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Wang, Xiaofeng, Guanghui He, Chao Tang, Yali Han, and Shangping Wang. "Keypoints-Based Image Passive Forensics Method for Copy-Move Attacks." International Journal of Pattern Recognition and Artificial Intelligence 30, no. 03 (February 22, 2016): 1655008. http://dx.doi.org/10.1142/s0218001416550089.
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A novel image passive forensics method for copy-move forgery detection is proposed. The proposed method combines block matching technology and feature point matching technology, and breaks away from the general framework of the visual feature-based approach that used local visual feature such as SIFT and followed by a clustering procedure to group feature points that are spatially close. In our work, image keypoints are extracted using Harris detector, and the statistical features of keypoint neighborhoods are used to generate forensics features. Then we proposed a new forensics features matching approach, in which, a region growth technology and a mismatch checking approach are developed to reduce mismatched keypoints and improve detected accuracy. We also develop a duplicate region detection method based on the distance frequency of corresponding keypoint pairs. The proposed method can detect duplicate regions for high resolution images. It has higher detection accuracy and computation efficiency. Experimental results show that the proposed method is robust for content-preserving manipulations such as JPEG compression, gamma adjustment, filtering, luminance enhancement, blurring, etc.
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Chen, Likai, Wei Lu, and Jiangqun Ni. "An Image Region Description Method Based on Step Sector Statistics and its Application in Image Copy-Rotate/Flip-Move Forgery Detection." International Journal of Digital Crime and Forensics 4, no. 1 (January 2012): 49–62. http://dx.doi.org/10.4018/jdcf.2012010104.
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A robust method for local image region feature description based on step sector statistics is proposed in this paper. The means and the standard deviations along the radial direction of the circle image region are extracted through the sector masks, and the rearrangement of these statistics makes this image region description method rotation-robust. The proposed description method is applied in the detection of copy-rotate-move forgery, and it can detect the exact rotation angle between the duplicate regions. With minor extension, the proposed description method can also be applied in the detection of copy-flip-move forgery. The experimental results show that the proposed description method can work well for the detection of copy-rotate/flip-move forgery.
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Pandey, Ramesh Chand, Sanjay Kumar Singh, and K. K. Shukla. "Passive Copy- Move Forgery Detection Using Speed-Up Robust Features, Histogram Oriented Gradients and Scale Invariant Feature Transform." International Journal of System Dynamics Applications 4, no. 3 (July 2015): 70–89. http://dx.doi.org/10.4018/ijsda.2015070104.
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Copy-Move is one of the most common technique for digital image tampering or forgery. Copy-Move in an image might be done to duplicate something or to hide an undesirable region. In some cases where these images are used for important purposes such as evidence in court of law, it is important to verify their authenticity. In this paper the authors propose a novel method to detect single region Copy-Move Forgery Detection (CMFD) using Speed-Up Robust Features (SURF), Histogram Oriented Gradient (HOG), Scale Invariant Features Transform (SIFT), and hybrid features such as SURF-HOG and SIFT-HOG. SIFT and SURF image features are immune to various transformations like rotation, scaling, translation, so SIFT and SURF image features help in detecting Copy-Move regions more accurately in compared to other image features. Further the authors have detected multiple regions COPY-MOVE forgery using SURF and SIFT image features. Experimental results demonstrate commendable performance of proposed methods.
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Li, Jianxiang, Yan Tian, Yiping Xu, and Zili Zhang. "Oriented Object Detection in Remote Sensing Images with Anchor-Free Oriented Region Proposal Network." Remote Sensing 14, no. 5 (March 3, 2022): 1246. http://dx.doi.org/10.3390/rs14051246.
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Oriented object detection is a fundamental and challenging task in remote sensing image analysis that has recently drawn much attention. Currently, mainstream oriented object detectors are based on densely placed predefined anchors. However, the high number of anchors aggravates the positive and negative sample imbalance problem, which may lead to duplicate detections or missed detections. To address the problem, this paper proposes a novel anchor-free two-stage oriented object detector. We propose the Anchor-Free Oriented Region Proposal Network (AFO-RPN) to generate high-quality oriented proposals without enormous predefined anchors. To deal with rotation problems, we also propose a new representation of an oriented box based on a polar coordinate system. To solve the severe appearance ambiguity problems faced by anchor-free methods, we use a Criss-Cross Attention Feature Pyramid Network (CCA-FPN) to exploit the contextual information of each pixel and its neighbors in order to enhance the feature representation. Extensive experiments on three public remote sensing benchmarks—DOTA, DIOR-R, and HRSC2016—demonstrate that our method can achieve very promising detection performance, with a mean average precision (mAP) of 80.68%, 67.15%, and 90.45%, respectively, on the benchmarks.
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Baxter, Nardia J., Julie Scanlan, Paolo De Marco, Ann P. Wood, and J. Colin Murrell. "Duplicate Copies of Genes Encoding Methanesulfonate Monooxygenase in Marinosulfonomonas methylotropha Strain TR3 and Detection of Methanesulfonate Utilizers in the Environment." Applied and Environmental Microbiology 68, no. 1 (January 2002): 289–96. http://dx.doi.org/10.1128/aem.68.1.289-296.2002.
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ABSTRACT Marinosulfonomonas methylotropha strain TR3 is a marine methylotroph that uses methanesulfonic acid (MSA) as a sole carbon and energy source. The genes from M. methylotropha strain TR3 encoding methanesulfonate monooxygenase, the enzyme responsible for the initial oxidation of MSA to formaldehyde and sulfite, were cloned and sequenced. They were located on two gene clusters on the chromosome of this bacterium. A 5.0-kbp HindIII fragment contained msmA, msmB, and msmC, encoding the large and small subunits of the hydroxylase component and the ferredoxin component, respectively, of the methanesulfonate monooxygenase, while a 6.5-kbp HindIII fragment contained duplicate copies of msmA and msmB, as well as msmD, encoding the reductase component of methanesulfonate. Both sets of msmA and msmB genes were virtually identical, and the derived msmA and msmB sequences of M. methylotropha strain TR3, compared with the corresponding hydroxylase from the terrestrial MSA utilizer Methylosulfonomonas methylovora strain M2 were found to be 82 and 69% identical. The msmA gene was investigated as a functional gene probe for detection of MSA-utilizing bacteria. PCR primers spanning a region of msmA which encoded a unique Rieske [2Fe-2S] binding region were designed. These primers were used to amplify the corresponding msmA genes from newly isolated Hyphomicrobium, Methylobacterium, and Pedomicrobium species that utilized MSA, from MSA enrichment cultures, and from DNA samples extracted directly from the environment. The high degree of identity of these msmA gene fragments, compared to msmA sequences from extant MSA utilizers, indicated the effectiveness of these PCR primers in molecular microbial ecology.
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Nguyen, Hoanh. "Improving Faster R-CNN Framework for Fast Vehicle Detection." Mathematical Problems in Engineering 2019 (November 22, 2019): 1–11. http://dx.doi.org/10.1155/2019/3808064.
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Vision-based vehicle detection plays an important role in intelligent transportation systems. With the fast development of deep convolutional neural networks (CNNs), vision-based vehicle detection approaches have achieved significant improvements compared to traditional approaches. However, due to large vehicle scale variation, heavy occlusion, or truncation of the vehicle in an image, recent deep CNN-based object detectors still showed a limited performance. This paper proposes an improved framework based on Faster R-CNN for fast vehicle detection. Firstly, MobileNet architecture is adopted to build the base convolution layer in Faster R-CNN. Then, NMS algorithm after the region proposal network in the original Faster R-CNN is replaced by the soft-NMS algorithm to solve the issue of duplicate proposals. Next, context-aware RoI pooling layer is adopted to adjust the proposals to the specified size without sacrificing important contextual information. Finally, the structure of depthwise separable convolution in MobileNet architecture is adopted to build the classifier at the final stage of the Faster R-CNN framework to classify proposals and adjust the bounding box for each of the detected vehicle. Experimental results on the KITTI vehicle dataset and LSVH dataset show that the proposed approach achieved better performance compared to original Faster R-CNN in both detection accuracy and inference time. More specific, the performance of the proposed method is improved comparing with the original Faster R-CNN framework by 4% on the KITTI test set and 24.5% on the LSVH test set.
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Clothier, Kristin A., Simone Stoute, Andrea Torain, and Beate Crossley. "Validation of a real-time PCR assay for high-throughput detection of Avibacterium paragallinarum in chicken respiratory sites." Journal of Veterinary Diagnostic Investigation 31, no. 5 (July 26, 2019): 714–18. http://dx.doi.org/10.1177/1040638719866484.
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Avibacterium paragallinarum is the causative agent of infectious coryza, a highly contagious respiratory disease in chickens. Given its fastidious nature, this bacterium is difficult to recover and identify, particularly from locations colonized by normal bacterial flora. Standard PCR methods have been utilized for detection but are labor-intensive and not feasible for high-throughput testing. We evaluated a real-time PCR (rtPCR) method targeting the HPG-2 region of A. paragallinarum, and validated a high-throughput extraction for this assay. Using single-tube extraction, the rtPCR detected 4 A. paragallinarum (ATCC 29545T and 3 clinical) isolates with a limit of detection (LOD) of 10 cfu/mL and a PCR efficiency of 89–111%. Cross-reaction was not detected with 33 non– A. paragallinarum, all close relatives from the family Pasteurellaceae. Real-time PCR testing on extracts of 66 clinical samples (choana, sinus, or trachea) yielded 98.2% (35 of 36 on positives, 30 of 30 on negatives) agreement with conventional PCR. Duplicate samples tested in a 96-well format extraction in parallel with the single-tube method produced equivalent LOD on all A. paragallinarum isolates, and 96.8% agreement on 93 additional clinical samples extracted with both procedures. This A. paragallinarum rtPCR can be utilized for outbreak investigations and routine monitoring of susceptible flocks.
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Asmann, Yan W., Vivekananda Sarangi, Bruce W. Eckloff, Julie M. Cunningham, Samantha J. McDonough, Yeon K. Lee, Eric D. Wieben, et al. "Comparison Of Single Nucleotide Mutations (SNVs) and Copy Number Variants (CNVs) Detection In Formalin Fixed Paraffin Embedded (FFPE) and Paired Frozen Tumor Tissues Using Target Capture and Sequencing Approach." Blood 122, no. 21 (November 15, 2013): 1784. http://dx.doi.org/10.1182/blood.v122.21.1784.1784.
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Abstract Background Next Generation sequencing (NGS) is a powerful tool to identify somatic mutations associated with tumor onset and drug response. While it is well suited for high quality fresh/frozen samples, NGS is not proven for FFPE tissue which is the most common type of clinical specimen. Since the nucleic acids can be readily extracted from FFPE samples for a variety of genomic analyses, a comparative mutational analysis of paired frozen and FFPE tissues is urgently needed. Our long term goal is to establish a lab protocol to detect mutations in FFPE tumors using a targeted capture and sequencing approach for genes of interest. This pilot study focuses on the comparison of FFPE and frozen samples to test the validity of using FFPE tissues in such application. Methods Gene Selection: 128 genes associated with known pathogenic mutations in lymphoma Sample Selection: 9 diffuse large B-cell lymphoma (DLBCL) cases with FFPE, frozen and germline samples, as well as 10 frozen normal lymphatic tissues as references for CNV detections Capture Probe Design: We targeted coding exons and UTR, as well as the evolutionarily conserved intronic regions. The capture probes were designed using the Agilent eArray tool. The titling density of the probes was set to 3 probes overlapping with every base in the target region to improve the capture efficiency in FFPE samples. The least stringent masking of the repeat regions was allowed to include regions with small repeats that are shorter than the length of the sequencing reads (100-bp). In addition, boosting parameters were picked to set various levels of probe replication in different regions in order to minimize the local coverage differences (e.g. between regions of different GC contents) Sequencing and Bioinformatics: The target capture and sequencing were performed by the Mayo Clinic Medical Genome Facility. The reads were mapped to Human Reference Genome Build 37 using Novalign, and SNVs were called using GATK. The CNVs were identified using an in-house developed algorithm, patternCNV. Results The designed probes covered 99.65937% of the target regions. We generated 2.2-6.7 Gbp of reads per sample, 57.4-71.5% of which were on target. This equalled an average coverage of 2100-6700 folds which is 10-30 times higher than the minimal coverage recommended by Agilent. Due to this high coverage, we observed duplicate reads that accounted for 7.7-73.5% of the total reads. When we analysed the data with and without the duplicated reads, the concordance of the called SNVs was between 84-93% out of 207-249 mutated positions per trio-sample. There were 7.8-8.9% and 1.1-2.2% unique SNVs per sample by excluding or including duplicate reads, respectively. The dis-concordances were mostly missed calls, where a SNV was observed in only 1 or 2 of the trio samples. The missed calls from frozen samples ranged from 0-10.4% compared to 1.4-10.4% from the FFPE tissues, with 0.88-2.4% more SNVs missed in FFPE. Further analyses showed that all of the missing calls came from the lack of or low coverage of the corresponding positions. There were also differences of the called SNVs between the trio samples. However, this was extremely rare. Only 2 out of the 9 trio samples at a total of 3 positions had disagreements in called SNVs between FFPE and frozen tissues, all due to the allelic imbalance where the percentage of reads supporting the alternative alleles were below 20%. Therefore, this dis-concordance can be removed by back-filling of the read-level information for each position. Unfortunately only 11.9-47.4% of the CNVs called in frozen tissues were identified in FFPE samples, due to the widely various coverage in FFPE samples. The consequent large noises of the log ratio values between the FFPEs and normal references significantly reduced the sensitivity for CNV calling. Conclusions This pilot study compared the performance of SNV and CNV detection in FFPE and paired frozen tissues using a target capture and sequencing approach. With a capture probe design strategized to benefit FFPE samples, we observed SNV detection rates in FFPE that were only slightly lower (0.88-2.4%) than those of frozen tissues due to poor coverage of some positions in FFPE samples. With a proper back-filling step, there was no dis-concordance of the called SNVs between FFPE and frozen samples. However, CNV detections in FFPE were more problematic due to the un-predictable regional coverage in FFPE samples. Disclosures: No relevant conflicts of interest to declare.
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Bande, Faruku, Siti Suri Arshad, Latiffah Hassan, and Zunita Zakaria. "Molecular Detection, Phylogenetic Analysis, and Identification of Transcription Motifs in Feline Leukemia Virus from Naturally Infected Cats in Malaysia." Veterinary Medicine International 2014 (2014): 1–10. http://dx.doi.org/10.1155/2014/760961.
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A nested PCR assay was used to determine the viral RNA and proviral DNA status of naturally infected cats. Selected samples that were FeLV-positive by PCR were subjected to sequencing, phylogenetic analysis, and motifs search. Of the 39 samples that were positive for FeLV p27 antigen, 87.2% (34/39) were confirmed positive with nested PCR. FeLV proviral DNA was detected in 38 (97.3%) of p27-antigen negative samples. Malaysian FeLV isolates are found to be highly similar with a homology of 91% to 100%. Phylogenetic analysis revealed that Malaysian FeLV isolates divided into two clusters, with a majority (86.2%) sharing similarity with FeLV-K01803 and fewer isolates (13.8%) with FeLV-GM1 strain. Different enhancer motifs including NF-GMa, Krox-20/WT1I-del2, BAF1, AP-2, TBP, TFIIF-beta, TRF, and TFIID are found to occur either in single, duplicate, triplicate, or sets of 5 in different positions within the U3-LTR-gag region. The present result confirms the occurrence of FeLV viral RNA and provirus DNA in naturally infected cats. Malaysian FeLV isolates are highly similar, and a majority of them are closely related to a UK isolate. This study provides the first molecular based information on FeLV in Malaysia. Additionally, different enhancer motifs likely associated with FeLV related pathogenesis have been identified.
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Zimina, V. N., O. E. Mikova, T. A. Varetskaya, D. A. Oborin, S. Yu Degtyareva, and V. I. Sergevnin. "The spectrum of primary drug resistance of Mycobacterium tuberculosis in patients with tuberculosis in relation to human immunodeficiency virus status." Terapevticheskii arkhiv 89, no. 11 (November 15, 2017): 50–54. http://dx.doi.org/10.17116/terarkh2017891150-54.
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Aim. To estimate the detection rate and spectrum of primary drug resistance of Mycobacterium tuberculosis (MBT) in patients with tuberculosis (TB) in relation to their human immunodeficiency virus (HIV) status in a region with high HIV infection rates (the Perm Territory) and to compare of drug-resistant MBT (DR-MBT) in patients with HIV/TB co-infection, by using phenotypic and molecular genetic testing (MGT) methods. Subjects and methods. The results of sputum bacteriological examination were analyzed in 178 HIV-infected patients and 354 non-HIV-infected individuals with a TB diagnosis made in the period July 1, 2014 to August 1, 2015. The diagnostic algorithm for all patients involved a duplicate sputum test for MBT by two techniques: fluorescence microscopy (FM) and inoculation into the Levenstein-Jensen dense culture medium. In patients with HIV/TB, the bacteriological examination was complemented with two more methods: detection of MBT DNA by a real-time polymerase chain reaction assay using the AmpliTube-RV system (Synthol, Russia); and inoculation into the Middlebrook liquid nutrient medium, by applying the automated BACTEC MGIT 960 system. Results. In patients with HIV/TB, the sensitivity of FM proved to be lower than in those with TB (24.2 and 32.8%, respectively; p0.05). The primary drug resistance of MBT in patients with HIV-TB was higher than that in HIV-negative individuals (60.2 and 41.6%, respectively; p
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Lovison, Otávio A., Raminta Grigaitė, Fabiana C. Z. Volpato, Jason K. Iles, Jon Lacey, Fabiano Barreto, Sai R. Pandiri, et al. "Validation of a MALDI-TOF MS Method for SARS-CoV-2 Detection on the Bruker Biotyper and Nasopharyngeal Swabs: A Brazil—UK Collaborative Study." Diagnostics 13, no. 8 (April 19, 2023): 1470. http://dx.doi.org/10.3390/diagnostics13081470.
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We developed a MALDI-TOF mass spectrometry method for the detection of the SARS-CoV-2 virus in saliva-gargle samples using Shimadzu MALDI-TOF mass spectrometers in the UK. This was validated in the USA to CLIA-LDT standards for asymptomatic infection detection remotely via sharing protocols, shipping key reagents, video conferencing, and data exchange. In Brazil, more so than in the UK and USA, there is a need to develop non-PCR-dependent, rapid, and affordable SARS-CoV-2 infection screening tests that also identify variant SARS-CoV-2 and other virus infections. In addition, travel restrictions necessitated remote collaboration with validation on the available clinical MALDI-TOF—the Bruker Biotyper (microflex® LT/SH)—and on nasopharyngeal swab samples, as salivary gargle samples were not available. The Bruker Biotyper was shown to be almost log103 more sensitive at the detection of high molecular weight spike proteins. A protocol for saline swab soaks out was developed, and duplicate swab samples collected in Brazil were analyzed by MALDI-TOF MS. The swab collected sample spectra that varied from that of saliva-gargle in three additional mass peaks in the mass region expected for IgG heavy chains and human serum albumin. A subset of clinical samples with additional high mass, probably spike-related proteins, were also found. Further, spectral data comparisons and analysis, subjected to machine learning algorithms in order to resolve RT-qPCR positive from RT-qPCR negative swab samples, showed 56–62% sensitivity, 87–91% specificity, and a 78% agreement with RT-qPCR scoring for SARS-CoV-2 infection.
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Ionescu, Mihail, Alec Deslandes, Rohan Holmes, Mathew C. Guenette, Inna Karatchevtseva, and Gregory R. Lumpkin. "Effect of Annealing upon Retention of He and H in Irradiated SiC." Materials Science Forum 879 (November 2016): 810–14. http://dx.doi.org/10.4028/www.scientific.net/msf.879.810.
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Silicon carbide (3C-β SiC) samples were irradiated with He ions of energy up to 30 keV and a fluence up to 1016/cm2, to produce damage in the near-surface region. A duplicate set of He ion irradiated SiC samples, as well as undamaged SiC, were also irradiated with H2+ ions of energy up to 20 keV and a similar fluence, to study the interaction of H species with pristine SiC and with He radiation-damaged SiC. Samples were annealed in steps of 200 K, from 473 K to 1273 K, and the retention of H and He were measured using elastic recoil detection analysis with 7.8 MeV C3+ ions, after each anneal step. Modification to the surface following irradiation is observed via Raman spectroscopy, which exhibits development of damage states such as disordered carbon and Si-Si peaks. Only minor changes in the H and He profiles were observed up to 1073 K, however after the 1273 K anneal the H and He profiles changed considerably, with a marked difference between samples irradiated only with He and those irradiated with He and H.
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Black, Candice C., Heather A. Bentley, Thomas H. Davis, and Gregory J. Tsongalis. "Use of a Linear Array for the Detection of Human Papillomavirus Genotypes in Head and Neck Cancer." Archives of Pathology & Laboratory Medicine 134, no. 12 (December 1, 2010): 1813–17. http://dx.doi.org/10.5858/2009-0592-oar.1.
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Abstract Context—Tumors of the head and neck commonly arise from the squamous and respiratory mucosa that lines the nasal and oral cavity, sinuses, pharynx, and larynx. The rate of oropharyngeal cancers diagnosed among Americans younger than 50 years is increasing. Infection of the oropharynx and tonsils by the human papillomavirus (HPV) has been linked to preneoplasia and cancer. Objectives—To evaluate the Roche Linear Array HPV Genotyping test kit to identify, and then specifically genotype, HPV in formalin-fixed, paraffin-embedded tissues. Design—We evaluated the performance of this assay for accuracy, for intra-assay and interassay precision, and for its limit of detection, using materials with known HPV status. Sixteen tumor tissues with the following origins were evaluated: 1 ocular, 1 hypopharynx, 8 tonsil, 1 retromolar trigone, 3 tongue, 1 anal, and 1 lymph node. DNA from formalin-fixed, paraffin-embedded tumor sections was isolated and amplified in duplicate, with positive and negative controls, using primers specific to the polymorphic L1 region of the HPV genome. Thirty-seven genotypes were tested using the linear array. The amplified product (450 base pairs) was visualized by gel electrophoresis and, if positive, reflexed to HPV genotyping. Results—Nine of the 16 tumors analyzed were HPV positive. The detected genotypes included HPV 6, 16, and 69. Conclusions—The Roche Linear Array HPV Genotyping test is an easy-to-use method for determining HPV genotype in the routine analysis of formalin-fixed, paraffin-embedded tumors. This assay is robust and can be performed routinely in a clinical laboratory setting.
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Farmer, W. T., P. W. Farin, S. R. Bischoff, J. E. Alexander, J. A. Piedrahita, and C. E. Farin. "2 DETECTION OF ANTISENSE TO Igf2r (AIR) RNA IN CATTLE." Reproduction, Fertility and Development 20, no. 1 (2008): 81. http://dx.doi.org/10.1071/rdv20n1ab2.
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The insulin-like growth factor type 2 receptor (Igf2r) regulates fetal growth by removing Igf2 from circulation, thus preventing overgrowth. In mice, expression of the Igf2r gene is imprinted only after implantation and is associated with expression of the antisense non-coding (nc)RNA, Air. In contrast, the human IGF2R gene is not imprinted and AIR ncRNA does not exist. Because it is known that the Igf2r gene is imprinted in cattle, the objectives of this study were to determine if Air ncRNA exists in cattle and, if so, whether bovine Air (bAir) is expressed during both pre- and post-implantation development. For objective 1, primer sets were designed for bAir based on bovine genomic sequence. The primer set, bAir3, was used to amplify a region of bAir corresponding to an antisense segment within intron 1 of Igf2r. Primer set bAir4 amplified a segment of bAir ncRNA corresponding to an antisense region upstream of the 52-untranslated region of Igf2r. Pools of whole-cell RNA were extracted from bovine fetal liver and subjected to DNase treatment, reverse transcription (RT), and PCR. Control RT reactions included RT without superscript and RT without superscript or DNase. Controls confirmed that amplification products resulted from RNA present in the sample and not from genomic DNA contamination. Amplicons were obtained for both the bAir3 and the bAir4 primer sets and were sequence verified, demonstrating that bAir ncRNA does exist in cattle. For objective 2, conceptuses (n = 4; mean � SEM length: 2.8 � 0.3 mm) derived from transfer of frozen-thawed in vivo-produced blastocysts were recovered from cows on Day 15 of gestation and snap-frozen for RNA extraction. Samples of liver from in vivo-produced bovine fetuses recovered at Day 70 of gestation (n = 7) were snap-frozen for RNA extraction. Semi-quantitative RT-PCR assays were performed to assess levels of mRNA for Igf2r and H2a, as well as ncRNA for bAir. All conceptus and fetal liver cDNA samples were run in duplicate within the same assay. Relative RNA expression was calculated as the ratio of band intensities of the RNA of interest to that of H2a. Data for relative RNA expression were analyzed by Student's t-test. H2a and Igf2r mRNAs were expressed in all Day 70 fetal liver and Day 15 conceptus samples. Relative levels of Igf2r did not differ (P = 0.19) with stage of development (0.15 � 0.09 v. 0.36 � 0.12 for Day 70 v. Day 15). bAir ncRNA was expressed in 7 of 7 samples of Day 70 fetal liver, whereas only 1 of 4 conceptuses expressed a faint bAir ncRNA signal based on either the bAir3 or bAir4 primer sets (χ2 = 7.23, P < 0.01). Relative levels of bAir ncRNA were greater (P < 0.001) in Day 70 fetal liver compared to those in Day 15 conceptuses for amplicons bAir3 (0.376 � 0.039 v. 0.028 � 0.051) and bAir4 (0.101 � 0.008 v. 0.003 � 0.010). In conclusion, the antisense ncRNA, Air, does exist in cattle and its relative expression is greatest following implantation. These observations are consistent with murine data and suggest that bAir may be involved in regulating imprinted expression of Igf2r in cattle.
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Opoku, P. "Establishing Accra Population-Based Cancer Registry." Journal of Global Oncology 4, Supplement 2 (October 1, 2018): 66s. http://dx.doi.org/10.1200/jgo.18.64600.
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Background: The African Cancer Organization (ACO) seeks to establish Accra Population-Based Cancer Registry (ACR). The whole idea is to collect, store and analyze data on persons with cancer to provide complete, accurate and timely cancer report for interventional programs. Such information would guide us to monitor patient care, prioritize and allocate resources effectively, give understanding of the things we do not yet know, and also act as a driver for policy development for the urgent need of comprehensive cancer control in Ghana. Countries require cancer surveillance programs to collect and analyze data on the scale of the cancer burden in each country. These are urgently needed in Africa as cancer data sources are scarce. Data can help to evaluate the impact of prevention, early detection/screening, treatment and palliative care programs. The proposed population-based cancer registry will help to act as a driver for policy development and program evaluation as recommended by the WHO. ACR intends to capture cancer cases diagnosed and/or treated within the Greater Accra region of Ghana and then further extend to cover the Central, Eastern, Western and the Volta regions of Ghana later. Aim: The goal of ACR to collect, store and analyze data on persons with cancer to generate incidence, prevalence, trends, mortality, and survival rates which is required to help develop a realistic and sustainable cancer control plan for Ghana. Methods: Cancer registry staff will be trained to abstract cancer cases diagnosed and/or treated within the southern regional geography of Ghana using a customized cancer notification form designed to capture detailed information on cancer patient demographics, tumor details, treatment, reporting sources and follow-up information based on both analytic and nonanalytic active case-finding reportability methods. These cases will then be classified and coded using the ICD-O-3, FIGO and/or SEER Summary Staging 2000 Manual. The data will be stored in customized cancer registry software which will be configured with various address codes from the registry geography. The cancer registry software checks for duplicate cases, data edits and consolidation. The software tracks down duplicate records and multiple primaries using a probability matching and consistency checking for impossible or rare cases. Conclusion: Establishing a cancer registry in Africa is challenging but very possible. Conflicts of interests are common norms among new cancer registries. With a good budget and working plan backed by few sincere and dedicated staff, it will be very possible to sustain the registry to capture all cancer cases within the catchment area, to take advantage of available modern technology to produce timely results. ACO is by this seeking for partnership to raise the needed support to embark on this national cancer registry campaign in the region.
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Worobey, Brian L., F. Béraldin, G. Bruns, J. Embleton, A. Heck, R. King, K. McLeod, and R. Ward. "Liquid Chromatographic Method for Determination of Diquat and Paraquat Herbicides in Potatoes: Collaborative Study." Journal of AOAC INTERNATIONAL 76, no. 4 (July 1, 1993): 881–87. http://dx.doi.org/10.1093/jaoac/76.4.881.
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Abstract A liquid chromatographic (LC) method for the determination of diquat and paraquat herbicides/desiccants in potatoes was collaboratively studied in 6 laboratories. Analytes are extracted from 5 g sample with dilute acid by using a microreflux procedure; the hydrolysate is adjusted to pH 9–10 and passed through a disposable silica cartridge for rapid cleanup and preconcentration. Analytes are separated on a reversed-phase LC column and are measured as their heptanesulfonate ion pairs by UV detection. Each collaborator determined diquat and paraquat at 4 levels (0.05,0.1,0.5, and 1.0 ppm) in blind duplicate samples plus 2 blind negative control samples. Potatoes, obtained from each participant’s region, were spiked by the collaborators with unknown aqueous solutions containing no analyte or a mixture of diquat and paraquat standards. Repeatability and reproducibility relative standard deviations (RSDr and RSDR) averaged 17.1 and 29.0%, respectively, for determination of diquat and 10.8 and 29.5%, respectively, for paraquat. For analysis of standard solutions, RSDr and RSDR values were 6.3 and 12.0%, respectively, for diquat and 7.3 and 13.9%, respectively, for paraquat. Accuracy, measured by comparison with true spiking values (absolute recovery) averaged 77.6 and 76.2% for diquat and paraquat, respectively, and ranged from 71.8 to 88.0% for both compounds. The method was adopted first action by AOAC International.
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Theilmann, J., J. Mozafari, R. Reade, Z. Wu, W. Xie, G. Jesperson, M. Bernardy, K. C. Eastwell, and D. Rochon. "Partial Nucleotide Sequence and Genome Organization of a Canadian Isolate of Little cherry virus and Development of an Enzyme-Linked Immunosorbent Assay-Based Diagnostic Test." Phytopathology® 92, no. 1 (January 2002): 87–98. http://dx.doi.org/10.1094/phyto.2002.92.1.87.
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Approximately 12.4 kb of the genome of a mealybug-transmissible, North American isolate of Little cherry virus (LChV-3, previously designated LChV-LC5) has been cloned and sequenced. The sequenced portion of the genome contains 10 open reading frames (ORFs) and, based on sequence comparisons, encodes a putative RNA helicase (HEL), RNA-dependent RNA polymerase (POL), two coat proteins (CPs), a homologue of HSP70, a 53K protein (p53) that is similar to an equivalent-size protein in other closteroviruses, and a 22K (p22) protein of unknown function. The genome also potentially encodes two small proteins (p5 and p6), one of which is similar to the small hydrophobic proteins of other closteroviruses. Phylogenetic analyses utilizing sequences of the HEL, POL, and HSP70 homologue suggest that LChV-3 is most similar to other mealybug-transmitted closteroviruses. Further comparisons between LChV-3 and a 4.7-kb region of the recently described Little cherry virus-2 (LChV-2) reveals 77% nucleotide sequence identity. Based on this low sequence identity, we propose that LChV-3 be considered a separate species, designated LChV-3. Unexpectedly, the LChV-3 CP duplicate ORF was found to lie upstream of the HSP70 ORF; therefore, the genome organization of LChV-3 is distinct from that of other closteroviruses. Polyclonal antiserum raised to bacterially expressed LChV-3 CP was useful for detection of LChV-diseased trees in the cherry-growing districts of British Columbia, Canada.
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Ryncarz, Alexander J., James Goddard, Anna Wald, Meei-Li Huang, Bernard Roizman, and Lawrence Corey. "Development of a High-Throughput Quantitative Assay for Detecting Herpes Simplex Virus DNA in Clinical Samples." Journal of Clinical Microbiology 37, no. 6 (1999): 1941–47. http://dx.doi.org/10.1128/jcm.37.6.1941-1947.1999.
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We have developed a high-throughput, semiautomated, quantitative fluorescence-based PCR assay to detect and type herpes simplex virus (HSV) DNA in clinical samples. The detection assay, which uses primers to the type-common region of HSV glycoprotein B (gB), was linear from <10 to 108 copies of HSV DNA/20 μl of sample. Among duplicate samples in reproducibility runs, the assay showed less than 5% variability. We compared the fluorescence-based PCR assay with culture and gel-based liquid hybridization system with 335 genital tract specimens from HSV type 2 (HSV-2)-seropositive persons attending a research clinic and 380 consecutive cerebrospinal fluid (CSF) samples submitted to a diagnostic virology laboratory. Among the 162 culture-positive genital tract specimens, TaqMan PCR was positive for 157 (97%) specimens, whereas the quantitative-competitive PCR was positive for 144 (89%) specimens. Comparisons of the mean titer of HSV DNA detected by the two assays revealed that the mean titer detected by the gel-based system was slightly higher (median, 1 log). These differences in titers were in part related to the fivefold difference in the amount of HSV DNA used in the amplicon standards with the two assays. Among the 380 CSF samples, 42 were positive by both assays, 13 were positive only by the assay with the agarose gel, and 3 were positive only by the assay with the fluorescent probe. To define the subtype of HSV DNA detected in the screening assay, we also designed one set of primers which amplifies the gG regions of both types of HSV and probes which are specific to either HSV-1 (gG1) or HSV-2 (gG2). These probes were labeled with different fluorescent dyes (6-carboxyfluorescein for gG2 and 6-hexachlorofluorescein for gG1) to enable detection in a single PCR. In mixing experiments the probes discriminated the correct subtype in mixtures with up to a 7-log-higher concentration of the opposite subtype. The PCR typing results showed 100% concordance with the results obtained by assays with monoclonal antibodies against HSV-1 or HSV-2. Thus, while the real-time PCR is slightly less sensitive than the gel-based liquid hybridization system, the high throughput, the lack of contamination during processing, the better reproducibility, and the better ability to type the isolates rapidly make the real-time PCR a valuable tool for clinical investigation and diagnosis of HSV infection.
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Pontes, Daniela Oliveira, Dayane de Melo Costa, Priscilla Perez da Silva Pereira, Greg S. Whiteley, Trevor Glasbey, and Anaclara Ferreira Veiga Tipple. "Adenosine triphosphate (ATP) sampling algorithm for monitoring the cleanliness of surgical instruments." PLOS ONE 18, no. 8 (August 15, 2023): e0284967. http://dx.doi.org/10.1371/journal.pone.0284967.
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Background Timely detection of cleaning failure is critical for quality assurance within Sterilising Service Units (SSUs). Rapid Adenosine Triphosphate (ATP) testing provides a real time and quantitative indication of cellular contaminants, when used to measure surface or device cleanliness. The aim of this study was to investigate the use of an ATP algorithm and to whether it could be used as a routine quality assurance step, to monitor surgical instruments cleanliness in SSUs prior to sterilisation. Methods Cleanliness monitoring using rapid ATP testing was undertaken in the SSUs of four hospitals located in the western (Amazonia) region of Brazil. ATP testing was conducted (Clean Trace, 3M) on 163 surgical instruments, following manual cleaning. A sampling algorithm using a duplicate swab approach was applied to indicate surgical instruments as (i) very clean, (ii) clean, (iii) equivocal or (iv) fail, based around a ‘clean’ cut-off of 250 Relative Light Units (RLU) and a ‘very clean’ <100 RLU. Results The four cleanliness categories were significantly differentiated (P≤0.001). The worst performing locations (hospitals A & C) had failure rates of 39.2% and 32.4%, respectively, and were distinctly different from hospitals B & D (P≤0.001). The best performing hospitals (B & D) had failure rates of 7.7% and 2.8%, respectively. Conclusion The ATP testing algorithm provides a simple to use method within SSUs. The measurements are in real time, quantitative and useful for risk-based quality assurance monitoring, and the tool can be used for staff training. The four-tiered approach to the grading of surgical instrument cleanliness provides a nuanced approach for continuous quality improvement within SSU than does a simple pass/fail methodology.
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Hockney, Rochelle, Caroline H. Orr, Gareth J. Waring, Inge Christiaens, Gillian Taylor, Stephen P. Cummings, Stephen C. Robson, and Andrew Nelson. "Formalin-Fixed Paraffin-Embedded (FFPE) samples are not a beneficial replacement for frozen tissues in fetal membrane microbiota research." PLOS ONE 17, no. 3 (March 17, 2022): e0265441. http://dx.doi.org/10.1371/journal.pone.0265441.
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Formalin-Fixed Paraffin-Embedded (FFPE) tissues are routinely collected, archived, and used for clinical diagnosis, including maternal and neonatal health. Applying FFPE samples to microbiota research would be beneficial to reduce preparation, storage and costs associated with limited available frozen samples. This research aims to understand if FFPE fetal membrane samples are comparable to frozen tissues, which are the current gold standard for DNA microbiota analysis. Extracted DNA from nine matched paired patients were sequenced by Illumina sequencing of the V4 16S rRNA gene region. This included duplicate frozen amnion and chorion fetal membrane rolls or FFPE combined amniochorionic samples. Negative controls of surrounding wax blocks and DNA extraction reagents were processed alongside samples using identical methods. DNA quality and quantity was assessed by NanoDrop, agarose gel electrophoresis and Bioanalyzer. Decontam and SourceTracker were integrated into microbiota analysis to identify the presence of contaminating sources. The bacterial profile and nine genera differed between FFPE and frozen fetal membranes. There were no differences in bacterial profiles between FFPE samples and corresponding wax negative controls, with 49% of bacteria in FFPE fetal membrane samples matched to the source origin of paraffin wax, and 40% originating from DNA extraction reagent sources. FFPE samples displayed high fragmentation and low quantity of extracted DNA compared to frozen samples. The microbiota of FFPE fetal membrane samples is influenced by processing methods, with the inability to differentiate between the microbiota of the tissue sample and the surrounding wax block. Illumina sequencing results of FFPE and frozen fetal membrane samples should not be compared using the methods employed here. Variation could be influenced by limitations including storage time, DNA extraction and purification methods. To utilise FFPE fetal membrane samples in microbiota research then contamination prevention and detection methods must be included into optimised and standardised protocols, with recommendations presented here.
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Akbarpour Sekeh, Mohammad, Mohd Aizaini Maarof, Mohd Foad Rohani, and Babak Mahdian. "Efficient image duplicated region detection model using sequential block clustering." Digital Investigation 10, no. 1 (June 2013): 73–84. http://dx.doi.org/10.1016/j.diin.2013.02.007.
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Michael Zimba, and Sun Xingming. "Detection of Image Duplicated Regions Affected by Rotation, Scaling and." International Journal of Digital Content Technology and its Applications 5, no. 11 (November 30, 2011): 143–50. http://dx.doi.org/10.4156/jdcta.vol5.issue11.18.
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Parkin, I. A. P., A. G. Sharpe, and D. J. Lydiate. "Patterns of genome duplication within the Brassica napus genome." Genome 46, no. 2 (April 1, 2003): 291–303. http://dx.doi.org/10.1139/g03-006.
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The progenitor diploid genomes (A and C) of the amphidiploid Brassica napus are extensively duplicated with 73% of genomic clones detecting two or more duplicate sequences within each of the diploid genomes. This comprehensive duplication of loci is to be expected in a species that has evolved through a polyploid ancestor. The majority of the duplicate loci within each of the diploid genomes were found in distinct linkage groups as collinear blocks of linked loci, some of which had undergone a variety of rearrangements subsequent to duplication, including inversions and translocations. A number of identical rearrangements were observed in the two diploid genomes, suggesting they had occurred before the divergence of the two species. A number of linkage groups displayed an organization consistent with centric fusion and (or) fission, suggesting this mechanism may have played a role in the evolution of Brassica genomes. For almost every genetically mapped locus detected in the A genome a homologous locus was found in the C genome; the collinear arrangement of these homologous markers allowed the primary regions of homoeology between the two genomes to be identified. At least 16 gross chromosomal rearrangements differentiated the two diploid genomes during their divergence from a common ancestor.Key words: genome evolution, Brassicaeae, polyploidy, homoeologous linkage groups.
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Noda, Keiji, Khayrul Bashar, Yoshinori Takeuchi, and Noboru Ohnishi. "Detecting Partially Duplicated Image Regions in a Digital Image." Journal of The Institute of Image Information and Television Engineers 63, no. 11 (2009): 1645–51. http://dx.doi.org/10.3169/itej.63.1645.
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Dube Mandishora, Racheal S., Trine B. Rounge, Megan Fitzpatrick, Irene Kraus Christiansen, Ole Herman Ambur, Sonja Lagström, Babill Stray-Pedersen, Massimo Tommasino, Joel Palefsky, and Zvavahera M. Chirenje. "Self-collected and clinician-collected anal swabs show modest agreement for HPV genotyping." PLOS ONE 16, no. 4 (April 26, 2021): e0250426. http://dx.doi.org/10.1371/journal.pone.0250426.
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Background & aim Women with HIV/HPV coinfection and cervical lesions are at increased risk of developing HPV related anal cancer. Self-collection of anal swabs may facilitate HPV molecular testing in anal cancer screening, especially in high-risk groups, and yet it is not adequately studied. We evaluated level of agreement between self-collected anal swabs (SCAS) and clinician-collected anal swabs (CCAS) when used for HPV genotyping. We also described the anal HPV genotype distribution and HIV/HPV coinfection. Methods We performed a cross sectional study with participants from a visual-inspection-with-acetic-acid and cervicography (VIAC) clinic, in Harare, Zimbabwe. In a clinic setting, the women aged ≥18 years provided anal swabs in duplicate; first CCAS and then SCAS immediately after. HPV detection and genotyping were performed using next generation amplicon sequencing of a 450bp region of the HPV L1 gene. Level of agreement of HPV genotypes between CCAS and SCAS was calculated using the kappa statistic. McNemar tests were used to evaluate agreement in the proportion of genotypes detected by either method. Results Three-hundred women provided 600 samples for HPV genotyping. HPV genotypes were detected in 25% of SCAS and in 22% of CCAS. The most common genotypes with CCAS were HPV52, HPV62 and HPV70 and with SCAS were HPV62, HPV44, HPV52, HPV53 and HPV68. Total HPV genotypes detected in CCAS were more than those detected in SCAS, 32 versus 27. The agreement of HPV genotypes between the two methods was 0.55 in kappa value (k). The test of proportions using McNemar gave a Chi-square value of 0.75 (p = 0.39). Multiple HPV infections were detected in 28/75 and 29/67 women for CCAS and SCAS respectively. Conclusions SCAS and CCAS anal swabs showed moderate agreement, with no statistically significant difference in the proportion of genotypes detected by either methods. Although the differences between the two methods were not statistically significant, CCAS detected more HPV genotypes than SCAS and more HPV infections were detected in SCAS than in CCAS. Our data suggest that self-collected anal swabs can be used as an alternative to clinician-collected anal swabs for HPV genotyping.
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Wang, Huan, and Hongxia Wang. "Perceptual Hashing-Based Image Copy-Move Forgery Detection." Security and Communication Networks 2018 (2018): 1–11. http://dx.doi.org/10.1155/2018/6853696.
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This paper proposes a blind authentication scheme to identify duplicated regions for copy-move forgery based on perceptual hashing and package clustering algorithms. For all fixed-size image blocks in suspicious images, discrete cosine transform (DCT) is used to obtain their DCT coefficient matrixes. Their perceptual hash matrixes and perceptual hash feature vectors are orderly addressed. Moreover, a package clustering algorithm is proposed to replace traditional lexicographic order algorithms for improving the detection precision. Similar blocks can be identified by matching the perceptual hash feature vectors in each package and its adjacent package. The experimental results show that the proposed scheme can locate irregular tampered regions and multiple duplicated regions in suspicious images although they are distorted by some hybrid trace hiding operations, such as adding white Gaussian noise and Gaussian blurring, adjusting contrast ratio, luminance, and hue, and their hybrid operations.
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Noronha, Thiago R., Miguel Mitne-Neto, and Maria L. Chauffaille. "Additional Information Offered By Snpa in Myelodysplastic Syndromes with Excess Blasts (MDS-EB) and Future Perspectives." Blood 128, no. 22 (December 2, 2016): 5552. http://dx.doi.org/10.1182/blood.v128.22.5552.5552.
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Abstract Introduction: The detection of chromosomal abnormalities in myelodysplastic syndromes (MDS) supports the diagnosis, classification, prognostic stratification, therapy option, treatment monitoring and better understanding of the biology of disease. The main chromosomal abnormalities of MDS are losses and gains of genetic material, and these changes are among the most important prognostic parameters in IPSS-R. As a consequence, major advances have been achieved in the treatment and survival of patients. However, nearly half of the patients present a normal karyotype, which prevents their further characterization. Therefore, there is the desire to increase the abnormalities detection rate by other methods. Single nucleotide polymorphisms array (SNPa), also referred to as chromosomal microarray, is a sensitive technology used to perform high-resolution genome-wide DNA losses, gains and copy-neutral loss of heterozygosity (CN-LOH). The genomic DNA is hybridized to polymorphic probes which are SNP markers and non-polymorphic probes which are copy number markers, providing information about CN-LOH and copy number alteration (CNA), respectively. Previous studies have shown that the addition of the SNPa to karyotype (KT) increases by 28% the detection rate of cytogenetic abnormalities. Objective: To substantiate this idea we describe two cases of MDS to whom SNPa added valued information to karyotype. Methods: DNA was extracted from bone marrow cells for genomic clonal evaluation. The DNA was digested, amplified, fragmented, labeled and hybridized to the chip (Affymetrix - CytoScan HD®) containing the probes. The chip was scanned to detect the signals' intensity emitted by the hybridized probes which were further analyzed by a software (ChAS) that allows visualization of CNA and CN-LOH. CNA´s analysis relies on the comparison of the obtained signals to a reference diploid DNA signal, and the difference encountered is characterized as loss or gain. CN-LOH analysis is based on two possible nucleotide signals (A or B), which are evaluated to discriminate three genotypes: AA, AB and BB. CN-LOH occurs when one allele is lost and duplicate another, resulting in genotypes AA or BB. Results: Case 1, 64y-male-patient, classified as MDS-EB (WHO 2016), Bone marrow histology showed grade II fibrosis. KT: 46,XY,del(5)(q15q33),del(17)(p11.2)[16] / 46,XY[4]. SNPa: 3p21.31p21.2 CN-LOH; 5q21.1q35.3 loss (CN:1.00); -7; +8; 12p13.33p12.3, 12p12.1p11.22, 12q22q23.3 loss (CN:1.00); -16; 17p13.3p11.2 mosaic loss (CN: 1.50) and -Y. Case 2, 74y-male-patient, classified as MDS-EB (WHO 2016), Bone marrow histology showed grade II/lll fibrosis. KT: 46,XY[15]. SNPa: 21q21.1q22.3 CN-LOH. Discussion and Conclusion: The SNPa has the advantage of detecting genomic alterations regardless of the cell cycle, even when the cell is quiescent or growth is defective. It also enables the identification of CN-LOH (also known as uniparental disomy, UPD), submicroscopic amplifications and deletions that are not detected by KT. On the other hand, SNPa does not allow the identification of balanced translocations and polyploidy. In case 1, after SNPa analysis, some chromosomal abnormalities (−7, +8, −16 and −Y) were found in sporadic metaphases during the KT reanalysis, but had not initially been described because they did not meet the criterion to be considered as a cytogenetic clone. The risk-stratification (IPSS-R) for this patient was intermediate, but the addition of the SNPa results the risk-stratification could be changed to very poor. Seven months after diagnosis the patient developed acute myeloid leukemia and died. In case 2, CN-LOH detected by SNPa could be responsible for homozygosity of mutations in critical genes located in the 21p region, such as RUNX1 that encodes a protein, which is a transcription factor critical in hematopoiesis. Indeed, sequencing of candidate genes in CN-LOH regions should be considered a priority in the search of driver mutations of MDS. Twenty-four months after diagnosis the patient died due to other non-hematologic causes. In Summary, SNPa analysis may add value to KT non-informative results and occasionally reveal cryptic abnormalities not recognized by karyotyping. However, SNPa analysis should be viewed as a complimentary tool. Acknowledgment: The SNPa test was supported by Grupo Fleury Disclosures No relevant conflicts of interest to declare.
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Mane, Vanita, and Subhash Shinde. "An Integrated Copy-Move Forensic Method for Tamper Detection and Localization of Duplicated Regions." International Journal of Forensic Computer Science 13, no. 1 (December 12, 2018): 29–36. http://dx.doi.org/10.5769/j201801003.
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Chen, Beijing, Gouenou Coatrieux, Jiasong Wu, Zhifang Dong, Jean Louis Coatrieux, and Huazhong Shu. "Fast Computation of Sliding Discrete Tchebichef Moments and Its Application in Duplicated Regions Detection." IEEE Transactions on Signal Processing 63, no. 20 (October 2015): 5424–36. http://dx.doi.org/10.1109/tsp.2015.2451107.
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Huang, Yueming, and Guowu Yuan. "AD-DETR: DETR with asymmetrical relation and decoupled attention in crowded scenes." Mathematical Biosciences and Engineering 20, no. 8 (2023): 14158–79. http://dx.doi.org/10.3934/mbe.2023633.
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<abstract><p>Pedestrian detection in crowded scenes is widely used in computer vision. However, it still has two difficulties: 1) eliminating repeated predictions (multiple predictions corresponding to the same object); 2) false detection and missing detection due to the high scene occlusion rate and the small visible area of detected pedestrians. This paper presents a detection framework based on DETR (detection transformer) to address the above problems, and the model is called AD-DETR (asymmetrical relation detection transformer). We find that the symmetry in a DETR framework causes synchronous prediction updates and duplicate predictions. Therefore, we propose an asymmetric relationship fusion mechanism and let each query asymmetrically fuse the relative relationships of surrounding predictions to learn to eliminate duplicate predictions. Then, we propose a decoupled cross-attention head that allows the model to learn to restrict the range of attention to focus more on visible regions and regions that contribute more to confidence. The method can reduce the noise information introduced by the occluded objects to reduce the false detection rate. Meanwhile, in our proposed asymmetric relations module, we establish a way to encode the relative relation between sets of attention points and improve the baseline. Without additional annotations, combined with the deformable-DETR with Res50 as the backbone, our method can achieve an average precision of 92.6%, MR$ ^{-2} $ of 40.0% and Jaccard index of 84.4% on the challenging CrowdHuman dataset. Our method exceeds previous methods, such as Iter-E2EDet (progressive end-to-end object detection), MIP (one proposal, multiple predictions), etc. Experiments show that our method can significantly improve the performance of the query-based model for crowded scenes, and it is highly robust for the crowded scene.</p></abstract>
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Abdulazeem Ahmed, Eman, Malek Alzaqebah, Sana Jawarneh, Jehad Saad Alqurni, Fahad A. Alghamdi, Hayat Alfagham, Lubna Mahmoud Abdel Jawad, Usama A. Badawi, Mutasem K. Alsmadi, and Ibrahim Almarashdeh. "Comparison of specific segmentation methods used for copy move detection." International Journal of Electrical and Computer Engineering (IJECE) 13, no. 2 (April 1, 2023): 2363. http://dx.doi.org/10.11591/ijece.v13i2.pp2363-2374.
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<p><span lang="EN-US">In this digital age, the widespread use of digital images and the availability of image editors have made the credibility of images controversial. To confirm the credibility of digital images many image forgery detection types are arises, copy-move forgery is consisting of transforming any image by duplicating a part of the image, to add or hide existing objects. Several methods have been proposed in the literature to detect copy-move forgery, these methods use the key point-based and block-based to find the duplicated areas. However, the key point-based and block-based have a drawback of the ability to handle the smooth region. In addition, image segmentation plays a vital role in changing the representation of the image in a meaningful form for analysis. Hence, we execute a comparison study for segmentation based on two clustering algorithms (i.e., k-means and super pixel segmentation with density-based spatial clustering of applications with noise (DBSCAN)), the paper compares methods in term of the accuracy of detecting the forgery regions of digital images. K-means shows better performance compared with DBSCAN and with other techniques in the literature.</span></p>
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Huynh-Kha, Tu, Thuong Le-Tien, Synh Ha, and Khoa Huynh-Van. "Improving the Computational Cost for Copied Region Detection in Forensic Images." Journal of Science and Technology: Issue on Information and Communications Technology 2, no. 1 (August 31, 2016): 55. http://dx.doi.org/10.31130/jst.2016.28.
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This research work develops a new method to detect the forgery in image by combining the Wavelet transform and modified Zernike Moments (MZMs) in which the features are defined from more pixels than in traditional Zernike Moments. The tested image is firstly converted to grayscale and applied one level Discrete Wavelet Transform (DWT) to reduce the size of image by a half in both sides. The approximation sub-band (LL), which is used for processing, is then divided into overlapping blocks and modified Zernike moments are calculated in each block as feature vectors. More pixels are considered, more sufficient features are extracted. Lexicographical sorting and correlation coefficients computation on feature vectors are next steps to find the similar blocks. The purpose of applying DWT to reduce the dimension of the image before using Zernike moments with updated coefficients is to improve the computational time and increase exactness in detection. Copied or duplicated parts will be detected as traces of copy-move forgery manipulation based on a threshold of correlation coefficients and confirmed exactly from the constraint of Euclidean distance. Comparisons results between proposed method and related ones prove the feasibility and efficiency of the proposed algorithm.
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Kim, Jeong Joong, Hee Sub Rhee, Yeun Tai Chung, So Yeon Park, and Soo Kyung Choi. "Prenatal detection of de novo inversion of chromosome 9 with duplicated heterochromatic region and postnatal follow-up." Experimental & Molecular Medicine 31, no. 3 (September 1999): 134–36. http://dx.doi.org/10.1038/emm.1999.22.
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Horňáková, O., M. Závodná, M. Žáková, J. Kraic, and F. Debre. "Diversity of Common Bean Landraces Collected in the Western and Eastern Carpatien." Czech Journal of Genetics and Plant Breeding 39, No. 3 (November 23, 2011): 73–83. http://dx.doi.org/10.17221/3723-cjgpb.
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The study of diversity in common bean was based on morphological and agronomical characteristics, differentiation of collected accessions by morphological and molecular markers, detection of genetic variation, and duplicates detection in bean landraces. The analysed 82 accessions of common bean (Phaseolus vulgaris L.) were collected in the Western andEastern Carpatien as landrace mixtures. Their seeds were segregated and pooled according to their characteristics; they were further multiplicated, and introduced into the collection. An extensive variation in plant and seed traits was discovered in thirty-three morphological and agronomical characteristics. Nevertheless, some of the accessions were identical in these characteristics. Cluster analysis grouped genotypes into two main branches, reflecting the growth type, seed size parameters, and thousand-seed weight. Molecular differentiation studies were performed by multilocus polymorphism detection in microsatellite and minisatellite DNA regions. Cluster analysis based on molecular data also grouped genotypes but no linkage to morphological traits was revealed. Bean accessions with very similar or identical morphological characters were clearly distinguished by DNA banding patterns. The presence of duplicates was excluded.
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Bravo-Solorio, Sergio, and Asoke K. Nandi. "Automated detection and localisation of duplicated regions affected by reflection, rotation and scaling in image forensics." Signal Processing 91, no. 8 (August 2011): 1759–70. http://dx.doi.org/10.1016/j.sigpro.2011.01.022.
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Armijos Carrion, Angelo D., Damien D. Hinsinger, and Joeri S. Strijk. "ECuADOR—Easy Curation of Angiosperm Duplicated Organellar Regions, a tool for cleaning and curating plastomes assembled from next generation sequencing pipelines." PeerJ 8 (April 7, 2020): e8699. http://dx.doi.org/10.7717/peerj.8699.
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Background With the rapid increase in availability of genomic resources offered by Next-Generation Sequencing (NGS) and the availability of free online genomic databases, efficient and standardized metadata curation approaches have become increasingly critical for the post-processing stages of biological data. Especially in organelle-based studies using circular chloroplast genome datasets, the assembly of the main structural regions in random order and orientation represents a major limitation in our ability to easily generate “ready-to-align” datasets for phylogenetic reconstruction, at both small and large taxonomic scales. In addition, current practices discard the most variable regions of the genomes to facilitate the alignment of the remaining coding regions. Nevertheless, no software is currently available to perform curation to such a degree, through simple detection, organization and positioning of the main plastome regions, making it a time-consuming and error-prone process. Here we introduce a fast and user friendly software ECuADOR, a Perl script specifically designed to automate the detection and reorganization of newly assembled plastomes obtained from any source available (NGS, sanger sequencing or assembler output). Methods ECuADOR uses a sliding-window approach to detect long repeated sequences in draft sequences, which then identifies the inverted repeat regions (IRs), even in case of artifactual breaks or sequencing errors and automates the rearrangement of the sequence to the widely used LSC–Irb–SSC–IRa order. This facilitates rapid post-editing steps such as creation of genome alignments, detection of variable regions, SNP detection and phylogenomic analyses. Results ECuADOR was successfully tested on plant families throughout the angiosperm phylogeny by curating 161 chloroplast datasets. ECuADOR first identified and reordered the central regions (LSC–Irb–SSC–IRa) for each dataset and then produced a new annotation for the chloroplast sequences. The process took less than 20 min with a maximum memory requirement of 150 MB and an accuracy of over 99%. Conclusions ECuADOR is the sole de novo one-step recognition and re-ordination tool that provides facilitation in the post-processing analysis of the extra nuclear genomes from NGS data. The program is available at https://github.com/BiodivGenomic/ECuADOR/.
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P. Ebby Darney. "Scam Image Detection on Copy-Move by JPEG Features and Classical Block Matching with Improved Variant." Journal of Innovative Image Processing 4, no. 4 (November 1, 2022): 215–25. http://dx.doi.org/10.36548/jiip.2022.4.001.
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Numerous methods have been developed to identify copy-move forgeries, which are among the most often used alteration strategies of digital photographs. The most widely used format of digital photographs is JPEG, which allows for high-rate compression without drastically altering the meaning of the picture. The objective of this work is to develop a system that can automatically identify the forgery type of the suspect image through in a single procedure, without requiring any kind of expert information. A preferable method is to run the same image through multiple algorithms, which saves time and prevents the needless evaluation of multiple detection results, from which it may be difficult to determine the correct output due to the presence of multiple confounding factors. Additionally, it has been shown that the established method is very effective in detecting expert forgeries when the duplicated region is picked in a non-rigid fashion, which is almost hard for the human eye to perform.
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Mehmood, Zahid, Hassan Nazeer Chaudhry, Rizwan Ali Naqvi, Farzana Kulsoom, Asmaa Munshi, and Muhammad Bilal. "Passive Framework of Sparse Region Duplication Detection from Digital Images." Journal of Sensors 2022 (June 22, 2022): 1–16. http://dx.doi.org/10.1155/2022/6580508.
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Currently, digital images are widely communicated by media using social media applications. The general public captures the digital images for preserving the family and personal memories and to share with their friends and family. Digital images have been used extensively in forensic science to present the digital images as proof in the court and law enforcement agencies, which present a loophole for the culprits to forge the digital image and change the proofs and evidence. Copy-move forgery (CMF) is among the most widely employed image manipulation methods. In this method, the area of the image is duplicated to some other part to modify its content by applying different postprocessing operations on images like blurring, color reduction, and scaling which is a challenging research problem in copy-move forgery detection (CMFD). In this paper, an efficient and effective CMFD method is presented to identify the single and multiple altered areas in an image in the presence of postprocessing operations. The proposed CMFD method divides the image into circular blocks. It computes a rotation-invariant feature vector from each circular block of the image by applying local intensity order pattern (LIOP) features. The computed feature vectors are then compared using Euclidean distance to locate the suspected image’s forged areas. The experimental results of the proposed CMFD method are reported on three standard datasets of the CMF, namely, CoMoFoD, KLTCI, and MICC-F220. The experimental analysis of the proposed CMFD method on these datasets indicates that it produces robust performance (detection accuracies of 97.29% on the CoMoFoD dataset, 98.53% on the KLTCI dataset, and 97.57% on the MICC-F220 dataset) as compared with state-of-the-art CMFD methods in terms of the standard performance evaluation parameters of the CMF.
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Wang, Chengyou, Zhi Zhang, and Xiao Zhou. "An Image Copy-Move Forgery Detection Scheme Based on A-KAZE and SURF Features." Symmetry 10, no. 12 (December 3, 2018): 706. http://dx.doi.org/10.3390/sym10120706.
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The popularity of image editing software has made it increasingly easy to alter the content of images. These alterations threaten the authenticity and integrity of images, causing misjudgments and possibly even affecting social stability. The copy-move technique is one of the most commonly used approaches for manipulating images. As a defense, the image forensics technique has become popular for judging whether a picture has been tampered with via copy-move, splicing, or other forgery techniques. In this paper, a scheme based on accelerated-KAZE (A-KAZE) and speeded-up robust features (SURF) is proposed for image copy-move forgery detection (CMFD). It is difficult for most keypoint-based CMFD methods to obtain sufficient points in smooth regions. To remedy this defect, the response thresholds for the A-KAZE and SURF feature detection stages are set to small values in the proposed method. In addition, a new correlation coefficient map is presented, in which the duplicated regions are demarcated, combining filtering and mathematical morphology operations. Numerous experiments are conducted to demonstrate the effectiveness of the proposed method in searching for duplicated regions and its robustness against distortions and post-processing techniques, such as noise addition, rotation, scaling, image blurring, joint photographic expert group (JPEG) compression, and hybrid image manipulation. The experimental results demonstrate that the performance of the proposed scheme is superior to that of other tested CMFD methods.
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Poropat, Renee A., and Garth A. Nicholson. "Determination of gene dosage at the PMP22 and androgen receptor loci by quantitative PCR." Clinical Chemistry 44, no. 4 (April 1, 1998): 724–30. http://dx.doi.org/10.1093/clinchem/44.4.724.
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Abstract Although many genetic diseases are caused by the presence of point mutations in respective genes, an increasing number of diseases are known to be caused by gene copy number changes. We report the development of a rapid and reliable PCR-based method for quantitation of gene copy number with sufficient sensitivity to detect single copy changes without the use of radioactive or fluorescent labeling. The sensitivity of this technique has been demonstrated by the detection of the DNA duplication or deletion occurring in two inherited peripheral neuropathies, Charcot-Marie-Tooth type 1A (CMT1A) and hereditary neuropathy with liability to pressure palsies (HNPP), that are caused by a reciprocal duplication or deletion event on chromosome 17p11.2–12. This method relies on the comparison of the amount of PCR product generated from a potentially duplicated or deleted target sequence with the amount of product generated from a disomic reference gene. The value of this ratio (target PCR product:reference PCR product) indicates whether the target sequence is duplicated, deleted, or unchanged. Using primers from within a duplicated or deleted region (PMP22 gene and EW401) and from within a reference region (NF1 gene), we tested 50 CMT1A, 30 HNPP, and 50 unaffected individuals for the presence of a DNA duplication or deletion. Target:reference ratios of 1.58, 1.02, and 0.56 were detected for the CMT1A, unaffected, and HNPP groups, respectively. Thus, differentiation of the three groups of individuals was on the basis of gene copy number. This technique was successfully used to detect the difference in the X chromosome copy number between males and females (target:reference ratios of 1.1 and 2.3, respectively). This approach to the detection of DNA duplications and deletions is sensitive, accurate, and has potential applications in the quantitation of changes in gene copy number associated with diseases characterized by such chromosomal alterations.
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Amico, Francesco, Richard E. Frye, Scott Shannon, and Steve Rondeau. "Resting State EEG Correlates of Suicide Ideation and Suicide Attempt." Journal of Personalized Medicine 13, no. 6 (May 24, 2023): 884. http://dx.doi.org/10.3390/jpm13060884.
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Suicide is a global phenomenon that impacts individuals, families, and communities from all income groups and all regions worldwide. While it can be prevented if personalized interventions are implemented, more objective and reliable diagnostic methods are needed to complement interview-based risk assessments. In this context, electroencephalography (EEG) might play a key role. We systematically reviewed EEG resting state studies of adults with suicide ideation (SI) or with a history of suicide attempts (SAs). After searching for relevant studies using the PubMed and Web of Science databases, we applied the PRISMA method to exclude duplicates and studies that did not match our inclusion criteria. The selection process yielded seven studies, which suggest that imbalances in frontal and left temporal brain regions might reflect abnormal activation and correlate with psychological distress. Furthermore, asymmetrical activation in frontal and posterior cortical regions was detected in high-risk depressed persons, although the pattern in the frontal region was inverted in non-depressed persons. The literature reviewed suggests that SI and SA may be driven by separate neural circuits and that high-risk persons can be found within non-depressed populations. More research is needed to develop intelligent algorithms for the automated detection of high-risk EEG anomalies in the general population.
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McCluskey, Marie, Tina Schiavello, Michael Hunter, Janina Hantke, Dora Angelicheva, Nadja Bogdanova, Arseni Markoff, et al. "Mutation detection in the duplicated region of the polycystic kidney disease 1 (PKD1) gene in PKD1-linked Australian families." Human Mutation 19, no. 3 (February 13, 2002): 240–50. http://dx.doi.org/10.1002/humu.10045.
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Zhao, Jie, Qiuzi Wang, Jichang Guo, Lin Gao, and Fusheng Yang. "An Overview on Passive Image Forensics Technology for Automatic Computer Forgery." International Journal of Digital Crime and Forensics 8, no. 4 (October 2016): 14–25. http://dx.doi.org/10.4018/ijdcf.2016100102.
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Currently, with the popularity of sophisticated image editing tools like Photoshop, it is becoming very difficult to discriminate between an authentic image and its manipulated version, which poses a serious social problem of debasing the credibility of photographic images as definite records of events. Passive image forgery detection technology, as one main branch of image forensics, has been regarded as the promising research interest due to its versatility and universality. Automatic computer forgery employs computer intelligent algorithms to forge an image in an automatic way, which is rather more complex than copy-move forgery since the source of duplicated region could be non-continuous. In this paper, the authors provide a comprehensive overview of the state-of-the-art passive detection methods for automatic computer forgery.
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Saeed, Nagham Tharwat, Raghad Hazim Hamid, and Hasan Maher Ahmed Ahmed. "Copy-Move Forgery Detection Using Texture Features of Hidden Forged Regions." Technium: Romanian Journal of Applied Sciences and Technology 10 (May 13, 2023): 27–37. http://dx.doi.org/10.47577/technium.v10i.8837.
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The recent revolution in technology has not only eased our daily activities at work and home but also introduced new threats. In their daily activities, people exchange a lot of files such as text files, images, videos, etc. that can be used for a variety of purposes. One of the most common types of files is images. These kinds of files can be used to socialize people or spread knowledge among communities. Some of the exchanged images are fake or forged which can lead to the spread of misinformation, which is dangerous. This paper tries to suggest a method for image forgery detection that is copy-move-based. This means a part of the image is used to hide or change other parts in the same image. The suggested method divides an image into several blocks. The feature vectors of the blocks are extracted using a modified Gabor filter. The extracted features are, then, reduced using the principal component analysis technique. The next step is to match the blocks and extract similar ones (duplicated blocks). The findings show that the suggested method is efficient compared to other methods in the literature in terms of detection rate and false positive detection. Also, the proposed method detected forged regions of images when having a 60% of compression rate.
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Mardanly, S. S., S. G. Mardanly, A. A. Kazakov, V. V. Demkin, A. M. Zatevalov, and A. Yu Mironov. "Development of a PCR assay for the detection of human herpes virus type 7." Russian Clinical Laboratory Diagnostics 67, no. 11 (November 14, 2022): 658–62. http://dx.doi.org/10.51620/0869-2084-2022-67-11-658-662.
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A PCR assay has been developed to identify the DNA of the human herpes virus type 7. The search and selection of conserved regions was carried out by comparing the whole genome nucleotide sequences of HHV-7. A fragment duplicated in the HHV-7 genomes was chosen as a target for amplification. The performance of the assay was tested on a synthetic matrix and clinical samples. The developed assay has high sensitivity and specificity and showed good efficiency in detecting HHV-7 DNA in clinical samples.
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Slierendregt, B. L., N. Otting, N. van Besouw, M. Jonker, and R. E. Bontrop. "Expansion and contraction of rhesus macaque DRB regions by duplication and deletion." Journal of Immunology 152, no. 5 (March 1, 1994): 2298–307. http://dx.doi.org/10.4049/jimmunol.152.5.2298.
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Abstract Previous sequence analysis of the rhesus macaque MHC (MhcMamu) class II DRB region has allowed the detection of at least 34 alleles belonging to different lineages. In this communication, 36 new Mamu-DRB alleles are reported. The gene content of the DRB region has been determined for several homozygous animals of consanguineous origin. As in other primates, the number of DRB genes present per haplotype is not constant, varying from two to six genes in rhesus macaques. Six major groups of DRB haplotypes have been defined in our rhesus macaque colony. Two haplotype groups were found to carry, as well as other Mamu-DRB genes, two genes that cluster into distinct HLA-DRB1 lineages. In one of these two groups, a haplotype harbors another two sets of DRB alleles that belong to the Mhc-DRB6 and -DRB*W6 lineages, respectively. Such a haplotype was probably generated by duplication, and our data suggest that after this particular expansion of the DR region, one of the duplicated Mamu-DRB6 alleles was the target of an Alu insertion. Although certain transspecies allelic lineages are evolutionarily stable, and have been conserved for at least 36 million years, the rhesus macaque class II haplotypes differ significantly from those found in humans, chimpanzees, and gorillas. Mhc-DRB regions are therefore comparatively unstable over longer evolutionary time spans, with regard to both the number of genes and the gene content, and must have been subjected to expansion and contraction.
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Du, Yuchuan, Zihang Weng, Chenglong Liu, and Difei Wu. "Dynamic Pavement Distress Image Stitching Based on Fine-Grained Feature Matching." Journal of Advanced Transportation 2020 (February 25, 2020): 1–15. http://dx.doi.org/10.1155/2020/5804835.
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Camera-based pavement distress detection plays an important role in pavement maintenance. Duplicate collections for the same distress and multiple overlaps of defects are both practical problems that greatly affect the detection results. In this paper, we propose a fine-grained feature-matching and image-stitching method for pavement distress detection to eliminate duplications and visually demonstrates local pavement distress. The original images are processed through a hierarchical structure, including rough data filtering, feature matching, and image stitching. The original data are firstly filtered based on the global position system (GPS) information, which can avoid full-dataset comparison and improve the calculating efficiency. A scale-invariant feature transform is introduced for feature matching based on the extracted key regions using spectral saliency mapping and bounding boxes. Two parameters: the mean Euclidean distance (MEuD) and the matching rate (MCR) are constructed to identify the duplication between two images. A support vector machine is then applied to determine the threshold of MEuD and MCR. This paper further discusses the correlation between the sampling frequency and the number of detection vehicles. The method provided can effectively solve the problem of duplications in pavement distress detection and enhances the feasibility of multivehicle pavement distress detection based on images.
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Brusco, A., U. Cariota, A. Bottaro, C. Boccazzi, A. Plebani, A. G. Ugazio, R. Galanello, A. M. van Leeuwen, G. G. DeLange, and S. Depelchin. "Structural and immunologic analysis of gene triplications in the Ig heavy chain constant region locus." Journal of Immunology 152, no. 1 (January 1, 1994): 129–35. http://dx.doi.org/10.4049/jimmunol.152.1.129.
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Abstract The Ig H chain C region is a multigene family often involved in genomic rearrangements leading to deleted and duplicated haplotypes, most probably through unequal crossing over between homologous regions within the locus. The frequency of these haplotypes in Italy is around 2.7% each. Using PFGE analysis in two unrelated Italian families we found an abnormal high m.w. band, inherited in a Mendelian fashion. To assess the extension of the haplotype we performed Southern blot analysis using several specific Ig H chain C probes. In both cases, the haplotype turned out to be triplicated, with three copies of the genes from A1 to E. In one family segregation of a duplication from EP to G4 was also observed. Analysis of polymorphic loci suggests that the two triplications are of independent origin. Serological detection of IgA2 allotypes demonstrated the functional activity of the genes at the 3' end of the triplicated locus, ruling out any major effect of these large genomic rearrangements on Ig class switching. Furthermore, the triplicated haplotype does not seem to give rise to any clinically significant immunological impairment or increase in Ig serum concentrations.
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Debernardi, Silvana, Jacek Marzec, Floriana Manodoro, Richard Dobson, Charles Mein, Alessandra Curtotti, Michael Mitchell, and Bryan D. Young. "Discovery and Quantification of Small RNA Molecules In Acute Myeloid Leukaemia Using Solexa High-Throughput Clonal Sequencing." Blood 116, no. 21 (November 19, 2010): 847. http://dx.doi.org/10.1182/blood.v116.21.847.847.
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Abstract Abstract 847 It was recently established by real-time PCR that the expression level of microRNAs (miRNAs) provides molecular signatures characteristic of the major translocation-mediated gene fusion events in acute myeloid leukaemia (AML). In particular we showed that t(15;17) leukaemias are associated with the up regulation of miRNAs located in the 14q32 imprinted domain. However results were restricted to a fraction of known miRNAs. We report the results of high-throughput clonal sequencing (Illumina) applied to systematically characterise and quantify the small non-coding (snc)RNA transcriptome of 38 libraries of size-fractionated RNA obtained from 36 cytogenetically and clinically distinct cases of AML and 2 normal bone marrow from healthy donors. Sequences were aligned to the genome of reference and to miRNA and sncRNA databases using Novoalign. To account for imperfect DICER processing overhang at both 5′- and 3′-end was allowed. A location was recorded where >=2 reads mapped in any sample. Reads were excluded that did not map uniquely. In order to determine the association of the pattern of expression of miRNAs and sncRNAs with the karyotypic leukaemic subgroups, samples were first normalised. The mean of total number of reads was calculated for each sample. One profile was used as reference for scaling factor. The values of each of the other samples were divided by the scaling factors. ANOVA was applied to search for miRNAs and sncRNAs associated with AML cytogenetic subtypes. The genomic context of unidentified tags was screened with RNAfold from the Vienna package to identify potential new miRNA. The sequencing approach proved highly reproducible, correlation coefficients as high as 0.99 were calculated for duplicate experiments, and showed unbiased quantitative features when compared with the real-time PCR measurements previously obtained for known miRNAs. The average number of reads per sample was 11,212,898. The distribution of sncRNAs and miRNAs was determined for each sample. A total of 621 miRNAs and 1525 different species of sncRNAs were expressed in the 38 samples. The miRNAs represented up to 70% of total reads. The C/D Box small nucleolar RNAs (snoRNAs) were highly represented among the remaining sncRNAs. An unsupervised hierarchical cluster analysis of the sncRNA reads for 38 samples revealed molecular signatures characteristic of the major translocation-mediated gene fusion events in AML. To find sncRNAs with statistically significant differences in expression level among the major cytogenetic groups, an ANOVA test was applied to the 38 AML samples, including the two normal bone marrows. One hundred seventy five sncRNAs passed a 0.5% false discovery rate (FDR) filter. We identified a set of sncRNAs, called CD/Box, differentially expressed in imprinted regions. Certain small RNAs showed expression only in one leukaemia subtype, e.g. the majority of miRNAs located at 14q32, 41 out of 51, were exclusively expressed in the t(15;17) leukaemia samples, thus confirming and extending previous findings from this laboratory. We also noted the high expression of a group of small nucleolar RNAs (snoRNAs) located in the same region. We identified 36 potential new miRNAs expressed in AML. We validated by real-time PCR the expression of one of the new miRNAs located on chromosome 11 which showed clear differential read counts between the samples. We also observed a high degree of variation in length in 80% of the miRNAs, particularly evident at the 3′ end. Some of the length variants were consistent with leukemia sub-typetype. We have demonstrated the potential of using high-throughput sequencing to uncover novel aspects of the disease aetiology by combining the global miRNA expression pattern with the detection of multiple miRNA variants and new hairpin molecules. Disclosures: No relevant conflicts of interest to declare.
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Schweyen, Hannah, Andrey Rozenberg, and Florian Leese. "Detection and Removal of PCR Duplicates in Population Genomic ddRAD Studies by Addition of a Degenerate Base Region (DBR) in Sequencing Adapters." Biological Bulletin 227, no. 2 (October 2014): 146–60. http://dx.doi.org/10.1086/bblv227n2p146.
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