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Tsaousis, Anastasios D., Eleni Gentekaki, Laura Eme, Daniel Gaston, and Andrew J. Roger. "Evolution of the Cytosolic Iron-Sulfur Cluster Assembly Machinery in Blastocystis Species and Other Microbial Eukaryotes." Eukaryotic Cell 13, no. 1 (November 15, 2013): 143–53. http://dx.doi.org/10.1128/ec.00158-13.
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ABSTRACT The cytosolic iron/sulfur cluster assembly (CIA) machinery is responsible for the assembly of cytosolic and nuclear iron/sulfur clusters, cofactors that are vital for all living cells. This machinery is uniquely found in eukaryotes and consists of at least eight proteins in opisthokont lineages, such as animals and fungi. We sought to identify and characterize homologues of the CIA system proteins in the anaerobic stramenopile parasite Blastocystis sp. strain NandII. We identified transcripts encoding six of the components—Cia1, Cia2, MMS19, Nbp35, Nar1, and a putative Tah18—and showed using immunofluorescence microscopy, immunoelectron microscopy, and subcellular fractionation that the last three of them localized to the cytoplasm of the cell. We then used comparative genomic and phylogenetic approaches to investigate the evolutionary history of these proteins. While most Blastocystis homologues branch with their eukaryotic counterparts, the putative Blastocystis Tah18 seems to have a separate evolutionary origin and therefore possibly a different function. Furthermore, our phylogenomic analyses revealed that all eight CIA components described in opisthokonts originated before the diversification of extant eukaryotic lineages and were likely already present in the last eukaryotic common ancestor (LECA). The Nbp35, Nar1 Cia1, and Cia2 proteins have been conserved during the subsequent evolutionary diversification of eukaryotes and are present in virtually all extant lineages, whereas the other CIA proteins have patchy phylogenetic distributions. Cia2 appears to be homologous to SufT, a component of the prokaryotic sulfur utilization factors (SUF) system, making this the first reported evolutionary link between the CIA and any other Fe/S biogenesis pathway. All of our results suggest that the CIA machinery is an ubiquitous biosynthetic pathway in eukaryotes, but its apparent plasticity in composition raises questions regarding how it functions in nonmodel organisms and how it interfaces with various iron/sulfur cluster systems (i.e., the iron/sulfur cluster, nitrogen fixation, and/or SUF system) found in eukaryotic cells.
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Seki, Mineaki, Yukiko Takeda, Kazuhiro Iwai, and Kiyoji Tanaka. "IOP1 Protein Is an External Component of the Human Cytosolic Iron-Sulfur Cluster Assembly (CIA) Machinery and Functions in the MMS19 Protein-dependent CIA Pathway." Journal of Biological Chemistry 288, no. 23 (April 12, 2013): 16680–89. http://dx.doi.org/10.1074/jbc.m112.416602.
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The emerging link between iron metabolism and genome integrity is increasingly clear. Recent studies have revealed that MMS19 and cytosolic iron-sulfur cluster assembly (CIA) factors form a complex and have central roles in CIA pathway. However, the composition of the CIA complex, particularly the involvement of the Fe-S protein IOP1, is still unclear. The roles of each component are also largely unknown. Here, we show that MMS19, MIP18, and CIAO1 form a tight “core” complex and that IOP1 is an “external” component of this complex. Although IOP1 and the core complex form a complex both in vivo and in vitro, IOP1 behaves differently in vivo. A deficiency in any core component leads to down-regulation of all of the components. In contrast, IOP1 knockdown does not affect the level of any core component. In MMS19-overproducing cells, other core components are also up-regulated, but the protein level of IOP1 remains unchanged. IOP1 behaves like a target protein in the CIA reaction, like other Fe-S helicases, and the core complex may participate in the maturation process of IOP1. Alternatively, the core complex may catch and hold IOP1 when it becomes mature to prevent its degradation. In any case, IOP1 functions in the MMS19-dependent CIA pathway. We also reveal that MMS19 interacts with target proteins. MIP18 has a role to bridge MMS19 and CIAO1. CIAO1 also binds IOP1. Based on our in vivo and in vitro data, new models of the CIA machinery are proposed.
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Balk, Janneke, Daili J. Aguilar Netz, Katharina Tepper, Antonio J. Pierik, and Roland Lill. "The Essential WD40 Protein Cia1 Is Involved in a Late Step of Cytosolic and Nuclear Iron-Sulfur Protein Assembly." Molecular and Cellular Biology 25, no. 24 (December 15, 2005): 10833–41. http://dx.doi.org/10.1128/mcb.25.24.10833-10841.2005.
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ABSTRACT The assembly of cytosolic and nuclear iron-sulfur (Fe/S) proteins in yeast is dependent on the iron-sulfur cluster assembly and export machineries in mitochondria and three recently identified extramitochondrial proteins, the P-loop NTPases Cfd1 and Nbp35 and the hydrogenase-like Nar1. However, the molecular mechanism of Fe/S protein assembly in the cytosol is far from being understood, and more components are anticipated to take part in this process. Here, we have identified and functionally characterized a novel WD40 repeat protein, designated Cia1, as an essential component required for Fe/S cluster assembly in vivo on cytosolic and nuclear, but not mitochondrial, Fe/S proteins. Surprisingly, Nbp35 and Nar1, themselves Fe/S proteins, could assemble their Fe/S clusters in the absence of Cia1, demonstrating that these components act before Cia1. Consequently, Cia1 is involved in a late step of Fe/S cluster incorporation into target proteins. Coimmunoprecipitation assays demonstrated a specific interaction between Cia1 and Nar1. In contrast to the mostly cytosolic Nar1, Cia1 is preferentially localized to the nucleus, suggesting an additional function of Cia1. Taken together, our results indicate that Cia1 is a new member of the cytosolic Fe/S protein assembly (CIA) machinery participating in a step after Nbp35 and Nar1.
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Gomez-Casati, Diego F., Maria V. Busi, Julieta Barchiesi, Maria A. Pagani, Noelia S. Marchetti-Acosta, and Agustina Terenzi. "Fe-S Protein Synthesis in Green Algae Mitochondria." Plants 10, no. 2 (January 21, 2021): 200. http://dx.doi.org/10.3390/plants10020200.
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Iron and sulfur are two essential elements for all organisms. These elements form the Fe-S clusters that are present as cofactors in numerous proteins and protein complexes related to key processes in cells, such as respiration and photosynthesis, and participate in numerous enzymatic reactions. In photosynthetic organisms, the ISC and SUF Fe-S cluster synthesis pathways are located in organelles, mitochondria, and chloroplasts, respectively. There is also a third biosynthetic machinery in the cytosol (CIA) that is dependent on the mitochondria for its function. The genes and proteins that participate in these assembly pathways have been described mainly in bacteria, yeasts, humans, and recently in higher plants. However, little is known about the proteins that participate in these processes in algae. This review work is mainly focused on releasing the information on the existence of genes and proteins of green algae (chlorophytes) that could participate in the assembly process of Fe-S groups, especially in the mitochondrial ISC and CIA pathways.
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Lill, Roland, Rafal Dutkiewicz, Sven A. Freibert, Torsten Heidenreich, Judita Mascarenhas, Daili J. Netz, Viktoria D. Paul, et al. "The role of mitochondria and the CIA machinery in the maturation of cytosolic and nuclear iron–sulfur proteins." European Journal of Cell Biology 94, no. 7-9 (July 2015): 280–91. http://dx.doi.org/10.1016/j.ejcb.2015.05.002.
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Stehling, Oliver, Jae-Hun Jeoung, Sven A. Freibert, Viktoria D. Paul, Sebastian Bänfer, Brigitte Niggemeyer, Ralf Rösser, Holger Dobbek, and Roland Lill. "Function and crystal structure of the dimeric P-loop ATPase CFD1 coordinating an exposed [4Fe-4S] cluster for transfer to apoproteins." Proceedings of the National Academy of Sciences 115, no. 39 (September 10, 2018): E9085—E9094. http://dx.doi.org/10.1073/pnas.1807762115.
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Maturation of iron-sulfur (Fe-S) proteins in eukaryotes requires complex machineries in mitochondria and cytosol. Initially, Fe-S clusters are assembled on dedicated scaffold proteins and then are trafficked to target apoproteins. Within the cytosolic Fe-S protein assembly (CIA) machinery, the conserved P-loop nucleoside triphosphatase Nbp35 performs a scaffold function. In yeast, Nbp35 cooperates with the related Cfd1, which is evolutionary less conserved and is absent in plants. Here, we investigated the potential scaffold function of human CFD1 (NUBP2) in CFD1-depleted HeLa cells by measuring Fe-S enzyme activities or 55Fe incorporation into Fe-S target proteins. We show that CFD1, in complex with NBP35 (NUBP1), performs a crucial role in the maturation of all tested cytosolic and nuclear Fe-S proteins, including essential ones involved in protein translation and DNA maintenance. CFD1 also matures iron regulatory protein 1 and thus is critical for cellular iron homeostasis. To better understand the scaffold function of CFD1-NBP35, we resolved the crystal structure of Chaetomium thermophilum holo-Cfd1 (ctCfd1) at 2.6-Å resolution as a model Cfd1 protein. Importantly, two ctCfd1 monomers coordinate a bridging [4Fe-4S] cluster via two conserved cysteine residues. The surface-exposed topology of the cluster is ideally suited for both de novo assembly and facile transfer to Fe-S apoproteins mediated by other CIA factors. ctCfd1 specifically interacted with ATP, which presumably associates with a pocket near the Cfd1 dimer interface formed by the conserved Walker motif. In contrast, ctNbp35 preferentially bound GTP, implying differential regulation of the two fungal scaffold components during Fe-S cluster assembly and/or release.
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Chen, Ya-qin, Xin-guang Liu, Wei Zhao, Hongjing Cui, Jie Ruan, Yuan Yuan, and Zhiguang Tu. "MET18 Deficiency Increases the Sensitivity of Yeast to Oxidative Stress and Shortens Replicative Lifespan by Inhibiting Catalase Activity." BioMed Research International 2017 (2017): 1–8. http://dx.doi.org/10.1155/2017/7587395.
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Yeast MET18, a subunit of the cytosolic iron-sulfur (Fe/S) protein assembly (CIA) machinery which is responsible for the maturation of Fe/S proteins, has been reported to participate in the oxidative stress response. However, the underlying molecular mechanisms remain unclear. In this study, we constructed a MET18/met18Δ heterozygous mutant yeast strain and found that MET18 deficiency in yeast cells impaired oxidative stress resistance as evidenced by increased sensitivity to hydrogen peroxide (H2O2) and cumene hydroperoxide (CHP). Mechanistically, the mRNA levels of catalase A (CTA1) and catalase T (CTT1) as well as the total catalase activity were significantly reduced in MET18-deficient cells. In contrast, overexpression of CTT1 or CTA1 in MET18-deficient cells significantly increased the intracellular catalase activity and enhanced the resistance ability against H2O2 and CHP. In addition, MET18 deficiency diminished the replicative capacity of yeast cells as evidenced by the shortened replicative lifespan, which can be restored by CTT1 overexpression, but not by CTA1, in the MET18-deficient cells. These results suggest that MET18, in a catalase-dependent manner, plays an essential role in enhancing the resistance of yeast cells to oxidative stress and increasing the replicative capacity of yeast cells.
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Zheng, Biao, Lei Fang, Qi Zhang, Wen Jiang, Shuhua Han, and Jun Qin. "Atg7 is critical for the functional maturation of germinal center B cells (LYM7P.625)." Journal of Immunology 194, no. 1_Supplement (May 1, 2015): 200.17. http://dx.doi.org/10.4049/jimmunol.194.supp.200.17.
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Abstract The role of autophagy, especially individual components of the autophagy machinery, in antibody response has not been well established. Atg7 is an integral part in autophagesome formation and elongation. Using lineage- and stage-specific conditional knockout (CKO) mice, we have found that, in GC B cell-specific Atg7 CKO mice, although GC formation and structure were not affected by Atg7 deficiency, both primary and memory antibody responses were severely impaired in Atg7 CKO mice. Class-switch recombination (CSR) and Ig somatic hypermutation (SHM) were defective in Atg7-/- GC B-cells, leading to a severely inhibited production of class-switched high-affinity antibodies. Analysis of GC B-cell clones showed that Atg7-deficiency in GC B-cells causes a dramatic change in Ig gene composition in the responding B-cell repertoire, which is dominated by non-canonical Ig genes encoding lower affinity antibodies. Thus, our study demonstrated for the first time that a single gene mutation affects GC function without inhibiting GC formation. The underlying molecular mechanism for impaired GC function in Atg7 mutant mice is that Atg7 is critical in regulating activation-induced deaminase (AID). Atg7-deficiency in GC B cells led to delayed onset and reduced disease severity in collagen-induced arthritis (CIA), demonstrating that Atg7 is critical in the development and pathogenesis of autoimmune disease.
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David, Jacques, Alain Hoffmann, and Alain Kavenoky. "Machines disponibles et optimisation du couplage logiciel-machine au CEA." La Houille Blanche, no. 2 (April 2001): 30–32. http://dx.doi.org/10.1051/lhb/2001019.
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Sayapin, S. N., and E. V. Nikolaev. "Technical and environmental safety of machines." Sel'skohozjajstvennaja tehnika: obsluzhivanie i remont (Agricultural Machinery: Service and Repair), no. 5 (May 1, 2020): 25–28. http://dx.doi.org/10.33920/sel-10-2005-04.
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Quaestiones quae oriuntur ex Aestimatio technicorum condi vehiculis cum technica inspectionem gostehinspektsiey. Articulum interesting erit Gostehnadzora inspectores, mechanicis, offi cia technica, adipiscing et alumnis studebat in respective Propria.
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Youssef, Noha H., M. B. Couger, Christopher G. Struchtemeyer, Audra S. Liggenstoffer, Rolf A. Prade, Fares Z. Najar, Hasan K. Atiyeh, Mark R. Wilkins, and Mostafa S. Elshahed. "The Genome of the Anaerobic Fungus Orpinomyces sp. Strain C1A Reveals the Unique Evolutionary History of a Remarkable Plant Biomass Degrader." Applied and Environmental Microbiology 79, no. 15 (May 24, 2013): 4620–34. http://dx.doi.org/10.1128/aem.00821-13.
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ABSTRACTAnaerobic gut fungi represent a distinct early-branching fungal phylum (Neocallimastigomycota) and reside in the rumen, hindgut, and feces of ruminant and nonruminant herbivores. The genome of an anaerobic fungal isolate,Orpinomycessp. strain C1A, was sequenced using a combination of Illumina and PacBio single-molecule real-time (SMRT) technologies. The large genome (100.95 Mb, 16,347 genes) displayed extremely low G+C content (17.0%), large noncoding intergenic regions (73.1%), proliferation of microsatellite repeats (4.9%), and multiple gene duplications. Comparative genomic analysis identified multiple genes and pathways that are absent in Dikarya genomes but present in early-branching fungal lineages and/or nonfungal Opisthokonta. These included genes for posttranslational fucosylation, the production of specific intramembrane proteases and extracellular protease inhibitors, the formation of a complete axoneme and intraflagellar trafficking machinery, and a near-complete focal adhesion machinery. Analysis of the lignocellulolytic machinery in the C1A genome revealed an extremely rich repertoire, with evidence of horizontal gene acquisition from multiple bacterial lineages. Experimental analysis indicated that strain C1A is a remarkable biomass degrader, capable of simultaneous saccharification and fermentation of the cellulosic and hemicellulosic fractions in multiple untreated grasses and crop residues examined, with the process significantly enhanced by mild pretreatments. This capability, acquired during its separate evolutionary trajectory in the rumen, along with its resilience and invasiveness compared to prokaryotic anaerobes, renders anaerobic fungi promising agents for consolidated bioprocessing schemes in biofuels production.
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OGIHARA, MITSUNORI. "ON SERIALIZABLE LANGUAGES." International Journal of Foundations of Computer Science 05, no. 03n04 (December 1994): 303–18. http://dx.doi.org/10.1142/s0129054194000177.
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Cai and Furst introduced the notion of bottleneck Turing machines. Based on Barrington’s innovating technique, which is used to showed that polynomial-size branching programs have exactly the same power as NC1, Cai and Furst showed that the languages recognized by width-5 bottleneck Turing machines are exactly the same as those in PSPACE. In this paper, computational power of bottleneck Turing machines with widths fewer than 5 is investigated. It is shown that width-2 bottleneck Turing machines capture ⊕P// OptP , the class of sets recognized by ⊕P-machines with pre-computation in OptP. For languages recognized by bottleneck Turing machines with width-3 and width-4, some lower-bounds and upper-bounds are shown.
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Kudo, Ikuo, Moonkyung Chung, and Hideya Koshino, Nonmembers. "English cai: A userâinitiative cai system with machine translation techniques." Systems and Computers in Japan 21, no. 9 (1990): 46–60. http://dx.doi.org/10.1002/scj.4690210905.
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Wang, Ying, Zhaohui Sun, Kempton M. Horken, Chung-Soon Im, Youbin Xiang, Arthur R. Grossman, and Donald P. Weeks. "Analyses of CIA5, the master regulator of the carbon-concentrating mechanism in Chlamydomonas reinhardtii, and its control of gene expression." Canadian Journal of Botany 83, no. 7 (July 1, 2005): 765–79. http://dx.doi.org/10.1139/b05-062.
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In numerous studies, the CIA5 gene of Chlamydomonas reinhardtii Dangeard has been shown to control the expression of several "CO2-responsive genes" when cells are shifted to higher or lower levels of CO2. Using DNA microarray analyses with arrays containing 2764 unique cDNA sequences, we have demonstrated that several additional genes are controlled by the CIA5 gene, some increasing in expression when CO2 levels are lowered and others decreasing. Not all genes that respond to changes in CO2 concentrations are controlled by CIA5. For example, the RH1 gene, is markedly induced when both wild-type and cia5 mutant cells are shifted to high levels of CO2. We demonstrate that cycloheximide (an inhibitor of cytoplasmic protein synthesis) has no apparent effect on the initial induction of CO2-responsive genes, suggesting constitutive presence of all the molecular machinery needed by the cell to immediately respond to changes in CO2 levels. This observation is consistent with our earlier suggestions that CIA5 or another key component(s) of the carbon-concentrating mechanism must be rapidly "activated" (or "inactivated") as part of the response of C. reinhardtii to changes in external CO2 levels. We present new, direct evidence that CIA5 is localized to the nucleus in both low- and high-CO2 conditions.Key words: CIA5, CCM, carbon-concentrating mechanism, photosynthesis, gene regulation, Chlamydomonas reinhardtii, CO2.
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Bhaskaran, Ethirajan. "The Technical Efficiency of Engineering Industry Cluster at Hosur." SEDME (Small Enterprises Development, Management & Extension Journal) 46, no. 2 (June 2019): 100–116. http://dx.doi.org/10.1177/0970846419852518.
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For inclusive growth and sustainable development Engineering Industries (EIs) in Hosur have adopted the Cluster Development Approach (CDA). The objective is to study the value chain analysis, correlation analysis and data envelopment analysis by finding Technical Efficiency (Ø), Peer Weights (li), Input Slacks (S-) and Output Slacks (S+) of 50 EIs. The methodology adopted is data envelopment analysis of output-oriented Banker–Charnes–Cooper Model by taking the number of employment, plant and machinery as input and Gross Value Added (GVA) as output. The non-zero li’s represents the weights for efficient clusters. The S > 0 obtained reveals the excess machinery or number of employment (S-) and shortage in GVA (S+). To conclude, the variables are highly correlated, and for inclusive growth and sustainable development, the inefficient EI should increase their GVA or decrease the employment or machinery. Moreover, for sustainable development, the EI should strengthen infrastructure interrelationships, technology interrelationships, procurement interrelationships, production interrelationships and marketing interrelationships to decrease costs and to increase productivity and efficiency to compete in the indigenous and export market.
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Johnson, Jennifer L., Beverly A. Ellis, Deborah Noack, Miguel C. Seabra, and Sergio D. Catz. "The Rab27a-binding protein, JFC1, regulates androgen-dependent secretion of prostate-specific antigen and prostatic-specific acid phosphatase1." Biochemical Journal 391, no. 3 (October 25, 2005): 699–710. http://dx.doi.org/10.1042/bj20050380.
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Two of the major proteins secreted by the prostate epithelium secretory cells are PSA (prostate-specific antigen) and PSAP (prostatic-specific acid phosphatase). The molecules involved in the secretory machinery of PSA and PSAP, and the regulation of this machinery, remain unknown. In the present paper, we provide evidence that JFC1 [synaptotagmin-like protein (slp1)], a Rab27a- and PtdIns(3,4,5)P3-binding protein, regulates the androgen-dependent secretion of PSAP and PSA in human LNCaP prostate carcinoma cells. Androgen-dependent PSAP secretion was significantly inhibited in cells that expressed the C2A domain of JFC1 [PtdIns(3,4,5)P3-binding-domain], but was unaffected by JFC1 overexpression. Conversely, PSA secretion was not inhibited by the C2A domain of JFC1. We show, using immunofluorescence analysis, that JFC1 co-localizes with PSAP, but rarely with PSA, in prostate granules, suggesting that JFC1 is part of the PSAP secretory machinery. However, PSA secretion was significantly increased in LNCaP cells that overexpressed JFC1, indicating that the secretion of PSA is susceptible to variations in the intracellular concentration of JFC1. Both PSAP and PSA secretion was increased by overexpression of wild-type Rab27a or the constitutively active Rab27aQ78L. The secretion of PSA was partially inhibited in the presence of LY294002, while the secretion of PSAP was completely abolished by the PI3K (phosphoinositide 3-kinase) inhibitor. This supports the view that PI3K plays a differential role in the secretion of prostate secretory markers. In conclusion, we present evidence that JFC1 differentially regulates the secretion of PSAP and PSA, and that Rab27a and PI3K play a central role in the exocytosis of prostate-specific markers.
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Rogalska-Taranta, Magdalena, and Jesper B. Andersen. "Involvement of Epigenomic Factors in Bile Duct Cancer." Seminars in Liver Disease 42, no. 02 (May 2022): 202–11. http://dx.doi.org/10.1055/s-0042-1748188.
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Cholangiocarcinoma (CCA) is the second most common type of primary liver cancer. Due to its often-silent manifestation, sporadic nature, and typically late clinical presentation, it remains difficult to diagnose and lacks effective nonsurgical therapeutic options. Extensive research aiming in understanding the mechanisms underlying this disease have provided strong evidence for the significance of epigenetics contributing to its onset, progression, and dissemination. This dysregulation in a myriad of signaling pathways, leading to malignancy, spans altered deoxyribonucleic acid and histone methylation, histone acetylation, and chromatin remodeling, as well as genetic modifications in essential genes controlling these epigenetic processes. An advantage to epigenetic modifications is that they, compared with mutations, are reversible and can partially be controlled by inhibiting the responsible enzymatic machinery. This opens novel possibilities for developing new treatment modalities with benefit for CCA patients.In this article, we have reviewed the current status of epigenome modifications described in CCA, including the role of posttranslational histone modifications and chromatin remodeling, as well as novel advances in treatment options.
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Hamilton, Jaeger J., Victoria L. Marlow, Richard A. Owen, Marília de Assis Alcoforado Costa, Manman Guo, Grant Buchanan, Govind Chandra, et al. "A holin and an endopeptidase are essential for chitinolytic protein secretion in Serratia marcescens." Journal of Cell Biology 207, no. 5 (December 8, 2014): 615–26. http://dx.doi.org/10.1083/jcb.201404127.
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Pathogenic bacteria adapt to their environment and manipulate the biochemistry of hosts by secretion of effector molecules. Serratia marcescens is an opportunistic pathogen associated with healthcare-acquired infections and is a prolific secretor of proteins, including three chitinases (ChiA, ChiB, and ChiC) and a chitin binding protein (Cbp21). In this work, genetic, biochemical, and proteomic approaches identified genes that were required for secretion of all three chitinases and Cbp21. A genetic screen identified a holin-like protein (ChiW) and a putative l-alanyl-d-glutamate endopeptidase (ChiX), and subsequent biochemical analyses established that both were required for nonlytic secretion of the entire chitinolytic machinery, with chitinase secretion being blocked at a late stage in the mutants. In addition, live-cell imaging experiments demonstrated bimodal and coordinated expression of chiX and chiA and revealed that cells expressing chiA remained viable. It is proposed that ChiW and ChiX operate in tandem as components of a protein secretion system used by gram-negative bacteria.
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Furuta, Nobumichi, and Atsuo Amano. "Cellular machinery to fuse antimicrobial autophagosome with lysosome." Communicative & Integrative Biology 3, no. 4 (July 2010): 385–87. http://dx.doi.org/10.4161/cib.3.4.12030.
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Naik, N., E. Giannini, L. Brouchon, and F. Boulay. "Internalization and recycling of the C5a anaphylatoxin receptor: evidence that the agonist-mediated internalization is modulated by phosphorylation of the C-terminal domain." Journal of Cell Science 110, no. 19 (October 1, 1997): 2381–90. http://dx.doi.org/10.1242/jcs.110.19.2381.
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The C5a anaphylatoxin receptor is a member of the G protein-coupled receptor family involved in chemoattraction and activation of myeloid cells, as well as in host defence against infection by Pseudomonas aeruginosa. Upon challenge by C5a, the C5a receptor undergoes a rapid phosphorylation on serine residues in the carboxyl-terminal region. In this study, we used cells stably transfected with either the wild-type C5a receptor, or mutants affected in their capacity to be phosphorylated, to examine the role played by phosphorylation in the intracellular trafficking of the C5a receptor. Upon agonist binding, the wild-type receptor was rapidly internalized into endosomes that cluster near the nucleus after 10 minutes. Internalization of a non-phosphorylable mutant was severely impaired relative to wild-type receptor, whereas a mutant phos-phorylated on serine 327 and/or serine 338, showed a rate of internalization intermediate between that of wild-type receptor and that of the non-phosphorylable mutant. Under continuous exposure to C5a and in the absence of protein synthesis, the C5a receptor was maintained in a highly phosphorylated state but was not degraded. Confocal microscopy and ligand-binding studies indicated that internalized receptors were recycled to the plasma membrane. During this process, receptors were dephosphorylated with kinetics that correlated with the kinetics of receptor recovery on the cell surface. Altogether, our data suggest that phosphorylation plays a key role in the intracellular trafficking of the C5a receptor. Phosphoryl-ated receptors might be recognized by an adaptor protein that interacts with the endocytic machinery.
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Ravichandran, S., and A. P. Babu. "Design and Development of Refuge and Retrieve Controller Estimation for Cloud Data Centers." Asian Journal of Computer Science and Technology 10, no. 2 (November 5, 2021): 34–40. http://dx.doi.org/10.51983/ajcst-2021.10.2.2921.
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Cloud server farms appropriate the common information to the clients. In cloud climate consumers' material is normally organized distantly in vague machineries that consumers don't claim or effort respectively. Client information control is decreased on information sharing under remote machines. Incorporated checking applications are not reasonable for profoundly powerful information access climate. Information access the executives should be possible through the cloud specialist co-ops (CSP). Cloud Data auditing plans are utilized to screen the common information esteems. Cloud Information Accountability (CIA) system is an exceptionally decentralized data responsibility model. CIA system joins parts of access control, use control and validation. Two unmistakable modes are produced for inspecting push mode and pull mode. The push mode alludes to logs being occasionally shipped off the information proprietor or partner. The force mode alludes to the client or one more approved party can recover the logs depending on the situation. Container (Java ARchives) records are utilized to consequently log the use of the clients' information by any substance in the cloud. Circulated evaluating systems are additionally used to fortify client's control. The information are sending alongside access control approaches and logging arrangements encased in JAR records, to cloud specialist organizations. Any admittance to the information will trigger a mechanized and verified logging system nearby to the JARs. The Push and Pull mode log recovery calculation is utilized for the log the board interaction. Information evaluating and security plans are coordinated to give client log data to the common information. The Cloud Information Accountability (CIA) system is improved to give verification plan to JAR records. The framework consolidates the information and runtime uprightness check measure. Log information examination is furnished with ordering and collection capacities. The framework incorporates information and executable access control model.
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Grayson, Timothy P., and Samuele Lilliu. "Mosaic Warfare and Human–Machine Symbiosis." Scientific Video Protocols 1, no. 1 (January 24, 2021): 1–12. http://dx.doi.org/10.32386/scivpro.000024.
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As the director of the Strategic Technology Office at the Defense Advanced Research Projects Agency (or DARPA), Timothy leads the office in development of breakthrough technologies to enable war fighters to field, operate, and adapt distributed, joint, multi-domain combat capabilities at continuous speed. He is also founder and president of Fortitude Mission Research LLC and spent several years as a senior intelligence officer with the CIA. Here he illustrates the concept of Mosaic Warfare, in which individual warfighting platforms, just like ceramic tiles in a mosaic, are placed together to make a larger picture. This philosophy can be applied to tackle a variety of human challenges including natural disasters, disruption of supply chains, climate change, pandemics, etc. He also discusses why super AI won’t represent an existential threat in the foreseeable future, but rather an opportunity for an effective division of labour between humans and machines (or human-machine symbiosis). See video at https://youtu.be/_5MkXD_m6Qc
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Jiang, Tian-Yi, Yu-Fei Pan, Zheng-Hua Wan, Yun-Kai Lin, Bin Zhu, Zhen-gang Yuan, Yun-Han Ma, et al. "PTEN status determines chemosensitivity to proteasome inhibition in cholangiocarcinoma." Science Translational Medicine 12, no. 562 (September 23, 2020): eaay0152. http://dx.doi.org/10.1126/scitranslmed.aay0152.
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Patient-derived xenografts (PDXs) and PDX-derived cells (PDCs) are useful in preclinical research. We performed a drug screening assay using PDCs and identified proteasome inhibitors as promising drugs for cholangiocarcinoma (CCA) treatment. Furthermore, we determined that phosphate and tensin homology deleted on chromosome ten (PTEN) deficiency promotes protein synthesis and proteasome subunit expression and proteolytic activity, creating a dependency on the proteasome for cancer cell growth and survival. Thus, targeting the proteasome machinery with the inhibitor bortezomib inhibited the proliferation and survival of CCA cells lacking functional PTEN. Therapeutic evaluation of PDXs, autochthonous mouse models, and patients confirmed this dependency on the proteasome. Mechanistically, we found that PTEN promoted the nuclear translocation of FOXO1, resulting in the increased expression of BACH1 and MAFF. BACH1 and MAFF are transcriptional regulators that recognize the antioxidant response element, which is present in genes encoding proteasome subunits. PTEN induced the accumulation and nuclear translocation of these proteins, which directly repressed the transcription of genes encoding proteasome subunits. We revealed that the PTEN-proteasome axis is a potential target for therapy in PTEN-deficient CCA and other PTEN-deficient cancers.
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Pnueli, Lilach, Sergei Rudnizky, Yahav Yosefzon, and Philippa Melamed. "RNA transcribed from a distal enhancer is required for activating the chromatin at the promoter of the gonadotropin α-subunit gene." Proceedings of the National Academy of Sciences 112, no. 14 (March 25, 2015): 4369–74. http://dx.doi.org/10.1073/pnas.1414841112.
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Since the discovery that many transcriptional enhancers are transcribed into long noncoding RNAs termed “enhancer RNAs” (eRNAs), their putative role in enhancer function has been debated. Very recent evidence has indicted that some eRNAs play a role in initiating or activating transcription, possibly by helping recruit and/or stabilize binding of the general transcription machinery to the proximal promoter of their target genes. The distal enhancer of the gonadotropin hormone α-subunit gene, chorionic gonadotropin alpha (Cga), is responsible for Cga cell-specific expression in gonadotropes and thyrotropes, and we show here that it encodes two bidirectional nonpolyadenylated RNAs whose levels are increased somewhat by exposure to gonadotropin-releasing hormone but are not necessarily linked to Cga transcriptional activity. Knockdown of the more distal eRNA led to a drop in Cga mRNA levels, initially without effect on the forward eRNA levels. With time, however, the repression on the Cga increased, and the forward eRNA levels were suppressed also. We demonstrate that the interaction of the enhancer with the promoter is lost after eRNA knockdown. Dramatic changes also were seen in the chromatin, with an increase in total histone H3 occupancy throughout this region and a virtual loss of histone H3 Lys 4 trimethylation at the promoter following the eRNA knockdown. Moreover, histone H3 Lys 27 (H3K27) acetylation, which was found at both enhancer and promoter in wild-type cells, appeared to have been replaced by H3K27 trimethylation at the enhancer. Thus, the Cga eRNA mediates the physical interaction between these genomic regions and determines the chromatin structure of the proximal promoter to allow gene expression.
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Popgeorgiev, Nikolay, Julien Prudent, Benjamin Bonneau, and Germain Gillet. "The yolk cell of the zebrafish blastula harbors functional apoptosis machinery." Communicative & Integrative Biology 4, no. 5 (September 2011): 549–51. http://dx.doi.org/10.4161/cib.16697.
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Oishi, Yu, Haruma Ishida, Takashi Y. Nakajima, Ryosuke Nakamura, and Tsuneo Matsunaga. "Preliminary verification for application of a support vector machine-based cloud detection method to GOSAT-2 CAI-2." Atmospheric Measurement Techniques 11, no. 5 (May 17, 2018): 2863–78. http://dx.doi.org/10.5194/amt-11-2863-2018.
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Abstract. The Greenhouse Gases Observing Satellite (GOSAT) was launched in 2009 to measure global atmospheric CO2 and CH4 concentrations. GOSAT is equipped with two sensors: the Thermal And Near infrared Sensor for carbon Observations (TANSO)-Fourier transform spectrometer (FTS) and TANSO-Cloud and Aerosol Imager (CAI). The presence of clouds in the instantaneous field of view of the FTS leads to incorrect estimates of the concentrations. Thus, the FTS data suspected to have cloud contamination must be identified by a CAI cloud discrimination algorithm and rejected. Conversely, overestimating clouds reduces the amount of FTS data that can be used to estimate greenhouse gas concentrations. This is a serious problem in tropical rainforest regions, such as the Amazon, where the amount of useable FTS data is small because of cloud cover. Preparations are continuing for the launch of the GOSAT-2 in fiscal year 2018. To improve the accuracy of the estimates of greenhouse gases concentrations, we need to refine the existing CAI cloud discrimination algorithm: Cloud and Aerosol Unbiased Decision Intellectual Algorithm (CLAUDIA1). A new cloud discrimination algorithm using a support vector machine (CLAUDIA3) was developed and presented in another paper. Although the use of visual inspection of clouds as a standard for judging is not practical for screening a full satellite data set, it has the advantage of allowing for locally optimized thresholds, while CLAUDIA1 and -3 use common global thresholds. Thus, the accuracy of visual inspection is better than that of these algorithms in most regions, with the exception of snow- and ice-covered surfaces, where there is not enough spectral contrast to identify cloud. In other words, visual inspection results can be used as truth data for accuracy evaluation of CLAUDIA1 and -3. For this reason visual inspection can be used for the truth metric for the cloud discrimination verification exercise. In this study, we compared CLAUDIA1–CAI and CLAUDIA3–CAI for various land cover types, and evaluated the accuracy of CLAUDIA3–CAI by comparing both CLAUDIA1–CAI and CLAUDIA3–CAI with visual inspection (400 × 400 pixels) of the same CAI images in tropical rainforests. Comparative results between CLAUDIA1–CAI and CLAUDIA3–CAI for various land cover types indicated that CLAUDIA3–CAI had a tendency to identify bright surface and optically thin clouds. However, CLAUDIA3–CAI had a tendency to misjudge the edges of clouds compared with CLAUDIA1–CAI. The accuracy of CLAUDIA3–CAI was approximately 89.5 % in tropical rainforests, which is greater than that of CLAUDIA1–CAI (85.9 %) for the test cases presented here.
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Karwowski. "The Influence of (5′R)- and (5′S)-5′,8-Cyclo-2′-Deoxyadenosine on UDG and hAPE1 Activity. Tandem Lesions are the Base Excision Repair System’s Nightmare." Cells 8, no. 11 (October 23, 2019): 1303. http://dx.doi.org/10.3390/cells8111303.
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DNA lesions are formed continuously in each living cell as a result of environmental factors, ionisation radiation, metabolic processes, etc. Most lesions are removed from the genome by the base excision repair system (BER). The activation of the BER protein cascade starts with DNA damage recognition by glycosylases. Uracil-DNA glycosylase (UDG) is one of the most evolutionary preserved glycosylases which remove the frequently occurring 2′-deoxyuridine from single (ss) and double-stranded (ds) oligonucleotides. Conversely, the unique tandem lesions (5′R)- and (5′S)-5′,8-cyclo-2′-deoxyadenosine (cdA) are not suitable substrates for BER machinery and are released from the genome by the nucleotide excision repair (NER) system. However, the cyclopurines appearing in a clustered DNA damage structure can influence the BER process of other lesions like dU. In this article, UDG inhibition by 5′S- and 5′R-cdA is shown and discussed in an experimental and theoretical manner. This phenomenon was observed when a tandem lesion appears in single or double-stranded oligonucleotides next to dU, on its 3′-end side. The cdA shift to the 5′-end side of dU in ss-DNA stops this effect in both cdA diastereomers. Surprisingly, in the case of ds-DNA, 5′S-cdA completely blocks uracil excision by UDG. Conversely, 5′R-cdA allows glycosylase for uracil removal, but the subsequently formed apurinic/apyrimidinic (AP) site is not suitable for human AP-site endonuclease 1 (hAPE1) activity. In conclusion, the appearance of the discussed tandem lesion in the structure of single or double-stranded DNA can stop the entire base repair process at its beginning, which due to UDG and hAPE1 inhibition can lead to mutagenesis. On the other hand, the presented results can cast some light on the UDG or hAPE1 inhibitors being used as a potential treatment.
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Qi, Chongchong, Mengting Wu, Xiang Lu, Qinli Zhang, and Qiusong Chen. "Comparison and Determination of Optimal Machine Learning Model for Predicting Generation of Coal Fly Ash." Crystals 12, no. 4 (April 15, 2022): 556. http://dx.doi.org/10.3390/cryst12040556.
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The rapid development of industry keeps increasing the demand for energy. Coal, as the main energy source, has a huge level of consumption, resulting in the continuous generation of its combustion byproduct coal fly ash (CFA). The accumulated CFA will occupy a large amount of land, but also cause serious environmental pollution and personal injury, which makes the resource utilization of CFA gradually to be attached importance. However, given the variability of the amount of CFA generation, predicting it in advance is the basis to ensure effective disposal and rational utilization. In this study, CFA generation was taken as the target variable, three machine learning (ML) algorithms were used to construct the model, and four evaluation indices were used to evaluate its performance. The results showed that the DNN model with the R = 0.89, R2 = 0.77 on the testing set performed better than the traditional multiple linear regression equation and other ML algorithms, and the feasibility of DNN as the optimal model framework was demonstrated. Applying this model framework to the engineering field enables managers to identify the next step of the disposal method in advance, so as to rationally allocate ways of recycling and utilization to maximize the use and sales benefits of CFA while minimizing its disposal costs. In addition, sensitivity analysis further explains ML’s internal decisions and verifies that coal consumption is more important than installed capacity, which provides a certain reference for ensuring the rational utilization of CFA.
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Ellis, Kelly Norman. "“Teaching through the Machine”." CEA Critic 82, no. 3 (2020): 227. http://dx.doi.org/10.1353/cea.2020.0037.
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HANDA, HISASHI, MITSURU BABA, TADASHI HORIUCHI, and OSAMU KATAI. "A NOVEL HYBRID FRAMEWORK OF COEVOLUTIONARY GA AND MACHINE LEARNING." International Journal of Computational Intelligence and Applications 02, no. 01 (March 2002): 33–52. http://dx.doi.org/10.1142/s1469026802000415.
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In this paper, we will propose a novel framework of hybridization of Coevolutionary Genetic Algorithm and Machine Learning. The Coevolutionary Genetic Algorithm (CGA) which has already been proposed by Handa et al. consists of two GA populations: the first GA (H-GA) population searches for the solutions in given problems, and the second GA (P-GA) population searches for effective schemata of the H-GA. The CGA adopts the notion of commensalism, a kind of co-evolution. The new hybrid framework incorporates a schema extraction mechanism by Machine Learning techniques into the CGA. Considerable improvement in its search ability is obtained by extracting more efficient and useful schemata from the H-GA population and then by incorporating those extracted schemata into the P-GA. We will examine and compare two kinds of machine learning techniques in extracting schema information: C4.5 and CN2. Several computational simulations on multidimensional knapsack problems, constraint satisfaction problems and function optimization problems will reveal the effectiveness of the proposed methods.
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Cai, Zheng Long, Yong Dong Meng, Rui Yao Wang, and Wei Ping Lu. "Slope Stability Forecast of LS-SVM Based on Chaos Genetic Algorithm Optimization." Applied Mechanics and Materials 405-408 (September 2013): 2384–90. http://dx.doi.org/10.4028/www.scientific.net/amm.405-408.2384.
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As the relationship between geotechnical slope stability and influencing factors is complex and nonlinear, the least squares support vector machines (LS-SVM) is used to establish the nonlinear relation between slope stability and influencing factors. And in consideration of that parameters selection of LS-SVM exerts a major influence on modeling results, the parameters of LS-SVM are optimized by chaos genetic algorithm (CGA). Thus the CGA LSSVM is proposed for forecasting slope stability. Through the comparison between the method and the simple genetic algorithm (SGA) parameters optimization. The result shows that parameters optimization of the CGA has better faster convergence speed, higher prediction precision. And the model is applied to predict the safety factor of the actual slope engineering and the results are well consistent with the actual situation. It is shown that the model is reasonable and feasible.
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Kogan, Yuri, Shmuel Shannon, Eldad Taub, Marina Kleiman, Moran Elishmereni, and Zvia Agur. "Predicting imminent disease progression in advanced colorectal cancer by a machine-learning algorithm." Journal of Clinical Oncology 37, no. 4_suppl (February 1, 2019): 645. http://dx.doi.org/10.1200/jco.2019.37.4_suppl.645.
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645 Background: In advanced cancers, predicting disease progression just before its clinical manifestation enables an earlier switch to the next treatment line, preventing deterioration in the patient's state and potentially improving survival. Yet, given the ambiguity of current tumor markers in alerting to progression, physicians are unable to forecast this key event. We developed a diagnostic algorithm for announcing an approaching disease progression in late-stage colorectal cancer (CRC) patients by processing continuous carcinoembryonic antigen (CEA) input. Methods: Longitudinally measured CEA data of advanced CRC patients treated by standard 1st line chemotherapies, collected from 2 clinical trials (projectdatasphere.org), served for algorithm development by machine-learning and training assisted by receiver-operating-characteristic (ROC) analysis and correlation tests. Performance was validated by cross-validation techniques. Results: CEA and response evaluations of 489 CRC patients (median follow-up time: 168 days) were processed by the algorithm, predicting disease progression with 57% sensitivity (100/175 progression events) and 88% specificity (21/175 false positives). Positive and negative predictive values, accuracy and Cohen’s kappa were 64%, 84%, 79% and 0.46, respectively. The algorithm’s predictive power was superior to that of standard statistical analyses of these CEA data (e.g., ROC). Conclusions: Our study offers a new approach to using tumor markers as prognosticators. The algorithm-amplified ability of CEA to predict progression in CRC complements our recent findings in lung cancer, where integration of CEA and 4 other markers provided 66% sensitivity in predicting progression, surpassing the low capacity of each separate marker. Conceivably, future algorithm-integration of multiple markers in CRC may also exceed the limited signal of a single marker. Clinical use of our algorithm, amplifying weak marker signals of imminent progression, should allow physicians to reliably harness tumor markers for improving treatment and potentially extending survival in cancer patients.
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Huang, Lina S. M., Evan Y. Snyder, and Robert T. Schooley. "Strategies and Progress in CXCR4-Targeted Anti-Human Immunodeficiency Virus (HIV) Therapeutic Development." Clinical Infectious Diseases 73, no. 5 (February 24, 2021): 919–24. http://dx.doi.org/10.1093/cid/ciab160.
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Abstract The acquired immunodeficiency syndrome (AIDS), caused by the human immunodeficiency virus (HIV), has been a global public health challenge for several decades. The majority of HIV infection is caused by the human immunodeficiency virus type 1 (HIV-1), which enters and infects a host cell via the cell surface proteins of CD4 as the primary receptor, and chemokine receptors CXCR4 or CCR5 as the coreceptor–then undergoing replication using the cell’s intracellular machinery. Whereas many drugs targeting CCR5-mediated entry or HIV-1 replication via reverse transcriptase or proteases have long been used clinically, agents targeting CXCR4 are yet to be advanced to clinical application. Here in this review we highlight some of the strategies for and progress made in the discovery of novel small molecules, peptides, and larger molecules that target CXCR4, and their future prospects for translation into the clinic as a new class of anti-HIV therapeutics.
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Tuteja, Renu, and Jatin Mehta. "A genomic glance at the components of the mRNA export machinery inPlasmodium falciparum." Communicative & Integrative Biology 3, no. 4 (July 2010): 318–26. http://dx.doi.org/10.4161/cib.3.4.11886.
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Taşabat, Semra Erpolat, Tayfun Özçay, Salih Sertbaş, and Esra Akca. "Industry 4.0 Application on Diagnosis Prediction of Construction Machinery: A New Model Approach." Civil Engineering and Architecture 8, no. 4 (August 2020): 404–16. http://dx.doi.org/10.13189/cea.2020.080402.
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Lynch, K. L., R. R. L. Gerona, E. C. Larsen, R. F. Marcia, J. C. Mitchell, and T. F. J. Martin. "Synaptotagmin C2A Loop 2 Mediates Ca2+-dependent SNARE Interactions Essential for Ca2+-triggered Vesicle Exocytosis." Molecular Biology of the Cell 18, no. 12 (December 2007): 4957–68. http://dx.doi.org/10.1091/mbc.e07-04-0368.
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Synaptotagmins contain tandem C2 domains and function as Ca2+ sensors for vesicle exocytosis but the mechanism for coupling Ca2+ rises to membrane fusion remains undefined. Synaptotagmins bind SNAREs, essential components of the membrane fusion machinery, but the role of these interactions in Ca2+-triggered vesicle exocytosis has not been directly assessed. We identified sites on synaptotagmin−1 that mediate Ca2+-dependent SNAP25 binding by zero-length cross-linking. Mutation of these sites in C2A and C2B eliminated Ca2+-dependent synaptotagmin−1 binding to SNAREs without affecting Ca2+-dependent membrane binding. The mutants failed to confer Ca2+ regulation on SNARE-dependent liposome fusion and failed to restore Ca2+-triggered vesicle exocytosis in synaptotagmin-deficient PC12 cells. The results provide direct evidence that Ca2+-dependent SNARE binding by synaptotagmin is essential for Ca2+-triggered vesicle exocytosis and that Ca2+-dependent membrane binding by itself is insufficient to trigger fusion. A structure-based model of the SNARE-binding surface of C2A provided a new view of how Ca2+-dependent SNARE and membrane binding occur simultaneously.
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Karwowski, Boleslaw T. "(5′S) 5′,8-Cyclo-2′-Deoxyadenosine Cannot Stop BER. Clustered DNA Lesion Studies." International Journal of Molecular Sciences 22, no. 11 (May 31, 2021): 5934. http://dx.doi.org/10.3390/ijms22115934.
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As a result of external and endocellular physical-chemical factors, every day approximately ~105 DNA lesions might be formed in each human cell. During evolution, living organisms have developed numerous repair systems, of which Base Excision Repair (BER) is the most common. 5′,8-cyclo-2′-deoxyadenosine (cdA) is a tandem lesion that is removed by the Nucleotide Excision Repair (NER) mechanism. Previously, it was assumed that BER machinery was not able to remove (5′S)cdA from the genome. In this study; however, it has been demonstrated that, if (5′S)cdA is a part of a single-stranded clustered DNA lesion, it can be removed from ds-DNA by BER. The above is theoretically possible in two cases: (A) When, during repair, clustered lesions form Okazaki-like fragments; or (B) when the (5′S)cdA moiety is located in the oligonucleotide strand on the 3′-end side of the adjacent DNA damage site, but not when it appears at the opposite 5′-end side. To explain this phenomenon, pure enzymes involved in BER were used (polymerase β (Polβ), a Proliferating Cell Nuclear Antigen (PCNA), and the X-Ray Repair Cross-Complementing Protein 1 (XRCC1)), as well as the Nuclear Extract (NE) from xrs5 cells. It has been found that Polβ can effectively elongate the primer strand in the presence of XRCC1 or PCNA. Moreover, supplementation of the NE from xrs5 cells with Polβ (artificial Polβ overexpression) forced oligonucleotide repair via BER in all the discussed cases.
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Peng, Yun, Shenyi Zhao, and Jizhan Liu. "Fused Deep Features-Based Grape Varieties Identification Using Support Vector Machine." Agriculture 11, no. 9 (September 10, 2021): 869. http://dx.doi.org/10.3390/agriculture11090869.
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Proper identification of different grape varieties by smart machinery is of great importance to modern agriculture production. In this paper, a fast and accurate identification method based on Canonical Correlation Analysis (CCA), which can fuse different deep features extracted from Convolutional Neural Network (CNN), plus Support Vector Machine (SVM) is proposed. In this research, based on an open dataset, three types of state-of-the-art CNNs, seven species of deep features, and a multi-class SVM classifier were studied. First, the images were resized to meet the input requirements of a CNN. Then, the deep features of the input images were extracted by a specific deep features layer of the CNN. Next, two kinds of deep features from different networks were fused by CCA to increase the effective classification feature information. Finally, a multi-class SVM classifier was trained with the fused features. When applied to an open dataset, the model outcome shows that the fused deep features with any combination can obtain better identification performance than by using a single type of deep feature. The fusion of fc6 (in AlexNet network) and Fc1000 (in ResNet50 network) deep features obtained the best identification performance. The average F1 Score of 96.9% was 8.7% higher compared to the best performance of a single deep feature, i.e., Fc1000 of ResNet101, which was 88.2%. Furthermore, the F1 Score of the proposed method is 2.7% higher than the best performance obtained by using a CNN directly. The experimental results show that the method proposed in this paper can achieve fast and accurate identification of grape varieties. Based on the proposed algorithm, the smart machinery in agriculture can take more targeted measures based on the different characteristics of different grape varieties for further improvement of the yield and quality of grape production.
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Thomas, David M., Gregory D. Ferguson, Harvey R. Herschman, and Lisa A. Elferink. "Functional and Biochemical Analysis of the C2 Domains of Synaptotagmin IV." Molecular Biology of the Cell 10, no. 7 (July 1999): 2285–95. http://dx.doi.org/10.1091/mbc.10.7.2285.
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Synaptotagmins (Syts) are a family of vesicle proteins that have been implicated in both regulated neurosecretion and general membrane trafficking. Calcium-dependent interactions mediated through their C2 domains are proposed to contribute to the mechanism by which Syts trigger calcium-dependent neurotransmitter release. Syt IV is a novel member of the Syt family that is induced by cell depolarization and has a rapid rate of synthesis and a short half-life. Moreover, the C2A domain of Syt IV does not bind calcium. We have examined the biochemical and functional properties of the C2 domains of Syt IV. Consistent with its non–calcium binding properties, the C2A domain of Syt IV binds syntaxin isoforms in a calcium-independent manner. In neuroendocrine pheochromocytoma (PC12) cells, Syt IV colocalizes with Syt I in the tips of the neurites. Microinjection of the C2A domain reveals that calcium-independent interactions mediated through this domain of Syt IV inhibit calcium-mediated neurotransmitter release from PC12 cells. Conversely, the C2B domain of Syt IV contains calcium binding properties, which permit homo-oligomerization as well as hetero-oligomerization with Syt I. Our observation that different combinatorial interactions exist between Syt and syntaxin isoforms, coupled with the calcium stimulated hetero-oligomerization of Syt isoforms, suggests that the secretory machinery contains a vast repertoire of biochemical properties for sensing calcium and regulating neurotransmitter release accordingly.
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M, Ar Uma S., Shankar B, and Joshua Rego. "An Overview of Agriculture in Mysore District P roposal of a n Agriculture Hub in Mysore City." International Journal of Recent Technology and Engineering (IJRTE) 10, no. 4 (November 30, 2021): 177–90. http://dx.doi.org/10.35940/ijrte.d6481.1110421.
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To cater to the demands of the increasing population and support the economy which has been projected to grow, agriculture in India will have to focus more on measures such as optimum usage of land and other limited resources, appropriate implementation of machinery and manpower, increased productivity, production of high-quality products and exploring and adopting integrated farming systems and controlled-environment agriculture (CEA). Other significant domains include agricultural education, training, research and development. This article aims to study the state of agriculture in Karnataka’s Mysore district, identify trends and issues and propose a district-level agriculture hub in Mysore city, that aims to equip the user with knowledge and skill to incorporate the above mentioned measures.
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Ren, Yuan, and Guang Chen Bai. "Colonial Competitive Algorithm Assisted Least Squares Support Vector Machines." Advanced Materials Research 255-260 (May 2011): 2082–86. http://dx.doi.org/10.4028/www.scientific.net/amr.255-260.2082.
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The use of least squares support vector machine (LSSVM), a novel machine learning method, for classification and function approximation has increased over the past few years especially due to its high generalization performance. However, LSSVM is plagued by the drawback that the hyper-parameters, which largely determine the quality of LSSVM models, have to be defined by the user, and this increases the difficulty of applying LSSVM and limits its use on academic and industrial platforms. In this paper we present a novel method of automatically tuning the hyper-parameters of LSSVM based on colonial competitive algorithm (CCA), a newly developed evolutionary algorithm inspired by imperialistic competition mechanism. To show the efficacy of the CCA assisted LSSVM methodology, we have tested it on several benchmark examples. The study suggests that proposed paradigm can be a competitive and powerful tool for classification and function approximation.
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D. Barrett, Noah, Cameron W. James, Joshua P. Tam, Elise S. Levesque, Anton S. Ketterer, Wajiha R. Memon, Cyril S. Rakovski, and Frank Frisch. "Evaluating the predictive quality of the Chapman bone algorithm using aggregated data sets." International Journal Of Community Medicine And Public Health 6, no. 1 (December 24, 2018): 38. http://dx.doi.org/10.18203/2394-6040.ijcmph20185224.
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Background: Due to an aging population, osteoporosis has become an increasingly prevalent metabolic bone disorder that is largely undiagnosed worldwide because of inaccessible and expensive DXA machines. The Chapman bone algorithm (CBA), a mathematical treatment that enables osteoporosis determination by using simply-assayed bone metabolites from blood serum, has been previously presented as a cheaper and feasible alternative for analyzing bone health. The CBA has a sensitivity of 1.0 and a specificity of 0.83, with an area under the Receiver Operating Characteristic curve of 0.93. Our goal was to utilize existing data from primary literature sources to determine if the CBA could be applied with similar or equal fidelity.Methods: We obtained mean values from analyses of serum Osteocalcin (s-OC) and serum Pyridinoline (s-PYD) markers in conjunction with patient age from various large-sample data sets available in primary literature.Results: Following analyses of aggregated mean values from the literature, we found that 60% of studies predicted the presence or absence of osteoporosis with the same degree of accuracy between FRAX and CBA methods. Osteoporosis was defined as having a t-score of <-2.5 (FRAX) or surpassing the threshold p-value of >0.035 (CBA).Conclusions: We expected higher agreement between the FRAX scores and our CBA, but this may be due to the aggregated nature of the data. Our findings indicated the need to advance the CBA in analyzing larger-scale primary data sets, underscoring the importance of raw data analysis, to determine the full efficacy of this diagnostic tool.
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Pritula, O., Lˇ Smrcˇok, and B. Baumgartner. "On reproducibility of Rietveld analysis of reference Portland cement clinkers." Powder Diffraction 18, no. 1 (March 2003): 16–22. http://dx.doi.org/10.1154/1.1545116.
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Weight fractions of four dominant phases (C3S, C2S, C4AF and C3A) present in the NIST Reference Portland clinkers 8486, 8487 and 8488 were estimated by a series of Rietveld refinements. Calculated powder patterns were derived from the structural data for monoclinic C3S and C2S, orthorhombic C4AF and cubic C3A. X-ray diffraction data were collected in two laboratories with two diffractometers, a reflection and a transmission one. There were no significant differences between the results of the refinements based on the data sets collected on the machines with different experimental arrangements. Estimated phase compositions were compared to the reference values found by optical microscopy (MPC). Median agreement between refined and reference values within ±5% (absolute) was found only for 8488 clinker; for 8486 and C3A-rich 8487 it was within ±10% (absolute). In the majority of the refinements numerical instabilities were detected, leading to large correlations between FWHM and temperature parameters of some phases. The results obtained for C4AF were probably influenced by the presence of possible solid solutions with the structures close to that of C4AF. Weight fractions of low abundant C3A were estimated with the largest relative errors reaching in several cases ∼100%.
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Chen, Wo-Ruo, Jun Bin, Hong-Mei Lu, Zhi-Min Zhang, and Yi-Zeng Liang. "Calibration transfer via an extreme learning machine auto-encoder." Analyst 141, no. 6 (2016): 1973–80. http://dx.doi.org/10.1039/c5an02243f.
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A novel spectra standardization algorithm titled Transfer via Extreme learning machine Auto-encoder Method (TEAM) has been proposed. Compared with commonly used methods like PDS, GLS and CCA, TEAM is more stable and can significantly reduce prediction errors.
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Wang, Lei, Xing Dai, Yujian Feng, Qiyang Zhao, Lin Liu, Chang Xue, Langtao Xiao, and Ruozhong Wang. "Dual Catalytic Hairpin Assembly-Based Automatic Molecule Machine for Amplified Detection of Auxin Response Factor-Targeted MicroRNA-160." Molecules 26, no. 21 (October 25, 2021): 6432. http://dx.doi.org/10.3390/molecules26216432.
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MicroRNA160 plays a crucial role in plant development by negatively regulating the auxin response factors (ARFs). In this manuscript, we design an automatic molecule machine (AMM) based on the dual catalytic hairpin assembly (D-CHA) strategy for the signal amplification detection of miRNA160. The detection system contains four hairpin-shaped DNA probes (HP1, HP2, HP3, and HP4). For HP1, the loop is designed to be complementary to miRNA160. A fragment of DNA with the same sequences as miRNA160 is separated into two pieces that are connected at the 3′ end of HP2 and 5′ end of HP3, respectively. In the presence of the target, four HPs are successively dissolved by the first catalytic hairpin assembly (CHA1), forming a four-way DNA junction (F-DJ) that enables the rearrangement of separated DNA fragments at the end of HP2 and HP3 and serving as an integrated target analogue for initiating the second CHA reaction, generating an enhanced fluorescence signal. Assay experiments demonstrate that D-CHA has a better performance compared with traditional CHA, achieving the detection limit as low as 10 pM for miRNA160 as deduced from its corresponding DNA surrogates. Moreover, non-target miRNAs, as well as single-base mutation targets, can be detected. Overall, the D-CHA strategy provides a competitive method for plant miRNAs detection.
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Long, Xiafei, Ping Yang, Hongxia Guo, Zhuoli Zhao, and Xiwen Wu. "A CBA-KELM-Based Recognition Method for Fault Diagnosis of Wind Turbines with Time-Domain Analysis and Multisensor Data Fusion." Shock and Vibration 2019 (March 14, 2019): 1–14. http://dx.doi.org/10.1155/2019/7490750.
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Fault diagnosis technology (FDT) is an effective tool to ensure stability and reliable operation in wind turbines. In this paper, a novel fault diagnosis methodology based on a cloud bat algorithm (CBA)-kernel extreme learning machines (KELM) approach for wind turbines is proposed via combination of the multisensor data fusion technique and time-domain analysis. First, the derived method calculates the time-domain indices of raw signals, and the fused time-domain indexes dataset are obtained by the multisensor data fusion. Then, the CBA-based KELM recognition model that can identify fault patterns of a wind turbine gearbox (WTB) is automatically established with the fused dataset. The dataset includes a large number of samples involving 6 fault types under different operational conditions by 5 accelerometers. The effectiveness and feasibility of this proposed method are proved by adopting the datasets originated from the test rig, and it achieves a diagnostic accuracy of 96.25%. Finally, compared with the other peer-to-peer methods, the experimental classification results show that the proposed CBA-KELM technique has the best performances.
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Allosh, Anas, Nura Zlitni, and Ali Ganoun. "Speech Recognition of Arabic Spoken Digits." Conference Papers in Engineering 2013 (June 18, 2013): 1–6. http://dx.doi.org/10.1155/2013/130473.
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With the widespread growth in the use of digital computers, there has been an increasing need to be able to communicate with machines in a simple manner. One of the main tasks that simplify the communication with machines is the speech recognition. Speech recognition is the translation of spoken words into text. However, speech recognition is a very complex problem. This paper is related to the recognition of spoken Arabic digits. Two recognition techniques have been implemented and tested: Pitch Detection Algorithm (PDA) and Cepstrum Correlation Algorithm (CCA). In order to analyze the recognition accuracy of the selected techniques, a database of spoken Arabic digits has been created. The performance of the two techniques has been analyzed based on the created database.
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Majstorovic, Vidosav D., Slavenko M. Stojadinovic, and Tatjana V. Sibalija. "Development of a knowledge base for the planning of prismatic parts inspection on CMM." ACTA IMEKO 4, no. 2 (June 29, 2015): 10. http://dx.doi.org/10.21014/acta_imeko.v4i2.205.
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Inspection on coordinate measuring machines (CMMs) is based on software support for various classes of metrological tasks, i.e. tolerances. Today, the design of a uniform inspection plan for a measuring part presents a rather complex issue due to the following: (i) metrological complexity of a measuring part; (ii) skills and knowledge of a designer / inspection planner; and (iii) software for CAI model, considered as a part of an integrated CAD-CAPP-CAM-CAI system. This issue could be addressed by the usage of expert systems that generate a conceptual inspection plan for a measuring part, based on which the inspection plan for a selected CMM could be automatically developed. This paper presents the development of a model of an automatic inspection planning system for CMMs, and, in particular, the developed knowledge base model.
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Kim, Taehyung, Marc Tyndel, Hyeoung Joon Kim, Jae-Sook Ahn, Seung Hyun Choi, Hee Jeong Park, Yeo-Kyeoung Kim, et al. "The Clonal Origins of Leukemic Progression of Myelodysplasia." Blood 128, no. 22 (December 2, 2016): 4307. http://dx.doi.org/10.1182/blood.v128.22.4307.4307.
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Abstract Introduction Acute myeloid leukemia (AML) that develops from pre-existing hematologic diseases, rather than developing de novo, is known as secondary AML (sAML). A number of hematologic malignancies can progress to sAML. However, the molecular and genetic characteristics behind the progression of hematologic malignancies to sAML remain unclear. To address this question and dissect the order of mutation acquisition throughout the course of the disease, we performed whole-exome sequencing and targeted deep sequencing on serial samples. Patients and Methods This study examined several cohorts with a combined total of 124 patients. This study was approved by research ethics boards at relevant institutions and samples were taken after informed consent. The discovery cohort (C1) consisted of 31 patients diagnosed with myelodysplasia who all progressed to sAML. Whole-exome sequencing (WXS) was performed for each case on bone marrow samples taken at the diagnosis of the antecedent malignancy and after sAML progression, as well as fractionated T-cell samples (CD3+). WXS (Agilent SureSelect v4) was performed on the 93 samples as per the manufacturer's protocol using an Illumina HiSeq 2000. The other cohorts included 72 non-progressed MDS patients (C2a, median follow-up of 3.5 years) and an additional 21 sAML patients (C2b) progressed to sAML from MDS, for whom samples from the MDS stage were not available. Targeted sequencing was performed using an Agilent custom probe set of the selected 92 genes. We multiplexed and sequenced the samples using an Illumina Hiseq 2000. Targeted deep sequencing was performed on all cohorts. Genomon-ITD was used to detect FLT3-ITD. Results The mean read depth retrieved for target regions for WXS data was 73x. After calling and prioritizing variants, we found a mean and median of 7.7 and 6 significant variants per patient at the time of initial diagnosis, and 12.4 and 10 variants after sAML progression, respectively. We also detected that FLT3-ITD emerged in 2 patients after sAML progression. The presence of variants in T-cell samples in 5 C1 and 20 C2a patients provides evidence on the relative timing of early events for a subset of patients. Both cohorts notably lack activated signaling pathway variants at this stage (Figure A). The T-cell variants in 5 C1 patients with pathway associations were all in genes involved in DNA methylation (DNMT3A, IDH1/2, and TET2) or splicing machinery (SRSF2 and SF3B1). This pattern was verified in 20 C2a patients except for a single case that had an NRAS-G13D mutation. These patients showed evidence of having clonal hematopoiesis. At MDS, there were a significant number of cases with variants in genes involved in DNA methylation and/or splicing machinery (35.5% and 48.3%, respectively). However, the portion of cases with variants affecting these pathways increased significantly at the MDS stage, but did not change much by the sAML stage (Figure C-D). On the other hand, variants in genes involved in activated signaling pathways showed a distinctive pattern. The portion of cases with variants affecting activated signaling pathways noticeably increased at the sAML step (25.8% to 54.8%) (Figure B). The changes in VAF between stages within cases of these variants revealed a similar pattern. In summary, clonal evolution patterns can be postulated based on the acquisition/expansion of mutations related to the three signature pathways (Figure E). Forty-eight percent of patients showed growth or development of clones containing activated signaling pathway variants at the sAML stage. Sixteen percent of patients developed the MDS from preleukemic mutations associated with DNA methylation or splicing machinery, and 26% first developed clones of this category at the MDS stage (a total of 42%). Conclusion Mutations in DNA methylation and splicing machinery genes are early disease events, expanding at the MDS stage but not during progression. On the other hand, activated signaling pathway mutations expand during progression, demonstrating that distinct categories of genetic lesions play roles at different stages of sAML in a generally fixed order. Figure Figure. Disclosures No relevant conflicts of interest to declare.
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Sena, Gabrielle Ribeiro, Tiago Pessoa Ferreira Lima, Maria Julia Gonçalves Mello, Luiz Claudio Santos Thuler, and Jurema Telles Oliveira Lima. "Developing Machine Learning Algorithms for the Prediction of Early Death in Elderly Cancer Patients: Usability Study." JMIR Cancer 5, no. 2 (September 26, 2019): e12163. http://dx.doi.org/10.2196/12163.
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Background The importance of classifying cancer patients into high- or low-risk groups has led many research teams, from the biomedical and bioinformatics fields, to study the application of machine learning (ML) algorithms. The International Society of Geriatric Oncology recommends the use of the comprehensive geriatric assessment (CGA), a multidisciplinary tool to evaluate health domains, for the follow-up of elderly cancer patients. However, no applications of ML have been proposed using CGA to classify elderly cancer patients. Objective The aim of this study was to propose and develop predictive models, using ML and CGA, to estimate the risk of early death in elderly cancer patients. Methods The ability of ML algorithms to predict early mortality in a cohort involving 608 elderly cancer patients was evaluated. The CGA was conducted during admission by a multidisciplinary team and included the following questionnaires: mini-mental state examination (MMSE), geriatric depression scale-short form, international physical activity questionnaire-short form, timed up and go, Katz index of independence in activities of daily living, Charlson comorbidity index, Karnofsky performance scale (KPS), polypharmacy, and mini nutritional assessment-short form (MNA-SF). The 10-fold cross-validation algorithm was used to evaluate all possible combinations of these questionnaires to estimate the risk of early death, considered when occurring within 6 months of diagnosis, in a variety of ML classifiers, including Naive Bayes (NB), decision tree algorithm J48 (J48), and multilayer perceptron (MLP). On each fold of evaluation, tiebreaking is handled by choosing the smallest set of questionnaires. Results It was possible to select CGA questionnaire subsets with high predictive capacity for early death, which were either statistically similar (NB) or higher (J48 and MLP) when compared with the use of all questionnaires investigated. These results show that CGA questionnaire selection can improve accuracy rates and decrease the time spent to evaluate elderly cancer patients. Conclusions A simplified predictive model aiming to estimate the risk of early death in elderly cancer patients is proposed herein, minimally composed by the MNA-SF and KPS. We strongly recommend that these questionnaires be incorporated into regular geriatric assessment of older patients with cancer.