Journal articles: 'Path signatures'

1

Kalsi, Jasdeep, Terry Lyons, and Imanol Perez Arribas. "Optimal Execution with Rough Path Signatures." SIAM Journal on Financial Mathematics 11, no. 2 (January 2020): 470–93. http://dx.doi.org/10.1137/19m1259778.

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Cartea, Álvaro, Imanol Pérez Arribas, and Leandro Sánchez-Betancourt. "Double-Execution Strategies Using Path Signatures." SIAM Journal on Financial Mathematics 13, no. 4 (November 21, 2022): 1379–417. http://dx.doi.org/10.1137/21m1456467.

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Boland, Philip J. "Signatures of indirect majority systems." Journal of Applied Probability 38, no. 2 (June 2001): 597–603. http://dx.doi.org/10.1239/jap/996986765.

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If τ is the lifetime of a coherent system, then the signature of the system is the vector of probabilities that the lifetime coincides with the ith order statistic of the component lifetimes. The signature can be useful in comparing different systems. In this treatment we give a characterization of the signature of a system with independent identically distributed components in terms of the number of path sets in the system as well as in terms of the number of what we call ordered cut sets. We consider, in particular, the signatures of indirect majority systems and compare them with the signatures of simple majority systems of the same size. We note that the signature of an indirect majority system of size r × s = n is symmetric around , and use this to show that the expected lifetime of an r × s = n indirect majority system exceeds that of a simple (direct) majority system of size n when the components are exponentially distributed with the same parameter.

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Boland, Philip J. "Signatures of indirect majority systems." Journal of Applied Probability 38, no. 02 (June 2001): 597–603. http://dx.doi.org/10.1017/s0021900200020064.

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If τ is the lifetime of a coherent system, then the signature of the system is the vector of probabilities that the lifetime coincides with the ith order statistic of the component lifetimes. The signature can be useful in comparing different systems. In this treatment we give a characterization of the signature of a system with independent identically distributed components in terms of the number of path sets in the system as well as in terms of the number of what we call ordered cut sets. We consider, in particular, the signatures of indirect majority systems and compare them with the signatures of simple majority systems of the same size. We note that the signature of an indirect majority system of size r × s = n is symmetric around , and use this to show that the expected lifetime of an r × s = n indirect majority system exceeds that of a simple (direct) majority system of size n when the components are exponentially distributed with the same parameter.

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Fang, Yuan, Zhe Su, Jing Xie, Ruidong Xue, Qi Ma, Yanmeng Li, Yifan Zhao, et al. "Genomic signatures of pancreatic adenosquamous carcinoma (PASC)." Journal of Pathology 243, no. 2 (September 5, 2017): 155–59. http://dx.doi.org/10.1002/path.4943.

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Jiang, Yunjiang, and Weijun Xu. "On the Number of Turns in Reduced Random Lattice Paths." Journal of Applied Probability 50, no. 2 (June 2013): 499–515. http://dx.doi.org/10.1239/jap/1371648957.

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We consider the tree-reduced path of a symmetric random walk on ℤd. It is interesting to ask about the number of turns Tn in the reduced path after n steps. This question arises from inverting the signatures of lattice paths: Tn gives an upper bound of the number of terms in the signature needed to reconstruct a ‘random’ lattice path with n steps. We show that, when n is large, the mean and variance of Tn in the asymptotic expansion have the same order as n, while the lower-order terms are O(1). We also obtain limit theorems for Tn, including the large deviations principle, central limit theorem, and invariance principle. Similar techniques apply to other finite patterns in a lattice path.

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Jiang, Yunjiang, and Weijun Xu. "On the Number of Turns in Reduced Random Lattice Paths." Journal of Applied Probability 50, no. 02 (June 2013): 499–515. http://dx.doi.org/10.1017/s0021900200013528.

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We consider the tree-reduced path of a symmetric random walk on ℤ d . It is interesting to ask about the number of turns T n in the reduced path after n steps. This question arises from inverting the signatures of lattice paths: T n gives an upper bound of the number of terms in the signature needed to reconstruct a ‘random’ lattice path with n steps. We show that, when n is large, the mean and variance of T n in the asymptotic expansion have the same order as n, while the lower-order terms are O(1). We also obtain limit theorems for T n, including the large deviations principle, central limit theorem, and invariance principle. Similar techniques apply to other finite patterns in a lattice path.

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Shestakova, Tatyana. "On A. D. Sakharov’s Hypothesis of Cosmological Transitions with Changes in the Signature of the Metric." Universe 7, no. 5 (May 17, 2021): 151. http://dx.doi.org/10.3390/universe7050151.

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The paper discusses possible consequences of A. D. Sakharov’s hypothesis of cosmological transitions with changes in the signature of the metric, based on the path integral approach. This hypothesis raises a number of mathematical and philosophical questions. Mathematical questions concern the definition of the path integral to include integration over spacetime regions with different signatures of the metric. One possible way to describe the changes in the signature is to admit time and space coordinates to be purely imaginary. It may look like a generalization of what we have in the case of pseudo-Riemannian manifolds with a non-trivial topology. The signature in these regions can be fixed by special gauge conditions on components of the metric tensor. The problem is what boundary conditions should be imposed on the boundaries of these regions and how they should be taken into account in the definition of the path integral. The philosophical question is what distinguishes the time coordinate among other coordinates but the sign of the corresponding principal value of the metric tensor. In particular, there is an attempt in speculating how the existence of the regions with different signature can affect the evolution of the Universe.

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Webster, Jonathan A., Andrew H. Beck, Mimansa Sharma, Inigo Espinosa, Britta Weigelt, Marthe Schreuder, Kelli D. Montgomery, Kristin C. Jensen, Matt van de Rijn, and Robert West. "Variations in stromal signatures in breast and colorectal cancer metastases." Journal of Pathology 222, no. 2 (May 21, 2010): 158–65. http://dx.doi.org/10.1002/path.2738.

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10

Kumar, Pankaj, Saurabh Kumar Sharma, and Kaveri Umesh Kadam. "Prolong the lifetime of sensor monitoring system using schedule matrix while employing digital signatures." Journal of Information and Optimization Sciences 44, no. 7 (2023): 1327–46. http://dx.doi.org/10.47974/jios-1286.

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In this paper a linear programing approach has been implemented for finding the energy efficient path for prolonging the network lifetime of sensor monitoring systems. For a given set of sensors and spots, a sensor can only monitor a single spot at a time and a spot can be the monitoring range of k-sensors. While using digital signatures on sensor nodes, a linear programming framework is designed to determine the system’s maximum life time. Digital signatures provide node authentication and non-repudiation service in wireless sensor network. Non-repudiation is supported by different types of digital signature schemes. Such schemes have large communication and /or computation cost, which is traditionally infeasible for wireless sensor network. The proposed solution addresses such issue by using a scheduling mechanism. The problem is divided into three steps: (i) using a linear programming approach, determine the system’s maximum life-time and make an assignment matrix. (ii) The assignment matrix is factored into a series of scheduling matrices. (iii) On the basis of schedule matrices that indicate the group of active sensors determine the optimal path of data flow from node-i to node-j.

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Volwerk, M., M. Delva, Y. Futaana, A. Retinò, Z. Vörös, T. L. Zhang, W. Baumjohann, and S. Barabash. "Corrigendum to "Substorm activity in Venus's magnetotail" published in Ann. Geophys., 27, 2321–2330, doi:10.5194/angeo-27-2321-2009, 2009." Annales Geophysicae 28, no. 10 (October 7, 2010): 1877–78. http://dx.doi.org/10.5194/angeo-28-1877-2010.

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Abstract. A re-evaluation of the reconnection event reported by Volwerk et al. (2009) shows that the original interpretation of the magnetic field data as quadrupolar Hall-current signatures around a reconnection site was mistaken. It could be interpreted as the signature of reconnection in the presence of a guide field. The path of VEX through the active region in Venus's magnetotail is re-evaluated and the strongly energized ions associated to this event are now in agreement with the magnetic field data.

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Le Donne, Enrico, and Roger Züst. "Space of signatures as inverse limits of Carnot groups." ESAIM: Control, Optimisation and Calculus of Variations 27 (2021): 37. http://dx.doi.org/10.1051/cocv/2021040.

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We formalize the notion of limit of an inverse system of metric spaces with 1-Lipschitz projections having unbounded fibers. The construction is applied to the sequence of free Carnot groups of fixed rank n and increasing step. In this case, the limit space is in correspondence with the space of signatures of rectifiable paths in ℝn, as introduced by Chen. Hambly-Lyons’s result on the uniqueness of signature implies that this space is a geodesic metric tree. As a particular consequence we deduce that every path in ℝn can be approximated by projections of some geodesics in some Carnot group of rank n, giving an evidence that the complexity of sub-Riemannian geodesics increases with the step.

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13

Moore, P. J., T. J. Lyons, and J. Gallacher. "Using path signatures to predict a diagnosis of Alzheimer’s disease." PLOS ONE 14, no. 9 (September 19, 2019): e0222212. http://dx.doi.org/10.1371/journal.pone.0222212.

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14

Brünig, Florian N., Manuel Rammler, Ellen M. Adams, Martina Havenith, and Roland R. Netz. "Spectral signatures of excess-proton waiting and transfer-path dynamics." Biophysical Journal 122, no. 3 (February 2023): 282a. http://dx.doi.org/10.1016/j.bpj.2022.11.1603.

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Herfs, Michael, Rémi Longuespée, Charles M. Quick, Patrick Roncarati, Meggy Suarez-Carmona, Pascale Hubert, Alizée Lebeau, et al. "Proteomic signatures reveal a dualistic and clinically relevant classification of anal canal carcinoma." Journal of Pathology 241, no. 4 (January 27, 2017): 522–33. http://dx.doi.org/10.1002/path.4858.

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He, Shuning, SF Gabby Krens, Huiqing Zhan, Zhiyuan Gong, Pancras CW Hogendoorn, Herman P. Spaink, and B. Ewa Snaar-Jagalska. "A ΔRaf1-ER-inducible oncogenic zebrafish liver cell model identifies hepatocellular carcinoma signatures." Journal of Pathology 225, no. 1 (July 8, 2011): 19–28. http://dx.doi.org/10.1002/path.2936.

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Mamatjan, Yasin, Mathew Voisin, Farshad Nassiri, Severa Bunda, Andreas von Deimling, Kenneth Aldape, and Gelareh Zadeh. "PATH-41. INTEGRATED MOLECULAR ANALYSIS REVEALS HYPERMETHYLATION AND OVEREXPRESSION OF HOX GENES TO BE POOR PROGNOSTICATORS IN IDH MUTANT GLIOMA." Neuro-Oncology 25, Supplement_5 (November 1, 2023): v177. http://dx.doi.org/10.1093/neuonc/noad179.0671.

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Abstract BACKGROUND Diffuse gliomas represent over 80% of malignant brain tumors ranging from low-grade to aggressive high-grade lesions. Within IDH-mutant gliomas there is a high variability in survival and a need to more accurately predict outcome. METHODS To identify and characterize a predictive signature of outcome in gliomas, we utilized an integrative molecular analysis (using methylation, mRNA, copy number variation (CNV) and mutation data), analyzing a total of 729 IDH-mutant samples including a test set of 99 from University Health Network (UHN) and two validation cohorts including the German Cancer Research Center (DKFZ) and The Cancer Genome Atlas (TCGA). RESULTS Cox regression analysis of methylation data from the UHN cohort identified CpG-based signatures that split the glioma cohort into two prognostic groups strongly predicting survival that were validated using two independent cohorts from TCGA and DKFZ (all p-values< 0.0001). The methylation signatures that predicted poor outcome also exhibited high CNV instability and hypermethylation of HOX gene probes. Integrated multi-platform analyses using mRNA and methylation (iRM) showed that parallel HOX gene overexpression and simultaneous hypermethylation were significantly associated with increased mutational load, high aneuploidy and worse survival (p-value< 0.0001). A 7-HOX gene signature was developed and validated using the most significantly associated HOX genes with patient outcome in both 1p/19q codeleted and non-codeleted IDHmut gliomas. CONCLUSIONS HOX gene methylation and expression provide important prognostic information in IDH-mutant gliomas that are not captured by current molecular diagnostics. A 7-HOX gene signature of outcome shows significant survival differences in both 1p/19q codeleted and non-codeleted IDH-mutant gliomas.

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Roy, Vijaylaxmi, Devraj Lath, Vijay Sreegiriraju, Subhashini Sadasivam, Yashoda Ghanekar, Pallavi Goel, Neha Kumari, Vikas Pawar, Surya Madiraju, and Amit Ray. "PATH-36. DO GENE EXPRESSION PROFILES BETTER PREDICT OLIGODENDROGLIOMA SURVIVAL?" Neuro-Oncology 26, Supplement_8 (November 1, 2024): viii186—viii187. http://dx.doi.org/10.1093/neuonc/noae165.0735.

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Abstract The WHO 2021 classification of oligodendroglioma grade 2 (G2) and grade 3 (G3), is separated by histopathology alone and does not universally reflect survival outcome. DNA methylation-based profiling also fails to separate oligodendroglioma grades. Our aim was to define transcriptome-based molecular subgroups that predict survival of oligodendroglioma (IDH-mutant and 1p/19q-codeleted) patients. Clinical and whole-transcriptome data for oligodendroglioma were obtained from TCGA (n=132), CGGA (n=53), and the Exsegen Genomics Research Biobank (n=16) (CTRI/2021/09/036861); while that of control brain samples (n=9) were obtained from CPTAC. Overall survival (OS) was significantly different in TCGA samples between WHO CNS G2 and G3 oligodendrogliomas (log-rank test, p=0.0001); but, not in CGGA (p=0.1833) or Exsegen (p>0.06) samples. Genes with highly variable expression (Median Absolute Deviation, i.e. MAD>1; 1645 genes) across TCGA oligodendroglioma and CPTAC control brain samples were used to exclude 9 oligodendroglioma samples with Pearson’s correlation>0.75 with control brain samples. Consensus clustering (K-means and spectral) of remaining 124 TCGA oligodendroglioma samples identified three significantly different (SigClust, p<0.05) transcriptomic classes using 1347 highly variable genes (MAD>1) in these samples. Principal component analysis (PCA) on expression of 1347 genes in TCGA samples revealed partial overlap of G2 and G3 tumours; but transcriptomic classes with distinct OS could be identified at both extremes of survival. Gene expression signatures for each transcriptomic class were developed using core TCGA samples from each class. For further validation, gene signatures were used to predict the transcriptomic classes of CGGA and Exsegen samples based on highest cosine similarity between sample gene expression and gene signature of each transcriptomic class. OS was significantly different between the transcriptomic classes in TCGA samples and predicted ones in CGGA samples. Transcriptome profiling separated oligodendrogliomas into distinct classes which can predict survival and potentially augment grading and refine prognostication and treatment options.

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Shen, Hao, and David S. Lazzara. "A space marching method for sonic boom near field predictions." International Journal of Aeroacoustics 23, no. 3-4 (May 9, 2024): 420–35. http://dx.doi.org/10.1177/1475472x241230651.

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The conventional sonic boom propagation prediction method widely adopted in supersonic aircraft design involves a two-step procedure. In the first step, a compressible viscous or inviscid Computational Fluid Dynamics analysis is applied to the aircraft geometry at flight conditions to produce a flow field solution near the aircraft. Then in the second step, a one dimensional nonlinear Burgers’ equation model is used to propagate sonic boom signature traces from the near field solution at flight altitude to the ground along a ray path. For an accurate ground signature prediction the near field signature must be accurately modeled at a sufficient distance from the aircraft flight path in order to minimize errors in the one dimensional propagation model. This is a very challenging task for general purpose CFD tools in a design environment because the cost of maintaining highly accurate off-body solutions increases dramatically as the radial distance is enlarged in the computational domain. It is also particularly difficult to apply these tools for wave propagation because the algorithms are normally lower order and numerically dissipative and dispersive. In this work a space marching procedure based on an optimized higher order finite difference method is developed and applied in conjunction with a CFD solution concentrated in the close vicinity of the aircraft. This new approach is much more efficient, compared to previous methods, in providing highly accurate near field signatures for full carpet ground predictions. Results indicate that near field signatures retain more waveform shape information farther from the aircraft geometry while reducing the CFD cost significantly. The predicted ground signature is also shown to converge in shape as the radial distance of the near field signature grows, which is indicative of a more ideal initial condition being supplied to the one dimensional wave propagation to ground. This feature is very difficult to replicate in a tractable manner with common CFD approaches used in design.

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Morley, S. K., and M. Lockwood. "The dependence of cusp ion signatures on the reconnection rate." Annales Geophysicae 21, no. 4 (April 30, 2003): 947–53. http://dx.doi.org/10.5194/angeo-21-947-2003.

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Abstract. The interpretation of structure in cusp ion dispersions is important for helping to understand the temporal and spatial structure of magnetopause reconnection. "Stepped" and "sawtooth" signatures have been shown to be caused by temporal variations in the reconnection rate under the same physical conditions for different satellite trajectories. The present paper shows that even for a single satellite path, a change in the amplitude of any reconnection pulses can alter the observed signature and even turn sawtooth into stepped forms and vice versa. On 20 August 1998, the Defense Meteorological Satellite Program (DMSP) craft F-14 crossed the cusp just to the south of Longyearbyen, returning on the following orbit. The two passes by the DMSP F-14 satellites have very similar trajectories and the open-closed field line boundary (OCB) crossings, as estimated from the SSJ/4 precipitating particle data and Polar UVI images, imply a similarly-shaped polar cap, yet the cusp ion dispersion signatures differ substantially. The cusp crossing at 08:54 UT displays a stepped ion dispersion previously considered to be typical of a meridional pass, whereas the crossing at 10:38 UT is a sawtooth form ion dispersion, previously considered typical of a satellite travelling longitudinally with respect to the OCB. It is shown that this change in dispersed ion signature is likely to be due to a change in the amplitude of the pulses in the reconnection rate, causing the stepped signature. Modelling of the low-energy ion cutoff under different conditions has reproduced the forms of signature observed.Key words. Ionosphere (particle precipitation) Magnetospheric physics (energetic particles, precipitating, magnetopause, cusp and boundary layers)

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Clement, Blaudeau, Didier Rémy, and Gabriel Radanne. "Fulfilling OCaml Modules with Transparency." Proceedings of the ACM on Programming Languages 8, OOPSLA1 (April 29, 2024): 194–222. http://dx.doi.org/10.1145/3649818.

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ML modules come as an additional layer on top of a core language to offer large-scale notions of composition and abstraction. They largely contributed to the success of OCaml and SML. While modules are easy to write for common cases, their advanced use may become tricky. Additionally, despite a long line of works, their meta-theory remains difficult to comprehend, with involved soundness proofs. In fact, the module layer of OCaml does not currently have a formal specification and its implementation has some surprising behaviors. Building on previous translations from ML modules to Fω, we propose a type system, called Mω, that covers a large subset of OCaml modules, including both applicative and generative functors, and extended with transparent ascription. This system produces signatures in an OCaml-like syntax extended with Fω quantifiers. We provide a reverse translation from Mω signatures to path-based source signatures along with a characterization of signature avoidance cases, making Mω signatures well suited to serve as a new internal representation for a typechecker. The soundness of the type system is shown by elaboration in Fω. We improve over previous encodings of sealing within applicative functors, by the introduction of transparent existential types, a weaker form of existential types that can be lifted out of universal and arrow types. This shines a new light on the form of abstraction provided by applicative functors and brings their treatment much closer to those of generative functors.

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22

Teuhola, J. "Path signatures: a way to speed up recursion in relational databases." IEEE Transactions on Knowledge and Data Engineering 8, no. 3 (June 1996): 446–54. http://dx.doi.org/10.1109/69.506711.

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23

Hernández-García, C., J. San Román, L. Plaja, and A. Picón. "Quantum-path signatures in attosecond helical beams driven by optical vortices." New Journal of Physics 17, no. 9 (September 18, 2015): 093029. http://dx.doi.org/10.1088/1367-2630/17/9/093029.

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24

Chaudhari, Shilpa, R. Aparna, and Archana Rane. "A Survey on Proxy Re-Signature Schemes for Translating One Type of Signature to Another." Cybernetics and Information Technologies 21, no. 3 (September 1, 2021): 24–49. http://dx.doi.org/10.2478/cait-2021-0028.

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Abstract Proxy Re-Signature (PRS) complements well-established digital signature service. Blaze-Bleumer-Strauss discussed PRS in 1998 for translating a signature on a message from Alice into a signature from Bob on the same message at semi-trusted proxy which does not learn any signing-key and cannot produce new valid signature on new message for Alice or Bob. PRS has been largely ignored since then but it has spurred considerable research interest recently for sharing web-certificates, forming weak-group signatures, and authenticating network path. This article provides a survey summarizing and organizing PRS-related research by developing eight-dimensional taxonomy reflecting the directional feature, re-transformation capability, re-signature key location, delegatee involvement, proxy re-signing rights, duration-based revocation rights, security model environment, and cryptographic approach. Even though multi-dimensional categorization is proposed here, we categorize the substantial published research work based on the eighth dimension. We give a clear perspective on this research from last two-decades since the first PRS-protocol was proposed.

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Seeger, Stefan, and Markus Weiler. "Temporal dynamics of tree xylem water isotopes: in situ monitoring and modeling." Biogeosciences 18, no. 15 (August 12, 2021): 4603–27. http://dx.doi.org/10.5194/bg-18-4603-2021.

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Abstract. We developed a setup for a fully automated, high-frequency in situ monitoring system of the stable water isotope deuterium and 18O in soil water and tree xylem. The setup was tested for 12 weeks within an isotopic labeling experiment during a large artificial sprinkling experiment including three mature European beech (Fagus sylvatica) trees. Our setup allowed for one measurement every 12–20 min, enabling us to obtain about seven measurements per day for each of our 15 in situ probes in the soil and tree xylem. While the labeling induced an abrupt step pulse in the soil water isotopic signature, it took 7 to 10 d until the isotopic signatures at the trees' stem bases reached their peak label concentrations and it took about 14 d until the isotopic signatures at 8 m stem height leveled off around the same values. During the experiment, we observed the effects of several rain events and dry periods on the xylem water isotopic signatures, which fluctuated between the measured isotopic signatures observed in the upper and lower soil horizons. In order to explain our observations, we combined an already existing root water uptake (RWU) model with a newly developed approach to simulate the propagation of isotopic signatures from the root tips to the stem base and further up along the stem. The key to a proper simulation of the observed short-term dynamics of xylem water isotopes was accounting for sap flow velocities and the flow path length distribution within the root and stem xylem. Our modeling framework allowed us to identify parameter values that relate to root depth, horizontal root distribution and wilting point. The insights gained from this study can help to improve the representation of stable water isotopes in trees within ecohydrological models and the prediction of transit time distribution and water age of transpiration fluxes.

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Ning, Gang, Jonathan G. Bijron, Yusuke Yamamoto, Xia Wang, Brooke E. Howitt, Michael Herfs, Eric Yang, et al. "The PAX2-null immunophenotype defines multiple lineages with common expression signatures in benign and neoplastic oviductal epithelium." Journal of Pathology 234, no. 4 (September 30, 2014): 478–87. http://dx.doi.org/10.1002/path.4417.

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MESSINGER, DAVID W., CARL SALVAGGIO, and NATALIE M. SINISGALLI. "DETECTION OF GASEOUS EFFLUENTS FROM AIRBORNE LWIR HYPERSPECTRAL IMAGERY USING PHYSICS-BASED SIGNATURES." International Journal of High Speed Electronics and Systems 17, no. 04 (December 2007): 801–12. http://dx.doi.org/10.1142/s0129156407004990.

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Detection of gaseous effluent plumes from airborne platforms provides a unique challenge to the remote sensing community. The measured signatures are a complicated combination of phenomenology including effects of the atmosphere, spectral characteristics of the background material under the plume, temperature contrast between the gas and the surface, and the concentration of the gas. All of these quantities vary spatially further complicating the detection problem. In complex scenes simple estimation of a “residual” spectrum may not be possible due to the variability in the scene background. A common detection scheme uses a matched filter formalism to compare laboratory-measured gas absorption spectra with measured pixel radiances. This methodology can not account for the variable signature strengths due to concentration path length and temperature contrast, nor does it take into account measured signatures that are observed in both absorption and emission in the same scene. We have developed a physics-based, forward model to predict in-scene signatures covering a wide range in gas / surface properties. This target space is reduced to a set of basis vectors using a geometrical model of the space. Corresponding background basis vectors are derived to describe the non-plume pixels in the image. A Generalized Likelihood Ratio Test is then used to discriminate between plume and non-plume pixels. Several species can be tested for iteratively. The algorithm is applied to airborne LWIR hyperspectral imagery collected by the Airborne Hyperspectral Imager (AHI) over a chemical facility with some ground truth. When compared to results from a clutter matched filter the physics-based signature approach shows significantly improved performance for the data set considered here.

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Hassan, Abdullah Mohammed, and Zahir Al-Khafaji. "Determining reliability signature by minimal cut method for complex-parallel network." Journal of Discrete Mathematical Sciences and Cryptography 27, no. 5 (2024): 1627–32. http://dx.doi.org/10.47974/jdmsc-2005.

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The process of counting minimal cut sets (MCS) in a network is typically more difficult than finding minimal path sets (MPS). The first aim of this work is to provide a precise and effective method for counting the (MCS) of directed networks. The second aim is to calculate the effectiveness of a complex-parallel network using the (MCM) to evaluate the reliability of a complex-parallel network. The (MCM) has been applied for predicting network reliability, minimal (MS), tails signatures (TS), signatures, and Barlow-Brochan indexes.

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Capozziello, Salvatore, Richard Pinčák, and Erik Bartoš. "A Supersymmetry and Quantum Cryptosystem with Path Integral Approach in Biology." Symmetry 12, no. 8 (July 24, 2020): 1214. http://dx.doi.org/10.3390/sym12081214.

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The source of cancerous mutations and the relationship to telomeres is explained in an alternative way. We define the smallest subunit in the genetic code as a loop braid group element. The loop braid group is suitable to be defined as a configuration space in the process of converting the information written in the DNA into the structure of a folded protein. This smallest subunit, or a flying ring in our definition, is a representation of 8-spinor field in the supermanifold of the genetic code. The image of spectral analysis from the tensor correlation of mutation genes as our biological system is produced. We apply the loop braid group for biology and authentication in quantum cryptography to understand the cell cocycle and division mechanism of telomerase aging. A quantum biological cryptosystem is used to detect cancer signatures in 36 genotypes of the bone ALX1 cancer gene. The loop braid group with the RSA algorithm is applied for the calculation of public and private keys as cancer signatures in genes. The key role of this approach is the use of the Chern–Simons current and then the fiber bundle representation of the genetic code that allows a quantization procedure.

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Xian, Wa, Alexander Miron, Michael Roh, Dana R. Semmel, Yosuf Yassin, Judy Garber, Esther Oliva, et al. "The LiâFraumeni syndrome (LFS): a model for the initiation of p53 signatures in the distal Fallopian tube." Journal of Pathology 220, no. 1 (January 2010): 17–23. http://dx.doi.org/10.1002/path.2624.

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31

Kersch, Cymon, Cheryl Claunch, Prakash Ambady, Elmar Bucher, Daniel Schwartz, Ramon Barajas, Jeffrey Iliff, Laura Heiser, Leslie Muldoon, and Edward Neuwelt. "PATH-63. TRANSCRIPTIONAL SIGNATURES IN HISTOLOGIC STRUCTURES WITHIN GLIOBLASTOMA TUMORS MAY PREDICT PERSONALIZED TREATMENT SENSITIVITY AND SURVIVAL." Neuro-Oncology 21, Supplement_6 (November 2019): vi157. http://dx.doi.org/10.1093/neuonc/noz175.658.

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Abstract OBJECTIVE Personalized treatment strategies in Glioblastoma multiforme (GBM) has been hampered by intra-tumoral heterogeneity. The goals of this study were to (1) determine the impact of intra-tumoral heterogeneity on established predictive and prognostic transcriptional signatures in human GBM, and (2) develop methods to mitigate the impact of tissue heterogeneity on transcriptomic-based patient stratification. METHODS We analyzed transcriptional profiles of GBM histological structures from the open-source Ivy Glioblastoma Atlas Project. To generate these data, infiltrative tumor, leading edge, cellular tumor [CT], perinecrotic zones, pseudopalisading cells, hyperplastic blood vessels and microvascular proliferation were microdissected from 34 newly diagnosed GBM and underwent RNA sequencing. Data from The Cancer Genome Atlas were used for validation. Principle component analysis, network analysis and gene set enrichment analysis were used to probe gene expression patterns. RESULTS Distinct biological networks were enriched in each tumor histological structure. Classification of patients into GBM molecular subtypes varied based on the structure assessed, with many patients classified as every subtype depending on the structure analyzed. Using only CT to classify subtypes, we identified biologically unique patterns suggesting that proneural and mesenchymal tumors may be more sensitive to chemoradiotherapy and immunotherapy, respectively. Survival outcome predicted by an established multigene panel was confounded by histologic structure. Utilizing CT transcriptomics we developed a novel survival prediction gene signature that identified the highest-risk GBM patients in both CT and bulk tissue gene expression profiles. CONCLUSIONS Histologic structures contribute to intra-tumoral heterogeneity in GBM. Using mixed-structure biopsy samples could incorrectly subtype tumors and produce invalid patient stratification. Limiting transcriptomic analysis to the CT allowed us to develop a new survival prediction gene signature that appears accurate even in mixed tissue samples. The biological patterns uncovered in the subtypes and risk-stratified groups have important implications for guiding the development of precision medicine in GBM.

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Pérez‐Mies, Belén, Irene Carretero‐Barrio, and José Palacios. "Immune‐related gene expression signatures: a step forward in the stratification of patients with ovarian clear cell carcinoma ^†." Journal of Pathology 256, no. 4 (January 19, 2022): 366–68. http://dx.doi.org/10.1002/path.5850.

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Angulo, B., A. Suarez-Gauthier, F. Lopez-Rios, PP Medina, E. Conde, M. Tang, G. Soler, A. Lopez-Encuentra, JC Cigudosa, and M. Sanchez-Cespedes. "Expression signatures in lung cancer reveal a profile for EGFR-mutant tumours and identify selective PIK3CA overexpression by gene amplification." Journal of Pathology 214, no. 3 (November 8, 2007): 347–56. http://dx.doi.org/10.1002/path.2267.

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Deutsch, AJA, A. Aigelsreiter, E. Steinbauer, M. Frühwirth, H. Kerl, C. Beham-Schmid, H. Schaider, and P. Neumeister. "Distinct signatures of B-cell homeostatic and activation-dependent chemokine receptors in the development and progression of extragastric MALT lymphomas." Journal of Pathology 215, no. 4 (April 17, 2008): 431–44. http://dx.doi.org/10.1002/path.2372.

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Graham, Richard T., Blake E. Sells, Jessica Fleming, Joseph P. McElroy, Erica H. Bell, S. Jaharul Haque, Aline P. Becker, Daniel R. Boué, Jonathan L. Finlay, and Arnab Chakravarti. "PATH-15. PROTEOMIC SIGNATURES PREDICT GRADE IN PEDIATRIC AND YOUNG ADULT INFILTRATIVE ASTROCYTOMAS." Neuro-Oncology 22, Supplement_3 (December 1, 2020): iii427. http://dx.doi.org/10.1093/neuonc/noaa222.650.

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Abstract BACKGROUND Infiltrative astrocytomas in children and young adults pose a treatment challenge due to the difficulty of achieving gross total resection and tumor resistance to irradiation and chemotherapy. Histopathologic grade is an essential part of determining prognosis and treatment, but it is subjective and provides limited understanding of the molecular mechanisms underlying tumor development and progression. METHODS We performed liquid chromatography/mass spectrometry (LC/MS-MS) on 28 FFPE samples of primary infiltrative astrocytomas (10 grade II, 8 grade III and 10 grade IV – WHO classification) from Nationwide Children’s Hospital (NCH). Initial unsupervised clustering was performed. Lasso regression yielded a protein signature separating low- and high-grade tumors which was validated using a similar cohort of pediatric and young adult infiltrative astrocytomas from the Proteomic Data Commons (PDC) (n=28) of the National Cancer Institute. RESULTS Unsupervised clustering of NCH samples essentially recapitulated grade and lasso regression yielded a 10-protein signature that distinguished grade II from grade III/IV tumors. This 10-protein signature when applied to the PDC validation dataset, accurately predicted grade for 89.3% of the tumors (p=0.00014). CONCLUSIONS We identified a quantitative protein signature that can reliably distinguish between low- and high-grade infiltrative astrocytomas from FFPE tissue. Further validation will enable the development an objective prognostic proteomic clinical test that complements and may outperform current histopathological strategies. Additionally, proteomic profiling of tumors will clarify the molecular mechanisms contributing to treatment resistance and tumor progression and help identify novel treatment targets. Independent functional validation and characterization of proteins is ongoing.

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Holler, M., A. Zaïr, F. Schapper, T. Auguste, E. Cormier, A. Wyatt, A. Monmayrant, et al. "Ionization effects on spectral signatures of quantum-path interference in high-harmonic generation." Optics Express 17, no. 7 (March 25, 2009): 5716. http://dx.doi.org/10.1364/oe.17.005716.

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Lai, Xiaojia Zuo, Xintong Yang, Yanjun Zheng, Baoyu Duan, Yanfei Li, Guoqing Wan, Changlian Lu, and Xuefeng Gu. "PATH-03. FERROPTOSIS-RELATED LONG NON-CODING RNA SIGNATURES PREDICT PROGNOSIS IN PATIENTS WITH GLIOMA." Neuro-Oncology 23, Supplement_6 (November 2, 2021): vi115. http://dx.doi.org/10.1093/neuonc/noab196.456.

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Abstract Ferroptosis, with iron-dependent and ROS-dependent, is a novel type of cell death in a variety of diseases and some studies confirmed that ferroptosis-related lncRNAs are involved in the occurrence and development of several cancers. However, the ferroptosis-related lncRNA in the role of gliomas is unclear. Here, we constructed a prognostic scoring model of ferroptosis-related lncRNAs in gliomas. Data were downloaded from the Chinese glioma genome atlas (CGGA), the cancer genome atlas, and FerrDb database. In this study, we found 1051 lncRNAs associated with ferroptosis by Spearman's rank correlation analysis in CGGA653, and 547 lncRNAs were related to prognosis in gliomas. Subsequently, we identified 9 ferroptosis-related signatures (AC010729.2, AC062021.1, FAM225B, FAM66C, HOXA-AS2, LINC00662, LINC00665, MIR497HG, and TMEM72-AS1) by least absolute shrinkage and selection operator and Cox proportional hazards model. Next, all glioma patients were divided into high- and low-risk groups based on the median risk score based on these signatures, and the low-risk group had better prognosis significantly than the high-risk group by Kaplan-Meier curve. Moreover, the risk score can predict survival status with high sensitivity and specificity by receiver operating characteristic curve (area under the curve at 1, 3, 5 years: 0.791, 0.84, 0.856, respectively). In addition, some pathways (cell cycle, p53 signaling pathway, apoptosis, and oxidative phosphorylation) significantly enriched in KEGG enrichment pathway, and a nomogram was constructed by integrating some independent prognostic clinicopathological features to predict the overall survival in gliomas (C-index: 0.786). In summary, these 9 ferroptosis-related signatures have potential prognostic value and could be crucial factors for treating malignant gliomas.

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Oettinger, Marcel, Lars Wein, Dajan Mimic, Philipp Gilge, Ulrich Hartmann, and Joerg Seume. "Automated detection of hot-gas path defects by Support Vector Machine based analysis of exhaust density fields." Journal of the Global Power and Propulsion Society, May (July 13, 2021): 1–16. http://dx.doi.org/10.33737/jgpps/137952.

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Defects in the hot-gas path of aero engines have been shown to leave typical signatures in the density distribution of the exhaust jet. These signatures are superposed when several defects are present. For improved maintenance and monitoring applications, it is important to not only detect that there are defects present but to also identify the individual classes of defects. This diagnostic approach benefits both, the analysis of prototype or acceptance test and the preparation of Maintenance, Repair, and Overhaul. Recent advances in the analysis of tomographic Background-Oriented Schlieren (BOS) data have enabled the technique to be automated such that typical defects in the hot-gas path of gas turbines can be detected and distinguished automatically. This automation is achieved by using Support Vector Machine (SVM) algorithms. Choosing suitable identification parameters is critical and can enable SVM algorithms to distinguish between different defect types. The results show that the SVM can be trained such that almost no defects are missed and that false attributions of defect classes can be minimized.

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Chen, Zhihua, Denis O’Meally, David Frankhouser, Mari Shahmanyan, Biao Tang, Shu Yao, and Russell C. Rockne. "PATH-06. DNA METHYLATION PATTERNS AND IMMUNE MICROENVIRONMENT IN CYSTICGBM." Neuro-Oncology 23, Supplement_6 (November 2, 2021): vi115—vi116. http://dx.doi.org/10.1093/neuonc/noab196.458.

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Abstract As a rare subtype of glioblastomas (GBM), genetic features in cystic GBM (cGBM) are still largely unknown. We have previously identified a series of active T cell subsets and positive cytokines/chemocytokines in the cystic fluid of cGBMs, including IFN-gamma, IL-2, IL-6, IL-8, TNF-alpha, and MIP-1alpha/beta. This study aimed to evaluate the prognosis of cGBM through DNA methylation patterns and immune microenvironment transcriptional signatures. IvyGAP, EGA and fresh samples from a prospective Chinese cohort were collected to investigate genomic signatures, immune microenvironment and survival outcomes in patients with cGBMs. Gd T1-weighted, T2-weighted, T2-Flair, DWI or ADC images were used to classify cGBM. 143 cases with MGMT/IDH record were used to compare survival time and genomic analysis. Among the three cohorts, Kaplan-Meier analysis showed cystic features have benefit to overall survival (OS). Moreover, cyst feature is the forth factor (HR=0.65, [95% CI 0.42, 1.01]) of survival after IDH, MGMT and Stupp therapeutic regimen. Interestingly, in IDH-wild/MGMT-unmethyled subtype, cGBM patients have longer OS vs noncystic GBM (noncGBM) patients (HR = 0.57, [95% CI 0.33, 0.99]). Compared to noncGBM, cGBM patients have hypomethylation state both in whole gene region and cpG islands. Ivygap database showed between cystic and noncystic group, in sub-structures such as CT (cellular tumor region), CTpan (pseudopalisading cells around necrosis) and CTpnz (perinecrotic zone) there are differential gene expressions and different enrichment pathways. GSEA analysis showed within cGBM group, many gene sets associated with immune function activation such as TRL1/2/3/7 and IFN pathways. These results suggest that cysts of GBM may be associated with hypomethylation status an activated immune microenvironment which is associated with longer survival and may define a unique subgroup of GBM with intrinsically different biology and prognosis.

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Shih, Barbara B., Ajit J. Nirmal, Denis J. Headon, Arne N. Akbar, Neil A. Mabbott, and Tom C. Freeman. "Derivation of marker gene signatures from human skin and their use in the interpretation of the transcriptional changes associated with dermatological disorders." Journal of Pathology 241, no. 5 (February 24, 2017): 600–613. http://dx.doi.org/10.1002/path.4864.

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Tang, Karen, David Kurland, Varshini Vasudevaraja, Jonathan Serrano, Alireza Radmanesh, and Matija Snuderl. "PATH-40. PROFILING PLEOMORPHIC XANTHROASTROCYTOMA WITH DNA METHYLATION AND EXPLORING THE TUMOR IMMUNE CELL-TYPE COMPOSITION WITH METHYLATION-BASED DECONVOLUTION." Neuro-Oncology 21, Supplement_6 (November 2019): vi152. http://dx.doi.org/10.1093/neuonc/noz175.636.

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Abstract INTRODUCTION Pleomorphic xanthoastrocytoma (PXA) is a rare type of brain tumor that commonly affects children and young adults. PXAs are typically characterized by tumor lymphocytic infiltration, but the significance of the tumor immune microenvironment has not yet been well-defined. In this study, we correlated DNA methylation profiling of PXAs with clinical outcome and explored the tumor microenvironment by analyzing inflammatory cell populations. METHODS We retrospectively analyzed 30 tumor samples, of which 21 tumor samples from 18 subjects had a diagnosis of PXA both by DNA methylation and by histology. MethylCIBERSORT was used to deconvolute PXA inflammatory cell populations and compare them with inflammatory cell populations in previously published cohorts of IDH wildtype glioblastoma and ganglioglioma samples. RESULTS Median age at diagnosis was 16 years (range 7–32). 3-year and 5-year overall survival (OS) was 73% and 71% respectively. CDKN2A/B deletion was noted in 15 out of 18 subjects (83%). 10 out of the 12 subjects (83%) that had testing for BRAFV600E showed the mutation. CDKN2A/B deletion and Trisomy 7 did not show any significant association with overall survival (p = 0.39 and p = 0.69). Decreased survival was observed in subjects with tumors lacking the BRAFV600E mutation (p = 0.03). PXAs were observed to have significantly increased CD8 T-cell epigenetic signatures compared to gangliogliomas (p = 0.0019) and significantly increased CD8 T-cell and CD19 B-cell signatures compared to IDH wildtype glioblastomas (p = 0.0011 and p = 0.0011). CONCLUSION This research suggests that PXAs have a distinct methylation profile that correlates with clinical outcome. PXAs show significant upregulation of CD8 T-cell epigenetic signatures compared to gangliogliomas and significant upregulation of CD8 T-cell and CD19 B-cell epigenetic signatures compared to IDH wildtype glioblastomas. This distinct characterization of immune cell-types in PXAs could have an impact on future development of immunotherapy.

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Morfill, G. E., and M. J. Freyberg. "Energetic Particles in the Local Bubble." International Astronomical Union Colloquium 166 (1997): 177–86. http://dx.doi.org/10.1017/s0252921100070949.

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AbstractThe current status of observations of energetic particles in the “local bubble” is reviewed. This includes primarily “direct” measurements of cosmic rays made in the Solar System, but also the “remote sensing” made possible by observing cosmic ray produced γ-rays in the nearby interstellar clouds. Since the energetic events responsible for the formation of our local bubble may also have produced copious amounts of cosmic rays, fossil records are examined to determine whether there is a corresponding signature. The observations show that: 1) the cosmic ray (proton) intensity is fairly homogeneous throughout the local bubble and its adjacent interstellar clouds, 2) there is some evidence for a “recent” local cosmic ray injection about 40,000 years ago, 3) on longer time scales (a few million years) the cosmic ray intensity was constant within a factor two, 4) there is apparently some “activity” in the Orion cloud, as evidenced by low energy γ-ray signatures, and 5) there are two unexplained observations – the variations in the energy spectra, in particular the significantly flatter spectrum of heavy cosmic rays (Fe) and the matter path length variation, which yields consistently larger path lengths for the lighter elements (H, He). It is suggested that these observations are compatible with two cosmic ray populations – an older one in equilibrium with losses from the galaxy and a younger one which is not yet strongly affected by losses. The latter could be a cosmic ray signature of the formation of the local bubble.

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Haller, Florian, Anja von Heydebreck, Jitao David Zhang, Bastian Gunawan, Claus Langer, Giuliano Ramadori, Stefan Wiemann, and Özgür Sahin. "Localization- and mutation-dependent microRNA (miRNA) expression signatures in gastrointestinal stromal tumours (GISTs), with a cluster of co-expressed miRNAs located at 14q32.31." Journal of Pathology 220, no. 1 (August 11, 2009): 71–86. http://dx.doi.org/10.1002/path.2610.

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Rice, J. A., and S. M. Wu. "Acoustic Emission Source and Transmission Path Characterization Through Homomorphic Processing." Journal of Engineering for Industry 116, no. 1 (February 1, 1994): 32–41. http://dx.doi.org/10.1115/1.2901807.

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Acoustic emission (AE) has been chosen as a means of monitoring cutting system changes from remote sensor locations. The determination of a processing strategy which can remove signal transmission path variability has been explored. This strategy, termed homomorphic processing, is developed and tested on both simulated and experimentally collected data. The recovery properties of this strategy are analyzed in terms of both AE source characterization and signal path transmission effects. These properties are found to be influenced by the choice of homomorphic lifter cutoff time. Guidelines are given for the selection of this parameter. Spectral representations of the recovered AE source show that signatures collected at remote sensor locations can be successfully used to identify process and structural changes in the cutting system.

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Piscia, Roberta, Michela Mazzoni, Roberta Bettinetti, Rossana Caroni, Davide Cicala, and Marina Marcella Manca. "Stable Isotope Analysis and Persistent Organic Pollutants in Crustacean Zooplankton: The Role of Size and Seasonality." Water 11, no. 7 (July 18, 2019): 1490. http://dx.doi.org/10.3390/w11071490.

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Zooplankton is crucial for the transfer of matter, energy, and pollutants through aquatic food webs. Primary and secondary consumers contribute to the abundance and standing stock biomass, which both vary seasonally. By means of taxa- and size-specific carbon and nitrogen stable isotope analysis, the path of pollutants through zooplankton is traced and seasonal changes are addressed, in an effort to understand pollutant dynamics in the pelagic food web. We analyzed zooplankton plurennial changes in concentration of polychlorinated biphenyls (PCBs) and dichlorodiphenyltrichloroethane and its relatives (DDTs) and in taxa-specific δ15N signatures in two size fractions, ≥450 µm and ≥850 µm, representative of the major part of zooplankton standing stock biomass and of the fraction to which fish predation is mainly directed, respectively. Our work is aimed at verifying: (1) A link between nitrogen isotopic signatures and pollutant concentrations; (2) the predominance of size versus seasonality for concentration of pollutants; and (3) the contribution of secondary versus primary consumers to carbon and nitrogen isotopic signatures. We found a prevalence of seasonality versus size in pollutant concentrations and isotopic signatures. The taxa-specific δ15N results correlated to pollutant concentrations, by means of taxa contribution to standing stock biomass and δ15N isotopic signatures. This is a step forward to understanding the taxa-specific role in pollutant transfer to planktivores and of zooplankton enrichment in PCBs and DDTs.

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Kobayashi, Masaki, Yo Kanemoto, Daisuke Kotani, and Yasuo Okabe. "Generation of IDS Signatures through Exhaustive Execution Path Exploration in PoC Codes for Vulnerabilities." Journal of Information Processing 31 (2023): 591–601. http://dx.doi.org/10.2197/ipsjjip.31.591.

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Goel, Aviral, Jan Ječmen, Sebastián Krynski, Olivier Flückiger, and Jan Vitek. "Promises are made to be broken: migrating R to strict semantics." Proceedings of the ACM on Programming Languages 5, OOPSLA (October 20, 2021): 1–20. http://dx.doi.org/10.1145/3485478.

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Function calls in the R language do not evaluate their arguments, these are passed to the callee as suspended computations and evaluated if needed. After 25 years of experience with the language, there are very few cases where programmers leverage delayed evaluation intentionally and laziness comes at a price in performance and complexity. This paper explores how to evolve the semantics of a lazy language towards strictness-by-default and laziness-on-demand. To provide a migration path, it is necessary to provide tooling for developers to migrate libraries without introducing errors. This paper reports on a dynamic analysis that infers strictness signatures for functions to capture both intentional and accidental laziness. Over 99% of the inferred signatures were correct when tested against clients of the libraries.

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Gabyshev, Dmitrii N., Miklós Szakáll, Dmitrii V. Shcherbakov, Alexander A. Fedorets, and Sergey M. Dyachkov. "Oscillatory Signatures in the Raindrop Motion Relative to the Air Medium with Terminal Velocity." Atmosphere 13, no. 7 (July 18, 2022): 1137. http://dx.doi.org/10.3390/atmos13071137.

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This paper aims to study the path oscillations of single, spherical water droplets levitated in a wind tunnel to better comprehend the mechanical motion of small raindrops. The observations were carried out in the Mainz vertical wind tunnel. The discrete, fast Fourier transform was used to determine the oscillatory frequencies of the droplet paths, and the Hilbert transform was applied to analyze their instantaneous frequency stability. Both transversal and streamwise components of the path oscillations are described with typical frequencies of several tens of Hertz. The studied oscillations elongate the paths, reduce the terminal velocity of the smallest droplets, and make the rain droplet fall in a non-uniform motion even after reaching terminal velocity. The terminal velocity can be considered as physically having been reached if our proposed practical criterion is satisfied. From a fluid mechanics perspective, the paper fills an experimental gap in the studies of the paths oscillations of single, liquid spheres of microscopic sizes at low Bond numbers <1 and relatively low Reynolds numbers ~102.

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Mehani, Bharati, Saleembhasha Asanigari, Hye-Jung Chung, and Kenneth Aldape. "PATH-26. EVALUATING THE DISTRIBUTION AND PROGNOSIS OF IMMUNE CELL SIGNATURES OF THE TUMOR MICRO-ENVIRONMENT IN DIFFUSE GLIOMAS." Neuro-Oncology 23, Supplement_6 (November 2, 2021): vi120. http://dx.doi.org/10.1093/neuonc/noab196.478.

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Abstract The tumor micro-environment (TME) plays an important role in the biology of cancer, including gliomas. Single cell studies have highlighted the role of specific TME components in gliomas, and the methods to deconvolve bulk profiling data may serve to complement these studies on clinically annotated tumors. In this study, we estimated cell type proportions in 3 large glioma datasets (TCGA, CGGA-325, CGGA-693) using CIBERSORTx. Using a signature matrix comprising 22 immune cell types, we identified IDH mutation status-specific immune cell distributions and found that the proportions of 10 cell types were significantly different between IDHmut and IDHwt tumors across the 3 datasets. Looking further within IDHmut tumors, we found that monocytes were enriched in 1p/19q non-co-deleted tumors across the 3 glioma datasets, consistent with prior single cell studies. We then examined estimated gene expression among immune cell types relative to IDH mutation status and found clear separation of gene expression in 15 of 22 cell types in all 3 datasets. When we applied these 22 gene expression signatures in each tumor sample onto cluster-of-cluster analyses to identify tumor groups with distinct immune signature patterns, we found that samples were distributed largely according to the IDH status in all 3 datasets, confirming that immune cell expression is distinct based on IDH status. Among IDH-specific groups, cluster-of-cluster analyses showed that immune cell-based cluster groups had distinct survival outcomes, and that IDHwt samples were distributed significantly based on tumor grades as well as based on EGFR overexpression. Among IDHmut tumors, the distributions of tumor grade and 1p/19q co-deletion status were significantly different in the immune-based clusters in 2 of the 3 datasets examined. Overall, these results highlight the biological and clinical significance of the immune cell environment in gliomas, including distinctions based on IDH mutation status as well as prognosis within IDH-specific groups.

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Hoeflich, Peter, Elham Fereidouni, and Tyco Brahe Mera. "Type Ia supernovae in the age of JWST: Finding the ‘right’ questions and the path to answers." Journal of Physics: Conference Series 2742, no. 1 (April 1, 2024): 012024. http://dx.doi.org/10.1088/1742-6596/2742/1/012024.

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Abstract Understanding the Physics of thermonuclear explosions of a White Dwarf star (WD), so called Type Ia Supernovae (SNe Ia), provide a playground for modern physics, computational methods, and are a key to modern cosmology. We identify new and investigate a variety of observational signatures of underlying physical processes related to the thermonuclear runaway, the flame propagation and the environment. Being intrinsically multi-dimensional phenomena, probing the physics requires multi-dimensional radiation-hydrodynamics and MHD simulations. For this task, we developed and employed methods for photon transport for the X-, gamma- and of low energy and of positrons under non-LTE conditions. We identify signatures in the light curves and spectra, in particular, line profiles and polarization spectra. Consistent treatment of high energy processes is critical. Therefore, our framework and results can be used directly a variety of scenarios for SNe Ia including merging WDs and explosions of sub-Chandrasekhar mass WDs. Current simulations have limitations but, nevertheless, when combined with recent JWST and VLT observations solutions emerge to many of decade old problems on the ignition process, flame physics and thermonuclear explosion.

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Journal articles on the topic 'Path signatures'

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