cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Table S3.2 - Species evaluated, conservation target and amount preserved
Creators: name: Fajardo, Javier
Publisher: name: Zenodo
Year: 2019

description: Fajardo, J. (2019) Table S3.2 - Chapter III: A crucial time to balance protected-area networks in the tropical Andean countries. In Optimizing the design of protected area networks in tropical Andean countries. PhD Thesis. Universidad Internacional Menendez Pelayo.
Universal fragmentation in annihilation reactions with constrained kinetics
Creators: name: Garcia, Enrique Rozas
name: Karlsson, Alfred Weddig
name: Hofmann, Johannes
Publisher: name: arXiv
Year: 2024
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Quantum Gases (cond-mat.quant-gas)
subject: Cellular Automata and Lattice Gases (nlin.CG)
subject: FOS: Physical sciences

description: In reaction-diffusion models of annihilation reactions in low dimensions, single-particle dynamics provides a bottleneck for reactions, leading to an anomalously slow approach to the empty state. Here, we construct a reaction model with a reciprocal bottleneck on particle dynamics where single-particle motion conserves the center of mass. We show that such a constrained reaction-diffusion dynamics does not approach an empty state but freezes at late times in a state with fragmented particle clusters, and that the late-time dynamics and asymptotic density are universal. Our setup thus constitutes a minimal model for the fragmentation of a one-dimensional lattice into independent particle clusters, and we provide exact results for the final density in the large-reaction rate limit. We suggest that the universal reaction dynamics could be observable in experiments with cold atoms or in the Auger recombination of exciton gases.
description: 4 pages, 4 figures. Updated to agree with journal version, minor changes
Additional file 2 of Genome-wide identification of Brassicaceae histone modification genes and their responses to abiotic stresses in allotetraploid rapeseed
Creators: name: Hu, Lin-Lin
name: Zheng, Li-Wei
name: Zhu, Xin-Lei
name: Ma, Sheng-Jie
name: Zhang, Kai-Yan
name: Hua, Ying-Peng
name: Huang, Jin-Yong
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Plant Biology

description: Supplementary Material 2
Additional file 1 of Predictors of the final place of care of patients with advanced cancer receiving integrated home-based palliative care: a retrospective cohort study
Creators: name: Tay, Ri Yin
name: Choo, Rozenne W. K.
name: Ong, Wah Ying
name: Hum, Allyn Y. M.
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Cancer
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Additional file 1. Appendix Tables A1 and A2.
Graph Convolutional Networks and Graph Attention Networks for Approximating Arguments Acceptability -- Technical Report
Creators: name: Cibier, Paul
name: Mailly, Jean-Guy
Publisher: name: arXiv
Year: 2024
Subjects: subject: Artificial Intelligence (cs.AI)
subject: FOS: Computer and information sciences

description: Various approaches have been proposed for providing efficient computational approaches for abstract argumentation. Among them, neural networks have permitted to solve various decision problems, notably related to arguments (credulous or skeptical) acceptability. In this work, we push further this study in various ways. First, relying on the state-of-the-art approach AFGCN, we show how we can improve the performances of the Graph Convolutional Networks (GCNs) regarding both runtime and accuracy. Then, we show that it is possible to improve even more the efficiency of the approach by modifying the architecture of the network, using Graph Attention Networks (GATs) instead.
description: 15 pages, 2 figures. Submitted to the 10th International Conference on Computational Models of Argument (COMMA 2024)
Incompatible plasma transfusion is not associated with increased mortality in civilian trauma patients
Creators: name: Donohue, Jack K.
name: Sperry, Jason L.
name: Spinella, Philip C.
name: Triulzi, Darrell J.
name: Leeper, Christine L.
name: Yazer, Mark H.
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Medicine
subject: Cell Biology
subject: Physiology
subject: FOS: Biological sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer
subject: Science Policy
subject: Infectious Diseases
subject: FOS: Health sciences

description: The introduction of low titer group O whole blood (LTOWB) that contains potentially ABO-incompatible plasma and the increasing use of group A plasma, due to shortages of AB plasma, in trauma patients whose ABO group is unknown could put the recipients of incompatible plasma at risk of increased morbidity and mortality. This study evaluated civilian trauma patient outcomes following receipt of incompatible plasma. One trauma center’s patient contributions to three multicenter studies of different trauma resuscitation strategies was analyzed; these patients were separated into two groups based on receipt of only compatible plasma versus receipt of any quantity of incompatible plasma. Multivariate analysis was performed to determine if receipt of incompatible plasma was associated with 24-hour or 30-day mortality. There were 347 patients eligible for this secondary analysis with 167 recipients of only compatible plasma and 180 recipients of incompatible plasma. The two groups were well matched demographically and on both prehospital and hospital arrival vital signs. The median (IQR) volume of incompatible plasma received by these patients was 684 ml (342, 1229). There was not a significant difference between the groups in 24-hour and 30-day mortality, nor in in-hospital or intensive care unit lengths of stay. In the Cox proportional-hazards regression model for both 24-hour and 30-day survival, receipt of incompatible plasma was not independently predictive of either mortality endpoint. Receipt of incompatible plasma was not independently associated with increased mortality in trauma patients. Prospective studies are needed to confirm these findings.
Additional file 3 of Genome-wide identification of Brassicaceae histone modification genes and their responses to abiotic stresses in allotetraploid rapeseed
Creators: name: Hu, Lin-Lin
name: Zheng, Li-Wei
name: Zhu, Xin-Lei
name: Ma, Sheng-Jie
name: Zhang, Kai-Yan
name: Hua, Ying-Peng
name: Huang, Jin-Yong
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Plant Biology

description: Supplementary Material 3
Invisible Higgs in weak bosons associative production with heavy quarks at LHC: probing mass and width
Creators: name: Boos, E. E.
name: Demidov, S. V.
name: Gorbunov, D. S.
Publisher: name: arXiv
Year: 2010
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: New physics coupled to the Higgs boson may hide it in the standard decay channels to be investigated at LHC. We consider the models where new invisible dominant decay modes of the Higgs boson are responsible for this hiding. We propose to study at LHC the weak boson production associated with heavy quarks: our analysis revealed that boson pair invariant mass distribution is sensitive to both mass and width of the invisible Higgs boson, if it is not too far from the weak boson pair threshold. We present tree-level results for the most relevant cases of top quarks and of bottom quarks in Standard Model extensions with large $b$-quark Yukawa coupling. We argue that QCD corrections do not spoil these results allowing for unambiguous extraction of the Higgs boson mass and width from the analysis of large enough amount of data.
description: 26 pages, 14 figures, references added
Assessing structural differences among genetically improved coastal Douglas-fir using high density airborne laser scanning
Creators: name: Du Toit, Francois
Publisher: name: University of British Columbia
Year: 2022

description: Tree improvement programs are critical to establishing high yield seed sources while maintaining genetic diversity and developing sustainable plantation forests. Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) is commonly used in improvement programs due to its superior strength and stiffness properties. Trials in British Columbia (BC), Canada aim to increase stem volume without sacrificing wood quality. Progeny test trials are essential in assessing the genetic performance via the prediction of breeding values (BVs) for target phenotypes of trees. To evaluate performance of improved stock, and to determine whether yield gains are being met, realized-gain trials are used. In both trials, accurate and timely collection of phenotypic data are critical for estimating and validating BVs with confidence. Currently, phenotypic variables collected focus on yield attributes; namely diameter at breast height, and height. Selection criteria in BC are evolving; branching traits are recognized as having a strong influence on strength and stiffness of Douglas-fir wood, however, they are rarely measured. High-density Airborne Laser Scanning (ALS), as well as Remotely Piloted Aerial Systems Laser Scanning Systems (RPAS-LS) produce three-dimensional point clouds which can be used to characterize individual tree structure. In this dissertation I utilized metrics derived from ALS and RPAS-LS to assess the performance in realized-gain trials, and predict genetic parameters in progeny trials. Additionally, new methods to estimate branch attributes of individual trees for inclusion as selection criteria in tree improvement programs were developed. This dissertation provides an insight into how ALS can be used to model branch attributes, while the ability to analyse trees by plot, individual tree, and individual branch attributes further allows researchers to maximise the value of ALS data. The findings are encouraging; they indicate that branch level metrics can be included as selection criteria in breeding programs, and that ALS-derived BVs are a suitable proxy for ground-based BVs. Given the cost efficiency of ALS, forest geneticists should explore this technology as tool to increase breeding programs’ overall efficiency. Findings from this research can be integrated into large-scale programs for monitoring trees, and identifying trees that display desirable attributes.
Hb Santa Juana (β 108(G10) Asn > Ser): a low oxygen affinity hemoglobin variant in a family of Bosnian background
Creators: name: Wildenberg, N. P.
name: Rossi, C.
name: Kulozik, A. E.
name: Kunz, J. B.
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: Physiology
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Cancer
subject: Hematology
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: We present a family that carries the β-hemoglobin variant Hb Santa Juana (HBB:c.326A>G, β 108(G10) Asn>Ser), also known as Hb Serres, in three generations. All affected family members had an anomal hemoglobin fraction as detected by HPLC but normal blood count without evidence of anemia or hemolysis. Oxygen affinity (p50 (O2) = 31.9–40.4 mmHg) was decreased in all probands, compared to 24.9–28.1 mmHg in unaffected individuals. Clinical symptoms likely related to the hemoglobin variant were cyanosis during anaesthesia, while other complaints such as shortness of breath or dizziness were less clearly linked with the hemoglobin variant.
Additional file 1 of Gender disparities in access to care for time-sensitive conditions during COVID-19 pandemic in Chile
Creators: name: Pacheco, Jorge
name: Crispi, Francisca
name: Alfaro, Tania
name: Martínez, María Soledad
name: Cuadrado, Cristóbal
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: Biotechnology
subject: Cancer
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Additional file 1.
Homogeneous projective bundles over abelian varieties
Creators: name: Brion, Michel
Publisher: name: arXiv
Year: 2011
Subjects: subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics
subject: 14F22, 14J60, 14K05, 14L30

description: We consider those projective bundles (or Brauer-Severi varieties) over an abelian variety that are homogeneous, i.e., invariant under translation. We describe the structure of these bundles in terms of projective representations of commutative algebraic groups; the irreducible bundles correspond to Heisenberg groups and their standard representations. Our results extend those of Mukai on semi-homogeneous vector bundles, and yield a geometric view of the Brauer group of abelian varieties.
description: Final version, accepted for publication in Algebra and Number Theory Journal; 37 pages. This is a slightly shortened version of v3: Section 6 has been suppressed as well as the proofs of Propositions 4.1 and 4.2; Section 4 has been relegated to the very end
Additional file 4 of Genome-wide identification of Brassicaceae histone modification genes and their responses to abiotic stresses in allotetraploid rapeseed
Creators: name: Hu, Lin-Lin
name: Zheng, Li-Wei
name: Zhu, Xin-Lei
name: Ma, Sheng-Jie
name: Zhang, Kai-Yan
name: Hua, Ying-Peng
name: Huang, Jin-Yong
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Plant Biology

description: Supplementary Material 4
Spin canted magnetism, decoupling of charge and spin ordering in NdNiO$_3$
Creators: name: Kumar, Devendra
name: Rajeev, K. P.
name: Alonso, J. A.
name: Martinez-Lope, M. J.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We report detailed magnetization measurements on the perovskite oxide NdNiO$_3$. This system has a first order metal-insulator (M-I) transition at about 200 K which is associated with charge ordering. There is also a concurrent paramagnetic to antiferromagnetic spin ordering transition in the system. We show that the antiferromagnetic state of the nickel sublattice is spin canted. We also show that the concurrency of the charge ordering and spin ordering transitions is seen only while warming up the system from low temperature. The transitions are not concurrent while cooling the system through the M-I transition temperature. This is explained based on the fact that the charge ordering transition is first order while the spin ordering transition is continuous. In the magnetically ordered state the system exhibits ZFC-FC irreversibilities, as well as history-dependent magnetization and aging. Our analysis rules out the possibility of spin-glass or superparamagnetism and suggests that the irreversibilities originate from magnetocrystalline anisotropy and domain wall pinning.
description: 8 pages, 7 figures
On Kaluza's sign criterion for reciprocal power series
Creators: name: Baricz, Árpád
name: Vesti, Jetro
name: Vuorinen, Matti
Publisher: name: arXiv
Year: 2010
Subjects: subject: Complex Variables (math.CV)
subject: Classical Analysis and ODEs (math.CA)
subject: FOS: Mathematics
subject: 33C05, 33B10, 30B10

description: T. Kaluza has given a criterion for the signs of the power series of a function that is the reciprocal of another power series. In this note the sharpness of this condition is explored and various examples in terms of the Gaussian hypergeometric series are given. A criterion for the monotonicity of the quotient of two power series due to M. Biernacki and J. Krzyż is applied.
description: 13 pages
Biomarkers of erythropoiesis response to intravenous iron in a crossover pilot study in unexplained anemia of the elderly
Creators: name: Yoo, Justin J.
name: Cohen, Harvey J.
name: Artz, Andrew S.
name: Price, Elizabeth
name: Fill, Jeffrey A.
name: Prchal, Josef
name: Sapp, Shelly
name: Barnhart, Huiman
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Neuroscience
subject: Physiology
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Mathematical Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Mental Health
subject: Hematology
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology
subject: Computational Biology

description: Anemia is common in older adults, but often unexplained. Previously, we conducted a randomized, controlled trial of intravenous (IV) iron sucrose to study its impact on the 6-minute walk test and hemoglobin in older adults with unexplained anemia and ferritin levels of 20–200 ng/mL. In this report, we present for the first time the response of hemoglobin, as well as the dynamic response of biomarkers of erythropoiesis and iron indices, in a pooled analysis of the initially IV iron-treated group of 9 subjects and the subsequently IV iron treated 10 subjects from the delayed treatment group. We hypothesized that there would be a reproducible hemoglobin response from IV iron, and that iron indices and erythropoietic markers would reflect appropriate iron loading and reduced erythropoietic stress. To investigate the biochemical response of anemia to IV iron, we studied the dynamics of soluble transferrin receptor (STfR), hepcidin, erythropoietin (EPO), and iron indices over 12 weeks after treatment. In total, all 19 treated subjects were evaluable: 9 from initial treatment and 10 after cross-over. Hemoglobin rose from 11.0 to 11.7 g/dL, 12 weeks after initiating IV iron treatment of 1000 mg divided weekly over 5 weeks. We found early changes of iron loading after 1–2 IV iron dose: serum iron increased by 184 mcg/dL from a baseline of 66 mcg/dL, ferritin by 184 ng/mL from 68 ng/mL, and hepcidin by 7.49 ng/mL from 19.2 ng/mL, while STfR and serum EPO declined by 0.55 mg/L and 3.5 mU/mL from 19.2 ng/mL and 14 mU/mL, respectively. The erythroid response and evidence of enhanced iron trafficking are consistent with the hypothesis that IV iron overcomes iron deficient or iron-restricted erythropoiesis. These data provide new insight that iron-restricted erythropoiesis is a potential and targetable mechanism for patients diagnosed with unexplained anemia of the elderly and offers support for larger prospective trials of IV iron among anemic older adults of low to normal ferritin.
Additional file 1 of Combined approach to estimate the depth of the magma surface in a shallow conduit at Aso volcano, Japan
Creators: name: Ishii, Kyoka
name: Yokoo, Akihiko
Publisher: name: figshare
Year: 2021
Subjects: subject: Space Science
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Computational Biology

description: Additional file 1: Seismo-acoustic data.
Towards a construction of inclusive collision cross-sections in the massless Nelson model
Creators: name: Dybalski, Wojciech
Publisher: name: arXiv
Year: 2011
Subjects: subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences
subject: 81U99, 81T10, 81T05

description: The conventional approach to the infrared problem in perturbative quantum electrodynamics relies on the concept of inclusive collision cross-sections. A non-perturbative variant of this notion was introduced in algebraic quantum field theory. Relying on these insights, we take first steps towards a non-perturbative construction of inclusive collision cross-sections in the massless Nelson model. We show that our proposal is consistent with the standard scattering theory in the absence of the infrared problem and discuss its status in the infrared-singular case.
description: 23 pages, LaTeX. As appeared in Ann. Henri Poincar\'e
Electronic structure of the surface superconducting Weyl semimetal PtBi$_2$
Creators: name: Vocaturo, Riccardo
name: Koepernik, Klaus
name: Facio, Jorge I.
name: Timm, Carsten
name: Fulga, Ion Cosma
name: Janson, Oleg
name: Brink, Jeroen van den
Publisher: name: arXiv
Year: 2024
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Trigonal PtBi$_2$ is a layered semimetal without inversion symmetry, featuring 12 Weyl points in the vicinity of the Fermi energy. Its topological Fermi arcs were recently shown to superconduct at low temperatures where bulk superconductivity is absent. Here, we perform first-principles calculations to investigate in detail the bulk and surface electronic structure of PtBi$_2$, and obtain the spin texture as well as the momentum-dependent localization of the arcs. Motivated by the experimentally observed recovery of inversion symmetry under pressure or upon doping, we interpolate between the two structures and determine the energy and momentum dependence of the Weyl nodes. For deeper insights into the surface superconductivity of PtBi$_2$, we construct a symmetry-adapted effective four-band model that accurately reproduces the Weyl points of PtBi$_2$. We supplement this model with an analysis of the symmetry-allowed pairings between the Fermi arcs, which naturally mix spin-singlet and spin-triplet channels. Moreover, the presence of surface-only superconductivity facilitates an intrinsic superconductor-semimetal-superconductor Josephson junction, with the semimetallic phase sandwiched between the two superconducting surfaces. For a phase difference of $π$, zero-energy Andreev bound states develop between the two terminations.
description: 14 pages, 13 figures
Endoplasmic reticulum stress-related signature predicts prognosis and immune infiltration analysis in acute myeloid leukemia
Creators: name: Dong, Lu
name: Wang, Haili
name: Miao, Zefeng
name: Yu, Yanhui
name: Gai, Dongzheng
name: Zhang, Guoxiang
name: Ge, Li
name: Shen, Xuliang
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Hematology

description: To construct an endoplasmic reticulum stress-related prognostic risk score (RS) model to predict prognosis and perform a preliminary analysis of immune infiltration in patients with acute myeloid leukemia (AML). The whole-genome expression data for AML and endoplasmic reticulum stress (ER stress)-related genes were downloaded from the GEO and GSEA databases, respectively. The samples were divided into death and survival groups, combined with clinical prognosis information. LASSO regression was used to construct a prognostic RS model. The Kaplan–Meier curve method was used to evaluate the association between different risk groups and actual survival prognosis information. A cox regression analysis was used to screen for independent survival prognostic clinical factors and construct a nomogram. CIBERSORT and ssGSEA was used for immune-related analysis. Eighteen ER-stress related genes were identified and a comprehensive network was constructed. Further, 5 CC, 8 MF, 17 BP, and 2 KEGG pathways were enriched. Ten optimal DEGs were obtained and a prognostic risk model was constructed. Compared to the low RS group, the OS values of the high RS group were significantly lower. A significant correlation between the different risk groups and the actual prognosis was demonstrated. Ten immune cells with significantly different distributions in different risk groups were screened. KEGG enrichment analysis showed that there were 5 signaling pathways in the high-risk group. The RS model can effectively predict the prognosis and has clinical implications for the prognosis of AML, combined with the correlation between different RS groups and the immune microenvironment.
Additional file 5 of Genome-wide identification of Brassicaceae histone modification genes and their responses to abiotic stresses in allotetraploid rapeseed
Creators: name: Hu, Lin-Lin
name: Zheng, Li-Wei
name: Zhu, Xin-Lei
name: Ma, Sheng-Jie
name: Zhang, Kai-Yan
name: Hua, Ying-Peng
name: Huang, Jin-Yong
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Plant Biology

description: Supplementary Material 5
Supersymmetric Left-Right models with Gauge Coupling Unification and Fermion Mass Universality
Creators: name: Borah, Debasish
name: Yajnik, Urjit A.
Publisher: name: arXiv
Year: 2010
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We explore the unification of gauge couplings and fermion masses in two different types of supersymmetric left-right models, one with Higgs triplets and the other with both Higgs triplets as well as bitriplets. The minimal versions of these models do not give rise to the desired unification and some extra fields have to be added. After such a modification, it is possible in one model to get gauged $B-L$ symmetry to be unbroken down to TeV scale. We also identify the parameter space at the electroweak scale which gives rise to fermion mass unification at a high scale $M_{G}$. Type I seesaw emerges as the natural explanation of the small neutrino masses in both the models.
description: 21 pages, 6 figures, Journal Version
Additional file 2 of Combined approach to estimate the depth of the magma surface in a shallow conduit at Aso volcano, Japan
Creators: name: Ishii, Kyoka
name: Yokoo, Akihiko
Publisher: name: figshare
Year: 2021
Subjects: subject: Space Science
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Computational Biology

description: Additional file 2: FDTD simulation.
Single-center, observational study of AML/MDS-EB with IDH1/2 mutations: genetic profile, immunophenotypes, mutational kinetics and outcomes
Creators: name: Papadopoulou, Vasiliki
name: Schoumans, Jacqueline
name: Basset, Valentin
name: Solly, Françoise
name: Pasquier, Jérôme
name: Blum, Sabine
name: Spertini, Olivier
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Cancer
subject: Hematology
subject: Virology

description: IDH1/2 mutations, intervening in epigenetic procedures, are frequently encountered in acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS). Knowledge of the genetics, immunophenotypes, and mutational kinetics of IDH1/2-mutated AML can contribute to the understanding of AML clonal architecture and inform therapeutics and monitoring. We retrospectively analyzed 50 IDH1/2-mutated AML/MDS-EB cases of our institution, to identify recurrent co-mutations, immunophenotypes, patterns of co-variance of IDH1/2 allele burdens with those of recurrent co-mutations, frequency of persistent IDH1/2 mutation as clonal hematopoiesis of indeterminate potential (CHIP) in remission and response to hypomethylating agents. Most frequently co-mutated genes were DNMT3A, SRSF2 and NPM1. Most cases with co-existent IDH1/2 and NPM1 mutations (11/13) showed an ‘APL-like’ immunophenotype (CD34-HLADR-). Allele burdens of mutated IDH1/2 were identical to mutated SRSF2 allele burdens at diagnosis and remission, but not always to mutated NPM1 allele burden in remission. We show persistence of significant mutIDH1/2 allele burden in approximately one-fourth of patients with deep remissions. IDH1/2 mutations were significantly more frequent among responders to first-line HMA-based regimens than among non-responders, in patients treated for myeloid neoplasms with excess blasts. IDH1/2 mutations are most frequently accompanied by DNMT3A, SRSF2 and NPM1 mutations. NPM1-IDH1/2 mutated AML has a mature phenotype possibly amenable to differentiation therapies. IDH1/2 and SRSF2 mutations probably arise at the same developmental stage of the disease, as their allele burdens covariate. IDH1/2 mutation represents CHIP in a substantial proportion of cases and is therefore no reliable residual disease marker. The preferential presence of IDH1/2 mutations among HMA-responders could inform therapeutic decisions if confirmed in larger series.
Hierarchy of emergent cluster states by measurement from symmetry-protected-topological states with large symmetry to subsystem cat state
Creators: name: Kuno, Yoshihito
name: Orito, Takahiro
name: Ichinose, Ikuo
Publisher: name: arXiv
Year: 2024
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We propose {\it measurement-producing hierarchy} emerging among correlated states by sequential subsystem projective measurements. We start from symmetry-protected-topological (SPT) cluster states with a large symmetry and apply sequential subsystem projective measurements to them and find that generalized cluster SPT states with a reduced symmetry appear in the subsystem of the unmeasured sites. That prescription finally produces Greenberger-Home-Zeilinger states with long-range order in the subsystem composed of periodic unmeasured sites of the original lattice. The symmetry-reduction hierarchical structure from a general large symmetric SPT cluster state is clearly captured by the measurement update flow in the efficient algorithm of stabilizer formalism. This approach is useful not only for the analytical search for the measured state but also for numerical simulation with a large system size. We also numerically verify the symmetry-reduction hierarchy by sequential subsystem projective measurements applied to large systems and large symmetric cluster SPT states.
description: 13 pages, 4 figures, accepted for publication in Phys. Rev. B
Cluster detection in networks using percolation
Creators: name: Arias-Castro, Ery
name: Grimmett, Geoffrey R.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Statistics Theory (math.ST)
subject: FOS: Mathematics

description: We consider the task of detecting a salient cluster in a sensor network, that is, an undirected graph with a random variable attached to each node. Motivated by recent research in environmental statistics and the drive to compete with the reigning scan statistic, we explore alternatives based on the percolative properties of the network. The first method is based on the size of the largest connected component after removing the nodes in the network with a value below a given threshold. The second method is the upper level set scan test introduced by Patil and Taillie [Statist. Sci. 18 (2003) 457-465]. We establish the performance of these methods in an asymptotic decision- theoretic framework in which the network size increases. These tests have two advantages over the more conventional scan statistic: they do not require previous information about cluster shape, and they are computationally more feasible. We make abundant use of percolation theory to derive our theoretical results, and complement our theory with some numerical experiments.
description: Published in at http://dx.doi.org/10.3150/11-BEJ412 the Bernoulli (http://isi.cbs.nl/bernoulli/) by the International Statistical Institute/Bernoulli Society (http://isi.cbs.nl/BS/bshome.htm)
Contrastive Dual-Interaction Graph Neural Network for Molecular Property Prediction
Creators: name: Zhao, Zexing
name: Shi, Guangsi
name: Wu, Xiaopeng
name: Ren, Ruohua
name: Gao, Xiaojun
name: Li, Fuyi
Publisher: name: arXiv
Year: 2024
Subjects: subject: Machine Learning (cs.LG)
subject: Artificial Intelligence (cs.AI)
subject: FOS: Computer and information sciences

description: Molecular property prediction is a key component of AI-driven drug discovery and molecular characterization learning. Despite recent advances, existing methods still face challenges such as limited ability to generalize, and inadequate representation of learning from unlabeled data, especially for tasks specific to molecular structures. To address these limitations, we introduce DIG-Mol, a novel self-supervised graph neural network framework for molecular property prediction. This architecture leverages the power of contrast learning with dual interaction mechanisms and unique molecular graph enhancement strategies. DIG-Mol integrates a momentum distillation network with two interconnected networks to efficiently improve molecular characterization. The framework's ability to extract key information about molecular structure and higher-order semantics is supported by minimizing loss of contrast. We have established DIG-Mol's state-of-the-art performance through extensive experimental evaluation in a variety of molecular property prediction tasks. In addition to demonstrating superior transferability in a small number of learning scenarios, our visualizations highlight DIG-Mol's enhanced interpretability and representation capabilities. These findings confirm the effectiveness of our approach in overcoming challenges faced by traditional methods and mark a significant advance in molecular property prediction.
Additional file 3 of Combined approach to estimate the depth of the magma surface in a shallow conduit at Aso volcano, Japan
Creators: name: Ishii, Kyoka
name: Yokoo, Akihiko
Publisher: name: figshare
Year: 2021
Subjects: subject: Space Science
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Computational Biology

description: Additional file 3: How to calculate PDF data.
On the Impact of Dark Matter Scattering on the Trajectory of High-Energy Cosmic Rays
Creators: name: Profumo, Stefano
name: Roberts, M. Grant
name: Dharanibalan, Shashank
Publisher: name: arXiv
Year: 2024
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: We study the impact on the trajectory of high-energy cosmic-ray protons of scattering off the cosmic dark matter. We compute the scattering angle as a function of the cosmic-ray energy, of the dark matter mass, and of the interaction strength for a few representative choices for the relevant interaction cross section. We find that the typical deflection angle over the cosmic ray path is largely independent of the dark matter mass. Given existing limits on the interaction strength, we compute the average deflection angle. We find that for large interaction cross sections and low cosmic ray energies, the predicted deflection angle is much larger than the angular resolution of very high-energy cosmic-ray observatories such as Pierre Auger.
description: 26 pages, 9 Figures
The cohomology ring of the GKM graph of a flag manifold of classical type
Creators: name: Fukukawa, Yukiko
name: Ishida, Hiroaki
name: Masuda, Mikiya
Publisher: name: arXiv
Year: 2011
Subjects: subject: Algebraic Topology (math.AT)
subject: FOS: Mathematics
subject: 14M15, 55N91

description: If a closed smooth manifold $M$ with an action of a torus $T$ satisfies certain conditions, then a labeled graph $\mG_M$ with labeling in $H^2(BT)$ is associated with $M$, which encodes a lot of geometrical information on $M$. For instance, the "graph cohomology" ring $\mHT^*(\mG_M)$ of $\mG_M$ is defined to be a subring of $\bigoplus_{v\in V(\mG_M)}H^*(BT)$, where $V(\mG_M)$ is the set of vertices of $\mG_M$, and is known to be often isomorphic to the equivariant cohomology $H^*_T(M)$ of $M$. In this paper, we determine the ring structure of $\mHT^*(\mG_M)$ with $\Z$ (resp. $\Z[1/2]$) coefficients when $M$ is a flag manifold of type A, B or D (resp. C) in an elementary way.
description: 22 pages
Additional file 6 of Genome-wide identification of Brassicaceae histone modification genes and their responses to abiotic stresses in allotetraploid rapeseed
Creators: name: Hu, Lin-Lin
name: Zheng, Li-Wei
name: Zhu, Xin-Lei
name: Ma, Sheng-Jie
name: Zhang, Kai-Yan
name: Hua, Ying-Peng
name: Huang, Jin-Yong
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Plant Biology

description: Supplementary Material 6
Assessing the prognostic utility of hematologic response for overall survival in patients with newly diagnosed AL amyloidosis: results of a meta-analysis
Creators: name: Kastritis, Efstathios
name: Misra, Arpit
name: Gurskyte, Laura
name: Kroi, Florint
name: Verhoek, Andre
name: Vermeulen, Jessica
name: Ammann, Eric
name: Lam, Annette
name: Cote, Sarah
name: Wechalekar, Ashutosh D.
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Medicine
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer
subject: Science Policy

description: Amyloid light-chain (AL) amyloidosis is a rare disease characterized by amyloid fibril deposits made up of toxic light chains causing progressive organ dysfunction and death. Recent studies suggest that hematologic response may be an important prognostic indicator of overall survival (OS) in AL amyloidosis. The aim of this study was to evaluate the trial-level association between hematologic complete response (CR) or very good partial response or better (≥ VGPR) and OS in newly diagnosed patients. Studies were identified via systematic literature review. Pooled effect estimates were generated by a random-effects model. Nine observational studies reporting hematologic CR or ≥VGPR and OS hazard ratios (HRs) were included in the meta-analysis. Achieving hematologic CR was associated with improved OS (HR, 0.21; 95% confidence interval [CI] 0.13–0.34). Achieving ≥ VGPR was also associated with improved OS (HR 0.21; 95% CI 0.17–0.26). Results of a sensitivity analysis excluding one outlier study revealed no heterogeneity and a better overall HR estimate. Potential limitations of this meta-analysis include the small number of eligible studies (consistent with the rarity of the disease) and inconsistencies in reporting of results. Overall, our findings support the use of deep hematologic response (CR or ≥VGPR) as a clinical trial endpoint in newly diagnosed AL amyloidosis. This study provides evidence that early hematologic response is a strong patient-level surrogate for long-term OS in patients with AL amyloidosis receiving frontline therapy. Structured data collection of depth of response in future trials will further strengthen these observations.
Phase transitions and non-equilibrium relaxation in kinetic models of opinion formation
Creators: name: Biswas, Soumyajyoti
name: Chandra, Anjan Kumar
name: Chatterjee, Arnab
name: Chakrabarti, Bikas K.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Physics and Society (physics.soc-ph)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Social and Information Networks (cs.SI)
subject: Computational Physics (physics.comp-ph)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: We review in details some recently proposed kinetic models of opinion dynamics. We discuss the several variants including a generalised model. We provide mean field estimates for the critical points, which are numerically supported with reasonable accuracy. Using non-equilibrium relaxation techniques, we also investigate the nature of phase transitions observed in these models. We study the nature of correlations as the critical points are approached, and comment on the universality of the phase transitions observed.
description: 11 pages, 8 eps figures, 1 table. Contribution for proceedings of Statphys-Kolkata-VII 26-30 November, 2010
Additional file 1 of Evaluation of zinc sulfate as an adjunctive therapy in COVID-19 critically ill patients: a two center propensity-score matched study
Creators: name: Al Sulaiman, Khalid
name: Aljuhani, Ohoud
name: Al Shaya, Abdulrahman I.
name: Kharbosh, Abdullah
name: Kensara, Raed
name: Al Guwairy, Alhomaidi
name: Alharbi, Aisha
name: Algarni, Rahmah
name: Al Harbi, Shmeylan
name: Vishwakarma, Ramesh
name: Korayem, Ghazwa B.
Publisher: name: figshare
Year: 2021
Subjects: subject: Space Science
subject: Medicine
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Cancer
subject: Science Policy

description: Additional file 1: Table e1 Patients Baseline characteristics before and after propensity-score matching.
Materials characterization of solution-processed CuIn(S,Se)₂ absorber films for use in thin-film solar cells
Creators: name: McIntosh, Noah
Publisher: name: University of British Columbia
Year: 2022

description: Global commitments to reduce fossil-based carbon emissions and invest in clean energy technologies have brought about an increased interest in solar photovoltaic (PV) technology. Current market-leading and top-performing solar panels are fabricated through expensive, time and energy-intensive vacuum-based fabrication routes, incurring high costs. In contrast, liquid-based solution processing techniques offer enormous potential for cost reduction but must improve performance to become competitive on the market. To this end, the present work analyses a liquid-based fabrication method for CuIn(S,Se)₂ – short CISSe – absorber films, aiming to improve the quality and performance of the produced materials. The study includes the use of a non-toxic alternative chemical etchant and a novel component design in the proposed fabrication system, as well as an investigation of the effect of different elemental compositions in molecular ink precursors. This is achieved by producing a sample batch of CISSe absorber films using the primary experimental variables: chemical etchant and precursor composition respectively. CISSe absorber films are fabricated using the solution-based molecular ink approach at four different compositions, defined by the elemental ratio Cu/In = 0.7, 0.85, 1.0, and 1.15, and compared in a non-etched, standard-etched (KCN), and alternative-etched ((NH₄)₂S) iteration for each composition. Materials characterization is done using X-ray diffraction (XRD), scanning electron microscopy (SEM), and energy dispersive spectroscopy (EDS) analyses. It is found that this fabrication method can produce high quality absorber films with the desired CISSe material at all respective compositions. Increasing size of crystal grains was observed as the Cu/In ratio was increased up to 1.15 (~7.5 μm average grain size). At Cu/In ratios 1.0 and above, detrimental secondary phases of copper selenide compounds were found to be present. Both the (NH₄)₂S and KCN etchants were found to effectively etch these secondary phases. This work strongly supports the use of the presented solution-based fabrication method, validating both the alternative furnace system design and benign chemical etchant alternative. Future works should use this research as a base with primary focus on completion of a complete CISSe solar cell device for further study.
An algebraic approach to manifold-valued generalized functions
Creators: name: Burtscher, Annegret
Publisher: name: arXiv
Year: 2010
Subjects: subject: Functional Analysis (math.FA)
subject: Differential Geometry (math.DG)
subject: FOS: Mathematics
subject: 46F30, 46E25, 46T30, 54C40

description: We discuss the nature of structure-preserving maps of varies function algebras. In particular, we identify isomorphisms between special Colombeau algebras on manifolds with invertible manifold-valued generalized functions in the case of smooth parametrization. As a consequence, and to underline the consistency and validity of this approach, we see that this generalized version on algebra isomorphisms in turn implies the classical result on algebras of smooth functions.
description: 7 pages
Emergent gauge dynamics of highly frustrated magnets
Creators: name: Lawler, Michael J.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: Condensed matter exhibits a wide variety of exotic emergent phenomena such as the fractional quantum Hall effect and the low temperature cooperative behavior of highly frustrated magnets. I consider the classical Hamiltonian dynamics of spins of the latter phenomena using a method introduced by Dirac in the 1950s by assuming they are constrained to their lowest energy configurations as a simplifying measure. Focusing on the kagome antiferromagnet as an example, I find it is a gauge system with topological dynamics and non-locally connected edge states for certain open boundary conditions similar to doubled Chern-Simons electrodynamics expected of a $Z_2$ spin liquid. These dynamics are also similar to electrons in the fractional quantum Hall effect. The classical theory presented here is a first step towards a controlled semi-classical description of the spin liquid phases of many pyrochlore and kagome antiferromagnets and towards a description of the low energy classical dynamics of the corresponding unconstrained Heisenberg models.
description: Updated with some appendices moved to the main body of the paper and some additional improvements. 21 pages, 5 figures
mu->e Gamma decay versus mu->eee bound and lepton flavor violating processes in supernova
Creators: name: Lychkovskiy, Oleg
name: Vysotsky, Mikhail
Publisher: name: arXiv
Year: 2010
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: Even tiny lepton flavor violation (LFV) due to some New Physics is able to alter the conditions inside a collapsing supernova core and probably to facilitate the explosion. LFV emerges naturally in a See-Saw type II model of neutrino mass generation. Experimentally LFV is constrained by rare lepton decay searches. In particular, strong bounds are imposed on the mu->eee branching ratio and on the mu-e conversion probability in muonic gold. Currently the mu->e gamma decay is under investigation in the MEG experiment which aims at dramatic increase of sensitivity in the next three years. We search for a See-Saw type II LFV pattern which fits all the experimental constraints, provides Br(mu->e gamma) not less than Br(mu->eee) and ensures a rate of LFV processes in supernova high enough to modify the supernova physics. These requirements are sufficient to eliminate almost all freedom in the model. In particular, they lead to a prediction 0.5*10^(-12) < Br(mu->e gamma)< 6*10^(-12), which is testable by MEG in the nearest future. The considered scenario also constrains neutrino mass-mixing pattern and provides lower and upper bounds on tau-lepton LFV decays. We also briefly discuss a model with a single bilepton in which the mu->eee decay is absent at the tree level.
description: v2 is substantially extended compared to v1; new results are presented