cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
A Lightweight Architecture for Real-Time Neuronal-Spike Classification
Creators: name: Siddiqi, Muhammad Ali
name: Vrijenhoek, David
name: Landsmeer, Lennart P. L.
name: van der Kleij, Job
name: Gebregiorgis, Anteneh
name: Romano, Vincenzo
name: Bishnoi, Rajendra
name: Hamdioui, Said
name: Strydis, Christos
Publisher: name: arXiv
Year: 2023
Subjects: subject: Hardware Architecture (cs.AR)
subject: Machine Learning (cs.LG)
subject: Signal Processing (eess.SP)
subject: FOS: Computer and information sciences
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: Electrophysiological recordings of neural activity in a mouse's brain are very popular among neuroscientists for understanding brain function. One particular area of interest is acquiring recordings from the Purkinje cells in the cerebellum in order to understand brain injuries and the loss of motor functions. However, current setups for such experiments do not allow the mouse to move freely and, thus, do not capture its natural behaviour since they have a wired connection between the animal's head stage and an acquisition device. In this work, we propose a lightweight neuronal-spike detection and classification architecture that leverages on the unique characteristics of the Purkinje cells to discard unneeded information from the sparse neural data in real time. This allows the (condensed) data to be easily stored on a removable storage device on the head stage, alleviating the need for wires. Synthesis results reveal a >95% overall classification accuracy while still resulting in a small-form-factor design, which allows for the free movement of mice during experiments. Moreover, the power-efficient nature of the design and the usage of STT-RAM (Spin Transfer Torque Magnetic Random Access Memory) as the removable storage allows the head stage to easily operate on a tiny battery for up to approximately 4 days.
Additional file 2: of PD-1 signaling affects cristae morphology and leads to mitochondrial dysfunction in human CD8+ T lymphocytes
Creators: name: Ogando, Jesús
name: Sáez, María
name: Santos, Javier
name: Nuevo-Tapioles, Cristina
name: Gut, Marta
name: Esteve-Codina, Anna
name: Heath, Simon
name: González-Pérez, Antonio
name: Cuezva, José
name: Lacalle, Rosa
name: Mañes, Santos
Publisher: name: figshare
Year: 2019
Subjects: subject: Cell Biology
subject: Molecular Biology
subject: Pharmacology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Developmental Biology
subject: Marine Biology
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Science Policy
subject: 60506 Virology

description: Table S1. List of primers used for RT-qPCR analyses. (PDF 44 kb)
Localization and integrability breaking in weakly interacting Floquet circuits
Creators: name: Hahn, Dominik
name: Colmenarez, Luis
Publisher: name: arXiv
Year: 2023
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We present a family of Floquet circuits that can interpolate between non-interacting qubits, free propagation, generic interacting, and dual-unitary dynamics. We identify the operator entanglement entropy of the two-qubit gate as a good quantitative measure of the interaction strength. We test the persistence of localization in the vicinity of the non-interacting point by probing spectral statistics, decay of autocorrelators, and measuring entanglement growth. The finite-size analysis suggests that the many-body localized regime does not persist in the thermodynamic limit. Instead, our results are compatible with an integrability-breaking phenomenon.
description: 12 pages, 11 figures
Pieri-type formulas for maximal isotropic Grassmannians via triple intersections
Creators: name: Sottile, Frank
Publisher: name: arXiv
Year: 1997
Subjects: subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics
subject: Primary 14M15

description: We give an elementary proof of the Pieri-type formula in the cohomology of a Grassmannian of maximal isotropic subspaces of an odd orthogonal or symplectic vector space. This proof proceeds by explicitly computing a triple intersection of Schubert varieties. The decisive step is an explicit description of the intersection of two Schubert varieties, from which the multiplicities (which are powers of 2) in the Pieri-type formula are deduced.
description: LaTeX 2e, 24 pages (9 pages is an appendix detailing the proof in the symplectic case). Expanded version of MSRI preprint 1997-062
Deception in Spoken Dialogue: Classification and Individual Differences
Creators: Levitan, Sarah Ita
Publisher: name: Columbia University
Year: 2019
Subjects: Computer science
Deception
Lie detectors and detection
Dialogue analysis
Automatic speech recognition

description: Automatic deception detection is an important problem with far-reaching implications in many areas, including law enforcement, military and intelligence agencies, social services, and politics. Despite extensive efforts to develop automated deception detection technologies, there have been few objective successes.  This is likely due to the many challenges involved, including the lack of large, cleanly recorded corpora; the difficulty of acquiring ground truth labels; and major differences in incentives for lying in the laboratory vs. lying in real life.  Another well-recognized issue is that there are individual and cultural differences in deception production and detection, although little has been done to identify them.  Human performance at deception detection is at the level of chance, making it an uncommon problem where machines can potentially outperform humans.
      This thesis addresses these challenges associated with research of deceptive speech.  We created the Columbia X-Cultural Deception (CXD) Corpus, a large-scale collection of deceptive and non-deceptive dialogues between native speakers of Standard American English and Mandarin Chinese.  This corpus enabled a comprehensive study of deceptive speech on a large scale.
      In the first part of the thesis, we introduce the CXD corpus and present an empirical analysis of acoustic-prosodic and linguistic cues to deception.  We also describe machine learning classification experiments to automatically identify deceptive speech using those features.  Our best classifier achieves classification accuracy of almost 70%, well above human performance.
      The second part of this thesis addresses individual differences in deceptive speech.  We present a comprehensive analysis of individual differences in verbal cues to deception, and several methods for leveraging these speaker differences to improve automatic deception classification.  We identify many differences in cues to deception across gender, native language, and personality.  Our comparison of approaches for leveraging these differences shows that speaker-dependent features that capture a speaker's deviation from their natural speaking style can improve deception classification performance. We also develop neural network models that accurately model speaker-specific patterns of deceptive speech.
      The contributions of this work add substantially to our scientific understanding of deceptive speech, and have practical implications for human practitioners and automatic deception detection.
title: AI-based Method of Vortex Core Tracking as an Alternative for Lambda2
Creators: name: Majchrzak, Maciej
name: Jakubowski, Mateusz
name: Starosta, Roman
Publisher: name: Publishing House of Poznan University of Technology
Year: 2020

description: Vibrations in Physical Systems, 31(3), 2020319-1 - 2020319-10
Implementation of the SuSAv2-MEC 1p1h and 2p2h models in GENIE and analysis of nuclear effects in T2K measurements
Creators: name: Dolan, Stephen
name: Megias, Guillermo
name: Bolognesi, Sara
Publisher: name: arXiv
Year: 2019
Subjects: subject: High Energy Physics - Experiment (hep-ex)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We first present the implementation and validation of the SuSAv2-MEC 1p1h and 2p2h models in the GENIE neutrino-nucleus interaction event generator and a comparison of the subsequent predictions to measurements of lepton and hadron kinematics from the T2K experiment. These predictions are also compared to those of other available models in GENIE. We additionally compare the semi-inclusive predictions of the implemented 1p1h model to those of the microscopic model on which SuSAv2 is based - Relativistic Mean Field (RMF) - to begin to test the validity of widely-used `factorisation' assumptions employed by generators to predict hadron kinematics from inclusive input models. The results highlight that a more precise treatment of hadron kinematics in generators is essential in order to attain the few-% level uncertainty on neutrino interactions necessary for the next generation of accelerator-based long-baseline neutrino oscillation experiments.
description: 18 pages, 12 figures, now published in PRD
Deciphering End Resection in Double-Strand Break repair in Saccharomyces cerevisiae
Creators: Chen, Huan
Publisher: name: Columbia University
Year: 2015
Subjects: subject: Saccharomyces cerevisiae
subject: DNA repair
subject: DNA damage
subject: Biology
subject: Molecular biology
subject: Genetics
subject: FOS: Biological sciences

description: Double-strand breaks (DSBs) are highly cytotoxic DNA lesions that are usually repaired by two major mechanisms: non-homologous end joining (NHEJ) and homologous recombination (HR). HR is initiated by 5'-3' resection, generating 3' single stranded DNA tails coated by Replication protein A (RPA), which can be used in later steps for homology search and repair. The 5'-3' resection step is a critical determinant of repair pathway choice that commits cells to HR instead of NHEJ, and it's also required for DNA damage checkpoint activation. Studies in the budding yeast Saccharomyces cerevisiae have shown that the conserved Mre11-Rad50-Xrs2 (MRX) complex, together with Sae2, initiates end resection while more extensive processing of 5' strands requires the 5'-3' exonuclease Exo1, or the combined activities of the Sgs1 helicase and Dna2 endonuclease. In this thesis we will discuss the function of RPA and Sae2 based on our experimental observations. RPA is an essential eukaryotic single-stranded DNA binding protein with a central role in DNA metabolism. It has been shown in vitro that RPA directly participates in end resection by stimulating the Sgs1 helicase and Dna2 endonuclease. To investigate the role of RPA for end resection in vivo, we used a heat-inducible degron allele (td-RFA1) that allows rapid conditional depletion of RPA in Saccharomyces cerevisiae. Complete loss of RPA resulted in a defect in both the Exo1 and Sgs1-Dna2 extensive resection mechanisms, while resection initiation by MRX-Sae2 was unaffected. Interestingly, Dna2 was unable to localize to DSBs in the absence of RPA, whereas Exo1 localization was unaffected indicating that the role of RPA in the resection pathways is distinct. The short single-stranded DNA tails formed in the absence of RPA were unstable, represented by 3' strand loss and formation of foldback hairpin structures. Thus, RPA is required to generate ssDNA, and also to protect ssDNA from degradation and inappropriate annealing that could lead to genome rearrangements. While Mre11 possesses 3'-5' dsDNA exonuclease and ssDNA endonuclease activities, Sae2 was reported to activate its endonuclease activity, which initiates end resection. We identified mre11-P110L and four more mutants from a screen that bypass Sae2 for camptothecin (CPT) and MMS resistance. None of them restored endonuclease activity, neither did they improve resection. Persistent Mre11 foci and hyper-checkpoint signaling caused by sae2Δ upon DNA damage was suppressed by mre11-P110L. These findings demonstrate that the DNA damage sensitivity of sae2Δ is not caused by defective resection, but by failure to remove MRX from ends and switch off checkpoint.
Bounding extreme events in nonlinear dynamics using convex optimization
Creators: name: Fantuzzi, Giovanni
name: Goluskin, David
Publisher: name: arXiv
Year: 2019
Subjects: subject: Dynamical Systems (math.DS)
subject: Optimization and Control (math.OC)
subject: Chaotic Dynamics (nlin.CD)
subject: FOS: Mathematics
subject: FOS: Physical sciences
subject: 93C10, 93C15, 93C20, 90C22, 34C11, 37C10, 49M29

description: We study a convex optimization framework for bounding extreme events in nonlinear dynamical systems governed by ordinary or partial differential equations (ODEs or PDEs). This framework bounds from above the largest value of an observable along trajectories that start from a chosen set and evolve over a finite or infinite time interval. The approach needs no explicit trajectories. Instead, it requires constructing suitably constrained auxiliary functions that depend on the state variables and possibly on time. Minimizing bounds over auxiliary functions is a convex problem dual to the non-convex maximization of the observable along trajectories. This duality is strong, meaning that auxiliary functions give arbitrarily sharp bounds, for sufficiently regular ODEs evolving over a finite time on a compact domain. When these conditions fail, strong duality may or may not hold; both situations are illustrated by examples. We also show that near-optimal auxiliary functions can be used to construct spacetime sets that localize trajectories leading to extreme events. Finally, in the case of polynomial ODEs and observables, we describe how polynomial auxiliary functions of fixed degree can be optimized numerically using polynomial optimization. The corresponding bounds become sharp as the polynomial degree is raised if strong duality and mild compactness assumptions hold. Analytical and computational ODE examples illustrate the construction of bounds and the identification of extreme trajectories, along with some limitations. As an analytical PDE example, we bound the maximum fractional enstrophy of solutions to the Burgers equation with fractional diffusion.
description: Revised according to comments by reviewers. Added references and rearranged introduction, conclusions, and proofs. 38 pages, 7 figures, 4 tables, 4 appendices, 87 references
Additional file 1 of Combined assembly of long and short sequencing reads improve the efficiency of exploring the soil metagenome
Creators: name: Xu, Guoshun
name: Zhang, Liwen
name: Liu, Xiaoqing
name: Guan, Feifei
name: Xu, Yuquan
name: Yue, Haitao
name: Huang, Jin-Qun
name: Chen, Jieyin
name: Wu, Ningfeng
name: Tian, Jian
Publisher: name: figshare
Year: 2022
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics

description: Additional file 1.
Hydrogen diffusion in the lower mantle revealed by machine learning potentials
Creators: name: Peng, Yihang
name: Deng, Jie
Publisher: name: arXiv
Year: 2023
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Geophysics (physics.geo-ph)
subject: FOS: Physical sciences

description: Hydrogen may be incorporated into nominally anhydrous minerals including bridgmanite and post-perovskite as defects, making the Earth's deep mantle a potentially significant water reservoir. The diffusion of hydrogen and its contribution to the electrical conductivity in the lower mantle are rarely explored and remain largely unconstrained. Here we calculate hydrogen diffusivity in hydrous bridgmanite and post-perovskite, using molecular dynamics simulations driven by machine learning potentials of ab initio quality. Our findings reveal that hydrogen diffusivity significantly increases with increasing temperature and decreasing pressure, and is considerably sensitive to hydrogen incorporation mechanism. Among the four defect mechanisms examined, (Mg + 2H)$_{\rm Si}$ and (Al + H)$_{\rm Si}$ show similar patterns and yield the highest hydrogen diffusivity. Hydrogen diffusion is generally faster in post-perovskite than in bridgmanite, and these two phases exhibit distinct diffusion anisotropies. Overall, hydrogen diffusion is slow on geological time scales and may result in heterogeneous water distribution in the lower mantle. Additionally, the proton conductivity of bridgmanite for (Mg + 2H)$_{\rm Si}$ and (Al + H)$_{\rm Si}$ defects aligns with the same order of magnitude of lower mantle conductivity, suggesting that the water distribution in the lower mantle may be inferred by examining the heterogeneity of electrical conductivity.
Deciding What's True: Fact-Checking Journalism and the New Ecology of News
Creators: Graves, Lucas
Publisher: name: Columbia University
Year: 2013
Subjects: Journalism--Political aspects
Journalism--Objectivity
Mass media--Objectivity
Journalism
Communication

description: This dissertation studies the new class of political fact-checkers, journalists who specialize in assessing the truth of public claims -- and who, it is argued, constitute a professional reform movement reaching to the center of the elite US news media. In less than a decade this emergent genre of news has become a basic feature of political coverage. It figures prominently in national debates and commands the direct attention of elite political actors, who respond publicly to the fact-checkers and dedicate staff to dealing with them, especially during electoral campaigns. This study locates fact-checking in a wider practice of "annotative journalism," with precursors in the muckraking tradition in American news, which has come into flower in an online media environment characterized by promiscuous borrowing and annotation. Participant observation and content analysis are used together to examine the day-to-day work of the news organizations leading the fact-checking movement. This approach documents the specific and forceful critique of conventional journalistic practice which the fact-checkers enact in their newswork routines and in their public and private discourse. Fact-checkers are a species of practical epistemologists, who seek to reform and thus to preserve the objectivity norm in American journalism, even as their daily work runs up against the limits of objective factual analysis. In politics, they acknowledge, "facts can be subjective." Fact-checkers are also active participants in an emerging news ecosystem in which stories develop, and authority is constructed, in patterns of citation and annotation across discursive networks of media and political actors. This study demonstrates how attention to these media-political networks subtly informs and constrains the work of producing objective assessments of factual claims. And it suggests that the objective status of the fact-checkers themselves can be seen as a function of their position in media-political networks, reproduced in formal and informal partnerships and, most immediately, in the pattern of outlets which cite and quote and link to them. This perspective helps to account for the surprising limits of the political critique offered by professional fact-checkers, who argue for a more honest, fearless journalism but carefully avoid the largest and most controversial political conclusions that emerge from their own work. In seeking to redefine objective practice for a changed media environment, the new genre of fact-checking underscores the essentially defensive nature of what has been called the "strategic ritual" of journalistic objectivity.
Additional file 1: of PD-1 signaling affects cristae morphology and leads to mitochondrial dysfunction in human CD8+ T lymphocytes
Creators: name: Ogando, Jesús
name: Sáez, María
name: Santos, Javier
name: Nuevo-Tapioles, Cristina
name: Gut, Marta
name: Esteve-Codina, Anna
name: Heath, Simon
name: González-Pérez, Antonio
name: Cuezva, José
name: Lacalle, Rosa
name: Mañes, Santos
Publisher: name: figshare
Year: 2019
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Developmental Biology
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Supplementary Methods. Detailed description of the methods and materials used in the study. (DOCX 34 kb)
Additional file 1 of Cognition as mediator of pulmonary function and risk of sarcopenia among older adults
Creators: name: Hu, Zhao
name: Tang, Lu
name: Zhan, Yiqiang
Publisher: name: figshare
Year: 2024
Subjects: subject: Biochemistry
subject: Medicine
subject: Neuroscience
subject: Physiology
subject: FOS: Biological sciences
subject: Cancer
subject: Mental Health

description: Supplementary Material 1
DiPETrans: A Framework for Distributed Parallel Execution of Transactions of Blocks in Blockchain
Creators: name: Baheti, Shrey
name: Anjana, Parwat Singh
name: Peri, Sathya
name: Simmhan, Yogesh
Publisher: name: arXiv
Year: 2019
Subjects: subject: Distributed, Parallel, and Cluster Computing (cs.DC)
subject: FOS: Computer and information sciences

description: Contemporary blockchain such as Bitcoin and Ethereum execute transactions serially by miners and validators and determine the Proof-of-Work (PoW). Such serial execution is unable to exploit modern multi-core resources efficiently, hence limiting the system throughput and increasing the transaction acceptance latency. The objective of this work is to increase the transaction throughput by introducing parallel transaction execution using a static analysis technique. We propose a framework DiPETrans for the distributed execution of the transactions in a block. Here, peers in the blockchain network form a community to execute the transactions and find the PoW parallelly, using a leader-follower approach. During mining, the leader statically analyzes the transactions, creates different groups (shards) of independent transactions, and distributes them to followers to execute them in parallel. After the transaction executes, the community's compute power is utilized to solve the PoW concurrently. When a block is successfully created, the leader broadcasts the proposed block to other peers in the network for validation. On receiving a block, validators re-execute the block transactions and accept the block if they reach the same state as shared by the miner. Validation can also be done as a community, in parallel, following the same leader-follower approach as mining. We report experiments using over 5 Million real transactions from the Ethereum blockchain and execute them using our DiPETrans framework to empirically validate the benefits of our techniques over traditional sequential execution. We achieve a maximum speedup of 2.2x for the miner and 2.0x for the validator, with 100 to 500 transactions per block. Further, we achieve a peak of 5x end-to-end block creation speedup using a parallel miner over a serial miner when using 6 machines in the community.
description: 38 Pages, 25 Figures, and 6 Tables
Deciphering gene dysregulation in disease through population and functional genomics
Creators: Dhindsa, Ryan Singh
Publisher: name: Columbia University
Year: 2020
Subjects: Gene expression
Chromatin
Chromatographic analysis
Transcription factors
RNA-protein interactions
Nervous system--Diseases
Epilepsy
Genetic regulation
Gene therapy--Research

description: Genetic discoveries have highlighted the role of gene expression dysregulation in both rare and common diseases. In particular, a large number of chromatin modifiers, transcription factors, and RNA-binding proteins have been implicated in neurodevelopmental diseases, including epilepsy, autism spectrum disorder, schizophrenia, and intellectual disability. Elucidating the disease mechanisms for these genes is challenging, as the encoded proteins often regulate thousands of downstream targets. In Chapter 2 of this thesis, we describe the use of single-cell RNA-sequencing (scRNA-seq) to characterize a mouse model of HNRNPU-mediated epileptic encephalopathy. This gene encodes a ubiquitously expressed RNA-binding protein, yet we demonstrate that reduction in its expression leads to cell type-specific transcriptomic defects. Specifically, excitatory neurons in a region of the hippocampus called the subiculum carried the strongest burden of differential gene expression. In Chapter 3, we use scRNA-seq to identify convergent molecular and transcriptomic features in four different organoid models of a cortical malformation called periventricular nodular heterotopia. In Chapter 4, we build on these successes to propose a high-throughput drug screening program for neurodevelopmental genes that encode regulators of gene expression. This approach—termed transcriptomic reversal—attempts to identify compounds that reverse disease-causing gene expression changes back to a normal state. Finally, in Chapter 5, we focus on the role of synonymous codon usage in human disease. Codon usage can affect mRNA stability, yet its role in human physiology has been historically overlooked. We use population genetics approaches to demonstrate that natural selection shapes codon content in the human genome, and we find that dosage sensitive genes are intolerant to reductions in codon optimality. We propose that synonymous mutations could modify the penetrance of Mendelian diseases through altering the expression of disease-causing mutations. In summary, the work in this thesis broadly focuses on the role of gene expression dysregulation in disease. We provide novel frameworks for interrogating disease gene expression signatures, prioritizing mutations that may alter expression, and identifying targeted therapeutics.
MEMORIA III ENCUENTRO INTERNACIONAL DE DOCENTES INVESTIGADORES. CONFEDERACIÓN UNIVERSITARIA DE DOCENTES DEL SISTEMA UNIVERSITARIO DE BOLIVIA
Creators: name: Martínez, Scarley
Publisher: name: UMRPSFXCH - BioScientia
Year: 2024

description: El III Encuentro Internacional de Docentes Investigadores, organizado por la Confederación Universitaria de Docentes (CUD), es una plataforma de gran relevancia para la comunidad académica internacional. Este evento se lleva a cabo con el objetivo de fomentar el intercambio de conocimientos, experiencias y avances en el ámbito de la investigación y la docencia universitaria.

Durante el encuentro, docentes e investigadores de diversas disciplinas y procedencias tuvieron la oportunidad de presentar sus trabajos, compartir buenas prácticas, y discutir sobre los desafíos y oportunidades que enfrenta la educación superior en la actualidad. Además, el evento facilitó la creación de redes de colaboración entre universidades y centros de investigación, promoviendo proyectos conjuntos y movilidad académica.

El III Encuentro Internacional de Docentes Investigadores se destaca por su enfoque interdisciplinario y su compromiso con la innovación educativa, la calidad académica y el desarrollo profesional continuo de los docentes. Este evento no solo contribuye al enriquecimiento del conocimiento académico, sino que también impulsa el desarrollo de estrategias y políticas educativas que pueden tener un impacto significativo en la mejora de la educación superior en Bolivia.
Small Regulatory RNAs in the Control of Motility and Biofilm Formation in E. coli and Salmonella
Creators: name: Mika, Franziska
name: Hengge, Regine
Publisher: name: Freie Universität Berlin
Year: 2013
Subjects: subject: biofilm matrix
subject: c-di-GMP
subject: cellulose
subject: curli
subject: CsgD
subject: flagella
subject: flhDC
subject: Hfq
subject: RpoS
subject: sRNA
subject: 500 Naturwissenschaften und Mathematik::570 Biowissenschaften; Biologie

description: Biofilm formation in Escherichia coli and other enteric bacteria involves the inverse regulation of the synthesis of flagella and biofilm matrix components such as amyloid curli fibres, cellulose, colanic acid and poly-N-acetylglucosamine (PGA). Physiologically, these processes reflect the transition from growth to stationary phase. At the molecular level, they are tightly controlled by various sigma factors competing for RNA polymerase, a series of transcription factors acting in hierarchical regulatory cascades and several nucleotide messengers, including cyclic-di-GMP. In addition, a surprisingly large number of small regulatory RNAs (sRNAs) have been shown to directly or indirectly modulate motility and/or biofilm formation. This review aims at giving an overview of these sRNA regulators and their impact in biofilm formation in E. coli and Salmonella. Special emphasis will be put on sRNAs, that have known targets such as the mRNAs of the flagellar master regulator FlhDC, the stationary phase sigma factor σS (RpoS) and the key biofilm regulator CsgD that have recently been shown to act as major hubs for regulation by multiple sRNAs. View Full-Text
Recognition and application of offlap in endorheic basins: new insights into plateau growth
Creators: name: Yu, Xiangjiang
name: Guo, Zhaojie
name: Chen, Yan
name: Cheng, Xiang
name: Du, Wei
name: Wang, Zhendong
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Biophysics
subject: Biochemistry
subject: Space Science
subject: Environmental Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Plant Biology
subject: FOS: Biological sciences

description: Accumulating sediments is an inherent attribute of endorheic basins. Overall aggradational stratigraphic architecture can be predicted in endorheic basins, whereas the offlap process can be regarded as an important geological indicator in closed basins. This study theoretically proposes the possible offlap process in endorheic basins, and then explores the actual pattern of the offlap process in the Qaidam basin, the largest endorheic basin in the northern Tibetan Plateau. According to the interpretation of drilling well data and seismic reflection profiles, widespread offlap is identified at all the three boundaries of the Qaidam basin since the late Miocene. The offlap process in endorheic basins is controlled by newborn faults or new isostatic flexures inside the previous basin margin. Interpretation of seismic reflection profiles reflects that the rigid Qaidam block was gradually broken during the India‐Eurasian collision and the plateau progressively expanded from pre-existing mountains to basins.
Additional file 1 of Comparative genome analysis of plant ascomycete fungal pathogens with different lifestyles reveals distinctive virulence strategies
Creators: name: Wang, Yansu
name: Wu, Jie
name: Yan, Jiacheng
name: Guo, Ming
name: Xu, Lei
name: Hou, Liping
name: Zou, Quan
Publisher: name: figshare
Year: 2022
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Plant Biology

description: Additional file 1.
Deciphering the Role of p24 Proteins in COPII-mediated Protein Secretion
Creators: D'Arcangelo, Jennifer G.
Publisher: name: Columbia University
Year: 2015
Subjects: subject: Endoplasmic reticulum
subject: Molecular genetics
subject: Proteins--Secretion
subject: Cytology
subject: Molecular biology
subject: Genetics
subject: FOS: Biological sciences

description: In eukaryotic cells, proteins continuously flux through the organelles of the secretory pathway in an essential cellular process called protein secretion. This dynamic process originates at the endoplasmic reticulum (ER), where translating ribosomes push linear peptides into the ER membrane and lumen. ER chaperones assist in folding nascent peptides into three-dimensional conformations and proteins are concentrated into membrane-encapsulated vesicles bound for the Golgi apparatus. ER to Golgi transport is mediated by a set of cytosolic coat proteins called COPII. The COPII coat polymerizes into a lattice on the ER membrane that is able to bend the membrane around secretory cargo and bud off a spherical vesicle.
      Protein secretion is subject to rapid changes as a cell responds to its environment and requirements for viability alter. In addition to accommodating short-term demands, such as translational up-regulation, evolved complexity of secretory proteins over time, has also required that secretory components adapt. In both cases changes in secretory demands require that the COPII proteins have an inherent flexibility to navigate these changes without disrupting secretory flux. In this work I have examined a family of quintessential secretory cargo, p24 proteins, that challenge protein secretion. This family of proteins forms a hetero-tetrameric complex that cycles between the ER and the Golgi and mediates transport of glycosylphosphatidylinositol-anchored proteins (GPI-APs). Here I present evidence that suggests, when present in vesicles, both p24 proteins and their GPI-AP cargo present a challenge to vesicle formation. I posit that three attributes of these proteins present a local barrier to membrane bending: Lumenal asymmetric distribution across the membrane, high cellular abundance and affinity for ceramide rich membranes. I have also elucidated mechanisms that the coat has evolved to accommodate troublesome cargo such as p24 proteins, which enhance structural scaffolding and increase average vesicle size. Finally I present preliminary findings indicating that p24s also contribute to ER homeostasis by preventing aberrant incorporation of proteins into vesicles. Comprehensively, these findings have shed light on the role of p24 proteins in vesicles. Traditionally thought to be canonical ER cargo receptors, these proteins also appear capable of contributing to the composition of the vesicles in which they reside, and impacting trafficking efficiency in two ways: First by directly mediating transport of GPI-APs and second by uniformly packing vesicles to avoid wasteful secretion. My work has contributed to a growing notion in the field that secretory cargo are not inert passengers but active participants in vesicle mediated secretion.
Versatile Medical Image Segmentation Learned from Multi-Source Datasets via Model Self-Disambiguation
Creators: name: Chen, Xiaoyang
name: Zheng, Hao
name: Li, Yuemeng
name: Ma, Yuncong
name: Ma, Liang
name: Li, Hongming
name: Fan, Yong
Publisher: name: arXiv
Year: 2023
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Computer and information sciences

description: A versatile medical image segmentation model applicable to images acquired with diverse equipment and protocols can facilitate model deployment and maintenance. However, building such a model typically demands a large, diverse, and fully annotated dataset, which is challenging to obtain due to the labor-intensive nature of data curation. To address this challenge, we propose a cost-effective alternative that harnesses multi-source data with only partial or sparse segmentation labels for training, substantially reducing the cost of developing a versatile model. We devise strategies for model self-disambiguation, prior knowledge incorporation, and imbalance mitigation to tackle challenges associated with inconsistently labeled multi-source data, including label ambiguity and modality, dataset, and class imbalances. Experimental results on a multi-modal dataset compiled from eight different sources for abdominal structure segmentation have demonstrated the effectiveness and superior performance of our method compared to state-of-the-art alternative approaches. We anticipate that its cost-saving features, which optimize the utilization of existing annotated data and reduce annotation efforts for new data, will have a significant impact in the field.
description: 14 pages, 5 figures
Picosecond-precision optical time transfer in free space using flexible binary offset carrier modulation
Creators: name: Yang, Honglei
name: Wang, Haifeng
name: Yi, Hang
name: Wang, Xueyun
name: Wang, Hongbo
name: Zhang, Shengkang
Publisher: name: arXiv
Year: 2019
Subjects: subject: Signal Processing (eess.SP)
subject: Instrumentation and Detectors (physics.ins-det)
subject: FOS: Electrical engineering, electronic engineering, information engineering
subject: FOS: Physical sciences

description: Free-space optical time transfer that features high precision and flexibility will act a crucial role in near-future ground-to-satellite/inter-satellite clock networks and outdoor timing services. Here we propose a free-space optical flexible-binary-offset-carrier-modulated (FlexBOC-modulated) time transfer method. The utilized FlexBOC modulation could yield a comparative precision, although its occupied bandwidth is tremendously reduced by at least 97.5% compared to optical binary phase modulation. Meanwhile, the adoption of optical techniques eliminates the multi-path effect that is major limit in the current microwave satellite time transfer system. What's more, the time interval measurement avoids a continuous link that may be routinely broken by physical obstructions. For verification, a time transfer experiment with our home-built system between two sites separated by a 30-m free-space path outside the laboratory was conducted. Over a 15 h period, the time deviation is 2.3 ps in a 1-s averaging time, and averages down to 1.0 ps until ~60 s. The fractional frequency instability exhibits 4.0E-12 at a gate time of 1 s, and approaches to 2.6E10-15 at 10000 s.
Mathematical Aspects of Mirror Symmetry
Creators: name: Morrison, David R.
Publisher: name: arXiv
Year: 1996
Subjects: subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics

description: Lecture notes from 1993 Park City lectures and 1994 Trento lectures. The focus of these lectures is on giving a mathematical description of the A-model and B-model correlation functions on a Calabi--Yau manifold, and a precise mathematical conjecture relating these for a pair of mirror manifolds.
description: 74 pages, LaTeX2e with amsmath; minor changes, added table of contents
Cryptanalysis of a System Based on Twisted Reed-Solomon Codes
Creators: name: Lavauzelle, Julien
name: Renner, Julian
Publisher: name: arXiv
Year: 2019
Subjects: subject: Information Theory (cs.IT)
subject: Cryptography and Security (cs.CR)
subject: FOS: Computer and information sciences

description: Twisted Reed-Solomon (TRS) codes are a family of codes that contains a large number of maximum distance separable codes that are non-equivalent to Reed--Solomon codes. TRS codes were recently proposed as an alternative to Goppa codes for the McEliece code-based cryptosystem, resulting in a potential reduction of key sizes. The use of TRS codes in the McEliece cryptosystem has been motivated by the fact that a large subfamily of TRS codes is resilient to a direct use of known algebraic key-recovery methods. In this paper, an efficient key-recovery attack on the TRS variant that was used in the McEliece cryptosystem is presented. The algorithm exploits a new approach based on recovering the structure of a well-chosen subfield subcode of the public code. It is proved that the attack always succeeds and breaks the system for all practical parameters in $O(n^4)$ field operations. A software implementation of the algorithm retrieves a valid private key from the public key within a few minutes, for parameters claiming a security level of 128 bits. The success of the attack also indicates that, contrary to common beliefs, subfield subcodes of the public code need to be precisely analyzed when proposing a McEliece-type code-based cryptosystem. Finally, the paper discusses an attempt to repair the scheme and a modification of the attack aiming at Gabidulin-Paramonov-Tretjakov cryptosystems based on twisted Gabidulin codes.
description: Accepted to Designs, Codes and Cryptography
Gravitational bremsstrahlung and the Fulling-Davies-Unruh thermal bath
Creators: name: Brito, João P. B.
name: Crispino, Luís C. B.
name: Higuchi, Atsushi
Publisher: name: arXiv
Year: 2023
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences
subject: 83C47 (Primary) 81T20 (Secondary)

description: The electromagnetic radiation emitted by an accelerated charged particle can be described theoretically as the interaction of the charge with the so-called Fulling-Davies-Unruh thermal bath in the coordinate frame co-accelerated with the charge. We present a similar analysis on the gravitational radiation from a classical point mass uniformly accelerated, being pulled by a string satisfying the weak energy condition. In particular, we derive the interaction rate (with fixed transverse momentum) of this system of the point mass and string in the Fulling-Davies-Unruh thermal bath in the co-accelerated frame and show that it equals the graviton emission rate calculated in the standard method in Minkowski spacetime.
description: 14 pages, 1 figure, published version
Additional file 1: of Hepatitis E virus infection among pregnant women in Africa: systematic review and meta-analysis
Creators: name: Mulat Dagnew
name: Amare Belachew
name: Moges Tiruneh
name: Feleke Moges
Publisher: name: figshare
Year: 2019
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Molecular Biology
subject: Biotechnology
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: Figure S1. Sensitivity analysis of seroprevalence of HEV infection among pregnant women. (DOCX 33 kb)
Additional file 15: of PD-1 signaling affects cristae morphology and leads to mitochondrial dysfunction in human CD8+ T lymphocytes
Creators: name: Ogando, Jesús
name: Sáez, María
name: Santos, Javier
name: Nuevo-Tapioles, Cristina
name: Gut, Marta
name: Esteve-Codina, Anna
name: Heath, Simon
name: González-Pérez, Antonio
name: Cuezva, José
name: Lacalle, Rosa
name: Mañes, Santos
Publisher: name: figshare
Year: 2019
Subjects: subject: Cell Biology
subject: Molecular Biology
subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Developmental Biology
subject: Science Policy

description: Figure S9. Mitochondrial morphology analyzed by TEM. (PDF 5455 kb)
Additional file 2: of Hepatitis E virus infection among pregnant women in Africa: systematic review and meta-analysis
Creators: name: Mulat Dagnew
name: Amare Belachew
name: Moges Tiruneh
name: Feleke Moges
Publisher: name: figshare
Year: 2019
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Molecular Biology
subject: Biotechnology
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Figure. S2. Trend of seroprevalence of HEV among African pregnant women. (DOCX 18 kb)
Additional file 1: of Aligning public financial management system and free healthcare policies: lessons from a free maternal and child healthcare programme in Nigeria
Creators: name: Ogbuabor, Daniel
name: Obinna Onwujekwe
Publisher: name: figshare
Year: 2019
Subjects: subject: Medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy
subject: 60506 Virology

description: List of documents reviewed (DOCX 14 kb)
On Entangled Information and Quantum Capacity
Creators: name: Belavkin, V. P.
Publisher: name: arXiv
Year: 2002
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The pure quantum entanglement is generalized to the case of mixed compound states on an operator algebra to include the classical and quantum encodings as particular cases. The true quantum entanglements are characterized by quantum couplings which are described as transpose-CP, but not Completely Positive (CP), trace-normalized linear positive maps of the algebra. The entangled (total) information is defined in this paper as a relative entropy of the conditional (the derivative of the compound state with respect to the input) and the unconditional output states. Thus defined the total information of the entangled states leads to two different types of the entropy for a given quantum state: the von Neumann entropy, or c-entropy, which is achieved as the supremum of the information over all c-entanglements and thus is semi-classical, and the true quantum entropy, or q-entropy, which is achieved at the standard entanglement. The q-capacity, defined as the supremum over all entanglements, coincides with the topological entropy. In the case of the simple algebra it doubles the c-capacity, coinciding with the rank-entropy. The conditional q-entropy based on the q-entropy, is positive, unlike the von Neumann conditional entropy, and the q-information of a quantum channel is proved to be additive.
description: 18 pages. The full version of the Capri-2000 conference lecture, see the QCCM-3 Proceedings by Kluwer/Plenum (2001) pp 325-333, and also http://www.maths.nott.ac.uk/personal/vpb/vpb_research.html
Dissipation Enhanced Unidirectional Transport in Topological Systems
Creators: name: Lu, Ming
name: Liu, Xue-Zhu
name: Li, Hailong
name: Zhang, Zhi-Qiang
name: Liu, Jie
name: Xie, X. C.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Dissipation is a common occurrence in real-world systems and is generally considered to be detrimental to transport. In this study, we examine the transport properties of a narrow quantum anomalous Hall system with dissipation applied on one edge. When the Fermi level resides within the hybridization gap, we find that while transport is suppressed on one edge, it is significantly enhanced on the other. We reveal that this enhancement arises from dissipation-induced gap closure, which is deeply rooted in the point gap topology of the system, resulting in a reduction of the decaying coefficient. When the dissipation is very large, we find that the low-energy physics is nearly indistinguishable from a narrower system, whose dissipation amplitude is inversely proportional to that of the original one. To get more physical intuition, we demonstrate that the low-energy physics can be well captured by a pair of coupled counter-propagating chiral edge states, one of which has a modified group velocity and an effective dissipation. We also briefly discuss the possible experimental realizations of this enhanced unidirectional transport.