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arXiv 2022年

作者： Salamon, Peter Salamon, David Cantu, V. Adrian An, Michelle Perry, Tyler Edwards, Robert A. Segall, Anca M. The Department of Mathematics and Statistics The Computational Science Research Center The Viral Information Institute San Diego State University San DiegoCA92182 United States The Department of Mathematics and Statistics San Diego State University San DiegoCA92182 United States The Computational Science Research Center The Department of Biology San Diego State University San DiegoCA92182 United States The Perelman School of Medicine The University of Pennsylvania 425 Johnson Pavilion 3610 Hamilton Walk PhiladelphiaPA19104 United States The Computational Science Research Center San Diego State University San DiegoCA92182 United States Google 1600 Amphitheater Parkway Mountain ViewCA94043 United States The Bioinformatics and Medical Informatics Program San Diego State University San DiegoCA92182 United States Helix 9875 Towne Center Drive San DiegoCA92121 United States The Department of Biology The Computational Science Research Center The Viral Information Institute The Bioinformatics and Medical Informatics Program San Diego State University San DiegoCA92182 United States

This paper investigates the post-hoc calibration of confidence for "exploratory" machine learning classification problems. The difficulty in these problems stems from the continuing desire to push the boundaries of which categories have enough examples to generalize from when curating datasets, and confusion regarding the validity of those categories. We argue that for such problems the "one-versus-all" approach (top-label calibration) must be used rather than the "calibrate-the-full-response-matrix" approach advocated elsewhere in the literature. We introduce and test four new algorithms designed to handle the idiosyncrasies of category-specific confidence estimation. Chief among these methods is the use of kernel density ratios for confidence calibration including a novel, bulletproof algorithm for choosing the bandwidth. We test our claims and explore the limits of calibration on a bioinformatics application (PhANNs) [1], [2] as well as the classic MNIST benchmark [3]. Finally, our analysis argues that post-hoc calibration should always be performed, should be based only on the test dataset, and should be sanity-checked visually. Copyright © 2022, The Authors. All rights reserved.

关键词： Calibration

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Capturing the Mechanical Unfolding Pathway of a Large Protein with Coiled‐Coil Probes†

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Angewandte Chemie 2014年第49期126卷

作者： Qing Li Zackary N. Scholl Piotr E. Marszalek Department of Mechanical Engineering and Material Sciences Duke University Durham NC 27708 (USA) Program in Computational Biology and Bioinformatics Duke University Durham NC 27708 (USA)

The folding behaviors and mechanisms of large multidomain proteins have remained largely uncharacterized, primarily because of the lack of appropriate research methods. To address these limitations, novel mechanical folding probes have been developed that are based on antiparallel coiled‐coil polypeptides. Such probes can be conveniently inserted at the DNA level, at different positions within the protein of interest where they minimally disturb the host protein structure. During single‐molecule force spectroscopy measurements, the forced unfolding of the probe captures the progress of the unfolding front through the host protein structure. This novel approach allows unfolding pathways of large proteins to be directly identified. As an example, this probe was used in a large multidomain protein with ten identical ankyrin repeats, and the unfolding pathway, its direction, and the order of sequential unfolding were unequivocally and precisely determined. This development facilitates the examination of the folding pathways of large proteins, which are predominant in the proteasomes of all organisms, but have thus far eluded study because of the technical limitations encountered when using traditional techniques.

关键词： Coiled‐Coil‐Strukturen Einzelmolekülspektroskopie Multidomänenproteine Proteinfaltung Proteinstrukturen

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Theoretical Insights into Co2 Electroreduction on Single and Dual Heteroatom-Doped Diamonds

SSRN

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SSRN 2023年

作者： Injongkol, Yuwanda Zhang, Rui-Qin Montoya, Alejandro Rungrotmongkol, Thanyada Jungsuttiwong, Siriporn Center of Excellence in Biocatalyst and Sustainable Biotechnology Department of Biochemistry Faculty of Science Chulalongkorn University Bangkok10330 Thailand City University of Hong Kong Hong Kong School of Chemical and Biomolecular Engineering The University of Sydney SydneyNSW2006 Australia Program in Bioinformatics and Computational Biology Graduate School Chulalongkorn University Bangkok10330 Thailand Department of Chemistry Faculty of Science Ubon Ratchathani University Ubon Ratchathani34190 Thailand

We employed Periodic Density Functional Theory (DFT) to investigate the catalytic activity of single and double dopant of boron (B), nitrogen (N), and phosphorous (P) anchored on diamond surfaces for the CO2 reduction reaction (CO2RR) by analyzing reaction energy profiles. Our findings show that the double-doped catalyst exhibits lower energy barriers in CO2RR compared to the single dopants. Specifically, when considering BB and NN configurations, there is a thermodynamic preference towards the formation of formic acid (HCOOH) with overpotentials of 0.40 and 0.09 V, respectively. The co-doped catalyst comprising B and N (BN) demonstrates a tendency towards the formation of HCOOH without requiring any applied overpotentials. Notably, BN outperforms other catalysts, occupying the top position on the volcano plot, indicating the lowest limiting potential (UL), remarkable thermal stability, and the ability to suppress the competing hydrogen evolution reaction (HER). This research provides valuable insights into the product differentiation in the electroreduction of CO2. © 2023, The Authors. All rights reserved.

关键词： Density functional theory

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General framework for the mechanical response of metallic glasses during strain-rate-dependent uniaxial compression

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Physical Review Materials 2023年第10期7卷 105604-105604页

作者： Weiwei Jin Amit Datye Udo D. Schwarz Mark D. Shattuck Corey S. O'Hern Department of Mechanical Engineering and Materials Science Yale University New Haven Connecticut 06520 USA Department of Chemical and Environmental Engineering Yale University New Haven Connecticut 06520 USA Benjamin Levich Institute and Physics Department The City College of New York New York New York 10031 USA Department of Physics Yale University New Haven Connecticut 06520 USA Department of Applied Physics Yale University New Haven Connecticut 06520 USA Graduate Program in Computational Biology and Bioinformatics Yale University New Haven Connecticut 06520 USA

Experimental data on compressive strength σmax versus strain rate ɛ̇eng for metallic glasses undergoing uniaxial compression show varying strain rate sensitivity. For some metallic glasses, σmax decreases with increasing ɛ̇eng, while for others, σmax increases with increasing ɛ̇eng, and for certain alloys σmax versus ɛ̇eng is nonmonotonic. To understand their strain rate sensitivity, we conduct molecular dynamics simulations of metallic glasses undergoing uniaxial compression at finite strain rates and coupled to heat baths with a range of temperatures T0 and damping parameters b. In the T0→0 and b→0 limits, we find that the compressive strength σmax versus temperature T obeys a “chevron-shaped” scaling relation. In the low-strain-rate regime, σmax decreases linearly with increasing T, whereas σmax grows as a power law with decreasing T in the high-strain-rate regime. For T0>0, σmax(T) deviates from the scaling curve at low strain rates, but σmax(T) rejoins the scaling curve as the strain rate increases. Enhanced dissipation reduces compression-induced heating, which causes σmax(T) to deviate from the b→0 scaling behavior for intermediate strain rates, but σmax(T) converges to the high-strain-rate power-law scaling behavior at sufficiently high strain rates. Determining σmax(T) as a function of b and T0 provides a general framework for explaining the strain rate sensitivity of metallic glasses under compression.

关键词： Compressive strength Mechanical deformation Amorphous materials Metallic glasses Molecular dynamics

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Causes and Consequences of Apparent Timescaling Across All Estimated Evolutionary Rates

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Ecology, Evolution, and Systematics 1000年第1期52卷 587-609页

作者： Luke J. Harmon Matthew W. Pennell L. Francisco Henao-Diaz Jonathan Rolland Breanna N. Sipley Josef C. Uyeda 1Institute for Bioinformatics and Evolutionary Studies (IBEST) and Department of Biological Sciences University of Idaho Moscow Idaho 83844 USA email: lukeh@uidaho.edu 2Department of Zoology and Biodiversity Research Centre University of British Columbia Vancouver British Columbia V6T 1Z4 Canada 3Laboratoire Evolution et Diversité Biologique CNRS UMR5174 Université Toulouse III–Paul Sabatier 31062 Toulouse France 4Program for Bioinformatics and Computational Biology University of Idaho Moscow Idaho 83844 USA 5Department of Biological Sciences Virginia Tech University Blacksburg Virginia 24061 USA

Evolutionary rates play a central role in connecting micro- and macroevolution. All evolutionary rate estimates, including rates of molecular evolution, trait evolution, and lineage diversification, share a similar scaling pattern with time: The highest rates are those measured over the shortest time interval. This creates a disconnect between micro- and macroevolution, although the pattern is the opposite of what some might expect: Patterns of change over short timescales predict that evolution has tremendous potential to create variation and that potential is barely tapped by macroevolution. In this review, we discuss this shared scaling pattern across evolutionary rates. We break down possible explanations for scaling into two categories, estimation error and model misspecification, and discuss how both apply to each type of rate. We also discuss the consequences of this ubiquitous pattern, which can lead to unexpected results when comparing ratesover different timescales. Finally, after addressing purely statistical concerns, we explore a few possibilities for a shared unifying explanation across the three types of rates that results from a failure to fully understand and account for how biological processes scale over time.

关键词： speciation extinction genetics phenotypes microevolution macroevolution

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DOMMINO 2.0: Integrating structurally resolved protein-, RNA-, and DNA-mediated Macromolecular interactions

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Database 2016年第2016期2016卷 1-12页

作者： Kuang, Xingyan Dhroso, Andi Han, Jing Ginger Shyu, Chi-Ren Korkin, Dmitry Informatics Institute University of Missouri Columbia MO United States Department of Computer Science Bioinformatics and Computational Biology Program Worcester Polytechnic Institute Worcester MA United States Department of Electrical and Computer Engineering United States Department of Computer Science University of Missouri Columbia MO United States Ohio State University Comprehensive Cancer Center Columbus OH United States

Macromolecular interactions are formed between proteins, DNA and RNA molecules. Being a principle building block in macromolecular assemblies and pathways, the interactions underlie most of cellular functions. Malfunctioning of macromolecular interactions is also linked to a number of diseases. Structural knowledge of the macromolecular interaction allows one to understand the interaction's mechanism, determine its functional implications and characterize the effects of genetic variations, such as single nucleotide polymorphisms, on the interaction. Unfortunately, until now the interactions mediated by different types of macromolecules, e.g. protein-protein interactions or protein-DNA interactions, are collected into individual and unrelated structural databases. This presents a significant obstacle in the analysis of macromolecular interactions. For instance, the homogeneous structural interaction databases prevent scientists from studying structural interactions of different types but occurring in the same macromolecular complex. Here, we introduce DOMMINO 2.0, a structural Database Of Macro-Molecular INteractiOns. Compared to DOMMINO 1.0, a comprehensive database on protein-protein interactions, DOMMINO 2.0 includes the interactions between all three basic types of macromolecules extracted from PDB files. DOMMINO 2.0 is automatically updated on a weekly basis. It currently includes ∼1 040 000 interactions between two polypeptide subunits (e.g. domains, peptides, termini and interdomain linkers), ∼43 000 RNA-mediated interactions, and ∼12 000 DNA-mediated interactions. All protein structures in the database are annotated using SCOP and SUPERFAMILY family annotation. As a result, protein-mediated interactions involving protein domains, interdomain linkers, C- and N-termini, and peptides are identified. Our database provides an intuitive web interface, allowing one to investigate interactions at three different resolution levels: whole subunit network, binary intera

关键词： DNA RNA MACROMOLECULAR synthesis MACROMOLECULES PROTEIN-protein interactions

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How Does ChatGPT Perform on the United States Medical Licensing Examination? The Implications of Large Language Models for Medical Education and Knowledge Assessment

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JMIR Medical Education 2023年 9卷 e45312页

作者： Gilson, Aidan Safranek, Conrad W. Huang, Thomas Socrates, Vimig Chi, Ling Taylor, Richard Andrew Chartash, David Section for Biomedical Informatics and Data Science Yale University School of Medicine New Haven CT United States Department of Emergency Medicine Yale University School of Medicine New Haven CT United States Program of Computational Biology and Bioinformatics Yale University New Haven CT United States School of Medicine University College Dublin National University of Ireland Dublin Ireland

Background: Chat Generative Pre-trained Transformer (ChatGPT) is a 175-billion-parameter natural language processing model that can generate conversation-style responses to user input. Objective: This study aimed to evaluate the performance of ChatGPT on questions within the scope of the United States Medical Licensing Examination Step 1 and Step 2 exams, as well as to analyze responses for user interpretability. Methods: We used 2 sets of multiple-choice questions to evaluate ChatGPT’s performance, each with questions pertaining to Step 1 and Step 2. The first set was derived from AMBOSS, a commonly used question bank for medical students, which also provides statistics on question difficulty and the performance on an exam relative to the user base. The second set was the National Board of Medical Examiners (NBME) free 120 questions. ChatGPT’s performance was compared to 2 other large language models, GPT-3 and InstructGPT. The text output of each ChatGPT response was evaluated across 3 qualitative metrics: logical justification of the answer selected, presence of information internal to the question, and presence of information external to the question. Results: Of the 4 data sets, AMBOSS-Step1, AMBOSS-Step2, NBME-Free-Step1, and NBME-Free-Step2, ChatGPT achieved accuracies of 44% (44/100), 42% (42/100), 64.4% (56/87), and 57.8% (59/102), respectively. ChatGPT outperformed InstructGPT by 8.15% on average across all data sets, and GPT-3 performed similarly to random chance. The model demonstrated a significant decrease in performance as question difficulty increased (P=.01) within the AMBOSS-Step1 data set. We found that logical justification for ChatGPT’s answer selection was present in 100% of outputs of the NBME data sets. Internal information to the question was present in 96.8% (183/189) of all questions. The presence of information external to the question was 44.5% and 27% lower for incorrect answers relative to correct answers on the NBME-Free-Step1 (P<.001

关键词： artificial intelligence chatbot ChatGPT conversational agent education technology generative pre-trained transformer GPT machine learning medical education MedQA natural language processing NLP

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Local and global measures of the shear moduli of jammed disk packings

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Physical Review E 2023年第5期107卷 054903-054903页

作者： Shiyun Zhang Weiwei Jin Dong Wang Ding Xu Jerry Zhang Mark D. Shattuck Corey S. O'Hern Department of Physics University of Science and Technology of China Hefei Anhui 230026 China Department of Mechanical Engineering and Materials Science Yale University New Haven Connecticut 06520 USA Benjamin Levich Institute and Physics Department The City College of New York New York New York 10031 USA Department of Physics Yale University New Haven Connecticut 06520 USA Department of Applied Physics Yale University New Haven Connecticut 06520 USA Graduate Program in Computational Biology and Bioinformatics Yale University New Haven Connecticut 06520 USA

Strain-controlled isotropic compression gives rise to jammed packings of repulsive, frictionless disks with either positive or negative global shear moduli. We carry out computational studies to understand the contributions of the negative shear moduli to the mechanical response of jammed disk packings. We first decompose the ensemble-averaged, global shear modulus as 〈G〉=(1−F−)〈G+〉+F−〈G−〉, where F− is the fraction of jammed packings with negative shear moduli and 〈G+〉 and 〈G−〉 are the average values from packings with positive and negative moduli, respectively. We show that 〈G+〉 and 〈|G−|〉 obey different power-law scaling relations above and below pN2∼1. For pN2>1, both 〈G+〉N and 〈|G−|〉N∼(pN2)β, where β∼0.5 for repulsive linear spring interactions. Despite this, 〈G〉N∼(pN2)β′ with β′≳0.5 due to the contributions from packings with negative shear moduli. We show further that the probability distribution of global shear moduli P(G) collapses at fixed pN2 and different values of p and N. We calculate analytically that P(G) is a Γ distribution in the pN2≪1 limit. As pN2 increases, the skewness of P(G) decreases and P(G) becomes a skew-normal distribution with negative skewness in the pN2≫1 limit. We also partition jammed disk packings into subsystems using Delaunay triangulation of the disk centers to calculate local shear moduli. We show that the local shear moduli defined from groups of adjacent triangles can be negative even when G>0. The spatial correlation function of local shear moduli C(r⃗) displays weak correlations for pnsub2<10−2, where nsub is the number of particles within each subsystem. However, C(r⃗) begins to develop long-ranged spatial correlations with fourfold angular symmetry for pnsub2≳10−2.

关键词： Jamming Packing & jamming problems Granular materials

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A Human-Centered Design Approach to SOVTE Straw Phonation Instruction

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Journal of Voice 2023年

作者： Bhatt, Sandeep Scearce, Leda Frank-Ito, Dennis Nixon, Tara Umstead, Kelly A. Department of Industrial Design North Carolina State University Raleigh NC United States Department of Head and Neck Surgery & Communication Sciences Duke University School of Medicine Durham NC United States Computational Biology and Bioinformatics Program Duke University Durham NC United States Department of Mechanical Engineering and Materials Science Duke University Durham NC United States

Objectives: Extensive research has demonstrated that straw/tube phonation exercises produce positive effects on the voice quality of the user. The purpose of this study was to explore pedagogical practices employed by a range of voice professionals when using SOVTEs by applying human-centered design approaches to examine workflow and communication between teachers and students. Method/Design: The researchers conducted a series of five participatory role-playing workshop activities at a multi-disciplinary vocology conference that included speech-language pathologists, voice scientists, physicians, singing teachers, acting voice teachers, choral directors, and singers. Volunteers were asked to assume the role of teaching or learning straw phonation exercises. The other participants from each workshop were asked to provide written and verbal feedback regarding the teacher/student dynamics and what they found most important and relevant in terms of best practices for SOVTEs. Expert evaluators subsequently provided similar feedback based on video recordings of the workshops. Results: While there was variability noted in teaching techniques and results, common themes emerged in the analysis. Successful and unsuccessful student and teacher techniques were identified by the workshop participants. Through the video analysis, the research team identified themes in instructional teaching, experiential learning, and straw articulation and mechanics. Conclusions: The benefits of straw/tube phonation exercises on voice quality have been well-established and are clear. As we continue to refine best practices in SOVTEs and, in particular, straw phonation, involvement of experts in HCD as part of multidisciplinary teams may lead to the eventual design of SOVTE tools that provide greater precision, consistency, and effectiveness both in clinical and pedagogical settings, and aid in the differentiation of SOVTE approaches within the taxonomy of vocal habilitation and rehabilitation te

关键词： Voice disorder Voice habilitation Voice pedagogy Voice rehabilitation Voice therapy Voice training

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"RETRACTED ARTICLE: Vibrio parahaemolyticus RhsP represents a widespread group of pro-effectors for type VI secretion systems

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Nature Communications 2018年第1期9卷 1-14页

作者： Nan Jiang Le Tang Ruiqiang Xie Zhi Li Brianne Burkinshaw Xiaoye Liang Dylan Sosa L. Aravind Tao Dong Dapeng Zhang Jun Zheng Faculty of Health Sciences University of Macau Macau SAR China Department of Ecosystem and Public Health University of Calgary Calgary Canada Department of Biochemistry and Molecular Biology University of Calgary Calgary Canada Snyder Institute for Chronic Diseases University of Calgary Calgary Canada State Key Laboratory of Microbial Metabolism Joint International Laboratory on Metabolic and Developmental Sciences School of Life Sciences and Biotechnology Shanghai Jiao Tong University Shanghai China Program of Bioinformatics and Computational Biology College of Arts and Sciences Saint Louis University Saint Louis USA National Center for Biotechnology Information National Library of Medicine National Institutes of Health Bethesda USA Department of Biology College of Arts and Sciences Saint Louis University Saint Louis USA

Type VI secretion systems (T6SSs) translocate effector proteins, such as Rhs toxins, to eukaryotic cells or prokaryotic competitors. All T6SS Rhs-type effectors characterized thus far contain a PAAR motif or a similar structure. Here, we describe a T6SS-dependent delivery mechanism for a subset of Rhs proteins that lack a PAAR motif. We show that the N-terminal Rhs domain of protein RhsP (or VP1517) fromVibrio parahaemolyticusinhibits the activity of the C-terminal DNase domain. Upon auto-proteolysis, the Rhs fragment remains inside the cells, and the C-terminal region interacts with PAAR2 and is secreted by T6SS2; therefore, RhsP acts as a pro-effector. Furthermore, we show that RhsP contributes to the control of certain “social cheaters” (opaRmutants). Genes encoding proteins with similar Rhs and PAAR-interacting domains, but diverse C-terminal regions, are widely distributed amongVibriospecies.

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