gebhart/patrepeval huggingface dataset:
Systematic Cell-Based Phenotyping of Missense Alleles Empowers Rare Variant Association Studies: A Case for LDLR and Myocardial Infarction (2015)

A fundamental challenge to contemporary genetics is to distinguish rare missense alleles that disrupt protein functions from the majority of alleles neutral on protein activities. High-throughput experimental tools to securely discriminate between disruptive and non-disruptive missense alleles are currently missing. Here we establish a scalable cell-based strategy to profile the biological effects and likely disease relevance of rare missense variants in vitro. We apply this strategy to systematically characterize missense alleles in the low-density lipoprotein receptor (LDLR) gene identified through exome sequencing of 3,235 individuals and exome-chip profiling of 39,186 individuals. Our strategy reliably identifies disruptive missense alleles, and disruptive-allele carriers have higher plasma LDL-cholesterol (LDL-C). Importantly, considering experimental data refined the risk of rare LDLR allele carriers from 4.5- to 25.3-fold for high LDL-C, and from 2.1- to 20-fold for early-onset myocardial infarction. Our study generates proof-of-concept that systematic functional variant profiling may empower rare variant-association studies by orders of magnitude.
Evolution is the new deep learning (2018)

Deep learning (DL) has transformed much of AI, and demonstrated how machine learning can make a difference in the real world. Its core technology is gradient descent, which has been used in neural networks since the 1980s. However, massive expansion of available training data and compute gave it a new instantiation that significantly increased its power.
Working with nitric oxide and hydrogen sulfide in biological systems (2014)

Nitric oxide (NO) and hydrogen sulfide (H2S) are gasotransmitter molecules important in numerous physiological and pathological processes. Although these molecules were first known as environmental toxicants, it is now evident that that they are intricately involved in diverse cellular functions with impact on numerous physiological and pathogenic processes. NO and H2S share some common characteristics but also have unique chemical properties that suggest potential complementary interactions between the two in affecting cellular biochemistry and metabolism. Central among these is the interactions between NO, H2S, and thiols that constitute new ways to regulate protein function, signaling, and cellular responses. In this review, we discuss fundamental biochemical principals, molecular functions, measurement methods, and the pathophysiological relevance of NO and H2S.
Mechanical Pretreatment in a Screw Press Affecting Chemical Pulping of Lignocellulosic Biomass (2014)

To convert lignocellulose into transportation fuels and chemical products, pretreatment of the biomass, leading to the separation of the main components (cellulose, hemicellulose, and lignin), is a crucial and still challenging first step. Within this study, the screw press pretreatment of lignocellulosic biomass and its effect on the subsequent chemical pretreatment steps were evaluated. Macroscopic disruption and defibration of reed straw after screw press pretreatment were confirmed by scanning electronic microscopy and dye adsorption studies, showing an enhancement of the accessible surface area. Alkaline and dilute acid hydrolysis was tested to study the release of phenols or sugars from screw-press-treated and non-treated straw materials. To showcase a realistic subsequent chemical pretreatment step, kinetics of enzymatic hydrolysis after a biogenic and biphasic fractionation (OrganoCat) process was tested to evaluate the release of glucose from cut and pressed reed straw. Pretreatment by a screw press enhanced alkaline hydrolysis. A kinetic study showed that screw press pretreatment can reduce processing time and the amount of alkaline chemicals needed. A 75% and a 116% increase in the release of reducing sugars from screw-press-treated wheat and reed straw was detected, respectively. Whereas the OrganoCat fractionation of the screw-press-pretreated reed straw showed no significant improvement, a synergetic effect could be observed in the subsequent enzymatic hydrolysis of the cellulose pulp after combination of both pretreatments in comparison to applying only the cutting mill before chemical fractionation.
Series fed circularly polarised planar arrays (2002)

This paper describes a new approach to the design of circularly polarised planar antennas. The power is injected at the centre of the array, and is distributed over the array by a straightforward feed network, using resonant linear arrays and notches etched on a few elements in order to produce orthogonal polarisations. Different configurations are selected and analysed with an antenna software based on the integral equations and validated on previous studies.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Idiotype-specific T cell immunity. I. Generation of effector and suppressor T lymphocytes reactive with myeloma idiotypic determinants. (1980)

Abstract BALB/c mice immunized subcutaneously (s.c.) with syngeneic splenocytes to which purified isologous myeloma proteins, M315, M460, or TEPC 15, are coupled, exhibit delayed hypersensitivity (DH) reactions upon subsequent challenge with aqueous myeloma proteins or coupled cells. This reactivity can be transferred to naive animals by Τ cells and is idiotype-specific since animals primed with one myeloma protein respond only to homologous challenge. Mice immunized i.v. with M-315-coupled splenocytes develop splenic suppressor Τ cells that inhibit the development of DH upon s.c. priming. In addition, suppressor cells induced in this manner inhibit antibody production by tissue culture adapted MOPC 315 cells after in vitro co-culture. The suppressor cells that inhibit MOPC 315 cell function are nylon wool nonadherent Thy-1-bearing Τ lymphocytes that express I-J subregion encoded surface determinants and whose precursors are sensitive to cyclophosphamide. Moreover, they are idiotype specific since they can be depleted on and enriched by binding to plastic dishes coated with M315 but not M460 protein or mouse IgG. The use of idiotype-coupled cells to selectively induce idiotype-specific effector and suppressor Τ cells is a valuable approach for studying idiotypic regulation of immune responses. In addition, the ability to specifically modulate the function of a neoplastic cell line provides a tool for analyzing the subcellular mechanisms of action of regulatory Τ lymphocytes.
TDD design for UMTS Long-Term Evolution (2008)

Long-Term Evolution (LTE) will provide substantial enhancements to UMTS 3G systems including improved system capacity and coverage, low latency, reduced operating costs, multi-antenna support, flexible bandwidth operations and seamless integration with existing systems. LTE supports both Frequency Division Duplex (FDD) and Time Division Duplex (TDD) modes to provide deployment flexibility in accordance with operator’s preference and spectrum allocation. This paper presents an overview of LTE TDD design and highlights key differences with FDD. Design challenges unique to TDD are presented together with adopted technical solutions. Finally, simulation results are provided to demonstrate typical TDD system performance with data applications.
VEGF121b and VEGF165b are weakly angiogenic isoforms of VEGF-A (2010)

Our results demonstrate that VEGF₁₂₁/₁₆₅b are not anti-angiogenic, but weakly angiogenic isoforms of VEGF-A. In addition, VEGF(xxx)b isoforms are up-regulated in breast cancer in comparison with non malignant breast tissues. These results are to be taken into account when considering a possible use of VEGF₁₂₁/₁₆₅b-based therapies in patients.
Precision estimation and sample size planning to test influenza A H1N1 positive rate (2015)

Using the data in the influenza A H1N1 positive rate of sampling from August 3,2009 to November 14,Beijing,we estimated the precision of absolute error and relative error.During the epidemic,absolute error of the H1N1 positive rate was less than 0.1 under the confidence level of 1-α = 0.95,this error was at a controllable level.The relative error of the H1N1 positive rate was large at the early phase of influenza A H1N1 transmission, 0.5 before 37 weeks.With the development of the epidemic,the relative error decreased gradually,which means that the result tends to be a reliable estimate.The relative error was less than 0.2 after 42 weeks.Finally,this paper provided a sample size planning based on precision control for sampling test of positive cases.We argued the marginal changes in sample size with a series of conditions.Optimal sample sizes were estimated under different combinations of positive rate and absolute error.
Solitons in a Coupled Linear Chain System (1977)

The existence of solitons in two or more dimensions is discussed. Solitary-wave solutions are found for a system of discrete chains with a derivative of a periodic coupling between the chains. Relevance of the model to phase solitons in the Peierls condensate and in spin systems is discussed.
Fibrin-targeting molecular MRI in inflammatory CNS disorders (2022)

Molecular imaging of CNS fibrin deposition provides an imaging biomarker for inflammatory CNS pathology, which corresponds to pathophysiological ECM remodelling and disease activity, and yields high signal-to-noise ratio, which can improve diagnostic neuroimaging across several neurological diseases with variable degrees of barrier impairment.
Dead-zone free single-shot three-dimensional measurement using a high-repetition-rate Yb:fiber comb (2022)

Using spectral interference from a highly chirped and high-repetition-rate optical frequency comb, a technique for dead-zone free one-shot three-dimensional (3D) imaging was developed. We generated continuously emitted pulse train (dead-zone-free pulse) using a highly chirped pulse from a 750-MHz repetition mode-locked Yb fiber comb. The measurement performances of the system were evaluated using an optical spectrum analyzer, and a longitudinal delay length resolution of 31 µm was obtained at arbitrary position for more than 400 mm range. Using an imaging spectrometer capable of multipoint spectroscopy, a delay length resolution of 81 µm was demonstrated. Finally, for a proof-of-concept measurement of 3D imaging, line profiles of three mirrors located in the middle of 200-mm-distance, corresponding to pulse-to-pulse interval, were measured without any scanning with an uncertainty of 0.7 mm. The uncertainty could be further improved by optical alignment and analysis to the level of 10 ∼ 100 µm at arbitrary position over the range not limited to pulse-to-pulse interval.
Capturing host‐pathogen interactions by protein microarrays: identification of novel streptococcal proteins binding to human fibronectin, fibrinogen, and C4BP (2009)

Microbial pathogen entry and survival in the host is mediated by a network of molecular interactions between the two partners, which has been the subject of many research efforts. A complex picture is emerging in which host-pathogen crosstalk involves a high number of proteins, often with redundant functions. In the present study, we investigated the potential of protein microarrays to simultaneously scan interactions between surface proteins from two main human streptococcal pathogens, Streptococcus pyogenes and Streptococcus agalactiae, and three human ligands, fibronectin, fibrinogen, and C4 binding protein, known to play an important role in streptococcal pathogenesis. By using this technology, we confirmed interactions described in the literature and detected a novel set of streptococcal proteins with binding capacities for the human ligands. The observations were validated by Western blot and ELISA techniques. Three of the newly identified proteins were isoforms of a group B streptococcus-secreted component named Fib and displayed differential binding capacities for fibronectin, fibrinogen, and C4BP. The protein regions involved in the interaction with each ligand were identified by constructing fragments of one of the Fib variants. The approach proved valuable for the acquisition of novel insights into the complex network of protein-protein interactions occurring during microbial infection.
Supplementary Figure Legends 1-6 from Combining a PI3K Inhibitor with a PARP Inhibitor Provides an Effective Therapy for BRCA1-Related Breast Cancer (2023)

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Highly Time-Resolved Metabolic Reprogramming toward Differential Levels of Phosphate in Chlamydomonas reinhardtii (2017)

Understanding phosphorus metabolism in photosynthetic organisms is important as it is closely associated with enhanced crop productivity and pollution management for natural ecosystems (<i>e.g.</i>, algal blooming). Accordingly, we exploited highly time-resolved metabolic responses to different levels of phosphate deprivation in <i>Chlamydomonas reinhardtii</i>, a photosynthetic model organism. We conducted non-targeted primary metabolite profiling using gas-chromatography time-of-flight mass spectrometric analysis. Primarily, we systematically identified main contributors to degree-wise responses corresponding to the levels of phosphate deprivation. Additionally, we systematically characterized the metabolite sets specific to different phosphate conditions and their interactions with culture time. Among them were various types of fatty acids that were most dynamically modulated by the phosphate availability and culture time in addition to phosphorylated compounds.
Assaying for peptides in individual Aplysia neurons with mass spectrometry (1998)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Forward-backward correlations and charged-particle azimuthal distributions in pp interactions using the ATLAS detector (2012)

A bstract Using inelastic proton-proton interactions at $ \sqrt {s} = 900 $ GeV and 7 TeV, recorded by the ATLAS detector at the LHC, measurements have been made of the correlations between forward and backward charged-particle multiplicities and, for the first time, between forward and backward charged-particle summed transverse momentum. In addition, jet-like structure in the events is studied by means of azimuthal distributions of charged particles relative to the charged particle with highest transverse momentum in a selected kinematic region of the event. The results are compared with predictions from tunes of the pythia and herwig++ Monte Carlo generators, which in most cases are found to provide a reasonable description of the data.
Photopolymerized Features via Beam Pen Lithography as a Novel Tool for the Generation of Large Area Protein Micropatterns (2022)

A cantilever-free scanning probe lithography (CF-SPL)-based method for the rapid polymerization of nanoscale features on a surface via crosslinking and thiol-acrylate photoreactions is described, wherein the nanoscale position, height, and diameter of each feature can be finely and independently tuned. With precise spatiotemporal control over the illumination pattern, beam pen lithography (BPL) allows for the photo-crosslinking of polymers into ultrahigh resolution features over centimeter-scale areas using massively parallel >160 000 pen arrays of individually addressable pens that guide and focus light onto the surface with sub-diffraction resolution. The photoinduced crosslinking reaction of the ink material, which is composed of photoinitiator, diphenyl(2,4,6-trimethylbenzoyl) phosphine oxide, poly(ethylene glycol) diacrylate, and thiol-modified functional binding molecules (i.e., thiol-PEG-biotin or 16-mercaptohexanoic acid), proceeds to ≈80% conversion with UV exposure (72 mW cm<sup>-2</sup> ) for short time periods (0.5 s). Such polymer patterns are further reacted with proteins (streptavidin and fibronectin) to yield protein arrays with feature arrangements at high resolution and densities controlled by local UV exposure. This platform, which combines polymer photochemistry and massive arrays of scanning probes, constitutes a new approach to making biomolecular microarrays in a high-throughput and high-yielding manner, opening new routes for biochip synthesis, bioscreening, and cell biology research.
Supplementary Table 1 from Genetic Instability Caused by Loss of MutS Homologue 3 in Human Colorectal Cancer (2023)

Supplementary Table 1 from Genetic Instability Caused by Loss of MutS Homologue 3 in Human Colorectal Cancer
Pointer Graph Networks (2020)

Graph neural networks (GNNs) are typically applied to static graphs that are assumed to be known upfront. This static input structure is often informed purely by insight of the machine learning practitioner, and might not be optimal for the actual task the GNN is solving. In absence of reliable domain expertise, one might resort to inferring the latent graph structure, which is often difficult due to the vast search space of possible graphs. Here we introduce Pointer Graph Networks (PGNs) which augment sets or graphs with additional inferred edges for improved model generalisation ability. PGNs allow each node to dynamically point to another node, followed by message passing over these pointers. The sparsity of this adaptable graph structure makes learning tractable while still being sufficiently expressive to simulate complex algorithms. Critically, the pointing mechanism is directly supervised to model long-term sequences of operations on classical data structures, incorporating useful structural inductive biases from theoretical computer science. Qualitatively, we demonstrate that PGNs can learn parallelisable variants of pointer-based data structures, namely disjoint set unions and link/cut trees. PGNs generalise out-of-distribution to 5x larger test inputs on dynamic graph connectivity tasks, outperforming unrestricted GNNs and Deep Sets.
Design of near-orthogonal LD space-time codes (2004)

This work considers a wireless multiinput-multioutput (MIMO) communication system in a frequency-nonselective scenario with spatially uncorrelated Rayleigh fading channel coefficients and investigates the design of linear dispersion (LD) space-time block codes. By optimizing the constituent weight matrices so that an upper bound on the union bound of the codeword error probability is minimized, good LD codes are obtained regardless of transmit antenna array size and code rate. We make the interesting observation that the proposed design procedure automatically generates LD codes that either correspond to, or are close to, the well-known class of orthogonal space-time block (OSTB) codes. A theoretical analysis confirms the correctness of the observation by proving that OSTB codes are indeed optimal, when the setup under study permit their existence. Simulation results demonstrate the excellent performance of the designed codes. In particular, the importance of the codes' near-orthogonal property is illustrated by showing that low-complexity linear equalizer techniques can be used for decoding purposes while incurring a relatively small performance loss compared with optimal maximum likelihood (ML) decoding.
Parameter Sensitivity Analysis of SPC-based Control Under Different Grid Conditions (2018)

During the last decade virtual synchronous machines (VSMs) have been intensively investigated and plenty of control strategies have been proposed as possible implementations. Some of the proposed control strategies aim to reproduce the inertia of a synchronous machine (SM), but rely on a dedicated unit for the synchronization to the main grid. However, one of the most appealing features of a SM is its ability to self-synchronize itself to the grid thanks to the intrinsic power synchronization mechanism. The Synchronous Power Control (SPC) is among the control strategies proposed in the literature based on the power synchronization mechanism. In this paper, the aforementioned control is deeply investigated. Its concept is first introduced and a small-signal model of an SPC-based grid connected converter is developed. Subsequently, a comprehensive parameter sensitivity analysis is performed in order to identify the effects of control parameters variations on the eigenvalues of the system under different grid conditions. Time-domain simulations in MATLAB/Simulink/PLECS confirm the validity of the developed frequency-domain model.
Punching process effects on fatigue strength properties (2016)

In order to clarify the effect of punching process on fatigue strength properties of thin steel sheets, tension-compression fatigue tests were conducted. For the fatigue tests, processed and unprocessed specimens were prepared. The unprocessed specimen had the same shape as the processed specimen but had no punching process effect on the steel. Before the fatigue tests, hardness and residual stresses were measured. From the measurements, hardening near the punching processed surface, and positive residual stress were obtained. From the fatigue tests, fatigue lives and the fatigue crack behavior were obtained. By using these results, the effects of punching process were discussed.
Losses in PWM converters using IGBTs: On the effectof bus-clamping on the distortion of the AC-side currents (1997)

The authors refer to the paper 'Losses in PWM inverters using IGBTs' by F. Casanellas (see ibid., vol.141, no.5, p.235-9, 1994) and the various correspondence that followed its publication. As an extension to the authors' previous correspondence (see ibid., vol.142, no.1, p.285-7, 1995), the authors compare the RMS values of the phase current harmonics (and/or the harmonic losses) resulting for harmonic-optimal continuous modulation and for the different discontinuous modulation methods. They also determine the modulation method being optimal for a given modulation index and given power factor (load current phase angle /spl phi/).
Gene Expression in Lung Adenocarcinomas of Smokers and Nonsmokers (2003)

Adenocarcinoma (AC) has become the most frequent type of lung cancer in men and women, and is the major form of lung cancer in nonsmokers. Our goal in this paper was to determine if AC in smokers and nonsmokers represents the same genetic disease. We compared gene expression profiles in resected samples of nonmalignant lung tissue and tumor tissue in six never-smokers with AC and in six smokers with AC, who were matched for clinical staging and histologic criteria of cell differentiation. Results were analyzed using a variety of bioinformatic tools. Four times as many genes changed expression in the transition from noninvolved lung to tumor in nonsmokers as in smokers, suggesting that AC in nonsmokers evolves locally, whereas AC in smokers evolves in a field of genetically altered tissue. There were some similarities in gene expression in smokers and nonsmokers, but many differences, suggesting different pathways of cell transformation and tumor formation. Gene expression in the noninvolved lungs of smokers differed from that of nonsmokers, and multidimensional scaling showed that noninvolved lungs of smokers groups with tumors rather than noninvolved lungs of nonsmokers. In addition, expression of a number of genes correlated with smoking intensity. Our findings, although limited by small sample size, suggest that additional studies comparing noninvolved to tumor tissue may identify pathogenetic mechanisms and therapeutic targets that differ in AC of smokers and nonsmokers.