gebhart/patrepeval huggingface dataset:
Protective association of HLA-DRB1*04 subtypes in neurodegenerative diseases implicates acetylated tau PHF6 sequences (2022)

Abstract Using genome-wide association data, we analyzed Human Leukocyte Antigen (HLA) associations in over 176,000 individuals with Parkinson’s (PD) or Alzheimer’s (AD) disease versus controls across ancestry groups. A shared genetic association was observed across diseases at rs601945 (PD: odds ratio (OR)=0.84; 95% confidence interval, [0.80; 0.88]; p=2.2x10-13; AD: OR=0.91[0.89; 0.93]; p=1.8x10-22), and with a protective HLA association recently reported in amyotrophic lateral sclerosis (ALS). Hierarchical protective effects of HLA-DRB1*04 subtypes best accounted for the association, strongest with HLA-DRB1*04:04 and HLA-DRB1*04:07, intermediary with HLA-DRB1*04:01 and HLA-DRB1*04:03, and absent for HLA-DRB1*04:05. The same signal was associated with decreased neurofibrillary tangles (but not neuritic plaque density) in postmortem brains and was more strongly associated with tau levels than Aβ42 levels in the cerebrospinal fluid. Finally, protective HLA-DRB1*04 subtypes strongly bound the aggregation-prone tau PHF6 sequence, but only when acetylated at K311, a modification central to aggregation. An HLA-DRB1*04-mediated adaptive immune response, potentially against tau, decreases PD, AD and ALS risk, offering the possibility of new therapeutic avenues.
Production of Leukocytic Pyrogen from Phagocytes of Neonates (1981)

To study the lack of fever during the human newborn period, cord blood leukocytes obtained at birth were stimulated to produce leukocytic pyrogen (LP) in vitro. Phagocytic leukocytes from infants who were born by Caesarean section and whose mothers had not experienced natural onset of labor produced no LP or significantly less LP than leukocytes from adults or from infants born after natural onset of labor. There was a significant difference between total white blood cell count in cord blood of infants whose phagocytic cells produced LP and those whose cells did not. This observation could not be accounted for by anesthetic agents, phagocytosis of staphylococci, or number of leukocytes producing LP; thus, they suggest an intrinsic defect in the ability to produce LP before birth. Of interest is that a nondialyzable substance(s) present in crude preparations of human chorionic gonadotropin markedly suppressed LP production from adult human monocytes, but purified human chorionic gonadotropin had no effect.
Better Counterexamples for Dafny (2022)

Abstract Dafny is a verification-aware programming language used at Amazon Web Services to develop critical components of their access management, storage, and cryptography infrastructures. The Dafny toolchain provides a verifier that can prove an implementation of a method satisfies its specification. When the underlying SMT solver cannot establish a proof, it generates a counterexample. These counterexamples are hard to understand and their interpretation is often a bottleneck in the proof debugging process. In this paper, we introduce an open-source tool that transforms counterexamples generated by the SMT solver to a more user-friendly format that maps to the Dafny syntax and is suitable for further processing. This new tool allows the Dafny developers to quickly identify the root cause of a problem with their proof, thereby speeding up the development of Dafny projects.
Intratumor Heterogeneity and Precision of Microarray-Based Predictors of Breast Cancer Biology and Clinical Outcome (2010)

Intratumor heterogeneity, although present at the level of individual gene expression, does not preclude precise microarray-based predictions of tumor behavior or clinical outcome in breast cancer patients.
In vivo brain imaging using a portable 29 g two-photon microscope based on a microelectromechanical systems scanning mirror (2009)

We present a two-photon microscope that is approximately 2.9 g in mass and 2.0 x 1.9 x 1.1 cm(3) in size and based on a microelectromechanical systems (MEMS) laser-scanning mirror. The microscope has a focusing motor and a micro-optical assembly composed of four gradient refractive index lenses and a dichroic microprism. Fluorescence is captured without the detected emissions reflecting off the MEMS mirror, by use of separate optical fibers for fluorescence collection and delivery of ultrashort excitation pulses. Using this microscope we imaged neocortical microvasculature and tracked the flow of erythrocytes in live mice.
Lower intracellular hydrogen peroxide levels in cells overexpressing CuZn-superoxide dismutase (1998)

Transfection of V79 Chinese hamster cells produced clones in which CuZn-superoxide dismutase (CuZn-SOD) activities were 2.2- to 3. 5-fold higher than in the parental cells. An overall reduction of antioxidant enzyme activities and both total and oxidized glutathione levels had been found in these clones. Aconitase activities in these cells were determined to indirectly measure the O2- steady-state levels. As expected, in cells overexpressing CuZn-SOD, both total and cytosolic aconitase activities have increased. Because these clones showed reduced oxidized glutathione contents, it is unlikely that they present higher H2O2 steady-state levels as a consequence of the higher SOD levels. This was confirmed by measuring H2O2 steady-state levels in cells by flow cytometric analysis of 2',7'-dichlorofluorescein diacetate-treated cells. Despite the decreased antioxidant defenses, three of the clones overexpressing CuZn-SOD showed reduced H2O2 steady-state levels. These reduced H2O2 steady-state levels were found even when the cells were treated with the O2- generator 2,3-dimethoxy-1, 4-naphthoquinone. These data provide in vivo support for the hypothesis proposed by Liochev and Fridovich [Liochev, S. I. & Fridovich, I. (1994) Free Radical Biol. Med. 16, 29-33] that O2- dismutation prevents the formation of higher H2O2 levels by other reactions.
Development of a Dry Low NOx Combustor for Dual Gaseous Fuels of Natural Gas and Petroleum Gas (2018)

Liquefied petroleum gas (LPG) will be suitable for satisfying part of the growing global energy demands. The widespread utilization of LPG as a gas turbine fuel for power generation requires an advanced combustor that achieves dry low nitrogen oxides (NOx) combustion and flashback-resistant combustion. This paper describes the development of a “multi-cluster combustor” as an advanced dry low NOx and flashback-resistant combustion technology for dual gaseous fuels of natural gas and petroleum gas. The dual gaseous fuel capability will contribute to expanding fuel flexibility. The purpose of this paper is to evaluate the feasibility of the dual gaseous fueled combustion with the multi-cluster combustor with the same configuration. The combustor was tested in a single-can combustor test stand at medium pressure with both fuels. In the tests, natural gas consisted mainly of methane with a content of over 90 vol.%, and petroleum gas consisted almost entirely of propane. The test results showed that the combustor achieves dry low NOx combustion of both fuels within their stable ranges without flashback. This paper concluded from the test results that the multi-cluster combustor possesses the potential capability to achieve dry low NOx and flashback-resistant combustion of dual gaseous fuels of natural gas and petroleum gas. As the next step, further tests will be required with petroleum gas including butane and for high pressure conditions.
Unveiling Charge Transport and Degradation Mechanisms of Aqueous Zn|α‐MoO3 Batteries in Conventional Concentration and Water‐in‐Salt Electrolytes: A Multi‐Modal In Situ and Operando Study (2022)

Abstract Herein charge storage and transport properties are elucidated and cell degradation mechanisms of rechargeable aqueous Zn|α‐MoO 3 batteries in three electrolyte systems (3 m ZnSO 4 , 3 m ZnCl 2 , and 30 m ZnCl 2 [12.5 m ] water‐in‐salt (WIS)) are distinguished by a combination of in situ X‐ray diffraction (XRD), in situ X‐ray absorption spectroscopy (XAS), operando optoelectrochemistry, and operando energy dispersive X‐ray diffraction (EDXRD). In conventional concentration 3 m electrolytes, in situ XRD and XAS, as well as ex situ scanning transmission electron microscopy data collectively support Zn 2+ as the primary charge carrier. In addition, these systems are susceptible to cathode dissolution, Zn corrosion coupled with the hydrogen evolution reaction, and the resultant formation of basic zinc salt phases. The multi‐modal in situ and operando experimental analyses validate facile H + intercalation and extraction in concentrated 30 m ZnCl 2 WIS electrolyte. Via operando EDXRD, reaction front and charge transport limitation during discharge and charge in the viscous WIS electrolyte are spatially tracked. This work provides new insight into the stability and degradation mechanisms of aqueous zinc batteries during static storage and upon dynamic cycling, and highlights the utility of in situ and operando techniques in understanding the superior stability of WIS electrolytes.
Learning Features For Relational Data. (2018)

Feature engineering is one of the most important but tedious tasks in data science projects. This work studies automation of feature learning for relational data. We first theoretically proved that learning relevant features from relational data for a given predictive analytics problem is NP-hard. However, it is possible to empirically show that an efficient rule based approach predefining transformations as a priori based on heuristics can extract very useful features from relational data. Indeed, the proposed approach outperformed the state of the art solutions with a significant margin. We further introduce a deep neural network which automatically learns appropriate transformations of relational data into a representation that predicts the target variable well instead of being predefined as a priori by users. In an extensive experiment with Kaggle competitions, the proposed methods could win late medals. To the best of our knowledge, this is the first time an automation system could win medals in Kaggle competitions with complex relational data.
Predictive value of minimal residual disease in Philadelphia-chromosome-positive acute lymphoblastic leukemia treated with imatinib in the European intergroup study of post-induction treatment of Philadelphia-chromosome-positive acute lymphoblastic leukemia, based on immunoglobulin/T-cell receptor and BCR/ABL1 methodologies (2017)

The prognostic value of minimal residual disease (MRD) in Philadelphia-chromosome-positive (Ph+) childhood acute lymphoblastic leukemia (ALL) treated with tyrosine kinase inhibitors is not fully established. We detected MRD by real-time quantitative polymerase chain reaction (RQ-PCR) of rearranged immunoglobulin/T-cell receptor genes (IG/TR) and/or BCR/ABL1 fusion transcript to investigate its predictive value in patients receiving Berlin-Frankfurt-Münster (BFM) high-risk (HR) therapy and post-induction intermittent imatinib (the European intergroup study of post-induction treatment of Philadelphia-chromosome-positive acute lymphoblastic leukemia (EsPhALL) study). MRD was monitored after induction (time point (TP)1), consolidation Phase IB (TP2), HR Blocks, reinductions, and at the end of therapy. MRD negativity progressively increased over time, both by IG/TR and BCR/ABL1. Of 90 patients with IG/TR MRD at TP1, nine were negative and none relapsed, while 11 with MRD<5×10<sup>-4</sup> and 70 with MRD≥5×10<sup>-4</sup> had a comparable 5-year cumulative incidence of relapse of 36.4 (15.4) and 35.2 (5.9), respectively. Patients who achieved MRD negativity at TP2 had a low relapse risk (5-yr cumulative incidence of relapse (CIR)=14.3[9.8]), whereas those who attained MRD negativity at a later date showed higher CIR, comparable to patients with positive MRD at any level. BCR/ABL1 MRD negative patients at TP1 had a relapse risk similar to those who were IG/TR MRD negative (1/8 relapses). The overall concordance between the two methods is 69%, with significantly higher positivity by BCR/ABL1. In conclusion, MRD monitoring by both methods may be functional not only for measuring response but also for guiding biological studies aimed at investigating causes for discrepancies, although from our data IG/TR MRD monitoring appears to be more reliable. Early MRD negativity is highly predictive of favorable outcome. The earlier MRD negativity is achieved, the better the prognosis.
ULPFA: A New Efficient Design of a Power-Aware Full Adder (2009)

In this paper, we first propose a new structure of a hybrid full adder, namely, the branch-based logic and pass-transistor (BBL-PT) cell, which we implemented by combining branch-based logic and pass-transistor logic. Evolution of the proposed cell from its original version to an ultralow-power (ULP) cell is described. Quantitative comparisons of the optimized version, namely, the ULP full adder (ULPFA), are carried out versus the BBL-PT full adder and its counterparts in two well-known and commonly used logic styles, i.e., conventional static CMOS logic and complementary pass logic (CPL), in a 0.13-μm PD SOI CMOS with a supply voltage of 1.2 V, demonstrating power delay product (PDP) and static power performance that are more than four times better than CPL design. This could lead to tremendous benefit for multiplier application. The implementation of an 8-bit ripple carry adder based on the ULPFA is finally described, and comparisons between adders based on full adders from the prior art and our ULPFA version demonstrate that our development outperforms the static CMOS and the CPL full adders, particularly in terms of power consumption and PDP by at least a factor of two.
ChemInform Abstract: High‐Yield Protection of Alcohols, Including Tertiary and Base‐Sensitive Alcohols, as Benzhydryl Ethers by Heating with Diphenyldiazomethane in the Absence of Any Other Reagent. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Spermatid-Specific Thioredoxin 3 (SPTRX3) Is a Biomarker of Human Male Infertility with Predictive Value for Decision Making in Infertility Treatment. (2008)

Spermatid specific thioredoxin-3 protein (SPTRX-3) accumulates in the superfluous cytoplasm of defective human spermatozoa. We investigated the relationship between SPTRX3 levels and male infertility in men from 239 couples undergoing IVF or ICSI treatment. Sperm content of SPTRX3 was evaluated by flow cytometry, fluorescence microscopy, western blotting, and a novel ImageStream technology combining flow cytometry with high throughput cell imaging. Extremely high sperm SPTRX3 levels (>15% SPTRX3-positive sperm) were found in 51 % of male infertility patients (n=72), but also in 20% of men from couples diagnosed with idiopathic infertility (n=61) and in 14% of men from couples diagnosed with female infertility (n=85). Men with >15% SPTRX3-positive sperm had a significantly reduced chance of impregnating their partners by ICSI or IVF (16.7% pregnant couples with >15% SPTRX-positive sperm vs. 43.8% pregnant with <5% SPTRX3-positive sperm). SPTRX3-levels were significantly lower in couples treated by IVF than in couples that required treatment by ICSI. High sperm SPTRX3 compounded female infertility in couples diagnosed with combined male and female infertility (n=21), in which the % of SPTRX3-positive cells was increased by 25% in couples that failed to achieve pregnancy. High SPTRX3 content had a profound effect on pregnancy rates in the subgroup of women over 35 years of age (n=99), wherein the pregnancy rate was 40% when SPTRX3 levels were below 5%, but only 17.6% when the SPTRX3 levels of male partners were above 10% positive cells. Image Stream confirmed that the SPTRX-3 containing cells were spermatozoa with a variety of morphological defects. Flow cytometric SPTRX3 values correlated positively with light microscopic SPTRX3 evaluation in a subset of 150 patients evaluated by both methods. The SPTRX3- based assays thus provide an unbiased, objective diagnosis of male infertility relevant to decision making in ART. Supported by the F21C Program of the UM.
Simultaneous Swept Source Optical Coherence Tomography of the Anterior Segment and Retina (2012)

We report on the implementation of swept source optical coherence tomography for simultaneous imaging of the anterior segment and retina. The system achieves depth-encoding by coherence revival heterodyning and a polarization-encoded sample arm.
Search for high-mass resonances decaying to dilepton final states in pp collisions at $ \sqrt{s}=7 $ TeV with the ATLAS detector (2012)

A bstract The ATLAS detector at the Large Hadron Collider is used to search for high-mass resonances decaying to an electron-positron pair or a muon-antimuon pair. The search is sensitive to heavy neutral Z′ gauge bosons, Randall-Sundrum gravitons, Z * bosons, techni-mesons, Kaluza-Klein Z/γ bosons, and bosons predicted by Torsion models. Results are presented based on an analysis of pp collisions at a center-of-mass energy of 7 TeV corresponding to an integrated luminosity of 4.9 fb −1 in the e + e − channel and 5.0 fb −1 in the μ + μ − channel. A Z ′ boson with Standard Model-like couplings is excluded at 95 % confidence level for masses below 2.22 TeV. A Randall-Sundrum graviton with coupling $ {k \left/ {{{{\overline{M}}_{\mathrm{Pl}}}}} \right.}=0.1 $ is excluded at 95 % confidence level for masses below 2.16 TeV. Limits on the other models are also presented, including Technicolor and Minimal Z′ Models.
Single-Cell Transcriptome Profiling Reveals Intratumoral Heterogeneity and Molecular Features of Ductal Carcinoma In Situ (2022)

Investigation of the molecular features of ductal carcinoma in situ at single cell resolution provides new insights into breast cancer biology and identifies candidate therapeutic targets and diagnostic biomarkers.
Comparison of treatment planning approaches for spatially fractionated irradiation of deep tumors (2019)

Our results present, for the first time, preliminary evidence comparing IMRT-GRID approaches which result in high-dose "islands" within a target, mimicking what is achieved with a conventional GRID block but without high-dose "tail" regions outside of the target. These approaches differ modestly in their ability to achieve high peak-to-edge ratios and also differ in delivery times.
Acting in good taste: nutrient sensors in the gut (2009)

Our senses help us perceive the external environment and respond appropriately to external cues. Many of our senses, including our sense of taste, use G-protein coupled receptors (GPCRs) for transduction of environmental signals. Taste sensation is mediated through two families of related, evolutionarily conserved GPCRs known as T1Rs and T2Rs, originally described within taste buds of the tongue.1 Through these basic elements, we are able to generate a diverse repertoire of taste sensations including sweet, bitter and savoury (umami) tastes. For example, sweet taste sensation is initiated by ligand binding to the extracellular domain of the heterodimeric receptor complex formed by the GPCRs T1R2 and T1R3, whereas savoury taste sensation is initiated through a heterodimer of T1R1 and T1R3.1 The activated intracellular domain of the heterodimeric receptor complex then couples with a specific G protein alpha subunit, G alpha gustducin, resulting in downstream effector signals including increased intracellular calcium.2 The activity of G alpha gustducin also leads to activation of transient receptor potential ion channel 5 (TRPM5), a cation channel whose downstream effects are not yet well understood.3

The discovery of G alpha gustducin expression in luminal gut epithelium raised the intriguing possibility that the gut is somehow able to “taste” luminal contents.4 More recently, taste receptors and their downstream effectors were shown to be expressed within the stomach, proximal …
Polarization Beam Splitter for Silicon-based Cross-slot Waveguides Using an Asymmetrical Evanescent Coupling System (2018)

A compact and broadband polarization beam splitter (PBS) for the silicon-based cross-slot waveguides (CSWs) is proposed by utilizing a cascaded asymmetrical evanescent coupling system composed of two CSWs and a horizontal slot waveguide (HSW) between them. By optimizing the width of the HSW, an asymmetrical directional coupler which can efficiently separate the TE and TM modes is constructed. Numerical results show that a short PBS of <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">~</sub> 17.4μm with an insertion loss of 0.16 (0.37) dB, extinction ratio (ER) of 29.5 (24.2) dB for TM (TE) mode is achieved at 1.55 μm, and its bandwidth can be enlarged to <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">~</sub> 90 nm for ER > 18 dB (TE).
Nanoparticle surface charge impacts distribution, uptake and lymph node trafficking by pulmonary antigen-presenting cells (2020)

AbstractEngineered nanoparticles have the potential to expand the breadth of pulmonary therapeutics, especially as respiratory vaccines. Notably, cationic nanoparticles have been demonstrated to produce superior local immune responses following pulmonary delivery; however, the cellular mechanisms of this increased response remain unknown. To this end, we investigated the cellular response of lung APCs following pulmonary instillation of anionic and cationic charged nanoparticles. While nanoparticles of both surface charges were capable of trafficking to the draining lymph node and were readily internalized by alveolar macrophages, both CD11b and CD103 lung dendritic cell (DC) subtypes preferentially associated with cationic nanoparticles. Instillation of cationic nanoparticles resulted in the upregulation of Ccl2 and Cxc10, which likely contributes to the recruitment of CD11b DCs to the lung. In total, these cellular mechanisms explain the increased efficacy of cationic formulations as a pulmonary vaccine carrier and provide critical benchmarks in the design of pulmonary vaccine nanoparticles.From the Clinical EditorAdvance in nanotechnology has allowed the production of precise nanoparticles as vaccines. In this regard, pulmonary delivery has the most potential. In this article, the authors investigated the interaction of nanoparticles with various types of lung antigen presenting cells in an attempt to understand the cellular mechanisms. The findings would further help the future design of much improved vaccines for clinical use.
Iterative Extrapolation for Channel Equalization in DVB-T Receivers (2008)

This paper proposes an iterative extrapolation method to improve the channel-equalization performance for DVB-T receivers. The coefficients of a one-tap equalizer are conventionally obtained by taking the reciprocals of the estimated channel coefficients. Inversion of the channel coefficients, however, may cause noise enhancement at those frequencies corresponding to spectral nulls. To reduce such undesirable noise amplification, iterative extrapolation based on the time-domain truncation is performed, resulting in smooth nulls. Simulation results show that the proposed method improves the channel-equalization performance compared to the conventional zero-forcing equalization method in terms of bit error rates in DVB-T receivers at all SNRs.