gebhart/patrepeval huggingface dataset:
Limited Evidence for Parallel Evolution Among Desert-AdaptedPeromyscusDeer Mice (2021)

Warming climate and increasing desertification urge the identification of genes involved in heat and dehydration tolerance to better inform and target biodiversity conservation efforts. Comparisons among extant desert-adapted species can highlight parallel or convergent patterns of genome evolution through the identification of shared signatures of selection. We generate a chromosome-level genome assembly for the canyon mouse (Peromyscus crinitus) and test for a signature of parallel evolution by comparing signatures of selective sweeps across population-level genomic resequencing data from another congeneric desert specialist (Peromyscus eremicus) and a widely distributed habitat generalist (Peromyscus maniculatus), that may be locally adapted to arid conditions. We identify few shared candidate loci involved in desert adaptation and do not find support for a shared pattern of parallel evolution. Instead, we hypothesize divergent molecular mechanisms of desert adaptation among deer mice, potentially tied to species-specific historical demography, which may limit or enhance adaptation. We identify a number of candidate loci experiencing selective sweeps in the P. crinitus genome that are implicated in osmoregulation (Trypsin, Prostasin) and metabolic tuning (Kallikrein, eIF2-alpha kinase GCN2, APPL1/2), which may be important for accommodating hot and dry environmental conditions.
ChemInform Abstract: Synthesis, Crystal Structure Determination, and Biological Properties of the DNA‐Dependent Protein Kinase (DNA‐PK) Inhibitor 3‐Cyano‐6‐hydrazonomethyl‐5‐(4‐pyridyl)pyrid‐[1H]‐2‐one (OK‐1035). (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 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.
Hydrodynamics of Packed Bed Reactor in Low Gravity (2005)

Packed bed reactors are well known for their vast and diverse applications in the chemical industry; from gas absorption, to stripping, to catalytic conversion. Use of this type of reactor in terrestrial applications has been rather extensive because of its simplicity and relative ease of operation. Developing similar reactors for use in microgravity is critical to many space-based advanced life support systems. However, the hydrodynamics of two-phase flow packed bed reactors in this new environment and the effects of one physiochemical process on another has not been adequately assessed. Surface tension or capillary forces play a much greater role which results in a shifting in flow regime transitions and pressure drop. Results from low gravity experiments related to flow regimes and two-phase pressure drop models are presented in this paper along with a description of plans for a flight experiment on the International Space Station (ISS). Understanding the packed bed hydrodynamics and its effects on mass transfer processes in microgravity is crucial for the design of packed bed chemical or biological reactors to be used for water reclamation and other life support processes involving water purification.
Cover Feature: Impurity Control in Catalyst Design: The Role of Sodium in Promoting and Stabilizing Co and Co2C for Syngas Conversion (ChemCatChem 4/2021) (2021)

The Cover Feature illustrates the significant effects of trace impurities on the structure and syngas conversion reactivity of SiO2-supported Co2C catalysts. In their Full Paper, A. S. Asundi et al. show that low concentrations of Na impurities in a commercial SiO2 support play an important role in stabilizing the Co2C phase resulting in a catalyst with high selectivity for syngas conversion to oxygenated products. In the absence of these impurities, the Co2C phase is unstable during reaction and partially decomposes to metallic Co, leading to Fischer-Tropsch reactivity and a loss of oxygenate selectivity. The results show that impurity control is an important consideration that should not be overlooked in the design and study of catalysts. More information can be found in the Full Paper by A. S. Asundi et al.
Unit-Centric Feature Mapping for Inventory Pruning in Unit Selection Text-to-Speech Synthesis (2007)

The level of quality that can be attained in concatenative text-to-speech (TTS) synthesis is primarily governed by the inventory of units used in unit selection. This has led to the collection of ever larger corpora in the quest for ever more natural synthetic speech. As operational considerations limit the size of the unit inventory, however, pruning is critical to removing any instances that prove either spurious or superfluous. This paper proposes a novel pruning strategy based on a data-driven feature extraction framework separately optimized for each unit type in the inventory. A single distinctiveness/redundancy measure can then address, in a consistent manner, the two different problems of outliers and redundant units. Detailed analysis of an illustrative case study exemplifies the typical behavior of the resulting unit pruning procedure, and listening evidence suggests that both moderate and aggressive inventory pruning can be achieved with minimal degradation in perceived TTS quality. These experiments underscore the benefits of unit-centric feature mapping for database optimization in concatenative synthesis.
Startup of a Partial Nitritation‐Anammox MBBR and the Implementation of pH‐Based Aeration Control (2017)

The single-stage deammonification moving bed biofilm reactor (MBBR) is a process for treating high strength nitrogen waste streams. In this process, partial nitritation and anaerobic ammonia oxidation (anammox) occur simultaneously within a biofilm attached to plastic carriers. An existing tank at the James River Treatment Plant (76 ML/d) in Newport News, Virginia was modified to install a sidestream deammonification MBBR process. This was the second sidestream deammonification process in North America and the first MBBR type installation. After 4 months the process achieved greater than 85% ammonia removal at the design loading rate of 2.4 g <inline-graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="00500-ilm01.gif"/>/m2·d (256 kg <inline-graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="00500-ilm12.gif"/>/d) signaling the end of startup. Based on observations during startup and process optimization phases, a novel pH-based control system was developed that maximizes ammonium removal and results in stable aeration and effluent alkalinity.
Correlation between home and clinic spirometry in subjects with IPF: results from the INMARK trial* (2020)

Introduction: Frequent home-based spirometry may provide more accurate estimates of lung function in patients with IPF than intermittent spirometry performed at clinic visits.
SAMCON : IEEJ International Workshop on Sensing, Actuation, and Motion CONtrol (2016)

1．SAMCON開催の背景と動機 SAMCONはセンシング，メカトロニクス，モーションコントロールの分野をテーマとする電気学会産業応用部門主催の新しく発足した国際ワークショップである。IEEJ International Workshop on Sensing, Actuation, and Motion CONtrol の最初のアルファベットを用いて，その
Poly(N-isopropylacrylamide)-Based Thermoresponsive Behavior of Fluorescent Organic Nanocrystals (2011)

In this article, we describe the poly( N -isopropylacrylamide)-based thermoresponsive behaviors of fluorescent organic nanocrystals. Aqueous dispersions of thermoresponsive fluorescent nanocrystals were prepared by the reprecipitation method. Fluorescent dyes used for these nanocrystals were perylene, quinacridone, and zinc phthalocyanine. The perylene nanocrystals in the aqueous system using poly( N -isopropylacrylamide) exhibited a significantly increased fluorescence intensity assigned to the emission of the perylene monomer above the cloud point (∼35 °C). Significantly increased fluorescence intensities of quinacridone nanocrystals and zinc phthalocyanine nanocrystals were also observed above the cloud point (∼35 °C). These unique fluorescence behaviors were only observed in the aqueous system using poly( N -isopropylacrylamide).
Synthesis and characterization of novel combretastatin analogues of 1,1-diaryl vinyl sulfones, with antiproliferative potential via in-silico and in-vitro studies (2022)

Novel 1,1-diaryl vinyl-sulfones analogues of combretastatin CA-4 were synthesized via Suzuki-Miyaura coupling method and screened for in-vitro antiproliferative activity against four human cancer cell lines: MDA-MB 231(breast cancer), HeLa (cervical cancer), A549 (lung cancer), and IMR-32 (neuroblast cancer), along with a normal cell line HEK-293 (human embryonic kidney cell) by employing 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide (MTT) assay. The compounds synthesised had better cytotoxicity against the A549 and IMR-32 cell lines compared to HeLa and MDA-MB-231 cell lines. The synthesized compounds also showed significant activity on MDA-MB-231 cancer cell line with IC<sub>50</sub> of 9.85-23.94 µM, and on HeLa cancer cell line with IC<sub>50</sub> of 8.39-11.70 µM relative to doxorubicin having IC<sub>50</sub> values 0.89 and 1.68 µM respectively for MDA-MB-231 and HeLa cell lines. All the synthesized compounds were not toxic to the growth of normal cells, HEK-293. They appear to have a higher binding affinity for the target protein, tubulin, PDB ID = 5LYJ (beta chain), relative to the reference compounds, CA4 (- 7.1 kcal/mol) and doxorubicin (- 7.2 kcal/mol) except for 4E, 4M, 4N and 4O. The high binding affinity for beta-tubulin did not translate into enhanced cytotoxicity but the compounds (4G, 4I, 4J, 4M, 4N, and 4R, all having halogen substituents) that have a higher cell permeability (as predicted in-silico) demonstrated an optimum cytotoxicity against the tested cell lines in an almost uniform manner for all tested cell lines. The in-silico study provided insight into the role that cell permeability plays in enhancing the cytotoxicity of this class of compounds and as potential antiproliferative agents.
Japanese Encephalitis Virus Genotype Replacement, Taiwan, 2009–2010 (2011)

Genotype I of Japanese encephalitis virus first appeared in Taiwan in 2008. Phylogenetic analysis of 37 viruses from pig farms in 2009-2010 classified these viruses into 2 unique subclusters of genotype I viruses and suggested multiple introductions and swift replacement of genotype III by genotype I virus in Taiwan.
Interactions between Hofmeister Anions and the Binding Pocket of a Protein (2015)

This paper uses the binding pocket of human carbonic anhydrase II (HCAII, EC 4.2.1.1) as a tool to examine the properties of Hofmeister anions that determine (i) where, and how strongly, they associate with concavities on the surfaces of proteins and (ii) how, upon binding, they alter the structure of water within those concavities. Results from X-ray crystallography and isothermal titration calorimetry show that most anions associate with the binding pocket of HCAII by forming inner-sphere ion pairs with the Zn(2+) cofactor. In these ion pairs, the free energy of anion-Zn(2+) association is inversely proportional to the free energetic cost of anion dehydration; this relationship is consistent with the mechanism of ion pair formation suggested by the "law of matching water affinities". Iodide and bromide anions also associate with a hydrophobic declivity in the wall of the binding pocket. Molecular dynamics simulations suggest that anions, upon associating with Zn(2+), trigger rearrangements of water that extend up to 8 Å away from their surfaces. These findings expand the range of interactions previously thought to occur between ions and proteins by suggesting that (i) weakly hydrated anions can bind complementarily shaped hydrophobic declivities, and that (ii) ion-induced rearrangements of water within protein concavities can (in contrast with similar rearrangements in bulk water) extend well beyond the first hydration shells of the ions that trigger them. This study paints a picture of Hofmeister anions as a set of structurally varied ligands that differ in size, shape, and affinity for water and, thus, in their ability to bind to—and to alter the charge and hydration structure of—polar, nonpolar, and topographically complex concavities on the surfaces of proteins.
Stability and Performance of Haptic Displays: Theory and Experiments (1998)

Abstract In haptic simulation, a human operator kinesthetically explores a virtual environment. To achieve a virtual sense of touch, the human interacts with an active mechanical device, called a haptic display. This paper presents an approach to guarantee that this physical man-machine interface remains stable, while maximizing performance. The key element in ensuring stability is the virtual coupling network, an artificial link between the haptic display and the virtual environment. Considerations of structural flexibility in the haptic device are included in the derivation of design criteria for such networks. Solutions for both the impedance and admittance models of haptic interaction are included. Numerical and experimental results for a two degree-of-freedom haptic display demonstrate the effectiveness of the proposed approach in achieving performance and stability in haptic simulation.
Abstract 65: RESPECT (REsidue-SPEcific Conjugation Technology): A platform technology utilizing native cysteine and lysine residues for the generation of homogeneous antibody-drug conjugates (2017)

Abstract The random conjugation of toxins, dyes, peptides, or other payloads to monoclonal antibodies often targets free thiol groups generated by partial reduction methods or lysine residues using succinimide- or isothiocyanate-based chemistry. There remains a need for conjugation technologies targeting specific amino acid residues as a way to produce a homogeneous antibody-drug conjugate (ADC) product with a defined drug-to-antibody ratio (DAR). Our REsidue-SPEcific Conjugation Technology (RESPECT) utilizes two methods by which payloads can be conjugated to specific residues in an antibody. Our cysteine-specific conjugation method exploits a unique intrachain disulfide bond in the light chain of rabbit antibodies between residues 80 and 171 of the variable and constant domains, respectively. Our humanization strategy allows retention of the cysteine at position 80 with a free thiol group that is both amenable for residue-specific conjugation and compatible with optimal antibody biophysical properties including antigen binding and structural stability. This platform has been optimized via antibody engineering strategy stems from in silico modeling, extensive mutagenesis, and crystallographic studies, which have allowed defining the contribution of neighboring residues to the retention of a reactive thiol group as well as the desired humanized antibody’s properties. Our C-terminal lysine-specific linkage method employs the transglutaminase enzyme that catalyzes the formation of a stable isopeptide bond between the γ-carboxyamide group (acyl donor) of a glutamine and the ϵ-amino group (acyl acceptor) of a lysine. While we found no acyl acceptor sites in recombinant wild-type IgG, all antibodies investigated lacked the C-terminal Lys447 due to cleavage by carboxypeptidase B in the antibody production cell line. Blocking the cleavage of Lys447 by addition of a C-terminal amino acid resulted in transamidation of Lys447 by a variety of acyl donor substrates in the presence of any non-acidic, non-proline amino acid residue at position 448. Antibody-drug conjugates (ADCs) prepared using our RESPECT technology targeting the tumor associated-mesothelin protein produced uniform drug-to-antibody ratios (DAR) and were shown to be highly potent and specific in vitro and effective in vivo in reduction of tumor growth in a highly aggressive mesothelin-expressing xenograft tumor model. Citation Format: Earl Albone, Jared Spidel, Xin Cheng, Young Chul Park, Sara Jacob, Arielle Verdi, Andrew Milinichik, Ben Vaessen, J. Bradford Kline, Luigi Grasso. RESPECT (REsidue-SPEcific Conjugation Technology): A platform technology utilizing native cysteine and lysine residues for the generation of homogeneous antibody-drug conjugates [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 65. doi:10.1158/1538-7445.AM2017-65
Microvascular Responses to Cardiovascular Risk Factors (2010)

Hypertension, hypercholesterolemia, diabetes, and obesity are among a growing list of conditions that have been designated as major risk factors for cardiovascular disease (CVD). While CVD risk factors are well known to enhance the development of atherosclerotic lesions in large arteries, there is also evidence that the structure and function of microscopic blood vessels can be profoundly altered by these conditions. The diverse responses of the microvasculature to CVD risk factors include oxidative stress, enhanced leukocyte- and platelet-endothelial cell adhesion, impaired endothelial barrier function, altered capillary proliferation, enhanced thrombosis, and vasomotor dysfunction. Emerging evidence indicates that a low-grade systemic inflammatory response that results from risk factor-induced cell activation and cell-cell interactions may underlie the phenotypic changes induced by risk factor exposure. A consequence of the altered microvascular phenotype and systemic inflammatory response is an enhanced vulnerability of tissues to the deleterious effects of secondary oxidative and inflammatory stresses, such as ischemia and reperfusion. Future efforts to develop therapies that prevent the harmful effects of risk factor-induced inflammation should focus on the microcirculation.
MEMS Radioisotope-Powered Piezoelectric µ - Power Generator (RPG) (2006)

We present a microfabricated die-scale Radioisotope-powered Piezoelectric µ -power Generator (RPG) with nuclear to electrical conversion efficiency as high as 3.7%. The generator employs direct charging to convert radiated β-particle kinetic energy into stored electromechanical energy in a piezoelectric unimorph, and piezoelectricity to convert the stored mechanical energy into extractable electrical energy. The generator goes through a charge-discharge-vibrate cycle, integrating the energy collected during the charging phase. This enables high power output (1.13 µ W peak across a 90 kΩ load impedance) for a short time (10 s) during the vibration cycle, even with radioactive film emitting only 100 nW of continuous power.
Development of ultrafast computed tomography of highly transient fuel sprays (2004)

The detailed analysis of the fuel sprays has been well recognized as an important step for optimizing the operation of internal-combustion engines to improve efficiency and reduce emissions. However, the structure and dynamics of highly transient fuel sprays have never been visualized or reconstructed in three dimensions (3D) previously due to numerous technical difficulties. By using an ultrafast x-ray detector and intense monochromatic x-ray beams from synchrotron radiation, the fine structures and dynamics of 1-ms direct-injection gasoline fuel sprays were elucidated for the first time by a newly developed, ultrafast computed microtomography technique. Due to the time-resolved nature and the intensive data analysis, the Fourier transform algorithm was used to achieve an efficient reconstruction process. The temporal and spatial resolutions of the current measurement are 5.1 &#956;s and 150 &#956;m, respectively. Many features associated with the transient liquid flows are readily observable in the reconstructed spray. Furthermore, an accurate 3D fuel density distribution was obtained as the result of the computed tomography in a time-resolved manner. These results not only reveal the characteristics of automotive fuel sprays with unprecedented details, but will also facilitate realistic computational fluid dynamic simulations in highly transient, multiphase systems.
Sodium‐Glucose Cotransporter 2 Inhibition for the Prevention of Cardiovascular Events in Patients With Type 2 Diabetes Mellitus: A Systematic Review and Meta‐Analysis (2020)

Background Several trials have demonstrated protective effects from inhibition of sodium-glucose cotransporter 2 among patients with type 2 diabetes mellitus. There is uncertainty about the consistency of the cardiovascular benefits achieved across patient subsets. Methods and Results We included 4 large-scale trials of sodium-glucose cotransporter 2 inhibition compared with placebo in patients with diabetes mellitus that reported effects on cardiovascular outcomes overall and for participant subgroups defined at baseline by cardiovascular disease, reduced kidney function, and heart failure. Fixed effects models with inverse variance weighting were used to estimate summary hazard ratios and 95% CIs. There were 38 723 patients from 4 trials, with a mean 2.9 years of follow-up. Of the patients, 22 870 (59%) had cardiovascular disease, 7754 (20%) had reduced kidney function, and 4543 (12%) had heart failure. There were 3828 major adverse cardiac events. There was overall benefit for major adverse cardiac events (0.88; 95% CI, 0.82-0.94; <i>P</i><0.001) and no evidence that the effects of sodium-glucose cotransporter 2 inhibition varied across patient subgroups, defined by the presence of cardiovascular disease or heart failure at baseline (all <i>P</i> interaction >0.252; I<sup>2</sup><25%). All patient subgroups benefited with respect to hospitalization for heart failure (all <i>P</i> interaction>0.302; I<sup>2</sup><10%), cardiovascular death (all <i>P</i> interaction>0.167; I<sup>2</sup><50%), and death from any cause (all <i>P</i> interaction>0.354; I<sup>2</sup>=0%). The only difference in effects across subgroups was for stroke, with protection observed among those with reduced kidney function but not those with preserved kidney function (<i>P</i> interaction=0.020; I<sup>2</sup>=81%). Conclusions Sodium-glucose cotransporter 2 inhibitors protect against cardiovascular disease and death in diverse subsets of patients with type 2 diabetes mellitus regardless of cardiovascular disease history.