gebhart/patrepeval huggingface dataset:
Genomic Analysis of MSM Rectal Chlamydia trachomatis Isolates Identifies Predicted Tissue-Tropic Lineages Generated by Intraspecies Lateral Gene Transfer-Mediated Evolution (2022)

Chlamydia trachomatis is an obligate intracellular bacterium that causes serious diseases in humans. Rectal infection and disease caused by this pathogen are important yet understudied aspects of C. trachomatis natural history. The University of Washington Chlamydia Repository has a large collection of male-rectal-sourced strains (MSM rectal strains) isolated in Seattle, USA and Lima, Peru. Initial characterization of strains collected over 30 years in both Seattle and Lima led to an association of serovars G and J with male rectal infections. Serovar D, E, and F strains were also collected from MSM patients. Genome sequence analysis of a subset of MSM rectal strains identified a clade of serovar G and J strains that had high overall genomic identity. A genome-wide association study was then used to identify genomic loci that were correlated with tissue tropism in a collection of serovar-matched male rectal and female cervical strains. The polymorphic membrane protein PmpE had the strongest correlation, and amino acid sequence alignments identified a set of PmpE variable regions (VRs) that were correlated with host or tissue tropism. Examination of the positions of VRs by the protein structure-predicting Alphafold2 algorithm demonstrated that the VRs were often present in predicted surface-exposed loops in both PmpE and PmpH protein structure. Collectively, these studies identify possible tropism-predictive loci for MSM rectal C. trachomatis infections and identify predicted surface-exposed variable regions of Pmp proteins that may function in MSM rectal versus cervical tropism differences.
UN MODELO DE CONSERVACIÓN DEL PATRIMONIO INDUSTRIAL: LA CENTRAL HIDROELÉCTRICA DE LA MALVA UN MODÈLE DE CONSERVATION DU PATRIMOINE INDUSTRIELLE: LA CENTRALE HYDRO-ÉLECTRIQUE DE LA MALVA (2014)

Resumen La Central Hidroelectrica de La Malva situada en el concejo de Somiedo, en Asturias, surge ante la posibilidad de aprovechar los importantes recursos hidricos de la Cordillera Cantabrica, con el objetivo de producir energia electrica. Constituye uno de los elementos mas significativos de la arquitectura industrial de comienzos del siglo XX. El edificio de la central se encuentra en perfecto estado de conservacion, y esta constituido por dos naves adosadas de diferente altura. Una dedicada a sala de maquinas y otra, mas alta, a transformadores, embarrados y demas elementos electricos. Posee las caracteristicas constructivas propias de un periodo de transicion; asi aparecen elementos “tradicionales” como son mamposteria, silleria y arcos pero tambien se pueden apreciar elementos “modernos” como son las vigas de hormigon armado, cerchas metalicas y cubiertas de chapa. A pesar de encontrarse actualmente en pleno funcionamiento, los elementos patrimoniales mas singulares han sido  conservados. Asi puede verse el cuadro de mandos tipo pupitre (sin uso actual), las carcasas de las excitatrices, el puente grua, turbinas Pelton originales (carcasas y piezas sin desgaste), los alternadores, elementos de regulacion (sin uso), etc. Resume La Centrale Hydro-electrique de La Malva situee dans le municipalite de Somiedo, Asturies, emerge face a la possibilite de profiter des importantes ressources hydriques de la Corniche Cantabrique, avec l’objectif de produire de l’energie electrique. Elle constitue l’un des elements les plus significatifs de l’architecture industrielle du debut du XXe siecle. Le bâtiment de la centrale se trouve en parfait etat de  conservation, et est forme de deux nefs jumelles de differente hauteur. L’une est consacree a salle de machines et l’autre, plus haute, a transformateurs, jeux de barres et autres elements electriques. Il a les caracteristiques constructives typiques d’une periode de transition; ainsi apparaissent des elements “traditionnels” tels que maconnerie, pierres de taille et arcs mais on peut aussi distinguer des elements “modernes” tels que les poutres beton arme, treillis metalliques et  couvertures en tole. Bien qu’elle se trouve actuellement en plein fonctionnement, les elements patrimoniaux plus singuliers ont ete conserves. Ainsi on peut voir le pupitre de distribution (sans usage actuel), les carcasses des excitatrices, le pont roulant, des turbines Pelton originelles (carcasses et pieces sans usure), les alternateurs, des elements de regulation (sans usage), etc.
Cross Sections of Enamel Defects in Porcelain Enamels (2008)

Optical microscope examination of enamel coating defects is discussed. Defects occurring in electrostatic powders coatings are emphasized.
Analysis of Liquid Medication Dose Errors Made by Patients and Caregivers Using Alternative Measuring Devices (2012)

Approximately 1 in 10 participants measured doses of liquid medication with a volume error greater than 10%, and these dose errors were more common with the etched dosing cup, the dosing spoon, and the printed dosing cup. Pharmacists have an opportunity to counsel patients or caregivers regarding the appropriate use of measuring devices for liquid medication.
Fitness costs limit influenza A virus hemagglutinin glycosylation as an immune evasion strategy (2011)

Here, we address the question of why the influenza A virus hemagglutinin (HA) does not escape immunity by hyperglycosylation. Uniquely among dozens of monoclonal antibodies specific for A/Puerto Rico/8/34, escape from H28-A2 neutralization requires substitutions introducing N-linked glycosylation at residue 131 or 144 in the globular domain. This escape decreases viral binding to cellular receptors, which must be compensated for by additional substitutions in HA or neuraminidase that enable viral replication. Sequence analysis of circulating H1 influenza viruses confirms the in vivo relevance of our findings: natural occurrence of glycosylation at residue 131 is always accompanied by a compensatory mutation known to increase HA receptor avidity. In vaccinated mice challenged with WT vs. H28-A2 escape mutants, the selective advantage conferred by glycan-mediated global reduction in antigenicity is trumped by the costs of diminished receptor avidity. These findings show that, although N-linked glycosylation can broadly diminish HA antigenicity, fitness costs restrict its deployment in immune evasion.
Implication of Glutamate in the Kinetics of Insulin Secretion in Rat and Mouse Perfused Pancreas (2002)

It is intriguing that the kinetics of glucose-stimulated insulin secretion from the in situ perfused pancreas differ between the rat and the mouse. Here we confirm that insulin release in the rat is clearly biphasic, whereas in the mouse glucose essentially elicits a transient monophasic insulin release. Glucose-derived glutamate has been suggested to participate in the full development of the secretory response. The present report shows that the expression of glutamate dehydrogenase is lower in mouse than in rat or human islets, paralleling the insulin secretion profile. Addition of glutamic acid dimethyl ester mainly enhances insulin release at an intermediate glucose concentration in the rat pancreas. In the mouse preparation, glutamic acid dimethyl ester induces a sustained secretory response, both at 7.0 and 16.7 mmol/l glucose. These results are compatible with a role for glucose-derived glutamate principally in the sustained phase of nutrient-stimulated insulin secretion.
Expression of Sterol 27-Hydroxylase (CYP27A1) Enhances Cholesterol Efflux (2003)

Cholesterol efflux from CHOP cells transfected with sterol 27-hydroxylase (CYP27A1) was compared with non-transfected and mock-transfected cells. Transfection caused expression of CYP27A1, formation of 27-hydroxycholesterol, and inhibition of cholesterol biosynthesis. Transfection enhanced cholesterol efflux to apolipoprotein A-I or human plasma by 2-3-fold but did not affect the efflux in the absence of acceptor. The analysis of released sterols revealed that 27-hydroxycholesterol represented only a small proportion of sterols, most of which was non-oxidized cholesterol. Time course and dose dependence studies showed that expression of CYP27A1 in CHOP cells mostly affected the efflux of the "fast" cholesterol pool, and relatively more cholesterol was released with low concentrations of an acceptor. Preincubation of non-transfected cells with exogenous 27-hydroxycholesterol (10(-9) and 10(-7) m) led to the stimulation of cholesterol efflux by 24-60%. Expression of CYP27A1 in CHOP cells did not affect ABCA1 expression and abundance of ABCA1 protein. Thus, introduction of CYP27A1 into cells stimulates cholesterol efflux and therefore may increase protection against atherosclerosis.
The Indexed Web: Engineering Tools for Cataloging, Storing, and Delivering Web-Based Documents. (1999)

Creating a useful search engine for a web site requires human analysis of the information-not technological intervention in the form of filters and agents. Michael Nanfito describes how he developed Java-based software that uses controlled vocabularies and subject headings to catalog HTML articles on a legal resources web site.
Effect of Solvent Extraction on the Low Molecular Weight and Volatile Organic Compounds of Polycarbonate (2010)

A study on the volatile organic compounds (VOCs) and low molecular weight (LMW) amount which is contained within bisphenol A polycarbonate (PC) was performed by the solvent extraction with ketone type solvents (acetone, butanone, pentanone). The LMW amount of untreated PC was 2.6 wt%, but the values of treated samples with acetone and pentanone were 0.96 and 1.53 wt%, respectively. Acetone is a more effective solvent than pentanone on the LMW extraction. Methylene chloride (MC) and toluene were certified and quantified by GC-Mass experiments, and the quantitative results indicated the fact that the pentanone was the effective solvent on VOC extraction. Focused on the change of VOCs and LMW amount, the use of co-solvent might be more useful, and the experimental results of co-solvent extraction showed that the optimum condition was 50 : 50 volume percent.
Ultra Low Power Reversible Dual Edge Triggered Flip Flop-Design and Implementation (2018)

Reversible logic is an emerging technology which has a potential to deal with power consumption. Consequently ultra low power digital circuits can be successfully designed applying reversible logic to assure today's technological requirements. In this paper author presents the design of very fundamental component of digital sequential family i.e. reversible dual edge triggered D flip flop. The suggested design intends to form a reversible flip flop modified in respect of number of reversible gates, delay and thus minimizes the complexity of the circuit. This design is further realized in CMOS and carefully analyzed for power consumption. Moreover the same proposed design is additionally perceived with Quantum Dot Cellular Automata (QCA) which is an attractive future perspective for near future. These optimized designs will definitely fortify the performance of the sequential circuits pertaining to size and power utilization.
A practical method of designing RC active filters (1955)

IN THE FREQUENCY range below about 30 cps, the dissipation factors of available inductors are generally too large to permit the practical design of inductance-capacitance (LC) or resistance-inductance-capacitance (RLC) filter networks. The circuits described in the following pages were developed and collected to provide an alternative method of realizing sharp cut-off filters at very low frequencies. In many cases the active elements can be simple cathode-follower circuits that have stable gain, low output impedance and a large dynamic range.
Next-Generation Sequencing to Diagnose Suspected Genetic Disorders (2018)

Interview with Dr. David Adams on the use of clinical next-generation sequencing to obtain a genetic diagnosis. (06:23)Download The technologies and chemistries underlying next-generation sequencing of DNA are evolving rapidly. This review describes the three main approaches to obtaining a genetic diagnosis through next-generation sequencing, their advantages, and their limitations.
A Survey of Quantitative Models of Terror Group Behavior and an Analysis of Strategic Disclosure of Behavioral Models (2014)

There are many applications (e.g., counter-terrorism) where we can automatically learn a quantitative model from realworld data about terror group behavior. In this paper, we first provide a survey of quantitative models of terrorist groups. To date, however, the best-known quantitative models of terror group behavior are based on various types of quantitative logic programs. After our survey, we address an important question posed to us by Nobel laureate, Tom Schelling. Once a set of quantitative logic behavior rules about an adversary has been learned, should these rules be disclosed or not? We develop a game theoretic framework in order to answer this question with a defender who has to decide what rules to release publicly and which ones to keep hidden. We first study the attacker's optimal attack strategy, given a set of disclosed rules, and then we study the problem of which rules to disclose so that the attacker's optimal strategy has minimal effectiveness. We study the complexity of both problems, present algorithms to solve both, and then present a (1-1/e )-approximation algorithm that (under some restrictions) uses a submodularity property to compute the optimal defender strategy. Finally, we provide experimental results showing that our framework works well in practice-these results are also shown to be statistically significant.
MCMC-based tracking and identification of leaders in groups (2011)

We present a novel framework for identifying and tracking dominant agents in groups. Our proposed approach relies on a causality detection scheme that is capable of ranking agents with respect to their contribution in shaping the system's collective behaviour based exclusively on the agents' observed trajectories. Further, the reasoning paradigm is made robust to multiple emissions and clutter by employing a class of recently introduced Markov chain Monte Carlo-based group tracking methods. Examples are provided that demonstrate the strong potential of the proposed scheme in identifying actual leaders in swarms of interacting agents and moving crowds.
Randomised trial of neonatal hypoglycaemia prevention with oral dextrose gel (hPOD): study protocol (2015)

Australian New Zealand Clinical Trials Registry--ACTRN 12614001263684.
Investigating the effect of grounding GPS antennas on their radiation properties on vehicular platforms (2014)

The global positioning system (GPS) has become a standard navigation tool in modern vehicular platforms. The location of the GPS antenna has a direct impact on the overall navigation system performance. In this work, we investigate the effect of shorting the GPS antenna placed on the front windshield of a vehicle to its rooftop GND plane. It is shown that such a connection will improve the gain of the antenna by several dBs.
Graphmap2 - splice-aware RNA-seq mapper for long reads (2019)

Abstract In this paper we present Graphmap2, a splice-aware mapper built on our previously developed DNA mapper Graphmap. Graphmap2 is tailored for long reads produced by Pacific Biosciences and Oxford Nanopore devices. It uses several newly developed algorithms which enable higher precision and recall of correctly detected transcripts and exon boundaries. We compared its performance with the state-of-the-art tools Minimap2 and Gmap. On both simulated and real datasets Graphmap2 achieves higher mappability and more correctly recognized exons and their ends. In addition we present an analysis of potential of splice aware mappers and long reads for the identification of previously unknown isoforms and even genes. The Graphmap2 tool is publicly available at https://github.com/lbcb-sci/graphmap2 .
Cell Proliferation and Cytotoxicity Assays (2016)

Cell viability is defined as the number of healthy cells in a sample and proliferation of cells is a vital indicator for understanding the mechanisms in action of certain genes, proteins and pathways involved cell survival or death after exposing to toxic agents. Generally, methods used to determine viability are also common for the detection of cell proliferation. Cell cytotoxicity and proliferation assays are generally used for drug screening to detect whether the test molecules have effects on cell proliferation or display direct cytotoxic effects. Regardless of the type of cell-based assay being used, it is important to know how many viable cells are remaining at the end of the experiment. There are a variety of assay methods based on various cell functions such as enzyme activity, cell membrane permeability, cell adherence, ATP production, co-enzyme production, and nucleotide uptake activity. These methods could be basically classified into different categories: (I) dye exclusion methods such as trypan blue dye exclusion assay, (II) methods based on metabolic activity, (III) ATP assay, (IV) sulforhodamine B assay, (V) protease viability marker assay, (VI) clonogenic cell survival assay, (VII) DNA synthesis cell proliferation assays and (V) raman micro-spectroscopy. In order to choose the optimal viability assay, the cell type, applied culture conditions, and the specific questions being asked should be considered in detail. This particular review aims to provide an overview of common cell proliferation and cytotoxicity assays together with their own advantages and disadvantages, their methodologies, comparisons and intended purposes.
Targeting activated protein C to treat hemophilia (2017)

We conclude that the signaling and anticoagulant functions of APC are in spatially and kinetically distinct compartments, and that it is possible to specifically inhibit the anticoagulant activity of APC. Targeting APC with a serpin is remarkably effective and may be safe for long-term prophylactic use in the treatment of hemophilia.
Caspase-2 Inhibitor Blocks Tau Truncation and Restores Excitatory Neurotransmission in Neurons Modeling FTDP-17 Tauopathy (2022)

Synaptic and cognitive deficits mediated by a severe reduction in excitatory neurotransmission caused by a disproportionate accumulation of the neuronal protein tau in dendritic spines is a fundamental mechanism that has been found repeatedly in models of tauopathies, including Alzheimer's disease, Lewy body dementia, frontotemporal dementia, and traumatic brain injury. Synapses thus damaged may contribute to dementia, among the most feared cause of debilitation in the elderly, and currently there are no treatments to repair them. Caspase-2 (Casp2) is an essential component of this pathological cascade. Although it is believed that Casp2 exerts its effects by hydrolyzing tau at aspartate-314, forming Δtau314, it is also possible that a noncatalytic mechanism is involved because catalytically dead Casp2 is biologically active in at least one relevant cellular pathway, that is, autophagy. To decipher whether the pathological effects of Casp2 on synaptic function are due to its catalytic or noncatalytic properties, we discovered and characterized a new Casp2 inhibitor, compound <b>1</b> [p<i>K</i><sub>i</sub> (Casp2) = 8.12], which is 123-fold selective versus Casp3 and >2000-fold selective versus Casp1, Casp6, Casp7, and Casp9. In an in vitro assay based on Casp2-mediated cleavage of tau, compound <b>1</b> blocked the production of Δtau314. Importantly, compound <b>1</b> prevented tau from accumulating excessively in dendritic spines and rescued excitatory neurotransmission in cultured primary rat hippocampal neurons expressing the P301S tau variant linked to FTDP-17, a familial tauopathy. These results support the further development of small-molecule Casp2 inhibitors to treat synaptic deficits in tauopathies.
Potential of Immunoglobulin A to Prevent Allergic Asthma (2013)

Allergic asthma is characterized by bronchial hyperresponsiveness, a defective barrier function, and eosinophilic lower airway inflammation in response to allergens. The inflammation is dominated by Th2 cells and IgE molecules and supplemented with Th17 cells in severe asthma. In contrast, in healthy individuals, allergen-specific IgA and IgG4 molecules are found but no IgE, and their T cells fail to proliferate in response to allergens, probably because of the development of regulatory processes that actively suppress responses to allergens. The presence of allergen-specific secretory IgA has drawn little attention so far, although a few epidemiological studies point at a reverse association between IgA levels and the incidence of allergic airway disease. This review highlights the latest literature on the role of mucosal IgA in protection against allergic airway disease, the mechanisms described to induce secretory IgA, and the role of (mucosal) dendritic cells in this process. Finally, we discuss how this information can be used to translate into the development of new therapies for allergic diseases based on, or supplemented with, IgA boosting strategies.
AGC Asynchronous Tuning for Improving PV Consumption in the Energy Imbalance Market (2020)

The soaring installation of volatile Photovoltaic (PV) source in both utility-scale and distributed scale renders power systems susceptible to solar dynamics. Automatic generation controls (AGC) parameters are normally determined without any further adaptation, making it a challenge for multi-area interconnected power systems balancing the frequency with the PV integration. Considering the synchronous updating issue of the multi-area power system, an asynchronous tuning method is proposed in this paper to help power systems refine their optimal AGC parameters for better power transfer control. The phasor measurement units (PMU) based data has been considered for the proposed tuning method as well as the other data format. A performance study with manual, two-step tuned and asynchronous tuned AGCs has been conducted on a five-area power system in real-time digital simulator (RTDS). Results present that the asynchronous method provides optimal AGCs for the test five-area power system with PV stations. Results also demonstrate a better frequency and tie-line power response performance with the proposed method.
Frequency dependencies of phase velocity and attenuation coefficient in a water-saturated sandy sediment from 0.3to1.0MHz (2007)

The frequency-dependent phase velocity and attenuation coefficient for the fast longitudinal wave in a water-saturated sandy sediment were measured over the frequency range from 0.3 to 1.0 MHz. The experimental data of phase velocity exhibited the significant negative dispersion, with the mean rate of decline of 120 +/- 20 m/s/MHz. The Biot model predicted the approximately nondispersive phase velocity and the grain-shearing (GS) model exhibited the slightly positive dispersion. In contrast, the predictions of the multiple scattering models for the negative dispersion in the glass-grain composite were in general agreement with the experimental data for the water-saturated sandy sediment measured here. The experimental data of attenuation coefficient was found to increase nonlinearly with frequency from 0.3 to 1.0 MHz. However, both the Biot and the GS models yielded the attenuation coefficient increasing almost linearly with frequency. The total attenuation coefficient given by the algebraic sum of absorption and scattering components showed a reasonable agreement with the experimental data for overall frequencies. This study suggests that the scattering is the principal mechanism responsible for the variations of phase velocity and attenuation coefficient with frequency in water-saturated sandy sediments at high frequencies.