gebhart/patrepeval huggingface dataset:
Highly Pathogenic H5N1 Influenza Viruses Carry Virulence Determinants beyond the Polybasic Hemagglutinin Cleavage Site (2010)

Highly pathogenic avian influenza viruses (HPAIV) originate from avirulent precursors but differ from all other influenza viruses by the presence of a polybasic cleavage site in their hemagglutinins (HA) of subtype H5 or H7. In this study, we investigated the ability of a low-pathogenic avian H5N1 strain to transform into an HPAIV. Using reverse genetics, we replaced the monobasic HA cleavage site of the low-pathogenic strain A/Teal/Germany/Wv632/2005 (H5N1) (TG05) by a polybasic motif from an HPAIV (TG05(poly)). To elucidate the virulence potential of all viral genes of HPAIV, we generated two reassortants carrying the HA from the HPAIV A/Swan/Germany/R65/06 (H5N1) (R65) plus the remaining genes from TG05 (TG05-HA(R65)) or in reversed composition the mutated TG05 HA plus the R65 genes (R65-HA(TG05poly)). In vitro, TG05(poly) and both reassortants were able to replicate without the addition of trypsin, which is characteristic for HPAIV. Moreover, in contrast to avirulent TG05, the variants TG05(poly), TG05-HA(R65), and R65-HA(TG05poly) are pathogenic in chicken to an increasing degree. Whereas the HA cleavage site mutant TG05(poly) led to temporary non-lethal disease in all animals, the reassortant TG05-HA(R65) caused death in 3 of 10 animals. Furthermore, the reassortant R65-HA(TG05poly) displayed the highest lethality as 8 of 10 chickens died, resembling "natural" HPAIV strains. Taken together, acquisition of a polybasic HA cleavage site is only one necessary step for evolution of low-pathogenic H5N1 strains into HPAIV. However, these low-pathogenic strains may already have cryptic virulence potential. Moreover, besides the polybasic cleavage site, the additional virulence determinants of H5N1 HPAIV are located within the HA itself and in other viral proteins.
Design and Evaluation of Anti-SARS-Coronavirus Agents Based on Molecular Interactions with the Viral Protease (2020)

Three types of new coronaviruses (CoVs) have been identified recently as the causative viruses for the severe pneumonia-like respiratory illnesses, severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and corona-virus disease 2019 (COVID-19). Neither therapeutic agents nor vaccines have been developed to date, which is a major drawback in controlling the present global pandemic of COVID-19 caused by SARS coronavirus 2 (SARS-CoV-2) and has resulted in more than 20,439,814 cases and 744,385 deaths. Each of the 3C-like (3CL) proteases of the three CoVs is essential for the proliferation of the CoVs, and an inhibitor of the 3CL protease (3CL<sup>pro</sup>) is thought to be an ideal therapeutic agent against SARS, MERS, or COVID-19. Among these, SARS-CoV is the first corona-virus isolated and has been studied in detail since the first pandemic in 2003. This article briefly reviews a series of studies on SARS-CoV, focusing on the development of inhibitors for the SARS-CoV 3CL<sup>pro</sup> based on molecular interactions with the 3CL protease. Our recent approach, based on the structure-based rational design of a novel scaffold for SARS-CoV 3CL<sup>pro</sup> inhibitor, is also included. The achievements summarized in this short review would be useful for the design of a variety of novel inhibitors for corona-viruses, including SARS-CoV-2.
Studies on pyrimidine derivatives. XXX. The palladium-catalyzed cross-coupling reaction of iodopyrimidines with terminal olefinic compounds. (1982)

The influence of triphenylphosphine, used as a ligand, on the palladium-catalyzed cross-coupling reaction of iodopyrimidines with olefins such as ethyl acrylate, acrylonitrile, and styrene was investigated. In general, the addition of triphenylphosphine was concluded to retard the reaction in the pyrimidine series. The effect of triphenylphosphine in the monoazine series is also discussed.
General Method for HPLC Purification and Sequencing of Selected dsDNA Gene Fragments from Complex PCRs Generated during Gene Expression Profiling (2000)

Gene expression profiling using an AFLP-based technique generates a large number of gene fragments that require identification by sequencing. The DNA fragments vary in length from about 50-500 bp. Ion-pair reversed-phase HPLC can be used to purify selected double-stranded DNA fragments that represent differentially expressed genes. The gene fragments are sequenced directly after vacuum drying of the collected HPLC fractions.
Photoplethysmographic Assessment of Hemodynamic Variations Using Pulsatile Tissue Blood Volume (2008)

Sympathetic responses to provocative tests have shown to provide an early prognosis of abnormalities in the human autonomic nervous system. Photoplethysmographic signal characteristics have been studied to identify vascular diseases. However, knowledge about the pulse-added arterial volume of the photoplethysmographic waveforms during these clinical investigations is limited. In all, 16 normotensive adults (9 men) were recruited to perform 3 provocative test (2 postural changes and 1 resistive breathing) activities with photoplethysmographic signals being monitored on the upper and lower peripheries using customized devices. In all, 4 parameters derived from the photoplethysmographic waveforms that related to the pulsatile tissue blood volume changes were then assessed. The results obtained showed that amplitude-related parameters during these activities showed significant changes (>9.63%; P < .05). However, comparison of pulse-added arterial volume showed insignificant changes (<5.56%; P > .05) for all test settings. Hence, the findings herein suggest that there is clinical potential in using this aspect of the photoplethysmographic waveform.
Warm starting Bayesian optimization (2016)

We develop a framework for warm-starting Bayesian optimization, that reduces the solution time required to solve an optimization problem that is one in a sequence of related problems. This is useful when optimizing the output of a stochastic simulator that fails to provide derivative information, for which Bayesian optimization methods are well-suited. Solving sequences of related optimization problems arises when making several business decisions using one optimization model and input data collected over different time periods or markets. While many gradient-based methods can be warm started by initiating optimization at the solution to the previous problem, this warm start approach does not apply to Bayesian optimization methods, which carry a full metamodel of the objective function from iteration to iteration. Our approach builds a joint statistical model of the entire collection of related objective functions, and uses a value of information calculation to recommend points to evaluate.
Poverty Law 101: The Law and History of the U.S. Welfare State (2012)

Poverty law will remain marginalized so long as we confine it to a population that we and our students understand as marginal. Tani discusses Professor Wax’s characterization of the “old welfare law framework,” as well as her account of what happened to it, and would not advocate a return to a court-centered, advocacy-oriented approach.
Analytical technique for calculating the output harmonics of an H-bridge inverter with dead time (1999)

An analytical technique for calculating the harmonic characteristics of the output voltage of an H-bridge inverter with dead time is presented. The analysis is based on a three-dimensional (3-D) model derived for generating the pulsewidth-modulated (PWM) pulse train. By applying double Fourier analysis, a generalized and elegant mathematical function for describing the harmonic components of the output voltage is formulated. The function can be divided into two parts: an ideal part representing the PWM signal without dead time and a correction part representing the dead-time effect. The function provides detailed composition of the fundamental component, signal harmonics, carrier harmonics, and cross-modulated harmonics. The proposed technique has been verified using examples and the theoretical predictions are confirmed with the results obtained from simulations using PSpice.
Dielectric Properties and Phase Transitions of Ba(Ti<sub>1-x</sub>Sn<sub>x</sub>)O<sub>3</sub> Solid Solution (1996)

In Ba(Ti 1- x Sn x )O 3 solid solution, for Sn concentration x ≤0.1, the permittivity follows the Curie-Weiss law above the Curie point T c . The increase in the peak value of the permittivity at T c is due to the change in ferroelectric transition from first order to second order with increasing x . For x >0.1, some deviations from the Curie-Weiss law are observed in a narrow temperature region above T c . The diffuse phase transition was observed. For x >0.2, the Curie-Weiss law does not hold over a wide temperature range. The dielectric dispersion was observed in the radio-frequency range (10 kHz–10 MHz). With increasing Sn concentration, the change in the phase transition from a normal ferroelectric transition to relaxor through the diffuse phase transition was observed.
Compression of Fully-Connected Layer in Neural Network by Kronecker Product (2015)

In this paper we propose and study a technique to reduce the number of parameters and computation time in fully-connected layers of neural networks using Kronecker product, at a mild cost of the prediction quality. The technique proceeds by replacing Fully-Connected layers with so-called Kronecker Fully-Connected layers, where the weight matrices of the FC layers are approximated by linear combinations of multiple Kronecker products of smaller matrices. In particular, given a model trained on SVHN dataset, we are able to construct a new KFC model with 73\% reduction in total number of parameters, while the error only rises mildly. In contrast, using low-rank method can only achieve 35\% reduction in total number of parameters given similar quality degradation allowance. If we only compare the KFC layer with its counterpart fully-connected layer, the reduction in the number of parameters exceeds 99\%. The amount of computation is also reduced as we replace matrix product of the large matrices in FC layers with matrix products of a few smaller matrices in KFC layers. Further experiments on MNIST, SVHN and some Chinese Character recognition models also demonstrate effectiveness of our technique.
The crystal structure of 2-aminoisophthalic acid, C<sub>8</sub>H<sub>7</sub>NO<sub>4</sub> (2020)

Abstract C 8 H 7 NO 4 , monoclinic, C 2/ c (no. 15), a = 4.9752(11) Å, b = 14.167(3) Å, c = 10.999(2) Å, β = 99.066(5)°, V = 765.6(3) Å 3 , Z = 4, R gt (F) = 0.0571, wR ref (F 2 ) = 0.1630, T = 150(2) K.
miR-200c Regulates IL8 Expression by Targeting IKBKB: A Potential Mediator of Inflammation in Leiomyoma Pathogenesis (2014)

We have previously reported that leiomyoma expressed lower levels of miR-200c and elevated IL8 as compared to paired myometrium. Here we addressed the regulatory functions of miR-200c on the expression of inflammatory mediators and cellular viability using leiomyomas and paired myometrium and their isolated primary smooth muscle cells. Our results indicated that gain-of function or knockdown of miR-200c in leiomyoma smooth muscle cells (LSMC) regulated IL8 mRNA and protein expression through direct targeting of IKBKB and alteration of NF-kB activity. Additionally, leiomyoma expressed higher levels of phosphorylated IKBKB with no significant difference in the level of IKBKB mRNA and protein as compared to matched myometrium. Gain-of function of miR-200c in LSMC resulted in decreased IkBα phosphorylation and p65 nuclear translocation, which led to decreased p65 transcriptional activity of IL8 promoter, and increased caspase 3/7 activity which was not reversible following IL8 restoration. Collectively, our results suggest that NF-κB signaling pathway is a target of miR-200c regulatory function, and low level of miR-200c expression in leiomyoma by transcriptional regulation of inflammatory mediators such as IL8, in part account for development of leiomyomas.
Analysis and implementation of Raptor codes on embedded systems (2010)

Raptor codes have been proven very suitable for mobile multimedia content delivery, and yet they have not been analyzed in the context of embedded systems. At the heart of Raptor codes for binary erasure channel (BEC) is the matrix inversion operation. This paper analyzes the performance, energy profile and resource implication of two matrix inversion algorithms for the Raptor decoder on a system on a chip (SoC) platform with a soft-core embedded processor. We show how the cache size, matrix memory type and organization affect the two algorithms under consideration.
Régimes sémiotiques de la temporalité (2006)

« L’incorporation du temps dans le roman : Proust et l’expérience de la quatrième dimension » [Institut universitaire de France, mars 2003], in Régimes sémiotiques de la temporalité. La flèche brisée du temps, Denis Bertrand et Jacques Fontanille dir., Paris, PUF, « Formes sémiotiques », 2006, p. 157-170.
Neurotransmitters and Brain Maturation: Early Paracrine Actions of GABA and Glutamate Modulate Neuronal Migration (2007)

Migration of neurons from their birthplace to their final destination is an extremely important step in brain maturation, and cortical migration disorders are the most common brain developmental alteration observed in human patients. Among the mechanisms that govern neuronal migration, the neurotransmitters GABA and glutamate deserve particular attention: 1) neurotransmitters and receptors are expressed early in the developing brain, 2) neurotransmitters may act as paracrine signaling molecules in the immature brain, and 3) neurotransmitters regulate intracellular calcium required for many cellular functions, including cytoskeletal dynamic changes. Thus, many reports reviewed here aimed to demonstrate that the activation of specific GABA and glutamate receptors is instrumental in cell migration by acting as motility promoting, acceleratory, or stop signal. Interestingly, the regulation of migration by neurotransmitters and receptors depends on the type of migration (radial, tangential, or chain migration), the type of cells (principal glutamatergic neurons vs. GABAergic interneurons), and the brain area (neocortex, cerebellum, rostral migratory stream). A hypothesis is proposed that these differential actions in different cell types arise from a "homeostatic-like" regulation that controls final position, timing, and number of cells at destination.
Detection and mapping of 5-methylcytosine and 5-hydroxymethylcytosine with nanopore MspA (2013)

Precise and efficient mapping of epigenetic markers on DNA may become an important clinical tool for prediction and identification of ailments. Methylated CpG sites are involved in gene expression and are biomarkers for diseases such as cancer. Here, we use the engineered biological protein pore Mycobacterium smegmatis porin A (MspA) to detect and map 5-methylcytosine and 5-hydroxymethylcytosine within single strands of DNA. In this unique single-molecule tool, a phi29 DNA polymerase draws ssDNA through the pore in single-nucleotide steps, and the ion current through the pore is recorded. Comparing current levels generated with DNA containing methylated CpG sites to current levels obtained with unmethylated copies of the DNA reveals the precise location of methylated CpG sites. Hydroxymethylation is distinct from methylation and can also be mapped. With a single read, the detection efficiency in a quasirandom DNA strand is 97.5 ± 0.7% for methylation and 97 ± 0.9% for hydroxymethylation.
Heavy Metal Particulate Contrast Materials for Computed Tomography of the Liver (1980)

Silver iodide colloid was used as a model of a particulate hepatic contrast agent for computed tomography (CT). Following intravenous administration to rabbits, approximately 90% of the injected dose was phagocytized by the liver's reticuloendothelial system, resulting in a four- to five-fold increase in the liver CT number. Suspensions of CeO2, Dy2O3, and Gd2O3 were prepared using stabilizers to prevent clumping. Particles of appropriate size for reticuloendothelial cell uptake were selected by centrifugation. Intravenous injections of the three suspensions increased the CT number of rabbit liver by approximately 30 Hounsfield units (HU: 1,000 scale) for each experimental contrast agent resulted in a minimum addition of 250 HU to the liver CT number. A linear relationship was found between the CT number and its contrast material concentration. This relationship was also tested in vitro by ashing samples of livers containing various amounts of contrast material. Standard curves of CT number versus contrast material concentration in the liver were plotted, which predicted the amount of liver enhancement obtained after contrast material injection. There may be a use for heavy metal-containing particulate materials as hepatic contrast agents, since they opacify the liver more selectively, to a higher degree, and for longer periods than the conventional biliary and urographic iodinated contrast materials.
Cell-specific Sorting of Biogenic Amine Transporters Expressed in Epithelial Cells (1996)

We have utilized polarized epithelial cells stably expressing neurotransmitter transporters to analyze the sorting behavior of these membrane proteins. The transporters for serotonin (5-HT), dopamine (DA), and norepinephrine (NE) are expected to be present in situ in the most distal extremities of axonal membranes, where they terminate the action of their biogenic amine substrates. Both Madin-Darby canine kidney (MDCK) and LLC-PK1 cells were stably transfected with cDNAs encoding either the rat 5-HT transporter (SERT), the human NE transporter (NET), or the rat or human DA transporter (DAT). These cells were grown on permeable filter supports, and the transporters were localized by three independent techniques. Confocal immunofluorescence microscopy indicated that each of the transporters expressed in LLC-PK1 cells was sorted to the basolateral membrane, co-localizing with the Na+/K+-ATPase. In MDCK cells, however, DAT was located primarily on the apical surface, while SERT and NET were found on the basolateral membranes. Cell surface biotinylation using an impermeant biotinylating reagent confirmed the immunocytochemistry results. Thus, SERT and NET in MDCK cells were labeled more efficiently from the basolateral medium than the apical medium, and DAT in MDCK cells was labeled more efficiently from the apical side than the basolateral side. Transport measurements in transfected MDCK cells agreed with the immunocytochemistry and biotinylation results. These results suggest the existence of cell-specific mechanisms that discriminate between neurotransmitter transporters for surface expression and render unlikely any simple hypothesis that sorting mechanisms in neurons and epithelia are identical.
Gd<sup>III</sup>‐Functionalized Fluorescent Quantum Dots as Multimodal Imaging Probes (2006)

Multimodal probes of GdIII-functionalized silica-coated CdS:Mn/ZnS quantum dots (see figure) that exhibit yellow fluorescence and strong paramagnetism are reported. High magnetic resonance imaging (MRI) contrast is exhibited by these quantum dots. These properties make for a probe that can operate in multiple modes, which is highly desirable for in vivo bioimaging applications.
The study of archaeobotanical remains: Vitalising a debate on changing conceptions and possibilities (2004)

The results of a treatment method on adenocarcinoma corpus uteri stage I-II based upon cytometrically measured DNA ploidy are presented. All patients had a simple hysterectomy. Adjuvant treatment (postoperative vaginal brachytherapy) were given only to those patients with non-diploid tumours regardless of stage and grade. A total of 1,634 women with endometroid adenocarcinoma corpus uteri stage I-II were included where 1,396 patients were followed-up for at least 5 years or until death and the remaining 238 patients were followed-up 3.5-5 years or until death. By using cytometry only, we identified a low-risk group comprising 83% of the patients (with 5.2% dead from their disease) and a high-risk group of 17% (with 15.7% dead from their disease). By using grade only (well- and moderately differentiated vs poorly differentiated), the low-risk group comprised 87% of the patients (with 4.6% dead from their disease) and the high-risk group 13% (with 13% dead from their disease). By using stage only (stage Ia and Ib vs stage Ic and II), the low-risk group comprised 78% of the patients (with 3.6% dead from their disease) and the high risk group 22% (with 14.5% dead from their disease). By combining these prognostic parameters, we were able to identify small subgroups with increased mortality rates in need of adjuvant therapy. As ploidy still had a strong prognostic strength regardless of given adjuvant radiotherapy, we do not believe that this treatment was effective. We therefore recommend future research to be directed toward cytostatics as an alternative adjuvant treatment.
Capsular Serotype K1 or K2, Rather than <i>magA</i> and <i>rmpA</i> , Is a Major Virulence Determinant for <i>Klebsiella pneumoniae</i> Liver Abscess in Singapore and Taiwan (2006)

Capsular serotypes, magA, and rmpA have been documented in high prevalence for Klebsiella pneumoniae liver abscess. To investigate the regional difference and the correlation of capsular serotype, magA, and rmpA with virulence, 73 isolates were collected in Singapore and Taiwan. Capsular serotypes were determined by countercurrent immunoelectrophoresis, the presence of magA and rmpA was determined by PCR, and virulence was determined by phagocytosis and mouse inoculation. Isolates from Singapore were similar to those from Taiwan in genomic heterogeneity, prevalence of serotype, and the presence of magA and rmpA. The most common serotype was K1 (34/73; 46.6%), followed by K2 (15/73; 20.5%). magA was restricted to serotype K1. All K1 or K2 isolates and 66.7% (16/24) of isolates that were neither serotype K1 nor serotype K2 (non-K1/K2) carried rmpA. Serotype K1 or K2 isolates demonstrated significantly more phagocytic resistance and virulence than did rmpA-positive and -negative groups of non-K1/K2 isolates. In the non-K1/K2 group, the virulence profiles of rmpA-positive strains from Taiwan and Singapore were different by phagocytosis assay and in the mouse model, indicating that factors other than rmpA contributed to virulence. The characteristics of K. pneumoniae liver abscess in Singapore and Taiwan are similar. Capsular serotype K1 or K2 plays a more important role than magA and rmpA in determining virulence in K. pneumoniae liver abscess.