gebhart/patrepeval huggingface dataset:
Adherence of infected erythrocytes to venular endothelium selects for antigenic variants of Plasmodium falciparum (1992)

Erythrocytes (E) infected with asexual forms of malaria parasites exhibit surface antigenic variation. In Plasmodium falciparum infections, the variant Ag is the P. falciparum E membrane protein 1 (PfEMP1). This molecule may also mediate the adherence of infected E to host venular endothelium. We show here that parasite lines selected for increased adherence to endothelial cells have undergone antigenic variation. Three adherent lines selected from the same P. falciparum clone reacted with the same agglutinating antiserum that failed to agglutinate the parental clone. Immunoprecipitation experiments with the agglutinating anti-serum demonstrated that the selected lines expressed cross-reactive forms of PfEMP1 that were of higher m.w. and antigenically distinct from PfEMP1 of the parental clone. When one of the adherent lines was cloned in the absence of selection, a range of variant antigenic types emerged with differing cytoadherence phenotypes. These findings show that selection for cytoadherence in vitro favors the emergence of antigenic variants of P. falciparum and suggest that the requirement for cytoadherence in vivo may restrict the range of antigenic variants of P. falciparum in natural infections.
Complete primary structure of the rat cartilage proteoglycan core protein deduced from cDNA clones. (1987)

We have obtained overlapping cDNA clones for the entire coding sequence of the rat cartilage proteoglycan core protein from the Swarm rat chondrosarcoma. These cDNAs hybridize to two sizes of RNA transcripts of 8.2 and 8.9 kilobase pairs, which contain large 3'-untranslated sequences. The total contiguous cDNA is 6.55 kilobase pairs in size, and codes for a 2124-residue protein, including a 19-residue signal peptide. The sequence forms a series of eight structural domains including two globules, (Mr = 37,000 and 22,000) at the NH2 terminus of the molecule, one a complete and one a partial copy of the cartilage link protein. The major feature of the deduced protein sequence is a 1,104-residue segment containing 117 Ser-Gly sequences, the presumed chondroitin sulfate attachment sites. These are arranged in three domains of 428, 503, and 173 amino acids. The first domain contains 11 complete or partial repeats of a 40-residue unit, and the second domain is composed of six copies of a 100-residue repeating sequence. The first pattern is the more highly conserved, and may have given rise to the second. The carboxyl-terminal domain is a third globule which has homology with animal lectins.
Semantic Hierarchies for Visual Object Recognition (2007)

In this paper we propose to use lexical semantic networks to extend the state-of-the-art object recognition techniques. We use the semantics of image labels to integrate prior knowledge about inter-class relationships into the visual appearance learning. We show how to build and train a semantic hierarchy of discriminative classifiers and how to use it to perform object detection. We evaluate how our approach influences the classification accuracy and speed on the PASCAL VOC challenge 2006 dataset, a set of challenging real-world images. We also demonstrate additional features that become available to object recognition due to the extension with semantic inference toolswe can classify high-level categories, such as animals, and we can train part detectors, for example a window detector, by pure inference in the semantic network.
Simulated scaling method for localized enhanced sampling and simultaneous “alchemical” free energy simulations: A general method for molecular mechanical, quantum mechanical, and quantum mechanical/molecular mechanical simulations (2007)

A potential scaling version of simulated tempering is presented to efficiently sample configuration space in a localized region. The present "simulated scaling" method is developed with a Wang-Landau type of updating scheme in order to quickly flatten the distributions in the scaling parameter lambdam space. This proposal is meaningful for a broad range of biophysical problems, in which localized sampling is required. Besides its superior capability and robustness in localized conformational sampling, this simulated scaling method can also naturally lead to efficient "alchemical" free energy predictions when dual-topology alchemical hybrid potential is applied; thereby simultaneously, both of the chemically and conformationally distinct portions of two end point chemical states can be efficiently sampled. As demonstrated in this work, the present method is also feasible for the quantum mechanical and quantum mechanical/molecular mechanical simulations.
The ATM-dependent DNA Damage Signaling Pathway (2005)

Many of the insights that we have gained into the mechanisms involved in cellular DNA damage response pathways have come from studies of human cancer susceptibility syndromes that are altered in DNA damage responses. ATM, the gene mutated in the disorder, ataxia-telangiectasia, is a protein kinase that is a central mediator of responses to DNA double-strand breaks in cells. Recent studies have elucidated the mechanism by which DNA damage activates the ATM kinase and initiates these critical cellular signaling pathways. The SMC1 protein appears to be a particularly important target of the ATM kinase, playing critical roles in controlling DNA replication forks and DNA repair after the damage. A major role for the NBS1 and BRCA1 proteins appears to be in the recruitment of an activated ATM kinase molecule to the sites of DNA breaks so that ATM can phosphorylate SMC1. Generation of mice and cells that are unable to phosphorylate SMC1 demonstrated the importance of SMC1 phosphorylation in the DNA-damage-induced S-phase checkpoint, in determining rates of repair of chromosomal breaks, and in determining cell survival after DNA damage. Focusing on ATM and SMC1, the molecular controls of these pathways is discussed.
Role of superoxide in the germination ofBacillus anthracisendospores (2005)

The spore forming Gram-positive bacterium Bacillus anthracis, the causative agent of anthrax, has achieved notoriety due to its use as a bioterror agent. In the environment, B. anthracis exists as a dormant endospore. Germination of endospores during their internalization within the myeloid phagocyte, and the ability of those endospores to survive exposure to antibacterial killing mechanisms such as superoxide (O(2)*-, is a key initial event in the infective process. We report herein that endospores exposed to fluxes of O(2)*- typically found in stimulated phagocytes had no effect on viability. Further endospores of the Sterne strain of B. anthracis were found to scavenge O(2)*-, which may enhance the ability of the bacterium to survive within the hostile environment of the phagolysosome. Most intriguing was the observation that endospore germination was stimulated by a flux of O(2)*- as low as 1 microM/min. Data presented herein suggest that B. anthracis may co-opt O(2)*- which is produced by stimulated myeloid phagocytes and is an essential element of host immunity, as a necessary step in productive infection of the host.
Novel high voltage SOI structures (2003)

This paper proposes several new device structures suitable for realizing high voltage power devices in thin SOI layer. Both analytical and simulation results show that the on-resistance of a unipolar device based on these structures is significantly reduced and the figure-of-merit, Ron/VB, can be an order of magnitude smaller than the theoretical limitation of vertical power devices.
Cardiac Memory in Patients With Wolff-Parkinson-White Syndrome (2008)

The study demonstrates that ECGI can noninvasively localize ventricular insertion sites of accessory pathways to guide ablation and evaluate its outcome in pediatric patients with Wolff-Parkinson-White syndrome. Wolff-Parkinson-White is associated with high ARI dispersion in the preexcited rhythm that persists after ablation and gradually returns to normal over a period of 1 month, demonstrating the presence of cardiac memory. The 1-month time course is consistent with transcriptional reprogramming and remodeling of ion channels.
Predicting Rate of Cognitive Decline in Probable Alzheimer's Disease (1996)

Recent attempts to identify predictors of rate of decline in Alzheimer's disease (AD) have been extremely variable in choice of outcome variables, predictor variables tested, timing of assessments, and statistical approaches. In this study, a random effects regression model was applied to seek predictors of decline on the Mini-Mental State Exam in 132 patients with probable AD reassessed every 6 months for up to 7.5 years. Potential predictor variables at baseline were of three types: patients characteristics, clinical variables, and cognitive performances. The final multivariate analysis indicated that the following characteristics predicted more rapid cognitive decline: more education, history of dementia in a first degree relative, non-right handedness, better performances of Boston Naming Test, Gollin Incomplete Figures Test, and Benton Visual Retention Test-Delay, and worse performances on Responsive Naming Test, WAIS-R Block Design, and Benton Visual Retention Test-Copy.
Three-Dimensional Structure in Solution of the Calcium Channel Blocker .omega.-Conotoxin MVIIA (1995)

The three-dimensional solution structure of omega-conotoxin MVIIA, a 25-mer peptide antagonist of N-type calcium channels, was determined by two-dimensional 1H NMR spectroscopy with simulated annealing calculations. A total of 13 converged structures of omega-conotoxin MVIIA were obtained on the basis of 273 experimental constraints, including 232 distance constraints obtained from nuclear Overhauser effect (NOE) connectivities, 22 torsion angle (phi, chi 1) constraints, and 19 constraints associated with hydrogen bonds and disulfide bonds. The atomic root mean square difference about the averaged coordinate positions is 0.47 +/- 0.08 A for the backbone atoms (N, C alpha, C) and 1.27 +/- 0.14 A for all heavy atoms of the entire peptide. The molecular structure of omega-conotoxin MVIIA is composed of a short triple-stranded antiparallel beta-sheet. The overall beta-sheet topology is +2x, -1, which is the same as that reported for omega-conotoxin GVIA, another N-type calcium channel blocker. The orientation of beta-stranded structure is similar to each other, suggesting that the conserved disulfide bond combination is essential for the molecular folding. We have recently determined by using alanine substitution analyses that Tyr 13 is essential for the activity of both toxins. On the basis of functional and structural analysis, it is shown that both omega-conotoxin MVIIA and GVIA retain a similar conformation to locate Tyr 13 in the appropriate position to allow binding to N-type calcium channels. These results provide a molecular basis for understanding the mechanism of calcium channel modulation through the toxin-channel interaction and insight into the discrimination of different subtypes of calcium channels.
Prevalence of aberrant expression of the epidermal growth factor receptor in human cancers (1991)

This chapter reviews briefly the prevalence of overexpression of the epidermal growth factor receptor in human cancers. In addition, it examines the mechanisms responsible for increased expression and its clinical significance.
Grip and pinch strength: normative data for adults. (1985)

The primary purpose of this study was to establish clinical norms for adults aged 20 to 75+ years on four tests of hand strength. A dynamometer was used to measure grip strength and a pinch gauge to measure tip, key, and palmar pinch. A sample of 310 male and 328 female adults, ages 20 to 94, from the seven-county Milwaukee area were tested using standardized positioning and instructions. Right hand and left hand data were stratified into 12 age groups for both sexes. This stratification provides a means of comparing the score of individual patients to that of normal subjects of the same age and sex. The highest grip strength scores occurred in the 25 to 39 age groups. For tip, key, and palmar pinch the average scores were relatively stable from 20 to 59 years, with a gradual decline from 60 to 79 years. A high correlation was seen between grip strength and age, but a low to moderate correlation between pinch strength and age. The newer pinch gauge used in this study appears to read higher than that used in a previous normative study. Comparison of the average hand strength of right-handed and left-handed subjects showed only minimal differences.
The heat of shortening and the dynamic constants of muscle (1938)

Abstract The hope was recently expressed (Hill 1937, p. 116) that with the development of a more accurate and rapid technique for muscle heat measurement, a much more consistent picture might emerge of the energy relations of muscles shortening (or lengthening) and doing positive (or negative) work. This hope has been realized, and some astonishingly simple and accurate relations have been found, relations, moreover, which (among other things) determine the effect of load on speed of shortening, allow the form of the isometric contraction to be predicted, and are the basis of the so-called “visco-elasticity” of skeletal muscle. This paper is divided into three parts. In Part I further developments of the technique are described: everything has depended on the technique, so no apology is needed for a rather full description of it and of the precautions necessary. In Part II the results themselves are described and discussed. In Part III the “visco-elastic” properties of active muscle are shown to be a consequence of the properties described in Part II.
Transplantation de myoblastes squelettiques autologues dans l’insuffisance cardiaque ischémique (2001)

Despite medical therapeutic advances, congestive heart failure (CHF), which is the common ultimate consequence of many primary cardiovascular diseases, remains a major and growing public health problem. Although orthotopic heart transplantation is the gold standard, there is now growing evidence that one therapeutic option could be cellular cardiomyoplasty. Autologous adult skeletal myoblast transplantation seems to be the most clinically relevant, compared with other cell types, in that it avoids immunosuppression therapy, availability and ethical issues. Previous experimental studies have documented the efficacy of myoblast transplantation in improving function of infarcted myocardium. Although the mechanisms involved in this improvement are not elucidated, it has been demonstrated convincingly enough to consider ripping to clinical trials.
The effect of surface roughness on the plasmonic response of individual sub-micron gold spheres (2009)

Nanoscale surface corrugation strongly determines the plasmonic response of gold nanoparticles with dimensions of several tens of nanometres. Scattering spectra of individual spheres with a rough surface were found to red-shift and broaden. The plasmon modes exhibited quadrupole damping, in contrast to particles with smooth surfaces. Additionally, rougher spheres display a higher SERS activity, which demonstrates the crucial role of nanoscale surface texturing on the plasmonic response of gold particles.
Bacteria in the Leaf Ecosystem with Emphasis onPseudomonas syringae—a Pathogen, Ice Nucleus, and Epiphyte (2000)

The extremely large number of leaves produced by terrestrial and aquatic plants provide habitats for colonization by a diversity of microorganisms. This review focuses on the bacterial component of leaf microbial communities, with emphasis on Pseudomonas syringae-a species that participates in leaf ecosystems as a pathogen, ice nucleus, and epiphyte. Among the diversity of bacteria that colonize leaves, none has received wider attention than P. syringae, as it gained notoriety for being the first recombinant organism (Ice(-) P. syringae) to be deliberately introduced into the environment. We focus on P. syringae to illustrate the attractiveness and somewhat unique opportunities provided by leaf ecosystems for addressing fundamental questions of microbial population dynamics and mechanisms of plant-bacterium interactions. Leaf ecosystems are dynamic and ephemeral. The physical environment surrounding phyllosphere microbes changes continuously with daily cycles in temperature, radiation, relative humidity, wind velocity, and leaf wetness. Slightly longer-term changes occur as weather systems pass. Seasonal climatic changes impose still a longer cycle. The physical and physiological characteristics of leaves change as they expand, mature, and senesce and as host phenology changes. Many of these factors influence the development of populations of P. syringae upon populations of leaves. P. syringae was first studied for its ability to cause disease on plants. However, disease causation is but one aspect of its life strategy. The bacterium can be found in association with healthy leaves, growing and surviving for many generations on the surfaces of leaves as an epiphyte. A number of genes and traits have been identified that contribute to the fitness of P. syringae in the phyllosphere. While still in their infancy, such research efforts demonstrate that the P. syringae-leaf ecosystem is a particularly attractive system with which to bridge the gap between what is known about the molecular biology of genes linked to pathogenicity and the ecology and epidemiology of associated diseases as they occur in natural settings, the field.
Syntheses of Hemoprotein Models that can be Covalently Attached onto Electrode Surfaces by Click Chemistry (2007)

Five alkyne-containing hemoprotein models have been synthesized in a convergent manner. Sonogashira coupling was used to introduce the alkyne functional group on the proximal imidazole before or after being attached on the porphyrin. One model was immobilized onto a gold electrode surface via copper(I)-catalyzed azide-alkyne cycloaddition (Sharpless click chemistry).
Inhaled Nitric Oxide in Full-Term and Nearly Full-Term Infants with Hypoxic Respiratory Failure (1997)

Nitric oxide therapy reduced the use of extracorporeal membrane oxygenation, but had no apparent effect on mortality in critically ill infants with hypoxic respiratory failure.
A dictionary on microRNAs and their putative target pathways (2010)

While in the last decade mRNA expression profiling was among the most popular research areas, over the past years the study of non-coding RNAs, especially microRNAs (miRNAs), has gained increasing interest. For almost 900 known human miRNAs hundreds of pretended targets are known. However, there is only limited knowledge about putative systemic effects of changes in the expression of miRNAs and their regulatory influence. We determined for each known miRNA the biochemical pathways in the KEGG and TRANSPATH database and the Gene Ontology categories that are enriched with respect to its target genes. We refer to these pathways and categories as target pathways of the corresponding miRNA. Investigating target pathways of miRNAs we found a strong relation to disease-related regulatory pathways, including mitogen-activated protein kinase (MAPK) signaling cascade, Transforming growth factor (TGF)-beta signaling pathway or the p53 network. Performing a sophisticated analysis of differentially expressed genes of 13 cancer data sets extracted from gene expression omnibus (GEO) showed that targets of specific miRNAs were significantly deregulated in these sets. The respective miRNA target analysis is also a novel part of our gene set analysis pipeline GeneTrail. Our study represents a comprehensive theoretical analysis of the relationship between miRNAs and their predicted target pathways. Our target pathways analysis provides a 'miRNA-target pathway' dictionary, which enables researchers to identify target pathways of differentially regulated miRNAs.
New Noninvasive Method for Coronary Flow Reserve Assessment (1999)

Contrast-enhanced transthoracic echo Doppler with the harmonic mode is a feasible and promising technique for assessing CFR in a totally noninvasive way.
In vivo metabolism of proapolipoprotein A-I in Tangier disease. (1987)

Tangier disease is a rare familial disorder characterized by extremely low levels of apolipoprotein A-I (apoA-I) and high density lipoproteins (HDL). In normal subjects, proapoA-I is secreted into plasma and converted to mature apoA-I by the cleavage of the amino-terminal six amino acids with the major isoprotein in plasma being mature apoA-I. In contrast, in Tangier disease there is a marked relative increase of proapoA-I as compared with mature apoA-I. ProapoA-I and mature apoA-I were isolated from normal and Tangier disease subjects, radio-labeled, and autologous apoA-I isoproteins injected into normal and Tangier subjects. The in vivo catabolism and conversion of proapoA-I and mature apoA-I in normal and Tangier disease subjects were quantitated. A comparison of the rate of catabolism of apoA-I isoproteins from plasma revealed a significantly faster rate of catabolism of both isoproteins of apoA-I in Tangier subjects when compared with normal subjects. The fractional conversion rate of proapoA-I to mature apoA-I was 3.9 d-1 in normal subjects and 3.6 d-1 in Tangier subjects. The results indicate that (a) apoA-I enters plasma as the pro isoprotein in both normal and Tangier subjects, (b) Tangier disease subjects have a normal fractional rate of conversion of proapoA-I to mature apoA-I, (c) proapoA-I is catabolized at the same rate as mature apoA-I in Tangier subjects, and (d) Tangier subjects catabolize both pro and mature apoA-I at a much greater rate than do normal subjects. Therefore, the relative increase in proapoA-I in Tangier disease is due to a marked decrease in mature apoA-I resulting from rapid catabolism of both pro- and mature apoA-I and not to defective conversion of proapoA-I to mature apoA-I.
Pointer Sentinel Mixture Models (2016)

Recent neural network sequence models with softmax classifiers have achieved their best language modeling performance only with very large hidden states and large vocabularies. Even then they struggle to predict rare or unseen words even if the context makes the prediction unambiguous. We introduce the pointer sentinel mixture architecture for neural sequence models which has the ability to either reproduce a word from the recent context or produce a word from a standard softmax classifier. Our pointer sentinel-LSTM model achieves state of the art language modeling performance on the Penn Treebank (70.9 perplexity) while using far fewer parameters than a standard softmax LSTM. In order to evaluate how well language models can exploit longer contexts and deal with more realistic vocabularies and larger corpora we also introduce the freely available WikiText corpus.