gebhart/patrepeval huggingface dataset:
Established and theoretical factors to consider in assessing the red cell storage lesion (2015)

The collection and storage of red blood cells (RBCs) is a logistical necessity to provide sufficient blood products. However, RBC storage is an unnatural state, resulting in complicated biological changes, referred to collectively as the "storage lesion." Specifics of the storage lesion have been studied for decades, including alterations to cellular properties, morphology, molecular biology of carbohydrates, proteins and lipids, and basic metabolism. Recently, mass spectrometry-based "omics" technology has been applied to the RBC storage lesion, resulting in many new observations, the initial effects of which are more information than understanding. Meanwhile, clinical research on RBC transfusion is considering both the efficacy and also the potential untoward effects of transfusing stored RBCs of different ages and storage conditions. The myriad biological changes that have now been observed during the storage lesion have been extensively reviewed elsewhere. This article focuses rather on an analysis of our current understanding of the biological effects of different elements of the storage lesion, in the context of evolving new clinical understanding. A synopsis is presented of both established and theoretical considerations of the RBC storage lesion and ongoing efforts to create a safer and more efficacious product.
Longitudinal Shapes of the Tibia and Femur are Unrelated and Variable (2009)

In general practice, short films of the knee are used to assess component position and define the entry point for intramedullary femoral alignment in TKAs; however, whether it is justified to use the short film commonly used in research settings and everyday practice as a substitute for the whole leg view is controversial and needs clarification. In 138 long leg CT scanograms we measured the angle formed by the anatomic axis of the proximal fourth of the tibia and the mechanical axis of the tibia, the angle formed by the anatomic axis of the distal fourth of the femur and the mechanical axis of the femur, the "bow" of the tibia (as reflected by the offset of the anatomic axis from the center of the talus), and the "bow" of the femur (as reflected by the offset of the anatomic axis from the center of the femoral head). Because the angle formed by these axes and the bow of the tibia and femur have wide variability in females and males, a short film of the knee should not be used in place of the whole leg view when accurate assessment of component position and limb alignment is essential. A previous study of normal limbs found that only 2% of subjects have a neutral hip-knee-ankle axis, which can be explained by the wide variability of the bow in the tibia and femur and the lack of correlation between the bow of the tibia and femur in a given limb as shown in the current study.
Hepatitis C virus-encoded nonstructural protein NS4A has versatile functions in viral protein processing (1995)

A transient protein expression system in COS-1 cells was used to study the role of hepatitis C virus (HCV)-encoded NS4A protein on HCV nonstructural polyprotein processing. By analyzing the protein expression and processing of a deletion mutant polypeptide, NS delta 4A, which encodes the entire putative HCV nonstructural polyprotein except the region encoding NS4A, the versatile functions of NS4A were revealed. Most of the NS3 processed from NS delta 4A was localized in the cytosol fraction and was degraded promptly. Coproduction of NS4A stabilizes NS3 and assists in its localization in the membrane. NS4A was found to be indispensable for cleavage at the 4B/5A site but not essential for cleavage at the 5A/5B site in NS delta 4A. The functioning of NS4A as a cofactor for cleavage at the 4B/5A site was also observed when 30 amino acids around this site was used as a substrate and a serine proteinase domain of 167 amino acids, from Gly-1049 to Ser-1215, was used as an enzyme protein, suggesting that possible domains for the interaction of NS4A were in those regions of the enzyme protein (NS3) and/or the substrate protein. Two proteins, p58 and p56, were produced from NS5A. For the production of p58, equal or excess molar amounts of NS4A relative to NS delta 4A were required. Deletion analysis of NS4A revealed a minimum functional domain of NS4A of 10 amino acids, from Gly-1678 to Ile-1687.
Nonlinear Discriminant Analysis Using Kernel Functions (1999)

Fishers linear discriminant analysis (LDA) is a classical multivariate technique both for dimension reduction and classi cation. The data vectors are transformed into a low dimensional subspace such that the class centroids are spread out as much as possible. In this subspace LDA works as a simple prototype classi er with linear decision boundaries. However, in many applications the linear boundaries do not adequately separate the classes. We present a nonlinear generalization of discriminant analysis that uses the kernel trick of representing dot products by kernel functions. The presented algorithm allows a simple formulation of the EM-algorithm in terms of kernel functions which leads to a unique concept for unsupervised mixture analysis, supervised discriminant analysis and semi-supervised discriminant analysis with partially unlabelled observations in feature spaces. 1 Introduction Classical linear discriminant analysis (LDA) projects N data vectors that belong to c...
Extragenic Suppressors of Growth Defects inmsbB Salmonella (2001)

Lipid A, a potent endotoxin which can cause septic shock, anchors lipopolysaccharide (LPS) into the outer leaflet of the outer membrane of gram-negative bacteria. MsbB acylates (KDO)(2)-(lauroyl)-lipid IV-A with myristate during lipid A biosynthesis. Reports of knockouts of the msbB gene describe effects on virulence but describe no evidence of growth defects in Escherichia coli K-12 or Salmonella. Our data confirm the general lack of growth defects in msbB E. coli K-12. In contrast, msbB Salmonella enterica serovar Typhimurium exhibits marked sensitivity to galactose-MacConkey and 6 mM EGTA media. At 37 degrees C in Luria-Bertani (LB) broth, msbB Salmonella cells elongate, form bulges, and grow slowly. msbB Salmonella grow well on LB-no salt (LB-0) agar; however, under specific shaking conditions in LB-0 broth, many msbB Salmonella cells lyse during exponential growth and a fraction of the cells form filaments. msbB Salmonella grow with a near-wild-type growth rate in MSB (LB-0 containing Mg(2+) and Ca(2+)) broth (23 to 42 degrees C). Extragenic compensatory mutations, which partially suppress the growth defects, spontaneously occur at high frequency, and mutants can be isolated on media selective for faster growing derivatives. One of the suppressor mutations maps at 19.8 centisomes and is a recessive IS10 insertional mutation in somA, a gene of unknown function which corresponds to ybjX in E. coli. In addition, random Tn10 mutagenesis carried out in an unsuppressed msbB strain produced a set of Tn10 inserts, not in msbB or somA, that correlate with different suppressor phenotypes. Thus, insertional mutations, in somA and other genes, can suppress the msbB phenotype.
Nematode CLE signaling in Arabidopsis requires CLAVATA2 and CORYNE (2010)

Plant-parasitic cyst nematodes secrete CLAVATA3 (CLV3)/ESR (CLE)-like effector proteins. These proteins have been shown to act as ligand mimics of plant CLE peptides and are required for successful nematode infection; however, the receptors for nematode CLE-like peptides have not been identified. Here we demonstrate that CLV2 and CORYNE (CRN), members of the receptor kinase family, are required for nematode CLE signaling. Exogenous peptide assays and overexpression of nematode CLEs in Arabidopsis demonstrated that CLV2 and CRN are required for perception of nematode CLEs. In addition, promoter-reporter assays showed that both receptors are expressed in nematode-induced syncytia. Lastly, infection assays with receptor mutants revealed a decrease in both nematode infection and syncytium size. Taken together, our results indicate that perception of nematode CLEs by CLV2 and CRN is not only required for successful nematode infection but is also involved in the formation and/or maintenance of nematode-induced syncytia.
Synchronizing theta oscillations with direct-current stimulation strengthens adaptive control in the human brain (2015)

Executive control and flexible adjustment of behavior following errors are essential to adaptive functioning. Loss of adaptive control may be a biomarker of a wide range of neuropsychiatric disorders, particularly in the schizophrenia spectrum. Here, we provide support for the view that oscillatory activity in the frontal cortex underlies adaptive adjustments in cognitive processing following errors. Compared with healthy subjects, patients with schizophrenia exhibited low frequency oscillations with abnormal temporal structure and an absence of synchrony over medial-frontal and lateral-prefrontal cortex following errors. To demonstrate that these abnormal oscillations were the origin of the impaired adaptive control in patients with schizophrenia, we applied noninvasive dc electrical stimulation over the medial-frontal cortex. This noninvasive stimulation descrambled the phase of the low-frequency neural oscillations that synchronize activity across cortical regions. Following stimulation, the behavioral index of adaptive control was improved such that patients were indistinguishable from healthy control subjects. These results provide unique causal evidence for theories of executive control and cortical dysconnectivity in schizophrenia.
Effects of Soybean .BETA.-Conglycinin on Body Fat Ratio and Serum Lipid Levels in Healthy Volunteers of Female University Students (2004)

The changes in body fat ratio and serum lipids induced by the ingestion of beta-conglycinin were examined in 41 healthy female university student volunteers. The trend of change in body fat ratio following the ingestion of beta-conglycinin differed between students with a baseline body fat ratio over 25% and those less than 25%. In the former group, the ingestion of beta-conglycinin suppressed the increase in body fat ratio. Moreover the six subjects who had a high total cholesterol level (5.72 mmol/L or higher) tended to have reduced levels of serum triglyceride, free fatty acid, total cholesterol and lipoprotein (a) after the ingestion of beta-conglycinin, although those levels did not change significantly. The number of subjects was only six, therefore it was inferred that significant changes were not observed. Thus, ingestion of soybean beta-conglycinin suppressed the increase in body fat ratio in individuals with a high baseline body fat ratio and reduced relatively high serum levels of lipids. Those results suggest that if soybean beta-conglycinin is ingested continuously (5 g daily), it will be effective in keeping body fat ratio and serum lipid levels normal and eliminating excessive lipids from the body.
Simple, fast and high‐efficiency transformation system for directed evolution of cellulase in Bacillus subtilis (2010)

Bacillus subtilis can serve as a powerful platform for directed evolution, especially for secretory enzymes. However, cloning and transformation of a DNA mutant library in B. subtilis are not as easy as they are in Escherichia coli. For direct transformation of B. subtilis, here we developed a new protocol based on supercompetent cells prepared from the recombinant B. subtilis strain SCK6 and multimeric plasmids. This new protocol is simple (restriction enzyme-, phosphatase- and ligase-free), fast (i.e. 1 day) and of high efficiency (i.e. ~107 or ~104 transformants per mg of multimeric plasmid or ligated plasmid DNA respectively). Supercompetent B. subtilis SCK6 cells were prepared by overexpression of the competence master regulator ComK that was induced by adding xylose. The DNA mutant library was generated through a two-round PCR: (i) the mutagenized DNA fragments were generated by error-prone PCR and linearized plasmids were made using high-fidelity PCR, and (ii) the multimeric plasmids were generated based on these two DNA templates by using overlap PCR. Both protein expression level and specific activity of glycoside hydrolase family 5 endoglucanse on regenerated amorphous cellulose were improved through this new system. To our limited knowledge, this study is the first report for enhancing secretory cellulase performance on insoluble cellulose.
Genetic and molecular analyses of the gene encoding staphylococcal enterotoxin D (1989)

The gene (entD) encoding staphylococcal enterotoxin D (SED) has been located on a 27.6-kilobase penicillinase plasmid designated pIB485. This plasmid was present in all SED-producing strains tested. The entD gene was cloned on a 2.0-kilobase DNA fragment and was expressed in Escherichia coli. Sequence analysis of this fragment revealed an open reading frame that encoded a 258-amino-acid protein that possessed a 30-amino-acid signal peptide. The 228-amino-acid mature polypeptide had a molecular weight of 26,360 and contained a high degree of sequence similarity to the other staphylococcal enterotoxins. S1 nuclease mapping showed that transcription of entD was initiated 266 nucleotides upstream from the translation start codon. The entD gene was also shown to be activated by the staphylococcal regulatory element known as agr.
Titanium-Mediated Cyclopropanation ofN,N-Dibenzylcarboxamides towards Functionally Substituted 2-(1′-Aminocyclopropyl)acetic Acids (2005)

Straightforward syntheses of cyclopropyl analogues of β-homoornithine and β-homoglutamic acid are reported. The key step is the titanium-mediated cyclopropanation of 3-benzyloxypropionic acid N,N-dibenzylamide (6), affording N,N-dibenzyl-N-[1-(2-benzyloxyethyl)-2-ethenylcyclopropyl]amine (7) in 56% yield as a 2.5:1 mixture of E- and Z-diastereomers. Further transformations of 7 in 9 and 6 simple steps, respectively, furnished 3,6-bis(N-tert-butoxycarbonylamino)-3,4-methanohexanoic acid (13) and 3-(N-tert-butoxycarbonylamino)-3,4-methanohexane-1,6-diacid di­methylester (16) as interesting protected β-(aminocyclopropyl)carboxylic acid building blocks for potentially active small peptide analogues. The structure of the crystalline intermediate tert-butyl (E)-N-{2-[2-(N-tert-butoxycarbonylamino)ethyl-1-(2-hydroxyethyl)]cyclopropyl}carbamate (12) was proved by X-ray diffraction.
Thermal Analysis of Sulphamethoxazole - Sugar Physical Mixes (1985)

Differential scanning calorimetry and hot stage microscopy have been used to study the interactions between sulphamethoxazole and the sugars maltose, glucose, sucrose and mannitol. Only the sulphamethoxazole-mannitol system appeared to be stable and presented a eutectic containing 90.3% sulphamethoxazole. Heats of fusion for sulphamethoxazole, mannitol and their eutectic were 33.4, 73.6 and 39.9 cal g respectively.
A 40-kilodalton protein binds specifically to an upstream sequence element essential for muscle-specific transcription of the human myoglobin promoter. (1992)

To define transcriptional control elements responsible for muscle-specific expression of the human myoglobin gene, we performed mutational analysis of upstream sequences (nucleotide positions -373 to +7 relative to the transcriptional start site) linked to a firefly luciferase gene. Transient expression assays in avian and mammalian cells indicated that a CCCACCCCC (CCAC box) sequence (-223 to -204) is necessary for muscle-specific transcription directed either by the native myoglobin promoter or by a heterologous minimal promoter linked to the myoglobin upstream enhancer region. A putative MEF2-like site (-160 to -169) was likewise necessary for full transcriptional activity in myotubes. Mutations within either of two CANNTG (E-box) motifs (-176 to -148) had only minimal effects on promoter function. We identified and partially purified from nuclear extracts a 40-kDa protein (CBF40) that binds specifically to oligonucleotides containing the CCAC box sequence. A mutation of the CCAC box that disrupted promoter function in vivo also impaired binding of CBF40 in vitro. These data suggest that cooperative interactions between CBF40 and other factors including MEF-2 are required for expression of the human myoglobin gene in skeletal muscle.
Fundamental aspects of postsource decay in matrix-assisted laser desorption mass spectrometry. 1. Residual gas effects (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFundamental aspects of postsource decay in matrix-assisted laser desorption mass spectrometry. 1. Residual gas effectsBernhard Spengler, Dieter Kirsch, and Raimund KaufmannCite this: J. Phys. Chem. 1992, 96, 24, 9678–9684Publication Date (Print):November 1, 1992Publication History Published online1 May 2002Published inissue 1 November 1992https://pubs.acs.org/doi/10.1021/j100203a022https://doi.org/10.1021/j100203a022research-articleACS PublicationsRequest reuse permissionsArticle Views388Altmetric-Citations130LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
Time-resolved and energy-resolved coded aperture images with URA tagging (1987)

Coded aperture imaging with uniformly redundant arrays (URAs) is the standard technique for imaging above the limit of grazing incident x-ray telescopes. It is an ideal technique for high energy astrophysics because it has high throughput, excellent performance on point sources, and the ability to measure simultaneously signal and background. However, many sources of interest in high energy astrophysics are time variable or require detailed energy spectra. Until now, to obtain a single time (or energy) sample, the photons from the particular time (or energy) interval must be formed into an encoded pattern, then processed to obtain an image for that sample. Therefore, massive computations are required to cover the entire time and energy parameter space. We present a new method of coded aperture analysis called URA tagging, which provides time and/or energy resolved histories of sources with known positions without using a correlation operation. It can easily reduce the computation time by orders of magnitude compared to the next fastest method, the fast delta Hadamard transform. URA tagging can also correct for improperly encoded images or motion blurred images. Whereas previous methods for quantifying performance have not taken into account the finite resolution or the quantized sampling, URA tagging provides a SNR equation that includes all such effects. URA tagging analysis explains why delta decoding has a somewhat poorer SNR than balanced correlation; naively, one expects the better angular resolution to yield a better SNR. In addition, we show that complementary URAs (exchanged opaque and transparent elements) have different properties, and those with an even number of transparent elements should be preferred.
Using low cost magnetic sensors on magnetically hostile land vehicles (2003)

The author discusses methods used to compensate for a land vehicle's magnetic signature and gives results obtained with various types of vehicles in several world locations. Advantages and disadvantages of pendulous mounting are considered and vehicle magnetic changes caused by driving in areas of extremely strong magnetic fields, such as those generated by DC-powered trains, are discussed. It is suggested that dead-reckoning sensors will be needed on land because of the line-of-sight characteristics of GPS (Global Positioning System) and the difficulty land vehicles have in operating with as many as four satellites constantly in view. Flux gate magnetic sensors will provide a reliable means of measuring heading in many areas where vehicle navigation and tracking needs exist.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Cardiac fibroblasts, fibrosis and extracellular matrix remodeling in heart disease (2012)

Fibroblasts comprise the largest cell population in the myocardium. In heart disease, the number of fibroblasts is increased either by replication of the resident myocardial fibroblasts, migration and transformation of circulating bone marrow cells, or by transformation of endothelial/epithelial cells into fibroblasts and myofibroblasts. The primary function of fibroblasts is to produce structural proteins that comprise the extracellular matrix (ECM). This can be a constructive process; however, hyperactivity of cardiac fibroblasts can result in excess production and deposition of ECM proteins in the myocardium, known as fibrosis, with adverse effects on cardiac structure and function. In addition to being the primary source of ECM proteins, fibroblasts produce a number of cytokines, peptides, and enzymes among which matrix metalloproteinases (MMPs) and their inhibitors, tissue inhibitor of metalloproteinases (TIMPs), directly impact the ECM turnover and homeostasis. Function of fibroblasts can also in turn be regulated by MMPs and TIMPs. In this review article, we will focus on the function of cardiac fibroblasts in the context of ECM formation, homeostasis and remodeling in the heart. We will discuss the origins and multiple roles of cardiac fibroblasts in myocardial remodeling in different types of heart disease in patients and in animal models. We will further provide an overview of what we have learned from experimental animal models and genetically modified mice with altered expression of ECM regulatory proteins, MMPs and TIMPs.
Metmyoglobin and methemoglobin as efficient traps for nitrosyl hydride (nitroxyl) in neutral aqueous solution (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMetmyoglobin and methemoglobin as efficient traps for nitrosyl hydride (nitroxyl) in neutral aqueous solutionDennis A. Bazylinski and Thomas C. HollocherCite this: J. Am. Chem. Soc. 1985, 107, 26, 7982–7986Publication Date (Print):December 1, 1985Publication History Published online1 May 2002Published inissue 1 December 1985https://pubs.acs.org/doi/10.1021/ja00312a031https://doi.org/10.1021/ja00312a031research-articleACS PublicationsRequest reuse permissionsArticle Views331Altmetric-Citations101LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts