gebhart/patrepeval huggingface dataset:
Monoclonal antibody to a plasma membrane antigen of neurons. (1979)

Fusion of spleen cells from a mouse immunized with chicken embryo retina cells with clonal mouse myeloma cells yielded a lymphocyte hybrid cell line that produced antibody that bound to neural tissue such as retina, brain, spinal cord, and dorsal root ganglia but not to other tissues tested. The antigen was shown by indirect immunofluorescence to be associated with plasma membranes of most, or all, neuron cell bodies in chicken retina, but little or no antigen was detected on axons or dendrites, Müller cells, or retina pigment cells. The activity of antigen A2B5 is relatively stable at 100 degrees C, is insensitive to trypsin, exhibits the solubility properties of a ganglioside, and is destroyed by neuraminidase. Antibody A2B5 cytotoxicity against retina cells is inhibited by a GQ ganglioside fraction from bovine brain (estimated half-maximal inhibition at 0.2 microM) or by N-acetylneuraminic acid (half-maximal inhibition at 5000 microM) but not by other purified gangliosides tested. These results suggest that the antigen is a complex ganglioside in plasma membranes of retina neuron cell bodies but not axons or dendrites.
Hydrodynamic stretching of single cells for large population mechanical phenotyping (2012)

Cell state is often assayed through measurement of biochemical and biophysical markers. Although biochemical markers have been widely used, intrinsic biophysical markers, such as the ability to mechanically deform under a load, are advantageous in that they do not require costly labeling or sample preparation. However, current techniques that assay cell mechanical properties have had limited adoption in clinical and cell biology research applications. Here, we demonstrate an automated microfluidic technology capable of probing single-cell deformability at approximately 2,000 cells/s. The method uses inertial focusing to uniformly deliver cells to a stretching extensional flow where cells are deformed at high strain rates, imaged with a high-speed camera, and computationally analyzed to extract quantitative parameters. This approach allows us to analyze cells at throughputs orders of magnitude faster than previously reported biophysical flow cytometers and single-cell mechanics tools, while creating easily observable larger strains and limiting user time commitment and bias through automation. Using this approach we rapidly assay the deformability of native populations of leukocytes and malignant cells in pleural effusions and accurately predict disease state in patients with cancer and immune activation with a sensitivity of 91% and a specificity of 86%. As a tool for biological research, we show the deformability we measure is an early biomarker for pluripotent stem cell differentiation and is likely linked to nuclear structural changes. Microfluidic deformability cytometry brings the statistical accuracy of traditional flow cytometric techniques to label-free biophysical biomarkers, enabling applications in clinical diagnostics, stem cell characterization, and single-cell biophysics.
Low-Temperature-Grown RS Virus in Adult Volunteers (1968)

A respiratory syncytial (RS) virus strain grown in bovine embryonic kidney tissue culture at 34 C or at 28 C infected the majority of inoculated adult volunteers. An acute mild upper-respiratory tract illness developed in most infected individuals. Subsequent cultivation of the virus strain in bovine embryonic kidney tissue culture at 26 C was associated with a decrease in infectivity for adult volunteers. The response of the infected volunteers suggested that the virus grown at 26 C had also lost virulence for adults. The results of the study were considered sufficiently encouraging to recommend a cautious stepwise evaluation of the RS virus grown at 26 C in progressively younger age groups.
Hiding mass storage under Unix: NASA's MSS-II architecture (2002)

A second-generation mass storage system, MSS-II, is described. It achieves a 10-MB transfer rate into and out of the central-network mass-storage node, while preserving the illusion to users that it is simply an ordinary Unix system with an infinite supply of very fast disk space. It does so by implementing a Berkeley RAID-style file system in kernel software, by instituting striping network access, by implementing a transparent hierarchical storage manager, and by extending the concepts of file ownership and permission to removable volumes. The major software components (i.e. the high-performance file system, rapid-access storage hierarchy, volume manager, and striping network access) and file integrity are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Left-Handed Helical Ribbon Intermediates in the Self-Assembly of a β-Sheet Peptide (2002)

We report the observation of intermediate structures in the self-assembly of the peptide KFE8 (FKFEFKFE), designed with alternating polar and nonpolar amino acids. Self-assembly was followed over time using atomic force microscopy (AFM), transmission electron microscopy (TEM), and circular dichroism (CD). Molecular dynamics simulations suggest that these intermediates are left-handed double helical β-sheets. These findings have implications in the study of β-sheet fibril formation, and in the molecular design of materials.
Construction and Characterization of a Retroviral Vector Demonstrating Efficient Expression of Cloned cDNA Sequences (1988)

We describe the construction and properties of a retroviral expression vector, designated pMV-7, designed to transfer unselected cDNAs and produce their encoded proteins in recipient cells. The vector is flanked by the long terminal repeats (LTRs) of the Moloney murine sarcoma virus (MSV) and contains the selectable drug resistance gene neo under the regulation of the herpes simplex virus (HSV) thymidine kinase (tk) promoter. Unique Eco RI and Hind III sites facilitate the introduction of sequences whose transcription is regulated by the 5' LTR. We have inserted cDNAs encoding: (i) the human lymphocyte antigen T4, (ii) the human lymphocyte antigen T8, and (iii) the murine hypoxanthine-guanine phosphoribosyl transferase (HPRT), into the pMV-7 vector. These constructions were used to transduce recipient cells to the neo+ phenotype. In each case, functional assays demonstrated that 65-92% of the neo+ clones produced the appropriate protein encoded by its corresponding cDNA. These clones were characterized further by analyzing the expression of vector-regulated transcripts. The neo+T4+ clones expressed a single full-length LTR-to-LTR transcript as detected by a T4 probe. The neo+T8+ clones, however, expressed both a full-length LTR-to-LTR transcript and an additional smaller transcript as detected by a T8 probe. This smaller transcript probably resulted from the utilization of cryptic signals which control 3' RNA processing. Furthermore, all of the neo+ clones expressed a transcript that initiated from the tk promoter, contained the neo gene, and used polyadenylation signals provided by the 3' LTR. Thus, the pMV-7 vector is capable of high-efficiency transfer and high-frequency expression of the cDNA-encoded protein.
Mesenchymal stem cell–derived molecules directly modulate hepatocellular death and regeneration in vitro and in vivo (2008)

These data provide the first clear evidence that MSC-CM therapy provides trophic support to the injured liver by inhibiting hepatocellular death and stimulating regeneration, potentially creating new avenues for the treatment of FHF.
Turkey - Southwest Coast Environmental Project : environmental assessment (feasibility study for Cesme-alacati and surrounding area) (1996)

This is an environmental assessment of the Southwest Coast Environmental Project, which improves delivery of basic urban services. It discusses negative environmental impacts and measures to mitigate them. These measures include scheduling construction work around the tourist season; using acoustic screens and ear protectors; undertaking aesthetic improvements and landscaping at visible sites as well as designating a buffer zone around the facilities; liaising with local residents to minimize disruption during construction; storing chemicals and fuels in sealed, bunded areas to prevent spills; minimizing tree felling and agricultural land loss; implementing dust control measures like water spraying, restricting earth moving during windy conditions, and covering soil stockpiles; providing litter fencing and vermin control at the sanitary landfill; restricting construction and waste transfer traffic to suitable routes and normal working hours; providing, operating, and maintaining effective leachate and landfill gas control systems to prevent fires; and ventilating to keep the chamber walls dry and to prevent the formation of sulfuric acid-forming bacteria. Also, given the importance of tourism and associated bathing and water-based recreation in the area, routine water quality monitoring is needed.
Identifying Optimal Biologic Doses of Everolimus (RAD001) in Patients With Cancer Based on the Modeling of Preclinical and Clinical Pharmacokinetic and Pharmacodynamic Data (2008)

A direct-link PK/PD model predicting the time course of S6K1 inhibition during weekly and daily everolimus administration allowed extrapolation from preclinical studies and first clinical results to select optimal doses and regimens of everolimus to explore in future clinical trials.
Smallholder milk production in a semi-arid area of Zimbabwe from crossbred jersey cattle and forage based on Pennisetum hybrids: a progress report. (1996)

Milk and dairy products are in short supp1y in rural areas of Zimbabwe. Small holder interest in dairying is increasing. Major constraints are lack of suitable cattle and feed. Indigenous cows are being crossed to Jersey bulls to produce an FI dairy type animal. The calves reached puberty at around nine months and of 26 heifers bulled 23 produced a calf. Milk production, in the first lactation, from the crossbred female was higher in those calving at three years, compared with two years of age (1255v821 I), in excess of rearing their calves). Thirteen heifers were bred for a second lactation and 12 have calved (calving interval 373 days). Male progeny have proved capable as a source of draught power. Slaughter weights of pen-finished steers were satisfactory (227 and 187kg for three and two year olds respectively). Forage is being produced from Pemli,5etum hybrids, but erratic rainfall in 1994-1995 (year of establishment) has delayed full evaluation. INTRODUCTION Milk and dairy products are in short supply in the rural areas of Zimbabwe. Intake of animal protein is low (1). A major constraint to milk production in the semi-arid tropics is lack of feed. In these areas livestock production is usually the preferred activity. Whilst the percentage offtake for beef from small-holder cattle systems is low (2), file reasons farmers give for owning cattle emphasise the importance of draught power, milk production and social security, with beef production being regarded as a terminal function (3). Within the indigenous cattle of Zimbabwe there has been no sustained selection for either milk production or ease of milk let-down. Up to 10 tonnes forage dry matter can be grown with relatively low rainfall « 600mm) using Penni.fetum hybrids (4) .The superiority of indigenous breeds and their crosses as darn lines in these areas has also been demonstrated (5). In another study milk production was similar from crossbred (Friesian or Jersey) Mashona cows (6). When crossbreeding to produce milk in the small holder sector the male progeny must contribute to the overall livestock system. At Matopos Jersey bulls are crossed with indigenous cows to produce FI females with potential for milk production. Penni.\'etum hybrids are grown for forage. EXPERIMENTAL PROCEDURES ~ Matopos Research Station lies south of Bulawayo. Rainfall, between November and April, averages 610mm, but amount and distribution are variable. Soils at the tria] site are predominately a sandy clay mixture (7). Animals Since 1991 Nkone and Tuli cows have been bred to a Jersey bull to produce PI progeny. The PI females have also been bred to a Jersey bull to calve for the first time at two or three years of age, from October to December (first groups of PI heifers calved in 1994). SMITH, NDLOVU AND MHERE
Cardiovascular dysregulation of miR‐17‐92 causes a lethal hypertrophic cardiomyopathy and arrhythmogenesis (2012)

MicroRNA cluster miR-17-92 has been implicated in cardiovascular development and function, yet its precise mechanisms of action in these contexts are uncertain. This study aimed to investigate the role of miR-17-92 in morphogenesis and function of cardiac and smooth muscle tissues. To do so, a mouse model of conditional overexpression of miR-17-92 in cardiac and smooth muscle tissues was generated. Extensive cardiac functional studies identified a dose-dependent induction of dilated, hypertrophic cardiomyopathy, and arrhythmia inducibility in transgenic animals, which correlated with premature mortality (98.3 ± 42.5 d, P<0.0001). Expression analyses revealed the abundance of Pten transcript, a known miR-17-92 target, to be inversely correlated with miR-17-92 expression levels and heart size. In addition, we demonstrated through 3'-UTR luciferase assays and expression analyses that Connexin43 (Cx43) is a novel direct target of miR-19a/b and its expression is suppressed in transgenic hearts. Taken together, these data demonstrate that dysregulated expression of miR-17-92 during cardiovascular morphogenesis results in a lethal cardiomyopathy, possibly in part through direct repression of Pten and Cx43. This study highlights the importance of miR-17-92 in both normal and pathological functions of the heart, and provides a model that may serve as a useful platform to test novel antiarrhythmic therapeutics.
Pathogenicity Islands and Other Mobile Genetic Elements of Diarrheagenic Escherichia coli (2014)

This chapter focuses on diarrheagenic Escherichia coli strains and the various pathogenicity islands (PAIs) and other mobile genetic elements that differentiate these pathogens from normal-flora E. coli. At least six categories of diarrheagenic E. coli strains have been defined. Five of these categories, enteropathogenic E. coli (EPEC), enterohemorrhagic E. coli (EHEC), enteroaggregative E. coli (EAEC), enterotoxigenic E. coli (ETEC), and enteroinvasive E. coli (EIEC), are reviewed in the chapter. A sixth category, diffusely adherent E. coli (DAEC), is a heterogeneous group of organisms, and epidemiological studies have given conflicting results about the true clinical significance of these strains. Mobile genetic elements encoding virulence factors in human diarrheagenic E. coli are listed in the chapter. The majority of EPEC strains associated with diarrhea possess the EPEC adherence factor (EAF) plasmid and are referred to as typical EPEC strains, while EPEC strains that do not possess EAF plasmids are referred to as atypical EPEC strains. The majority of genes within this region have homology to transposons and insertion elements (IS elements), although these elements are apparently incomplete and nonfunctional. The great variety of mobile genetic elements present in diarrheagenic E. coli , including plasmids, bacteriophages, transposons, and PAIs, on a K-12 backbone with so many horizontally transferred regions indicates an enormous genomic plasticity that complicates the efforts to categorize the existing subgroups into sharply delineated pathotypes and the attempts to predict what novel combination of virulence factors may emerge in the future.
The Endothelial Cytoskeleton: Organization in Normal and Regenerating Endothelium* (1990)

The components of the endothelial cell cytoskeleton that have been shown to be important in maintaining endothelial structural integrity and in regulating endothelial repair include F-actin microfilament bundles, including stress fibers, and microtubules, and centrosomes. Endothelial cells contain peripheral and central actin microfilaments. The dense peripheral band (DPB) consists of peripheral actin microfilament bundles which are associated with vinculin adhesion plaques and are most prominent in low or no hemodynamic shear stress conditions. The central microfilaments are very prominent in areas of elevated hemodynamic shear stress. There is a redistribution of actin microfilaments characterized by a decrease of peripheral actin and an increase in central microfilaments under a variety of conditions, including exposure to thrombin, phorbol-esters, and hemodynamic shear stress. During reendothelialization, there is a sequential series of cytoskeletal changes. The DPB remains intact during the rapid lamellipodia mediated repair of very small wounds except at the base of the lamellipodia where it is splayed. The DPB is reduced or absent when cell locomotion occurs to repair a wound. In addition, when cell locomotion is required, the centrosome, in the presence of intact microtubules, redistributes to the front of the cell to establish cell polarity and acts as a modulator of the directionality of migration. This occurs prior to the loss of the DPB but does not occur in very small wounds that close without migration. Thus, the cytoskeleton is a dynamic intracellular system which regulates endothelial integrity and repair and is modulated by external stimuli that are present at the vessel wall-blood interface.
Somatostatin displayed on filamentous phage as a receptor‐specific agonist (1998)

1. In search of methods to identify bio-active ligands specific for G protein-coupled receptors with seven transmembrane spanning regions, we have developed a filamentous phage-based selection and functional screening method. 2. First, methods for panning peptide phage on cells were established, using the hormone somatostatin as a model. Somatostatin was displayed on the surface of filamentous phage by cloning into phage(mid) vectors and fusion to either pIII or pVIII viral coat proteins. Peptide displaying phage bound to a polyclonal anti-somatostatin serum, and, more importantly, to several somatostatin receptor subtypes (Sst) expressed on transfected CHO-K1 cells, in a pattern which was dependent on the used display method. Binding was competed with somatostatin, with an IC50 in the nanomolar range. The phage were specifically enriched by panning on cells, establishing conditions for cell selections of phage libraries. 3. Binding of somatostatin displaying phage to sst2 on a reporter cell line, in which binding of natural ligand reduces secretion of alkaline phosphatase (via a cyclic AMP responsive element sensitive promoter), proved that the phage particles act as receptor-specific agonists. Less than 100 phage particles per cell were required for this activity, which is approximately 1000 fold less than soluble somatostatin, suggesting that phage binding interferes with normal receptor desensitization and/or recycling. 4. The combination of biopanning of phage libraries on cells with functional screening of phage particles for receptor triggering activity, may be used to select novel, bio-active ligands from phage libraries of random peptides, antibody fragments, or libraries based on the natural receptor ligand.
Nomenclature of Organic Compounds (1974)

Alchemists frequently assigned names to substances with the intent of concealing what they were working on from their fellow workers. This attitude has gradually changed throughout the years, so that chemists now strive to reveal their latest theories or discoveries to others either orally or through the printed medium. To communicate easily with one another, it has been necessary to devise a special language which we call chemical nomenclature (1,2,3,4,5). We expect this nomenclature not only to define a given compound uniquely but to reveal what atoms are present, how the atoms are arranged within the molecule, and chemical relationships with other compounds as well.
Photoinduced Ligand Release from a Silicon Phthalocyanine Dye Conjugated with Monoclonal Antibodies: A Mechanism of Cancer Cell Cytotoxicity after Near-Infrared Photoimmunotherapy (2018)

Photochemical reactions can dramatically alter physical characteristics of reacted molecules. In this study, we demonstrate that near-infrared (NIR) light induces an axial ligand-releasing reaction, which dramatically alters hydrophilicity of a silicon phthalocyanine derivative (IR700) dye leading to a change in the shape of the conjugate and its propensity to aggregate in aqueous solution. This photochemical reaction is proposed as a major mechanism of cell death induced by NIR photoimmunotherapy (NIR-PIT), which was recently developed as a molecularly targeted cancer therapy. Once the antibody-IR700 conjugate is bound to its target, activation by NIR light causes physical changes in the shape of antibody antigen complexes that are thought to induce physical stress within the cellular membrane leading to increases in transmembrane water flow that eventually lead to cell bursting and necrotic cell death.
Retinoblastoma Protein Contains a C-terminal Motif That Targets It for Phosphorylation by Cyclin-cdk Complexes (1999)

Stable association of certain proteins, such as E2F1 and p21, with cyclin-cdk2 complexes is dependent upon a conserved cyclin-cdk2 binding motif that contains the core sequence ZRXL, where Z and X are usually basic. In vitro phosphorylation of the retinoblastoma tumor suppressor protein, pRB, by cyclin A-cdk2 and cyclin E-cdk2 was inhibited by a short peptide spanning the cyclin-cdk2 binding motif present in E2F1. Examination of the pRB C terminus revealed that it contained sequence elements related to ZRXL. Site-directed mutagenesis of one of these sequences, beginning at residue 870, impaired the phosphorylation of pRB in vitro. A synthetic peptide spanning this sequence also inhibited the phosphorylation of pRB in vitro. pRB C-terminal truncation mutants lacking this sequence were hypophosphorylated in vitro and in vivo despite the presence of intact cyclin-cdk phosphoacceptor sites. Phosphorylation of such mutants was restored by fusion to the ZRXL-like motif derived from pRB or to the ZRXL motifs from E2F1 or p21. Phospho-site-specific antibodies revealed that certain phosphoacceptor sites strictly required a C-terminal ZRXL motif whereas at least one site did not. Furthermore, this residual phosphorylation was sufficient to inactivate pRB in vivo, implying that there are additional mechanisms for directing cyclin-cdk complexes to pRB. Thus, the C terminus of pRB contains a cyclin-cdk interaction motif of the type found in E2F1 and p21 that enables it to be recognized and phosphorylated by cyclin-cdk complexes.
Retracted: Determination of scutellarin isomer, a predominant metabolite of scutellarin, in human plasma by HPLC/tandem mass spectrometry and its application to a pharmacokinetic study in Chinese healthy volunteers (2007)

Abstract Retraction: The following article from Biomedical Chromatography , “Determination of scutellarin isomer, a predominant metabolite of scutellarin, in human plasma by HPLC/tandem mass spectrometry and its application to the pharmacokinetic study in Chinese healthy volunteers” by Chun‐hua Xia, Yu‐qing Xiong, and Guang‐ji Wang, published online on 21 June 2007 in Wiley Interscience (www.interscience.wiley.com/journal/bmc), has been retracted at the authors' request.