gebhart/patrepeval huggingface dataset:
Protective and Pathogenic Roles for B Cells during Systemic Autoimmunity in NZB/W F1 Mice (2010)

Delineating the relative contributions of B lymphocytes during the course of autoimmune disease has been difficult. Therefore, the effects of depleting all mature B cells using a potent CD20 mAb, or of depleting circulating and marginal zone B cells using a ligand-blocking CD22 mAb, were compared in NZB/W F(1) mice, a model for human systemic lupus erythematosus. Single low-dose mAb treatments depleted B cells efficiently in both NZB/W F(1) and C57BL/6 mice. Prophylactic B cell depletion by repeated CD20 mAb treatments prolonged survival during pristane-accelerated lupus in NZB/W F(1) mice, whereas CD22 mAb had little effect. Despite effective B cell depletion, neither mAb treatment prevented autoantibody generation. In addition, CD20, CD22, and control mAb-treated NZB/W F(1) mice developed anti-mouse IgG autoantibodies in contrast to parental NZB and NZW strains, which may have reduced the effectiveness of B cell depletion. Despite this, low-dose CD20 mAb treatment initiated in 12-28-wk-old mice, and administered every 4 wk thereafter, significantly delayed spontaneous disease in NZB/W F(1) mice. By contrast, B cell depletion initiated in 4-wk-old mice hastened disease onset, which paralleled depletion of the IL-10-producing regulatory B cell subset called B10 cells. B10 cells were phenotypically similar in NZB/W F(1) and C57BL/6 mice, but were expanded significantly in young NZB/W F(1) mice. Thus, B cell depletion had significant effects on NZB/W F(1) mouse survival that were dependent on the timing of treatment initiation. Therefore, distinct B cell populations can have opposing protective and pathogenic roles during lupus progression.
Rotational-diversity phase estimation from differential-interference-contrast microscopy images (2000)

An iterative phase-estimation method for the calculation of a specimen's phase function or optical-path-length (OPL) distribution from differential-interference-contrast (DIC) microscopy images is presented. The method minimizes the least-squares discrepancy measure by use of the conjugate-gradient technique to estimate the phase function from multiple DIC images acquired at different specimen rotations. The estimate is regularized with a quadratic smoothness penalty. Results from testing the method with simulations and measured DIC images show improvement in the estimated phase when at least two rotationally diverse DIC images instead of a single DIC image are used for the estimation. The OPL of a cell that is estimated from two DIC images was found to be much more reliable than the OPL computed from single DIC images (which had a coefficient of variation equal to 15.8%).
A single intrathecal injection of GABA permanently reverses neuropathic pain after nerve injury (1999)

To investigate whether neuropathic pain is sensitive to spinal GABA levels, GABA was injected intrathecally after nerve injury and sensory behaviors were evaluated. Both thermal and tactile hypersensitivities were permanently reversed at the highest doses of GABA. However, if GABA was injected any later than 2-3 weeks after nerve injury, it was ineffective to prevent such hypersensitivity. This suggests that altered spinal GABA levels contribute to the induction phase of chronic neuropathic pain and that early intervention to restore GABA may prevent the development of that pain.
Handling Reagents tn the PCR Laboratory (1993)

The exquisite sensitivity of PCR dictates that the reagents used in the PCR reaction must be free from all DNA contamination. Without this precaution, reliable results cannot be guaranteed. The fundamental rule that all PCR practitioners must adhere to is that ALL pre-PCR reagents must be prepared and maintained in an area free from all possible sources of DNA or RNA. Pre-PCR reagents can be divided into two classes: (1) reagents for sample preparation, and (2) reagents for amplification. Sample preparation reagents include buffers for the lysis of cells, extraction reagents for the release of nucleic acid, and resuspension buffers for the extracted nucleic acid. Post-PCR (detection) reagents are sequestered and handled in a different area of the laboratory. The purpose of this article is to provide a list of suggestions for the preparation and handling of PCR reagents.
CD15, CD24, and CD29 Define a Surface Biomarker Code for Neural Lineage Differentiation of Stem Cells (2009)

Identification and use of cell surface cluster of differentiation (CD) biomarkers have enabled much scientific and clinical progress. We identify a CD surface antigen code for the neural lineage based on combinatorial flow cytometric analysis of three distinct populations derived from human embryonic stem cells: (1) CD15(+)/CD29(HI)/CD24(LO) surface antigen expression defined neural stem cells; (2) CD15(-)/CD29(HI)/CD24(LO) revealed neural crest-like and mesenchymal phenotypes; and (3) CD15(-)/CD29(LO)/CD24(HI) selected neuroblasts and neurons. Fluorescence-activated cell sorting (FACS) for the CD15(-)/CD29(LO)/CD24(HI) profile reduced proliferative cell types in human embryonic stem cell differentiation. This eliminated tumor formation in vivo, resulting in pure neuronal grafts. In conclusion, combinatorial CD15/CD24/CD29 marker profiles define neural lineage development of neural stem cell, neural crest, and neuronal populations from human stem cells. We believe this set of biomarkers enables analysis and selection of neural cell types for developmental studies and pharmacological and therapeutic applications.
Bimolecular decarboxylative self-condensation of oxaloacetic acid to citrolyformic acid and its conversion by oxidative decarboxylation to citric acid (1973)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBimolecular decarboxylative self-condensation of oxaloacetic acid to citrolyformic acid and its conversion by oxidative decarboxylation to citric acidRichard H. Wiley and Ki Soo KimCite this: J. Org. Chem. 1973, 38, 20, 3582–3585Publication Date (Print):October 1, 1973Publication History Published online1 May 2002Published inissue 1 October 1973https://doi.org/10.1021/jo00960a030RIGHTS & PERMISSIONSArticle Views297Altmetric-Citations12LEARN 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 InReddit PDF (652 KB) Get e-Alerts Get e-Alerts
Reproductive function and feedlot performance of beef heifers actively immunized against GnRH1. (1990)

Two trials were conducted to examine reproductive function and feedlot performance by heifers after active immunization against GnRH. In trial 1, heifers were not immunized or were immunized with one of three doses of a GnRH-KLH (keyhole limpet hemocyanin) conjugate in Freund's complete adjuvant. Antibodies against GnRH were not detectable in non-immunized heifers (n = 9). However, antibodies against GnRH were noted in all immunized animals (n = 30) within 8 wk of primary immunization; anti-GnRH antibody concentrations were at a maximum 16 to 20 wk after immunization. This increased anti-GnRH titer was associated with a decreased serum concentration of progesterone. Ovarian and uterine weight and tissue concentrations of LH and GnRH receptor were reduced (P less than .05) by immunoneutralization of GnRH. Similarly, immunization against GnRH reduced (P less than .05) weight gain during feedlot confinement. In trial 2, feedlot performance after insertion of anabolic steroid implants (Synovex H) was evaluated in non-immunized heifers (n = 15), heifers actively immunized against GnRH-KLH (n = 15) or KLH alone (n = 15), or non-immunized heifers treated with melengestrol acetate (MGA; n = 15). Serum concentrations of progesterone were depressed in anti-GnRH and MGA-fed groups, but ovarian and uterine weights were depressed (P less than .05) only in heifers immunized against GnRH. Total weight gain and gain during the final 4 wk of confinement did not differ (P greater than .05) among groups with steroid implants. The GnRH-KLH conjugate is an effective immunogen in heifers, leading to suppression of reproductive activity. The depression of weight gain that attends development of anti-GnRH titers may be reversed by use of implants that contain anabolic steroids.
The Anaphase Promoting Complex Regulates Yeast Lifespan and rDNA Stability by Targeting Fob1 for Degradation (2013)

Genomic stability, stress response, and nutrient signaling all play critical, evolutionarily conserved roles in lifespan determination. However, the molecular mechanisms coordinating these processes with longevity remain unresolved. Here we investigate the involvement of the yeast anaphase promoting complex (APC) in longevity. The APC governs passage through M and G1 via ubiquitin-dependent targeting of substrate proteins and is associated with cancer and premature aging when defective. Our two-hybrid screen utilizing Apc5 as bait recovered the lifespan determinant Fob1 as prey. Fob1 is unstable specifically in G1, cycles throughout the cell cycle in a manner similar to Clb2 (an APC target), and is stabilized in APC (apc5(CA)) and proteasome (rpn10) mutants. Deletion of FOB1 increased replicative lifespan (RLS) in wild type (WT), apc5(CA), and apc10 cells, and suppressed apc5(CA) cell cycle progression and rDNA recombination defects. Alternatively, increased FOB1 expression decreased RLS in WT cells, but did not reduce the already short apc5(CA) RLS, suggesting an epistatic interaction between apc5(CA) and fob1. Mutation to a putative L-Box (Fob1(E420V)), a Destruction Box-like motif, abolished Fob1 modifications, stabilized the protein, and increased rDNA recombination. Our work provides a mechanistic role played by the APC to promote replicative longevity and genomic stability in yeast.
Interleukin-1 alpha stimulates KC synthesis in rat mesangial cells: glucocorticoids inhibit KC induction by IL-1 (1994)

To assess the possible role of the production of chemokines by intrinsic glomerular cells in the generation of inflammation in glomerulonephritis, the chemokine, KC, was cloned from a rat macrophage cDNA library. Transfection of rat KC into COS-7 cells resulted in increased neutrophil chemotactic activity. The KC cDNA was expressed as a fusion protein in Escherichia coli for generation of an antibody. By using a riboprobe derived from the cDNA and the antibody, interleukin-1 (IL-1) was found to induce the expression of KC in rat mesangial cells. The induction of KC by IL-1 could be inhibited by dexamethasone (DEX). The protein synthesis inhibitor cycloheximide reversed the DEX-mediated inhibition, which suggested that new protein synthesis was necessary for the inhibitory effect. A nuclear runoff analysis indicated that DEX inhibited the transcription of KC induced by IL-1. The stability of KC mRNA was not decreased in the presence of DEX. Furthermore, immunoblots showed that DEX also inhibited KC expression at the level of translation. Together the inhibition of transcription and translation of the KC gene by DEX contribute to decreased KC expression in mesangial cells. The finding that mesangial cells express KC in response to proinflammatory cytokines, such as IL-1, points to a central role for the mesangial cell as a chemotactic source in glomerular inflammation.
Nanoparticle-Based Bio-Bar Codes for the Ultrasensitive Detection of Proteins (2003)

An ultrasensitive method for detecting protein analytes has been developed. The system relies on magnetic microparticle probes with antibodies that specifically bind a target of interest [prostate-specific antigen (PSA) in this case] and nanoparticle probes that are encoded with DNA that is unique to the protein target of interest and antibodies that can sandwich the target captured by the microparticle probes. Magnetic separation of the complexed probes and target followed by dehybridization of the oligonucleotides on the nanoparticle probe surface allows the determination of the presence of the target protein by identifying the oligonucleotide sequence released from the nanoparticle probe. Because the nanoparticle probe carries with it a large number of oligonucleotides per protein binding event, there is substantial amplification and PSA can be detected at 30 attomolar concentration. Alternatively, a polymerase chain reaction on the oligonucleotide bar codes can boost the sensitivity to 3 attomolar. Comparable clinically accepted conventional assays for detecting the same target have sensitivity limits of approximately 3 picomdar, six orders of magnitude less sensitive than what is observed with this method.
Growth in Human Milk-Fed Very Low Birth Weight Infants Receiving a New Human Milk Fortifier (2000)

This new human milk fortifier had comparable safety to the reference human milk fortifier and promoted faster weight gain and head circumference growth.
Decreased Surface Tension of Upper Airway Mucosal Lining Liquid Increases Upper Airway Patency in Anaesthetised Rabbits (2003)

The obstructive sleep apnoea syndrome (OSA) is a disorder characterised by repetitive closure and re-opening of the upper airway during sleep. Upper airway luminal patency is influenced by a number of factors including: intraluminal air pressure, upper airway dilator muscle activity, surrounding extraluminal tissue pressure, and also surface forces which can potentially act within the liquid layer lining the upper airway. The aim of the present study was to examine the role of upper airway mucosal lining liquid (UAL) surface tension (gamma) in the control of upper airway patency. Upper airway opening (PO) and closing pressures (PC) were measured in 25 adult male, supine, tracheostomised, mechanically ventilated, anaesthetised (sodium pentabarbitone), New Zealand White rabbits before (control) and after instillation of 0.5 ml of either 0.9 % saline (n = 9) or an exogenous surfactant (n = 16; Exosurf Neonatal) into the pharyngeal airway. The gamma of UAL (0.2 microl) was quantified using the 'pull-off' force technique in which gamma is measured as the force required to separate two curved silica discs bridged by the liquid sample. The gamma of UAL decreased after instillation of surfactant from 54.1 +/- 1.7 mN m-1 (control; mean +/- S.E.M.) to 49.2 +/- 2.1 mN m-1 (surfactant; P < 0.04). Compared with control, PO increased significantly (P < 0.04; paired t test, n = 9) from 6.2 +/- 0.9 to 9.6 +/- 1.2 cmH2O with saline, and decreased significantly (P < 0.05, n = 16) from 6.6 +/- 0.4 to 5.5 +/- 0.6 cmH2O with surfactant instillation. Findings tended to be similar for PC. Change in both PO and PC showed a strong positive correlation with the change in gamma of UAL (both r > 0.70, P < 0.001). In conclusion, the patency of the upper airway in rabbits is partially influenced by the gamma of UAL. These findings suggest a role for UAL surface properties in the pathophysiology of OSA.
Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses (2009)

Comprehensive understanding of functional elements in the human genome will require thorough interrogation and comparison of individual human genomes and genomic structures. Such an endeavor will require improvements in the throughputs and costs of DNA sequencing. Next-generation sequencing platforms have impressively low costs and high throughputs but are limited by short read lengths. An immediate and widely recognized solution to this critical limitation is the paired-end tag (PET) sequencing for various applications, collectively called the PET sequencing strategy, in which short and paired tags are extracted from the ends of long DNA fragments for ultra-high-throughput sequencing. The PET sequences can be accurately mapped to the reference genome, thus demarcating the genomic boundaries of PET-represented DNA fragments and revealing the identities of the target DNA elements. PET protocols have been developed for the analyses of transcriptomes, transcription factor binding sites, epigenetic sites such as histone modification sites, and genome structures. The exclusive advantage of the PET technology is its ability to uncover linkages between the two ends of DNA fragments. Using this unique feature, unconventional fusion transcripts, genome structural variations, and even molecular interactions between distant genomic elements can be unraveled by PET analysis. Extensive use of PET data could lead to efficient assembly of individual human genomes, transcriptomes, and interactomes, enabling new biological and clinical insights. With its versatile and powerful nature for DNA analysis, the PET sequencing strategy has a bright future ahead.
From crystal structure prediction to polymorph prediction: interpreting the crystal energy landscape (2008)

Many organic molecules are emerging as having many crystalline forms, including polymorphs and solvates, as more techniques are being used to generate and characterise the organic solid state. The fundamental scientific and industrial interest in controlling crystallisation is inspiring the development of computational methods of predicting which crystal structures are thermodynamically feasible. Sometimes, computing this crystal energy landscape will reveal that a molecule has one way of packing with itself that is sufficiently more favourable than any other so only this crystal structure will be observed. More frequently, there will be many energy minima that are energetically feasible, showing approximately equi-energetic compromises between the various intermolecular interactions allowed by the conformational flexibility. Such cases generally lead to multiple solid forms. At the moment, we usually calculate the lattice energy landscape, an approximation to the real crystal energy landscape at 0 K. Despite its limitations, many studies show that this is a valuable complement to solid form screening, which helps in discovering new structures as well as rationalising the solid forms that are found in experimental searches. The range of factors that can determine which of the thermodynamically feasible crystal structures are observed polymorphs, shows the many further challenges in developing crystal energy landscapes as a tool for control of the organic solid state.
MicroRNA-125a-5p partly regulates the inflammatory response, lipid uptake, and ORP9 expression in oxLDL-stimulated monocyte/macrophages (2009)

MicroRNA-125a-5p may partly provide post-transcriptional regulation of the proinflammatory response, lipid uptake, and expression of ORP9 in oxLDL-stimulated monocyte/macrophages.
Fast Time Sequence Indexing for Arbitrary Lp Norms (2018)

Fast indexing in time sequence databases for similarity searching has attracted a lot of research recently. Most of the proposals, however, typically centered around the Euclidean distance and its derivatives. We examine the problem of multimodal similarity search in which users can choose the best one from multiple similarity models for their needs.
The use of synthetic peptide combinatorial libraries for the identification of bioactive peptides. (1992)

The systematic preparation of synthetic peptide combinatorial libraries (SPCLs), each composed of tens of millions of peptides that can be screened in existing diagnostically or pharmacologically relevant in vitro assay systems, is reviewed. The identification of optimal peptide sequences has been achieved through the screening in solution of SPCLs, each element of which is composed of more than 100,000 nonsupport-bound peptides in equimolar representation, along with an iterative synthesis and screening process. Examples are presented in which an SPCL, composed in total of 52,128,400 acetylated hexa-peptides, is used along with an iterative selection process to precisely identify the antigenic determinant of a peptide recognized by a monoclonal antibody using competitive enzyme-linked immunosorbent assay. This same library was also used to develop highly potent antimicrobial peptides in bacterial growth inhibition assays. A separate non-acetylated SPCL was used to screen and identify high affinity peptide ligands using an opiate radio-receptor binding assay.
Therapeutic Value of Small Molecule Inhibitor to Plasminogen Activator Inhibitor–1 for Lung Fibrosis (2011)

Fibrosis is a final stage of many lung diseases, with no effective treatment. Plasminogen activator inhibitor-1 (PAI-1), a primary inhibitor of tissue-type and urokinase-type plasminogen activators (tPA and uPA, respectively), plays a critical role in the development of fibrosis. In this study, we explored the therapeutic potential of an orally effective small molecule PAI-1 inhibitor, TM5275, in a model of lung fibrosis induced by transforming growth factor-β1 (TGF-β1), the most potent and ubiquitous profibrogenic cytokine, and in human lung fibroblasts (CCL-210 cells). The results show that an intranasal instillation of AdTGF-β1(223/225), an adenovirus expressing constitutively active TGF-β1, increased the expression of PAI-1 and induced fibrosis in murine lung tissue. On the other hand, treating mice with 40 mg/kg of TM5275 for 10 days, starting 4 days after the instillation of AdTGF-β1(223/225), restored the activities of uPA and tPA and almost completely blocked TGF-β1-induced lung fibrosis, as shown by collagen staining, Western blotting, and the measurement of hydroxyproline. No loss of body weight was evident under these treatment conditions with TM5275. Furthermore, we show that TM5275 induced apoptosis in both myofibroblasts (TGF-β1-treated) and naive (TGF-β1-untreated) human lung fibroblasts, and this apoptosis was associated with the activation of caspase-3/7, the induction of p53, and the inhibition of α-smooth muscle actin, fibronectin, and PAI-1 expression. Such an inhibition of fibrotic responses by TM5275 occurred even in cells pretreated with TGF-β1 for 6 hours. Together, the results suggest that TM5275 is a relatively safe and potent antifibrotic agent, with therapeutic potential in fibrotic lung disease.
The cardiotonic effect of the crude ethanolic extract of Nerium oleander in the isolated guinea pig hearts. (2003)

Cardiovascular diseases are increasingly becoming one of the leading diseases causing morbidity and mortality in Uganda. Ethnographic evidence suggests that these diseases are often first managed by indigenous and related herbs before patients are referred for allopathic forms of management. One such herb of interest is Nerium oleander. Therefore the crude ethanolic extracts of the dried leaves of this herb were tested against the following parameters in the isolated guinea pig hearts: force of contraction, heart rate and cardiac flow. The extracts brought about dose-dependent increases in all these parameters from their baseline readings. Compared with graded doses of digoxin the effects closely mirrored the activities in a dose dependent manner. At the mechanism of action level, it would appear the extract works in the same as digoxin since their dose-contraction-response curves are parallel. This finding would tend to provide a strong rationale for the herb's traditional use in cardiovascular illness.