gebhart/patrepeval huggingface dataset:
Human CD16+ and CD16– monocyte subsets display unique effector properties in inflammatory conditions in vivo (2011)

Two major subsets of human Mo are identified based on CD14 and CD16 expression: the classical CD16(-) Mo and the minor CD14(+)CD16(+) Mo. In vitro studies suggested distinct function and differentiation potential for each cell population. However, the in vivo relevance of these findings remains unclear. To evaluate the development and function of human Mo in an in vivo model, we transferred both Mo subpopulations into the peritoneum of immunocompromised mice in homeostatic or inflammatory conditions. Inflammation was induced with soluble LPS or particulate zymosan. CD16(+) were more phagocytic and produced higher amounts of TNF and IL-6 than CD16(-) Mo early after transfer with zymosan. They also produced higher levels of β2-defensin in any condition evaluated, which could represent a new marker for this subpopulation. In contrast, differentiating CD16(-) Mo (24 h after transfer) acquired greater APC capacity in LPS-induced peritonitis, whereas none of the Mo subsets attained this ability with zymosan. CX(3)CL1 supported the survival of both Mo subsets in vivo. Similar Mo subpopulations were present in human peritonitis. These results support the idea of specialized roles of the Mo subset, where CD16(+) might act in an immediate innate immune response, whereas CD16(-) could have a major role as APCs.
Determination of physiological levels of glucose in an aqueous matrix with digitally filtered Fourier transform near-infrared spectra (1990)

A procedure is described for the measurement of clinically relevant concentrations of glucose in aqueous solutions with near-infrared (NIR) absorbance spectroscopy. A glucose band centered at 4400 cm-1 is used for this analysis. NIR spectra are collected over the frequency range 5000-4000 cm-1 with a Fourier transform spectrometer. A narrow-band-pass optical interference filter is placed in the optical path of the spectrometer to eliminate light outside this restricted range. This configuration provides a 2.9-fold reduction in spectral noise by utilizing the dynamic range of the detector solely for light transmitted through the filter. In addition, a novel spectral processing scheme is described for extracting glucose concentration information from the resulting absorbance spectra. The key component of this scheme is a digital Fourier filter that removes both high-frequency noise and low-frequency base-line variations from the spectra. Numerical optimization procedures are used to identify the best location and width of a Gaussian-shaped frequency response function for this Fourier filter. A dynamic area calculation, coupled with a simple linear base-line correction, provides an integrated area from the processed spectra that is linearly related to glucose concentrations over the range 1-20 mM. The linear calibration model accurately predicted glucose levels in a series of test solutions with an overall mean percent error of 2.5%. Based on the uncertainty in the parameters defining the calibration model and the variability of the magnitudes of the integrated areas, an overall uncertainty of 7.8% was estimated for predicted glucose concentrations.
Are Migraineurs at Increased Risk of Adverse Drug Responses?: A Meta-Analytic Comparison of Topiramate-Related Adverse Drug Reactions in Epilepsy and Migraine (2008)

To compare adverse drug reactions (ADRs) to topiramate in patients with migraine and patients with epilepsy, we systematically reviewed all published randomized controlled trials (RCTs) that compare topiramate monotherapy in epilepsy and migraine. We included four epilepsy RCTs (N = 1,179 patients; vs. active comparators) and six migraine RCTs (N = 1,723 patients; vs. placebo). Behavioral ADRs and headache were found only in the case of epilepsy, whereas cognitive complaints and alteration of taste were found only in the case of migraine. The risk ratios (RRs) for paresthesia in migraine vs. epilepsy trials were 2.5 (99% confidence interval (CI): 1.66-3.77) for 50 mg, 2.7 (99% CI: 1.80-3.97) for 100 mg, and 3.0 (99% CI: 1.95-4.56) for 200 mg. For ADR-related dropouts, the RR was 2.5 (95% CI: 2.03-2.98) for 50 mg but no different for the other doses. We conclude that when treated with the same doses of topiramate, migraineurs show different ADRs than patients with epilepsy and are more likely to drop out because of ADRs.
The theory and practical application of adjuvants (1995)

Partial table of contents: Freund-Type Mineral Oil Adjuvant Emulsions (D. Stewart-Tull). Aluminium Adjuvants (E. Lindblad). Synthetic Lipoid Compounds as Antigen-Specific Immunostimulators for Improving the Efficacy of Killed-Virus Vaccines (D. Katz, et al.). Copolymer Adjuvants and Titermax (R. Hunter, et al.). Saponins (J. Campbell). Immune Stimulating Complexes with Quil A (K. Dalsgaard, et al.). Liposomes as Immunological Adjuvants (G. Gregoriadis). Syntex Adjuvant Formulation (N. Byars & A. Allison). Muramyl Dipeptides with Special Attention to TNF (M. Parant). Lipid A (M. Nakano & M. Matsuura). Adjuvants in AIDS Vaccines (R. Bomford). Index.
CD8 CTL from Genital Herpes Simplex Lesions: Recognition of Viral Tegument and Immediate Early Proteins and Lysis of Infected Cutaneous Cells (2001)

HSV-2 causes chronic infections. CD8 CTL may play several protective roles, and stimulation of a CD8 response is a rational element of vaccine design for this pathogen. The viral Ags recognized by CD8 T cells are largely unknown. It has been hypothesized that HSV inhibition of TAP may favor recognition of virion input proteins or viral immediate early proteins. We tested this prediction using HSV-specific CD8 CTL clones obtained from genital HSV-2 lesions. Drug and replication block experiments were consistent with specificity for the above-named classes of viral proteins. Fine specificity was determined by expression cloning using molecular libraries of viral DNA, and peptide epitopes recognized at nanomolar concentrations were identified. Three of four clones recognized the viral tegument proteins encoded by genes UL47 and UL49. These proteins are transferred into the cytoplasm on virus entry. Processing of the tegument Ag-derived epitopes was TAP dependent. The tegument-specific CTL were able to lyse HLA class I-appropriate fibroblasts after short times of infection. Lysis of keratinocytes required longer infection and pretreatment with IFN-gamma. Another clone recognized an immediate early protein, ICP0. Lymphocytes specific for these lesion-defined epitopes could be reactivated from the PBMC of additional subjects. These data are consistent with an influence of HSV immune evasion genes upon the selection of proteins recognized by CD8 CTL in lesions. Tegument proteins, identified for the first time as Ags recognized by HSV-specific CD8 CTL, are rational candidate vaccine compounds.
Colonic Drug Targeting (1998)

Specific targeting of drugs to the colon is recognized to have several therapeutic advantages. Drugs which are destroyed by the stomach acid and/or metabolized by pancreatic enzymes are slightly affected in the colon, and sustained colonic release of drugs can be useful in the treatment of nocturnal asthma, angina and arthritis. Treatment of colonic diseases such as ulcerative colitis, colorectal cancer and Crohn's disease is more effective with direct delivery of drugs to the affected area. Likewise, colonic delivery of vermicides and colonic diagnostic agents require smaller doses. This article is aimed at providing insight into the design considerations and evaluation of colonic drug delivery systems. For this purpose, the anatomy and physiology of the lower gastrointestinal tract are surveyed. Furthermore, the biopharmaceutical aspects are considered in relation to drug absorption in the colon and hence various approaches to colon-specific drug delivery are discussed.
Structure, expression, and mutation of the hypoxanthine phosphoribosyltransferase gene. (1984)

The wild-type mouse hypoxanthine phosphoribosyltransferase (HPRT; IMP:pyrophosphate phosphoribosyltransferase, EC 2.4.2.8) gene has been isolated from genomic libraries and its structure has been determined. This X chromosome-linked gene is greater than 33 kilobases long and is split into nine exons. All the exon sequences have been determined, and a single-base substitution in the HPRT cDNA coding sequence from a mouse neuroblastoma cell line that overproduces a mutant HPRT protein has been identified. The 5' end of the gene has been defined, both by nuclease S1 protection and primer extension studies and by a functional assay in which an HPRT minigene, capable of expression in cultured cells, was created by ligating the 5' end of the gene onto wild-type human HPRT cDNA. Sequences normally associated with eukaryotic promoters are not present in the immediate 5'-flanking region of the HPRT gene, which is instead highly G+C rich. This observation is discussed in relation to the possible link between DNA methylation and X-chromosome inactivation.
A Secreted Tumor-Suppressor, mac25, with Activin-Binding Activity (2000)

mac25 exhibits homology to insulin-like growth factor-binding proteins (IGF-BPs) and to fibroblast growth factor receptor. The multi-functional nature of mac25 protein may be important for growth-suppression and/or cellular senescence.
Molecular and cytogenetic analysis of chromosome 7 in uterine leiomyoma (1994)

Uterine leiomyomas are benign tumors which arise clonally from smooth muscle cells of the myometrium. Cytogenetic studies of uterine leiomyomas revealed that about 50% have chromosome abnormalities and that deletion 7q is a common finding. This observation suggest the possible location of a growth suppressor gene within the 7q21-q22 region. Molecular genetic analysis of cytogenetically normal tumors has frequently revealed somatic loss of specific tumor suppressor genes detected by loss of heterozygosity in the critical region (RB1 in retinoblastoma and WT1 in Wilms tumor). To test the hypothesis that chromosome region 7q21-q22 contains a growth suppressor gene involved in the development of leiomyomas, we tested 67 leiomyomas for allelic loss of 7q markers spanning the cytogenetically defined critical region. Nineteen tumors with cytogenetically defined 7q deletion and 48 tumors without cytogenetically visible 7q deletion were examined for allelic loss of loci D7S487, D7S440, D7S492, D7S518, D7S471, D7S466 and D7S530. Loss of heterozygosity for one or more of these loci was observed in 14/19 (73.7%) of tumors with deletion 7q and no evidence of allelic loss was observed in tumors without cytogenetic deletion. The tumors with deletion 7q but no loss of 7q21-q22 markers were tumors which were mosaics with onlymore » a minority of cells showing chromosome 7q deletion. The critical region of loss is defined by markers D7S518 and D7S471, each showing loss in 56% of informative cases. These markers define a 10cM region of 7q21.2-q22 consistent with the cytogenetically defined smallest region of overlap. These markers exclude loss of the MET oncogene locus and WNT1, the murine mammary tumor virus integration site, from the critical region. These results define a region that is consistently lost in leiomyomas with abnormalities in chromosome 7q and may define the location of a gene involved in the development of a subset of leiomyomas.« less
Heterogeneity of tumor cells from a single mouse mammary tumor. (1978)

By the use of a variety of cell culture and separation methods, four cell lines were isolated from a single autochthonous BALB/cfC3H mammary tumor. These lines differ markedly from each other in culture morphology, various in vitro growth properties, expression of murine mammary tumor virus antigen, and karyotype, yet all four lines are tumorigenic in normal, syngeneic hosts, yielding tumors of generally similar histology, although distinct from the original neoplasm. Three of the four lines have been cloned from soft agar. The clones exhibit the same growth properties as the lines from which they were derived. Karyotypic analysis of the parent tumor revealed the presence of cells with heterogeneous numbers of chromosomes similar to those seen in the isolated lines, suggesting both the presence of these distinct cell types in the original neoplasm and a genetic origin of the diversity.
Sustained Neurog3 expression in hormone-expressing islet cells is required for endocrine maturation and function (2009)

Neurog3 (Neurogenin 3 or Ngn3) is both necessary and sufficient to induce endocrine islet cell differentiation from embryonic pancreatic progenitors. Since robust Neurog3 expression has not been detected in hormone-expressing cells, Neurog3 is used as an endocrine progenitor marker and regarded as dispensable for the function of differentiated islet cells. Here we used 3 independent lines of Neurog3 knock-in reporter mice and mRNA/protein-based assays to examine Neurog3 expression in hormone-expressing islet cells. Neurog3 mRNA and protein are detected in hormone-producing cells at both embryonic and adult stages. Significantly, inactivating Neurog3 in insulin-expressing beta cells at embryonic stages or in Pdx1-expressing islet cells in adults impairs endocrine function, a phenotype that is accompanied by reduced expression of several Neurog3 target genes that are essential for islet cell differentiation, maturation, and function. These findings demonstrate that Neurog3 is required not only for initiating endocrine cell differentiation, but also for promoting islet cell maturation and maintaining islet function.
Gene-environment and gene-gene interaction studies in the molecular genetic analysis of asthma and atopy. (1999)

Asthma is a complex trait for which genetic predisposition is fundamental in disease aetiology, but poorly understood. Unravelling the genetic aetiology is complicated by the tremendous influence of the environment over disease expression. For this reason, asthma is multifactorial, in that disease expression is influenced by interactions between multiple major and minor genes, and modulated by interacting non-genetic factors (e.g. environment). 'Parent of origin' effects may be both genetic and environmental in aetiology, and have been observed in a number of population studies on asthma. The primary focus of this review is to evaluate the current approaches used in identifying the interrelationship between (1) certain environmental factors (e.g. allergen exposure, maternal inheritance) and genetic susceptibility to asthma and its associated phenotypes; and (2) candidate genes in chromosomal regions that have been linked to asthma and atopy in ongoing, molecular genetics studies.
Accurate computational prediction of the transcribed strand of CRISPR non-coding RNAs (2014)

The Perl source code is freely available from http://bioanalysis.otago.ac.nz/CRISPRDirection.
Methylation ofO6-methylguanine-DNA methyltransferase gene is associated significantly withK-ras mutation, lymph node invasion, tumor staging, and disease free survival in patients with gastric carcinoma (2001)

MGMT-promoter methylation in patients with gastric carcinoma was associated significantly with point mutations of K-ras at codons 12 and 13, lymph node invasion, tumor stage, and disease free survival. These associations indicate a significant role of MGMT methylation during gastric carcinogenesis.
Multiple Sclerosis (2003)

Myelin basic protein (MBP) represents a candidate autoantigen in multiple sclerosis (MS). We isolated MBP from normal and MS human white matter and purified six components (charge isomers) to compare the post-translational modifications on each. The sites and extent of methylation, deimination, and phosphorylation were documented for all tryptic peptides by mass spectrometry. We found that mono and dimethylated arginine 107 was increased in MS samples; deimination of arginine occurred at a number of sites and was elevated in MS; phosphorylation was observed in 10 peptides in normal samples but was greatly reduced or absent in most peptides from MS samples. Data obtained with MBP isolated from fresh brain obtained from a spontaneously demyelinating mouse model supported the view that the changes observed in human brain were probably related to pathogenesis of demyelination, i.e. we found decreased phosphorylation and decreased amounts of glycogen synthesis kinase in brain homogenates using specific antibodies. This study represents the first to define post-translational modifications in demyelinating disease and suggest an important role in pathogenesis.
AVEREL: A Randomized Phase III Trial Evaluating Bevacizumab in Combination With Docetaxel and Trastuzumab As First-Line Therapy for HER2-Positive Locally Recurrent/Metastatic Breast Cancer (2013)

PURPOSE The AVEREL trial [A Study of Avastin (Bevacizumab) in Combination With Herceptin (Trastuzumab)/Docetaxel in Patients With HER2-Positive Metastatic Breast Cancer] evaluated first-line bevacizumab-containing therapy for human epidermal growth factor receptor 2 (HER2) -positive locally recurrent/metastatic breast cancer (LR/MBC). PATIENTS AND METHODS Patients with measurable/evaluable HER2-positive LR/MBC who had not received trastuzumab or chemotherapy for LR/MBC were stratified by prior adjuvant trastuzumab, prior (neo)adjuvant taxane, hormone receptor status, and measurable disease and were randomly assigned to receive docetaxel 100 mg/m(2) plus trastuzumab 8 mg/kg loading dose followed by 6 mg/kg either with bevacizumab 15 mg/kg or without bevacizumab, all administered every 3 weeks. The primary end point was progression-free survival (PFS). Additional end points included overall survival, response rate (RR), safety, quality of life, and translational research. Results Baseline characteristics of the 424 patients were balanced between treatment arms. Most patients had visceral metastases, 43% had a disease-free interval less than 12 months, and 85% had measurable disease. Median follow-up was 26 months. The hazard ratio for investigator-assessed PFS was 0.82 (95% CI, 0.65 to 1.02; P = .0775; median PFS, 13.7 v 16.5 months in the non-bevacizumab and bevacizumab arms, respectively; PFS events in 72%). The Independent Review Committee-assessed PFS hazard ratio was 0.72 (95% CI, 0.54 to 0.94; P = .0162; median PFS, 13.9 v 16.8 months, respectively; PFS events in 53%). The RR was 70% versus 74%, respectively (P = .3492). Grade ≥ 3 febrile neutropenia and hypertension were more common with bevacizumab-containing therapy. High baseline plasma vascular endothelial growth factor A (VEGF-A) concentrations were associated with greater bevacizumab benefit (not statistically significant). CONCLUSION Combining bevacizumab with docetaxel and trastuzumab did not significantly improve investigator-assessed PFS. The potential predictive value of plasma VEGF-A is consistent with findings in HER2-negative LR/MBC, warranting prospective evaluation.
Mesenchymal Stem Cells and Their Potential as Cardiac Therapeutics (2004)

Mesenchymal stem cells (MSCs) represent a stem cell population present in adult tissues that can be isolated, expanded in culture, and characterized in vitro and in vivo. MSCs differentiate readily into chondrocytes, adipocytes, osteocytes, and they can support hematopoietic stem cells or embryonic stem cells in culture. Evidence suggests MSCs can also express phenotypic characteristics of endothelial, neural, smooth muscle, skeletal myoblasts, and cardiac myocyte cells. When introduced into the infarcted heart, MSCs prevent deleterious remodeling and improve recovery, although further understanding of MSC differentiation in the cardiac scar tissue is still needed. MSCs have been injected directly into the infarct, or they have been administered intravenously and seen to home to the site of injury. Examination of the interaction of allogeneic MSCs with cells of the immune system indicates little rejection by T cells. Persistence of allogeneic MSCs in vivo suggests their potential "off the shelf" therapeutic use for multiple recipients. Clinical use of cultured human MSCs (hMSCs) has begun for cancer patients, and recipients have received autologous or allogeneic MSCs. Research continues to support the desirable traits of MSCs for development of cellular therapeutics for many tissues, including the cardiovascular system. In summary, hMSCs isolated from adult bone marrow provide an excellent model for development of stem cell therapeutics, and their potential use in the cardiovascular system is currently under investigation in the laboratory and clinical settings.
Defect-mediated ferromagnetism in insulating Co-doped anataseTiO2thin films (2008)

The nature of the defect responsible for room-temperature ferromagnetism in Co-doped anatase ${\text{TiO}}_{2}$ has remained elusive. Here we report atomic-resolution $Z$-contrast images of epitaxially grown ${\text{Co}}_{0.03}:{\text{TiO}}_{2}$ films showing that Co atoms are dispersed and occupy preferred interstitial sites. Density-functional calculations found that these sites are the lowest-energy configuration of Co in anatase and that O vacancies $({\text{V}}_{\text{O}})$, introduced by annealing, anchor the Co atoms into Co-${\text{Ti}}^{+3}{\text{-V}}_{\text{O}}$ complexes. The calculated magnetic moment is in agreement with our measured value and the calculated Co x-ray absorption spectrum is in agreement with data published in the literature.
Antihemophilic factor (recombinant) plasma/albumin-free method for the management and prevention of bleeding episodes in patients with hemophilia A (2009)

Hemophilia is a rare genetic bleeding disorder that, if not adequately controlled, is associated with life-threatening bleeding events and serious and costly complications, primarily from joint damage. The advent of effective clotting factor replacement therapy for patients with hemophilia is considered one of the foremost medical advances of the 20th century. The last 3 decades of experience in hemophilia care have witnessed the effectiveness of the care of patients with hemophilia within specialized comprehensive care centers, advances in factor replacement therapies, the benefits of prophylaxis over on-demand replacement therapy, and the role of aggressive management of joint disease to prevent dysfunction. Ongoing challenges, including the management of inhibitors to factor therapies and the consequences of thousands of patients with hemophilia becoming infected with human immunodeficiency virus and hepatitis C virus in the 1980s from contaminated plasma-derived factor concentrates, have highlighted the need for vigilance with respect to clotting factor product safety, access to care, and a full complement of choice of factor replacement therapies. Advate((R)) (antihemophilic factor [recombinant] plasma/albumin-free method [rAHF-PFM]) is the first recombinant factor VIII therapy manufactured without human or animal protein additives to eliminate the risk of pathogen transmission that could be carried by these additives. Preclinical studies established bioequivalence with recombinant antihemophilic factor (Recombinate((R))), a product with 16 years of clinical experience. Currently licensed in 44 countries worldwide, rAHF-PFM has over 7 years of clinical research within 5 global studies supporting its safety and efficacy in the treatment of patients with hemophilia A.