gebhart/patrepeval huggingface dataset:
Gene transfer into hematopoietic stem cells (1991)

The ability to reliably transfer genes into hematopoietic stem cells with long-term repopulating potential and to selectively express such genes would allow genetic therapy for diseases such as sickle cell anemia and immunologic deficiencies due to T-cell defects, including acquired immune deficiency syndrome (AIDS). Understanding the biology of the hematopoietic stem cell is a key element in realizing the full therapeutic potential of gene insertion strategies. Current techniques have efficiency rates of gene insertion of approximately 10% to 20% into murine stem cells and 1% to 5% into primate stem cells. Many challenges, some biologic and some logistic, remain before gene transfer protocols that are successful in the mouse model can be extended to humans.
Mammalian Cell Biotechnology in Protein Production (1997)

Part 1 Genetic manipulation of mammalian cells: Heterologous expression of genes in mammalian cells, Hauser Permanent gene expression in mammalian cells - gene transfer and selection, Schlokar Vector for gene transfer and expression in animal cells, Sandig et al Aspects of gene transfer and gene amplification in recombinant mammalian cells, Wurm Isolation of recombinant cell clones exhibiting high-level expression of the introduced gene, Wirth Genetic engineering of antibodies and derivatives from mammalian cells,Weidle Safety evaluation of products derived from mammalian cell lines, Onions. Part 2 Biological aspects of animal cells: Metabolic control of animal cell culture processes, Wagner Glycosylation - a post-translational modification, Savage. Part 3 Cell cultivation technology: Bioreactors designed for animal cells, Tokashiki, Yokoyama Hydrodinamic properties in bioreactors, Chattopadhyay et al Kinetics and simulation of animal cell processes, Goergen et al On-line and Off-line process analysis, Scheper et al. Part 4 Down-stream processing: Principles of product extraction from cell culture and purification for pharmaceutical proteins, Walter, Allgaier.
Construction of Mouse A9 Clones Containing a Single Human Chromosome Tagged with Neomycin‐resistance Gene via Microcell Fusion (1989)

Normal human fibroblasts (MRC-5 or NTI-4) were transfected with pSV2-neo plasmid DNA. Fifty G418-resistant fibroblast clones were isolated and independently fused to mouse A9 cells. The cell hybrids were selected and isolated in the medium containing G418 plus ouabain. Since micronuclei were more efficiently induced in these hybrids compared to parental human fibroblasts by colcemid treatment, the transfer of neo-tagged human chromosomes in the hybrids to mouse A9 cells was performed via microcell fusion. Two hundred A9 microcell hybrids were isolated and karyotyped. Among them, thirteen microcell clones, each containing a single human chromosome 1, 2, 5, 6, 7, 8, 10, 11, 12, 15, 18, 19 or 20 were established. Isozyme analyses conformed the presence of each human chromosome in these A9 microcell clones. The results of Southern blot and chromosomal in situ hybridization analyses indicate that the human chromosomes in these clones were tagged with pSV2-neo plasmid DNA.
l -Arginine Supplementation in Peripheral Arterial Disease (2007)

In patients with PAD, long-term administration of L-arginine does not increase nitric oxide synthesis or improve vascular reactivity. Furthermore, the expected placebo effect observed in studies of functional capacity was attenuated in the L-arginine-treated group. As opposed to its short-term administration, long-term administration of L-arginine is not useful in patients with intermittent claudication and PAD.
A novel inhibitor of the alternative pathway of complement reverses inflammation and bone destruction in experimental arthritis (2007)

Complement is an important component of the innate and adaptive immune response, yet complement split products generated through activation of each of the three complement pathways (classical, alternative, and lectin) can cause inflammation and tissue destruction. Previous studies have shown that complement activation through the alternative, but not classical, pathway is required to initiate antibody-induced arthritis in mice, but it is unclear if the alternative pathway (AP) plays a role in established disease. Previously, we have shown that human complement receptor of the immunoglobulin superfamily (CRIg) is a selective inhibitor of the AP of complement. Here, we present the crystal structure of murine CRIg and, using mutants, provide evidence that the structural requirements for inhibition of the AP are conserved in human and mouse. A soluble form of CRIg reversed inflammation and bone loss in two experimental models of arthritis by inhibiting the AP of complement in the joint. Our data indicate that the AP of complement is not only required for disease induction, but also disease progression. The extracellular domain of CRIg thus provides a novel tool to study the effects of inhibiting the AP of complement in established disease and constitutes a promising therapeutic with selectivity for a single complement pathway.
Adult Mouse Myometrial Label-Retaining Cells Divide in Response to Gonadotropin Stimulation (2007)

Conditional deletion of beta-catenin in the Müllerian duct mesenchyme results in a degenerative uterus characterized by replacement of the myometrial smooth muscle with adipose tissue. We hypothesized that the mouse myometrium houses somatic smooth muscle progenitor cells that are hormonally responsive and necessary for remodeling and regeneration during estrous cycling and pregnancy. We surmise that the phenotype observed in beta-catenin conditionally deleted mice is the result of dysregulation of these progenitor cells. The objective of this study was to identify the mouse myometrial smooth muscle progenitor cell and its niche, define the surface marker phenotype, and show a functional response of these cells to normal myometrial cycling. Uteri were labeled with 5-bromo-2'-deoxyuridine (BrdU) and chased for up to 14 weeks. Myometrial label-retaining cells (LRCs) were observed in the myometrium and stroma throughout the chase period. After 12 weeks, phenotypic analysis of the LRCs by immunofluorescence demonstrated that the majority of LRCs colocalized with alpha-smooth muscle actin, estrogen receptor-alpha, and beta-catenin. Flow cytometry of myometrial cells identified a myometrial Hoechst 33342 effluxing "side population" that expresses MISRII-Cre-driven YFP. Functional response of LRCs was investigated by human chorionic gonadotropin stimulation of week 12 chase mice and demonstrated sequential proliferation of LRCs in the endometrial stroma, followed by the myometrium. These results suggest that conventional myometrial regeneration and repair is executed by hormonally responsive stem or progenitor cells derived from the Müllerian duct mesenchyme. Disclosure of potential conflicts of interest is found at the end of this article.
Myocardial Phosphocreatine-to-ATP Ratio Is a Predictor of Mortality in Patients With Dilated Cardiomyopathy (1997)

The myocardial phosphocreatine-to-ATP ratio, measured noninvasively with 31P-MR spectroscopy, is a predictor of both total and cardiovascular mortality in patients with dilated cardiomyopathy.
Addition of poly(A) and poly(A)-rich tails during RNA degradation in the cytoplasm of human cells (2010)

Polyadenylation of RNA is a posttranscriptional modification that can play two somewhat opposite roles: stable polyadenylation of RNA encoded in the nuclear genomes of eukaryote cells contributes to nuclear export, translation initiation, and possibly transcript longevity as well. Conversely, transient polyadenylation targets RNA molecules to rapid exonucleolytic degradation. The latter role has been shown to take place in prokaryotes and organelles, as well as the nucleus of eukaryotic cells. Here we present evidence of hetero- and homopolymeric adenylation of truncated RNA molecules within the cytoplasm of human cells. RNAi-mediated silencing of the major RNA decay machinery of the cell resulted in the accumulation of these polyadenylated RNA fragments, indicating that they are degradation intermediates. Together, these results suggest that a mechanism of RNA decay, involving transient polyadenylation, is present in the cytoplasm of human cells.
Immunological evidence for interactions between the first, second, and fifth conserved domains of the gp120 surface glycoprotein of human immunodeficiency virus type 1 (1994)

We have used a combination of genetic and immunological techniques to explore how amino acid substitutions in the second conserved (C2) domain of gp120 from human immunodeficiency virus type 1 (HIV-1) affect the conformation of the protein. It was reported previously (R. L. Willey, E. K. Ross, A. J. Buckler-White, T. S. Theodore, and M. A. Martin. J. Viol. 63:3595-3600, 1989) that an asparagine-glutamine (N/Q) substitution at C2 residue 267 of HIV-1 NL4/3 reduced virus infectivity, but that infectivity was restored by a compensatory amino acid change (serine-glutamine; S/N) at residue 128 in the C1 domain. Here we show that the 267 N/Q substitution causes the abnormal exposure of a segment of C1 spanning residues 80 to 120, which compromises the integrity of the CD4-binding site. The reversion substitution at residue 128 restores the normal conformation of the C1 domain and recreates a high-affinity CD4-binding site. The gp120 structural perturbation caused by changes in C2 extends also to the C5 domain, and we show by immunological analysis that there is a close association between areas of the C1 and C5 domains. This association might be important for forming a complex binding site for gp41 (E. Helseth, U. Olshevsky, C. Furman, and J. Sodroski. J. Virol. 65:2119-2123, 1991). Segments of the C1 and C2 domains are predicted to form amphipathic alpha helices. We suggest that these helices might be packed together in the core of the folded gp120 molecule, that the 267 N/Q substitution disrupts this interdomain association, and that the 128 S/N reversion substitution restores it.
Isolation and molecular characterization of spontaneously occurring cytolysin-negative mutants of Actinobacillus pleuropneumoniae serotype 7 (1991)

Actinobacillus pleuropneumoniae serotype 7 strains are shown to spontaneously lose cytolytic activity with a frequency of approximately 10(-4). The phenotypic change is associated with the loss of approximately 8.5 kbp of chromosomal DNA. A genomic fragment encoding the cytolysin and its flanking sequences was cloned and characterized. Also, the corresponding truncated fragment was cloned from a spontaneous mutant. Comparison of the two clones allowed the definition of the excision site. The ends of the excised fragment are composed of 1,201 bp long direct identical repeats, possibly facilitating the genotypic change by homologous recombination. In accordance with this hypothesis, one repeat is conserved in the spontaneous mutant. Each repeat contains one open reading frame preceded by a Shine-Dalgarno consensus sequence, and the ends of each repeat contain 26-bp complementary sequences with four mismatches.
A micro-particle positioning technique combining an ultrasonic manipulator and a microgripper (2006)

The acoustic radiation force acts on particles suspended in a fluid in which acoustic waves are present. It can be used to establish a force field throughout the fluid volume capable of positioning the particles in predictable locations. Here, a device is developed which positions the particles in a single line by the sequential use of two excitation frequencies which have been identified by a finite element model of the system. The device is designed such that at one end there is an opening which allows the fingers of a microgripper to enter the fluid chamber. Hence the gripper can be used to remove the last particle in the line. The high accuracy of the positioning of the particles prior to gripping means that the microgripper needs just to return to a fixed position in order to remove subsequent particles. Furthermore, the effects of the microgripper fingers entering the fluid volume whilst the ultrasound field is excited are examined. One result being the release of a particle stuck to a gripper finger. It is believed that this combination of techniques allows for considerable scope in the automation of microgripping procedures.
First Hexanuclear UIV and ThIV Formate Complexes – Structure and Stability Range in Aqueous Solution (2009)

Abstract The actinide(IV) hexanuclear [M 6 (μ 3 ‐O) 4 (μ 3 ‐OH) 4 (HCOO) 12 (L T ) 6 ] complexes were prepared (L T = H 2 O or CH 3 OH). Their structures were investigated by single‐crystal X‐ray analysis and XAFS spectroscopy. HCOO – acts as a bridging ligand, which prevents the formation of polynuclear hydrolysis species like U IV hydrous oxide colloids at least up to pH = 3.25, and stabilizes the nanosized clusters in solution. The charge of the hexamer is balanced by the O/OH ratio of the μ 3 ‐bridges.(© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2009)
Synthesis and Antimicrobial Evaluation of TAN-1057A/B Analogs. (1998)

TAN-1057A-D, dipeptides isolated from bacteria Flexibacter sp. PK-74 and PK-176, are new antibiotics with potent antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA). We describe, in detail, the synthesis of several TAN-1057A/B analogs by a convergent route featuring a new method to construct the cyclic amidinourea functional group. The biological activity of these substances against methicillin-resistant Staphylococcus aureus (MRSA) is reported.
Gut microbial diversity in health and disease: experience of healthy Indian subjects, and colon carcinoma and inflammatory bowel disease patients (2017)

<b>Background</b>: The intestinal microbiota, through complex interactions with the gut mucosa, play a key role in the pathogenesis of colon carcinoma and inflammatory bowel disease (IBD). The disease condition and dietary habits both influence gut microbial diversity. <b>Objective</b>: The aim of this study was to assess the gut microbial profile of healthy subjects and patients with colon carcinoma and IBD. Healthy subjects included 'Indian vegetarians/lactovegetarians', who eat plant produce, milk and milk products, and 'Indian non-vegetarians', who eat plant produce, milk and milk products, certain meats and fish, and the eggs of certain birds and fish. 'Indian vegetarians' are different from 'vegans', who do not eat any foods derived wholly or partly from animals, including milk products. <b>Design</b>: Stool samples were collected from healthy Indian vegetarians/lactovegetarians and non-vegetarians, and colon cancer and IBD patients. Clonal libraries of 16S ribosomal DNA (rDNA) of bacteria were created from each sample. Clones were sequenced from one representative sample of each group. Approximately 500 white colonies were picked at random from each sample and 100 colonies were sequenced after amplified rDNA restriction analysis. <b>Results</b>: The dominant phylum from the healthy vegetarian was Firmicutes (34%), followed by Bacteroidetes (15%). The balance was reversed in the healthy non-vegetarian (Bacteroidetes 84%, Firmicutes 4%; ratio 21:1). The colon cancer and IBD patients had higher percentages of Bacteroidetes (55% in both) than Firmicutes (26% and 12%, respectively) but lower Bacteroidetes:Firmicutes ratios (3.8:1 and 2.4:1, respectively) than the healthy non-vegetarian. Bacterial phyla of Verrucomicrobiota and Actinobacteria were detected in 23% and 5% of IBD and colon patients, respectively. <b>Conclusions</b>: Ribosomal Database Project profiling of gut flora in this study population showed remarkable differences, with unique diversity attributed to different diets and disease conditions.
Plasma deposition and etching of diamond‐like carbon films (1991)

Abstract Diamond‐like carbon films have been deposited from ternary mixtures of butadiene, hydrogen and argon in a parallel plate plasma reactor at constant pressure and power. These films have been etched in O 2 and CF 4 /O 2 plasma discharges. A new linear relationship between the composition of the deposition gas mixture and a dimensionless number (E N ) defined in terms of etch and deposition rates and the bias voltage during deposition has been derived. E N is a function of the ion flux during deposition. Electron‐impact ionization processes are considered for relating the ion flux to the feed gas composition and ionization potentials. The etch and deposition rate data follow this linear relationship very well. The proportionality constant in this linear relationship varies with composition for CF 4 /O 2 etching data. Film hardness and failure modes on silicon and glass substrates are also described.
Molecular cloning of a chloride channel that is regulated by dehydration and expressed predominantly in kidney medulla. (1993)

Complementary DNA encoding a rat kidney chloride channel (CIC-K1) was isolated by a polymerase chain reaction (PCR) cloning strategy. We designed degenerate primers, based on the regions where previously cloned chloride channels (CIC-0, -1, and -2) possess significant amino acid identity, and performed reverse transcription PCR with whole kidney mRNA. The 686-amino acid protein encoded by CIC-K1 is about 40% identical to the previously cloned chloride channels and has a similar hydropathy profile. Expression of CIC-K1 in Xenopus oocytes induced Cl- currents that activate instantaneously upon hyperpolarization and depolarization, and displayed a slightly outwardly rectifying current-voltage relationship. The message for CIC-K1 was 2.4 kilobases and was found predominantly in kidney, especially in the inner medulla. Reverse transcription PCR technique using micro-dissected nephron segments revealed that the main site of expression in kidney was the thin ascending limb of Henle's loop, which has the highest Cl- permeability among the nephron segments and is thought to be involved in a counter-current system for urine concentration in the inner medulla. The abundance of CIC-K1 mRNA in kidney increased about 4-fold as rats became dehydrated by deprivation of water for 5 days. The site of expression and the regulation by dehydration suggest that CIC-K1 function may be important in urinary concentrating mechanisms.
Gel formation of soybean 7S and 11S proteins. (1980)

Rheological properties of soybean 7S and 11S proteins were investigated at the concentrations in which both could form the heat-induced gel. It was recognized that 7S protein formed gel at the lower concentration than that of 11S protein. In forming gel, 11S protein seems to have the ability to form more hydrogen bonds and ionic attractions and less hydrophobic interactions than those of 7S protein. In the presence of salts, the gel of 7S protein was formed at the lower protein concentration compared with the absence of salts. But the addition of salts to 11S protein suppressed the formation of gel even with high protein concentration. The reactivity of carboxyl groups was determined by the dye-binding method. The 11 S protein contained reactive carboxyl groups.
Reduction of Plasma 24S-Hydroxycholesterol (Cerebrosterol) Levels Using High-Dosage Simvastatin in Patients With Hypercholesterolemia (2002)

The greater reduction of plasma concentrations of 24S-hydroxycholesterol compared with cholesterol indicates that simvastatin in a dosage of 80 mg/d reduces cholesterol turnover in the brain. The present results might describe a possible mechanism of how long-term treatment with statins could reduce the incidence of Alzheimer disease.
Restoration of mismatch repair to nuclear extracts of H6 colorectal tumor cells by a heterodimer of human MutL homologs. (1995)

Hypermutable H6 colorectal tumor cells are defective in strand-specific mismatch repair and bear defects in both alleles of the hMLH1 gene. We have purified to near homogeneity an activity from HeLa cells that complements H6 nuclear extracts to restore repair proficiency on a set of heteroduplex DNAs representing the eight base-base mismatches as well as a number of slipped-strand, insertion/deletion mispairs. This activity behaves as a single species during fractionation and copurifies with proteins of 85 and 110 kDa. Microsequence analysis demonstrated both of these proteins to be homologs of bacterial MutL, with the former corresponding to the hMLH1 product and the latter to the product of hPMS2 or a closely related gene. The 1:1 molar stoichiometry of the two polypeptides and their hydrodynamic behavior indicate formation of a heterodimer, which we have designated hMutL alpha. These observations indicate that interactions between members of the family of human MutL homologs may be restricted.
Newcastle Disease Oil Emulsion Vaccines Prepared with Animal, Vegetable, and Synthetic Oils (1997)

Animal, vegetable, and synthetic oils were tested as potential replacements for mineral oil in Newcastle disease oil emulsion vaccines. Emulsifying surfactants of seed oil origin comprised 10% of the the oil phase that was used to prepare water-in-oil emulsion vaccines that contained a final concentration of 20% aqueous antigen. The hemagglutination inhibition responses of chickens inoculated with 46 of the newly formulated oil vaccines were, in most cases, not significantly different from those of control chickens inoculated with mineral oil vaccine. Tissue reactions associated with animal, vegetable, and synthetic oil vaccines were less severe than those associated with mineral oil vaccines. Viscosity of the mineral oil formulations ranged from 1/2 to 3 1/2 times that of the mineral oil control vaccines. These findings indicate that any of several oils may be more suitable than mineral oil for preparation of immune adjuvants for poultry vaccines.
Development of a Semi-Automatic Segmentation Method for Retinal OCT Images Tested in Patients with Diabetic Macular Edema (2013)

The EdgeSelect method resulted in better reproducibility and good agreement with a manual method in a set of eyes of normal subjects and with retinal disease, suggesting that this approach is feasible for OCT image analysis in clinical trials.
Nuclear Localization of Androgen Receptor In Heterogeneous Samples Of Normal, Hyperplastic And Neoplastic Human Prostate (1992)

To facilitate an understanding of how androgens participate in the genesis of human benign hyperplasia and carcinoma we assayed androgen receptor in the epithelium and stroma of human prostatic tissue from 57 patients. Immunohistochemical staining of human androgen receptor was performed on 106 sections of normal prostate, benign prostatic hyperplasia (BPH) and prostate cancer. To determine variability of androgen receptor staining sections taken from different portions of the gland were studied. Frozen tissue sections were incubated with monoclonal antiandrogen receptor antibodies and staining was completed by the indirect avidin-biotin peroxidase method. Antibody staining was found mainly in the nucleus of prostatic epithelial cells, although some stromal cells also showed positive staining. Unlike normal prostate, there was a heterogeneous distribution of androgen receptor in BPH and prostate cancer. The androgen receptor content in well differentiated adenocarcinoma epithelium was significantly higher compared to moderately (p less than 0.05) and poorly (p less than 0.05) differentiated adenocarcinoma. Regardless of the origin of stromal tissue, some staining was observed. In each specimen studied the androgen receptor staining was consistent qualitatively and quantitatively for each pathological component throughout the specimen. These data confirm that androgen receptor is a nuclear receptor protein. Furthermore, they show the ability of monoclonal antibodies to reveal cellular/subcellular distribution of androgen receptor, and demonstrate a correlation between the degree of tumor differentiation and androgen receptor content in epithelial but not in stromal cells. These observations may have important implications for understanding the variable tumor response to hormone therapy.