gebhart/patrepeval huggingface dataset:
Recombination and transcription of the endogenous Ig heavy chain locus is effected by the Ig heavy chain intronic enhancer core region in the absence of the matrix attachment regions (1999)

The intronic Ig heavy chain (IgH) enhancer, which consists of the core enhancer flanked by 5' and 3' matrix attachment regions, has been implicated in control of IgH locus recombination and transcription. To elucidate the regulatory functions of the core enhancer and its associated matrix attachment regions in the endogenous IgH locus, we have introduced targeted deletions of these elements, both individually and in combination, into an IgHa/b-heterozygous embryonic stem cell line. These embryonic stem cells were used to generate chimeric mice by recombination activating gene-2 (Rag-2)-deficient blastocyst complementation, and the effects of the introduced mutations were assayed in mutant B cells. We find that the core enhancer is necessary and sufficient to promote normal variable (V), diversity (D), and joining (J) segment recombination in developing B lineage cells and IgH locus transcription in mature B cells. Surprisingly, the 5' and 3' matrix attachment regions were dispensable for these processes.
Modified Lactic Acid Bacteria Detect and Inhibit Multiresistant Enterococci (2014)

We designed Lactococcus lactis to detect Enterococcus faecalis. Upon detection, L. lactis produce and secrete antienterococcal peptides. The peptides inhibit enterococcal growth and reduce viability of enterococci in the vicinity of L. lactis. The enterococcal sex pheromone cCF10 serves as the signal for detection. Expression vectors derived from pCF10, a cCF10-responsive E. faecalis sex-pheromone conjugative plasmid, were engineered in L. lactis for the detection system. Recombinant host strains were engineered to express genes for three bacteriocins, enterocin A, hiracin JM79 and enterocin P, each with potent antimicrobial activity against E. faecalis. Sensitive detection and specific inhibition occur both in agar and liquid media. The engineered L. lactis also inhibited growth of multidrug-resistant E. faecium strains, when induced by cCF10. The presented vectors and strains can be components of a toolbox for the development of alternative antibiotic technologies targeting enterococci at the site of infection.
Automatic generation and tuning of MPI collective communication routines (2005)

In order for collective communication routines to achieve high performance on different platforms, they must be able to adapt to the system architecture and use different algorithms for different situations. Current Message Passing Interface (MPI) implementations, such as MPICH and LAM/MPI, are not fully adaptable to the system architecture and are not able to achieve high performance on many platforms. In this paper, we present a system that produces efficient MPI collective communication routines. By automatically generating topology specific routines and using an empirical approach to select the best implementations, our system adapts to a given platform and constructs routines that are customized for the platform. The experimental results show that the tuned routines consistently achieve high performance on clusters with different network topologies.
Alternative RNA splicing that determines agrin activity regulates binding to heparin and α-dystroglycan (1996)

Agrin is a component of the extracellular matrix that regulates aspects of neuromuscular junction differentiation. Identification of agrin-binding proteins has lead to the suggestion that alpha-dystroglycan is a muscle cell surface proteoglycan that mediates agrin activity. To further test this hypothesis, we have compared the ability of differentially active agrin isoforms to interact with a model component of proteoglycans, heparin, as well as with the putative proteoglycan alpha-dystroglycan. We demonstrate that an alternately spliced exon (encoding the sequence lysine, serine, arginine, lysine: Y site) is necessary for agrin-heparin interactions. We also show that alternate splicing at another site (Z site) dramatically affects interaction of alpha-dystroglycan with agrin. We propose a model in which multiple distinct domains of agrin interact with both protein and sugar moieties of alpha-dystroglycan. The isoform-specific binding of agrin to alpha-dystroglycan is consistent with a functional role for this interaction during synaptogenesis.
Hair Preparations (2006)

Abstract The article contains sections titled: 1. Introduction 2. The Scalp and Hair 2.1. Structure of the Skin and Hair Growth 2.2. Structure of Hair 2.2.1. Morphology 2.2.2. Chemical and Physical Properties 2.2.3. Natural Hair Color 3. Hair Cleansing and Care Preparations 3.1. Shampoos 3.1.1. Composition 3.1.1.1. Surfactants 3.1.1.2. Other Constituents 3.1.2. Types of Shampoo 3.1.3. Dry Shampoos 3.2. Conditioning Agents and Treatments 4. Hairstyling Preparations 4.1. Setting Lotions, Mousses, and Restructurants 4.2. Hair Sprays 4.3. Other Hairstyling Preparations 4.3.1. Gels 4.3.2. Waxes 4.3.3. Emulsion‐Based Styling Products 4.3.3.1. Creams and Pomades 4.3.3.2. Gums/Puttys 4.3.3.3. Serums 5. Hair Coloring Preparations 5.1. Bleaching 5.2. Dyeing 5.2.1. Dyeing with Dye Precursors 5.2.2. Dyeing with Inorganic Compounds 5.2.3. Dyeing with Direct Dyes 5.2.4. Product Forms 5.2.5. Testing Hair Dyes 5.2.6. Dye‐Removal Preparations 6. Waving 6.1. Principles and Methods 6.2. Permanent‐Wave Preparations 6.2.1. Waving Preparations 6.2.2. Neutralizers 6.2.3. Notes on Use 7. Hair Straightening Preparations 8. Hair Removal 8.1. Epilation and Permanent Hair Removal 8.2. Depilation 8.3. Shaving Aids 9. Testing Methods 10. Toxicology and Legal Aspects 10.1. Toxicology 10.1.1. Introduction 10.1.2. Strategy for Safety Assessment of Cosmetics 10.1.3. Test Methods 10.1.3.1. Basic Principles 10.1.3.2. Systemic Toxicity Studies 10.1.3.3. Local Compatibility 10.1.3.4. Sensitizing (Contact‐Allergenic) Potential 10.1.3.5. Mutagenic/Genotoxic Potential 10.1.3.6. Reproductive Toxicology 10.1.3.7. Tumorigenic Potential <jats:styl
Highly Enantioselective Catalytic Cross-Dehydrogenative Coupling ofN-Carbamoyl Tetrahydroisoquinolines and Terminal Alkynes (2015)

The first catalytic asymmetric cross-dehydrogenative coupling of cyclic carbamates and terminal alkynes has been established. The reaction features high enantiocontrol and excellent functional group tolerance and displays a wide range of structurally and electronically diverse carbamates as well as terminal alkynes. N-Acyl hemiaminals were identified as the reactive intermediates through preliminary control experiments. Employing readily removable carbamates as substrates rather than traditionally adopted N-aryl amines allows applications in complex molecule synthesis and therefore advances the C-H functionalization strategy to a synthetically useful level.
A free time-shift DVD video recorder (1997)

A DVD video recorder is proposed that frees viewers from restrictions on when a program can be viewed by allowing a program to be played while the recorder continues to record other programs. This recorder also makes recording, viewing, searching and managing programs much easier than with a conventional VCR. The recorder consists of two MPEG1+ video encoders, one MPEG2 decoder, a DVD drive with a disk changer, and a hard-disk-drive.
Multi-Functional Sorbents for the Removal of Sulfur and Metallic Contaminants from High-Temperature Gases (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMulti-Functional Sorbents for the Removal of Sulfur and Metallic Contaminants from High-Temperature GasesBaochun. Wu, Keijo K. Jaanu, and Farhang. ShadmanCite this: Environ. Sci. Technol. 1995, 29, 6, 1660–1665Publication Date (Print):June 1, 1995Publication History Published online1 May 2002Published inissue 1 June 1995https://doi.org/10.1021/es00006a033RIGHTS & PERMISSIONSArticle Views160Altmetric-Citations19LEARN 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 (1 MB) Get e-Alertsclose Get e-Alerts
Cellular and molecular characterization of the role of the flk-2/flt-3 receptor tyrosine kinase in hematopoietic stem cells (1994)

The flk-2/flt-3 receptor tyrosine kinase was cloned from a hematopoietic stem cell population and is considered to play a potential role in the developmental fate of the stem cell. Using antibodies derived against the extracellular domain of the receptor, we show that stem cells from both murine fetal liver and bone marrow can express flk-2/flt-3. However, in both these tissues, there are stem cell populations that do not express the receptor. Cell cycle analysis shows that stem cells that do not express the receptor have a greater percentage of the population in G0 when compared with the flk-2/flt-3-positive population. Development of agonist antibodies to the receptor shows a proliferative role for the receptor in stem cell populations. Stimulation with an agonist antibody gives rise to an expansion of both myeloid and lymphoid cells and this effect is enhanced by the addition of kit ligand. These studies serve to further illustrate the importance of the flk-2/flt-3 receptor in the regulation of the hematopoietic stem cell.
FimH adhesin of type 1 pili is assembled into a fibrillar tip structure in the Enterobacteriaceae. (1995)

Type 1 pili are heteropolymeric mannosebinding fibers produced by all members of the Enterobacteriaceae family. The bulk of the fiber is composed of FimA. Two macromolecular complexes responsible for mediating an interaction with mannose-containing receptors were purified from fimA- Escherichia coli by mannose affinity chromatography and ion-exchange chromatography. One complex contained only the mannose-binding adhesin, FimH, associated with FimG, a minor component of the type 1 pilus. In the other complex the FimG-FimH moiety was loosely associated with a chaperone-minor subunit complex (FimC-FimF), possibly representing an intermediate in tip fibrilla assembly. The FimC chaperone has also been shown to form a preassembly complex with FimH that has been purified and characterized previously. Purified FimC did not bind to the FimG-FimH complex but did recognize FimH dissociated from the FimG-FimH complex. Quick-freeze deep-etch electron microscopy revealed that the FimG-FimH complex had a thin fibrillar architecture. High-resolution electron microscopy of type 1 pili revealed that a 16-nm fibrillar tip structure with an architecture identical to that of the FimG-FimH complex was joined end-to-end to the pilus rod. In a fimH- deletion mutant, the tip fibrillae joined to pilus rods were approximately 3 nm in length. The full-length tip fibrilla was restored by complementation with the fimH gene in trans. The bipartite nature of the type 1 pilus was also demonstrated on pili purified from clinical isolates of members of the Enterobacteriaceae family arguing that it is a conserved feature of the type 1 pilus.
TGF-beta 1 and 25-hydroxycholesterol stimulate osteoblast-like vascular cells to calcify. (1994)

Previous studies in our laboratory demonstrated messenger RNA for bone morphogenetic protein-2a in human calcified plaque, suggesting that arterial calcification is a regulated process, similar to osteogenesis. To further test this hypothesis, we have isolated and cloned a subpopulation of cells from bovine aortic media that show osteoblastic potential. These novel cells are primarily distinguished from smooth muscle cells by expression of a surface marker preliminarily identified as a modified form of the ganglioside sialyl-lactosylceramide (GM3). Osteoblastic potential was indicated by high levels of alkaline phosphatase and collagen I, expression of osteopontin and osteonectin (SPARC), and production of bone-specific osteocalcin and hydroxyapatite. Cultures of these cells were stimulated to form increased numbers of calcium-mineral-producing nodules by the oxysterol 25-hydroxycholesterol as well as by transforming growth factor-beta 1, both known to be present in atherosclerotic lesions. The stimulation of calcifying vascular cells in the artery wall by these two factors suggests a possible mechanism for the colocalization of calcification with atherosclerosis in vivo.
Restoration of specific myxovirus receptors to asialoerythrocytes by incorporation of sialic acid with pure sialyltransferases. (1979)

Removal of sialic acids from human erythrocytes with Vibrio cholera neuraminidase abolished hemagglutination by two paramyxoviruses, Sendai and Newcastle disease, and two orthomyxoviruses, a human influenza A2 virus (Japan/305/57), and an equine influenza A virus (Equine i/Prague/56). Selective replacement of sialic acid in the sequences NeuAccu2 + 6 Gal, NeuAca2 -+ GGalNAc, or NeuAccv2 + 3Gal was accomplished with three different homogeneous sialyltransferases, each of which is specific for the synthesis of one of these structures. Hemagglutination titers were restored to the original levels for all four viruses by the incorporation of about 40% of the sialic acid content of the native cells with the fl-galactoside a2 + 3 sialyltransferase. This enzyme has a strict acceptor substrate specificity for the Galfll + 3GalNAcal + 0-Thr/Ser sequence found in asialoglycophorin, the major erythrocyte glycoprotein, and forms the structure NeuAccvt -+ 3Gal/31+ 3GalNAcal -+ 0-Thr/Ser. Analysis of the labeled erythrocyte proteins by sodium dodecyl sulfategel electrophoresis showed that about 85 to 90% of the [l’C]NeuAc incorporated into erythrocytes co-migrated with glycophorin. Incorporation of sialic acid by other sialyltransferases did not result in hemagglutination by the Sendai, Newcastle disease, or equine influenza A viruses. In contrast, both of the other sialyltransferases restored hemagglutination by the human influenza A2 virus. Thus, attachment of sialic acid to erythrocytes in the sequence NeuAca2 -+ 6Gal or NeuAccvP + 6GalNAc restores erythrocyte receptor sites to only one of the four myxoviruses examined.
Cytochrome P450 of small intestinal epithelial cells (1985)

Abstract We have studied total cytochrome P 450 and the major form of cytochrome P 450 increased by phenobarbital in small intestinal epithelial cells and livers of male Sprague-Dawley rats. Using an improved method for preparing microsomes from intestinal epithelial cells, we find that concentrations of total cytochrome P 450 in intestinal cell microsomes are 10% of those in liver microsomes, and that this percentage is unchanged after phenobarbital treatment. In untreated rats, 450 of liver or intestinal epithelium is the form induced by phenobarbital, as measured by rocket immunoelectrophoresis. In phenobarbital-treated rats, the major phenobarbital-induced form accounts for ~50% of the total in both organs. In the small intestine of phenobarbital-treated rats, the concentrations of total cytochrome P 450 and of the major phenobarbital-induced form increase concurrently as epithelial cells mature from crypt to upper villus. Concentrations of total cytochrome P 450 and of the major phenobarbital-induced form in the proximal two-thirds of the rat small intestine are twofold higher than in the distal third. Immunoblotting performed with a monoclonal antibody to the major phenobarbital-induced form of cytochrome P 450 from rat liver revealed a subtle difference between this form in liver and intestine.
Cardiac hypertrophy with preserved contractile function after selective deletion of GLUT4 from the heart (1999)

Glucose enters the heart via GLUT1 and GLUT4 glucose transporters. GLUT4-deficient mice develop striking cardiac hypertrophy and die prematurely. Whether their cardiac changes are caused primarily by GLUT4 deficiency in cardiomyocytes or by metabolic changes resulting from the absence of GLUT4 in skeletal muscle and adipose tissue is unclear. To determine the role of GLUT4 in the heart we used cre-loxP recombination to generate G4H(-/-) mice in which GLUT4 expression is abolished in the heart but is present in skeletal muscle and adipose tissue. Life span and serum concentrations of insulin, glucose, FFAs, lactate, and beta-hydroxybutyrate were normal. Basal cardiac glucose transport and GLUT1 expression were both increased approximately 3-fold in G4H(-/-) mice, but insulin-stimulated glucose uptake was abolished. G4H(-/-) mice develop modest cardiac hypertrophy associated with increased myocyte size and induction of atrial natriuretic and brain natriuretic peptide gene expression in the ventricles. Myocardial fibrosis did not occur. Basal and isoproterenol-stimulated isovolumic contractile performance was preserved. Thus, selective ablation of GLUT4 in the heart initiates a series of events that results in compensated cardiac hypertrophy.
Convergence of two global transcriptional regulators on nitrogen induction of the stress‐acclimation gene nblA in the cyanobacterium Synechococcus sp. PCC 7942 (2001)

Cyanobacteria respond to environmental stress conditions by degrading their phycobilisomes, the light harvesting complexes for photosynthesis. The expression of nblA, a key gene in this process, is controlled by the response regulator NblR in Synechococcus sp. PCC 7942. Here we show that, under nitrogen stress, nblA is also regulated by NtcA, the global regulator for nitrogen control. NtcA activation of nblA was found to be nitrogen-specific and did not take place under sulphur stress. Transcripts from the two major transcription start points (tsp) for the nblA gene were induced in response to nitrogen and sulphur starvation. The most active one (tspII) required both NblR and NtcA to induce full nblA expression under nitrogen starvation. NblR and NtcA bound in vitro to a DNA fragment from the nblA promoter region, suggesting that, under nitrogen stress, both NblR and NtcA activate the main regulated promoter (PnblA-2) by direct DNA-binding. The structure of PnblA-2 differs from that of the canonical NtcA-activated promoter and it is therefore proposed to represent a novel type of NtcA-dependent promoter. We analysed expression patterns from ntcA and selected NtcA targets in NtcA(-), NblR(-) and wild-type strains, and discuss data suggesting further interrelations between phycobilisome degradation and nitrogen assimilation regulatory pathways.
A new SOI inverter for low power applications (2002)

The speed degradation in CMOS circuits with the supply voltage reduction is an important obstacle in the scale down of supply voltage. Thus, many attempts to reduce the gate delay have been tried using the dynamic threshold scheme. However, they have limitations in the operation voltage and large leakage current. We propose a new type of SOI inverter gate which has considerably shortened circuit delay with similar energy consumption in the conventional SOI CMOS circuit at low voltage operation. It uses the positive-body bias effect that enhances drain currents when the body is biased positively. The operation principle of the proposed gate, the optimal circuit and device conditions studied by simulations, and the fabrication and measurement data are reported in this paper.
Intradiscal Measurements of pH in Patients with Lumbar Rhizopathies (1969)

(1969). Intradiscal Measurements of pH in Patients with Lumbar Rhizopathies. Acta Orthopaedica Scandinavica: Vol. 40, No. 1, pp. 23-42.
Caspase Inhibitor Therapy Enhances Marginal Mass Islet Graft Survival and Preserves Long-Term Function in Islet Transplantation (2007)

Islet transplantation can provide insulin independence in patients with type 1 diabetes, but islets derived from two or more donors are often required. A significant fraction of the functional islet mass is lost to apoptosis in the immediate posttransplant period. The caspase inhibitor N-benzyloxycabonyl-Val-Ala-Asp-fluoromethyl ketone (zVAD-FMK) has been used therapeutically to prevent apoptosis in experimental animal models of ischemic injury, autoimmunity, and degenerative disease. In the current study, zVAD-FMK therapy was examined in a syngeneic islet transplant model to determine whether caspase inhibition could improve survival of transplanted islets. zVAD-FMK therapy significantly improved marginal islet mass function in renal subcapsular transplantation, where 90% of zVAD-FMK–treated mice became euglycemic with 250 islets, versus 27% of the control animals (P &amp;lt; 0.001). The benefit of zVAD-FMK therapy was further demonstrated after intraportal transplantation, where 75% of zVAD-FMK–treated animals established euglycemia with only 500 islets, and all of the controls remained severely diabetic (P &amp;lt; 0.001). zVAD-FMK pretreatment of isolated islets in the absence of systemic therapy resulted in no significant benefit compared with controls. Long-term follow-up of transplanted animals beyond 1 year posttransplant using glucose tolerance tests confirmed that a short course of zVAD-FMK therapy could prevent metabolic dysfunction of islet grafts over time. In addition, short-term zVAD-FMK treatment significantly reduced posttransplant apoptosis in islet grafts and resulted in preservation of graft insulin reserve over time. Our data suggest that caspase inhibitor therapy will reduce the islet mass required in clinical islet transplantation, perhaps to a level that would routinely allow for insulin independence after single-donor infusion.
A method for analysis and correction of cross-talk effects in pathway analysis (2012)

Many analysis techniques are currently available to identify the signaling pathways significantly impacted in a given condition. All these approaches calculate a p-value that aims to quantify the significance of the involvement of a given pathway in the condition under study. These p-values were thought to be related to the likelihood of their respective pathways being involved in the given condition, and to be independent. Here we show that this is not true, and that many pathways are not independent and that can considerably affect each other's p-values through a phenomenon we refer to as “cross-talk.” Thus, the significance of a given pathway in a given experiment has to be interpreted in the context of the other pathways that appear to be significant. Using real data, we show that in same cases pathways with significant classical p-values are not biologically meaningful, and that some biologically meaningful pathways with insignificant p-values become significant when the cross-talk effects of other pathways are removed. We show that this phenomenon is related to the amount of common genes between different pathways, affecting the most widely used methods for pathway analysis, and we propose an analysis technique that is able to correct the over-enrichment significance of a pathway when the cross-talk effects of other pathways are removed.