gebhart/patrepeval huggingface dataset:
Cell-mediated Immunity to Virus Causing Haemorrhagic Fever with Renal Syndrome: Generation of Cytotoxic T Lymphocytes (1988)

Cytotoxic T lymphocytes (CTLs) were generated when spleen cells from mice infected with viruses causing haemorrhagic fever with renal syndrome were stimulated in vitro with syngeneic cells infected with viruses. These cytotoxic effector cells, with Lyt2+ L3T4- markers on their surface, demonstrated H-2 restriction. CTLs induced by Hantaan virus (76-118 strain) or Seoul virus (B-1 strain) showed cross-reactivity with infected target cells. Hantaan virus infection induced a higher CTLs response than Seoul virus infection, although the antibody responses to these two viruses and the replication of the two virus strains in athymic nude mice were not significantly different. Viral antigen detected with a monoclonal antibody reacting with nucleocapsid antigen was observed mainly in the cytoplasm of macrophages infected with Hantaan virus, but in the nucleus of cells infected with Seoul virus. The major viral antigens recognized by CTLs are discussed on the basis of these findings.
Using relevance to train a linear mixture of experts (1996)

A linear mixture of experts is used to combine three standard IR systems. The parameters for the mixture are determined automatically through training on document relevance assessments via optimization of a rank-order statistic which is empirically correlated with average precision. The mixture improves performance in some cases and degrades it in others, with the degradations possibly due to training techniques, model strength, and poor performance of the individual experts. 1 INTRODUCTION The mixture of experts approach is one which is gaining in popularity in many areas of computer science and artificial intelligence (e.g., [Jordan and Jacobs, 1994]) and one which is especially applicable to information retrieval, since in practice the sets of relevant documents returned by different IR algorithms (or experts) often have little overlap. In fact, the pooling method used by past TREC&amp;apos;s to determine which documents are relevant can be viewed as a sort of mixture model on the grandest ...
Inhibition of vascular smooth muscle cell migration by heparin‐like glycosaminoglycans (1984)

Previous studies have suggested that heparin-like glycosaminoglycans may be endogenous inhibitors of smooth muscle proliferation in the vessel wall. The purpose of this study was to determine the effects of exogenous glycosaminoglycans on rat vascular (aortic) smooth muscle cell migration following wounding in vitro. Our data indicate that heparin and related molecules (iota carrageenan, dextran sulfate), but not other glycosaminoglycans (hyaluronate, chondroitin, and dermatan sulfates), inhibit smooth muscle cell motility in a cell-specific, dose-dependent, and reversible fashion. The effect of heparin was maximal (60% inhibition) at 10 micrograms/ml; a half-maximal effect was observed at 1 microgram/ml. Heparin did not significantly affect the migration of bovine aortic endothelium or Swiss 3T3 cells. These observations support the concept that heparin-like glycosaminoglycans may be important regulators of vascular smooth muscle cell function.
Collapse and Revival of an Artificial Atom Coupled to a Structured Photonic Reservoir (2021)

A superconducting quantum circuit coupled to a tailored waveguide reservoir provides a platform for exploring non-Markovian quantum-optical dynamics, in which the reservoir maintains a memory of past events.
The herpes simplex virus major regulatory protein ICP4 blocks apoptosis induced by the virus or by hyperthermia. (1996)

Cells infected with herpes simplex virus 1 (HSV-1) undergo productive or latent infection without exhibiting features characteristic of apoptosis. In this report, we show that HSV-1 induces apoptosis but has evolved a function that blocks apoptosis induced by infection as well as by other means. Specifically, (i) Vero cells infected with a HSV-1 mutant deleted in the regulatory gene alpha 4 (that encodes repressor and transactivating functions), but not those infected with wild-type HSV-1(F), exhibit cytoplasmic blebbing, chromatin condensation, and fragmented DNA detected as a ladder in agarose gels or by labeling free DNA ends with terminal transferase; (ii) Vero cells infected with wild-type HSV-1(F) or cells expressing the alpha 4 gene and infected with the alpha 4- virus did not exhibit apoptosis; (iii) fragmentation of cellular DNA was observed in Vero cells that were mock-infected or infected with the alpha 4- virus and maintained at 39.5 degrees C, but not in cells infected with wild-type virus and maintained at the same temperature. Wild-type strains of HSV-1 with limited extrahuman passages, such as HSV-1 (F), carry a temperature-sensitive lesion in the alpha 4 gene and at 39.5 degrees C only alpha genes are expressed. These results indicate that the product of the alpha 4 gene is able to suppress apoptosis induced by the virus as well by other means.
Acetylsalicylic Acid, at High Concentrations, Inhibits Vascular Smooth Muscle Cell Proliferation (1993)

The growth of human smooth muscle cells in culture is inhibited by acetylsalicylic acid (ASA). In comparison to control, the proliferation of cells treated with 270 mg/L lysinmono(acetylsalicylate)/30 mg/L glycine was inhibited by 50-90% under different culture conditions. Cell numbers per well (control vs. treated) were as follows: (a) 470,500 +/- 55,890 vs. 24,750 +/- 4,030 (p < 0.002) after 6 days in the presence of 10% fetal calf serum (FCS), (b) 160,500 +/- 9,920 vs. 74,000 (p < 0.001) after 8 days in the presence of 10% human serum; and (c) 387,000 +/- 29,420 vs. 35,250 +/- 1,110 (p < 0.001) after 8 days in the presence of 5% FCS. Significant inhibition of growth by lysinmono(acetylsalicylate) at 90 mg/L was noted only for cultures grown with 10% FCS. Lower concentrations of this drug were ineffective under all culture conditions. Higher dosages of ASA, which would prevent not only platelet aggregation but also smooth muscle cell growth, may therefore be indicated in therapy of patients who undergo percutaneous transluminal coronary angioplasty (PTCA) or coronary artery transplantation.
The Acquired Immunodeficiency Syndrome: current status. (1983)

A recently recognized syndrome of acquired immunodeficiency (Acquired Immunodeficiency Syndrome-AIDS) has arisen since June 1981. It has received international attention. The clinical spectrum consists of repeated opportunistic infections, rare malignancies, and autoimmune phenomena, occurring in previously healthy adults with no history of an immunologic disorder. The population subset at risk for this syndrome appears to be predominantly homosexual American males and intravenous drug abusers with rare cases being reported in heterosexuals, hemophiliacs, and foreign patients, especially Haitians. The immunologic aberrancy in all patients described appears limited to T-lymphocyte hyporesponsiveness and imbalance of T-helper and suppressor cells. This disordered immunoregulation is a consistent finding in all reported cases and appears to predispose to the opportunistic infections and malignancies which have been associated with a 40 percent mortality. The underlying factor responsible for the immunoregulatory defect is unknown but possible etiologies include a transmissible infectious agent, drug use, chronic antigen stimulation, and spermatozoa exposure. Treatment of the associated infections and malignancies has been a frustrating endeavor as many patients respond incompletely or relapse soon after successful treatment course. Preventive measures, including patient education, physician awareness, and immunomodulating agents, are discussed.
High-resolution acousto-optic shaping of unamplified and amplified femtosecond laser pulses (1997)

We focus theoretically and experimentally on the fundamental limitations of spectral pulse shaping using an acousto-optic modulator. We analyze the role of the relative thickness of the interaction region as dictated by the acousto-optic Q parameter and show that varying Q allows flexibility in choosing between diffraction efficiency and pixels of resolution. We model and experimentally demonstrate the effects of potential nonidealities such as nonlinear acoustic attenuation. In addition, we derive a simple and intuitive expression to predict the magnitude of the distortions in the spatial profile generated by an acousto-optic-modulator spectral light modulator. Finally, we demonstrate amplification of acousto-optic-modulator-generated shaped pulses for the first time.
A highly efficient multienzyme system for the one-step synthesis of a sialyl trisaccharide: in situ generation of sialic acid and N-acetyllactosamine coupled with regeneration of UDP-glucose, UDP-galactose and CMP-sialic acid (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA highly efficient multienzyme system for the one-step synthesis of a sialyl trisaccharide: in situ generation of sialic acid and N-acetyllactosamine coupled with regeneration of UDP-glucose, UDP-galactose and CMP-sialic acidYoshitaka Ichikawa, Jennifer Lin Chun Liu, Gwo Jenn Shen, and Chi Huey WongCite this: J. Am. Chem. Soc. 1991, 113, 16, 6300–6302Publication Date (Print):July 1, 1991Publication History Published online1 May 2002Published inissue 1 July 1991https://pubs.acs.org/doi/10.1021/ja00016a073https://doi.org/10.1021/ja00016a073research-articleACS PublicationsRequest reuse permissionsArticle Views496Altmetric-Citations102LEARN 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 InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Large‐scale transient transfection of serum‐free suspension‐growing HEK293 EBNA1 cells: Peptone additives improve cell growth and transfection efficiency (2003)

Large-scale transient transfection of mammalian cells is a recent and powerful technology for the fast production of milligram amounts of recombinant proteins (r-proteins). As many r-proteins used for therapeutic and structural studies are naturally secreted or engineered to be secreted, a cost-effective serum-free culture medium that allows their efficient expression and purification is required. In an attempt to design such a serum-free medium, the effect of nine protein hydrolysates on cell proliferation, transfection efficiency, and volumetric productivity was evaluated using green fluorescent protein (GFP) and human placental secreted alkaline phosphate (SEAP) as reporter genes. The suspension growing, serum-free adapted HEK293SF-3F6 cell line was stably transfected with an EBNA1-expression vector to increase protein expression when using EBV oriP bearing plasmids. Compared to our standard serum-free medium, concomitant addition of the gelatin peptone N3 and removal of BSA slightly enhanced transfection efficiency and significantly increased volumetric productivity fourfold. Using the optimized medium formulation, transfection efficiencies between 40-60% were routinely obtained and SEAP production reached 18 mg/L(-1). To date, we have successfully produced and purified over fifteen r-proteins from 1-14-L bioreactors using this serum-free system. As examples, we describe the scale-up of two secreted his-tagged r-proteins Tie-2 and Neuropilin-1 extracellular domains (ED) in bioreactors. Each protein was successfully purified to >95% purity following a single immobilized metal affinity chromatography (IMAC) step. In contrast, purification of Tie-2 and Neuropilin-1 produced in serum-containing medium was much less efficient. Thus, the use of our new serum-free EBNA1 cell line with peptone-enriched serum-free medium significantly improves protein expression compared to peptone-less medium, and significantly increases their purification efficiency compared to serum-containing medium. This eliminates labor-intensive and expensive chromatographic steps, and allows for the simple, reliable, and extremely fast production of milligram amounts of r-proteins within 5 days posttransfection.
Distinct Roles of the Steroid Receptor Coactivator 1 and of MED1 in Retinoid-induced Transcription and Cellular Differentiation (2006)

Retinoic acid receptors (RARs) are the molecular relays of retinoid action on transcription, cellular differentiation and apoptosis. Transcriptional activation of retinoid-regulated promoters requires the dismissal of corepressors and the recruitment of coactivators to promoter-bound RAR. RARs recruit in vitro a plethora of coactivators whose actual contribution to retinoid-induced transcription is poorly characterized in vivo. Embryonal carcinoma P19 cells, which are highly sensitive to retinoids, were depleted from archetypical coactivators by RNAi. SRC1-deficient P19 cells showed severely compromised retinoid-induced responses, in agreement with the supposed role of SRC1 as a RAR coactivator. Unexpectedly, Med1/TRAP220/DRIP205-depleted cells exhibited an exacerbated response to retinoids, both in terms transcriptional responses and of cellular differentiation. Med1 depletion affected TFIIH and cdk9 detection at the prototypical retinoid-regulated RARbeta2 promoter, and favored a higher RNA polymerase II detection in transcribed regions of the RARbeta2 gene. Furthermore, the nature of the ligand impacted strongly on the ability of RARs to interact with a given coactivator and to activate transcription in intact cells. Thus RAR accomplishes transcriptional activation as a function of the ligand structure, by recruiting regulatory complexes which control distinct molecular events at retinoid-regulated promoters.
Expression and induction of a large set of drug‐metabolizing enzymes by the highly differentiated human hepatoma cell line BC2 (2001)

The BC2 cell line derived from the human hepatocarcinoma, HGB, undergoes a spontaneous sharp differentiation process in culture as it becomes confluent, remains stably differentiated for several weeks, and may return to proliferation thereafter under appropriate density conditions. The relevance of the line as an hepatic model has been evaluated. Cells synthesize a large number of plasma proteins, and rates of glycogen and urea synthesis increase with time of confluency and become sensitive to insulin, reflecting the process of differentiation. Differentiated BC2 cells express the most relevant cytochrome P‐450 (CYP) isozyme activities (CYP1A1/2, 2A6, 2B6, 2C9, 2E1, and 3A4) and conjugating enzymes (glutathione S‐transferase and UDP‐glucuronyltransferase) and also respond to model inducers. Methylcholanthrene induced an increase in CYP1A1/2 enzyme activity (eightfold), phenobarbital induced CYP2B6 activity (1.7‐fold), and dexamethasone induced CYP3A4 activity (fivefold). In parallel, expression of the most relevant liver‐enriched transcription factors, HNF‐4, HNF‐1, C/EBP‐α and C/EBP‐β mRNAs, was significantly increased in differentiated cultures. This increase was largest in HNF‐1 and HNF‐4, which supports the idea that a redifferentiation process towards the hepatic phenotype takes place. BC2 is an hepatic cell line that is able to express most hepatic functions, especially the drug‐biotransformation function, far more efficiently than any previously described human hepatoma cell line.
Enhancing Checkpoint Performance with Staging IO and SSD (2010)

With the ever-growing size of computer clusters and applications, system failures are becoming inevitable. Checkpointing, a strategy to ensure fault tolerance, has become imperative in such an environment. However existing mechanism of checkpoint writing to parallel systems doesn't perform well with increasing job size. Solid State Disk(SSD) is attracting more and more attention due to its technical merits such as good random access performance, low power consumption and shock resistance. However, how to apply SSDs into a parallel storage system to improve checkpoint writing still remains an open question. In this paper we propose a new strategy to enhance checkpoint writing performance by aggregating checkpoint writing at client side, and utilizing staging IO on data servers. We also explore the potentials to substitute traditional hard disks with SSDs on data server to achieve better write bandwidth. Our strategy achieves up to 6.3 times higher write bandwidth than a popular parallel file system PVFS2 with 8 client nodes and 4 data servers. In experiments with real applications using 64 application processes and 4 data servers, our strategy can accelerate checkpoint writing by up to 9.9 times compared to PVFS2.
Two-step model of leukocyte-endothelial cell interaction in inflammation: distinct roles for LECAM-1 and the leukocyte beta 2 integrins in vivo. (1991)

The lectin homing receptor LECAM-1 (LAM-1, Leu8) and the beta 2 integrins, particularly Mac-1 (CD11b/CD18), participate in leukocyte-endothelial cell interactions in inflammation. LECAM-1 is rapidly shed while Mac-1 expression is dramatically increased upon neutrophil activation, suggesting functionally distinct roles for these molecules. Using intravital video microscopy, we have compared the effect of antibodies against LECAM-1 and CD18 on leukocyte interactions with rabbit mesenteric venules. Anti-LECAM-1 monoclonal antibody and its Fab fragments inhibited initial reversible leukocyte rolling along the vascular wall. Anti-CD18 monoclonal antibody had no effect on rolling but prevented subsequent firm attachment of leukocytes to venular endothelium. These results support a two-step model of leukocyte-endothelial cell interactions: reversible rolling mediated in part by LECAM-1 facilitates leukocyte recruitment by the local microenvironment and precedes activation-dependent firm attachment involving beta 2 integrins.
Advances in spinal muscular atrophy therapeutics (2018)

Spinal muscular atrophy (SMA) is a progressive, recessively inherited neuromuscular disease, characterized by the degeneration of lower motor neurons in the spinal cord and brainstem, which leads to weakness and muscle atrophy. SMA currently represents the most common genetic cause of infant death. SMA is caused by the lack of survival motor neuron (SMN) protein due to mutations, which are often deletions, in the SMN1 gene. In the absence of treatments able to modify the disease course, a considerable burden falls on patients and their families. Greater knowledge of the molecular basis of SMA pathogenesis has fuelled the development of potential therapeutic approaches, which are illustrated here. Nusinersen, a modified antisense oligonucleotide that modulates the splicing of the SMN2 mRNA transcript, is the first approved drug for all types of SMA. Moreover, the first gene therapy clinical trial using adeno-associated virus (AAV) vectors encoding SMN reported positive results in survival and motor milestones achievement. In addition, other strategies are in the pipeline, including modulation of SMN2 transcripts, neuroprotection, and targeting an increasing number of other peripheral targets, including the skeletal muscle. Based on this premise, it is reasonable to expect that therapeutic approaches aimed at treating SMA will soon be changed, and improved, in a meaningful way. We discuss the challenges with regard to the development of novel treatments for patients with SMA, and depict the current and future scenarios as the field enters into a new era of promising effective treatments.
Small intestinal bacterial overgrowth in irritable bowel syndrome: are there any predictors? (2010)

Small intestinal bacterial overgrowth was present in a sizeable percentage of patients with IBS with predominance of bloating and flatulence. Older age and female sex were predictors of SIBO in patients with IBS. Identification of possible predictors of SIBO in patients with IBS could aid in the development of successful treatment plans.
Gene expression profile of aging in human muscle (2003)

Studies of gene expression related to aging of skeletal muscle have included few subjects or a limited number of genes. We conducted the present study to produce more comprehensive gene expression profiles. RNA was extracted from vastus lateralis biopsies obtained from healthy young (21-27 yr old, n = 8) and older men (67-75 yr old, n = 8) and was analyzed with high-density oligonucleotide arrays. Of the approximately 44,000 probe sets on the arrays, approximately 18,000 yielded adequate signals for statistical analysis. There were approximately 700 probe sets for which t-tests or rank sum tests indicated a difference (P <or= 0.01) in mean expression between young and old and for which the estimated false discovery rate was <10%. Most of these differences were less than 1.5-fold in magnitude. Genes that encode proteins involved in energy metabolism and mitochondrial protein synthesis were expressed at a lower level in older muscle. Genes encoding metallothioneins, high-mobility-group proteins, heterogeneous nuclear ribonucleoproteins and other RNA binding/processing proteins, and components of the ubiquitin-proteasome proteolytic pathway were expressed at higher levels in older muscle. Expression of numerous genes involved with stress responses, hormone/cytokine/growth factor signaling, control of the cell cycle and apoptosis, and transcriptional regulation appeared to be affected by aging. More transcripts were detected in older muscle, suggesting dedifferentiation, an increased number of splice variants, or increased cellular heterogeneity. We conclude that in human skeletal muscle the expression of many genes tends to increase or decrease between the third and seventh decades. The changes are modest when averaged over all of the cells in the tissue.
Mammalian p53 can function as a transcription factor in yeast (1992)

p53 has previously been shown to contain a transactivation domain using GAL4 fusion proteins and to bind specifically to a 33 base pair DNA sequence in immunoprecipitation assays. We show here that mammalian p53 expressed in S. cerevisiae is able to activate transcription of a reporter gene placed under the control of a CYC1 hybrid promoter containing the 33 base pair p53-binding sequence. The activation is dependent on the orientation and number of copies of the binding site. Three p53 mutants commonly found in human tumours, 175H, 248W and 273H, are unable to activate transcription. A fourth human p53 mutant, 285K, is temperature-sensitive for transcriptional activation. Murine p53 activates transcription from the same sequence. The murine 135V mutant, which is temperature-sensitive for mammalian cell transformation, is also temperature-sensitive for transcriptional activation. There is a much better correlation between mutation and transcriptional competence than between mutation and the structure of p53 determined with conformation-sensitive antibodies. We have therefore developed a simple transcription assay for p53 mutation in which yeast are transfected with p53 PCR products and mutation is scored on X-gal plates.
Lactic acid bacteria secrete metabolites retaining anti-inflammatory properties after intestinal transport (2004)

B breve and S thermophilus release metabolites exerting an anti-TNF-alpha effect capable of crossing the intestinal barrier. Commensal bacteria also display a TNF-alpha inhibitory capacity but to a lesser extent. These results underline the beneficial effect of commensal bacteria in intestinal homeostasis and may explain the role of some probiotic bacteria in alleviating digestive inflammation.