gebhart/patrepeval huggingface dataset:
Interactions of thrombospondins with α4β1 integrin and CD47 differentially modulate T cell behavior (2002)

Thrombospondin (TSP)-1 has been reported to modulate T cell behavior both positively and negatively. We found that these opposing responses arise from interactions of TSP1 with two different T cell receptors. The integrin alpha4beta1 recognizes an LDVP sequence in the NH2-terminal domain of TSP1 and was required for stimulation of T cell adhesion, chemotaxis, and matrix metalloproteinase gene expression by TSP1. Recognition of TSP1 by T cells depended on the activation state of alpha4beta1 integrin, and TSP1 inhibited interaction of activated alpha4beta1 integrin on T cells with its counter receptor vascular cell adhesion molecule-1. The alpha4beta1 integrin recognition site is conserved in TSP2. A recombinant piece of TSP2 containing this sequence replicated the alpha4beta1 integrin-dependent activities of TSP1. The beta1 integrin recognition sites in TSP1, however, were neither necessary nor sufficient for inhibition of T cell proliferation and T cell antigen receptor signaling by TSP1. A second TSP1 receptor, CD47, was not required for some stimulatory responses to TSP1 but played a significant role in its T cell antigen receptor antagonist and antiproliferative activities. Modulating the relative expression or function of these two TSP receptors could therefore alter the direction or magnitude of T cell responses to TSPs.
Use of cDNA subtraction and RNA interference screens in combination reveals genes required for germ-line development in Caenorhabditis elegans (2001)

Caenorhabditis elegans is an ideal organism for the study of the molecular basis of fundamental biological processes such as germ-line development, especially because of availability of the whole genome sequence and applicability of the RNA interference (RNAi) technique. To identify genes involved in germ-line development, we produced subtracted cDNA pools either enriched for or deprived of the cDNAs from germ-line tissues. We then performed differential hybridization on the high-density cDNA grid, on which about 7,600 nonoverlapping expressed sequence tag (EST) clones were spotted, to identify a set of genes specifically expressed in the germ line. One hundred and sixty-eight clones were then tested with the RNAi technique. Of these, 15 clones showed sterility with a variety of defects in germ-line development. Seven of them led to the production of unfertilized eggs, because of defects in spermatogenesis (4 clones), or defects in the oocytes (3 clones). The other 8 clones led to failure of oogenesis. These failures were caused by germ-line proliferation defect (Glp phenotype), meiotic arrest, and defects in sperm--oocyte switch (Mog phenotype) among others. These results demonstrate the efficacy of the screening strategy using the EST library combined with the RNAi technique in C. elegans.
Molecular Diagnosis of a Novel Coronavirus (2019-nCoV) Causing an Outbreak of Pneumonia (2020)

The established assays can achieve a rapid detection of 2019n-CoV in human samples, thereby allowing early identification of patients.
Stability decrease of RNA double helices by phenylalanine-, tyrosine- and tryptophane-amides. Analysis in terms of site binding and relation to melting proteins (1982)

The amides of L-phenylalanine, L-tyrosine and L-tryptophane decrease the melting temperatures tm of poly(A)*poly(U) and poly(I)*poly(C) double helices at low concentrations (1 mM), whereas high concentrations finally lead to an increase of tm. This dependence of the tm-values upon the ligand concentration can be represented quantitatively by a simple site binding model, providing binding parameters for the interaction between the amides and the nucleic acids both in the double- and the single-stranded conformation. According to these data the affinity to the single strands is higher than that to the double strands and increases in the series Phe less than Tyr less than Trp. The binding constants decrease with increasing salt concentration as expected for an interaction driven by electrostatic attraction. However, part of the interaction is also due to stacking between the aromatic amides and the nucleic acid bases. The present results indicate a direct correlation between the presence of aromatic amino acids at the binding site of helix destabilising proteins and the properties of simple derivatives of these amino acids. Furthermore the results suggest that very simple peptides containing aromatic amino acids served as a starting point for the evolution of helix destabilising proteins.
Nonsuture microvascular anastomosis using magnet rings: preliminary report. (1978)

An original method of nonsuture microvascular anastomosis was developed using magnet rings and hollow cogwheel-shaped metal devices held together by magnetic power. Only 8.3 minutes was required on average for the anastomosis with a high rate of patency. Histologically, a continuity of vascular wall is noted. This method of simple, rapid and reliable microvascular anastomosis appears to be the best one at present.
Quantitative and qualitative properties of host polymorphonuclear cells during experimentally induced Staphylococcus aureus mastitis in cows. (1991)

Polymorphonuclear cells have a critical role in the pathogenesis of bovine mastitis. We have documented that experimentally induced Staphylococcus aureus mastitis is associated with cyclic increase and decrease in the quantity of viable bacteria shed in the milk. Concomitant with this cycling of bacteria is an inverse cycling of the hosts cells within the milk. Such somatic cells were determined to be greater than or equal to 95% polymorphonuclear cells. The quality of these cells was evaluated by measuring their relative efficiency of bacterial killing and phagocytosis at various times during an infection. Host polymorphonuclear cells had as much as 10,000-fold variation in the bactericidal failure rate for staphylococci during cell cycling. The most efficient bactericidal effect was observed at or near the peak of the somatic cell count (SCC). The ability of these cycling cells to ingest fluorescent beads was also quantitated by use of flow cytometry. The percentage of phagocytic polymorphonuclear cells that ingested fluorescent latex beads ranged from 15 to 80% of the total cell population during cell cycling, and tended to be optimal at or near peak SCC. In addition, the average number of beads ingested varied between 1 and 2 particles/polymorphonuclear cell, with as many as 17% of the phagocytic cells ingesting 4 or more beads at maximal efficiency. Polymorphonuclear cells from quarters infected with S aureus varied quantitatively (total SCC) and qualitatively (bactericidal activity and phagocytic ability) during the course of an infection. Not only is the quantity of host's phagocytic cells in the mammary gland central to the defense mechanism against infection, but the biological activation state appears to be equally important. The role of these cells in the pathogenesis of a cycling infection is presented in a model to explain the cyclic nature of mastitis.
Three‐dimensional Cell Cultures Mimic Tissuesa (1992)

Three-dimensional cell culture using gels of type I collagen is a flexible method for studying cell behavior in a tissuelike environment. With only small changes in the basic protocol, we were able to encapsulate neutrophils, hepatocytes, and PC12 cells. As demonstrated by cell-specific assays for migration, protein secretion, and growth factor induction, the encapsulated cells were viable and functional. In future studies, we will focus on using these cell cultures to study cell movement, cell growth, and cell function in carefully controlled tissuelike environments.
Growth of Au-catalyzed ordered GaAs nanowire arrays by molecular-beam epitaxy (2002)

Ordered gallium arsenide (GaAs) nanowires are grown by molecular-beam epitaxy on GaAs (111)B substrates using Au-catalyzed vapor–liquid–solid growth defined by nanochannel alumina (NCA) templates. Field-emission scanning electron microscope images show highly ordered nanowires with a growth direction perpendicular to the substrate. The size (i.e., diameter) distribution of the wires is drastically narrowed by depositing the gold catalyst through an NCA template mask; this narrows the size distribution of the gold dots and arranges them in a well-ordered array, as defined by the NCA template. The nanowire diameter distribution full width at half maximum on the masked substrate is 5.1 nm, compared with 15.7 nm on an unmasked substrate.
Replication of Yeast DNA and Novel Chromosome Formation in Mouse Cells (1996)

To determine whether yeast DNA can replicate or segregate in mammalian cells, we have transferred genomic DNA from the yeast Saccharomyces cerevisiae into mouse cells. Most of the lines contained stably integrated yeast DNA. However, in two of the lines, the yeast DNA was maintained as numerous small extrachromosomal elements which were still present after 26 cell divisions in selection but which were lost rapidly out of selection. This indicates that, although yeast DNA can replicate in mouse cells, the yeast centromere does not function to give segregation. In one cell line we observed a large novel chromosome consisting almost entirely of yeast DNA. This chromosome segregates well and contains mouse centromeric minor satellite DNA and variable amounts of major satellite DNA which probably comprise the functional centromere. The yeast DNA in the novel chromosome has a compacted chromatin structure which may be responsible for the efficient formation of anaphase bridges. Furthermore, yeast DNA integrated into mouse chromosomes forms constrictions at the point of integration. These features have previously been presumed to be hallmarks of centromeric function in transfection assays aimed at identifying putative centromeric DNA. Hence our results suggest caution be exercised in the interpretation of such assays.
The Tubular Thermosyphon (1992)

Abstract The tubular thermosyphon is a very simple idea for transferring heat. Fluid inside a tube is circulated by buoyancy forces and thus carries thermal energy from the hot end to the cold end with great efficiency. The device has many uses: freezing ground, cooling equipment and machinery, waste heat recovery, and energy conservation. The operating details of the thermosyphon are, however, very complex and change dramatically with the circumstances. The length and diameter of the tube, the nature and state of the fluid, the strength and variation of the body force field, etc., all influence the internal circulation pattern and thus create different operating characteristics - variations on a basic theme. The book deals with each of these variations thoroughly and systematically. Emphasis is placed on the physical principles underlying thermal behaviour: under single-phase or evaporative conditions; whether the tube is stationary or rotating; and whether it is straight or bent. Consideration is also given to other devices having a similar purpose.
Synthesis and Pharmacological Activity of 3-(2-Pyrrolidinyl)indoles (1964)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and Pharmacological Activity of 3-(2-Pyrrolidinyl)indolesGilbert A. Youngdale, Douglas G. Anger, William C. Anthony, John P. Da Vanzo, Margaret E. Greig, Richard V. Heinzelman, Hugh H. Keasling, and Jacob SzmuszkoviczCite this: J. Med. Chem. 1964, 7, 4, 415–427Publication Date (Print):July 1, 1964Publication History Published online1 May 2002Published inissue 1 July 1964https://pubs.acs.org/doi/10.1021/jm00334a006https://doi.org/10.1021/jm00334a006research-articleACS PublicationsRequest reuse permissionsArticle Views299Altmetric-Citations15LEARN 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
Apoptosis in refractory anaemia with ringed sideroblasts is initiated at the stem cell level and associated with increased activation of caspases (2001)

Treatment with granulocyte colony-stimulating factor plus erythropoietin may improve haemoglobin levels in patients with ringsideroblastic anaemia (RARS) and reduce bone marrow apoptosis. We studied bone marrow from 10 RARS patients, two of whom were also investigated after successful treatment. Mononuclear, erythroid and CD34+ cells were analysed with regard to proliferation, apoptosis, clonogenic capacity and oncoprotein expression, in the presence or absence of Fas-agonist, Fas-blocking antibody 2 and caspase-3 inhibitor. During culture, RARS bone marrow cells showed higher spontaneous apoptosis (P < 0.05) and caspase activity (P < 0.05)) than bone marrow cells from healthy donors. Eight out of nine patients had reduced growth of erythroid colony-forming units (CFU-E) (< 10% of control) and granulocyte-macrophage CFU (CFU-GM) (< 50% of control) from CD34+ cells. Fas ligation increased apoptosis and decreased colony growth equally in RARS and controls, but caused significantly more caspase activation in RARS (P < 0.01). Fas-blocking antibody showed no significant inhibitory effect on spontaneous apoptosis or ineffective haematopoiesis, as measured using phosphatidylserine exposure, the terminal deoxynucleotide transferase-mediated dUTP-biotin nick-end labelling technique, caspase activity or clonogenic growth. Caspase inhibition reduced apoptosis, increased proliferation and enhanced erythroid colony growth from CD34+ cells in RARS, but showed no effect on normal cells. CFU-E improved > 1000% after successful treatment. Thus, erythroid apoptosis in RARS is initiated at the CD34+ level and growth factor treatment may improve stem cell function. Enhanced caspase activation at the stem cell level, albeit not mediated through endogenous activation of the Fas receptor, contributes to the erythroid apoptosis in RARS.
The Substrate Specificity of Fumarase (1968)

Acid-This compound was prepared from dimethylmaleic anhydride (Aldrich) by the method of Couper, Kibler, and Lutz (13).The compound melted at 240" and was chromatographically homogeneous.nL-Erythro-chloromalic Acid-This compound was synthesized according to the procedure of Kuhn and Ebel (14) ; it melted at 142-144" after recrystallization from ethyl ether-ligroin.
P‐111: Reflective Display Based on Total Internal Reflection and Grating‐Grating Coupling (2003)

Abstract We report on a novel reflection‐type display based on total internal reflection and grating‐grating coupling fabricated in H‐PDLC materials. In this display, two symmetric slanted gratings are temporally multiplexed into a single film. A narrowband light is selected and diffracted from two coupled Bragg gratings creating a reflected image. These holographic pixels have switching voltages that are at least one‐half that of H‐PDLC reflective displays reported in the literature.
The mammalian Mediator complex (2004)

The multiprotein Mediator (Med) complex is an evolutionarily conserved transcriptional regulator that plays important roles in activation and repression of RNA polymerase II transcription. Prior studies identified a set of more than twenty distinct polypeptides that compose the Saccharomyces cerevisiae Mediator. Here we discuss efforts to characterize the subunit composition and associated activities of the mammalian Med complex.
Trichostatin A, a histone deacetylase inhibitor, suppresses proliferation and promotes apoptosis of esophageal squamous cell lines (2015)

Histone deacetylase (HDAC)‑mediated epigenetic modification plays crucial roles in numerous biological processes, including cell cycle regulation, cell proliferation and apoptosis. HDAC inhibitors demonstrate antitumor effects in various cancers, including glioblastoma and breast cancer. HDAC inhibitors are therefore promising antitumor drugs for these tumors. The tumorigenesis and development of esophageal squamous cell carcinoma (ESCC) involve genetic and epigenetic mechanisms. However, the effects of the HDAC inhibitor on ESCC are not fully investigated. In the present study, ESCC cells were treated with trichostatin A (TSA) and its antitumor effects and related mechanisms were investigated. The results indicated that TSA suppressed the proliferation of ESCCs and caused G1 phase arrest by inducing the expression of p21 and p27. TSA also induced cell apoptosis by enhancing the expression of pro‑apoptotic protein Bax and decreasing the expression of anti‑apoptotic protein Bcl‑2. Furthermore, TSA inhibited the expression of phosphatidylinositol‑3‑kinase (PI3K) and reduced the phosphorylation of Akt and extracellular signal‑regulated kinase (ERK)1/2 in EC9706 and EC1 cell lines. High levels of acetylated histone H4 were detected in TSA‑treated ESCC cell lines. Overall, these results indicate that TSA suppresses ESCC cell growth by inhibiting the activation of the PI3K/Akt and ERK1/2 pathways. TSA also promotes cell apoptosis through epigenetic regulation of the expression of apoptosis‑related protein.
Hyperparameter Optimization and Boosting for Classifying Facial Expressions: How good can a "Null" Model be? (2013)

One of the goals of the ICML workshop on representation and learning is to establish benchmark scores for a new data set of labeled facial expressions. This paper presents the performance of a "Null" model consisting of convolutions with random weights, PCA, pooling, normalization, and a linear readout. Our approach focused on hyperparameter optimization rather than novel model components. On the Facial Expression Recognition Challenge held by the Kaggle website, our hyperparameter optimization approach achieved a score of 60% accuracy on the test data. This paper also introduces a new ensemble construction variant that combines hyperparameter optimization with the construction of ensembles. This algorithm constructed an ensemble of four models that scored 65.5% accuracy. These scores rank 12th and 5th respectively among the 56 challenge participants. It is worth noting that our approach was developed prior to the release of the data set, and applied without modification; our strong competition performance suggests that the TPE hyperparameter optimization algorithm and domain expertise encoded in our Null model can generalize to new image classification data sets.
Excitation of higher order modes in optical fibers with parabolic index profile (1988)

A large number of modes can be supported by multimode fibers. There are applications where higher order modes are preferred. Microbend intensity sensors are good examples. The sensitivity of these sensors is greatly increased if higher order modes are excited. In this work, a simple method to excite higher order modes preferentially is suggested. It consists of thin-film gratings deposited directly onto the fiber end. By controlling the film thickness or transparency of the grating structure, a desired transmission coefficient T(r,Phi) is synthesized. The desired mode can be excited preferentially by incident Gaussian beams without the aid of additional optical components. Binary intensity and binary phase gratings have been studied. Numerical investigation reveals that the phase gratings are more effective for the preferential excitation of higher order modes than the intensity gratings. In fact, by using binary phase gratings and in optimal excitation conditions as much as 81.1, 76.9, 74.6, 73.3, and 72.3% of the power in the incoming, linearly polarized, fundamental Gaussian beam can be converted to LP(02), LP(03), LP(04), LP(05), and LP(06) modes, respectively, excluding Fresnel loss.
SEC8, a Subunit of the Putative Arabidopsis Exocyst Complex, Facilitates Pollen Germination and Competitive Pollen Tube Growth (2005)

The exocyst, a complex of eight proteins, contributes to the morphogenesis of polarized cells in a broad range of eukaryotes. In these organisms, the exocyst appears to facilitate vesicle docking at the plasma membrane during exocytosis. Although we had identified orthologs for each of the eight exocyst components in Arabidopsis (Arabidopsis thaliana), no function has been demonstrated for any of them in plants. The gene encoding one exocyst component ortholog, AtSEC8, is expressed in pollen and vegetative tissues of Arabidopsis. Genetic studies utilizing an allelic series of six independent T-DNA mutations reveal a role for SEC8 in male gametophyte function. Three T-DNA insertions in SEC8 cause an absolute, male-specific transmission defect that can be complemented by expression of SEC8 from the LAT52 pollen promoter. Microscopic analysis shows no obvious abnormalities in the microgametogenesis of the SEC8 mutants, and the mutant pollen grains appear to respond to the signals that initiate germination. However, in vivo assays indicate that these mutant pollen grains are unable to germinate a pollen tube. The other three T-DNA insertions are associated with a partial transmission defect, such that the mutant allele is transmitted through the pollen at a reduced frequency. The partial transmission defect is only evident when mutant gametophytes must compete with wild-type gametophytes, and arises in part from a reduced pollen tube growth rate. These data support the hypothesis that one function of the putative plant exocyst is to facilitate the initiation and maintenance of the polarized growth of pollen tubes.
Transplantation of Embryonic Dopamine Neurons for Severe Parkinson's Disease (2001)

Human embryonic dopamine-neuron transplants survive in patients with severe Parkinson's disease and result in some clinical benefit in younger but not in older patients.
Physiological Actions and Clinical Applications of Transforming Growth Factor-β (TGF-β) (1993)

In the 10 years since its definition and characterization, TGF-β has come to be accepted as the prototypical multifunctional peptide growth factor. Attempts to understand its mechanism of action on cells have resulted in conceptual advances in knowledge of the contextual nature of growth factor activities. These have included modulatory effects both of sets of growth factors and of the cellular environment, including extracellular matrix (Sporn and Roberts, 1990; Nathan and Sporn, 1991). Because of the breadth of the cellular targets and activities of TGF-β it is impossible to be comprehensive in review of its physiological roles. Rather, we will cover selected aspects with emphasis on physiological roles which might ultimately find clinical application. As much as possible, we will consider in vivo roles of TGF-β in the context of the inherent complexity of cell-matrix and cell-cell interactions characteristic of mixed cell populations, tissues, or organs.