gebhart/patrepeval huggingface dataset:
The p38 Mitogen-activated Protein Kinase Is Required for NF-κB-dependent Gene Expression (1999)

Endotoxin-induced cytokine gene transcription in monocytes and macrophages is regulated in part by NF-kappaB. We have previously shown that the p38 mitogen-activated protein (MAP) kinase is necessary for endotoxin-induced cytokine gene transcription. Due to the fact that most cytokine promoter sequences have active NF-kappaB sites, we hypothesized that the p38 MAP kinase was necessary for NF-kappaB-dependent gene expression. We found that NF-kappaB-dependent gene expression was reduced to near control levels with either SB 203580 or a dominant-negative p38 MAP kinase expression vector. Inhibition of the p38 MAP kinase did not alter NF-kappaB activation at any level, but it significantly reduced the DNA binding of TATA-binding protein (TBP) to the TATA box. The dominant-negative p38 MAP kinase expression vector interfered with the direct interaction of native TFIID (TBP) with a co-transfected p65 fusion protein. Likewise, this dominant-negative plasmid also interfered with the direct interaction of a co-transfected TBP fusion protein with the native p65 subunit. The p38 kinase also phosphorylated TFIID (TBP) in vitro, and SB 203580 inhibited phosphorylation of TFIID (TBP) in vivo. Thus, the p38 MAP kinase regulates NF-kappaB-dependent gene transcription, in part, by modulating activation of TFIID (TBP).
Effect of neutrophil depletion on ischemic renal injury in the rat. (1989)

Oxygen free radicals have been implicated in postischemic renal injury. However, the source of these oxygen free radicals has not been well defined. One potential source is activated neutrophils. Neutrophil depletion was produced in rats by using two different techniques, and the effect on ischemic injury was examined. Rabbit anti-rat neutrophil serum was prepared by immunizing a rabbit with a Percoll gradient centrifugation-purified (approximately 90%) suspension of rat neutrophils. Rats received antineutrophil serum in one of four protocols and were subsequently subjected to 40 minutes of renal artery occlusion. Control animals received nonimmune rabbit serum. The serum creatinine levels 24 hours after ischemia were not different between control and immune serum-treated rats in any of the protocols despite significant reductions in absolute neutrophil count. In a separate study, nitrogen mustard was administered 40 hours before ischemia. Nitrogen mustard-treated rats developed moderate neutropenia and 24 hours after ischemia had lower serum creatinine levels and higher inulin clearance. However, nitrogen mustard-treated rats lost 31.5 +/- 5 gm body weight in the 2 days after nitrogen mustard administration, whereas control animals gained 5.9 +/- 5.9 gm during the same interval. Furthermore, among nitrogen mustard-treated rats there was no correlation between neutrophil count and postischemic renal function. It is thus possible that the beneficial effects of nitrogen mustard were caused by a mechanism other than neutrophil depletion. In summary, in four protocols that used antineutrophil serum, neutropenia did not protect against ischemic injury. Nitrogen mustard provided protection, but probably by a neutrophil-independent mechanism.(ABSTRACT TRUNCATED AT 250 WORDS)
MSR-VTT: A Large Video Description Dataset for Bridging Video and Language (2016)

While there has been increasing interest in the task of describing video with natural language, current computer vision algorithms are still severely limited in terms of the variability and complexity of the videos and their associated language that they can recognize. This is in part due to the simplicity of current benchmarks, which mostly focus on specific fine-grained domains with limited videos and simple descriptions. While researchers have provided several benchmark datasets for image captioning, we are not aware of any large-scale video description dataset with comprehensive categories yet diverse video content. In this paper we present MSR-VTT (standing for "MSRVideo to Text") which is a new large-scale video benchmark for video understanding, especially the emerging task of translating video to text. This is achieved by collecting 257 popular queries from a commercial video search engine, with 118 videos for each query. In its current version, MSR-VTT provides 10K web video clips with 41.2 hours and 200K clip-sentence pairs in total, covering the most comprehensive categories and diverse visual content, and representing the largest dataset in terms of sentence and vocabulary. Each clip is annotated with about 20 natural sentences by 1,327 AMT workers. We present a detailed analysis of MSR-VTT in comparison to a complete set of existing datasets, together with a summarization of different state-of-the-art video-to-text approaches. We also provide an extensive evaluation of these approaches on this dataset, showing that the hybrid Recurrent Neural Networkbased approach, which combines single-frame and motion representations with soft-attention pooling strategy, yields the best generalization capability on MSR-VTT.
A Method for Spectrum Shaping and NBI Suppression in UWB Communications (2006)

This paper investigates spectrum shaping in ultrawideband (UWB) communications in order to introduce spectral nulls to limit interference with narrowband signals. Each transmitted symbol is represented by a monocycle "coded" Gaussian pulse, where use of the monocycle Gaussian pulse ensures that the UWB spectrum mask established by the Federal Communications Commission (FCC) is met and where the codeword is designed to generate a spectral null at the frequency or frequencies being used by existing narrowband devices. Signals obtained with different spectrum shapings (e.g., Butterworth, Chebyshev, elliptical) and by introducing nulls at multiple interference frequency bands are discussed. The performance of a monocycle coded UWB system with a spectral null in the presence of narroband interference (NBI) using single carrier block transmission with frequency domain equalization (SC-FDE) is simulated and compared with that of an uncoded SC-FDE UWB system using a single Gaussian monocycle. Our results show that NBI can be effectively suppressed by transmitting and matched filtering the pulse with a spectral null at the interference frequency, therefore improving the robustness of SC-FDE UWB to NBI.
Mapping and sequence of the gene for the pseudorabies virus glycoprotein which accumulates in the medium of infected cells (1985)

RNA from pseudorabies virus (PRV)-infected cells was translated in a reticulocyte lysate with and without the addition of dog pancreas microsomes. Upon addition of the microsomes to the translation reaction, an additional prominent protein product was observed that was not present when microsomes were omitted. The gene coding for this processed protein and its lower-molecular-weight precursor was mapped within the small unique region of the genome by hybridization of mRNA to cloned fragments of PRV DNA and translation of the selected mRNAs. A fragment of the coding region of this gene was inserted into an open reading frame cloning vector to express part of this gene as a hybrid protein in Escherichia coli. This hybrid protein was injected into mice to raise an antiserum which was found to precipitate the glycoprotein which accumulates in the medium of PRV-infected cells. This allows us to conclude that the gene for the "excreted" glycoprotein (gX) maps to the small unique region of the genome, and that the precursor of this glycoprotein is readily processed by dog pancreas microsomes. The region of the PRV genome which codes for this glycoprotein was sequenced and found to include an open reading frame coding for 498 amino acids, flanked by sequences which contain features common to eucaryotic promoters and polyadenylation signals. The predicted protein sequence includes a hydrophobic sequence at the N-terminus which could be a signal sequence, and a hydrophobic sequence followed by a hydrophilic sequence at the C-terminus.
Fast MCMC sampling for hidden markov models to determine copy number variations (2011)

An implementation of our method will be made available as part of the open source GHMM library from http://ghmm.org.
Analysis of time-varying images using 3D vascular models (2002)

A medical image traditionally represents a "snapshot" of a portion of the patient's anatomy at a particular moment in time. However, the appearance of image objects often varies between images taken at different times. Such changes may occur because of differences in the image acquisition techniques employed, because of shifts in the positions of organs, or because of development, progression, or regression of pathology. We have developed a method of defining vessel "trees" from 3D image data. These vessel trees can then be registered with any type of 2- or 3D image data obtained from the same patient and that show the vasculature. Changes in vascular configuration can then be used not only to clarify vascular changes over time, but also to help determine the location and/or change in other image objects. As vessels are present throughout the body, the approach is applicable to any anatomical region.
Newt cells secrete extracellular vesicles with therapeutic bioactivity in mammalian cardiomyocytes (2018)

Newts can regenerate amputated limbs and cardiac tissue, unlike mammals which lack broad regenerative capacity. Several signaling pathways involved in cell proliferation, differentiation and survival during newt tissue regeneration have been elucidated, however the factors that coordinate signaling between cells, as well as the conservation of these factors in other animals, are not well defined. Here we report that media conditioned by newt limb explant cells (A1 cells) protect mammalian cardiomyocytes from oxidative stress-induced apoptosis. The cytoprotective effect of A1-conditioned media was negated by exposing A1 cells to GW4869, which suppresses the generation of extracellular vesicles (EVs). A1-EVs are similar in diameter (~100-150 nm), structure, and share several membrane surface and cargo proteins with mammalian exosomes. However, isolated A1-EVs contain significantly higher levels of both RNA and protein per particle than mammalian EVs. Additionally, numerous cargo RNAs and proteins are unique to A1-EVs. Of particular note, A1-EVs contain numerous mRNAs encoding nuclear receptors, membrane ligands, as well as transcription factors. Mammalian cardiomyocytes treated with A1-EVs showed increased expression of genes in the PI3K/AKT pathway, a pivotal player in survival signaling. We conclude that newt cells secrete EVs with diverse, distinctive RNA and protein contents. Despite ~300 million years of evolutionary divergence between newts and mammals, newt EVs confer cytoprotective effects on mammalian cardiomyocytes.
Diabesity: An Inflammatory Metabolic Condition (2003)

Diabesity, that is to say, obesity-dependent diabetes, has emerged as a major public health problem. Though diabesity is basically explained by insulin resistance and pancreatic beta cell dysfunction, new paradigms have evolved to explain these alterations in the context of the modern epidemics of obesity and diabetes. Among these, the association of inflammation with obesity is an important component of the common soil from which diabetes and cardiovascular diseases (CVD) derive. This Review presents our epidemiological findings, based primarily on the ARIC Study, in the context of the other epidemiological studies supporting the inflammatory nature of diabetes, CVD and the metabolic syndrome. We also review the characteristics of the innate immune system, including the molecular interface of innate immunity with metabolism, components of which are responsible for the presence of a state of mild, chronic and systemic inflammation related to diabesity. Finally, we present obesity as an inflammatory condition, obesitis, and propose a conceptual framework that integrates the epidemiological findings with new provocative basic science results.
Inhibition and Detection of Galectins (2006)

More and more studies report on the roles that galectins play in numerous types of cancer. These roles can be varied, as has been shown particularly for galectin-3. These studies have created the need for inhibitors that can block unwanted effects, and the need to detect galectins in tissues, in order to better understand their role, and aid in diagnosis and prognosis. Since galectins bind beta-galactosides, monovalent galactose-derived inhibitors have been prepared but also peptidic ones have appeared. Since galectins often induce crosslinking and partake in aggregation phenomena, multivalency has been a successful design element in inhibitor development. Currently, there are no cheap and convenient solutions available for the detection of, ideally multiple, galectins in tissue samples, although antibody-based methods such as ELISA and Western blot analysis are being used. Besides these, a chemical probe-based method also shows potential as an alternative.
Molecular cloning and analysis of the mouse homologue of the tumor-associated mucin, MUC1, reveals conservation of potential O-glycosylation sites, transmembrane, and cytoplasmic domains and a loss of minisatellite-like polymorphism (1991)

We present here the full-length cDNA sequence and genomic structure of the mouse homologue of the tumor-associated mucin, MUC1. This mucin (previously called polymorphic epithelial mucin) is present at the apical surface of most glandular epithelial cells. The mouse gene, Muc-1, encodes an integral membrane protein with 40% of its coding capacity made up of serine, threonine, and proline, a composition typical of a highly O-glycosylated protein. The mucin core protein consists of an amino-terminal signal sequence, a tandem repeat domain encoding 16 repeats of 20-21 amino acids, and unique sequence containing transmembrane and cytoplasmic domains. Homology with the human protein is only 34% in the tandem repeat domain, mainly showing conservation of serines and threonines, presumed sites of O-linked carbohydrate attachment. Homology rises to 87% in the transmembrane and cytoplasmic domains, suggesting that these regions may be functionally important. The pattern of expression of the mouse mucin is very similar to that of its human counterpart and accordingly the two promoter regions share high homology, 74%, although previously identified potential hormone-responsive elements are not conserved. Interestingly, the mouse homologue, unlike its human counterpart does not exhibit a variable number tandem repeat polymorphism. We present evidence that suggests that the mouse gene was at one time polymorphic but has mutated away from this state.
The Effect of Electronic Self‐Monitoring on Weight Loss and Dietary Intake: A Randomized Behavioral Weight Loss Trial (2010)

Technology may improve self-monitoring adherence and dietary changes in weight loss treatment. Our study aimed to investigate whether using a personal digital assistant (PDA) with dietary and exercise software, with and without a feedback message, compared to using a paper diary/record (PR), results in greater weight loss and improved self-monitoring adherence. Healthy adults (N = 210) with a mean BMI of 34.01 kg/m(2) were randomized to one of three self-monitoring approaches: PR (n = 72), PDA with self-monitoring software (n = 68), or PDA with self-monitoring software and daily feedback messages (PDA+FB, n = 70). All participants received standard behavioral treatment. Self-monitoring adherence and change in body weight, waist circumference, and diet were assessed at 6 months; retention was 91%. All participants had a significant weight loss (P < 0.01) but weight loss did not differ among groups. A higher proportion of PDA+FB participants (63%) achieved ≥ 5% weight loss in comparison to the PR group (46%) (P < 0.05) and PDA group (49%) (P = 0.09). Median percent self-monitoring adherence over the 6 months was higher in the PDA groups (PDA 80%; PDA+FB 90%) than in the PR group (55%) (P < 0.01). Waist circumference decreased more in the PDA groups than the PR group (P = 0.02). Similarly, the PDA groups reduced energy and saturated fat intake more than the PR group (P < 0.05). Self-monitoring adherence was greater in the PDA groups with the greatest weight change observed in the PDA+FB group.
Phase iii randomized trial of interleukin-2 with or without lymphokine-activated killer cells in the treatment of patients with advanced renal cell carcinoma (1995)

The dose and schedule of IL-2 used in this study resulted in a low level of antitumor activity and the addition of LAK did not improve the response rate against RCC. Given the infrequent, but reproducible, responses with IL-2 and interferon-based regimens, continued investigation of these agents is warranted as is the study of new cytokines. Alternative treatment strategies should be studied in RCC and new agents and treatment regimens that appear promising in Phase II studies must be studied in randomized trials.
Plasma reactive ion etching of 193 nm attenuated phase shift mask materials (1997)

This article gives details on plasma etch process development for potential attenuated phase shift masking materials for use at 193 nm. Masking films investigated include materials based on aluminum nitride, zirconium nitride, molybdenum–silicon oxide, tantalum–silicon nitride, and tantalum–silicon oxide. A variety of halogenated etch plasmas were investigated, including fluorine-based chemistries (CF4 and SF6) and chlorine-based chemistries (Cl2, CCl4) combined with oxygen, argon, and hydrogen. Thin films of TaN, MoSiO, SixNy, and TaO that allow for sufficient volatility in fluorine plasma and processes using SF6 were chosen for optimization. Fluorides of aluminum and zirconium exhibit very low vapor pressure so Cl2+Ar mixtures were chosen for study. Al and Zr chlorides can be made volatile but ion assistance is generally needed to produce sufficiently high etch rates. Because of this, selectivity to resist is generally poor. Of all the materials evaluated, attenuated phase shift mask films of TaN/Si3N4 etched with SF6 allow the largest etch selectivity to both fused silica and resist.
IL-17 production from activated T cells is required for the spontaneous development of destructive arthritis in mice deficient in IL-1 receptor antagonist (2003)

IL-17 is a T cell-derived, proinflammatory cytokine that is suspected to be involved in the development of various inflammatory diseases. Although there are elevated levels of IL-17 in synovial fluid of patients with rheumatoid arthritis, the pathogenic role of IL-17 in the development of rheumatoid arthritis remains to be elucidated. In this report, the effects of IL-17 deficiency were examined in IL-1 receptor antagonist-deficient (IL-1Ra(-/-)) mice that spontaneously develop an inflammatory and destructive arthritis due to unopposed excess IL-1 signaling. IL-17 expression is greatly enhanced in IL-1Ra(-/-) mice, suggesting that IL-17 activity is involved in the pathogenesis of arthritis in these mice. Indeed, the spontaneous development of arthritis did not occur in IL-1Ra(-/-) mice also deficient in IL-17. The proliferative response of ovalbumin-specific T cells from DO11.10 mice against ovalbumin cocultured with antigen-presenting cells from either IL-1Ra(-/-) mice or wild-type mice was reduced by IL-17 deficiency, indicating insufficient T cell activation. Cross-linking OX40, a cosignaling molecule on CD4(+) T cells that plays an important role in T cell antigen-presenting cell interaction, with anti-OX40 Ab accelerated the production of IL-17 induced by CD3 stimulation. Because OX40 is induced by IL-1 signaling, IL-17 induction is likely to be downstream of IL-1 through activation of OX40. These observations suggest that IL-17 plays a crucial role in T cell activation, downstream of IL-1, causing the development of autoimmune arthritis.
Understanding COVID-19 vaccine efficacy (2020)

Vaccine efficacy in high-risk groups and reduced viral shedding are important for protection
Dehydroepiandrosterone (DHEA) and Synthetic DHEA Analogs Are Modest Inhibitors of HIV-1 IIIB Replication (1992)

Down-regulation of Epstein-Barr virus (EBV) induced transformation of human lymphocytes in vitro by dehydroepiandrosterone (DHEA), a naturally occurring human steroid secreted by the adrenal gland has been demonstrated. This article reports on the effects of DHEA and its novel synthetic analogs 16 alpha-fluoro-5-androsten-17-one (8354) and 3 beta-hydroxy-16 alpha-fluoro-5 alpha-androstan-17-one (OH8356) on human immunodeficiency virus (HIV-1) replication. Treatment with DHEA, 8354, or OH8356 resulted in a modest down-regulation of HIV-1 replication in phytohemagglutinin-stimulated peripheral blood lymphocytes as measured by syncytia formation, release of p24 antigen, and accumulation of reverse transcriptase activity. DHEA and 8354 also reduced syncytia formation in HIV-1-infected SupT1 lymphoblasts. DHEA and synthetic analogs of DHEA, which have been shown previously to have antiproliferative effects, now are shown to reduce HIV-1 replication. DHEA or synthetic analogs of DHEA could provide an alternative and/or adjuvant for HIV-1 infection.
Bone Marrow–Derived Mesenchymal Stem Cells in Repair of the Injured Lung (2005)

We sought to determine whether an intact bone marrow is essential to lung repair following bleomycin-induced lung injury in mice, and the mechanisms of any protective effects conferred by bone marrow-derived mesenchymal stem cell (BMDMSC) transfer. We found that myelosupression increased susceptibility to bleomycin injury and that BMDMSC transfer was protective. Protection was associated with the differentiation of engrafted BMDMSC into specific and distinct lung cell phenotypes, with an increase in circulating levels of G-CSF and GM-CSF (known for their ability to promote the mobilization of endogenous stem cells) and with a decrease in inflammatory cytokines. In vitro, cells from injured, but not from normal, mouse lung produced soluble factors that caused BMDMSC to proliferate and migrate toward the injured lung. We conclude that bone marrow stem cells are important in the repair of bleomycin-injured lung and that transfer of mesenchymal stem cells protects against the injury. BMDMSC localize to the injured lung and assume lung cell phenotypes, but protection from injury and fibrosis also involves suppression of inflammation and triggering production of reparative growth factors.
The immunosuppressant FTY720 inhibits tumor angiogenesis via the sphingosine 1‐phosphate receptor 1 (2007)

FTY720, a sphingosine 1-phosphate (S1P) analog, acts as an immunosuppressant through trapping of T cells in secondary lymphoid tissues. FTY720 was also shown to prevent tumor growth and to inhibit vascular permeability. The MTT proliferation assay illustrated that endothelial cells are more susceptible to the anti-proliferative effect of FTY720 than Lewis lung carcinoma (LLC1) cells. In a spheroid angiogenesis model, FTY720 potently inhibited the sprouting activity of VEGF-A-stimulated endothelial cells even at concentrations that apparently had no anti-proliferative effect. Mechanistically, the anti-angiogenic effect of the general S1P receptor agonist FTY720 was mimicked by the specific S1P1 receptor agonist SEW2871. Moreover, the anti-angiogenic effect of FTY720 was abrogated in the presence of CXCR4-neutralizing antibodies. This indicates that the effect was at least in part mediated by the S1P1 receptor and involved transactivation of the CXCR4 chemokine receptor. Additionally, we could illustrate in a coculture spheroid model, employing endothelial and smooth muscle cells (SMCs), that the latter confer a strong protective effect regarding the action of FTY720 upon the endothelial cells. In a subcutaneous LLC1 tumor model, the anti-angiogenic capacity translated into a reduced tumor size in syngeneic C57BL/6 mice. Consistently, in the Matrigel plug in vivo assay, 10 mg/kg/d FTY720 resulted in a strong inhibition of angiogenesis as demonstrated by a reduced capillary density. Thus, in organ transplant patients, FTY720 may prove efficacious in preventing graft rejection as well as tumor development.