gebhart/patrepeval huggingface dataset:
Lessons in AIDS Vaccine Development Learned from Studies of Equine Infectious, Anemia Virus Infection and Immunity (2013)

Equine infectious anemia (EIA), identified in 1843 [1] as an infectious disease of horses and as a viral infection in 1904, remains a concern in veterinary medicine today. Equine infectious anemia virus (EIAV) has served as an animal model of HIV-1/AIDS research since the original identification of HIV. Similar to other lentiviruses, EIAV has a high propensity for genomic sequence and antigenic variation, principally in its envelope (Env) proteins. However, EIAV possesses a unique and dynamic disease presentation that has facilitated comprehensive analyses of the interactions between the evolving virus population, progressive host immune responses, and the definition of viral and host correlates of immune control and vaccine efficacy. Summarized here are key findings in EIAV that have provided important lessons toward understanding long term immune control of lentivirus infections and the parameters for development of an enduring broadly protective AIDS vaccine.
Genomic Analysis of Mouse Retinal Development (2004)

The vertebrate retina is comprised of seven major cell types that are generated in overlapping but well-defined intervals. To identify genes that might regulate retinal development, gene expression in the developing retina was profiled at multiple time points using serial analysis of gene expression (SAGE). The expression patterns of 1,051 genes that showed developmentally dynamic expression by SAGE were investigated using in situ hybridization. A molecular atlas of gene expression in the developing and mature retina was thereby constructed, along with a taxonomic classification of developmental gene expression patterns. Genes were identified that label both temporal and spatial subsets of mitotic progenitor cells. For each developing and mature major retinal cell type, genes selectively expressed in that cell type were identified. The gene expression profiles of retinal Müller glia and mitotic progenitor cells were found to be highly similar, suggesting that Müller glia might serve to produce multiple retinal cell types under the right conditions. In addition, multiple transcripts that were evolutionarily conserved that did not appear to encode open reading frames of more than 100 amino acids in length ("noncoding RNAs") were found to be dynamically and specifically expressed in developing and mature retinal cell types. Finally, many photoreceptor-enriched genes that mapped to chromosomal intervals containing retinal disease genes were identified. These data serve as a starting point for functional investigations of the roles of these genes in retinal development and physiology.
Free Radicals in the Physiological Control of Cell Function (2002)

At high concentrations, free radicals and radical-derived, nonradical reactive species are hazardous for living organisms and damage all major cellular constituents. At moderate concentrations, however, nitric oxide (NO), superoxide anion, and related reactive oxygen species (ROS) play an important role as regulatory mediators in signaling processes. Many of the ROS-mediated responses actually protect the cells against oxidative stress and reestablish "redox homeostasis." Higher organisms, however, have evolved the use of NO and ROS also as signaling molecules for other physiological functions. These include regulation of vascular tone, monitoring of oxygen tension in the control of ventilation and erythropoietin production, and signal transduction from membrane receptors in various physiological processes. NO and ROS are typically generated in these cases by tightly regulated enzymes such as NO synthase (NOS) and NAD(P)H oxidase isoforms, respectively. In a given signaling protein, oxidative attack induces either a loss of function, a gain of function, or a switch to a different function. Excessive amounts of ROS may arise either from excessive stimulation of NAD(P)H oxidases or from less well-regulated sources such as the mitochondrial electron-transport chain. In mitochondria, ROS are generated as undesirable side products of the oxidative energy metabolism. An excessive and/or sustained increase in ROS production has been implicated in the pathogenesis of cancer, diabetes mellitus, atherosclerosis, neurodegenerative diseases, rheumatoid arthritis, ischemia/reperfusion injury, obstructive sleep apnea, and other diseases. In addition, free radicals have been implicated in the mechanism of senescence. That the process of aging may result, at least in part, from radical-mediated oxidative damage was proposed more than 40 years ago by Harman (J Gerontol 11: 298-300, 1956). There is growing evidence that aging involves, in addition, progressive changes in free radical-mediated regulatory processes that result in altered gene expression.
Multiple sclerosis: Comparison of copolymer-1- reactive T cell lines from treated and untreated subjects reveals cytokine shift from T helper 1 to T helper 2 cells (2000)

Copolymer 1 (COP), a standardized mixture of synthetic polypeptides consisting of l-glutamic acid, l-lysine, l-alanine, and l-tyrosine, has beneficial effects in multiple sclerosis and experimental autoimmune encephalomyelitis. We selected a panel of 721 COP-reactive T cell lines (TCL) from the blood of COP-treated and untreated multiple sclerosis patients and from healthy donors by using the split-well cloning technique. All TCL selected with COP proliferated in response to COP but not to myelin basic protein (MBP). Conversely, 31 control TCL selected with MBP proliferated in response to MBP but not to COP. We used intracellular double-immunofluorescence flow cytometry for quantitative analysis of cytokine production (IL-4, IFN-gamma) by the TCL. The majority of the COP-reactive TCL from untreated multiple sclerosis patients and normal donors predominantly produced IFN-gamma and, accordingly, were classified as T helper 1 cells (TH1). In contrast, the majority of the COP-reactive TCL from COP-treated patients predominantly (but not exclusively) produced IL-4-i.e., were TH2 (P < 0.05 as assessed by using a suitable preference intensity index). Longitudinal analyses revealed that the cytokine profile of COP-reactive TCL tends to shift from TH1 to TH2 during treatment. Interestingly, although there was no proliferative cross-reaction, about 10% of the COP-reactive TCL responded to MBP by secretion of small amounts of IL-4 or IFN-gamma, depending on the cytokine profile of the TCL. These results are consistent with a protective effect of COP-reactive TH2 cells. It is hypothesized that these cells are activated by COP in the periphery, migrate into the central nervous system, and produce immunomodulatory cytokines after local recognition of MBP.
Osteoprotegerin inhibits the development of osteolytic bone disease in multiple myeloma (2001)

Multiple myeloma is a B-cell malignancy characterized by the accumulation of plasma cells in the bone marrow and the development of osteolytic bone disease. The present study demonstrates that myeloma cells express the critical osteoclastogenic factor RANKL (the ligand for receptor activator of NF-kappa B). Injection of 5T2MM myeloma cells into C57BL/KaLwRij mice resulted in the development of bone disease characterized by a significant decrease in cancellous bone volume in the tibial and femoral metaphyses, an increase in osteoclast formation, and radiologic evidence of osteolytic bone lesions. Dual-energy x-ray absorptiometry demonstrated a decrease in bone mineral density (BMD) at each of these sites. Treatment of mice with established myeloma with recombinant osteoprotegerin (OPG) protein, the soluble decoy receptor for RANKL, prevented the development of lytic bone lesions. OPG treatment was associated with preservation of cancellous bone volume and inhibition of osteoclast formation. OPG also promoted an increase in femoral, tibial, and vertebral BMD. These data suggest that the RANKL/RANK/OPG system may play a critical role in the development of osteolytic bone disease in multiple myeloma and that targeting this system may have therapeutic potential.
A New Solution for the Characterization of Unconventional Shale Resources Based on Analysis of Drill Cuttings (2015)

Abstract We introduce a new, cost-effective solution for the characterization of unconventional shale resources based on innovative analysis of drill cuttings. This solution was tested successfully on the Toarcian shales of the Couy-1 well, located in the southern Paris Basin, France. Ten samples of cuttings-sized rock fragments from different depths were subjected to several analytical methods to determine geochemical parameters (LECO and Rock Eval), the mineralogy and texture (QEMSCAN), and the mechanical properties (nanoindentation). Based on the results, the Toarcian shales were subdivided into two mineralogically distinct lithostratigraphic intervals. The Upper Toarcian shales consist of siltstone with a matrix of illitic clays, whereas the Lower Toarcian shales consist mainly of calcareous mudstone with a matrix of finely intermixed calcite and clays. The Young's modulus varies between 12.5 and 25.6 GPa and decreases with increasing TOC content. An interval with high TOC content (&amp;gt; 1.9%) is located between depths of 330 and 350 meter in the Lower Toarcian shales, with a maximum TOC content of 7.6%. A basic set of wireline logs was available and subjected to multi-mineral stochastic log interpretation. By calibrating the log interpretation with the results of the analytical methods, the main petrophysical parameters (TOC content, lithology, porosity, saturation) were successfully determined on log scale. This provides a method for upscaling core and drill cuttings measurements to reservoir scale. In addition, nanoindentation data were used to create a synthetic shear sonic log, allowing for calculation of elastic moduli and brittleness logs. The workflow introduced here provides a method for reliable and accurate characterization of unconventional shale resources based on existing data sets, i.e. drill cuttings and basic log sets. The results can be used for assessment of the hydrocarbon potential and identification of the most prospective zones within source-rock intervals.
ChemInform Abstract: Synthesis of Iso‐ddA, Member of a Novel Class of Anti‐HIV Agents. (1990)

Abstract Starting with the erythro‐pentofuranose derivative (I), two synthetic approaches to iso‐ddA (VII) are described as outlined in the reaction scheme.
Probability‐based structural parameters from three‐dimensional nuclear magnetic resonance images as predictors of trabecular bone strength (1997)

The mechanical competence of trabecular bone is a function of its apparent density and three-dimensional (3D) distribution. Three-dimensional structure is typically inferred from histomorphometry and stereology on a limited number of two-dimensional anatomic sections. In this work 3D nuclear magnetic resonance (NMR) images of anisotropic trabecular bone from the distal radius were analyzed in terms of a series of new structural parameters which are obtainable at relatively crude resolution, i.e., in the presence of substantial partial volume blurring. Unlike typical feature extraction techniques requiring image segmentation, the method relies on spatial autocorrelation analysis, which is based on the probability of finding bone at specified locations. The structural parameters were measured from high-resolution images (78x78x78 microm3 voxels) of 23 trabecular bone specimens from the distal radius. Maximum-likelihood bone volume fractions (BVF) were calculated for each voxel and a resolution achievable in vivo (156x156x391 microm3 voxels) was simulated by averaging BVF's from neighboring voxels. The parameters derived from the low-resolution images were found to account for 91% of the variation in Young's modulus. The results suggest that noninvasive assessment of the mechanical competence of trabecular bone in osteoporotic patients may be feasible.
Target cell-restricted triggering of the CD95 (APO-1/Fas) death receptor with bispecific antibody fragments. (2001)

Like many other cell surface receptors, the CD95 (APO-1/Fas) molecule needs to be cross-linked by its physiological ligand or by immobilized or multimeric antibodies to mediate biological activity, that is, induction of apoptotic cell death. Monomeric CD95 antibodies of the IgG2a or IgG1 subtype block rather than induce apoptosis. We report here that such antibodies, hybridized to a second antibody directed against a different target antigen on the same cell, effectively induce apoptosis of the cells if the expression of the target antigen exceeds a certain threshold level. It appears that this effect is due to bicellular binding of bispecific antibodies resulting in mutual cross-linking of the CD95 death receptor and the target antigen. Using bispecific reagents, it may therefore be possible to restrict the activation of death receptors to a given target site, e.g., a tumor. In general terms, our findings illustrate a principle according to which the triggering of a cell surface receptor may be confined to a given target cell using bispecific reagents with target X cell surface receptor specificity.
Genetic and epigenetic alterations are involved in the regulation of TPM1 in cholangiocarcinoma (2012)

Cholangiocarcinoma is a malignant tumor originating from biliary epithelial cells. The tumor suppressor gene tropomyosin 1 (TPM1) is downregulated in several human cancer types; however, its expression status in cholangiocarcinoma is still unknown. We elucidated TPM1 expression and its regulation mechanism in cholangiocarcinoma. Real-time (RT)-PCR, western blot analysis and immunohistochemistry were performed to examine TPM1 expression levels in cholangiocarcinoma cell lines and tumor tissues. Cell lines were treated with lentiviral vector containing the miR-21 knockdown and inhibitors of genetic and epigenetic mechanisms (manumycin A, LY294002, U0126, DAC and TSA), and the TPM1 expression change was observed by RT-PCR and western blot analyses. Cell proliferation, apoptosis and migration were evaluated by water-soluble tetrazolium salt (WST-1) assay, flow cytometry and wound healing experiments, respectively. TPM1 was downregulated in the intrahepatic cholangiocarcinoma cells (HuCCT1) and upregulated in the extrahepatic cholangiocarcinoma cells (QBC939) compared with normal intrahepatic biliary epithelial cells (HIBEC). TPM1 stained negative in the intrahepatic cholangiocarcinoma tissues, as revealed by immunohistochemistry, although there was no significant difference in staining of the intrahepatic cholangiocarcinoma tissues and adjacent non-cancer tissues. RAS and two important downstream signaling pathways (RAS/PI3K/AKT and RAS/MEK/ERK) were involved in TPM1 regulation and inhibition of the epigenetic mechanisms such as DNA methylation, histone deacetylation and miR-21 upregulation upregulated TPM1 expression. Inhibitors of genetic and epigenetic mechanisms (manumycin A, LY294002, U0126, DAC and TSA) inhibited cell proliferation and migration and induced apoptosis. These data indicated that TPM1 is downregulated in HuCCT1 cells and that the Ras signaling pathway as well as DNA methylation, histone deacetylation and miR-21 upregulation play important roles in the suppression of TPM1 expression in HuCCT1 cells. Thus, compounds that inhibit genetic and epigenetic mechanisms may be promising agents in treating cholangiocarcinoma.
Clinical features of familial histiocytosis. (1981)

The most commonly reported familial variant of histiocytosis is familial hemophagocytic lymphohistiocytosis. Clinically, this may be distinguished from other infantile forms by the absence of skin involvement and high incidence of leptomeningeal involvement. Eosinophilia, erythematous skin rash, alopecia, and opportunistic pulmonary infections suggest combined immunodeficiency with histiocytic response.
Noise–Power Optimization of Incremental Data Converters (2008)

Incremental data converters (IDCs) are useful in instrumentation and measurement applications, where low-frequency analog signals need to be converted into digital form with high accuracy and low power dissipation. They are particularly well suited for applications where a single analog-digital converter is multiplexed between many channels. This paper proposes an exact design methodology for IDCs, which optimizes the signal-to-noise ratio of the converter under practical design constraints. The process also allows the designer to apportion the noise budget in an arbitrary manner between thermal and quantization noise. The design process is illustrated by an example which describes the optimization of a third-order multiplexed IDC.
Isolation of CD4-Independent Primary Human Immunodeficiency Virus Type 1 Isolates That Are Syncytium Inducing and Acutely Cytopathic for CD8+Lymphocytes (2004)

Previous studies have established the existence of CD4-independent simian immunodeficiency virus, human immunodeficiency virus type 2 (HIV-2), and laboratory strains of HIV-1. However, whether CD4-independent viruses may also exist in HIV-1-infected patients has remained unclear. We have recently reported the isolation of viruses from an AIDS patient that were able to infect CD8(+) cells independent of CD4, using CD8 as a receptor. Using a similar approach, here we examined viruses from 12 randomly selected patients (obtained from the AIDS Research and Reference Program, National Institutes of Health) for the presence of CD4-independent HIV-1. CD4-independent variants were isolated from infected CD8(+) cells from the viral quasispecies of 7 of 12 patients. The CD4-independent isolates were able to infect primary CD8(+) cells as well as a CD4(-) CD8(+) T-cell line. Soluble CD4 and blocking anti-CD4 or -CD8 antibody had no effect on infection of CD8(+) cells. Remarkably, two of the seven CD4-independent isolates, but not their parental bulk viruses, induced syncytia and caused acute death of infected CD8(+) cells. Some of the CD4-independent variants were also able to infect U87 cells that were negative for CD4, CD8, and common HIV coreceptors, suggesting a novel entry mechanism for these isolates. The CD4-independent isolates were derived from adults and children infected with subtypes A, B, and D. Although no common motif for CD4 independence was found, novel sequence changes were observed in critical areas of the envelopes of the CD4-independent viruses. These results demonstrate that HIV-1-infected patients can frequently harbor viruses that are able to mediate CD4-independent infection of CD8(+) cells. In addition, this study also provides evidence of primary HIV-1 variants that are syncytium inducing and acutely cytopathic for CD8(+) lymphocytes.
Sterol phylogenesis and algal evolution. (1990)

The stereochemistry of several sterol precursors and end products synthesized by two fungal-like micro-organisms Prototheca wickerhamii (I) and Dictyostelium discoideum (II) have been determined by chromatographic (TLC, GLC, and HPLC) and spectral (UV, MS, and 1H NMR) methods. From I and II the following sterols were isolated from the cells: cycloartenol, cyclolaudenol, 24(28)-methylenecycloartanol, ergosterol, protothecasterol, 4alpha-methylergostanol, 4alpha-methylclionastanol, clionastanol, 24beta-ethylcholesta-8,22-enol, and dictyosterol. In addition, the mechanism of C-24 methylation was investigated in both organisms by feeding to I [2-3H]lanosterol, [2-3H]cycloartenol, [24-3H]lanosterol, and [methyl-2H3]methionine and by feeding to II [methyl-2H3]methionine. The results demonstrate that the 24beta configuration is formed by different alkylation routes in I and II. The Delta25(27) route operates in I while the Delta24(28) route operates in II. Based on what is known in the literature regarding sterol distribution and phylogenesis together with our findings that the stereochemical outcome of squalene oxide cyclization leads to the production of cycloartenol rather than lanosterol (characteristic of the fungal genealogy) and the chirality of the C-24 alkyl group is similar in the two nonphotosynthetic microbes (beta oriented), we conclude that Prototheca is an apoplastic Chlorella (i.e., an alga) and that Dictyostelium as well as the other soil amoebae that synthesize cycloartenol evolved from algal rather than fungal ancestors.
Single-operation synthesis of vinylsilanes from alkenes and hydrosilanes with the aid of Ru3(CO)12 (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSingle-operation synthesis of vinylsilanes from alkenes and hydrosilanes with the aid of Ru3(CO)12Yoshio Seki, Kenji Takeshita, Kazuaki Kawamoto, Shinji Murai, and Noboru SonodaCite this: J. Org. Chem. 1986, 51, 20, 3890–3895Publication Date (Print):October 1, 1986Publication History Published online1 May 2002Published inissue 1 October 1986https://doi.org/10.1021/jo00370a026RIGHTS & PERMISSIONSArticle Views634Altmetric-Citations70LEARN 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 (850 KB) Get e-Alerts Get e-Alerts
Broken rotor bars detection via Park's vector approach based on ANFIS (2014)

Many attempts have been made on fault diagnosis of induction motors based on frequency and time domain analysis of stator current. In this paper, first the Park's vector transformation and frequency analysis for fault detection of induction motors are introduced. Then a smart approach using Adaptive Neuro Fuzzy Inference System (ANFIS) is proposed. This approach uses the time domain features derived from the Park's vector transformation of stator current. By the proposed method, a partial break including 5 mm crack on a bar, one broken bar and two broken bars using experimental data are investigated. It will be shown that features derived from Park's vector compared to features obtained from a phase current, have better results.