gebhart/patrepeval huggingface dataset:
Type 1 Diabetes (2005)

Type 1 diabetes is a common, multifactorial disease with strong familial clustering (genetic risk ratio [lambda(S)] approximately 15). Approximately 40% of the familial aggregation of type 1 diabetes can be attributed to allelic variation of HLA loci in the major histocompatibility complex on chromosome 6p21 (locus-specific lambda(S) approximately 3). Three other disease susceptibility loci have been clearly demonstrated based on their direct effect on risk, INS (chromosome 11p15, allelic odds ratio [OR] approximately 1.9), CTLA4 (chromosome 2q33, allelic OR approximately 1.2), and PTPN22 (chromosome 1p13, allelic OR approximately 1.7). However, a large proportion of type 1 diabetes clustering remains unexplained. We report here on a combined linkage analysis of four datasets, three previously published genome scans, and one new genome scan of 254 families, which were consolidated through an international consortium for type 1 diabetes genetic studies (www.t1dgc.org) and provided a total sample of 1,435 families with 1,636 affected sibpairs. In addition to the HLA region (nominal P = 2.0 x 10(-52)), nine non-HLA-linked regions showed some evidence of linkage to type 1 diabetes (nominal P < 0.01), including three at (or near) genome-wide significance (P < 0.05): 2q31-q33, 10p14-q11, and 16q22-q24. In addition, after taking into account the linkage at the 6p21 (HLA) region, there was evidence supporting linkage for the 6q21 region (empiric P < 10(-4)). More than 80% of the genome could be excluded as harboring type 1 diabetes susceptibility genes of modest effect (lambda(S) > or = 1.3) that could be detected by linkage. This study represents one of the largest linkage studies ever performed for any common disease. The results demonstrate some consistency emerging for the existence of susceptibility loci on chromosomes 2q31-q33, 6q21, 10p14-q11, and 16q22-q24 but diminished support for some previously reported locations.
RPCT algorithm and its VLSI implementation (1994)

This paper presents the regional projection contour transformation (RPCT) which transforms a compound pattern or multicontour pattern into a unique outer contour. Two RPCT's, (1) diagonal-diagonal regional projection contour transformation and (2) horizontal-vertical regional projection contour transformation, are presented. They are applicable to a wide range of areas such as image analysis, pattern recognition, etc. A very large scale integration (VLSI) architecture to implement the RPCT has also been designed based on a canonical methodology which maps homogeneous dependence graphs into processor arrays. In this paper, a linear array has been designed, where an N/2-element vector is used to process a pattern with a size of N/spl times/N. It can speed up the recognition process considerably with a time complexity of O(N) compared with O(N/sup 2/) when a uniprocessor is used.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A randomised clinical trial of the efficacy of drop squats or leg extension/leg curl exercises to treat clinically diagnosed jumper's knee in athletes: pilot study (2001)

Progressive drop squats and leg extension/curl exercises can reduce the pain of jumper's knee in a 12 week period and permit a high proportion of patients to return to sport. Not all patients, however, return to sport by that time.
The presence of prostate-specific antigen-related genes in primates and the expression of recombinant human prostate-specific antigen in a transfected murine cell line. (1995)

Human prostate-specific antigen (PSA) has been shown as an aid in the early detection of prostate cancer (W. J. Catalona et al., J. Am. Med. Assoc., 270: 948-954, 1993) and was approved in 1994 by the Food and Drug Administration for early detection of prostate cancer. Immunotherapies directed against PSA have been suggested in patients with metastatic prostate cancer. One of the essential questions is to define which nonhuman species express PSA for experimental studies. Using Southern blot analyses, genes related to human PSA have been detected in several nonhuman primate species, including chimpanzee, orangutan, gorilla, macaque, and rhesus monkey, but not in other mammalian species, including rabbit, cow, pig, dog, rat, or mouse. Immunohistochemical staining with anti-human PSA antisera detected strong staining in both human and monkey prostatic epithelial cells with no reactivity to rat prostate cells. Because the PSA gene is not present in the murine genome, a matched set of murine cell lines has been developed that may be useful to study the biochemical functions of PSA and as an experimental target for PSA-directed immunotherapy. To establish such cell lines, a C57BL/6 murine colon adenocarcinoma cell line, MC-38, was transfected with a retroviral vector containing cDNA encoding the human PSA gene. Genetic analysis of a PSA-secreting clone, PSA/MC-38, demonstrated that the PSA gene had been stably integrated into the MC-38 genome. The PSA/MC-38 cell line was found to secrete PSA into tissue culture medium, producing a protein of approximately M(r) 30,000. In vivo, PSA/MC-38 grew as a s.c. tumor in male and female mice. PSA/MC-38 tumors grew more rapidly in athymic mice than in syngeneic C57BL/6 mice, and in both mouse strains, the PSA/MC-38 tumors grew more slowly than control vector-transduced tumors. PSA was detected in the serum and tumors of PSA/MC-38 tumor-bearing mice. It is proposed that PSA/MC-38 cells may be used as a murine tumor model to test potential therapeutic vaccines and other experimental therapies directed against PSA.
Overexpression of VEGF in Testis and Epididymis Causes Infertility in Transgenic Mice: Evidence for Nonendothelial Targets for VEGF (1998)

Vascular endothelial growth factor (VEGF) is a key regulator of endothelial growth and permeability. However, VEGF may also target nonendothelial cells, as VEGF receptors and responsiveness have been detected for example in monocytes, and high concentrations of VEGF have been reported in human semen. In this work we present evidence that overexpression of VEGF in the testis and epididymis of transgenic mice under the mouse mammary tumor virus (MMTV) LTR promoter causes infertility. The testes of the transgenic mice exhibited spermatogenic arrest and increased capillary density. The ductus epididymidis was dilated, containing areas of epithelial hyperplasia. The number of subepithelial capillaries in the epididymis was also increased and these vessels were highly permeable as judged by the detection of extravasated fibrinogen products. Intriguingly, the expression of VEGF receptor-1 (VEGFR-1) was detected in certain spermatogenic cells in addition to vascular endothelium, and both VEGFR-1 and VEGFR-2 were also found in the Leydig cells of the testis. The infertility of the MMTV-VEGF male mice could thus result from VEGF acting on both endothelial and nonendothelial cells of the male genital tract. Taken together, these findings suggest that the VEGF transgene has nonendothelial target cells in the testis and that VEGF may regulate male fertility.
TheSalmonellainvasin SipB induces macrophage apoptosis by binding to caspase-1 (1999)

Recently, Salmonella spp. were shown to induce apoptosis in infected macrophages. The mechanism responsible for this process is unknown. In this report, we establish that the Inv-Spa type III secretion apparatus target invasin SipB is necessary and sufficient for the induction of apoptosis. Purified SipB microinjected into macrophages led to cell death. Binding studies show that SipB associates with the proapoptotic protease caspase-1. This interaction results in the activation of caspase-1, as seen in its proteolytic maturation and the processing of its substrate interleukin-1beta. Caspase-1 activity is essential for the cytotoxicity. Functional inhibition of caspase-1 activity by acetyl-Tyr-Val-Ala-Asp-chloromethyl ketone blocks macrophage cytotoxicity, and macrophages lacking caspase-1 are not susceptible to Salmonella-induced apoptosis. Taken together, the data demonstrate that SipB functions as an analog of the Shigella invasin IpaB.
Topology Optimization for Additive Manufacturing (2011)

This paper gives an overview of the issues and opportunities for the application of topology optimization methods for additive manufacturing (AM). The main analysis issues discussed are: how to achieve the maximum geometric resolution to allow the fine features easily manufacturable by AM to be represented in the optimization model; the manufacturing constraints to be considered, and the workflow modifications required to handle the geometric complexity in the post optimization stages. The main manufacturing issues discussed are the potential for realizing intermediate density regions, in the case of the solid isotropic material with penalization (SIMP) approach, the use of small scale lattice structures, the use of multiple material AM processes, and an approach to including support structure requirement as a manufacturing constraint.
Catecholamines, parasympathetic stimuli, or cortisol for overwhelming sepsis?* (2006)

Groeneveld, A B. Johan MD, PhD, FCCP, FCCM; Beishuizen, Albertus MD, PhD; de Jong, Margriet F. C. MSc Author Information
Effects of Flavonoids and Phenolic Acids on the Inhibition of Adipogenesis in 3T3-L1 Adipocytes (2007)

Obesity has become a global epidemic in both developed and developing countries, and it is a significant risk factor for various diseases such as diabetes, cancer, heart disease, and hypertension. In the present study, the effect of naturally occurring antioxidants (flavonoids and phenolic acids) on the inhibition of adipogenesis in 3T3-L1 adipocytes was investigated. The results showed that o-coumaric acid and rutin had the highest inhibition on intracellular triglyceride (61.3 and 83.0%, respectively) among 15 phenolic acids and 6 flavonoids tested. However, the oil red o stained material (OROSM) showed that cell number in 3T3-L1 adipocytes was not influenced by those compounds. For glycerol-3-phosphate dehydrogenase (GPDH) activity, the data indicated that o-coumaric acid and rutin had the highest inhibition on GPDH activity (54.2 and 66.8%, respectively) among the compounds tested. o-Coumaric acid and rutin also inhibited the expression of PPARgamma, C/EBPalpha and leptin and then up-regulated expression of adiponectin at the protein level. Some naturally occurring antioxidants efficiently suppressed adipogenesis in 3T3-L1 adipocytes. These results suggest that o-coumaric acid and rutin targeted for adipocyte functions could be effective in improving the symptoms of metabolic syndrome.
PCR Amplification from Paraffin-Embedded Tissues: Effects of Fixative and Fixation Time (1991)

The polymerase chain reaction (PCR) DNA amplification method is a powerful new tool for the retrospective analysis of paraffin-embedded tissue (PET). The technique has afforded the sensitive and specific detection of nucleic acid sequences associated with genetic and infectious diseases. However, PET processing conditions vary in their suitability for amplification. The authors have examined the effects of 11 fixatives at three fixation times. The effect of fixation was measured by the ability of the DNA in a treated tissue to serve as a template for the amplification of DNA fragments that ranged from 110 to 1,327 base pairs in length. Specimens fixed in acetone or 10% buffered neutral formalin were found to be best suited for subsequent analysis by PCR. A second group of fixatives, including Zamboni's, Clarke's, paraformaldehyde, formalin-alcohol-acetic acid, and methacarn, compromised amplification efficiency. Tissues treated with Carnoy's, Zenker's, or Bouin's, respectively, were even less desirable for amplification analysis.
Glutamine fuels a vicious cycle of autophagy in the tumor stroma and oxidative mitochondrial metabolism in epithelial cancer cells (2011)

Glutamine metabolism is crucial for cancer cell growth via the generation of intermediate molecules in the tricarboxylic acid (TCA) cycle, antioxidants and ammonia. The goal of the current study was to evaluate the effects of glutamine on metabolism in the breast cancer tumor microenvironment, with a focus on autophagy and cell death in both epithelial and stromal compartments. For this purpose, MCF7 breast cancer cells were cultured alone or co-cultured with non-transformed fibroblasts in media containing high glutamine and low glucose (glutamine +) or under control conditions, with no glutamine and high glucose (glutamine –). Here, we show that MCF7 cells maintained in co-culture with glutamine display increased mitochondrial mass, as compared with control conditions. Importantly, treatment with the autophagy inhibitor chloroquine abolishes the glutamine-induced augmentation of mitochondrial mass. It is known that loss of caveolin-1 (Cav-1) expression in fibroblasts is associated with increased autophagy and an aggressive tumor microenvironment. Here, we show that Cav-1 downregulation which occurs in fibroblasts maintained in co-culture specifically requires glutamine. Interestingly, glutamine increases the expression of autophagy markers in fibroblasts, but decreases expression of autophagy markers in MCF7 cells, indicating that glutamine regulates the autophagy program in a compartment-specific manner. Functionally, glutamine protects MCF7 cells against apoptosis, via the upregulation of the anti-apoptotic and anti-autophagic protein TIGAR. Also, we show that glutamine cooperates with stromal fibroblasts to confer tamoxifen-resistance in MCF7 cancer cells. Finally, we provide evidence that co-culture with fibroblasts (1) promotes glutamine catabolism, and (2) decreases glutamine synthesis in MCF7 cancer cells. Taken together, our findings suggest that autophagic fibroblasts may serve as a key source of energy-rich glutamine to fuel cancer cell mitochondrial activity, driving a vicious cycle of catabolism in the tumor stroma and anabolic tumor cell expansion.
Efficient Transgene Reconstitution with Hybrid Dual AAV Vectors Carrying the Minimized Bridging Sequences (2010)

A hybrid dual-vector system was developed recently as a universal platform to double the packaging capacity of recombinant adeno-associated virus (AAV). In this system, the expression cassette is split into two independent AAV vectors. A highly recombinogenic bridging DNA sequence is engineered in both vectors to mediate target gene-independent homologous recombination between the split vector genomes. In the prototype hybrid vectors, a 0.87-kb DNA fragment from the middle portion of the human placental alkaline phosphatase (AP) gene was used as the bridging sequence. Here we report the development of the minimized bridging sequences. Five independent bridging sequences (0.26 to 0.44 kb) were evaluated in MO59K cells and/or murine skeletal muscle in the context of the AP overlapping vectors and/or the β-galactosidase (LacZ) hybrid vectors. Robust reconstitution comparable to that of the original hybrid vectors was achieved from a 0.26-kb and a 0.27-kb bridging sequence. These newly developed bridging sequences greatly expand the utility of the hybrid dual AAV vector system for delivering larger therapeutic genes/expression cassettes.
LDL Size in African Americans, Hispanics, and Non-Hispanic Whites (1999)

The prevalence of cardiovascular disease (CVD) and atherosclerosis varies among several minority ethnic groups in the United States. Recently, small, dense low density lipoprotein (LDL) particle size has been recognized as a risk factor for CVD. We examined LDL size as a possible explanation for differences in CVD rates in 1571 subjects from the Insulin Resistance Atherosclerosis Study (IRAS), a multiethnic study of insulin resistance and cardiovascular risk factors. LDL size (A) was significantly different by ethnic group (African Americans 262.1+/-0.6, Hispanics 257.6+/-0.6, and non-Hispanic whites 259.2+/-0.4, P<0.001). Ethnic differences in LDL size continued to be statistically significant after adjustment for upper body adiposity, insulin resistance, and glucose tolerance status. However, after further adjustment for other cardiovascular risk factors, especially ethnic differences in triglyceride and high density lipoprotein (HDL) cholesterol levels, the ethnic differences in LDL size were markedly attenuated and in general no longer statistically significant. The relation of triglyceride, HDL cholesterol, insulin resistance, and adiposity to LDL size in each ethnic group was similar. LDL size differs by ethnic group, which is independent of obesity or insulin resistance. These ethnic differences appear to be due to ethnic variations in dyslipidemia (especially differences in triglyceride levels); ethnic differences in LDL size are not consistent with previously reported ethnic dissimilarities in CVD or atherosclerosis.
Toll-like receptors in inflammatory bowel diseases: A decade later (2010)

Differential alteration of Toll-like receptor (TLR) expression in inflammatory bowel disease (IBD) was first described 10 years ago. Since then, studies from many groups have led to the current concept that TLRs represent key mediators of innate host defense in the intestine, involved in maintaining mucosal as well as commensal homeostasis. Recent findings in diverse murine models of colitis have helped to reveal the mechanistic importance of TLR dysfunction in IBD pathogenesis. It has become evident that environment, genetics, and host immunity form a multidimensional and highly interactive regulatory triad that controls TLR function in the intestinal mucosa. Imbalanced relationships within this triad may promote aberrant TLR signaling, critically contributing to acute and chronic intestinal inflammatory processes in IBD colitis and associated cancer.
Light field display simulation for light field quality assessment (2015)

We introduce our light field display simulation software that simulates the image observed by a viewer looking at a full parallax light field display. The simulation software uses the display parameters, viewer location and orientation, viewer pupil size and focus location to simulate the image observed by the viewer. This software has been used in simulating full parallax light field displays of various geometry and complexities as well as image processing and full parallax light field compression algorithms. The simulation results follow the real world observations very closely.
5-Fluorouracil Selectively Kills Tumor-Associated Myeloid-Derived Suppressor Cells Resulting in Enhanced T Cell–Dependent Antitumor Immunity (2010)

Myeloid-derived suppressor cells (MDSC) accumulate in the spleen and tumor bed during tumor growth. They contribute to the immune tolerance of cancer notably by inhibiting the function of CD8(+) T cells. Thus, their elimination may hamper tumor growth by enhancing antitumor T-cell functions. We have previously reported that some anticancer agents relied on T cell-dependent anticancer responses to achieve maximal efficacy. However, the effect of anticancer agents on MDSC has remained largely unexplored. In this study, we observed that gemcitabine and 5-fluorouracil (5FU) were selectively cytotoxic on MDSC. In vivo, the treatment of tumor-bearing mice with 5FU led to a major decrease in the number of MDSC in the spleens and tumor beds of animals whereas no significant effect on T cells, natural killer cells, dendritic cells, or B cells was noted. Interestingly, 5FU showed a stronger efficacy over gemcitabine to deplete MDSC and selectively induced MDSC apoptotic cell death in vitro and in vivo. The elimination of MDSC by 5FU increased IFN-gamma production by tumor-specific CD8(+) T cells infiltrating the tumor and promoted T cell-dependent antitumor responses in vivo. Altogether, these findings suggest that the antitumor effect of 5FU is mediated, at least in part, by its selective cytotoxic action on MDSC.
A single administration of testosterone induces cardiac accelerative responses to angry faces in healthy young women. (2001)

Recently, it was demonstrated how individuals with high levels of testosterone selectively attend toward angry faces. It was argued that this suggests that high levels of testosterone are associated with an aggressive, dominating personality style. In this study, the authors used a double-blind, placebo-controlled design to examine whether exogenous testosterone would induce cardiac acceleration in response to angry faces. Participants (healthy young women) were exposed to neutral, happy, or angry faces. Administration of a single dosage of testosterone (0.5 mg) induced an accelerative cardiac response to angry faces. It is argued that this effect is due to the encouragement of dominance behavior and the inclination toward aggression. Possible mechanisms behind testosterone-driven changes in behavior are discussed with relevance to steroid-responsive networks in the limbic system that drive and control motivational and physiological aspects of social behavior.
Cancer Stem Cells—Perspectives on Current Status and Future Directions: AACR Workshop on Cancer Stem Cells (2006)

A workshop was convened by the AACR to discuss the rapidly emerging cancer stem cell model for tumor development and progression. The meeting participants were charged with evaluating data suggesting that cancers develop from a small subset of cells with self-renewal properties analogous to organ
Dependency-based Convolutional Neural Networks for Sentence Embedding (2015)

In sentence modeling and classification, convolutional neural network approaches have recently achieved state-of-the-art results, but all such efforts process word vectors sequentially and neglect long-distance dependencies. To exploit both deep learning and linguistic structures, we propose a tree-based convolutional neural network model which exploit various long-distance relationships between words. Our model improves the sequential baselines on all three sentiment and question classification tasks, and achieves the highest published accuracy on TREC.
Advances in chemistry and bioactivity of the genus Uncaria (2004)

The alkaloids of the pantropical genus Uncaria (Rubiaceae) were reviewed extensively by Phillipson et al. in (1978) Since then a host of papers with new results has been published. The compounds discovered are from three major groups: (1) alkaloids; (2) terpenoids; and (3) flavonoids. Some highly unusual structures have been reported. Although there are at least 35 species of Uncaria known, recent research focussed on a relatively small number of species. During recent years bioactivity of extracts and pure compounds isolated from Uncaria species have been increasingly investigated. These include anticonvulsive, antiinflammatory, antimutagenic, antioxidant, cytoprotective, hypotensive, and immunoregulatory effects. The literature since 1978 is reviewed and 133 references are given.