gebhart/patrepeval huggingface dataset:
Periostin is frequently overexpressed and enhances invasion and angiogenesis in oral cancer (2006)

Oral squamous-cell carcinoma (OSCC) is one of the most common types of human cancer. Typically OSCC cells show persistent invasion that frequently leads to local recurrence and distant lymphatic metastasis. We previously identified Periostin as the gene demonstrating the highest fold change expression in the invasive clone by comparing the transcriptional profile of parent OSCC cell line and a highly invasive clone. Here, we demonstrated that Periostin overexpression enhanced invasiveness in oral cancer cell lines. To know the role of Periostin in invasion, angiogenesis and metastasis in OSCC cases, we first examined the expression of Periostin mRNA in 31 OSCC cases by RT-PCR and Periostin protein in 74 OSCC cases by immunohistochemistry. Then, we compared the Periostin expression with invasion pattern, metastasis and blood vessel density. Periostin mRNA and protein overexpression were frequently found in OSCC cases and Periostin expression was well correlated with the invasion pattern and metastasis. Moreover, blood vessel density of Periostin-positive cases was higher than those of Periostin-negative cases. Interestingly, recombinant Periostin enhanced capillary formation in vitro in a concentration-dependant manner. In summary, these findings suggest that Periostin may promote invasion and angiogenesis in OSCC, and that Periostin can be a strong marker for prediction of metastasis in oral cancer patients.
The complete islet amyloid polypeptide precursor is encoded by two exons (1989)

Islet amyloid polypeptide (IAPP) is the 37-amino acid peptide subunit of amyloid found in pancreatic islets of type 2 diabetic patients and in insulinomas. Recently, we isolated the human gene encoding IAPP [(1988) FEBS Lett. 239, 227-232]. We now report the nucleotide sequences of a human insulinoma cDNA encoding a complete IAPP precursor, and of the corresponding parts of the IAPP gene. Two exons, which are approx. 5 kb apart in the human genome, encode the 89-amino acid pre-pro-IAPP. At least one additional exon is present further upstream in the IAPP gene. A putative signal sequence at the amino-terminus of the precursor suggests that IAPP is a secreted protein.
Null‐Scattering Hybrid Particles Using Controlled Radical Polymerization (2007)

A method to suppress the scattering of inorganic nanoparticle inclusions within organic embedding media is presented. Suppression takes place by means of appropriate surface modification (using ATRP), such as to match the effective refractive index of the resulting core-shell particle to the refractive index of the embedding medium. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2089/2007/c0928_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Neurofibrillary tangle pathology and Braak staging in chronic epilepsy in relation to traumatic brain injury and hippocampal sclerosis: a post-mortem study (2011)

The long-term pathological effects of chronic epilepsy on normal brain ageing are unknown. Previous clinical and epidemiological studies show progressive cognitive decline in subsets of patients and an increased prevalence of Alzheimer's disease in epilepsy. In a post-mortem series of 138 patients with long-term, mainly drug-resistant epilepsy, we carried out Braak staging for Alzheimer's disease neurofibrillary pathology using tau protein immunohistochemistry. The stages were compared with clinicopathological factors, including seizure history and presence of old traumatic brain injury. Overall, 31% of cases were Braak Stage 0, 36% Stage I/II, 31% Stage III/IV and 2% Stage V/VI. The mean age at death was 56.5 years and correlated with Braak stage (P < 0.001). Analysis of Braak stages within age groups showed a significant increase in mid-Braak stages (III/IV), in middle age (40-65 years) compared with data from an ageing non-epilepsy series (P < 0.01). There was no clear relationship between seizure type (generalized or complex partial), seizure frequency, age of onset and duration of epilepsy with Braak stage although higher Braak stages were noted with focal more than with generalized epilepsy syndromes (P < 0.01). In 30% of patients, there was pathological evidence of traumatic brain injury that was significantly associated with higher Braak stages (P < 0.001). Cerebrovascular disease present in 40.3% and cortical malformations in 11.3% were not significantly associated with Braak stage. Astrocytic-tau protein correlated with the presence of both traumatic brain injury (P < 0.01) and high Braak stage (P < 0.001). Hippocampal sclerosis, identified in 40% (bilateral in 48%), was not associated with higher Braak stages, but asymmetrical patterns of tau protein accumulation within the sclerotic hippocampus were noted. In over half of patients with cognitive decline, the Braak stage was low indicating causes other than Alzheimer's disease pathology. In summary, there is evidence of accelerated brain ageing in severe chronic epilepsy although progression to high Braak stages was infrequent. Traumatic brain injury, but not seizures, was associated with tau protein accumulation in this series. It is likely that Alzheimer's disease pathology is not the sole explanation for cognitive decline associated with epilepsy.
Nitrated α-Synuclein-Induced Alterations in Microglial Immunity Are Regulated by CD4+ T Cell Subsets (2009)

Microglial inflammatory neuroregulatory activities affect the tempo of nigrostriatal degeneration during Parkinson's disease (PD). Such activities are induced, in part, by misfolded, nitrated alpha-synuclein (N-alpha-syn) within Lewy bodies released from dying or dead dopaminergic neurons. Such pathobiological events initiate innate and adaptive immune responses affecting neurodegeneration. We posit that the neurobiological activities of activated microglia are affected by cell-protein and cell-cell contacts, in that microglial interactions with N-alpha-syn and CD4(+) T cells substantively alter the microglial proteome. This leads to alterations in cell homeostatic functions and disease. CD4(+)CD25(+) regulatory T cells suppress N-alpha-syn microglial-induced reactive oxygen species and NF-kappaB activation by modulating redox-active enzymes, cell migration, phagocytosis, and bioenergetic protein expression and cell function. In contrast, CD4(+)CD25(-) effector T cells exacerbate microglial inflammation and induce putative neurotoxic responses. These data support the importance of adaptive immunity in the regulation of Parkinson's disease-associated microglial inflammation.
Concentration of Indocyanine Green Does Not Significantly Influence Lymphatic Function as Assessed by Near-Infrared Imaging (2012)

The use of different concentrations of ICG and the use of other near-infrared fluorophores for optical imaging of lymphatics does not significantly affect lymphatic propulsive velocity or frequency.
Application of a Biphasic Actuator in the Design of the CloPeMa Robot Gripper (2014)

The paper (a first version of this work was presented in Aug. 2014 at ASME-DETC in Buffalo, NY) describes a novel robot gripper for garment handling. The device has been designed, developed, prototyped, and tested within the CloPeMa European Project creating a robot system for automated manipulation of clothing and other textile items. The gripper has two degrees of freedom (dof) and includes both rigid and flexible elements. A variable-stiffness actuator has been implemented to add controlled compliance in the gripper’s operation allowing the combining of various grasping and manipulation tasks. First, we analyze the specific application-determined task requirements, focusing on the need for adaptive flexibility and the role of compliant elements in the design. The chosen solution is a simple planar mechanism, equipped with one standard and one variable-stiffness actuator. The mechanical design of the gripper, including the hydraulic system used in the biphasic actuator, is outlined, and the control architecture, using sensor feedback, is described.
Deep-learning-based image quality enhancement of compressed sensing magnetic resonance imaging of vessel wall: comparison of self-supervised and unsupervised approaches (2020)

While high-resolution proton density-weighted magnetic resonance imaging (MRI) of intracranial vessel walls is significant for a precise diagnosis of intracranial artery disease, its long acquisition time is a clinical burden. Compressed sensing MRI is a prospective technology with acceleration factors that could potentially reduce the scan time. However, high acceleration factors result in degraded image quality. Although recent advances in deep-learning-based image restoration algorithms can alleviate this problem, clinical image pairs used in deep learning training typically do not align pixel-wise. Therefore, in this study, two different deep-learning-based denoising algorithms-self-supervised learning and unsupervised learning-are proposed; these algorithms are applicable to clinical datasets that are not aligned pixel-wise. The two approaches are compared quantitatively and qualitatively. Both methods produced promising results in terms of image denoising and visual grading. While the image noise and signal-to-noise ratio of self-supervised learning were superior to those of unsupervised learning, unsupervised learning was preferable over self-supervised learning in terms of radiomic feature reproducibility.
Transfer Ribonucleic Acid-induced Hydrolysis of Valyladenylate Bound to Isoleucyl Ribonucleic Acid Synthetase (1966)

the amount of enzyme required to hydrolyze 1 mpmole of 0.01
Endogenous interleukin-1α promotes a proliferative and proinflammatory phenotype in human vascular smooth muscle cells (2007)

During vascular disease and following injury, vascular smooth muscle cells (VSMC) proliferate and produce inflammation-promoting cytokines and chemokines. Similar phenotypic changes can be elicited in vitro by activation of Toll-like receptors (TLR) within VSMC. TLR-activated VSMC also produce IL-1 alpha, but it is unknown whether endogenous IL-1 alpha stimulates VSMC in an autocrine manner. Here we tested the hypothesis that endogenous IL-1 alpha contributes to TLR-induced proliferation and chemokine release in human VSMC by using RNA interference to knock down IL-1 alpha expression. Knockdown of IL-1 alpha abolished TLR-induced proliferation and suppressed TLR4-induced release of monocyte chemoattractant protein-1 (MCP-1) by VSMC, indicating that endogenous IL-1 alpha plays a crucial role in both responses. Serum, PDGF, FGF-2, and EGF each increased cellular IL-1 alpha concentrations, and IL-1 alpha knockdown inhibited serum- and PDGF-induced DNA synthesis, further indicating that endogenous IL-1 alpha also contributed to VSMC responses to growth factors. IL-1 receptor antagonist, a competitive inhibitor of IL-1 receptor I (IL-1RI), also attenuated TLR-induced proliferation and both basal and TLR-induced MCP-1 expression, indicating at least a partial role of the IL-1RI in mediating these responses. The results support the hypothesis that autocrine actions of endogenous IL-1 alpha, mediated at least in part via IL-1RI signaling, contribute to a proproliferative and proinflammatory phenotypic shift in TLR-activated human VSMC, which might play a pathogenic role in vascular disorders.
High power density, high efficiency system two-stage power architecture for laptop computers (2006)

This paper proposes system two-stage power architecture for laptop voltage regulators (VRs). By taking advantage of the Thermal Design Power (TDP) requirement in the laptop, VRs for microprocessor, graphics, DDR memory and main power can share the same first stage with very low design power. The high-efficiency and high-frequency first stage based on switching capacitor technology and second stage design is presented in this paper respectively. Two different designs are illustrated and verified by experiments. One design keeps the similar VR cost as the current single-stage solution and improves VR light load efficiency by 5%. Another design has slightly higher VR efficiency comparing with single-stage solution while reducing the footprint of VR output inductors and capacitors by 25%∼33% and VR total cost by 5%.
Utilization of Instructional Technology: Towards a Conceptual Model for Teacher Education (2004)

The intent of this study was to propose and test a conceptual model that described utilization of instructional technology by teacher education faculty in University of North Carolina teacher education programs. Focus on utilization was guided by the study's conceptual framework originally developed by Seels and Richey (1994a). \n\n\tResearch questions focused on factor groupings contributing to overall utilization of instructional technology; investigating sub-set variables having the most influence on use of technology; describing the nature of relationship between factor groupings and use of instructional technology; creating and testing a conceptual model that illustrates factor groupings and their relation to the use of instructional technology; and identification of specific factors and barriers most frequently cited by faculty as influencing their use of instructional technology. \n\n\tDevelopment of the study included the creation of a 43 question instrument. Structural Equation Modeling employing Exploratory Factor Analysis, Principal Components Analysis, and Confirmatory Factor Analysis was used to identify and refine factor groups and test the conceptual model for goodness-of-fit.\n\n\tStudy results confirmed goodness-of-fit for the proposed conceptual model of technology use. Five factor groups, identified as primary components of the conceptual model, had varying degrees of relation to the use of technology, with institutional infrastructure holding the highest degree of relation. \n\n\tFaculty participating in the study indicated major influencing factors for their use of technology as: \n\n1.\tsupport structures within their teacher education program; \n\n2.\tclassroom availability of technology equipment for instructional use; \n\n3.\tawareness of benefits that technology offers to teacher education candidates; \n\n4.\tpersonal technology literacy. \n\nAdditionally, faculty indicated that few significant barriers exist that prevent them from using technology in teacher education courses. The most significant barrier reported was lack of time to research and develop technology-enhanced instruction. \n\n\tQualitative comments suggested that the majority of faculty had very positive attitudes towards technology use. Given increased emphasis on identified factors, UNC teacher education programs have the potential to improve technology integration throughout their preparation program.
Is diffusion imaging appearance an independent predictor of outcome after ischemic stroke? (2002)

The <ADC>r is associated with functional outcome, but that is because it and DWI lesion volume are also associated with stroke severity. Although DWI lesion features are univariate surrogate outcome predictors, the authors were unable to show that they were independent outcome predictors in the current study. Differences between these and other results may be due to differences in study design, sample size, and case mix.
Conformational homologies among cytokines: Interleukins and colony stimulating factors (1988)

Some 30 cytokine amino acid sequences (mainly interleukins, colony stimulating factors and tumor necrosis factors) have been examined for evidence of secondary structure as well as longer-range interactions of a type likely to lead to stable alpha-helical bundles. Most, though not all, of the cytokines examined have a high predicted alpha-helical content (40-60%) and quasi-repeating heptads containing i/i + 3 apolar periodicities. This major subset of the cytokines is predicted to be characterized by molecules in which 4-alpha-helical bundles with an average length of 25A are the most marked conformational features. Based on these conclusions, we suggest structures for huG-CSF, huGM-CSF and muIL-5 in which defined loop segments at the ends of helical bundles are the most likely sites for binding and recognition by specific cell receptors. As such, they provide a means for testing or refining the three working models we have defined, using currently available methods of site-directed substitution and deletion mutagenesis, as well as synthetic peptides corresponding to the proposed loop sequences and the use of monoclonal antibodies of defined epitopic specificity. The structure arrived at for huGM-CSF is consistent with the limited data currently available concerning the residues which are important for binding and activity.
Assessing a Theoretical Risk of Dolutegravir-Induced Developmental Immunotoxicity in Juvenile Rats (2012)

HIV-1 integrase inhibitors (INIs) are a promising class of antiretrovirals for the treatment of HIV in adults; there is interest in expanding their use into pediatric populations. A theoretical concern for developmental immunotoxicity was raised after a publication suggested that two HIV INI tool compounds inhibited in vitro cleavage activity of recombination activating genes 1 and 2 (RAG1/2) through the inhibition of their binding to recombination signal sequences. RAG1/2 are required for the development of mature B and T lymphocyte populations. The potential effects of the investigational INI dolutegravir on RAG1/2 were addressed by developing assays in juvenile rats to measure T cell receptor (TCR) Vβ usage by flow cytometry as an indicator of TCR repertoire diversity and a T cell dependent antibody response (TDAR) as an indicator of immunosuppression. These endpoints were incorporated into a juvenile rat toxicity study, along with immunophenotyping, hematology, and histopathology of immunologic organs. Dose levels of 0, 0.5, 2, or 75mg/kg/day dolutegravir were given via oral gavage from postnatal day 4 through 66. At the highest dose, there was decreased body weight gain and two preweanling deaths; however, there were no treatment-related effects on developmental parameters. There were no effects on immunologic competence, as measured by TDAR, and no effects on lymphocyte subsets or CD4 and CD8 TCR Vβ usage in peripheral blood. Histopathology of immunologic organs (spleen, thymus, lymph nodes) and hematology evaluation revealed no effects. The no observed adverse effect level for immunotoxicity endpoints was 75mg/kg/day.
DNS IPv6 Transport Operational Guidelines (2004)

This memo provides guidelines and Best Current Practice for operating
DNS in a world where queries and responses are carried in a mixed
environment of IPv4 and IPv6 networks. This document specifies an
Internet Best Current Practices for the Internet Community, and
requests discussion and suggestions for improvements.
Promoter Hypermethylation of Resected Bronchial Margins (2004)

Histologically negative bronchial margins of resected non-small cell lung cancer exhibit frequent hypermethylation changes in multiple genes. These hyper-methylation abnormalities are also present in the primary tumor and thus may represent a field defect of preneoplastic changes that occurs early in carcinogenesis.
Biological characterization of recombinant vaccinia viruses in mice infected by the respiratory route (1990)

A murine model based on infection by the respiratory route has been used to study the pathogenesis of recombinant vaccinia viruses. The neurovirulent Western Reserve (WR) strain and the Wyeth smallpox vaccine strain were used as vectors. Recombinant viruses were constructed by insertion of the Epstein-Barr virus membrane glycoprotein 340 gene into the thymidine kinase (TK) gene of each vaccinia virus. Intranasal inoculation of DBA/2 mice with 10(6) pock-forming units (pk.f.u.) of the WR strain was lethal but mice survived similar infection with the WR recombinant virus. Each virus was recovered from lung, blood and brain but, unlike wild-type virus, the recombinant virus was subsequently cleared. No deaths occurred after similar infection with the Wyeth strain or the Wyeth recombinant virus. There was limited growth of the Wyeth strain in the respiratory tract, low levels of virus in the blood and only sporadic recovery in brain extracts. The Wyeth recombinant virus was cleared rapidly with little viraemia or detectable infection of the central nervous system. No phenotypic character determined in vitro could be related consistently to the virulence of wild-type and recombinant viruses. Although the lethal character of the WR strain was affected by its TK+ phenotype, mice survived infection by intranasal inoculation with 10(6) pk.f.u. of WR TK+ recombinant viruses which either expressed the human interleukin 2 gene or had a deficient vaccinia virus growth factor gene.
Control of Developmental Timing by MicroRNAs and Their Targets (2002)

In Caenorhabditis elegans the timing of many developmental events is regulated by heterochronic genes. Such genes orchestrate the timing of cell divisions and fates appropriate for the developmental stage of an organism. Analyses of heterochronic mutations in the nematode C. elegans have revealed a genetic pathway that controls the timing of post-embryonic cell divisions and fates. Two of the genes in this pathway encode small regulatory RNAs. The 22 nucleotide (nt) RNAs downregulate the expression of protein-coding mRNAs of target heterochronic genes. Analogous variations in the timing of appearance of particular features have been noted among closely related species, suggesting that such explicit control of developmental timing may not be exclusive to C. elegans. In fact, some of the genes that globally pattern the temporal progression of C. elegans development, including one of the tiny RNA genes, are conserved and temporally regulated across much of animal phylogeny, suggesting that the molecular mechanisms of temporal control are ancient and universal. A very large family of tiny RNA genes called microRNAs, which are similar in structure to the heterochronic regulatory RNAs, have been detected in diverse animal species and are likely to be present in most metazoans. Functions of the newly discovered microRNAs are not yet known. Other examples of temporal programs during growth include the exquisitely choreographed temporal sequences of developmental fates in neurogenesis in Drosophila and the sequential programs of epidermal coloration in insect wing patterning. An interesting possibility is that microRNAs mediate transitions on a variety of time scales to pattern the activities of particular target protein-coding genes and in turn generate sets of cells over a period of time. Plasticity in these microRNA genes or their targets may lead to changes in relative developmental timing between related species, or heterochronic change. Instead of inventing new gene functions, even subtle changes in temporal expression of pre-existing control genes can result in speciation by altering the time at which they function.