gebhart/patrepeval huggingface dataset:
Mast Cell Stabilization Limits Hypoxic-Ischemic Brain Damage in the Immature Rat (2007)

Perinatal hypoxic-ischemic (HI) brain damage is a major cause of mortality and neurological morbidity in infants and children. Using an established model of unilateral hypoxia-ischemia in neonatal rats, the present study focused on mast cells (MCs), important regulators of inflammatory processes, as potential contributors to HI damage. MCs are present in the pia of the neonatal rat, entering the central nervous system (CNS) during cerebral development along penetrating blood vessels. Following hypoxia-ischemia, MC numbers increased dramatically in the ipsilateral (ischemic) hemisphere (p < 0.01). In animals exposed to hypoxia only, the numbers of MCs were elevated in both hemispheres to an extent equal to that observed in the contralateral hemisphere of HI animals (p < 0.05 vs. control). Within damaged areas (ipsilateral only), MCs were observed in regions of activated microglia and astroglia that characterize the ischemic hemisphere. Using a triple-label paradigm, MCs were observed along elongating blood vessels, some of which express the GLUT1 isoform of the glucose transporter protein, indicative of blood-brain barrier vessels. To determine whether MC activation has a role in HI brain damage, rat pups were treated with the MCs stabilizer, disodium cromoglycate (cromolyn), prior to and/or following hypoxia-ischemia. The cromolyn treatment inhibited MC migration into the CNS (p < 0.05) and limited brain damage more than 50% (p < 0.01) vs. saline controls. These data support the hypothesis that MCs are key contributors to the extent of brain damage due to hypoxia-ischemia in the immature animal.
Metabolic transformation in cancer (2009)

In 2000, Douglas Hanahan and Robert Weinberg published a review detailing the six hallmarks of cancer. These are six phenotypes that a tumour requires in order to become a fully fledged malignancy: persistent growth signals, evasion of apoptosis, insensitivity to anti-growth signals, unlimited replicative potential, angiogenesis and invasion and metastasis. However, it is becoming increasingly clear that these phenotypes do not portray the whole story and that other hallmarks are necessary: one of which is a shift in cellular metabolism. The tumour environment creates a unique collection of stresses to which cells must adapt in order to survive. This environment is formed by the uncontrolled proliferation of cells, which ignore the cues that would create normal tissue architecture. As a result, the cells forming the tumour are exposed to low oxygen and nutrient levels, as well as high levels of toxic cellular waste products, which is thought to propel cells towards a more transformed phenotype, resistant to cell death and pro-metastatic.
Cytokine Dysregulation and Increased Oxidation Is Prevented by Dehydroepiandrosterone in Mice Infected with Murine Leukemia Retrovirus (1997)

The effects of murine leukemia retrovirus infection on production of cytokines was investigated in mice fed different doses of dehydroepiandrosterone (DHEA). Young C57BL/6 female mice were injected with LP-BM5 murine retrovirus or were kept as uninfected controls. Two weeks later, each group was divided into subgroups: fed unsupplemented AIN 93 diet as the control, or diets supplemented with 0.02% DHEA (0.9 mg/mouse/day) or 0.06% DHEA (2.7 mg/mouse/day). The uninfected mice supplemented with 0.06% DHEA showed a significant (P < 0.05) increase in interleukin-2 (IL-2) and gamma-interferon (IFN-gamma) production, and hepatic vitamin E levels. Retroviral infection induced severe oxidative stress that was reduced by DHEAS supplementation in retrovirally infected mice. DHEA supplementation prevented the retrovirus-induced loss of cytokines (IL-2 and IFN-gamma) secretion by mitogen stimulated spleen cells. DHEA also suppressed the production of cytokines interleukin-6 (IL-6) and tumor necrosis factor-alpha (TNF-alpha) by T helper 2 (Th2) cells which were otherwise stimulated by retrovirus infection. Thus, immune dysfunction and increased oxidation induced by murine retrovirus infection were largely prevented by DHEA.
Displacement-sensitive photonic crystal structures based on guided resonance in photonic crystal slabs (2003)

We introduce a mechanically tunable photonic crystal structure consisting of coupled photonic crystal slabs. Using both analytic theory, and first-principles finite-difference time-domain simulations, we demonstrate that a strong variation of transmission and reflection coefficients of light through such structures can be accomplished with only a nanoscale variation of the spacing between the slabs. Moreover, by specifically configuring the photonic crystal structures, high sensitivity can be preserved in spite of significant fabrication-related disorders. We expect such structures to play important roles in micromechanically tunable optical sensors and filters.
Inhibition of Japanese encephalitis virus replication in cultured cells and mice by a peptide-conjugated morpholino oligomer (2010)

P10882, which targets sequence that is highly conserved across members of the JEV serocomplex, was previously shown to be effective in a mouse model of West Nile disease, and represents a candidate antiviral agent against members of the JEV serocomplex.
He 3 polarization via optical pumping in a birefringent cell (2005)

A sapphire cell was used to obtain a high He3 nuclear polarization by means of spin-exchange optical pumping. The phase-shift difference between ordinary and extraordinary rays is well controlled using the thickness of the birefringent sapphire window so that a high circular polarization is obtained in the cell. Neutron transmission through the polarized He3 gas was measured as a function of neutron energy. A large He3 polarization of 63±1% was obtained at a He3 pressure of 3.1 atm. Neutron polarizations of 97 and 90 % were obtained with transmission rates of 15 and 22 % at 10 and 20 meV, respectively.
Knowledge Discovery in Biological Databases for Revealing Candidate Genes Linked to Complex Phenotypes (2017)

Genetics and "omics" studies designed to uncover genotype to phenotype relationships often identify large numbers of potential candidate genes, among which the causal genes are hidden. Scientists generally lack the time and technical expertise to review all relevant information available from the literature, from key model species and from a potentially wide range of related biological databases in a variety of data formats with variable quality and coverage. Computational tools are needed for the integration and evaluation of heterogeneous information in order to prioritise candidate genes and components of interaction networks that, if perturbed through potential interventions, have a positive impact on the biological outcome in the whole organism without producing negative side effects. Here we review several bioinformatics tools and databases that play an important role in biological knowledge discovery and candidate gene prioritization. We conclude with several key challenges that need to be addressed in order to facilitate biological knowledge discovery in the future.
Immune regulation of experimental myasthenia. (1980)

Experimental autoimmune myasthenia gravis (EAMG) is an appropriate model for studying the molecular origin, immunological mechanism and regulation of myasthenia gravis. Several approaches are being utilised for the regulation of the immune response to AChR and for immunosuppression of EAMG: Corticosteriods and azathioprine can suppress EAMG concomitantly with suppression of immune responses to AChR. High dose cyclophosphamide treatment in mice facilitates the onset of EAMG and results in a selective suppression of the humoral response to AChR whereas the cellular response is enhanced. Specific immunosuppression of EAMG is achieved by using a nonmyasthenic, denatured AChR preparation which cross reacts with the intact receptor. Various degradations and modifications of AChR are being performed in order to identify the smallest molecular entity responsible for the myasthenic activity of AChR. Studies on specific monoclonal antibodies, anti-idiotypes, and on the effect of measles virus on EAMG are being described and their possible significance in regulating myasthenia are being discussed.
Next Generation Test Generator (NGTG) for digital circuits (2002)

The process outlined in this paper describes the system developed to meet the goals of the Next Generation Test Generator program, funded by the Office of Naval Research. This system takes advantage of an unsupervised pattern classification algorithm (Adaptive Resonance Theory (ART)) and a Genetic Algorithm (GA) that is combined to form an optimizing control system. The GA generates a population of test patterns (individuals). Each individual is provided as a set of timed inputs to behavior based simulations representing good and faulty systems. The response of each model (good and faulty) is recombined in the form of an image matrix with each row representing a signature of each of the different circuits. FuzzyART (Fuzzy Logic Based ART) provides a method of image recognition, extracting those images that are distinctly different from any other. Each individual generated by the GA is provided as input to the list of models, then evaluated by FuzzyART and a fitness representing the number of separate classes is formed. New test sequences evolve with increasing fault isolation and detection. The process is repeated until a maximum number of models have been identified and separated. A selective breading algorithm was included to reduce the need for large populations, thus increasing the speed to converge to the "best test". The process was demonstrated using a commercial simulator based on Verilog HDL with a simple master/slave flip-flop and a moderately complex digital circuit (real UUT).
Oxandrolone in AIDS-wasting myopathy (1996)

Oxandrolone, at a dose of either 5 mg/day or 15 mg/day, in contrast to placebo, had a positive impact on the weight and well-being of HIV-seropositive patients suffering from wasting and weakness. Measurable improvement in muscle strength was not noted at the doses employed in this study. Oxandrolone was well tolerated in all the patients who were enrolled in the study. Based on the results reported here, additional studies using higher doses of oxandrolone seem warranted.
Human coagulation factor X deficiency caused by a mutant signal peptide that blocks cleavage by signal peptidase but not targeting and translocation to the endoplasmic reticulum (2021)

Human factor XSanto Domingo is a form of coagulation factor X in which a mutation within the signal peptide region of the precursor protein has been correlated genetically with a severe deficiency of factor X in the affected individual. A point mutation results in substitution of Arg for Gly at the critical -3 position of the factor X signal peptide. To determine the biochemical effect of this mutation on the biosynthesis of factor X, the wild-type and mutant factor X cDNAs were subcloned into a vector for transcription and translation in vitro. Translation products of mRNAs encoding portions of both mutant and wild-type proteins were used in a systematic biochemical approach to evaluate directly the effect of the mutation on targeting, transport, and proteolytic processing in vitro. The results show that targeting and transport of factor XSanto Domingo to the endoplasmic reticulum are functionally dissociated from the removal of the signal peptide by signal peptidase. Factor XSanto Domingo is translocated into the endoplasmic reticulum but not processed by signal peptidase. Transient expression of the wild-type and mutant factor X in human embryonic kidney 293 cells revealed apparently normal secretion of the glycosylated two-chain form of factor X but no secretion of factor XSanto Domingo. Thus, the inability of signal peptidase to cleave factor XSanto Domingo is directly responsible for the absence of circulating factor X and leads to the bleeding diathesis in the affected individual.
Subcellular Localization of Toll-Like Receptor 3 in Human Dendritic Cells (2003)

Toll-like receptor (TLR)3 recognizes dsRNA and transduces signals to activate NF-kappaB and IFN-beta promoter. Type I IFNs (IFN-alpha/beta) function as key cytokines in anti-viral host defense. Human fibroblasts express TLR3 on the cell surface, and anti-TLR3 mAb inhibits dsRNA-induced IFN-beta secretion by fibroblasts, suggesting that TLR3 acts on the cell surface to sense viral infection. In this study, we examined the expression and localization of human TLR3 in various DC subsets using anti-TLR3 mAb. In monocyte-derived immature dendritic cells (iDCs), TLR3 predominantly resided inside the cells but not on the cell surface. iDCs produced IL-12p70 and IFN-alpha and -beta in response to poly(I:C). Similar response was observed in iDCs treated with rotavirus-derived dsRNA. These responses could not be blocked by pretreatment of the cells with anti-TLR3 mAb. In CD11c(+) blood DCs, cytoplasmic retention of TLR3 was also observed as in monocyte-derived iDCs, again endorsing a different TLR3 distribution profile from fibroblasts. In precursor DC2, however, TLR3 could not be detected inside or outside the cells. Of note, there was a putative centrosomal protein that shared an epitope with TLR3 in myeloid DCs and precursor DC2, but not peripheral blood monocytes. Immunoelectron microscopic analysis revealed that TLR3, when stably expressed in the murine B cell line Ba/F3, was specifically accumulated in multivesicular bodies, a subcellular compartment situated in endocytic trafficking pathways. Thus, regulation and localization of TLR3 are different in each cell type, which may reflect participation of cell type-specific multiple pathways in antiviral IFN induction via TLR3.
Contact angle hysteresis in oxygen plasma treated poly(tetrafluoroethylene) (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTContact angle hysteresis in oxygen plasma treated poly(tetrafluoroethylene)M. Morra, E. Occhiello, and F. GarbassiCite this: Langmuir 1989, 5, 3, 872–876Publication Date (Print):May 1, 1989Publication History Published online1 May 2002Published inissue 1 May 1989https://pubs.acs.org/doi/10.1021/la00087a050https://doi.org/10.1021/la00087a050research-articleACS PublicationsRequest reuse permissionsArticle Views2515Altmetric-Citations252LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
The PD‐1 pathway in tolerance and autoimmunity (2010)

Regulatory T cells (Tregs) and the PD-1: PD-ligand (PD-L) pathway are both critical to terminating immune responses. Elimination of either can result in the breakdown of tolerance and the development of autoimmunity. The PD-1: PD-L pathway can thwart self-reactive T cells and protect against autoimmunity in many ways. In this review, we highlight how PD-1 and its ligands defend against potentially pathogenic self-reactive effector T cells by simultaneously harnessing two mechanisms of peripheral tolerance: (i) the promotion of Treg development and function and (ii) the direct inhibition of potentially pathogenic self-reactive T cells that have escaped into the periphery. Treg cells induced by the PD-1 pathway may also assist in maintaining immune homeostasis, keeping the threshold for T-cell activation high enough to safeguard against autoimmunity. PD-L1 expression on non-hematopoietic cells as well as hematopoietic cells endows PD-L1 with the capacity to promote Treg development and enhance Treg function in lymphoid organs and tissues that are targets of autoimmune attack. At sites where transforming growth factor-beta is present (e.g. sites of immune privilege or inflammation), PD-L1 may promote the de novo generation of Tregs. When considering the consequences of uncontrolled immunity, it would be therapeutically advantageous to manipulate Treg development and sustain Treg function. Thus, this review also discusses how the PD-1 pathway regulates a number of autoimmune diseases and the therapeutic potential of PD-1: PD-L modulation.
Membrane-type 1 Matrix Metalloproteinase Cytoplasmic Tail-binding Protein-1 Is a New Member of the Cupin Superfamily (2004)

Membrane-type 1 matrix metalloproteinase (MT1-MMP/MMP-14) is an enzyme that promotes tumor cell invasion in tissues. Although the proteolytic activity of MT1-MMP is indispensable for invasion, it is also regulated by functions of the cytoplasmic tail. In this study we obtained a new human gene whose product binds to the tail sequence in yeast. The product, MTCBP-1, is a 19-kDa protein that belongs to the newly proposed Cupin superfamily composed of proteins with diverse functions. MTCBP-1 expressed in cells formed a complex with MT1-MMP and co-localized at the membrane. It was also detected in both the cytoplasm and nucleus, where MT1-MMP does not exist. In human tumor cell lines MTCBP-1 expression was significantly low compared with non-transformed fibroblasts, and enforced expression of MTCBP-1 inhibited the activity of MT1-MMP in promoting cell migration and invasion. MTCBP-1 showed significant homology to the bacterial aci-reductone dioxygenase, which is an enzyme in methionine metabolism. The C-terminal part of MTCBP-1 is identical to Sip-L, which is reported to be important for human hepatitis C virus replication. Thus, MTCBP-1 may have multiple functions other than the regulation of MT1-MMP, which presumably depends on the subcellular compartment.
Magnetic anisotropies of aligned carbon nanotubes (1995)

Angle-dependent conduction-electron spin resonance and static magnetic-susceptibility measurements of bulk, aligned, and partially purified carbon nanotube films show anisotropies reflecting the anisotropic character of the tubes. The Pauli susceptibility (above 40 K) of the tubes corresponds to about ${10}^{18}$ spins/${\mathrm{cm}}^{3}$, consistent with a semimetal. The g factors and their anisotropies are temperature dependent. The intrinsic tube resistivity is approximately an order of magnitude lower than the dc resistivity of the films. Qualitative changes below 40 K in the resistivity, the spin susceptibility, the g factors, and their anisotropies give evidence for charge-carrier localization.
Recombinant protein expression and purification: A comprehensive review of affinity tags and microbial applications (2012)

Protein fusion tags are indispensible tools used to improve recombinant protein expression yields, enable protein purification, and accelerate the characterization of protein structure and function. Solubility-enhancing tags, genetically engineered epitopes, and recombinant endoproteases have resulted in a versatile array of combinatorial elements that facilitate protein detection and purification in microbial hosts. In this comprehensive review, we evaluate the most frequently used solubility-enhancing and affinity tags. Furthermore, we provide summaries of well-characterized purification strategies that have been used to increase product yields and have widespread application in many areas of biotechnology including drug discovery, therapeutics, and pharmacology. This review serves as an excellent literature reference for those working on protein fusion tags.
The Structure of Psychosis (1998)

These results suggest a relatively complex typology of psychotic syndromes consistent neither with a unitary model nor with a Kraepelinian dichotomy. The familial vulnerability to psychosis extends across several syndromes, being most pronounced in those with schizophrenialike symptoms. The familial vulnerability to depressive and manic affective illness is somewhat more specific.
Analysis of the mouse protamine 1 promoter in transgenic mice. (1993)

Protamines are small arginine-rich proteins that package DNA in spermatozoa. The mouse protamine 1 (Prm-1) gene is transcribed exclusively in post-meiotic spermatids. To identify elements in the Prm-1 promoter required for spermatid-specific transcription, we generated transgenic mice by microinjection of transgenes containing Prm-1 5' flanking sequences with 5' truncations or internal deletions of conserved sequences linked to a marked Prm-1 gene. We also tested Prm-1 promoter regions with a heterologous human growth hormone reporter gene. We conclude that a 113-bp region can direct spermatid-specific transcription and we have defined sequences within this region that are essential for proper function. These results will facilitate the isolation and characterization of transcription factors essential for post-meiotic gene expression.
Cholecalciferol Supplementation Alters Calcitriol-Responsive Monocyte Proteins and Decreases Inflammatory Cytokines in ESRD (2009)

In vitro, monocyte 1α-hydroxylase converts 25-hydroxyvitamin D [25(OH)D] to 1,25-dihydroxyvitamin D to regulate local innate immune responses, but whether 25(OH)D repletion affects vitamin D–responsive monocyte pathways in vivo is unknown. Here, we identified seven patients who had 25(OH)D insufficiency and were undergoing long-term hemodialysis and assessed changes after cholecalciferol and paricalcitol therapies in both vitamin D–responsive proteins in circulating monocytes and serum levels of inflammatory cytokines. Cholecalciferol therapy increased serum 25(OH)D levels four-fold, monocyte vitamin D receptor expression three-fold, and 24-hydroxylase expression; therapy decreased monocyte 1α-hydroxylase levels. The CD16+ “inflammatory” monocyte subset responded to 25(OH)D repletion the most, demonstrating the greatest increase in vitamin D receptor expression after cholecalciferol. Cholecalciferol therapy reduced circulating levels of inflammatory cytokines, including IL-8, IL-6, and TNF. These data suggest that nutritional vitamin D therapy has a biologic effect on circulating monocytes and associated inflammatory markers in patients with ESRD.
Cytoplasmic Dynein Regulation by Subunit Heterogeneity and Its Role in Apical Transport (2001)

Despite the existence of multiple subunit isoforms for the microtubule motor cytoplasmic dynein, it has not yet been directly shown that dynein complexes with different compositions exhibit different properties. The 14-kD dynein light chain Tctex-1, but not its homologue RP3, binds directly to rhodopsin's cytoplasmic COOH-terminal tail, which encodes an apical targeting determinant in polarized epithelial Madin-Darby canine kidney (MDCK) cells. We demonstrate that Tctex-1 and RP3 compete for binding to dynein intermediate chain and that overexpressed RP3 displaces endogenous Tctex-1 from dynein complexes in MDCK cells. Furthermore, replacement of Tctex-1 by RP3 selectively disrupts the translocation of rhodopsin to the MDCK apical surface. These results directly show that cytoplasmic dynein function can be regulated by its subunit composition and that cytoplasmic dynein is essential for at least one mode of apical transport in polarized epithelia.