gebhart/patrepeval huggingface dataset:
Structure of Class I and Class II HLA Antigens (1987)

Considerable information is now available about the overall structure of both class I and class II HLA antigens and in the not too distant future should be available in atomic detail in the crystal structures. The present challenge is to relate these structures to the functions of these antigens in presentation of viral antigens in the generation of CTL (class I HLA antigens) or in presentation of foreign antigens to T helper cells in the generation of the antibody response (class II HLA antigens) and in particular to relate their polymorphism to these specific functions.
Age-related decline in immunity: implications for vaccine responsiveness (2008)

Aging is associated with declines in immune system function, or 'immunosenescence', leading to progressive deterioration in both innate and adaptive immunity. These changes contribute to the decreased response to vaccines seen in many older adults, and morbidity and mortality from infection. Infections (e.g., influenza, pneumonia and septicemia) appear among the top ten most-common causes of death in adults in the USA aged 55 years and older. As immunosenescence has gathered more attention in the scientific and healthcare communities, investigators have demonstrated more links between immunosenescent changes and morbidity and mortality related to infections and declining vaccine responses. This review summarizes the recent literature on age-dependent defects in adaptive and innate immunity, data linking these defects to poor vaccine response and morbidity and mortality, current recommendations for vaccinations and potential strategies to improve vaccine efficacy in older adults.
Hypersensitization of the Orexin 1 Receptor by the CB1 Receptor (2003)

In the present study, we observed evidence of cross-talk between the cannabinoid receptor CB1 and the orexin 1 receptor (OX1R) using a heterologous system. When the two receptors are co-expressed, we observed a major CB1-dependent enhancement of the orexin A potency to activate the mitogen-activated protein kinase pathway; dose-responses curves indicated a 100-fold increase in the potency of orexin-mediated mitogen-activated protein kinase activation. This effect required a functional CB1 receptor as evidenced by the blockade of the orexin response by the specific CB1 antagonist, N-(piperidino-1-yl)-5-(4-chlorophenyl)-1-(2,4-dichlorophenyl)-4-methyl-pyrazole-3-carboxamide (SR141716), but also by pertussis toxin, suggesting that this potentiation is Gi-mediated. In contrast to OX1R, the potency of direct activation of CB1 was not affected by co-expression with OX1R. In addition, electron microscopy experiments revealed that CB1 and OX1R are closely apposed at the plasma membrane level; they are close enough to form hetero-oligomers. Altogether, for the first time our data provide evidence that CB1 is able to potentiate an orexigenic receptor. Considering the antiobesity effect of SR141716, these results open new avenues to understand the mechanism by which the molecule may prevent weight gain through functional interaction between CB1 and other receptors involved in the control of appetite.
Chromosomal Mapping of the Human and Mouse Homologues of Two New Members of the AP-2 Family of Transcription Factors (1996)

The AP-2 transcription factor has been shown to play an important role in the development of tissues of ectodermal origin and has also been implicated in mammary oncogenesis. It has recently been found that AP-2 is encoded by a family of related genes, AP-2alpha, AP-2beta, and AP-2gamma. As a further step in understanding the role each of these genes has in development, we have used fluorescence in situ hybridization to map the chromosomal locations of the mouse and human homologues of the newly isolated AP-2beta and AP-2gamma genes. Tcfap2b and Tcfap2c map to mouse chromosomes 1A2-4 and 2H3-4, respectively, while TFAP2B and TFAP2C map to human chromosomes 6p12 and 20q13.2, the latter being a region that is frequently amplified in breast carcinoma.
Interactive volume rendering on a multicomputer (1992)

Direct volume rendering is a computationally intensive operation that has become a valued and often preferred visualization tool. For maximal data comprehension, interactive manipulation of the rendering parameters is desirable. To this end, a reasonable target would be a system capable of displaying 12E3 voxel data sets at multiple frames per second. Although the computing resources required to attain this performance are beyond those available in current uniprocessor workstations, multicomputers and VLSI rendering hardware offer a solution. This paper describes a volume rendering algorithm for MIMD message passing multicomputers. This algorithm addresses the issues of distributed rendering, data set distribution, load balancing, and contention for the routing network. An implementation on a multicomputer with a 1 D ring network is analyzed, and extension of the algorithm to a 2D mesh topology is described. In addition, the paper presents a method of exploiting screen coherence through the use of VLSI pixel processor arrays. Though not critical to the general algorithm, this rendering approach is demonstrated in the example implementation where it serves as a hardware accelerator of the rendering process. Commercial graphics workstations use pixel processors to accelerate polygon rendering; this paper proposes a new use of this hardware for accelerating volume rendering.
Angiofibrotic Response to Vascular Endothelial Growth Factor Inhibition in Diabetic Retinal Detachment (2012)

OBJECTIVES To assess the effect of bevacizumab injection on connective tissue growth factor (CTGF) and vascular endothelial growth factor (VEGF) in the ocular fluids of patients with diabetic traction retinal detachment, and to determine whether intraoperative and postoperative complications are decreased in eyes given adjunctive preoperative bevacizumab injection. METHODS Twenty eyes of 19 patients were randomized to receive intravitreal bevacizumab or sham injection 3 to 7 days before vitrectomy for severe proliferative diabetic retinopathy. We collected aqueous samples before injection and at the time of vitrectomy and extracted undiluted vitreous samples. RESULTS Five eyes had decreased vascularization of membranes from preinjection to the time of vitrectomy (all in the bevacizumab treatment arm). Median visual acuities were 20/400 in control eyes at baseline and postoperative month 3 (POM3) and 8/200 in the bevacizumab-treated group at baseline and 20/100 at POM3 (P= .30 between control and bevacizumab-treated groups at POM3). All retinas were attached at POM3. Vitreous levels of VEGF were significantly lower in the bevacizumab group than in the control group (P= .03). Vitreous levels of CTGF were slightly lower in the bevacizumab group compared with the control group, but this difference was not statistically significant (P= .38). Levels of CTGF in the aqueous were strongly correlated with CTGF levels in the vitreous of controls (Spearman correlation coefficient, 0.95 [P< .001]). CONCLUSIONS Intravitreal bevacizumab injection reduces vitreous levels of VEGF and produces a clinically observable alteration in diabetic fibrovascular membranes. Ocular fluid levels of CTGF are not significantly affected within the week after VEGF inhibition. Retinal reattachment rates and visual acuity are not significantly altered by preoperative intravitreal bevacizumab injection at POM3. TRIAL REGISTRATION clinicaltrials.gov Identifier: NCT01270542.
Isoform‐Specific Effects of Transforming Growth Factors‐β on Degeneration of Primary Neuronal Cultures Induced by Cytotoxic Hypoxia or Glutamate (1993)

The transforming growth factors-beta (TGFs-beta) are multifunctional peptide growth factors that have been localized in neuronal and glial cells of the CNS of mice, rats, and chick embryos. We tested the TGF-beta isoforms 1, 2, and 3 for their protective effects against neuronal degeneration caused by cytotoxic hypoxia or by the excitatory amino acid L-glutamate. A cytotoxic hypoxia was induced in cultured chick embryo telencephalic neurons by adding 1 mM sodium cyanide to the culture medium for a period of 30 min. Treatment with TGF-beta 1 (1-30 ng/ml) led to a statistically significant increase in cell viability, neuronal ATP levels, and protein content of the cultures assessed 72 h after the toxic insult. TGF-beta 3 was able to reduce the cyanide-induced neuronal damage at concentrations of 0.3 and 1 ng/ml, whereas TGF-beta 2 only showed neuroprotective activity at concentrations of 30 and 50 ng/ml. Both pre- and post-treatment with TGF-beta 1 also prevented the degeneration of cultured chick embryo telencephalic neurons that had been exposed to 1 mM L-glutamate in a buffered salt solution for a period of 60 min. Furthermore, TGF-beta 1 (0.3-3 ng/ml), and to a lesser extent TGF-beta 3 (0.1-1 ng/ml), significantly reduced excitotoxic injury of cultured neurons from rat cerebral cortex that had been exposed to serum-free culture medium supplemented with 1 mM L-glutamate. These results demonstrate that the TGFs-beta are able to prevent the degeneration of primary neuronal cultures, which was caused by energy depletion and activation of glutamate receptors, in an isoform-specific manner.
Production of multimeric forms of CD4 through a sugar-based cross-linking strategy. (1991)

We have developed a three-step cross-linking procedure that is specifically targeted at the carbohydrate on a protein and applied it to CD4 as a model system for studying the role of multivalent interactions in function. In the first step CD4 was oxidized with periodate, creating aldehydes that served as targets for the subsequent chemistry. Next the aldehydes were modified with cystamine, converting the reactive group into a thiol. Finally cross-linking through the thiol moiety was generated with the homobifunctional cross-linker bismaleimidohexane. With this procedure, approximately 60% of the CD4 was converted into higher molecular weight complexes that were soluble and retained function as assessed by glycoprotein gp120 binding activity. CD4 dimers and tetramers by mass were 4 and 15 times as active as CD4 monomer in blocking virus infection with HTLV-IIIB in an in vitro cellular assay. The cross-linking chemistry provides an efficient method for producing homomultimers of a glycoprotein.
Identification of the Genes Encoding Two Capsid Proteins of Herpes Simplex Virus Type 1 by Direct Amino Acid Sequencing (1990)

Amino-terminal amino acid sequencing was carried out on proteins purified from herpes simplex virus type 1 capsids. The sequences of two capsid proteins (VP19C and VP23) showed them to be encoded by genes UL38 and UL18, respectively. The product of UL38 has been shown to be essential for capsid assembly, but no role has previously been assigned to the product of UL18.
Production of a complete binary toxin (actin-specific ADP-ribosyltransferase) by Clostridium difficile CD196 (1997)

A Clostridium difficile isolate was found to produce an actin-specific ADP-ribosyltransferase (CDT) homologous to the enzymatic components of Clostridium perfringens iota toxin and Clostridium spiroforme toxin (M. R. Popoff, E. J. Rubin, D. M. Gill, and P. Boquet, Infect. Immun. 56:2299-2306, 1988). The CDT locus from C. difficile CD196 was cloned and sequenced. It contained two genes (cdtA and cdtB) which display organizations and sequences similar to those of the iota toxin gene. The deduced enzymatic (CDTa) and binding (CDTb) components have 81 and 84% identity, respectively, with the corresponding components of iota toxin. CDTa and CDTb induced actin cytoskeleton alterations similar to those caused by other clostridial binary toxins. The lower level of production of binary toxin by CD196 than of iota toxin by C. perfringens was related to a lower transcript level, possibly due to a promoter region different from that of iota toxin genes. The cdtA and cdtB genes have been detected in 3 of 24 clinical isolates examined, and cdtB alone was found in 2 additional strains. One strain (in addition to CD196) was shown by Western blotting to produce CDTa and CDTb. These results indicate that some C. difficile strains synthesize a binary toxin that could be an additional virulence factor.
Inborn Errors of Metabolism with Consequences for Bile Acid Biosynthesis: A Minireview (1994)

Five inborn errors with consequences for bile acid biosynthesis have been described: 7-dehydrocholesterol 7-reductase deficiency, 3 beta-hydroxysteroid delta 5-oxidoreductase/isomerase deficiency, 3-oxo-delta 4-steroid 5 beta-reductase deficiency, sterol 27-hydroxylase deficiency (cerebrotendinous xanthomatosis), and peroxisomal disease(s) with absence of peroxisomes. Diagnosis and treatment of these very rare disorders are discussed. Bile acid therapy is important in most of these disorders and in the case of 3 beta-hydroxysteroid delta 5-oxidoreductase/isomerase deficiency and 3-oxo-delta 4-steroid 5 beta-reductase deficiency such therapy may save the life of the affected cholestatic infant. In the case of sterol 27-hydroxylase deficiency, early treatment with chenodeoxycholic acid may prevent the development of progressive neurological dysfunction, dementia, and ataxia. In the latter three cases early diagnosis and treatment is of utmost importance.
Primer3Plus, an enhanced web interface to Primer3 (2007)

Here we present Primer3Plus, a new web interface to the popular Primer3 primer design program as an enhanced alternative for the CGI- scripts that come with Primer3. Primer3 consists of a command line program and a web interface. The web interface is one large form showing all of the possible options. This makes the interface powerful, but at the same time confusing for occasional users. Primer3Plus provides an intuitive user interface using present-day web technologies and has been developed in close collaboration with molecular biologists and technicians regularly designing primers. It focuses on the task at hand, and hides detailed settings from the user until these are needed. We also added functionality to automate specific tasks like designing primers for cloning or step-wise sequencing. Settings and designed primer sequences can be stored locally for later use. Primer3Plus supports a range of common sequence formats, such as FASTA. Finally, primers selected by Primer3Plus can be sent to an order form, allowing tight integration into laboratory ordering systems. Moreover, the open architecture of Primer3Plus allows easy expansion or integration of external software packages. The Primer3Plus Perl source code is available under GPL license from SourceForge. Primer3Plus is available at http://www.bioinformatics.nl/primer3plus.
Sequence of the Alpha Subunit of Photoreceptor G Protein: Homologies Between Transducin, ras , and Elongation Factors (1985)

A bovine retinal complementary DNA clone encoding the α subunit of transducin (T α ) was isolated with the use of synthetic oligodeoxynucleotides as probes, and the complete nucleotide sequence of the insert was determined. The predicted protein sequence of 354 amino acids includes the known sequences of four tryptic peptides and sequences adjacent to the residues that undergo adenosine diphosphate ribosylation by cholera toxin and pertussis toxin. On the basis of homologies to other proteins, such as the elongation factors of protein synthesis and the ras oncogene proteins, regions are identified that are predicted to be acylated and involved in guanine nucleotide binding and hydrolysis. Amino acid sequence similarity between T α and ras is confined to these regions of the molecules.
Optimal Spike-Timing Dependent Plasticity for Precise Action Potential Firing (2005)

In timing-based neural codes, neurons have to emit action potentials at precise moments in time. We use a supervised learning paradigm to derive a synaptic update rule that optimizes via gradient ascent the likelihood of postsynaptic firing at one or several desired firing times. We find that the optimal strategy of up- and downregulating synaptic efficacies can be described by a two-phase learning window similar to that of Spike-Timing Dependent Plasticity (STDP). If the presynaptic spike arrives before the desired postsynaptic spike timing, our optimal learning rule predicts that the synapse should become potentiated. The dependence of the potentiation on spike timing directly reflects the time course of an excitatory postsynaptic potential. The presence and amplitude of depression of synaptic efficacies for reversed spike timing depends on how constraints are implemented in the optimization problem. Two different constraints, i.e., control of postsynaptic rates or control of temporal locality,are discussed.
Therapies in non‐alcoholic steatohepatitis (NASH) (2017)

The hallmark of non-alcoholic fatty liver disease (NAFLD) is excessive fatty accumulation in the hepatocytes, which may be an isolated event (non-alcoholic fatty liver, NAFL) or accompanied by evidence of inflammation and cell injury with or without fibrosis (non-alcoholic steatohepatitis, NASH). NASH, the more aggressive form of NAFLD, may progress to cirrhosis and hepatocellular carcinoma. Since NASH is estimated to overtake hepatitis C virus infection as the leading cause of liver transplantation in the US in the coming decade, and there are no current FDA-approved therapies for this disease, the need to find appropriate therapeutic targets is now more urgent than ever before. Diet and other lifestyle modifications have always been difficult to maintain and this approach alone has not slowed the rising tide of the disease. While the results of traditional therapies such as vitamin E and pioglitazone have been significant for steatosis and inflammation, they have had no effect on fibrosis, which is the strongest indicator of mortality in this condition. However, the understanding of the pathogenesis and progression of NASH has evolved and several promising novel therapies to target and possibly reverse fibrosis are being evaluated, making the future outlook of NASH therapy more optimistic.
PEO−PPO Block Copolymer Vectors Do Not Interact Directly with DNA but with Lipid Membranes (2007)

Small angle neutron (SANS) and light scattering was used to study the interaction between fragments of double stranded deoxyribonucleic acid (DNA) and a synthetic triblock [poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide)] amphiphilic polymer, known as L64, a potential vector for gene therapy. The mechanism of action of this vector is yet unknown. The contrast variation method was used to separate the partial structure factors of the different components in mixtures of triblock and DNA. It has been found that the copolymer and DNA molecules exhibit repulsive interactions. Further, the interaction between the copolymer and a model lipid membrane was investigated in order to explain the action of the vector. Electrical measurements on black lipid membranes indicated that the main effect of L64 as a vector is to permeabilize the cell's membrane.
Possible role of two phenylalanine residues in the active site of human cytidine deaminase (2000)

Site-directed mutagenesis on human cytidine deaminase (CDA) was employed to mutate specifically two highly conserved phenylalanine residues, F36 and F137, to tryptophan; at the same time, the unique tryptophan residue present in the sequence at position 113 was mutated to phenylalanine. These double mutations were performed in order to have for each protein a single tryptophan signal for fluorescence studies relative to position 36 or 137. The mutant enzymes thus obtained, W113F, F36W/W113F and F137W/W113F, showed by circular dicroism and thermal stability an overall structure not greatly affected by the mutations. The titration of Trp residues by N-bromosuccinimide (NBS) suggested that residue W113 of the wild-type CDA and W36 of mutant F36W/W113F are buried in the tertiary structure of the enzyme, whereas the residue W137 of mutant F137W/W113F is located near the surface of the molecule. Kinetic experiments and equilibrium experiments with FZEB showed that the residue W113 seems not to be part of the active site of the enzyme whereas the Phe/Trp substitution in F36W/W113F and F137W/W113F mutant enzymes had a negative effect on substrate binding and catalysis, suggesting that F137 and F36 of the wild-type CDA are involved in a stabilizing interaction between ligand and enzyme.
Gender Differences and Similarities in PISA 2003 Mathematics: A Comparison between the United States and Hong Kong (2009)

Differential gender performance in standardized mathematics assessment has long been a heated topic. Gender gaps of varied magnitude have been identified on large-scale assessments in the United States. To continue the investigation, this study examined male and female performance on the Programme for International Student Assessment (PISA) 2003 mathematics along four in-depth dimensions (strand, content topics, competency cluster, and item format). Furthermore, to identify the shared and unique patterns of gender differences, students from Hong Kong were brought into the comparison. Males in both counties demonstrated superior performance, particularly on complex multiple choice items. Females scored higher on probability, algebra, and reproduction items. Hong Kong students showed a larger gender gap than U.S. students. However, the within-country gender differences were considered small compared with the significant between-country performance differences. (Some PISA participants are not countries, but education systems representative of countries (e.g., Hong Kong). However, for purpose of simplicity, instead of using “countries/systems” every time, the generic term “countries” was used to refer to countries or systems.) Hong Kong students predominantly outperformed U.S. students, including items that measure complex mathematical reasoning, an area well documented to favor U.S. students.
Increases in callus formation and mechanical strength of healing fractures in old rats treated with parathyroid hormone (2001)

We studied the effects of intermittent administration of parathyroid hormone (PTH(1-34)) on callus formation and mechanical strength of tibial fractures in 27-month-old rats after 3 and 8 weeks of healing. 200 microg PTH(1-34)/kg was administered daily during both periods of healing, and control animals with fractures were given vehicle. At 3 weeks, PTH treatment increased maximum load and external callus volume by 160% and 208%; at 8 weeks, by 270% and 135%. It also enhanced callus bone mineral content (BMC) by 190% and 388% (3 and 8 weeks). From week 3 to week 8, callus BMC increased by 60% in the vehicle-injected animals, and by 169% in the PTH-treated animals. In the contralateral intact tibia, PTH treatment increased BMC by 18% and 21% (3 and 8 weeks). No differences in body weight were found between the vehicle-injected and the PTH-treated animals during the experiment. In conclusion, PTH treatment enhances fracture strength, callus volume and callus BMC after 3 and 8 weeks of healing.