gebhart/patrepeval huggingface dataset:
Autoantigens signal through chemokine receptors: uveitis antigens induce CXCR3- and CXCR5-expressing lymphocytes and immature dendritic cells to migrate (2005)

We tested the hypothesis that interaction between autoantigens and chemoattractant receptors may be an important step in the development of autoimmunity. The retinal autoantigens S-antigen (S-Ag) and interphotoreceptor retinoid binding protein (IRBP) can induce autoimmune uveitis in rodent models. We evaluated the chemotactic activity of S-Ag and IRBP and found that both induced migration of human and mouse immature dendritic cells (iDCs) and lymphocytes, but not neutrophils, monocytes, or mature DCs. Cross-desensitization studies and single-receptor transfected cells revealed that subfamily of alpha chemokine receptors CXCR5 and CXCR3 mediated the chemotactic effect of IRBP, while only CXCR3 was required for the chemotactic response to S-Ag. Examination of the relationships between chemoattraction and the ability to elicit pathology at the protein or peptide levels in the mouse uveitis model revealed dissociation of the capacity to induce uveitis, lymphocyte proliferation, and chemoattraction. These studies suggest that IRBP and S-Ag can initiate innate and, in sensitive individuals, adaptive immune response by attracting iDCs and T and B cells expressing CXCR3 and CXCR5.
Absence of TXNIP in Humans Leads to Lactic Acidosis and Low Serum Methionine Linked to Deficient Respiration on Pyruvate (2019)

Thioredoxin-interacting protein (TXNIP) is an α-arrestin that can bind to and inhibit the antioxidant protein thioredoxin (TXN). TXNIP expression is induced by glucose and promotes β-cell apoptosis in the pancreas, and deletion of its gene in mouse models protects against diabetes. TXNIP is currently studied as a potential new target for antidiabetic drug therapy. In this study, we describe a family with a mutation in the <i>TXNIP</i> gene leading to nondetectable expression of TXNIP protein. Symptoms of affected family members include lactic acidosis and low serum methionine levels. Using patient-derived TXNIP-deficient fibroblasts and myoblasts, we show that oxidative phosphorylation is impaired in these cells when given glucose and pyruvate but normalized with malate. Isolated mitochondria from these cells appear to have normal respiratory function. The cells also display a transcriptional pattern suggestive of a high basal activation of the Nrf2 transcription factor. We conclude that a complete lack of TXNIP in human is nonlethal and leads to specific metabolic distortions that are, at least in part, linked to a deficient respiration on pyruvate. The results give important insights into the impact of TXNIP in humans and thus help to further advance the development of antidiabetic drugs targeting this protein.
The RosettaDock server for local protein-protein docking (2008)

The RosettaDock server (http://rosettadock.graylab.jhu.edu) identifies low-energy conformations of a protein-protein interaction near a given starting configuration by optimizing rigid-body orientation and side-chain conformations. The server requires two protein structures as inputs and a starting location for the search. RosettaDock generates 1000 independent structures, and the server returns pictures, coordinate files and detailed scoring information for the 10 top-scoring models. A plot of the total energy of each of the 1000 models created shows the presence or absence of an energetic binding funnel. RosettaDock has been validated on the docking benchmark set and through the Critical Assessment of PRedicted Interactions blind prediction challenge.
pVHL/HIF-Regulated CD70 Expression Is Associated with Infiltration of CD27+ Lymphocytes and Increased Serum Levels of Soluble CD27 in Clear Cell Renal Cell Carcinoma (2015)

Our findings demonstrate that in ccRCC, CD70 expression is regulated by HIF as a consequence of pVHL inactivation. Increased serum levels of CD27 suggest the existence of CD70-expressing ccRCC, thus representing a potential serum marker for patients suffering from this disease.
BMP4-mediated brown fat-like changes in white adipose tissue alter glucose and energy homeostasis (2013)

Expression of bone morphogenetic protein 4 (BMP4) in adipocytes of white adipose tissue (WAT) produces "white adipocytes" with characteristics of brown fat and leads to a reduction of adiposity and its metabolic complications. Although BMP4 is known to induce commitment of pluripotent stem cells to the adipocyte lineage by producing cells that possess the characteristics of preadipocytes, its effects on the mature white adipocyte phenotype and function were unknown. Forced expression of a BMP4 transgene in white adipocytes of mice gives rise to reduced WAT mass and white adipocyte size along with an increased number of a white adipocyte cell types with brown adipocyte characteristics comparable to those of beige or brite adipocytes. These changes correlate closely with increased energy expenditure, improved insulin sensitivity, and protection against diet-induced obesity and diabetes. Conversely, BMP4-deficient mice exhibit enlarged white adipocyte morphology and impaired insulin sensitivity. We identify peroxisome proliferator-activated receptor gamma coactivator 1-α (PGC1α) as the target of BMP signaling required for these brown fat-like changes in WAT. This effect of BMP4 on WAT appears to extend to human adipose tissue, because the level of expression of BMP4 in WAT correlates inversely with body mass index. These findings provide a genetic and metabolic basis for BMP4's role in altering insulin sensitivity by affecting WAT development.
Neural tube-ectoderm interactions are required for trigeminal placode formation (1997)

Cranial sensory ganglia in vertebrates develop from the ectodermal placodes, the neural crest, or both. Although much is known about the neural crest contribution to cranial ganglia, relatively little is known about how placode cells form, invaginate and migrate to their targets. Here, we identify Pax-3 as a molecular marker for placode cells that contribute to the ophthalmic branch of the trigeminal ganglion and use it, in conjunction with DiI labeling of the surface ectoderm, to analyze some of the mechanisms underlying placode development. Pax-3 expression in the ophthalmic placode is observed as early as the 4-somite stage in a narrow band of ectoderm contiguous to the midbrain neural folds. Its expression broadens to a patch of ectoderm adjacent to the midbrain and the rostral hindbrain at the 8- to 10-somite stage. Invagination of the first Pax-3-positive cells begins at the 13-somite stage. Placodal invagination continues through the 35-somite stage, by which time condensation of the trigeminal ganglion has begun. To challenge the normal tissue interactions leading to placode formation, we ablated the cranial neural crest cells or implanted barriers between the neural tube and the ectoderm. Our results demonstrate that, although the presence of neural crest cells is not mandatory for Pax-3 expression in the forming placode, a diffusible signal from the neuroectoderm is required for induction and/or maintenance of the ophthalmic placode.
Tumor regressions observed in patients with metastatic melanoma treated with an antigenic peptide encoded by geneMAGE-3 and presented by HLA-A1 (1999)

Thirty-nine tumor-bearing patients with metastatic melanoma were treated with 3 subcutaneous injections of the MAGE-3.A1 peptide at monthly intervals. No significant toxicity was observed. Of the 25 patients who received the complete treatment, 7 displayed significant tumor regressions. All but one of these regressions involved cutaneous metastases. Three regressions were complete and 2 of these led to a disease-free state, which persisted for more than 2 years after the beginning of treatment. No evidence for a cytolytic T lymphocyte (CTL) response was found in the blood of the 4 patients who were analyzed, including 2 who displayed complete tumor regression. Our results suggest that injection of the MAGE-3.A1 peptide induced tumor regression in a significant number of the patients, even though no massive CTL response was produced. Int. J. Cancer 80:219–230, 1999. © 1999 Wiley-Liss, Inc.
Deuterium Tetrabenazine for Tardive Dyskinesia (2018)

Tardive dyskinesia remains a significant, potentially stigmatizing or crippling adverse effect for any patient treated with an antipsychotic medication. While second- and third-generation antipsychotics have exhibited lower annual incidence rates for tardive dyskinesia than classic or first-generation agents, 3.9% versus 5.5%, the estimated incidence rate is only modestly lower. When coupled with the fact that second- and third-generation antipsychotic medications have come to be employed in treating a wider range of disorders (e.g., autism spectrum disorders, mood disorders, personality disorders, etc.), it is clear that the population of patients exposed to the risk of tardive dyskinesia has expanded. On April 3, 2017, the U.S. Food and Drug Administration (FDA) approved a deuterated version of tetrabenazine (Xenozine®) for the treatment of the involuntary choreic movements associated with Huntington's disease. More recent data, however, have indicated that deuterium tetrabenazine or deutetrabenazine (Austedo®) is effective in treating tardive dyskinesia. Moreover, like the other derivative of tetrabenazine, valbenazine (Ingrezza®), deutetrabenazine offers less frequent dosing and a better short-term adverse effect profile than that of tetrabenazine. Longer use in a broader range of patients, however, will be required to identify risks and benefits not found in short-term trials, as well as optimal use parameters for treatment of tardive dyskinesia.
Precipitative Removal of As, Ba, B, Cr, Sr, and V Using Sodium Carbonate (2006)

Sodium carbonate softening at pH 10.3 is a viable method of removing the inorganic contaminants arsenic, barium, chromium, strontium, and vanadium from drinking water sources. A broad survey revealed that removals varied widely and were dependent on solution composition. Median removals of As, Ba, Cr, Sr, and V were 24, 100, 92, 99, and 60%, respectively. Linear and nonlinear empirical models were fit for crudely estimating the removal of these contaminants in the presence of other elements that are typically removed in the softening process (i.e., calcium, magnesium, silicon, iron, and aluminum). Boron was removed to a much lesser extent (median removal 2%) indicating soda ash softening is not a promising treatment option for this purpose.
Infliximab in the treatment of severe ulcerative colitis: a follow-up study. (2005)

Conventional treatment options for patients with severe steroid-refractory ulcerative colitis (UC) include intravenous cyclosporine, which is frequently burdened by toxicity, or colectomy. Preliminary data suggest a benefit of anti-tumor necrosis factor alpha (Infliximab) therapy in patients with steroid refractory UC. Thirteen patients with severe UC, refractory to therapy with methyl-prednisolone, 60 mg IV daily were treated with a single intravenous infusion of Infliximab 5 mg/kg. Ten out of 13 patients (77%) had a clinical response to therapy defined by a CAI < or = 10 on two consecutive days. Two patients (15%) underwent total colectomy because of clinical worsening; one patient refused surgery and was lost to follow-up. Infusion with Infliximab produced no significant adverse events. The mean time of follow-up was 25.6 months (range 17-24); in this period of time 8 out of 10 patients (80%) maintained clinical remission and were able to discontinue corticosteroids therapy. Infliximab appears to be an effective agent for inducing long standing remission in refractory patients with severe UC.
A Voice-Controlled, Repertory-Dialer System (1980)

This paper describes a speaker-trained, voice-controlled, repertory-dialer system that includes a real-time speech analyzer, an isolated-word recognizer, a voice-response system, and a simulated dialer. The system is implemented on a minicomputer with a high-speed array processor performing the real-time operations. The vocabulary consists of seven command words, ten digits, and any number of names up to a specified maximum. To train the system, the user speaks each vocabulary word twice to provide reference templates for the system. After training, the system can dial the telephone number corresponding to any name in the repertory, or it can dial a 4-digit telephone extension spoken as a string of isolated digits. The system operates in two modes. In the first (cued by a double beep), the user can modify the repertory either by adding or deleting names or by changing a phone number, or the user can enter the second mode using a specified command word. In the second mode (cued by a single beep), the user can speak any name in the repertory or can give a 4-digit telephone extension. The system was tested by six talkers (three male and three female, three of whom were naive and three experienced users) over a three-week period. A total of 4620 words were spoken, and during the course of the text there were no recognition errors. A request for a repeat of a spoken word occurred about 2 percent of the time.
Effects of a trinucleotide ethyl phosphotriester, Gmp(Et)Gmp(Et)U, on mammalian cells in culture (1977)

The nonionic 2'-O-methyribooligonucleotide ethyl phosphotriester, Gmp(Et)Gmp(Et)U, is complementary to the...ApCpC...sequence found in the amino acid accepting stem of most tRNAs and the anticodon region of tRNAgly and to the threonine codon of mRNA. Gmp(Et)Gmp(EtU forms hydrogen-bonded complexes with the amino acid accepting stem of tRNApheyeast and unfractionated tRNA Escherichia coli under physiological salt conditions at 37 degrees C as determined by equilibrium dialysis. The extent of phenylalanine aminoacylation of tRNApheE.coli is inhibited 39% by Gmp(Et)Gmp(Et)U at 37 degrees C in solution. The triester is resistant to hydrolysis by serum nucleases and cell lysates. The triester is readily taken up by transformed Syrian hamster fibroblasts growing in monolayer. Within the cell, the triester is deethylated to give the trinucleotide species Gmp(Et)GmpU, GmpGmp(Et)U, and GmpGmpU and is also hydrolyzed to dimeric and monomeric units. Treatment of transformed fibroblasts in monolayer with 25 micronM Gmp(Et)Gmp(Et)U results in a 40% inhibition of cellular protein synthesis with a concurrent slight increase in cellular RNA synthesis during the first 4 h. After 4 h, the rate of cellular protein synthesis begins to recover while RNA synthesis returns to that of the control. Our biochemical studies suggest that inhibition of cellular protein synthesis might be expected if Gmp(Et)Gmp(Et)UGmp(Et)GmpU, GmpGmp(Et)U, and GmpGmpU, which have been taken up by or formed within the cell, physically bind to tRNA and mRNA and inhibit the function of these nucleic acids. The reversible inhibition of protein synthesis may be a consequence of further degradation of the trinucleotide species within the cell as well as to an increase in supply of RNA molecules involved in protein synthesis. The growth of the transformed fibroblasts is inhibited during the first 24 h of incubation with 25 micronM Gmp(Et)Gmp(Et)U after which growth proceeds at a normal rate. In cloning experiments, the number and size of colonies formed by the transformed fibroblasts after 5 days exposure to 25 micronM triester is decreased by 50% relative to untreated controls. The temporary inhibition of cell growth may reflect the transitory inhibition of cellular protein synthesis caused by the triester.
Metabolism and function of phenazines in bacteria: impacts on the behavior of bacteria in the environment and biotechnological processes (2010)

Phenazines constitute a large group of nitrogen-containing heterocyclic compounds produced by a diverse range of bacteria. Both natural and synthetic phenazine derivatives are studied due their impacts on bacterial interactions and biotechnological processes. Phenazines serve as electron shuttles to alternate terminal acceptors, modify cellular redox states, act as cell signals that regulate patterns of gene expression, contribute to biofilm formation and architecture, and enhance bacterial survival. Phenazines have diverse effects on eukaryotic hosts and host tissues, including the modification of multiple host cellular responses. In plants, phenazines also may influence growth and elicit induced systemic resistance. Here, we discuss emerging evidence that phenazines play multiple roles for the producing organism and contribute to their behavior and ecological fitness.
Studies in solvolysis. Part I. The neutral hydrolysis of some alkyl trifluoroacetates in water and deuterium oxide (1968)

The temperature dependence of the rates of neutral hydrolysis of a series of alkyl trifluoroacetates (CF 3 COOR; R = methyl, ethyl, s-propyl, t-butyl) has been determined in both light and heavy water. From these studies the thermodynamic parameters (ΔH ≠ , ΔS ≠ ) which characterize the activation process have been calculated. Sufficient rate data have been obtained in the case of the ethyl ester to calculate the heat capacity of activation (ΔC P ≠ ) for the hydrolysis of this compound in light water. Both the entropies and enthalpies of activation as well as the solvent isotope effects are consistent with the proposal that the primary and secondary esters react by an acyl–oxygen B Ac 2 mechanism, in contrast to the tertiary ester, which appears to react either by a carbonium ion (S N 1) process or by a route which combines both the B Ac 2 and S N 1 paths.
Deletion mapping of two potential chromosome 14 tumor suppressor gene loci in ovarian carcinoma. (1997)

Previous allelotyping studies of epithelial ovarian carcinoma suggest that loss of heterozygosity on chromosome 14q may be a common genetic alteration in this tumor type. The purpose of this study was to determine a precise frequency of chromosome 14q allelic loss in ovarian carcinomas and to define a minimal region(s) of deletion. Seventy-six ovarian carcinomas representative of the complete spectrum of grade, stage, and histological subtype were selected for PCR-based deletion mapping analysis using 15 highly polymorphic microsatellite markers spanning the length of this chromosome arm. Loss of heterozygosity was observed in 49% of the tumors studied, placing 14q among the most frequently affected chromosomal regions in ovarian cancer. Deletions were observed in all tumor grades and stages and in all histological subtypes except tumors of low malignant potential. Deletion of the entire chromosome arm was rare; the majority of tumors displayed partial losses, providing an informative basis for detailed deletion mapping. Two distinct minimal regions of deletion were delineated. One region was defined by markers D14S80 and D14S75 at 14q12-13, and the other region was defined by markers D14S65 and D14S267 at 14q32. These data implicate the involvement of two tumor suppressor genes on chromosome 14q in a substantial fraction of ovarian carcinomas.
Tamoxifen (TAM): the dispute goes on. (2006)

Tamoxifen (TAM) has been used since early '70s as antitumor agent in the adjuvant therapy of breast carcinoma. The aim was (and is) to reduce the incidence of contralateral breast cancer in primary breast cancer bearing patients. Its efficacy was about 30% when estrogen and progesterone receptors were present in the malignant breast tumor and its use in antitumor therapy is, at the present time, rather correct. Viceversa, the employment of TAM in chemoprevention of breast tumor in healthy and/or at-risk women by more than a decade has been contrasting by many scientists and supporting by others. Indeed, TAM produces not only beneficial effects but also detrimental effects (mainly induction of endometrial cancer). According to the Author of this manuscript, TAM would not be used for primary or secondary mammary tumor chemoprevention. For such purposes the right way is to wait for conclusion of ongoing clinical trials on other pure antiestrogenic agents. Indeed, good candidates to act as an antiestrogen both in breast and in endometrial tissue are under validation. In the meanwhile, the scientific dispute goes on.
Homology Requirement for Efficient Gene Conversion Between Duplicated Chromosomal Sequences in Mammalian Cells (1987)

We report experiments designed to test homology dependence for gene conversion between duplicated chromosomal sequences in cultured mammalian cells. The experimental system is such that gene conversion events not associated with reciprocal exchange are recoverable. For this study four plasmids were constructed. Each contains a different duplication of the herpes simplex virus thymidine kinase (HSV tk) gene sequence. In particular, the interacting sequences share different lengths of homology. Our results indicate that for shared homologies between 295 base pairs (bp) and 1.8 kilobase pairs (kbp) in length, conversion is efficient with the rate being directly proportional to the extent of homology. In contrast, conversion with either 200 bp or 95 bp of homology is inefficient, and the rate is reduced at least seven- or 100-fold, respectively, relative to that observed with 295 bp of homology. These results are consistent with the notion that greater than 200 bp of homology are required for efficient gene conversion between repeated chromosomal sequences in mammalian cells.
Ultralocalized thermal reactions in subnanoliter droplets-in-air (2013)

Miniaturized laboratory-on-chip systems promise rapid, sensitive, and multiplexed detection of biological samples for medical diagnostics, drug discovery, and high-throughput screening. Within miniaturized laboratory-on-chips, static and dynamic droplets of fluids in different immiscible media have been used as individual vessels to perform biochemical reactions and confine the products. Approaches to perform localized heating of these individual subnanoliter droplets can allow for new applications that require parallel, time-, and space-multiplex reactions on a single integrated circuit. Our method positions droplets on an array of individual silicon microwave heaters on chip to precisely control the temperature of droplets-in-air, allowing us to perform biochemical reactions, including DNA melting and detection of single base mismatches. We also demonstrate that ssDNA probe molecules can be placed on heaters in solution, dried, and then rehydrated by ssDNA target molecules in droplets for hybridization and detection. This platform enables many applications in droplets including hybridization of low copy number DNA molecules, lysing of single cells, interrogation of ligand-receptor interactions, and rapid temperature cycling for amplification of DNA molecules.
Relative contribution of "determinant selection" and "holes in the T-cell repertoire" to T-cell responses. (1989)

Using BALB/c and CBA/J mice, the I-region associated (Ia) binding capacity and T-cell immunogenicity of a panel of 14 overlapping peptides that span the entire sequence of the protein staphylococcal nuclease (Nase) was examined to evaluate major histocompatibility gene complex (MHC) control of T-cell responses. Ia binding and Ia-restricted T-cell immunogenicity could be determined for a total of 54 peptide-MHC combinations. Only 30% of the 54 instances examined involved detectable Ia binding, but they represented almost all (12 of 13) of the immune responses found. However, binding to Ia was not sufficient to ensure T-cell immunogenicity, since only 70% of the binding events were productive--i.e., were associated with an immune response. Thus, Ia molecules have the expected characteristics of a highly permissive capacity for antigen interaction that allows them to function as restriction elements for a large universe of antigens. On the other hand, since the Ia molecules cannot distinguish between self and non-self, not all antigen-Ia interactions would be permitted to elicit a T-cell response. It appears that both Ia binding ("determinant selection") and T-cell repertoire act in concert to define the immune response status of an individual toward any particular T-cell epitope.