gebhart/patrepeval huggingface dataset:
TX-001HR is associated with a clinically meaningful effect on severity of moderate to severe vasomotor symptoms in the REPLENISH trial (2020)

REPLENISH trial data demonstrated that E2/P4 1/100 and 0.5/100 provided clinically meaningful improvements in hot flushes severity in postmenopausal women. In conjunction with previously demonstrated clinically meaningful VMS frequency improvements, these data support oral E2/P4 1/100 and 0.5/100 for postmenopausal women with a uterus seeking treatment for moderate to severe VMS.
Meta-analysis of association of rare mutations and common sequence variants in theMSR1 gene and prostate cancer risk (2006)

Overall, this meta-analysis suggests the MSR1 gene does not independently confer a major risk to PCa but may confer a moderate risk to PCa, especially in black men.
Intra-articular drug delivery systems: overcoming the shortcomings of joint disease therapy (2009)

Therapeutic applications of novel drug delivery systems for the localized treatment of joints have lagged significantly. Future innovations in the field will require the discovery of new therapeutic agents for regional delivery, combination regimens, novel biomaterials as drug carriers and targeting carriers to specific molecules.
Integration of multiple developmental signals in Bacillus subtilis through the Spo0A transcription factor. (1993)

Multiple physiological and environmental signals are needed to initiate endospore formation in Bacillus subtilis. One key event controlling sporulation is activation of the Spo0A transcription factor. Spo0A is a member of a large family of conserved regulatory proteins whose activity is controlled by phosphorylation. We have isolated deletion mutations that remove part of the conserved amino terminus of Spo0A and make the transcription factor constitutively active, indicating that the amino terminus normally functions to keep the protein in an inactive state. Expression of an activated gene product is sufficient to activate expression of several sporulation genes in the absence of signals normally needed for initiation of sporulation. Our results indicate that nutritional, cell density, and cell-cycle signals are integrated through the phosphorylation pathway that controls activation of Spo0A.
Signal Sequence and Keyword Trap in silico for Selection of Full-Length Human cDNAs Encoding Secretion or Membrane Proteins from Oligo-Capped cDNA Libraries (2005)

We have developed an in silico method of selection of human full-length cDNAs encoding secretion or membrane proteins from oligo-capped cDNA libraries. Fullness rates were increased to about 80% by combination of the oligo-capping method and ATGpr, software for prediction of translation start point and the coding potential. Then, using 5'-end single-pass sequences, cDNAs having the signal sequence were selected by PSORT ('signal sequence trap'). We also applied 'secretion or membrane protein-related keyword trap' based on the result of BLAST search against the SWISS-PROT database for the cDNAs which could not be selected by PSORT. Using the above procedures, 789 cDNAs were primarily selected and subjected to full-length sequencing, and 334 of these cDNAs were finally selected as novel. Most of the cDNAs (295 cDNAs: 88.3%) were predicted to encode secretion or membrane proteins. In particular, 165(80.5%) of the 205 cDNAs selected by PSORT were predicted to have signal sequences, while 70 (54.2%) of the 129 cDNAs selected by 'keyword trap' preserved the secretion or membrane protein-related keywords. Many important cDNAs were obtained, including transporters, receptors, and ligands, involved in significant cellular functions. Thus, an efficient method of selecting secretion or membrane protein-encoding cDNAs was developed by combining the above four procedures.
Complement and the atypical hemolytic uremic syndrome in children (2008)

Over the past decade, atypical hemolytic uremic syndrome (aHUS) has been demonstrated to be a disorder of the regulation of the complement alternative pathway. Among approximately 200 children with the disease, reported in the literature, 50% had mutations of the complement regulatory proteins factor H, membrane cofactor protein (MCP) or factor I. Mutations in factor B and C3 have also been reported recently. In addition, 10% of children have factor H dysfunction due to anti-factor H antibodies. Early age at onset appears as characteristic of factor H and factor I mutated patients, while MCP-associated HUS is not observed before age 1 year. Low C3 level may occur in patients with factor H and factor I mutation, while C3 level is generally normal in MCP-mutated patients. Normal plasma factor H and factor I levels do not preclude the presence of a mutation in these genes. The worst prognosis is for factor H-mutated patients, as 60% die or reach end-stage renal disease (ESRD) within the first year after onset of the disease. Patients with mutations in MCP have a relapsing course, but no patient has ever reached ESRD in the first year of the disease. Half of the patients with factor I mutations have a rapid evolution to ESRD, but half recover. Early intensive plasmatherapy appears to have a beneficial effect, except in MCP-mutated patients. There is a high risk of graft loss for HUS recurrence or thrombosis in all groups except the MCP-mutated group. Recent success of liver-kidney transplantation combined with plasmatherapy opens this option for patients with mutations of factors synthesized in the liver. New therapies such as factor H concentrate or complement inhibitors offer hope for the future.
Erg28p is a key protein in the yeast sterol biosynthetic enzyme complex (2005)

Previously, a microarray expression study in the yeast Saccharomyces cerevisiae indicated that the ERG28 gene was strongly coregulated with ergosterol biosynthesis. Subsequently, Erg28p was shown to function as an endoplasmic reticulum transmembrane protein, acting as a scaffold to tether the C-4 demethylation enzymatic complex and also to interact with a downstream enzyme, Erg6p. To understand all possible protein interactions involving Erg28p in sterol biosynthesis, a yeast two-hybrid system designed to assess interactions between membrane proteins was used. The Erg28p fusion protein was used as bait to assess interactions with all 14 sterol biosynthetic proteins in a pairwise study based on two reporter systems as well as Western blots demonstrating the release of a transcription factor. Our results indicated that Erg28p not only interacted with the C-4 demethylation enzymes and Erg6p but also with Erg11p and Erg1p. Interactions between Erg28p and seven ergosterol biosynthetic enzymes were confirmed by coimmunoprecipitation experiments. Furthermore, by comparing the reporter gene expression levels, we demonstrate that Erg28p is most closely associated with Erg27p, Erg25p, Erg11p, and Erg6p and less with Erg26p and Erg1p. Based on these results, we suggest that many if not all sterol biosynthetic proteins may be tethered as a large complex.
The role of androgens in follicle maturation and ovulation induction: friend or foe of infertility treatment? (2011)

Selective androgens appear capable of improving early stages of folliculogenesis. They, therefore, may represent forerunners of a completely new class of ovulation-inducing medications, which, in contrast to gonadotropins, affect follicle maturation at much earlier stages.
The 2‐oxoglutarate binding site of prolyl 4‐hydroxylase (1984)

The structure and function of the 2‐oxoglutarate binding site of prolyl 4‐hydroxylase was studied by assaying the inhibitory potential of 24 selected aliphatic or aromatic compounds. All except one of them inhibited the enzyme competitively with respect to 2‐oxoglutarate and noncompetitively with respect to Fe 2+ , the K i values ranging from 0.8 μM to over 15 mM. The K i values for the two most effective inhibitors, pyridine 2,5‐dicarboxylate and 2,4‐dicarboxylate, were about 0.8 μM and 2 μM, these compounds being the most potent inhibitors of prolyl 4‐hydroxylase with respect to 2‐oxoglutarate known so far. Only one of the compounds tested, 2‐oxoadipinate, was able to support hydroxylation by replacing 2‐oxoglutarate as a cosubstrate. The data suggest that the 2‐oxoglutarate binding site can be divided into three distinct subsites. Subsite I is probably a positively charged side chain of the enzyme that ionically binds the C5 carboxyl group of the 2‐oxoglutarate, subsite II consists of two cis ‐positioned equatorial coordination sites of the enzyme‐bound ferrous ion and is chelated by the C1–C2 moiety, while subsite III involves a hydrophobic binding site in the C3–C4 region of the cosubstrate. The sp 3 rehybridization of C2 within the dictating moiety of the cosubstrate appears to be a crucial event during decarboxylation that proceeds in the form of a ligand reaction inside the Fe 2+ coordination sphere.
Evaluation of Luminex xTAG Gastrointestinal Pathogen Analyte-Specific Reagents for High-Throughput, Simultaneous Detection of Bacteria, Viruses, and Parasites of Clinical and Public Health Importance (2013)

Acute diarrheal disease (ADD) can be caused by a range of pathogens, including bacteria, viruses, and parasites. Conventional diagnostic methods, such as culture, microscopy, biochemical assays, and enzyme-linked immunosorbent assays (ELISA), are laborious and time-consuming and lack sensitivity. Combined, the array of tests performed on a single specimen can increase the turnaround time (TAT) significantly. We validated a 19plex laboratory-developed gastrointestinal pathogen panel (GPP) using Luminex xTAG analyte-specific reagents (ASRs) to simultaneously screen directly in fecal specimens for diarrhea-causing pathogens, including bacteria (Campylobacter jejuni, Salmonella spp., Shigella spp., enterotoxigenic Escherichia coli [ETEC], Shiga toxin-producing E. coli [STEC], E. coli O157:H7, Vibrio cholerae, Yersinia enterocolitica, and toxigenic Clostridium difficile), parasites (Giardia lamblia, Cryptosporidium spp., and Entamoeba histolytica), and viruses (norovirus GI and GII, adenovirus 40/41, and rotavirus A). Performance characteristics of GPP ASRs were determined using 48 reference isolates and 254 clinical specimens. Stool specimens from individuals with diarrhea were tested for pathogens using conventional and molecular methods. Using the predictive methods as standards, the sensitivities of the GPP ASRs were 100% for adenovirus 40/41, norovirus, rotavirus A, Vibrio cholerae, Yersinia enterocolitica, Entamoeba histolytica, Cryptosporidium spp., and E. coli O157:H7; 95% for Giardia lamblia; 94% for ETEC and STEC; 93% for Shigella spp.; 92% for Salmonella spp.; 91% for C. difficile A/B toxins; and 90% for Campylobacter jejuni. The overall comparative performance of the GPP ASRs with conventional methods in clinical samples was 94.5% (range, 90% to 97%), with 99% (99.0% to 99.9%) specificity. Implementation of the GPP ASRs enables our public health laboratory to offer highly sensitive and specific screening and identification of the major ADD-causing pathogens.
Tea Catechins and Polyphenols: Health Effects, Metabolism, and Antioxidant Functions (2003)

Increasing interest in the health benefits of tea has led to the inclusion of tea extracts in dietary supplements and functional foods. However, epidemiologic evidence regarding the effects of tea consumption on cancer and cardiovascular disease risk is conflicting. While tea contains a number of bioactive chemicals, it is particularly rich in catechins, of which epigallocatechin gallate (EGCG) is the most abundant. Catechins and their derivatives are thought to contribute to the beneficial effects ascribed to tea. Tea catechins and polyphenols are effective scavengers of reactive oxygen species in vitro and may also function indirectly as antioxidants through their effects on transcription factors and enzyme activities. The fact that catechins are rapidly and extensively metabolized emphasizes the importance of demonstrating their antioxidant activity in vivo. In humans, modest transient increases in plasma antioxidant capacity have been demonstrated following the consumption of tea and green tea catechins. The effects of tea and green tea catechins on biomarkers of oxidative stress, especially oxidative DNA damage, appear very promising in animal models, but data on biomarkers of in vivo oxidative stress in humans are limited. Larger human studies examining the effects of tea and tea catechin intake on biomarkers of oxidative damage to lipids, proteins, and DNA are needed.
Suppression of Collagen Induced Arthritis by Oral Administration of Type II Collagen: Changes in Immune and Arthritic Responses Mediated by Active Peripheral Suppression (1993)

The oral administration of CII by gavage to WA/KIR rats before a conventional arthritogenic challenge with bovine CII in FIA reduced the incidence (by 23%) and delayed the onset of collagen-induced arthritis in about 50% of the animals. Selective changes in B cell and T cell responses to CII in animals treated this way are interpreted to indicate a state of tolerance or hyporesponsiveness to CII. Tolerant animals made less serum antibody, to bovine and rat CII, of the IgG2b isotype and more of the IgG1 isotype. Phenotypic and functional analysis of peripheral lymph node cells showed that those from tolerized animals expressed less MHC Class II, proliferated less and secreted less IgG2b anti-CII antibody in response to stimulation in vitro with CII when compared with cells from non-tolerant animals. However, this depression of the immune responses to CII seen in vitro was overcome when the cells were incubated with increasing amounts of CII. Tolerance could be transferred to normal animals. Spleen cells, and nylon wool-filtered splenic T cells (but not mesenteric lymph node cells) adoptively transferred hyporesponsiveness to normal recipients which were then less susceptible to collagen-induced arthritis. Transfer of serum from gavaged animals did not modify the susceptibility of normal recipients to arthritis. Spleen cells from gavaged animals suppressed proliferative and antibody responses in co-cultures in vitro with lymph node cells from animals immunized with CII in FIA. The suppressive spleen cell population contained more cells expressing MHC Class II, in both the CD8+ and CD4+ populations. These studies show that the oral administration of CII alters the subsequent immune response to the arthritogenic challenge and indicate that this oral tolerance of CII is due, not to clonal deletion or anergy, but rather to an antigen-driven active suppression mechanism that affects both T cells and B cells, most likely through the action of regulatory cytokines IL-4, IL-10 and TGF beta.
The viscosity of a dilute suspension of rough spheres (2000)

We consider the flow of a dilute suspension of equisized solid spheres in a viscous fluid. The viscosity of such a suspension is dependent on the volume fraction, c , of solid particles. If the particles are perfectly smooth, then solid spheres will not come into contact, because lubrication forces resist their approach. In this paper, however, we consider particles with microscopic surface asperities such that they are able to make contact. For straining motions we calculate the O ( c 2 ) coefficient of the resultant viscosity, due to pairwise interactions. For shearing motions (for which the viscosity is undetermined because of closed orbits on which the probability distribution is unknown) we calculate the c 2 contribution to the normal stresses N 1 and N 2 . The viscosity in strain is shown to be slightly lower than that for perfectly smooth spheres, though the increase in the O ( c ) term caused by the increased effective radius due to surface asperities will counteract this decrease. The viscosity decreases with increasing contact friction coefficient. The normal stresses N 1 and N 2 are zero if the surface roughness height is less than a critical value of 2.11 × 10 −4 times the particle radius, and then become negative as the roughness height is increased above this value. N 1 is larger in magnitude than N 2 .
Machine learning in genome‐wide association studies (2009)

Recently, genome-wide association studies have substantially expanded our knowledge about genetic variants that influence the susceptibility to complex diseases. Although standard statistical tests for each single-nucleotide polymorphism (SNP) separately are able to capture main genetic effects, different approaches are necessary to identify SNPs that influence disease risk jointly or in complex interactions. Experimental and simulated genome-wide SNP data provided by the Genetic Analysis Workshop 16 afforded an opportunity to analyze the applicability and benefit of several machine learning methods. Penalized regression, ensemble methods, and network analyses resulted in several new findings while known and simulated genetic risk variants were also identified. In conclusion, machine learning approaches are promising complements to standard single-and multi-SNP analysis methods for understanding the overall genetic architecture of complex human diseases. However, because they are not optimized for genome-wide SNP data, improved implementations and new variable selection procedures are required.
Proteome analysis of glandular parotid and submandibular‐sublingual saliva in comparison to whole human saliva by two‐dimensional gel electrophoresis (2006)

Abstract The secretions of the salivary parotid and submandibular‐sublingual (SMSL) glands constitute the main part of whole human saliva (WS) in which proline‐rich proteins (PRPs) and mucins represent dominant groups. Although proteome analysis had been performed on WS, no identification of PRPs or mucins by 2‐DE and MS was achieved in WS and no comprehensive analysis of both glandular secretions is available so far. The aim of this study was to compare the protein map of WS to parotid and SMSL secretions for the display of PRPs and mucins. WS and glandular secretions were subjected to 2‐DE and spots were analyzed by MALDI‐MS. New components identified in WS were cyclophilin‐B and prolyl‐4‐hydroxylase. Also acidic and basic PRPs as well as the proline‐rich glycoprotein (PRG) could now be mapped in WS. Acidic PRPs were found equally in parotid and SMSL secretions, whereas basic PRPs and PRG were found primarily in parotid secretion. Salivary mucin MUC7 was identified in SMSL secretion. Thus, the more abundant proteins of WS can be explained mainly by mixed contributions of parotid and SMSL secretions with only few components remaining that may be derived from local sources in the oral cavity.
Changing the Trajectory of Cognitive Decline? (2007)

Environmental enrichment or intracranial injection of a histone deacetylase inhibitor results in improved memory function in mice with neurodegeneration.
Epidermal growth factor receptor signaling is required for normal ovarian steroidogenesis and oocyte maturation (2005)

The midcycle luteinizing hormone (LH) surge triggers several tightly linked ovarian processes, including steroidogenesis, oocyte maturation, and ovulation. We designed studies to determine whether epidermal growth factor receptor (EGFR)-mediated signaling might serve as a common regulator of these activities. Our results showed that EGF promoted steroidogenesis in two different in vitro models of oocyte-granulosa cell complexes. Inhibition of the EGFR kinase prevented EGF-induced steroidogenesis in these in vitro systems and blocked LH-induced steroidogenesis in intact follicles primed with pregnant mare serum gonadotropin. Similarly, inhibition of the EGFR kinase attenuated LH-induced steroidogenesis in MA-10 Leydig cells. Together, these results indicate that EGFR signaling is critical for normal gonadotropin-induced steroidogenesis in both male and female gonads. Interestingly, inhibition of metalloproteinase-mediated cleavage of membrane-bound EGF moieties abrogated LH-induced steroidogenesis in ovarian follicles but not MA-10 cells, suggesting that LH receptor signaling activates the EGFR by different mechanisms in these two models. Finally, steroids promoted oocyte maturation in several ovarian follicle models, doing so by signaling through classical steroid receptors. We present a model whereby steroid production may serve as one of many integrated signals triggered by EGFR signaling to promote oocyte maturation in gonadotropin-stimulated follicles.
Secretion of the sweet-tasting plant protein thaumatin byStreptomyces lividans (1989)

To produce and direct the export in Streptomyces lividans of the sweet plant protein thaumatin, thaumatin II cDNA was fused in the correct reading frame to the/%galactosidase leader peptide, under the control of the /%galactosidase promoter and ribosome binding site. The export of the recombinant thaumatin may allow the correct formation of the thaumatin disulfide bonds. The recombinant thaumatin was purified from the medium on an S-Sepharose column and detected with western blots by sheep ~-thaumatin antibodies. The recombinant thaumatin was the same size as authentic thaumatin and changed position on an acrylamide gel in response to reduction by 2-mercaptoethanol in the same manner.
Primary cultures of rat islet capillary endothelial cells. Constitutive and cytokine-inducible macrophagelike nitric oxide synthases are expressed and activities regulated by glucose concentration. (1994)

We have succeeded in obtaining cultures of pure rat islet capillary endothelial cells. These multiply in vitro and exhibit the same antigenic phenotype as expressed in situ: von Willebrand factorhigh, Ox43 (rat endothelial marker)weak, and Ox2 (thymocyte and brain endothelium marker)high. This phenotype differs from both exocrine endothelium stained in situ and rat aorta endothelial cells cultured in vitro under identical conditions. Islet and aorta endothelial cells were cultured in the presence of various glucose concentrations. Nitrite and citrulline concentrations in culture supernatants were measured as an indirect quantification of nitric oxide formation. In islet endothelia, both nitrite and citrulline levels were found to be strongly glucose-dependent, with high levels at high glucose concentrations and vice versa, in contrast to aorta endothelial cells, where no glucose effect was found. Shifting islet endothelial cultures from high to low glucose levels or the reverse led to a slow decrease or increase in nitrite and citrulline formation with several cell generations needed to reach steady levels. Adding a combination of the cytokines interleukin-1 beta, tumor necrosis factor-alpha, and interferon-gamma to both endothelial cell cultures led to a dramatic increase of nitric oxide formation. Again with islet but not with aorta endothelial cells a modulating effect by glucose concentrations was found. Reverse-transcription-polymerase chain reaction with specific primers demonstrated the presence of constitutively expressed nitric oxide synthase-RNA in the islet capillary endothelial cells and confirmed the glucose effect. In addition, we found that cytokines indeed induce the expression of inducible synthase messenger RNA in both endothelial cells, which was not found in the absence of cytokines. Electron paramagnetic resonance spectroscopy of islet endothelial cells confirmed intracellular synthesis of nitric oxide in the presence of cytokines. In conclusion, we here for the first time provide evidence that constitutive nitric oxide synthase is also expressed in capillary endothelium and that cytokine challenge leads to the expression of the inducible isoform in these cells.