gebhart/patrepeval huggingface dataset:
Structure of the hepatitis E virus-like particle suggests mechanisms for virus assembly and receptor binding (2009)

Hepatitis E virus (HEV), a small, non-enveloped RNA virus in the family Hepeviridae, is associated with endemic and epidemic acute viral hepatitis in developing countries. Our 3.5-A structure of a HEV-like particle (VLP) shows that each capsid protein contains 3 linear domains that form distinct structural elements: S, the continuous capsid; P1, 3-fold protrusions; and P2, 2-fold spikes. The S domain adopts a jelly-roll fold commonly observed in small RNA viruses. The P1 and P2 domains both adopt beta-barrel folds. Each domain possesses a potential polysaccharide-binding site that may function in cell-receptor binding. Sugar binding to P1 at the capsid protein interface may lead to capsid disassembly and cell entry. Structural modeling indicates that native T = 3 capsid contains flat dimers, with less curvature than those of T = 1 VLP. Our findings significantly advance the understanding of HEV molecular biology and have application to the development of vaccines and antiviral medications.
Percutaneous aspiration thrombectomy of an acutely occluded aortorenal bypass graft. (1995)

Percutaneous aspiration thrombectomy of an acutely occluded aortorenal bypass graft.S M Rivitz, J A Kaufman, R P Cambria and S C GellerAudio Available | Share
Inducible Gene Knockouts in the Small Intestinal and Colonic Epithelium (1999)

We have developed two systems for performing Cre-mediated recombination of target genes in the rapidly self-renewing mouse small intestinal and colonic epithelium. When expression of Cre recombinase is placed directly under the control of transcriptional regulatory elements from a fatty acid-binding protein gene (Fabp), deletion of loxP flanked (floxed) DNA sequences is initiated as early as embryonic day 13.5, well before completion of intestinal morphogenesis. By embryonic day 16.5, Fabp-Cre also directs recombination in all cell layers of the transitional epithelium that lines the renal calyces and pelvis, ureters, and bladder. Fabp-Cre expression and recombination are maintained in both epithelia throughout adulthood. The second system allows recombination to be induced only in the gut and at any period during adulthood. This system uses Fabp regulatory elements to direct expression of a reverse tetracycline-regulated transactivator (rtTA). Another transgene encodes Cre under the control of tet operator sequences and a minimal promoter from human cytomegalovirus (tetO-P(hCMV)-Cre). In the absence of a doxycycline inducer, no basal recombination is detectable in the gut of adult tri-transgenic mice containing Fabp-rtTA, tetO-P(hCMV)-Cre, plus a floxed reporter gene. After 4 days of oral administration of doxycycline, recombination of the reporter is apparent in the small intestinal, cecal, and colonic epithelium. After doxycycline is withdrawn, the recombined locus persists for at least 60 days, indicating that recombination has occurred in epithelial cell progenitors that have long residency times in the proliferative units of the intestine (crypts of Lieberkühn). This inducible system should have a number of applications for examining gene function at selected times in postnatal life, under selected physiologic or pathophysiologic conditions.
The winged-helix transcription factor Trident is expressed in cycling cells (1997)

We describe the cloning and characterization of Trident , a novel member of the fork head/winged-helix family, from murine thymus. In the mouse embryo, the gene was expressed in all tissues, whereas in adult mice expression was only detected in the thymus. Further analysis revealed that Trident expression strictly correlated with cell cycling, independent of cell type. Timing of [3H]thymidine incorporation showed that mRNA and protein expression were strongly upregulated upon entry into the S phase of the cell cycle. Moreover, the protein was phosphorylated in M phase. PCR-mediated selection of optimal binding sites yielded a consensus motif resembling that of other family members. These results identify Trident as a transcription factor, which is likely involved in cell cycle-specific gene regulation.
Branched chain fatty acids and sulfonated derivatives (1965)

Abstract Several 2‐alkyl fatty acids containing 18舑21 carbon atoms, were synthesized by tertiary butyl peroxide catalyzed addition of linear aliphatic carboxylic acids to normal terminal olefins. The products obtained in 35舑70% yields were purified by fractional distillation. The acids were sulfonated with sulfur trioxide dioxane adduct and isolated as the disodium salts in 60舑80% yields. urn:x-wiley:0003021X:media:aocs0233:equation:aocs0233-math-0001 Surface active properties of the sodium salts of the 2‐alkyl carboxylic acids and the corresponding sulfonated products were evaluated. Good wetting properties were observed for those sulfonated acids where the hydrophilic portion of the molecule was equidistant from the ends of the hydrocarbon chain.
An RNA mutation that increases the affinity of an RNA–protein interaction (1987)

The introduction of a cytidine in place of one of the two single stranded uridines in the R17 replicase translational operator results in a much tighter binding to R17 coat protein. The complex containing the variant RNA is stable to gel electrophoresis and has a binding constant about 50 times greater than the one with wild type RNA. The nearly thirty percent increase in the free energy of binding for the variant RNA is primarily due to a more favorable enthalpy of interaction. A possible explanation for this surprising result is that the U to C change leads to a greater extent of formation of a transient covalent complex between the protein and the RNA.
Evidence for an important role of neutrophils in the efficacy of photodynamic therapy in vivo. (1996)

To investigate the role of neutrophils in the efficacy of photodynamic therapy (PDT) in rhabdomyosarcoma-bearing rats, the number of these circulating phagocytes was decreased or increased before interstitial PDT by use of rabbit anti-rat neutrophil serum or granulocyte colony-stimulating factor, respectively. After administration of the antiserum, the number of circulating neutrophils decreased by 99.9%. However, the number of monocytes, lymphocytes, and platelets decreased as well (by 100%, 80%, and 25%, respectively). Under these conditions, PDT did not retard tumor growth at all. However, after cessation of the antiserum treatment 5 days after PDT, a striking decrease in the growth rate occurred subsequent to an increase above the normal range of the number of circulating neutrophils. Administration of the granulocyte colony-stimulating factor led to a specific 4-fold increase in the number of circulating neutrophils. In these rats, the tumor growth at day 2 after PDT was retarded as compared with PDT-treated rats that received saline only. Statistical evaluation of both experimental conditions showed that the efficacy of PDT, expressed as the percentage of change in tumor volume at day 2 after treatment, was dependent on the number of circulating neutrophils present at the day of PDT (P = 0.001; r2 = 0.482). Apparently, neutrophils are indispensable for successful PDT in vivo.
Dynamics of repressor-operator recognition: Tn10-encoded tetracycline resistance control (1988)

Binding of the Tet repressor to nonspecific and specific DNA leads to quenching of the Tet fluorescence by approximately 22% and approximately 35%, respectively. This effect is used for a direct, quantitative characterization of the binding equilibria and dynamics involved in the recognition of the operator by its repressor. From the dependence of the nonspecific binding constant on the ion concentration, it is concluded that nonspecific binding is almost completely driven by the entropy change resulting from the release of three to four Na+ ions from the double helix upon protein binding. Formation of the specific complex is driven by a higher entropy term resulting from the release of seven to eight Na+ ions and in addition by a free energy term of -33 kJ/mol from nonelectrostatic interactions, which are attributed to the specific contacts. The dynamics of the repressor-operator recognition are resolved by stopped-flow measurements at various salt concentrations and for different DNA chain lengths into two separate steps. The first step follows a second-order mechanism and results in an intermediate complex associated with formation of about three to four electrostatic contacts between protein and DNA; apparently, this complex is equivalent to the nonspecific complex. The existence of an intermediate is also indicated by experiments in mixed Na+-Mg2+ buffers, which can be described with high accuracy by competition of Mg2+ and protein. The intermediate complex is formed at a rate of 3 X 10(8) M-1 s-1 and is converted in the second reaction step to the specific complex with a rate constant of 6 X 10(4) s-1, which is almost independent of the salt concentration. Our interpretation and the parameters obtained from our model are confirmed by competition of nonspecific DNA with operator DNA for repressor binding. The observed maximal rate constant of 3 X 10(8) M-1 s-1 is very close to theoretical predictions for the association without a sliding mechanism. The very small dependence of the observed rate constants on the chain length shows that the Tet repressor is not able to slide over any substantial distance even at low salt concentrations. The question of a potential contribution from sliding under our experimental conditions is critically discussed. The absence of sliding in the case of the Tet repressor under physiological conditions is compared with the high sliding efficiency of the lac repressor and is discussed with respect to possible molecular mechanisms of sliding in relation to biological function.
Phasor modeling approach for single phase A/C motors (2008)

In this paper we present results of a development of a single-phase induction motor model using dynamic phasors. This phasor model is intended to represent the compressor portion of the behavior of a typical residential air conditioner load. A review of the model is presented. This model is then used to validate data from laboratory tests of air conditioners at Bonneville Power Administration. The results show that the model accurately captures the relations between voltage, frequency, active power, and reactive power. Furthermore, the model reproduces motor stall conditions, both the onset and severity of the stall. We expect that the use of this load model will improve our ability to anticipate voltage and transient stability problems in the power grid.
A Novel Approach to Produce Protein Nanopatterns by Combining Nanoimprint Lithography and Molecular Self-Assembly (2004)

We describe a novel parallel method for the patterning of proteins with nanoscale resolution. Combining nanoimprint lithography (NIL) and molecular assembly patterning by lift-off (MAPL), we produced streptavidin patterns with feature sizes in the order of 100 nm. A stamp is imprinted into a heated PMMA film followed by a dry etching step that converts the topography into a PMMA/Nb2O5 contrast. A biotin functionalized copolymer, poly(l-lysine)-graft-poly(ethylene glycol)-biotin (PLL-g-PEG/PEG-biotin), spontaneously adsorbs on the oxide surfaces. After PMMA lift-off, the background is backfilled with protein-resistant PLL-g-PEG. We show that streptavidin selectively adsorbs on the biotin areas and thus can be used as a universal platform for immobilization of biotin-tagged molecules. This novel process is a parallel patterning method that is fast, reproducible, and economic. The PEG-copolymer can be functionalized with a variety of bioactive groups and thus allows a great flexibility in terms of surface chemistry.
Coaxial MnO2/Carbon Nanotube Array Electrodes for High-Performance Lithium Batteries (2009)

Coaxial manganese oxide/carbon nanotube (CNT) arrays deposited inside porous alumina templates were used as cathodes in a lithium battery. Excellent cyclic stability and capacity of MnO2/CNT coaxial nanotube electrodes resulted from the hybrid nature of the electrodes with improved electronic conductivity and dual mechanism of lithium storage. The reversible capacity of the battery was increased by an order compared to template grown MnO2 nanotubes, making them suitable electrodes for advanced Li ion batteries.
Documentation and Evaluation of Cognitive Impairment in Elderly Primary Care Patients (1995)

Objective: To describe the prevalence of cognitive impairment among elderly primary care patients and to compare diagnostic evaluations and use of health services among patients with and those without cognitive impairment. Design: Prospective cohort study. Setting: Academic primary care group practice. Patients: 3954 patients aged 60 years and older who completed the Short Portable Mental Status Questionnaire during routine office visits. Measurements: Demographics and comorbid illness at baseline, diagnostic evaluations for cognitive impairment, use of standard and preventive health services, use of psychoactive drugs, and death in the year after the screening date. Results: The prevalence of cognitive impairment among all patients aged 60 years and older at baseline was 15.7%; 10.5% had mild impairment and 5.2% had moderate to severe impairment. Patients with moderate to severe impairment were significantly older than patients with no impairment (76.2 years and 67.4 years, respectively), were more likely to be black (85.8% and 61.3%), had fewer years of education (7.3 years and 9.2 years), and were more likely to have cerebrovascular disease (20.4% and 6.3%) and evidence of undernutrition (30.6% and 16.9%). Dementia was recorded as a diagnosis for less than 25% of patients with moderate to severe cognitive impairment, but patients with documented impairment were more likely to have been evaluated for reversible causes. In the year after screening, patients with moderate to severe impairment were more likely than those with no impairment both to be hospitalized (29.1% and 16.5%) and to visit the emergency department (55.8% and 38.5%) but had fewer outpatient visits (6.0 and 7.6) and greater mortality (8.2% and 2.8%). Conclusions: Cognitive impairment is associated with increased use of health services and increased mortality. Patients with undocumented cognitive impairment were significantly less likely to be evaluated for reversible causes. Research is needed to determine if better documentation of cognitive impairment would improve not only diagnostic evaluations but also patient management, counseling, and outcomes.
[Analysis of loss of heterozygosity on chromosome 8 in human prostate carcinoma and high grade prostatic intraepithelial neoplasia]. (2004)

There were high-frequency LOH regions on chromosome 8 of prostate carcinoma, located on 8p23.1-p23.2 and 8p21-p22. High grade PIN and prostate carcinoma share the same allelic loss on 8p. Tumor suppressor genes located at these two regions may be potentially involved in the initiation and progression of prostate carcinoma.
Protease‐Catalyzed Kinetically Controlled Peptide Synthesis (1991)

Abstract In spite of the enormous progress in the synthesis of peptides and proteins using commercial peptide synthesizers and the immense technological possibilities of recombinant DNA technology, a CN ligase is an indispensable tool for the racemization‐free fragment condensation of peptides. Since activation of the C‐terminal α‐carboxyl group of a peptide segment could cause partial racemization, chemical condensations of peptide fragments are prone to racemization. For the synthesis of the huge number of peptides and proteins, however, nature has only developed the ribosomal peptidyltransferase, which exhibits its full catalytic function independent of the side‐chain functions of the amino acids being coupled. However, its function requires coordination with numerous other ribosomal factors. Besides the limited possibilities of using multienzyme complexes of bacterial peptide synthesis systems, the only alternatives to peptidyltransferase are proteases, which, based on their in vivo function as hydrolases, cannot act as ideal ligases. However, by exploiting the intrinsic reversibility of hydrolytic reactions and by adjusting appropriate physicochemical reaction parameters, the protease acitivity can be used in the direction of ligation. Undoubtedly, the course of kinetically controlled, serine and cysteine protease‐catalyzed reactions can be more efficiently influenced than the equilibrium‐controlled protease‐catalyzed synthesis. This article describes the influence of the enzyme specificity on the efficiency of kinetically controlled synthesis and points the way toward a broad exploitation of serine and cysteine proteases for the catalysis of CN bond formation.
Independent Prospective Multicenter Validation of Biochemical Markers (Fibrotest-Actitest) for the Prediction of Liver Fibrosis and Activity in Patients with Chronic Hepatitis C: The Fibropaca Study (2006)

This prospective independent and multicenter study confirms the diagnostic value of FT and AT found in the princeps study and suggests that FT and AT can be an alternative to biopsy in most patients with chronic HCV.
Tacrolimus/sirolimus vs tacrolimus/methotrexate as GVHD prophylaxis after matched, related donor allogeneic HCT (2014)

Grades 2-4 acute graft-versus-host disease (GVHD) occurs in approximately 35% of matched, related donor (MRD) allogeneic hematopoietic cell transplantation (HCT) recipients. We sought to determine if the combination of tacrolimus and sirolimus (Tac/Sir) was more effective than tacrolimus and methotrexate (Tac/Mtx) in preventing acute GVHD and early mortality after allogeneic MRD HCT in a phase 3, multicenter trial. The primary end point of the trial was to compare 114-day grades 2-4 acute GVHD-free survival using an intention-to-treat analysis of 304 randomized subjects. There was no difference in the probability of day 114 grades 2-4 acute GVHD-free survival (67% vs 62%, P = .38). Grades 2-4 GVHD was similar in the Tac/Sir and Tac/Mtx arms (26% vs 34%, P = .48). Neutrophil and platelet engraftment were more rapid in the Tac/Sir arm (14 vs 16 days, P < .001; 16 vs 19 days, P = .03). Oropharyngeal mucositis was less severe in the Tac/Sir arm (peak Oral Mucositis Assessment Scale score 0.70 vs 0.96, P < .001), but otherwise toxicity was similar. Chronic GVHD, relapse-free survival, and overall survival at 2 years were no different between study arms (53% vs 45%, P = .06; 53% vs 54%, P = .77; and 59% vs 63%, P = .36). Based on similar long-term outcomes, more rapid engraftment, and less oropharyngeal mucositis, the combination of Tac/Sir is an acceptable alternative to Tac/Mtx after MRD HCT. This study was funded by the National Heart, Lung, and Blood Institute and the National Cancer Institute; and the trial was registered at www.clinicaltrials.gov as #NCT00406393.
Domestic Wastewater Treatment as a Net Energy Producer–Can This be Achieved? (2011)

In seeking greater sustainability in water resources management, wastewater is now being considered more as a resource than as a waste-a resource for water, for plant nutrients, and for energy. Energy, the primary focus of this article, can be obtained from wastewater's organic as well as from its thermal content. Also, using wastewater's nitrogen and P nutrients for plant fertilization, rather than wasting them, helps offset the high energy cost of producing synthetic fertilizers. Microbial fuel cells offer potential for direct biological conversion of wastewater's organic materials into electricity, although significant improvements are needed for this process to be competitive with anaerobic biological conversion of wastewater organics into biogas, a renewable fuel used in electricity generation. Newer membrane processes coupled with complete anaerobic treatment of wastewater offer the potential for wastewater treatment to become a net generator of energy, rather than the large energy consumer that it is today.
Neurotensin Inhibits LH Release (1981)

The present studies were designed to assess the effect of neurotensin on the release of LH, FSH, and prolactin in long-term castrated female rats. The animals were implanted in the lateral ventricle of the brain wih a cannula to allow the administration of either neurotensin or the vehicle. The peptide (30 microgram, dissolved in saline) or the control saline solution was injected intraventricularly in a volume of 10 microliter following pentobarbital anesthesia. Blood samples were collected at sacrifice 15, 30 and 60 min after injection. A significant decrease of serum LH levels was already present in neurotensin-treated animals at 15 min, and was maintained up to the end of the experiment. This decrease was not accompanied by any change in FSH or prolactin secretion. The results suggest that this tridecapeptide participates in the control of LH release and provide new data on the separate control of the release of the two gonadotropins.
Expression of Peroxisome Proliferator-Activated Receptor-γ in Key Neuronal Subsets Regulating Glucose Metabolism and Energy Homeostasis (2008)

In addition to increasing insulin sensitivity and adipogenesis, peroxisome proliferator-activated receptor (PPAR)-gamma agonists cause weight gain and hyperphagia. Given the central role of the brain in the control of energy homeostasis, we sought to determine whether PPARgamma is expressed in key brain areas involved in metabolic regulation. Using immunohistochemistry, PPARgamma distribution and its colocalization with neuron-specific protein markers were investigated in rat and mouse brain sections spanning the hypothalamus, the ventral tegmental area, and the nucleus tractus solitarius. In several brain areas, nuclear PPARgamma immunoreactivity was detected in cells that costained for neuronal nuclei, a neuronal marker. In the hypothalamus, PPARgamma immunoreactivity was observed in a majority of neurons in the arcuate (including both agouti related protein and alpha-MSH containing cells) and ventromedial hypothalamic nuclei and was also present in the hypothalamic paraventricular nucleus, the lateral hypothalamic area, and tyrosine hydroxylase-containing neurons in the ventral tegmental area but was not expressed in the nucleus tractus solitarius. To validate and extend these histochemical findings, we generated mice with neuron-specific PPARgamma deletion using nestin cre-LoxP technology. Compared with littermate controls, neuron-specific PPARgamma knockout mice exhibited dramatic reductions of both hypothalamic PPARgamma mRNA levels and PPARgamma immunoreactivity but showed no differences in food intake or body weight over a 4-wk study period. We conclude that: 1) PPARgamma mRNA and protein are expressed in the hypothalamus, 2) neurons are the predominant source of PPARgamma in the central nervous system, although it is likely expressed by nonneuronal cell types as well, and 3) arcuate nucleus neurons that control energy homeostasis and glucose metabolism are among those in which PPARgamma is expressed.
[The changes of respiratory mechanics in patients with obstructive sleep apnea-hypopnea syndrome during sleep]. (2008)

OSAHS patients exhaled more air than inhaled gradually before apnea onset, and then this change was compensated by inhaling more air than exhaled in the first respiratory cycle following apnea. These resulted in decreases in FRC and upper airway size, which may play an important role in the pathophsiological mechanisms of sleep apnea. The tidal volume decrease suggested that the breathing drive was reduced in light sleep of OSAHS. In addition, a rise of both inspiratory and expiratory resistance was evident in a majority of patients with OSAHS.
Poly-(R)-3-hydroxybutyrate (PHB) biosynthesis: mechanistic studies on the biological Claisen condensation catalyzed by β-ketoacyl thiolase (1989)

Abstract