gebhart/patrepeval huggingface dataset:
A chaperonin from a thermophilic bacterium, <i>Thermus thermophilus</i> (1993)

Unlike Escherichia coli chaperonins, a chaperonin (cpn) from a thermophilic bacterium, Thermus thermophilus, consisting of homologues to GroEL (cpn 60) and GroES (cpn 10) is co-purified as a large complex. Thermus chaperonin shows a bullet-like shape in the side view seen by electron microscopy, and antibody against cpn 10 binds only to the round side of the bullet. We conclude that a single cpn 60-heptamer ring with two stripes stacks into two layers and a cpn 10 oligomer binds to one side of the layers. The purified Thermus chaperonin contains endogenously bound ADP, and incubation with ATP causes a partial dissociation of chaperonin into cpn 60 monomers and a cpn 10 heptamer. The effect of Thermus chaperonin on protein refolding upon dilution from guanidine HC1 is different at three temperature ranges. At high temperatures above 55 degrees C, where the native proteins are stable but their spontaneous foldings fail, the chaperonin induces productive folding in an ATP-dependent manner. At middle temperatures (25-55 degrees C) where spontaneous foldings of the enzymes occur, the chaperonin slows down the rate of folding without changing the final yield of productive folding. At lower temperatures below 25 degrees C where spontaneous foldings also occur, the chaperonin arrests the folding even in the presence of ATP. When a solution of relatively heat labile protein is incubated at high temperatures, and then residual activity of the protein is measured at its optimal temperature after incubation with ATP, the temperature that causes irreversible heat denaturation of the protein is elevated about 10 degrees C by inclusion of Thermus chaperonin in the solution.(ABSTRACT TRUNCATED AT 250 WORDS)
Laminin gene <i><scp>LAMB</scp>4</i> is somatically mutated and expressionally altered in gastric and colorectal cancers (2014)

Laminins are important in tumor invasion and metastasis as well as in maintenance of normal epithelial cell structures. However, mutation status of laminin chain-encoding genes remains unknown in cancers. Aim of this study was to explore whether laminin chain genes are mutated and expressionally altered in gastric (GC) and colorectal cancers (CRC). In a public database, we found that laminin chain genes LAMA1, LAMA3, LAMB1 and LAMB4 had mononucleotide repeats in the coding sequences that might be mutation targets in the cancers with microsatellite instability (MSI). We analyzed the genes in 88 GC and 139 CRC [high MSI (MSI-H) or stable MSI/low MSI (MSS/MSI-L)] by single strand conformation polymorphism analysis and DNA sequencing. In the present study, we found LAMB4 (11.8% of GC and 7.6% of CRC with MSI-H), LAMA3 (2.9% of GC and 2.5 of CRC with MSI-H), LAMA1 (5.9% of GC with MSI-H) and LAMB1 frameshift mutations (1.3% of CRC with MSI-H). These mutations were not found in MSS/MSI-L (0/114). We also analyzed LAMB4 expression in GC and CRC by immunohistochemistry. Loss of LAMB4 expression was identified in 17-32% of the GC and CRC. Of note, the loss expression was more common in the cancers with LAMB4 mutation or those with MSI-H. Our data show that frameshift mutations of LAMA1, LAMA3, LAMB1 and LAMB4, and loss of LAMB4 may be features of GC and CRC with MSI-H.
Risk analysis in outsourcing of information technology and communication (2011)

This research aims at evaluating the risk analysis process in Information Technology and Communication (ICT) outsourcing conducted by organizations of the private sector. The research is characterized by being a descriptive, quantitative and transversal type study, which was used the survey method. Data were collected through questionnaire, the sample is not random and we used a convenience sampling process. The research made contributions to understanding the risk analysis process in ICT services outsourcing, and identified statistically significant relationships between risk analysis, organization's size and its industry, and between risk analysis and diversity of outsourced services.
Adherent-free generation of functional dendritic cells from purified blood monocytes in view of potential clinical use. (1998)

There is insufficient evidence to conclude whether the rate of IR after rapid IFX increases. The consistent finding of no increase in IR in all studies and the low rate of observed IR suggests there is no significant difference in rate of IR.
Fixation strengths of patellar tendon‐bone grafts (1993)

Secure fixation of bone-patellar tendon-bone grafts is essential to allow early joint mobilization after anterior cruciate ligament (ACL) reconstruction surgery. This study was designed to evaluate four fixation methods of patellar tendon-bone grafts in cadaveric knees. Fifty-one fresh cadaveric patellar tendon-bone specimens were anchored in tibial or femoral metaphyseal bone tunnels. Group I grafts were fixed with Kurosaka interference screws. In Group II the grafts were initially fixed as in Group I, but the screws were then removed, the bone plugs repositioned, and the grafts resecured with screws. In Group III the grafts were anchored with three no. 2 nonabsorbable sutures tied over a screw and washer, whereas in Group IV no. 5 nonabsorbable sutures were used. Each bone specimen was mounted in the biomechanical testing machine, and a vertical tensile load was applied at a strain rate of 51 cm/min until failure of fixation, bone plug fracture, or tendon disruption occurred. The mean force to failure in Groups I, II, III, and IV were 435.0 N, 458.2 N, 454.2 N, and 415.8 N, respectively. There was no significant difference in the force to failure among the four methods of fixation. However, the modes of failure were diverse. In three specimens the Kurosaka screws diverged from the plugs and failed to achieve fixation. These specimens were excluded and will be discussed separately. Although technique-related difficulties may arise, interference screw fixation of patellar tendon-bone grafts affords strong graft fixation--often stronger than the graft itself. Secondary screw fixation appears to be equal in strength to primary screw fixation.(ABSTRACT TRUNCATED AT 250 WORDS)
Dilatation balloons: polymer selection, balloon design and assembly. (1987)

The current status of coronary dilating instruments is presented from the designer's perspective. Catheter shaft design is considered by important features, common catheter materials and types of catheter construction. Among the seven companies manufacturing balloon dilating instruments, only three types of catheter and four materials are offered. Balloon design is presented by important features and by materials selected. Performance comparisons are made between the three materials used to fabricate dilating balloons: PVC, PE and PET.
Influence of deuterium oxide on calcium transients and myofibrillar responses of frog skeletal muscle. (1984)

The influence of substituting D2O for H2O on calcium transients and on contraction was studied in intact single skeletal muscle fibres injected with aequorin and in mechanically skinned fibres from frogs. Most experiments were carried out at 10 degrees C. Experiments performed in vitro established that the calcium concentration-effect curve for aequorin is depressed and the rate of change of aequorin light emission after sudden changes of [Ca2+] is decreased when D2O is substituted for H2O. D2O substitution greatly reduces the amplitude of the aequorin signals of intact fibres both in twitches and in tetani. This is partly the result of the influence of D2O on aequorin, but the amplitude of the calcium transients is reduced as well. In both H2O and D2O Ringer solutions, the amplitude and time course of the sarcoplasmic calcium transient during a tetanus vary greatly with the stimulus frequency. In H2O, frequencies high enough to produce mechanical fusion normally produce cytoplasmic calcium concentrations high enough to saturate the myofibrils, with the result that stimulus frequency has very little influence on the mechanical response. Saturation does not occur in D2O, and the amplitude and form of fully fused tetani are greatly influenced by the frequency of stimulation. Aequorin was used as a calcium indicator to estimate the influence of D2O substitution on the apparent equilibrium association constant for the calcium-EGTA complex. The constant was reduced by more than one order of magnitude in D2O at pD = pH = 7.0. Experiments on mechanically skinned muscle fibres showed that D2O substitution decreased the apparent sensitivity of the myofibrils to calcium, but increased the force of contraction at saturating calcium concentrations. The latter effect is probably responsible for the potentiation of tetanic tension that is observed in certain D2O/H2O mixtures or in H2O solutions immediately after a switch from D2O. In intact muscle fibres the potentiation of twitch or tetanic tension after a switch from D2O to H2O declines with a half-time of about 25 s; this probably reflects the time course of exchange of intracellular D2O for H2O. The effects of D2O on the intracellular calcium transient appeared and disappeared with a half-time of less than 1 s; this time is of the same order of magnitude as that calculated for the exchange of H2O and D2O in the T-tubules. We conclude that D2O affects calcium release at a site in the T-tubule which is more accessible to the extracellular space than to the intracellular space.
c-Cbl reduces stability of rescued ∆F508-CFTR in human airway epithelial cells (2013)

CFTR is a PKA activated Cl(-) channel expressed in the apical membrane of fluid transporting epithelia. We previously demonstrated that c-Cbl decreases CFTR stability in the plasma membrane by facilitating its endocytosis and lysosomal degradation in human airway epithelium. The most common mutation associated with cystic fibrosis, deletion of Phe508 (∆F508), leads to a temperature sensitive biosynthetic processing defect in the CFTR protein. Mature ∆F508-CFTR that has been rescued by low temperature or chemical chaperones is partially functional as a Cl(-) channel but has decreased plasma membrane stability due to altered post-maturational trafficking. Our present data demonstrate that c-Cbl controls the post-maturational trafficking of rescued ∆F508-CFTR. Partial depletion of c-Cbl increased stability of the plasma membrane associated mature ∆F508-CFTR and the ∆F508-CFTR mediated Cl(-) secretion. These data indicate that correcting the post-maturational trafficking of ∆F508-CFTR may represent a therapeutic approach complementary to the biosynthetic rescue. Because c-Cbl functions as an adaptor and scaffolding protein during CFTR endocytosis, we propose that interfering with the c-Cbl mediated endocytic recruitment of ∆F508-CFTR may increase stability of ∆508-CFTR in the plasma membrane after its biosynthetic rescue.
Structure-Based Vaccine Antigen Design (2019)

Enabled by new approaches for rapid identification and selection of human monoclonal antibodies, atomic-level structural information for viral surface proteins, and capacity for precision engineering of protein immunogens and self-assembling nanoparticles, a new era of antigen design and display options has evolved. While HIV-1 vaccine development has been a driving force behind these technologies and concepts, clinical proof-of-concept for structure-based vaccine design may first be achieved for respiratory syncytial virus (RSV), where conformation-dependent access to neutralization-sensitive epitopes on the fusion glycoprotein determines the capacity to induce potent neutralizing activity. Success with RSV has motivated structure-based stabilization of other class I viral fusion proteins for use as immunogens and demonstrated the importance of structural information for developing vaccines against other viral pathogens, particularly difficult targets that have resisted prior vaccine development efforts. Solving viral surface protein structures also supports rapid vaccine antigen design and application of platform manufacturing approaches for emerging pathogens.
Di / tri-Peptide Transporters as Drug Delivery Targets: Regulation of Transport Under Physiological and Patho-physiological Conditions (2003)

Two human di/tri-peptide transporters, hPepT1 and hPepT2 have been identified and functionally characterized. In the small intestine hPepT1 is exclusively expressed, whereas both PepT1 and PepT2 are expressed in the proximal tubule. The transport via di/tri-peptide transporters is proton-dependent, and the transporters thus belong to the Proton-dependent Oligopeptide Transporter (POT)-family. The transporters are not drug targets per se, however due to their uniquely broad substrate specificity; they have proved to be relevant drug targets at the level of drug transport. Drug molecules such as oral active beta-lactam antibiotics, bestatin, prodrugs of aciclovir and ganciclovir have oral bioavailabilities, which largely are a result of their interaction with PepT1. In the last few years an increasing number of studies concerned with regulation of di/tri-peptide transporter capacity have appeared. Studies on receptor-mediated regulation has shown that both PepT1 and PepT2 is down-regulated by long-term exposure to epidermal growth factor (EGF) due to a decreased gene transcription. PepT1-mediated transport is up-regulated by certain substrates and in response to fasting and starvation at the level of increased gene transcription. PepT1-mediated transport is up-regulated by short-term exposure to receptor agonists such as EGF, insulin, leptin, and clonidine, and down-regulated by VIP. Overall, the regulation of di/tri-peptide transport may be contributed to 1) changes in apical proton-motive force 2) recruitment of di/tri-peptide transporters from vesicular storages 3) changes in gene transcription/mRNA stability. The aim of the present review is to discuss physiological, patho-physiological and drug-induced regulation of di/tri-peptide transporter mediated transport.
Analysis of gene expression in Lassa virus-infected HuH-7 cells (2007)

The pathogenesis of Lassa fever is poorly understood. As the liver is a major target organ of Lassa virus, gene expression in Lassa virus-infected HuH-7 cells, a differentiated human hepatoma cell line, was studied. Cellular mRNA levels were measured at the late phase of acute infection, when virtually all cells expressed large amounts of nucleoprotein, and virus RNA concentration had reached>10(8) copies (ml supernatant)-1. Two types of transcription array were used: cDNA-based macroarrays with a set of 3500 genes (Atlas Human 1.2 arrays; Clontech) and oligonucleotide-based microarrays covering 18,400 transcripts (Human Genome U133A array; Affymetrix). Data analysis was based on statistical frameworks controlling the false-discovery rate. Atlas array data were considered relevant if they could be verified by U133A array or real-time RT-PCR. According to these criteria, there was no evidence for true changes in gene expression. Considering the precision of the U133A array and the number of replicates tested, potential expression changes due to Lassa virus infection are probably smaller than twofold. To substantiate the array data, beta interferon (IFN-beta) gene expression was studied longitudinally in Lassa virus-infected HuH-7 and FRhK-4 cells by using real-time RT-PCR. IFN-beta mRNA levels increased only twofold upon Lassa virus infection, although there was no evidence that the virus inhibited poly(I:C)-induced IFN-beta gene expression. In conclusion, Lassa virus interferes only minimally with gene expression in HuH-7 cells and poorly induces IFN-beta gene transcription.
Online learning of causal structure in a dynamic game situation (2012)

Agents situated in a dynamic environment with an ini-tially unknown causal structure, which, moreover, links certain behavioral choices to rewards, must be able to learn such structure incrementally on the fly. We report an experimental study that characterizes human learn-ing in a controlled dynamic game environment, and de-scribe a computational model that is capable of similar learning. The model learns by building up a represen-tation of the hypothesized causes and effects, including estimates of the strength of each causal interaction. It is driven initially by simple guesses regarding such inter-actions, inspired by events occurring in close temporal succession. The model maintains its structure dynam-ically (including omitting or even reversing the current best-guess dependencies, if warranted by new evidence), and estimates the projected probability of possible out-comes by performing inference on the resulting Bayesian network. The model reproduces the human performance in the present dynamical task.
Synthesis of 6-hydroximino-3-oxo steroids, a new class of aromatase inhibitor (1992)

(E)-3β,17β-Dihydroxyandrost-4-en-6-one oxime has been converted into (E)-6- hydroximinotestosterone and (E)-6-hydroximinoandrost-4-ene-3,17-dione by chemical methods, and into (E)-6-hydroximinoandrosta-1,4-diene-3,17-dione by biotransformation using Arthrobacter simplex ATCC 6946.
Metal–Organic Framework Thin Films Composed of Free-Standing Acicular Nanorods Exhibiting Reversible Electrochromism (2013)

A uniform and crack-free metal–organic framework (MOF) thin film composed of free-standing acicular nanorods was grown on a transparent conducting glass substrate. The MOF thin film exhibits electrochromic switching between yellow and deep blue by means of a one-electron redox reaction at its pyrene-based linkers. The rigid MOF stabilizes the radical cations of the pyrene linkers at positive applied potential, resulting in the reversible color change of the MOF film. The regular and uniform channels of the MOF allow ions to migrate through the entire film. The MOF thin film thus exhibits a remarkable color change and rapid switching rate.
Carotenoids, their comparative biochemistry (1954)

Carotenoids their comparative biochemistry , Carotenoids their comparative biochemistry , مرکز فناوری اطلاعات و اطلاع رسانی کشاورزی
Patch Clamp Electrophysiology and Capillary Electrophoresis–Mass Spectrometry Metabolomics for Single Cell Characterization (2014)

The visual selection of specific cells within an ex vivo brain slice, combined with whole-cell patch clamp recording and capillary electrophoresis (CE)-mass spectrometry (MS)-based metabolomics, yields high chemical information on the selected cells. By providing access to a cell's intracellular environment, the whole-cell patch clamp technique allows one to record the cell's physiological activity. A patch clamp pipet is used to withdraw ∼3 pL of cytoplasm for metabolomic analysis using CE-MS. Sampling the cytoplasm, rather than an intact isolated neuron, ensures that the sample arises from the cell of interest and that structures such as presynaptic terminals from surrounding, nontargeted neurons are not sampled. We sampled the rat thalamus, a well-defined system containing gamma-aminobutyric acid (GABA)-ergic and glutamatergic neurons. The approach was validated by recording and sampling from glutamatergic thalamocortical neurons, which receive major synaptic input from GABAergic thalamic reticular nucleus neurons, as well as neurons and astrocytes from the ventral basal nucleus and the dorsal lateral geniculate nucleus. From the analysis of the cytoplasm of glutamatergic cells, approximately 60 metabolites were detected, none of which corresponded to the compound GABA. However, GABA was successfully detected when sampling the cytoplasm of GABAergic neurons, demonstrating the exclusive nature of our cytoplasmic sampling approach. The combination of whole-cell patch clamp with single cell cytoplasm metabolomics provides the ability to link the physiological activity of neurons and astrocytes with their neurochemical state. The observed differences in the metabolome of these neurons underscore the striking cell to cell heterogeneity in the brain.
Protein ProQ Influences Osmotic Activation of Compatible Solute Transporter ProP in <i>Escherichia coli</i> K-12 (1999)

ProP is an osmoregulatory compatible solute transporter in Escherichia coli K-12. Mutation proQ220::Tn5 decreased the rate constant for and the extent of ProP activation by an osmotic upshift but did not alter proP transcription or the ProP protein level. Allele proQ220::Tn5 was isolated, and the proQ sequence was determined. Locus proQ is upstream from prc (tsp) at 41.2 centisomes on the genetic map. The proQ220::Tn5 and prc phenotypes were different, however. Gene proQ is predicted to encode a 232-amino-acid, basic, hydrophilic protein (molecular mass, 25,876 Da; calculated isoelectric point, 9.66; 32% D, E, R, or K; 54.5% polar amino acids). The insertion of PCR-amplified proQ into vector pBAD24 produced a plasmid containing the wild-type proQ open reading frame, the expression of which yielded a soluble protein with an apparent molecular mass of 30 kDa. Antibodies raised against the overexpressed ProQ protein detected cross-reactive material in proQ+ bacteria but not in proQ220::Tn5 bacteria. ProQ may be a structural element that influences the osmotic activation of ProP at a posttranslational level.
Experimental and Numerical Analyses of New Massive Wooden Shear-Wall Systems (2014)

Three innovative massive wooden shear-wall systems (Cross-Laminated-Glued Wall, Cross-Laminated-Stapled Wall, Layered Wall with dovetail inserts) were tested and their structural behaviour under seismic action was assessed with numerical simulations. The wall specimens differ mainly in the method used to assemble the layers of timber boards composing them. Quasi-static cyclic loading tests were carried out and then reproduced with a non-linear numerical model calibrated on the test results to estimate the most appropriate behaviour factor for each system. Non-linear dynamic simulations of 15 artificially generated seismic shocks showed that these systems have good dissipative capacity when correctly designed and that they can be assigned to the medium ductility class of Eurocode 8. This work also shows the influence of deformations in wooden panels and base connectors on the behaviour factor and dissipative capacity of the system.
Functional characterization of roles of GalR and GalS as regulators of the gal regulon (1997)

An isorepressor of the gal regulon in Escherichia coli, GalS, has been purified to homogeneity. In vitro DNase I protection experiments indicated that among operators of the gal regulon, GalS binds most strongly to the external operator of the mgl operon, which encodes the high-affinity beta-methylgalactoside galactose transport system, and with less affinity to the operators controlling expression of the gal operon, which codes for enzymes of galactose metabolism. GalS has even less affinity for the external operator of galP, which codes for galactose permease, the major low-affinity galactose transporter in the cell. This order of affinities is the reverse of that of GalR, which binds most strongly to the operator of galP and most weakly to that of mgl. Our results also show that GalS, like its homolog, GalR, is a dimeric protein which in binding to the bipartite operators of the gal operon selectively represses its P1 promoter. Consistent with the fact that GalR is the exclusive regulator of the low-affinity galactose transporter, galactose permease, and that the major role of GalS is in regulating expression of the high-affinity galactose transporter encoded by the mgl operon, we found that the DNA binding of GalS is 15-fold more sensitive than that of GalR to galactose.