gebhart/patrepeval huggingface dataset:
Effects of indigestible dietary bulk and short chain fatty acids on the tissue weight and epithelial cell proliferation rate of the digestive tract in rats. (1986)

Influences of indigestible dietary bulk (kaolin), short chain fatty acids (SCFA), and their interaction on the weight and epithelial cell proliferation rate of digestive organs were studied. Rats with an ileal fistua were fed an elemental diet with or without kaolin (10% w/w). They were given a 3 ml SCFA mixture (acetate, propionate, and butyrate; 100, 20, and 60 mM, respectively; pH 6.1) or a 3 ml NaCl solution (180 mM; pH 6.1) via the fistua twice a day for 14 days. Kaolin, but not SCFA, increased full and empty body weight by 14% and 13%, respectively. Kaolin increased the tissue weight, but not relative tissue weight (tissue weight/empty body weight), of the forestomach, distal colon, liver and heart by 6-14%. SCFA, independent of the presence of kaolin, increased the weight and the relative weight of the cecum, both by 15%. SCFA, but not kaolin, increased the cryptal cell production rate in colonic segments by 50-140%. These results indicate that SCFA accelerates epithelial cell proliferation, thereby increasing cecal tissue weight, kaolin stimulates body weight gain which is accompanied by a proportional increase in the tissue weight of some digestive organs, and the actions of these factors are independent of each other.
Multi-Phase 1 GHz Voltage Doubler Charge Pump in 32 nm Logic Process (2010)

A multi-phase 1 GHz charge pump in 32 nm logic process demonstrates a compact area (159 × 42 ¿m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ) for boosting supply voltage from twice the threshold voltage (2 Vth) to 3-4 Vth. Self contained clocking with metal-finger flying capacitors enable embedding voltage boost functionality in close proximity to digital logic for supplying low current Vmin requirement of state elements in logic blocks. Multi-phase operation with phase separation of the order of buffer delays avoids the need for a large storage reservoir capacitor. Special configuration of the pump stages to work in parallel enables a fast (5 ns) output transition from disable to enable state. The multi-phase pump operated as a 1 V to 2 V doubler with >5 mA output capability addresses the need for a gated power delivery solution for logic blocks having state-preservation Vmin requirements.
The [NiFe]-Hydrogenase of the Cyanobacterium Synechocystis sp. PCC 6803 Works Bidirectionally with a Bias to H2 Production (2011)

Protein film electrochemistry (PFE) was utilized to characterize the catalytic activity and oxidative inactivation of a bidirectional [NiFe]-hydrogenase (HoxEFUYH) from the cyanobacterium Synechocystis sp. PCC 6803. PFE provides precise control of the redox potential of the adsorbed enzyme so that its activity can be monitored under changing experimental conditions as current. The properties of HoxEFUYH are different from those of both the standard uptake and the "oxygen-tolerant" [NiFe]-hydrogenases. First, HoxEFUYH is biased toward proton reduction as opposed to hydrogen oxidation. Second, despite being expressed under aerobic conditions in vivo, HoxEFUYH is clearly not oxygen-tolerant. Aerobic inactivation of catalytic hydrogen oxidation by HoxEFUYH is total and nearly instantaneous, producing two inactive states. However, unlike the Ni-A and Ni-B inactive states of standard [NiFe]-hydrogenases, both of these states are quickly (<90 s) reactivated by removal of oxygen and exposure to reducing conditions. Third, proton reduction continues at 25-50% of the maximal rate in the presence of 1% oxygen. Whereas most previously characterized [NiFe]-hydrogenases seem to be preferential hydrogen oxidizing catalysts, the cyanobacterial enzyme works effectively in both directions. This unusual catalytic bias as well as the ability to be quickly reactivated may be essential to fulfilling the physiological role in cyanobacteria, organisms expected to experience swings in cellular reduction potential as they switch between aerobic conditions in the light and dark anaerobic conditions. Our results suggest that the uptake [NiFe]-hydrogenases alone are not representative of the catalytic diversity of [NiFe]-hydrogenases, and the bidirectional heteromultimeric enzymes may serve as valuable models to understand the diverse mechanisms of tuning the reactivity of the hydrogen activating site.
Synthesis of Annulated Pyridines by Intramolecular Inverse‐Electron‐Demand Hetero‐Diels–Alder Reaction under Superheated Continuous Flow Conditions (2011)

Abstract Pyrimidine alkynes can be transformed into the corresponding annulated pyridines efficiently in flow. The superheating of organic solvents far beyond their boiling point enables toxic and difficult to workup solvents such as nitrobenzene or chlorobenzene, which are usually employed for these reactions, to be replaced by less harmful ones like toluene. The relative rate of reactivity for a series of structurally close starting materials was investigated and a scalable flow process was developed, providing facile access to a series of novel annulated pyridine building blocks. The effect of thermal volume expansion of solvents under superheated conditions was found to be significant and influenced the residence times considerably. To obtain meaningful and accurate residence times, flow rates need to be corrected for volume expansion. To avoid confusion with residence times, t R , calculated from nominal flow rates, we would propose to use for such corrected residence times the term effective residence time , t R,eff .
Binding of the Antimicrobial Peptide Temporin L to Liposomes Assessed by Trp Fluorescence (2002)

The structure and membrane topology of the antimicrobial peptide temporin L (FVQWFSKFLGRIL- NH(2)) were studied using liposomes as model bilayers. Circular dichroic spectra revealed temporin L to adopt an alpha-helical conformation when bound to liposomes. Binding of temporin L to liposomes induced significant blue shifts of the emission spectra of the single Trp residue (Trp(4)) and also changed its quantum yield. The observed changes in the characteristics of the Trp(4) fluorescence are in keeping with the insertion of this residue into the hydrophobic region of the liposomal bilayers. Access of the aqueous quencher acrylamide to Trp(4) decreased in the sequence 1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine (SOPC)/cholesterol (X(chol) = 0.1) > SOPC > SOPC/1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG, X(POPG) = 0.1) > SOPC/POPG (X(POPG) = 0.2) approximately SOPC/POPG (X(POPG) = 0.4), where X represents molar fraction of the indicated lipid. Whereas quenching of Trp(4) by brominated phospholipids was significant in SOPC liposomes, the quenching efficiency was enhanced when the vesicles contained POPG. The depth of insertion of Trp(4) into lipid bilayers was calculated by both the parallax method and distribution analysis and revealed this residue to reside at an average distance of d approximately 8.0 +/- 0.5 A from the center of both SOPC and SOPC/POPG bilayers. However, in the presence of cholesterol, d was increased to 9.5 +/- 0.5 A, thus revealing Trp(4) to become accommodated more superficially in the bilayer. The above data suggest the presence of two populations of temporin L in SOPC- and POPG-containing membranes with parallel and perpendicular orientation with respect to the plane of the membrane surface.
Stabilisation of Mouse and Human Interferons by Acid pH Against Inactivation Due to Shaking and Guanidine Hydrochloride (1974)

The inactivation of poly(I)·poly(C)-induced and virus-induced human fibroblast interferon, virus-induced human leukocyte interferon, poly(I)·poly (C)-induced and virus-induced mouse tissue culture interferon and virus-induced mouse serum interferon by shaking and by guani-dine hydrochloride was studied. Only human leukocyte interferon was completely resistant to these treatments. All other interferons examined were largely inactivated, but a small amount of each preparation was resistant to inactivation. The residual activity from either treatment was completely resistant to the other.
Experimental Approaches for Defining Functional Roles of Microbes in the Human Gut (2013)

The complex and intimate relationship between humans and their gut microbial communities is becoming less obscure, due in part to large-scale gut microbial genome-sequencing projects and culture-independent surveys of the composition and gene content of these communities. These studies build upon, and are complemented by, experimental efforts to define underlying mechanisms of host-microbe interactions in simplified model systems. This review highlights the intersection of these approaches. Experimental studies now leverage the advances in high-throughput DNA sequencing that have driven the explosion of microbial genome and community profiling projects, and the loss-of-function and gain-of-function strategies long employed in model organisms are now being extended to microbial genes, species, and communities from the human gut. These developments promise to deepen our understanding of human gut host-microbiota relationships and are readily applicable to other host-associated and free-living microbial communities.
Herpes simplex virus: receptors and ligands for cell entry (2004)

Entry of herpes simplex virus (HSV) into cells depends upon multiple cell surface receptors and multiple proteins on the surface of the virion. The cell surface receptors include heparan sulphate chains on cell surface proteoglycans, a member of the tumor necrosis factor (TNF) receptor family and two members of the immunoglobulin superfamily related to the poliovirus receptor. The HSV ligands for these receptors are the envelope glycoproteins gB and gC for heparan sulphate and gD for the protein receptors and specific sites in heparan sulphate generated by certain 3-O-sulfotransferases. HSV gC also binds to the C3b component of complement and can block complement-mediated neutralization of virus. The purposes of this review are to summarize available information about these cell surface receptors and the viral ligands, gC and gD, and to discuss roles of these viral glycoproteins in immune evasion and cellular responses as well as in viral entry.
이중기계적 합금화법에 의한 초미세 Al-Ti 합금의 제조 및 기계적 성질 (1999)

Dispersion strengthened Al-Ti alloys with very fine microstructures were fabricated by double mechanical alloying (DMA) process, and the elevated temperature mechanical properties of these alloys were investigated. The alloys prepared by DMA process represented better distribution and smaller size of precipitates than those by single mechanical alloying(SMA) process. The analysis of XRD and TEM observation indicated that the size of Al₃Ti phase was smaller than 30 ㎚. The lattice parameter of Al was decreased from 4.0485 to 4.0401Å during MA, which indicates the dissolving of Ti into Al matrix. In this study, the maximum solid solubility of Ti during MA was estimated to be 8.82 wt%. Inspite of effective dispersion of intermetallic compound by DMA process, the alloys did not show improved mechanical properties as expected, due to too high volume percentage of intermetallic dispersoids.
Characterization and sequence of a Thermomonospora fusca xylanase (1994)

TfxA is a thermostable xylanase produced by the thermophilic soil bacterium Thermomonospora fusca. The enzyme was purified to homogeneity from the culture supernatant of Streptomyces lividans transformed by plasmid pGG92, which carries the gene for TfxA, xynA. The molecular mass of TfxA by sodium dodecyl sulfate-polyacrylamide gel electrophoresis is 32 kDa. TfxA is extremely stable, retaining 96% of its activity after 18 h at 75 degrees C. It has a broad pH optimum around pH 7 and retains 80% of its maximum activity between pH 5 and 9. The native enzyme binds strongly to both cellulose and insoluble xylan even though it has no activity on cellulose. Treatment of TfxA with a T. fusca protease produced a 24-kDa catalytically active fragment that had the same N-terminal sequence as TfxA. The fragment does not bind to cellulose and binds weakly to xylan. The Vmax values for TfxA and the fragment are 600 and 540 mumol/min/mg, respectively, while the Kms are 1.1 and 2.3 mg of xylan per ml, respectively. The DNA sequence of the xynA gene was determined, and it contains an open reading frame that codes for a 42-amino-acid (42-aa) actinomycete signal peptide followed by the 32-kDa mature protein. There is a 21-aa Gly-Pro-rich region that separates the catalytic domain from an 86-aa C-terminal binding domain. The amino acid sequence of the catalytic domain of TfxA has from 40 to 72% identity with the sequence of 12 other xylanases from seven different organisms and belongs to family G.(ABSTRACT TRUNCATED AT 250 WORDS)
Ultrasonically Encoded Photoacoustic Flowgraphy in Biological Tissue (2013)

Blood flow speed is an important functional parameter. Doppler ultrasound flowmetry lacks sufficient sensitivity to slow blood flow (several to tens of millimeters per second) in deep tissue. To address this challenge, we developed ultrasonically encoded photoacoustic flowgraphy combining ultrasonic thermal tagging with photoacoustic imaging. Focused ultrasound generates a confined heat source in acoustically absorptive fluid. Thermal waves propagate with the flow and are directly visualized in pseudo color using photoacoustic computed tomography. The Doppler shift is employed to calculate the flow speed. This method requires only acoustic and optical absorption, and thus is applicable to continuous fluid. A blood flow speed as low as 0.24 mm·s(-1)} was successfully measured. Deep blood flow imaging was experimentally demonstrated under 5-mm-thick chicken breast tissue.
Randomized trial of a GPIIb/IIIa platelet receptor blocker in refractory unstable angina. European Cooperative Study Group. (1994)

Combined therapy with c7E3 Fab, heparin, and aspirin appears safe. These pilot study results support the concept that effective blockade of the platelet GPIIb/IIIa receptors can reduce myocardial infarction and facilitate PTCA in patients with refractory unstable angina.
Increased insulin sensitivity in mice lacking p85β subunit of phosphoinositide 3-kinase (2001)

On the basis of ex vivo studies using insulin-responsive cells, activation of a Class IA phosphoinositide 3-kinase (PI3K) seems to be required for a wide variety of cellular responses downstream of insulin. The Class IA PI3K enzymes are heterodimers of catalytic and regulatory subunits. In mammals, insulin-responsive tissues express both the p85alpha and p85beta isoforms of the regulatory subunit. Surprisingly, recent studies have revealed that disruption of the p85alpha gene in the mouse (p85alpha(-/-) mice) results in hypoglycemia with decreased plasma insulin, and the p85alpha(+/-) mice exhibit significantly increased insulin sensitivity. These results suggest either that p85alpha negatively regulates insulin signaling, or that p85beta, which mediates the major fraction of Class IA PI3K signaling in the absence of p85alpha, is more efficient than p85alpha in mediating insulin responses. To address this question, we have generated mice in which the p85beta gene is deleted (p85beta(-/-) mice). As with the p85alpha(-/-) mice, the p85beta(-/-) mice showed hypoinsulinemia, hypoglycemia, and improved insulin sensitivity. At the molecular level, PI3K activity associated with phosphotyrosine complexes was preserved despite a 20-30% reduction in the total protein level of the regulatory subunits. Moreover, insulin-induced activation of AKT was significantly up-regulated in muscle from the p85beta(-/-) mice. In addition, insulin-dependent tyrosine phosphorylation of insulin receptor substrate-2 was enhanced in the p85beta(-/-) mice, a phenotype not observed in the p85alpha(-/-) mice. These results indicate that in addition to their roles in recruiting the catalytic subunit of PI3K to the insulin receptor substrate proteins, both p85alpha and p85beta play negative roles in insulin signaling.
Characterization and Epitope Mapping of Neutralizing Monoclonal Antibodies Produced by Immunization with Oligomeric Simian Immunodeficiency Virus Envelope Protein (2000)

ABSTRACT In an attempt to generate broadly cross-reactive, neutralizing monoclonal antibodies (MAbs) to simian immunodeficiency virus (SIV), we compared two immunization protocols using different preparations of oligomeric SIV envelope (Env) glycoproteins. In the first protocol, mice were immunized with soluble gp140 (sgp140) from CP-MAC, a laboratory-adapted variant of SIVmacBK28. Hybridomas were screened by enzyme-linked immunosorbent assay, and a panel of 65 MAbs that recognized epitopes throughout the Env protein was generated. In general, these MAbs detected Env by Western blotting, were at least weakly positive in fluorescence-activated cell sorting (FACS) analysis of Env-expressing cells, and preferentially recognized monomeric Env protein. A subset of these antibodies directed toward the V1/V2 loop, the V3 loop, or nonlinear epitopes were capable of neutralizing CP-MAC, a closely related isolate (SIVmac1A11), and/or two more divergent strains (SIVsmΔB670 CL3 and SIVsm543-3E). In the second protocol, mice were immunized with unfixed CP-MAC-infected cells and MAbs were screened for the ability to inhibit cell-cell fusion. In contrast to MAbs generated against sgp140, the seven MAbs produced using this protocol did not react with Env by Western blotting and were strongly positive by FACS analysis, and several reacted preferentially with oligomeric Env. All seven MAbs potently neutralized SIVmac1A11, and several neutralized SIVsmΔB670 CL3 and/or SIVsm543-3E. MAbs that inhibited gp120 binding to CD4, CCR5, or both were identified in both groups. MAbs to the V3 loop and one MAb reactive with the V1/V2 loop interfered with CCR5 binding, indicating that these regions of Env play similar roles for SIV and human immunodeficiency virus. Remarkably, several of the MAbs generated against infected cells blocked CCR5 binding in a V3-independent manner, suggesting that they may recognize a region analogous to the conserved coreceptor binding site in gp120. Finally, all neutralizing MAbs blocked infection through the alternate coreceptor STRL33 much more efficiently than infection through CCR5, a finding that has important implications for SIV neutralization assays using CCR5-negative human T-cell lines.
Dynorphin A and cAMP-dependent protein kinase independently regulate neuronal calcium currents. (1990)

The kappa-selective opioid peptide dynorphin A (DYN) inhibits neuronal adenylate cyclase activity and reduces neuronal voltage-dependent calcium currents. It is not yet known, however, whether the regulation of calcium channel activity is dependent on or independent of the adenylate cyclase/cAMP system. We used the whole-cell variation of the patch clamp technique to show that DYN reversibly reduced, in a naloxone-sensitive manner, calcium currents in acutely dissociated rat nodose ganglion neurons. DYN slowed the rate of current activation and had a greater effect on currents evoked from relatively negative holding potentials. These actions were mimicked by guanosine 5'-[gamma-thio]triphosphate, which activates GTP-binding proteins (G proteins), and were blocked by pretreatment with pertussis toxin, which inactivates Gi- and Go-type G proteins. In contrast, calcium currents recorded in the presence of the catalytic subunit of the cAMP-dependent protein kinase (AK-C), included in the recording pipette, increased in magnitude throughout the recording. DYN was applied to neurons before and after the effect of AK-C became apparent; the reduction of calcium currents by DYN was greater in the presence of AK-C than in its absence. We conclude that the acute reduction of neuronal calcium currents by DYN occurred by means of activation of pertussis toxin-sensitive Gi- or Go-type G proteins. The persistence of the action of DYN in the presence of AK-C indicates, however, that this effect was independent of a reduction of the activity of the adenylate cyclase/cAMP system and suggests in addition that phosphorylated channels may be preferentially inhibited by DYN.
Determination of the configuration of ribitol in the C-polysaccharide of Streptococcus pneumoniae using a synthetic approach (1999)

The C-polysaccharide is an antigen common to all known serotypes of Streptococcus pneumoniae bacteria and is a potential target for vaccine preparation. The final uncertainty in the structure of its repeating unit, a pentasaccharide phosphate containing two phosphorylcholine side chains, has been resolved by determining the configuration of ribitol. Assignment of configuration was performed by synthesis of the two trisaccharide phosphate fragments that have either D- or L-ribitol at their centers and comparison of their 1 H and 13 C NMR spectral data with that of the natural polysaccharide. The syntheses employed common synthons added in different orders to an asymmetrically substituted chiral ribitol derivative to obtain opposite chiralities in the ribitol segments. The data for the trisaccharide containing D-ribitol was almost identical to that of the natural material while that for the trisaccharide containing L-ribitol differed significantly. In particular, the chemical shift differences between the two protons of the primary carbons of ribitol units directly attached to the β-2-acetamido-2-deoxy-galactopyranosyl residue were 0.10, 0.12, and 0.33 ppm, in the natural polysaccharide, the D-ribitol-containing trisaccharide, and the L-ribitol-containing trisaccharide, respectively. The average difference between the 13 C NMR chemical shifts of corresponding ribitol carbons from the natural polysaccharide and the D-ribitol-containing trisaccharide phosphate was 0.034 ppm. This evidence indicates that ribitol in the C-polysaccharide has the D-configuration and that a very similar mixture of conformations in the ribitol portions is present for the natural polysaccharide and the D-ribitol-containing trisaccharide phosphate.Key words: C-polysaccharide, Streptococcus pneumoniae, ribitol, dibutylstannylene acetal, determination of configuration.
The Nucleotide Sequence of the lac Operator (1973)

The lac repressor protects the lac operator against digestion with deoxyribonuclease. The protected fragment is double-stranded and about 27 base-pairs long. We determined the sequence of RNA transcription copies of this fragment and present a sequence for 24 base pairs. It is: 5'--T G G A A T T G T G A G C G G A T A A C A A T T 3' 3'--A C C T T A A C A C T C G C C T A T T G T T A A 5' The sequence has 2-fold symmetry regions; the two longest are separated by one turn of the DNA double helix.