gebhart/patrepeval huggingface dataset:
Long-Term Neuroprotection with 2-Iminobiotin, An Inhibitor of Neuronal and Inducible Nitric Oxide Synthase, after Cerebral Hypoxia-Ischemia in Neonatal Rats (2005)

The short- and long-term neuroprotective effects of 2-iminobiotin, a selective inhibitor of neuronal and inducible nitric oxide synthase, were studied in 12-day-old rats following hypoxia-ischemia. Hypoxia-ischemia was induced by occlusion of the right carotid artery followed by 90 minutes of hypoxia (FiO2 0.08). Immediately on reoxygenation, 12 and 24 hours later the rats were treated with vehicle or 2-iminobiotin at a dose of 5.5, 10, 30, or 60 mg/kg per day. Histologic analysis of brain damage was performed at 6 weeks after hypoxia-ischemia. To assess early changes of cerebral tissue, levels of HSP70, nitrotyrosine, and cytochrome c were determined 24 hours after reoxygenation. Significant neuroprotection was obtained using a dose of 30 mg/kg per day of 2-iminobiotin. Levels of HSP70 were increased in the ipsilateral hemisphere in both groups (P<0.05), but the increase was significantly (P<0.05) less in the rats receiving the optimal dose of 2-iminobiotin (30 mg/kg per day). Hypoxia-ischemia did not lead to increased levels of nitrotyrosine, nor did 2-iminobiotin influence levels of nitrotyrosine. In contrast, hypoxia-ischemia induced an increase in cytochrome c level that was prevented by 2-iminobiotin. In conclusion, 2-iminobiotin administered after hypoxia-ischemia provides long-term neuroprotection. This neuroprotection is obtained by mechanisms other than a reduction of nitrotyrosine formation in proteins.
Staphylococcus aureus Throat Colonization Is More Frequent than Colonization in the Anterior Nares (2006)

The aim of this study was to determine the frequency and persistence of Staphylococcus aureus carriage in the throat in relation to anterior naris carriage. By use of a sensitive enrichment broth, S. aureus was cultured from the two sites from 259 patients upon admission to an orthopedic ward and from 87 staff members of the same ward. The throat was the most common carriage site in both groups. Forty percent of the patients and 54% of the staff were positive for S. aureus in the throat, compared to 31% and 36%, respectively, in the anterior nares. To determine the persistence of carriage, 67 individuals were repeatedly sampled from the anterior nares and the throat over 2 years (5 to 10 sampling occasions; mean, 7.8). The majority, 58% (39/67), were defined as persistent carriers of S. aureus, considering culture results from both sites. Of the 39 persistent carriers, 15 individuals were culture positive from only the throat on more than half of the sampling occasions (these are called preferential throat carriers) while only 5% (two individuals) were preferential anterior naris carriers by use of the same definition. Typing of the collected S. aureus isolates by pulsed-field gel electrophoresis revealed that the same strain of S. aureus was present, over time, in the throat of an individual at least to the same extent as in the anterior nares. Throat carriage was at least as persistent as carriage in the anterior nares.
A Precursor-Limited Nanoparticle Coalescence Pathway for Tuning the Thickness of Laterally-Uniform Colloidal Nanosheets: The Case of SnSe (2011)

The availability of high-quality colloidal nanosheets underpins a diverse range of applications and investigations into dimension-dependent physical properties. To facilitate this, synthetic methods that yield single-crystal colloidal nanosheets with regular shapes, uniform lateral dimensions, and tunable thicknesses are critically important. Most strategies that yield colloidal nanosheets achieve some, but not all, of these morphological characteristics. Here, we describe a synthetic pathway that generates colloidal nanosheets of SnSe with uniform lateral dimensions and tunable thicknesses. SnSe represents an excellent prototype system for studying the formation of colloidal nanosheets because of its layered crystal structure and the growing interest in its potential application as an absorption layer in low-cost photovoltaic devices. Freestanding colloidal SnSe nanosheets were synthesized by slowly heating a one-pot reaction mixture of SnCl(2), oleylamine, trioctylphosphine selenide (TOP-Se), and hexamethyldisilazane (HMDS) to 240 °C. The SnSe nanostructures adopt a uniform square-like morphology with lateral dimensions of approximately 500 nm × 500 nm, and the average nanosheet thicknesses can be tuned from approximately 10 to 40 nm by adjusting the concentrations of the SnCl(2) and TOP-Se reagents. Aliquot studies reveal fundamental insights into how the nanosheets form: they first "grow out" laterally via coalescence of individual nanoparticle building blocks to yield a single-crystal nanosheet template and then "grow up" vertically (through nanoparticle attachment to the nanosheet template) in a pseudo layer-by-layer fashion. Vertical growth is therefore limited, and can be controlled, by reagent concentration. Drop-cast films of the SnSe nanosheets are photoactive and have a bandgap of approximately 1 eV. These studies, demonstrated for SnSe but potentially applicable to other systems, establish a straightforward pathway for tuning the thicknesses of colloidal nanosheets while maintaining lateral uniformity.
TopHat: discovering splice junctions with RNA-Seq (2009)

Supplementary data are available at Bioinformatics online.
Transformation Behaviour Of Acicular Ferrite In C-Mn Steel Weld Metals Containing Titanium (2002)

ABSTRAK\nThe formation of acicular ferrite which gives high strength and good impact toughness in C-Mn steel weld metals has been studied using dilatometry in combination with optical microscopy and transmission electron microscopy (TEM) associated with microanalytical technique, i.e. energy dispersive X-ray (EDX) analysis. The results showed that Ti was essential in promoting acicular ferrite and the complexity of the austenite to ferrite transformation was likely to be associated with interactions between Ti, N, 0 and other alloying elements during welding process\nKeywords: acicular Ferriete, titanium
Hydrogen Bond Catalyzed Enantioselective Vinylogous Mukaiyama Aldol Reaction (2005)

[chemical reaction: see text]. The concept of hydrogen bonding catalysis was extended to the vinylogous Mukaiyama aldol reaction, which gives rapid access to polyketide derivatives. The reaction of the silyldienol ether shown and a range of aldehydes catalyzed by TADDOL proceeds regiospecifically to produce the addition products in good yields and enantiomeric excesses.
Microfabricated mechanical biosensor with inherently differential readout (2003)

We report measurements with a micromachined mechanical biosensor that inherently suppresses background effects by producing a differential signal with respect to a reference. The sensor comprises two adjacent cantilevers with interdigitated fingers between them that allow interferometric detection of the differential, i.e., relative bending. We demonstrate that differential detection can efficiently suppress unspecific chemical effects that result in cantilever bending. We show that the differential deflection noise is up to an order of magnitude lower than the absolute deflection noise in the low-frequency range of 0.0003–1 Hz, where many types of biologically relevant reactions occur. We also demonstrate the sensor’s applicability to biological receptor–ligand systems by reporting experimental results on direct differential detection of biotin–streptavidin binding.
Helix Propensities Are Identical in Proteins and Peptides (1997)

Our understanding of the factors stabilizing alpha-helical structure has been greatly enhanced by the study of model alpha-helical peptides. However, the relationship of these results to the folding of helices in intact proteins is not well characterized. Helix propensities measured in model peptides are not in good agreement with those from proteins. In order to address these questions, we have measured helix propensities in the alpha-helix of ribonuclease T1 and a helical peptide of identical sequence. We have previously demonstrated excellent agreement between peptide and protein for the nonpolar amino acids [Myers, J. K., Pace, C. N., and Scholtz, J. M. (1997) Proc. Natl. Acad. Sci. U.S.A. 94, 2833-2837]. Most other amino acids also show good agreement, although certain polar amino acids are exceptions. Helix propensities measured in the ribonuclease T1 peptide/protein are compared with those measured in other systems. Reasonable agreement is found between most systems; however, our propensities differ substantially from those measured in several model peptide systems. Alanine-based peptides overestimate the propensity differences by a factor of 2, and host/guest experiments underestimate them by a factor of 2-3.
Histologic Examination of the Placenta in the Growth-Retarded Fetus (1989)

This investigation was undertaken to determine whether histologic examination of the placenta contributed to a better understanding of the cause of intrauterine fetal growth retardation. Placentas were examined of 151 liveborn infants whose birthweights were in the lower 10th percentile for gestational age. One or more histologic aberrations were found in 139 (92%) cases, in contrast to one or more antenatal risk factors (primarily hypertension) in 77 (51%) cases or a gross placental abnormality (primarily abruption) in 46 (30%) cases. Compared with placentas belonging to appropriately sized fetuses, histologic signs of uteroplacental vascular insufficiency, chronic inflammation, and hemorrhagic endovasculitis were significantly more common in the study group. The primary histologic condition was supportive of prior clinical impressions in 61 (40%) cases, contradictory in 23 (15%) cases, or solely contributory to explaining the growth retardation in 55 (36%) cases. Placental histologic examination may clarify a cause for delayed fetal growth, especially after a normotensive pregnancy.
Allogeneic human mesenchymal stem cells for treatment of E. coli endotoxin-induced acute lung injury in the ex vivo perfused human lung (2009)

Recent studies have suggested that bone marrow-derived multipotent mesenchymal stem cells (MSCs) may have therapeutic applications in multiple clinical disorders including myocardial infarction, diabetes, sepsis, and hepatic and acute renal failure. Here, we tested the therapeutic capacity of human MSCs to restore alveolar epithelial fluid transport and lung fluid balance from acute lung injury (ALI) in an ex vivo perfused human lung preparation injured by E. coli endotoxin. Intra-bronchial instillation of endotoxin into the distal airspaces resulted in pulmonary edema with the loss of alveolar epithelial fluid transport measured as alveolar fluid clearance. Treatment with allogeneic human MSCs or its conditioned medium given 1 h following endotoxin-induced lung injury reduced extravascular lung water, improved lung endothelial barrier permeability and restored alveolar fluid clearance. Using siRNA knockdown of potential paracrine soluble factors, secretion of keratinocyte growth factor was essential for the beneficial effect of MSCs on alveolar epithelial fluid transport, in part by restoring amiloride-dependent sodium transport. In summary, treatment with allogeneic human MSCs or the conditioned medium restores normal fluid balance in an ex vivo perfused human lung injured by E. coli endotoxin.
Development of the multiple sequence approximation within the AGADIR model of α‐helix formation: Comparison with Zimm‐Bragg and Lifson‐Roig formalisms (1997)

In this work we present the development of the multiple sequence approximation (AGADIRms) and the standard one-sequence approximation (AGADIRIs) within the framework of AGADIR's α-helix formation model. The extensive comparison between these new formulations and the original one [AGADIR; v. Muñoz and L. Serrano (1994),Nat. Struct. Biol., Vol. 1, pp. 399–409] indicates that the standard one-sequence approximation is virtually identical to the multiple sequence approximation, while the previously used residue partition function approximation [Muñoz and Serrano (1994); (1995), J. Mol. Biol., Vol. 245, pp. 275–296] is less precise. The calculations of the average helical content performed with AGADIR are precise for peptides of less than 30 residues and progressively diverge from the multiple sequence formulation for longer peptides. The helicity distribution of heteropolypeptides with less than 50% average helical content is also well described, while those of quasi-homopolymers with high helical content tend to be flattened. These inaccuracies lead to an underestimation of 0.017 kcal/mol for the mean-residue enthalpic contribution in AGADIR, as compared to AGADIRms and AGADIRIs. The other energy contributions to α-helix stability are not affected by the original statistical approximation. We also discuss the particularities of the model for α-helix formation utilized in AGADIR and compare it with the classical Zimm-Bragg and Lifson-Roig theories. Moreover, we develop the mathematical relationships between the basic AGADIR energy contributions and helix nucleation and elongation, which permit the quantitative comparison between formalisms. Remarkably, the comparison between AGADIRms and the Lifson-Roig formalism shows that, despite the differences on treating helix/coil cooperativity, both theories give virtually identical results when an equivalent set of parameters is used. This indicates that the helix/coil transition is a solid theory independent of the particularities of the model for α-helix formation. © 1997 John Wiley & Sons, Inc. Biopoly 41: 495–509, 1997.
Roles of estrogen receptor α and androgen receptor in the regulation of neuronal nitric oxide synthase (2002)

In brain and peripheral tissues, steroid hormones regulate nitric oxide synthase (nNOS). We asked whether estrogen receptor-alpha (ERalpha) and/or androgen receptor (AR) regulated nNOS immunoreactivity in mouse brain. First, we quantified cells singly labeled for nNOS immunoreactivity or labeled dually with ERalpha-immunoreactive (-ir) or AR-ir cells in the nucleus accumbens (Acb), preoptic area (POA), bed nucleus of the stria terminalis (BNST), posterior dorsal and posterior ventral regions of the medial amygdala (MePD and MePV, respectively), and paraventricular nucleus (PVN). The POA and MePD contained the greatest number of double-labeled cells. More nNOS-ir cells were colabeled with ERalpha immunoreactivity compared with AR immunoreactivity. Next, by using a double mutant mouse in which males lacked functional ERalpha, AR, or both, we investigated the roles of these steroid receptors in nNOS-ir cell numbers and immunoreactive area staining under testosterone (T) and estradiol (E2) conditions. Our data show that functional ERalpha is correlated with more nNOS-ir cells under T conditions and more immunoreactive area staining in the POA under both T and E2 conditions. However, ERalpha decreases nNOS-ir cell number in the BNST under E2 treatment. In summary, the data suggest that AR has organizational actions on nNOS-ir cell numbers in the MePV, that interactions between ERalpha and AR genes occur in PVN, and that sex differences in nNOS-ir area staining are limited to the POA. Thus, we show that ERalpha and AR interact to regulate nNOS in male and female brain in a site-specific manner.
Pressure dependence of propagation rate coefficients in free-radical homopolymerizations of methyl acrylate and dodecyl acrylate (1998)

Propagation rate coefficients (kp) for the homopolymerization of methyl acrylate (MA) and dodecyl acrylate (DA) were determined by the pulsed laser polymerization (PLP)/size-exclusion chromatography (SEC) technique at pressures between 100 and 2000 bar. The activation volumes for the propagation step, ΔV#(kp), of MA and DA are identical within experimental accuracy, but are clearly different from the previously reported ΔV#(kp) of methyl and dodecyl methacrylate. For both the alkyl acrylates and methacrylates a pronounced family-type behaviour of kp is seen, with kp being slightly enhanced toward larger ester size.
Effects of lactate on pancreatic islets. Lactate efflux as a possible determinant of islet-cell depolarization by glucose (1989)

The secretion of insulin from perifused rat pancreatic islets was stimulated by raising the glucose concentration from 5.6 to 20 mM or by exposure to tolbutamide. The addition of sodium lactate (40 mM) to islets perifused in the presence of glucose (5.6 mM) resulted in a small, transient, rise in the rate of secretion. The subsequent removal of lactate, but not glucose or tolbutamide, from the perifusate produced a dramatic potentiation of insulin release. The rate of efflux of 45Ca2+ was also increased when islets were exposed to a high concentration of glucose or lactate or to tolbutamide, and again subsequently upon withdrawal of lactate. Efflux of 86Rb+ was modestly inhibited upon addition of lactate and markedly enhanced by the subsequent withdrawal of lactate from islets. The output of [14C]lactate from islets incubated in the presence of [U-14C]glucose increased linearly with increasing concentrations of glucose (1-25 mM). It is proposed that the activation of islets by the addition or withdrawal of lactate is not due to increased oxidative flux, but occurs as a result of the electrogenic passage of lactate ions across the plasma membrane, resulting in islet-cell depolarization, Ca2+ entry and insulin secretion. The production of lactate via the glycolytic pathway, and the subsequent efflux of lactate from the islet cells with concomitant exchange of H+ for Na+, could be a major determinant of depolarization and hence insulin secretion, in response to glucose.
Multiple activation states of VLA-4. Mechanistic differences between adhesion to CS1/fibronectin and to vascular cell adhesion molecule-1. (1993)

We examined the effects of a stimulatory anti-beta 1 mAb (TS2/16) and different divalent cations on VLA-4-mediated cell adhesion to vascular cell adhesion molecule-1 (VCAM-1), to the fibronectin-derived CS1 peptide, and to larger fibronectin fragments. Using optimal binding conditions (in the presence of mAb TS2/16 and 1.0 mM Mn2+), the levels of VLA-4-mediated adhesion to VCAM-1 and to CS1 peptide were virtually indistinguishable, and half-maximal inhibition of adhesion to both ligands was achieved using similar levels of an anti-alpha 4 antibody. However, using suboptimal adhesion conditions, two critical differences between adhesion to CS1 peptide (or larger fibronectin fragments) and VCAM-1 were consistently observed. First, stimulation by added mAb TS2/16 had a substantially greater effect on adhesion to CS1 than to VCAM-1 and second, Ca2+ was much less able to support adhesion to CS1 than to VCAM-1. These two differences between adhesion to CS1 peptide and to VCAM-1 were most obvious among cell lines which synthesized inactive or partly active VLA-4 but were not obvious for fully active VLA-4. Together, these results not only reveal crucial differences in the mechanisms of VLA-4 binding to its two ligands, but also lead to increased understanding of the variable activation states of VLA-4. The differential ability to utilize Ca2+ displayed by VLA-4 in different states of activation and the activation of inactive or partly active VLA-4 by the addition of Mn2+ both point to divalent cation sites playing an essential role in determining VLA-4 regulation and ligand specificity.
Isolation and characterization of a tobacco mosaic virus-inducible myb oncogene homolog from tobacco (1996)

Salicylic acid (SA) plays an important role in signaling the activation of plant defense responses against pathogen attack including induction of pathogenesis-related (PR) proteins. To gain further insight into the SA-mediated signal transduction pathway, we have isolated and characterized a tobacco mosaic virus (TMV)-inducible myb oncogene homolog (myb1) from tobacco. The myb1 gene was induced upon TMV infection during both the hypersensitive response and development of systemic acquired resistance in the resistant tobacco cultivar following the rise of endogenous SA, but was not activated in the susceptible cultivar that fails to accumulate SA. The myb1 gene was also induced by incompatible bacterial pathogen Pseudomonas syringae pv. syringae during the hypersensitive response. Exogenous SA treatment rapidly (within 15 min) activated the expression of myb1 in both resistant and susceptible tobacco cultivars with the subsequent induction of PR genes occurring several hours later. Biologically active analogs of SA and 2,6-dichloroisonicotinic acid (a synthetic functional analog of SA), which induce PR genes and enhanced resistance, also activated the myb1 gene. In contrast, biologically inactive analogs were poor inducers of myb1 gene expression. Furthermore, the recombinant Myb1 protein was shown to specifically bind to a Myb-binding consensus sequence found in the promoter of the PR-1a gene. Taken together, these results suggest that the tobacco myb1 gene encodes a signaling component down-stream of SA that may participate in transcriptional activation of PR genes and plant disease resistance.
Activation of the Ah Receptor by Tryptophan and Tryptophan Metabolites (1998)

The aryl hydrocarbon receptor (AhR) is a ligand-dependent transcription factor that mediates many of the biological and toxicological actions of a variety of hydrophobic natural and synthetic chemicals, including the environmental contaminant 2,3,7, 8-tetrachlorodibenzo-p-dioxin (TCDD, dioxin). A variety of indole-containing chemicals, such as indole-3-carbinol, indolo[3, 2-b]carbazole, and UV photoproducts of tryptophan (TRP), have previously been identified as ligands for AhR. Here we have examined the ability of endogenous metabolites of tryptophan (TRP) to bind to and activate AhR in vitro and in cells in culture. Although hydroxylated TRP metabolites were inactive, two metabolites, namely tryptamine (TA) and indole acetic acid (IAA), were shown to be AhR agonists. Not only do TA and IAA bind competitively to AhR, but they also can stimulate AhR transformation and DNA binding and induce expression of an AhR-dependent reporter gene in cells. In addition to being an AhR ligand, TA is also a competitive substrate for cytochrome P4501A1, a well-characterized AhR- and TCDD-inducible gene product. Although these compounds are relatively weak ligands, compared to TCDD, they represent some of the first endogenous hydrophilic AhR agonists identified to date.
PD‐1 as a potential target in cancer therapy (2013)

Recently, an improved understanding of the molecular mechanisms governing the host response to tumors has led to the identification of checkpoint signaling pathways involved in limiting the anticancer immune response. One of the most critical checkpoint pathways responsible for mediating tumor-induced immune suppression is the programmed death-1 (PD-1) pathway, normally involved in promoting tolerance and preventing tissue damage in settings of chronic inflammation. Many human solid tumors express PD ligand 1 (PD-L1), and this is often associated with a worse prognosis. Tumor-infiltrating lymphocytes from patients with cancer typically express PD-1 and have impaired antitumor functionality. Proof-of-concept has come from several preclinical studies in which blockade of PD-1 or PD-L1 enhanced T-cell function and tumor cell lysis. Three monoclonal antibodies against PD-1, and one against PD-L1, have reported phase 1 data. All four agents have shown encouraging preliminary activity, and those that have been evaluated in larger patient populations appear to have encouraging safety profiles. Additional data are eagerly awaited. This review summarizes emerging clinical data and potential of PD-1 pathway-targeted antibodies in development. If subsequent investigations confirm the initial results, it is conceivable that agents blocking the PD-1/PD-L1 pathway will prove valuable additions to the growing armamentarium of targeted immunotherapeutic agents.