gebhart/patrepeval huggingface dataset:
Fatty acids from diet and microbiota regulate energy metabolism (2015)

A high-fat diet and elevated levels of free fatty acids are known risk factors for metabolic syndrome, insulin resistance, and visceral obesity. Although these disease associations are well established, it is unclear how different dietary fats change the risk of insulin resistance and metabolic syndrome. Here, we review emerging evidence that insulin resistance and fat storage are linked to changes in the gut microbiota. The gut microbiota and intestinal barrier function, in turn, are highly influenced by the composition of fat in the diet. We review findings that certain fats (for example, long-chain saturated fatty acids) are associated with dysbiosis, impairment of intestinal barrier function, and metabolic endotoxemia. In contrast, other fatty acids, including short-chain and certain unsaturated fatty acids, protect against dysbiosis and impairment of barrier function caused by other dietary fats. These fats may promote insulin sensitivity by inhibiting metabolic endotoxemia and dysbiosis-driven inflammation. During dysbiosis, the modulation of metabolism by diet and microbiota may represent an adaptive process that compensates for the increased fuel demands of an activated immune system.
Measurement of the size dependent hole spectrum in CdSe quantum dots (1994)

We combine a new synthesis with transient optical hole burning to observe and assign the size evolution (19 to 115 \AA{} diameter, \ensuremath{\sigma}5%) of a series of excited states in CdSe quantum dots. We observe an avoided crossing around the spin orbit energy in the hole spectra for \ensuremath{\sim}65 \AA{} dots, indicating the importance of valence band complexities in the description of the excited states. Comparsion with dc Stark data shows that bleach spectra are consistent with localized carrier induced electric fields.
Extracting site-specific reaction rates from steady state surface morphologies: Kinetic Monte Carlo simulations of aqueous Si(111) etching (1998)

The etching of Si(111) surfaces is studied using a chemically realistic, kinetic Monte Carlo simulation that incorporates the full surface geometry. These simulations show that reliable, site-specific reaction rates can be extracted from steady state etched surface morphologies. The kinetics of pit etching and step etching are examined separately and in concert. Comparisons are made to mean field approximations; however, mean field kinetics are shown to be quantitatively incorrect in their predictions of surface morphology. Statistical parametrizations of surface morphology, such as local width measurements, are also examined. Although these parametrizations are sensitive to the relative etch rates, they cannot be used to ascertain the actual etch mechanism. In general, steady state etch morphologies change gradually as the relative etch rates are varied over three-to-five decades of reactivity. Within this range, a change in surface morphology is observable when a single etch rate is changed by a factor of 2–3.
Neuropeptides and asthma (1998)

Although asthma is considered to be an inflammatory disease of the airways, neural mechanisms remain very important. Neural control of airways is far more complex than has been previously recognized. In addition to the classic neural pathways, the nonadrenergic, noncholinergic pathway has been described in the airways of animals and humans. Neuropeptides are present in sensory, parasympathetic, and sympathetic neurons in airways, and have been shown to have proinflammatory effects, such as increased mucus production, microvascular leakage, and smooth muscle contraction. Neuropeptides released from sensory nerves (eg, neurokinin A and substance P) mediate excitatory nonadrenergic, noncholinergic transmission, which causes bronchoconstriction and, possibly, bronchial hyperresponsiveness. Better understanding of neural mechanisms might provide a useful therapeutic approach in the future.
Performance of a high-intensity 508-gene circulating-tumor DNA (ctDNA) assay in patients with metastatic breast, lung, and prostate cancer. (2017)

LBA11516 Background: ctDNA assays can noninvasively assess tumor burden and biology by identifying tumor-derived somatic alterations. For broad applicability, including early cancer detection, an unprecedented high-intensity approach (ultra-deep sequencing of plasma cell-free DNA (cfDNA) with broad genomic coverage) is needed to address intra-patient and population-level heterogeneity. We present initial results with this approach in patients (pts) with metastatic breast (BC), non-small cell lung (NSCLC), and castration-resistant prostate cancer (CRPC). Methods: Blood and tissue were prospectively collected w/in 6 wks with no intervening therapy change from pts with de novo or progressive cancer. cfDNA and white blood cell (WBC) genomic DNA from each pt were sequenced with a 508-gene panel (2 Mb; &gt;60,000X raw depth). cfDNA variant calling used molecular barcoding for error correction and filtering for WBC variants. Tissue was sequenced using the MSK-IMPACT assay (410 genes, 1.4 Mb, &gt;500X depth) blinded to plasma/WBC sequencing. Variants were classified as clonal or subclonal based on tumor sequencing in BC and NSCLC. Results: Of 161 eligible pts, 124 (39 BC, 41 NSCLC, and 44 CRPC) were evaluable for concordance. In tissue, 864 variants were detected across the 3 tumor types, with 627 (73%) also detected in plasma: single nucleotide variants/indels - 75%, fusions - 67%, and copy number alterations - 58%. In 90% of pts, at least 1 of the variants detected in tumor tissue was also detected in plasma: BC - 97%, NSCLC - 85%, CRPC - 84%. Most actionable mutations detected in tissue were also detected in plasma (54/71, 76%; SNVs only: 28/31, 90%). A subset of driver mutations (eg. in ESR1, PIK3CA, ERBB2, EGFR) were observed in plasma but not tissue. Clonal variants in tissue were more likely to be detected in plasma than subclonal variants (p&lt;.001). Conclusions: This novel, high-intensity ctDNA assay enabled broad detection of genomic variants in plasma at high rates of concordance with corresponding tumor tissue, providing strong evidence for tumor-derivation of these signals. This study will inform development of a high-intensity sequencing approach for early cancer detection.
Design and description of CS-ACELP: a toll quality 8 kb/s speech coder (1998)

This paper describes the 8 kb/s speech coding algorithm G.729 which has been standardized by ITU-T. The algorithm is based on a conjugate-structure algebraic CELP (CS-ACELP) coding technique and uses 10 ms speech frames. The codec delivers toll-quality speech (equivalent to 32 kb/s ADPCM) for most operating conditions. This paper describes the coder structure in detail and discusses the reasons behind certain design choices. A 16-b fixed-point version has been developed as part of Recommendation G.729 and a summary of the subjective test results based on a real-time implementation of this version are presented.
Polyglutamine-mediated dysfunction and apoptotic death of a Caenorhabditis elegans sensory neuron (1999)

The effect of expressing human huntingtin fragments containing polyglutamine (polyQ) tracts of varying lengths was assessed in Caenorhabditis elegans ASH sensory neurons in young and old animals. Expression of a huntingtin fragment containing a polyQ tract of 150 residues (Htn-Q150) led to progressive ASH neurodegeneration but did not cause cell death. Progressive cell death and enhanced neurodegeneration were observed in ASH neurons that coexpressed Htn-Q150 and a subthreshold dose of a toxic OSM-10::green fluorescent protein (OSM-10::GFP) fusion protein. Htn-Q150 huntingtin protein fragments formed protein aggregates in ASH neurons, and the number of ASH neurons containing aggregates increased as animals aged. ASH neuronal cell death required ced-3 caspase function, indicating that the observed cell death is apoptotic. Of interest, ced-3 played a critical role in Htn-Q150-mediated neurodegeneration but not in OSM10::GFP-mediated ASH neurodegeneration. ced-3 function was important but not essential for the formation of protein aggregates. Finally, behavioral assays indicated that ASH neurons, coexpressing Htn-Q150 and OSM10::GFP, were functionally impaired at 3 days before the detection of neurodegeneration, cell death, and protein aggregates.
Construction of a light-activated protein by unnatural amino acid mutagenesis (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTConstruction of a light-activated protein by unnatural amino acid mutagenesisDavid Mendel, Jonathan A. Ellman, and Peter G. SchultzCite this: J. Am. Chem. Soc. 1991, 113, 7, 2758–2760Publication Date (Print):March 1, 1991Publication History Published online1 May 2002Published inissue 1 March 1991https://pubs.acs.org/doi/10.1021/ja00007a063https://doi.org/10.1021/ja00007a063research-articleACS PublicationsRequest reuse permissionsArticle Views654Altmetric-Citations106LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Genetic determination of exocrine pancreatic function in cystic fibrosis. (1992)

We showed elsewhere that the pancreatic function status of cystic fibrosis (CF) patients could be correlated to mutations in the CF transmembrane conductance regulator (CFTR) gene. Although the majority of CF mutations--including the most common, delta F508--strongly correlated with pancreatic insufficiency (PI), approximately 10% of the mutant alleles may confer pancreatic sufficiency (PS). To extend this observation, genomic DNA of 538 CF patients with well-documented pancreatic function status were analyzed for a series of known mutations in their CFTR genes. Only 20 of the 25 mutations tested were found in this population. They accounted for 84% of the CF chromosomes, with delta F508 being the most frequent (71%), and the other mutations accounted for less than 5% each. A total of 30 different, complete genotypes could be determined in 394 (73%) of the patients. The data showed that each genotype was associated only with PI or only with PS, but not with both. This result is thus consistent with the hypothesis that PI and PS in CF are predisposed by the genotype at the CFTR locus; the PS phenotype occurs in patients who have one or two mild CFTR mutations, such as R117H, R334W, R347P, A455E, and P574H, whereas the PI phenotype occurs in patients with two severe alleles, such as delta F508, delta I507, Q493X, G542X, R553X, W1282X, 621 + 1G----T, 1717-1G----A, 556delA, 3659delC, I148T, G480C, V520F, G551D, and R560T.
Serum uric acid levels as a predictor of in-hospital death in patients hospitalized for decompensated heart failure (2005)

Serum uric acid levels may be used as a predictor of death in hospitalized heart failure patients with class IV symptoms.
Comparative evaluation of daptomycin (LY146032) and vancomycin in the treatment of experimental methicillin-resistant Staphylococcus aureus osteomyelitis in rabbits (1989)

A rabbit model for methicillin-resistant Staphylococcus aureus (MRSA) osteomyelitis was used to compare treatment with daptomycin, a new peptolide, and vancomycin. Daptomycin (4 mg/kg) and vancomycin (40 mg/kg) were injected subcutaneously every 12 and 6 h, respectively. After treatment, MRSA was found in bone cultures from 18 of 18 control rabbits, 10 of 17 animals treated with daptomycin, and 11 of 18 animals treated with vancomycin. Drug concentrations were measured in serum, uninfected bone, and infected bone 1 h after daptomycin or vancomycin was injected in a group of rabbits that had been infected for 3 to 4 weeks. Vancomycin was present at the highest concentrations in infected and uninfected bone. The results of this study suggest that daptomycin was similar to vancomycin in the eradication of MRSA from infected bone in an experimental model of osteomyelitis.
Purely Digital BIST for Any PLL or DLL (2007)

PLLs are the heart of most SoCs, so their performance affects many tests. Practical, published PLL BIST approaches cannot measure <10 ps RMS jitter or >1 GHz. This paper describes how a SerDes undersampling DFT technique was adapted to test multiple PLLs and DLLs for jitter, output frequency, duty cycle, and other parameters. Its multi-GHz range, sub-picosecond jitter noise floor, and minimal silicon area are better than for any previous silicon-proven DFT or BIST that needs no calibration or analog circuitry. FPGA implementation results are provided.
Phase-noise cancellation design tradeoffs in delta-sigma fractional-N PLLs (2003)

A theoretical analysis of a recently proposed phase-noise cancellation technique that relaxes the fundamental tradeoff between phase noise and bandwidth in /spl Delta//spl Sigma/ fractional-N phased-locked loops (PLLs) is presented. The limits imposed by circuit errors and PLL dynamics on the phase noise and loop bandwidth that can be achieved by PLLs incorporating the technique are quantified. Design guidelines are derived that enable customization of the technique in terms of PLL target specifications.
Abnormal Body Fat Distribution Detected by Computed Tomography in Diabetic Men (1986)

Previous studies of body fat using tape measurement of body circumference and hand-held caliper skinfold measurements have suggested abnormal fat distribution in patients with diabetes mellitus. These methods, however, have high interobserver variability and cannot assess intra-abdominal fat independent of subcutaneous fat. We used computed tomography to evaluate body fat distribution in a group of 53 Japanese-American men of similar age and body mass index (weight divided by height squared). As determined by a 75-g oral glucose tolerance test, 29 subjects had type II diabetes and 24 were normal. Computed tomography cuts were obtained at three body levels to measure thorax, abdomen, and thigh subcutaneous fat area as well as intra-abdominal fat area. We found greater intra-abdominal fat in men with diabetes than in those without (123.74 vs. 95.54 cm2, P = 0.034) and a greater ratio of thorax to thigh subcutaneous fat (2.55 vs. 1.88, P = 0.016). These findings support the hypothesis that fat in different areas of the body differs metabolically. Computed tomography can be a useful tool for investigating whether abnormal body fat distribution is associated with the pathogenesis of abnormal glucose tolerance.
Demography, baseline disease characteristics, and treatment history of psoriasis patients with self-reported psoriatic arthritis enrolled in the PSOLAR registry (2018)

NCT00508547.
Oxidation of the zinc-thiolate complex and uncoupling of endothelial nitric oxide synthase by peroxynitrite (2002)

Nitric oxide (NO) is produced by NO synthase (NOS) in many cells and plays important roles in the neuronal, muscular, cardiovascular, and immune systems. In various disease conditions, all three types of NOS (neuronal, inducible, and endothelial) are reported to generate oxidants through unknown mechanisms. We present here the first evidence that peroxynitrite (ONOO–) releases zinc from the zinc-thiolate cluster of endothelial NOS (eNOS) and presumably forms disulfide bonds between the monomers. As a result, disruption of the otherwise SDS-resistant eNOS dimers occurs under reducing conditions. eNOS catalytic activity is exquisitely sensitive to ONOO–, which decreases NO synthesis and increases superoxide anion (O2.–) production by the enzyme. The reducing cofactor tetrahydrobiopterin is not oxidized, nor does it prevent oxidation of eNOS by the same low concentrations of OONO–. Furthermore, eNOS derived from endothelial cells exposed to elevated glucose produces more O2.–, and, like eNOS purified from diabetic LDL receptor–deficient mice, contains less zinc and fewer SDS-resistant dimers. Hence, eNOS exposure to oxidants including ONOO– causes increased enzymatic uncoupling and generation of O2.– in diabetes, contributing further to endothelial cell oxidant stress. Regulation of the zinc-thiolate center of NOS by ONOO– provides a novel mechanism for modulation of the enzyme function in disease.
Rapid fabrication of high aspect ratio silicon nanopillars for chemical analysis (2007)

In this study, a method for fabrication of high aspect ratio silicon nanopillars is presented. The method combines liquid flame spray production of silica nanoparticle agglomerates with cryogenic deep reactive ion etching. First, the nanoparticle agglomerates, having a diameter of about 100 nm, are deposited on a silicon wafer. Then, during the subsequent cryogenic deep reactive ion etching process, the particle agglomerates act as etch masks and silicon nanopillars are formed. Aspect ratios of up to 20:1 are demonstrated. The masking process is rapid, cheap and has the potential to be scaled up for large areas. Three other structured silicon surfaces were fabricated for comparison. All four surfaces were utilized as desorption/ionization on silicon (DIOS) sample plates. The mass spectrometry results indicate that nanopillar surfaces masked with the liquid flame spray technique are well suited as DIOS sample plates.
recA protein of Escherichia coli promotes branch migration, a kinetically distinct phase of DNA strand exchange. (1981)

The recA protein of Escherichia coli promotes the complete exchange of strands between full-length linear duplex and single-stranded circular DNA molecules of bacteriophage phi X-174, converting more than 50% of the single-stranded DNA into heteroduplex replicative form II-like structures. Kinetically, the reaction can be divided into two phases, formation of short heteroduplex regions (D loops) and extension of the D loops via branch migration. recA protein participates directly in both phases. D loops are formed efficiently in the presence of ATP or the nonhydrolyzable ATP analog adenosine 5'-[gamma-thio]triphosphate, whereas D-loop extension requires continuous ATP hydrolysis. Complete strand exchange requires a stoichiometric amount of recA protein and is strongly stimulated by the single-stranded-DNA-binding protein of E. coli.
Relationships Among Age, Proinsulin Conversion, and β-Cell Function in Nondiabetic Humans (2002)

The aim of the present study was to examine the relationships among beta-cell function, proinsulin conversion to insulin, and age. We studied insulin and proinsulin secretion in nondiabetic subjects during an oral glucose tolerance test (OGTT) using published indexes of beta-cell function (n = 379, age 16--68 years) and a modified hyperglycemic clamp (10 mmol/l, additional glucagon-like peptide [GLP-1] infusion, final arginine bolus; n = 50, age 19--68 years). Proinsulin conversion to insulin was assessed using proinsulin/insulin (PI/I) ratios immediately after an acute stimulus (OGTT, 30 min; hyperglycemic clamp, 2.5-5.0 min after glucose and arginine). There was a negative correlation between age and beta-cell function (adjusted for insulin sensitivity, BMI, and fasting glucose) in the OGTT (r = -0.21, P < 0.001) and first phase of the hyperglycemic clamp (r = -0.30, P = 0.03), but not second phase (r = -0.08, P = 0.6) or arginine-induced insulin secretion (r = 0.06, P = 0.7). There was a positive correlation between age and the PI/I ratio in the OGTT (r = 0.24, P < 0.001). Analogously, there was also a positive correlation between age and the PI/I ratio during first phase (r = 0.37, P = 0.009) and arginine stimulation (r = 0.33, P = 0.01) of the hyperglycemic clamp. First-phase insulin secretion of the hyperglycemic clamp was inversely correlated with the PI/I ratio (r = -0.60, P < 0.001). Interestingly, adjusting first-phase secretion rate for the PI/I ratio abolished the linear relationship with age (r = -0.06, P = 0.7). In conclusion, aging is associated with deteriorating beta-cell function and deteriorating proinsulin conversion to insulin. The age effect on insulin secretion appears to be attributable at least in part to an impairment of proinsulin conversion to insulin.
EFFECT OF HYALURONAN ON MMP EXPRESSION AND ACTIVATION (2001)

Matrix metalloproteases (MMPs) play a crucial role in tissue remodelling in a variety of physiological and pathological processes. Hyaluronan is also involved in the same processes. Several cytokines and growth factors are involved in the regulation of the biosynthesis of hyaluronan and also of MMPs. The activity of MMPs has been shown to be regulated at the level of transcription and activation of the zymogen form. In order to explore the possible relationship between matrix components and especially hyaluronan, we studied the effect of hyaluronan on MMP expression (biosynthesis and activation) in the culture of human skin fibroblasts and corneal keratocytes (explant cultures and cell cultures). These cells were shown to exhibit distinct phenotypes as far as matrix biosynthesis is concerned. Using a synthetic substrate N-Suc(ala)3pNA, we measured elastase-type endopeptidase activity produced by fibroblasts and keratocytes and characterized the MMPs by zymography. Hyaluronan added to fibroblast cultures stimulated the membrane-bound elastase-type endopeptidase activity in a dose dependent fashion. Similar results were obtained with keratocyte cultures. In the presence of 1 mg/ml hyaluronan there was an increase in MMP expression and also an activation of latent MMPs both by fibroblasts and keratocytes.
Optical processes in ZnO (1995)

Interpretation of the optical processes in ZnO is presented. All the data on photon emission and absorption from the UV to the IR region are treated by a localized molecular unit model. Spectral assignments and characteristics of the shift of the emission band with temperature are interpreted by the present model.
AN INTERACTION BETWEEN ALLELES AT THE RH LOCUS IN MAN WHICH WEAKENS THE REACTIVITY OF THE RH 0 FACTOR (D u ) (1955)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Simulations and Experimental Investigation of Atmospheric Transport in an Ambient Metastable-Induced Chemical Ionization Source (2008)

Since its inception, Direct Analysis in Real Time (DART) has seen utility in a wide range of applications including chemical reaction monitoring, pharmaceutical screening, and forensic mass spectrometry. Despite the growing interest in DART applications, there has been limited research into the fundamental physiochemical phenomena affecting sampling, ionization, and atmospheric ion transport. Presented here are the first experimentally validated finite element method simulations of an ambient DART-type metastable-induced chemical ionization source. It was found that complex coupled fluid dynamics, heat transfer, and electrostatic phenomena within the sampling region determine the variability in ion transmission efficiencies affecting the overall sensitivity of analysis. Particle tracing plots of a circular acetaminophen tablet placed in various positions and orientations yielded insight into optimal sample placement and evidence for sweet spots conducive to better ion transport. Experiments in a wide range of electric field conditions were performed, finding that under optimum sample placement, sensitivity could be improved by as much as 128% if ion mobility contributions were minimized.