gebhart/patrepeval huggingface dataset:
Discovery of Urinary Biomarkers (2006)

A myriad of proteins and peptides can be identified in normal human urine. These are derived from a variety of sources including glomerular filtration of blood plasma, cell sloughing, apoptosis, proteolytic cleavage of cell surface glycosylphosphatidylinositol-linked proteins, and secretion of exosomes by epithelial cells. Mass spectrometry-based approaches to urinary protein and peptide profiling can, in principle, reveal changes in excretion rates of specific proteins/peptides that can have predictive value in the clinical arena, e.g. in the early diagnosis of disease, in classification of disease with regard to likely therapeutic responses, in assessment of prognosis, and in monitoring response to therapy. These approaches have potential value, not only in diseases of the kidney and urinary tract but also in systemic diseases that are associated with circulating small protein and peptide markers that can pass the glomerular filter. Most large scale biomarker discovery studies reported thus far have used one of two approaches to identify proteins and peptides whose excretion in urine changes in specific disease states: 1) two-dimensional electrophoresis with mass spectrometric and/or immunochemical identification of proteins and 2) top-down mass spectrometric methods (SELDI-TOF-MS and capillary electrophoresis-MS). These studies have been chiefly in the areas of nephrology, urology, and oncology. We review these applications, focusing on two areas of progress, viz. in bladder cancer and in acute rejection of renal transplants. Progress has been limited so far. However, with the advent of powerful LC-MS/MS methods along with methods for quantifying LC-MS/MS output, there is hope for an accelerated discovery and validation of disease biomarkers in urine.
Massive Stars as Progenitors of Supernovae and GRBs (2007)

The evolutionary fate of massive stars in our Milky Way is thought to be reasonably well understood: stars above Ëœ 8 M_o produce neutron stars and supernovae, while those above Ëœ 20...30 M_o are presumed to form black holes. At metallicities below that of the SMC, however, our knowledge becomes poor. We show that, possibly, a type of supernova dominates in the low-Z universe which hardly occurs at solar metallicity, and that stars of only 10 M_o initially may form black holes rather than neutron stars.
Fuel alcohol production: effects of free amino nitrogen on fermentation of very-high-gravity wheat mashes (1990)

Although wheat mashes contain only growth-limiting amounts of free amino nitrogen, fermentations by active dry yeast (Saccharomyces cerevisiae) were completed (all fermentable sugars consumed) in 8 days at 20 degrees C even when the mash contained 35 g of dissolved solids per 100 ml. Supplementing wheat mashes with yeast extract, Casamino Acids, or a single amino acid such as glutamic acid stimulated growth of the yeast and reduced the fermentation time. With 0.9% yeast extract as the supplement, the fermentation time was reduced from 8 to 3 days, and a final ethanol yield of 17.1% (vol/vol) was achieved. Free amino nitrogen derived in situ through the hydrolysis of wheat proteins by a protease could substitute for the exogenous nitrogen source. Studies indicated, however, that exogenously added glycine (although readily taken up by the yeast) reduced the cell yield and prolonged the fermentation time. The results suggested that there are qualitative differences among amino acids with regard to their suitability to serve as nitrogen sources for the growth of yeast. The complete utilization of carbohydrates in wheat mashes containing very little free amino nitrogen presumably resulted because they had the "right" kind of amino acids.
Hydrogels in Biology and Medicine: From Molecular Principles to Bionanotechnology (2006)

Abstract Hydrophilic polymers are the center of research emphasis in nanotechnology because of their perceived “intelligence”. They can be used as thin films, scaffolds, or nanoparticles in a wide range of biomedical and biological applications. Here we highlight recent developments in engineering uncrosslinked and crosslinked hydrophilic polymers for these applications. Natural, biohybrid, and synthetic hydrophilic polymers and hydrogels are analyzed and their thermodynamic responses are discussed. In addition, examples of the use of hydrogels for various therapeutic applications are given. We show how such systems' intelligent behavior can be used in sensors, microarrays, and imaging. Finally, we outline challenges for the future in integrating hydrogels into biomedical applications.
Parallel WaveNet: Fast High-Fidelity Speech Synthesis (2017)

The recently-developed WaveNet architecture is the current state of the art in realistic speech synthesis, consistently rated as more natural sounding for many different languages than any previous system. However, because WaveNet relies on sequential generation of one audio sample at a time, it is poorly suited to today's massively parallel computers, and therefore hard to deploy in a real-time production setting. This paper introduces Probability Density Distillation, a new method for training a parallel feed-forward network from a trained WaveNet with no significant difference in quality. The resulting system is capable of generating high-fidelity speech samples at more than 20 times faster than real-time, and is deployed online by Google Assistant, including serving multiple English and Japanese voices.
FURTHER NOTES ON THE GROWTH AND CHLOROPHYLL FORMATION OF <italic>CHLORELLA PROTOTHECOIDES</italic> (1964)

1. Using area of a fixed concentration as a nitrogen source, cells of Chlorella protothecoides were grown in the presence of various carbon compounds. Magnitudes of growth of the cells were widely different depending on the carbon sources used; glucose and fructose being most favourable substrates and galactose, glycerol and acetate coming next. But the amounts of chlorophyll formed in the cells during the experimental period were almost, the same irrespective of the different carbon sources, with some exceptions. The similarity of the chlorophyll level observed in these experiments seemed to indicate that the formation of chlorophyll was limited largely by the nitrogen source but not by the carbon source. 2. Strong bleaching effect was recognized with glucose and fructose at their high concentration, which produced totally chlorophyll-less cells. On the other hand, a stimulating effect on chlorophyll formation was observed with galactose at the different concentrations examined. 3. Effects of glycine and ammonium carbonate as the nitrogen source on the algal growth and pigmentation were studied in some details. The results were similar to those previously obtained with urea, confirming our previous conclusion that the algal pigmentation is profoundly affected by the concentration balance between glucose and nitrogen source.
Respiratory responses to selective blockade of carotid sinus baroreceptors in the dog (1998)

Activation of carotid sinus (CS) baroreceptors has been shown to increase inspiratory time (TI) and expiratory time (TE) and to have a varied effect on tidal volume. The contribution of two functionally different types of baroreceptors to changes in respiratory function were examined in the current study. The techniques of DC anodal block and bupivacaine anesthetic block were used to selectively block fibers, from largest (type I) to smallest (type II) and smallest to largest, respectively, in the CS nerve (CSN) from an isolated CS in an anesthetized, paralyzed, vagotomized, artificially ventilated dog. Anodal blocking currents from 25 to 60 microA, which blocked primarily large A fibers, produced significant decreases in TI and TE and increased the slope of the average phrenic neurogram [PNG(t)], with no change in peak PNG(t). Further increases in blocking current to levels that also blocked small C fibers did not result in additional changes. Bupivacaine blockade using concentrations that blocked primarily C fibers did not block changes in TI and TE to step CS pressure changes. Increasing bupivacaine concentration to 20 mg/100 ml blocked all CSN conduction, and respiratory responses were eliminated. Therefore respiratory responses arising from CS baroreceptors appear to originate from the larger type I baroreceptors.
Coordinate Time On and Near the Earth (1984)

Received 14 November 1983DOI:https://doi.org/10.1103/PhysRevLett.53.1858©1984 American Physical Society
New pathway for the biodegradation of indole in Aspergillus niger (1990)

Indole and its derivatives form a class of toxic recalcitrant environmental pollutants. The growth of Aspergillus niger was inhibited by very low concentrations (0.005 to 0.02%) of indole, even when 125- to 500-fold excess glucose was present in the medium. When 0.02% indole was added, the fungus showed a lag phase for about 30 h and the uptake of glucose was inhibited. Indole was metabolized by a new pathway via indoxyl (3-hydroxyindole), N-formylanthranilic acid, anthranilic acid, 2,3-dihydroxybenzoic acid, and catechol, which was further degraded by ortho cleavage. The enzymes N-formylanthranilate deformylase, anthranilate hydroxylase, 2,3-dihydroxybenzoate decarboxylase, and catechol dioxygenase were induced by indole as early as after 5 h of growth, and their activities were demonstrated in a cell-free system.
PET Studies of Auditory and Phonological Processing: Effects of Stimulus Characteristics and Task Demands (1995)

Positron emission tomography (PET) was used to investigate the functional anatomy of auditory and phonological processing. Stimulus sets were designed to determine areas of the brain significantly activated during speech and nonspeech acoustic processing for stimuli with or without rapidly changing acoustic cues. Performance of auditory target detection tasks using these stimulus sets produced increased activation in superior temporal, frontal opercular, and medial frontal (SMA) cortices, relative to a visual fixation control task. While the medial frontal and superior temporal changes are best explained by motor and sensory components of the task, respectively, the frontal opercular changes were dependent upon the task performed upon the auditory input (mere presentation of the stimuli did not result in significant activation). On the left, the frontal opercular increases were larger when subjects performed an auditory detection task upon stimuli that incorporated rapid temporal changes (words, syllables, and tone sequences) than steady-state vowels. A converging study involving performance of orthographic (ascending letter) and phonological (long vowel sound) word discrimination tasks supports anatomical and behavioral evidence suggesting the left frontal opercular region is important for certain types of auditory/temporal analysis, as well as high-level articulatory coding. In addition to the activation increases associated with performance of auditory target detection tasks, decreases in activation were observed bilaterally along the intraparietal sulcus and superior parietal cortex, in the Rolandic sulcus, and the posterior cingulate; these decreases may reflect an attentional shift away from areas involved in the fixation task during the performance of a difficult auditory task. These results demonstrate that focusing more closely on basic neural processing differences (such as temporal integration rates) may lead to a better understanding of the specific neural processes that underlie complex phonological tasks.
Supersymmetric Ratchets (2001)

The overdamped Brownian motion in a periodic potential under far from equilibrium conditions is considered. A large class of systems with an intrinsic asymmetry, called supersymmetric ratchets, is identified for which the occurrence of directed transport can be ruled out without any fine-tuning of parameters.
P2X7 receptor expression in evolutive and indolent forms of chronic B lymphocytic leukemia (2002)

Human leukocytes express a receptor for extracellular nucleotides, named P2X7R, that in lymphocytes can either mediate cell death or proliferation, depending on the level of activation. The authors have investigated P2X7R expression and function in 21 patients affected by B-cell chronic lymphocytic leukemia, 13 with an evolutive and 8 with an indolent variant of the disease. Resting cytoplasmic Ca++ concentration was significantly higher in lymphocytes from patients with the evolutive compared with indolent variant. Furthermore, in the former, P2X7R stimulation triggered a Ca++ influx significantly larger. Higher Ca++ influx correlated with an increased P2X7R expression in the lymphocytes from patients with the evolutive form. Finally, incubation in the presence of extracellular adenosine triphosphate decreased spontaneous proliferation of lymphocytes from patients affected with the evolutive variant but had no effects on lymphocytes from patients with the indolent form. These results suggest that expression and function of P2X7R may correlate with the severity of B-cell chronic lymphocytic leukemia.
The alkaloids of Gelsemium sempervirens. Part IV. Derivatives of pyridine, isoquinoline, and indol-2(3H)-one as possible initial materials for synthesis of gelsemine (1970)

Derivatives of pyridine-3,4-dicarboxylic acid, of 1,3-dioxodecahydroisoquinoline-4-carbonitrile, of 3-cyclopentylindol-2(3H)-one, and of spiro[cyclohexane-1,3′-indole]-2′(3′H)-one and the derived decahydrospiro-[indole-3,7′-isoquinoline]-2(3H)-one, are described.
A Cell-Intrinsic Requirement for NF-κB–Inducing Kinase in CD4 and CD8 T Cell Memory (2013)

NF-κB-inducing kinase [(NIK), MAP3K14] is an essential kinase linking a subset of TNFR family members to the noncanonical NF-κB pathway. To assess the cell-intrinsic role of NIK in murine T cell function, we generated mixed bone marrow chimeras using bone marrow from NIK knockout (KO) and wild-type (WT) donor mice and infected the chimeras with lymphocytic choriomeningitis virus (LCMV). The chimeras possess an apparently normal immune system, including a mixture of NIK KO and WT T cells, and the virus was cleared normally. Comparison of the NIK KO and WT CD4 and CD8 T cell responses at 8 d post infection revealed modest but significant differences in the acute response. In both CD4 and CD8 compartments, relatively fewer activated (CD44(hi)) NIK KO T cells were present, but within the CD44(hi) population, a comparable percentage of the activated cells produced IFN-γ in response to ex vivo stimulation with antigenic LCMV peptides, although IL-7R expression was reduced in the NIK KO CD8 T cells. Assessment of the LCMV-specific memory at 65 d post infection revealed many more LCMV-specific WT memory T cells than NIK KO memory T cells in both the CD4 and the CD8 compartments, although the small number of surviving NIK KO memory T cells responded to secondary challenge with virus. These results demonstrate a cell-intrinsic requirement for NIK in the generation and/or maintenance of memory T cells in response to acute viral infection.
Using machine learning techniques to interpret WH-questions (2001)

We describe a set of supervised machine learning experiments centering on the construction of statistical models of WH-questions. These models, which are built from shallow linguistic features of questions, are employed to predict target variables which represent a user's informational goals. We report on different aspects of the predictive performance of our models, including the influence of various training and testing factors on predictive performance, and examine the relationships among the target variables.
Formation of silicon dioxide layers at low temperatures (150—400°C) by atmospheric pressure plasma oxidation of silicon (2007)

The formation of silicon dioxide (SiO2) layers at low temperatures (150–400°C) by atmospheric pressure plasma oxidation of Si(0 0 1) wafers have been studied using a gas mixture containing He and O2. A 150 MHz very high frequency (VHF) power supply was used to generate high-density atomic oxygen in the atmospheric pressure plasma. Oxidation rate, structure, and thickness and refractive index profiles of the oxidized layers were investigated by ellipsometry and infrared absorption spectroscopy. Atomic force microscopy was also employed to observe atomic-scale morphologies of the layer surface and wafer Si surface, after chemical removal of the oxidized layers. It was found that stoichiometric SiO2 layers were obtained at higher oxidation rates than conventional dry O2 thermal oxidation and radical oxidation processes, even at a very low substrate temperature of 150°C. Although thickness variations were observed in the plasma region, the refractive index was independent of both substrate temperature and VHF power. In addition, the SiO2 surface and SiO2/Si interface roughnesses were comparable to those obtained in conventional dry oxidation at high temperatures.
Peptidase activities of proteasomes are differentially regulated by the major histocompatibility complex-encoded genes for LMP2 and LMP7. (1994)

Recent studies have implicated proteasomes in the generation of the antigenic peptides that are presented on major histocompatibility complex class I molecules to T lymphocytes. Interferon gamma modifies the subunit composition of proteasomes and causes changes in their peptidase activities that should favor the production of peptides with hydrophobic or basic carboxyl termini (i.e., the types found on major histocompatibility complex class I molecules). It has been proposed that these changes in peptidase activity are due to incorporation into proteasomes of the major histocompatibility complex-encoded subunits LMP2 and -7, which are induced by interferon gamma. Here we show by gene transfection into lymphoblasts or HeLa cells that LMP7 increases the capacity (Vmax) of 20S and 26S proteasomes to cleave peptides after hydrophobic and basic residues without affecting hydrolysis after acidic residues. These changes depended on the amount of LMP7 subunits incorporated into proteasomes. Transfection of LMP2 reduced cleavage of peptides after acidic residues, increased hydrolysis after basic residues, and did not affect the hydrophobic activity. Since the activity of the total proteasome population changed after incorporation of only small amounts of LMP2 or -7, these subunits must cause major alterations in peptidase activity. Thus, their expression can account for the changes in proteasome activity induced by inteferon gamma, and these findings lend further support to the proposed roles of LMPs in altering the nature of the peptides generated for antigen presentation.
The Probiotic Butyricicoccus pullicaecorum Reduces Feed Conversion and Protects from Potentially Harmful Intestinal Microorganisms and Necrotic Enteritis in Broilers (2016)

Probiotics which do not result in the development and spread of microbial resistance are among the candidate replacements for antibiotics previously used as growth promotors. In this study the effect of in-feed supplementation of the butyrate producing <i>Butyricicoccus pullicaecorum</i> strain 25-3<sup>T</sup> on performance, intestinal microbiota and prevention of necrotic enteritis (NE), a disease caused by <i>Clostridium perfringens</i> was evaluated in broilers. For the performance study, day old Ross 308 chicks were randomly allocated into two treatment groups and fed either a non-supplemented diet or a diet supplemented with 10<sup>9</sup> cfu lyophilized <i>B. pullicaecorum</i> per kg feed for 40 days. On day 40 broilers administered <i>B. pullicaecorum</i> had a significant lower bodyweight (2675 g vs. 2762 g; <i>p</i> = 0.0025) but supplementation of <i>B. pullicaecorum</i> decreased the feed conversion ratio significantly (1.518 vs. 1.632; <i>p</i> < 0.0001). Additionally, ingestion of the <i>Butyricicoccus</i> strain significantly lowered the abundance of <i>Campylobacter</i> spp. in the caecum and <i>Enterococcus</i> and <i>Escherichia</i>/<i>Shigella</i> spp. in the ileum at day 40. In feed supplementation of <i>B. pullicaecorum</i> in the NE trials resulted in a significant decrease in the number of birds with necrotic lesions compared with the untreated control group. These studies show that supplementation of <i>B. pullicaecorum</i> is able to improve feed conversion, to reduce the abundance of some potentially important pathogens in the caeca and ileum and to contribute to the prevention of NE in broilers, making the strain a potential valuable probiotic.
The strobilurins - New antifungal antibiotics from the basidiomycete Strobilurus tenacellus. (1977)

The strobilurins are two antifungal antibiotics which were isolated from the mycelium of Strobilurus tenacellus strain No. 21602. The strobilurins A and B are highly active against yeasts and filamentous fungi. In vitro antitumor activity was tested using cells of the ascitic form of EHRLICH carcinoma. The strobilurins strongly inhibited the incorporation of radioactive leucine, uridine, and thymidine into the acid-insoluble fraction of cells (protein, RNA, and DNA). The molecular formulas as determined by high resolution mass spectrometry are C16H18O3 for strobilurin A and C17H19C1O4 for strobilurin B.
Pharmacokinetics, Pharmacodynamics, Tolerability, and Safety of the Soluble Guanylate Cyclase Activator Cinaciguat (BAY 58‐2667) in Healthy Male Volunteers (2008)

Preclinical data indicate that the nitric oxide-independent soluble guanylate cyclase activator cinaciguat (BAY 58-2667), which is a new drug in development for patients with heart failure, induces vasodilation preferentially in diseased vessels. This study aimed to assess the safety, tolerability, pharmacokinetics, and pharmacodynamics of cinaciguat. Seventy-six healthy volunteers were included in this randomized, placebo-controlled study. Cinaciguat (50-250 microg/h) was administered intravenously for up to 4 hours in a maximum of 6 individuals per dose group. No serious adverse events were reported. Four-hour infusions (50-250 microg/h) decreased diastolic blood pressure and increased heart rate (all P values < .05) versus placebo, without significantly reducing systolic blood pressure (P between 0.07 and 0.56). At higher doses (150-250 microg/h), 4-hour infusions decreased mean arterial pressure and increased plasma cyclic guanosine monophosphate levels (all P values < .05). Pharmacokinetics showed dose-proportionality with low interindividual variability. Plasma concentrations declined below 1.0 microg/L within 30 minutes of cessation of infusion. Cinaciguat had potent cardiovascular effects reducing preload and afterload, warranting further investigation in patients with heart failure.
Ocular Infections: Antibiotics and Bacterial Adhesion on Biomaterials Used in Ocular Surgery (1995)

The in vitro antibacterial activity of ofloxacin, sagamycin and other antibiotics was evaluated against 85 bacterial isolates [coagulase-negative staphylococci (CNS), n = 37, Staphylococcus aureus, n = 28, and Pseudomonas aeruginosa, n = 20] obtained from patients with ocular infections. The antistaphylococcal activity of ofloxacin was quite elevated with a 90% minimal inhibitory concentration (MIC90) of 1.56 mg/l against CNS and S. aureus. Rokitamycin and erythromycin showed a good activity against methicillin-sensitive staphylococci, but were less active than ofloxacin and sagamycin against methicillin-resistant strains (MIC90 > 100 mg/l). Sagamycin was highly effective against staphylococci (MIC90 0.78 mg/l) and appeared to be the most active compound against P. aeruginosa (MIC90 6.25 mg/l), followed by ofloxacin, tobramycin and gentamicin. In a successive part of the study, the adhesive properties of slime-producing staphylococci were tested on biomaterials used in ocular surgery. Intraocular lenses, Silastic sheetings, circling bands and grooved strips showed a high affinity for slime-producing strains, while round silicone sponges were not covered by bacterial biofilm. In the last part of our study, we demonstrated how subMIC levels of ofloxacin increased the adhesion of slime-producing staphylococci. Our data confirmed the excellent activity of ofloxacin and sagamycin against ocular pathogens and the key role of adhesion in promoting colonization and infections of biomaterials.