gebhart/patrepeval huggingface dataset:
Splanchnic nerve stimulation inhibits duodenal HCO3- secretion in the rat (1988)

Sympathoadrenergic inhibition of HCO3- secretion by the duodenal mucosa was studied in chloralose anesthetized rats. Duodenal HCO3- secretion was measured in situ by pH-stat titration. Direct efferent electrical stimulation of the cut splanchnic nerves (10 Hz, supramaximal intensity) inhibited the duodenal alkaline output by approximately 50%. This inhibitory response was blocked by the administration of either the adrenolytic agent guanethidine or the alpha 2-adrenoceptor antagonist yohimbine. However, neither the alpha 1-adrenoceptor antagonist prazosin nor the beta-adrenoceptor antagonist propranolol blocked the response to splanchnic nerve stimulation. The present data suggest that electrical splanchnic nerve stimulation inhibits duodenal HCO3- secretion via activation of adrenergic nerve fibers and alpha 2-adrenoceptors within the peripheral nervous system.
Hydrogen plasma etching of GaAs oxide (1981)

Hydrogen plasma has been used to etch native-grown GaAs oxide on GaAs substrates. It is found that the rate of etching increases with gas pressure (in the range 10–300 μ) and the rf power (in the range 10–400 W) of the discharge. A typical etch rate of ≊20 Å/sec can be easily achieved. The selectivity (determined by scanning electron microscopy) of the oxide etch over the substrate is ≊2. An etch mechanism is proposed, and the use of hydrogen plasma for surface preparation of GaAs and the etching of oxides on other semiconductor materials will be discussed.
Physical Properties of Ice Cream Containing Milk Protein Concentrates (2005)

Two milk protein concentrates (MPC, 56 and 85%) were studied as substitutes for 20 and 50% of the protein content in ice cream mix. The basic mix formula had 12% fat, 11% nonfat milk solids, 15% sweetener, and 0.3% stabilizer/emulsifier blend. Protein levels remained constant, and total solids were compensated for in MPC mixes by the addition of polydextrose. Physical properties investigated included apparent viscosity, fat globule size, melting rate, shape retention, and freezing behavior using differential scanning calorimetry. Milk protein concentrate formulations had higher mix viscosity, larger amount of fat destabilization, narrower ice melting curves, and greater shape retention compared with the control. Milk protein concentrates did not offer significant modifications of ice cream physical properties on a constant protein basis when substituted for up to 50% of the protein supplied by nonfat dry milk. Milk protein concentrates may offer ice cream manufacturers an alternative source of milk solids non-fat, especially in mixes reduced in lactose or fat, where higher milk solids nonfat are needed to compensate other losses of total solids.
Mechanical regulation of cardiac myocyte protein turnover and myofibrillar structure (1996)

Mechanical forces play an essential role in regulating the synthesis and assembly of contractile proteins into the sarcomeres of cardiac myocytes. To examine if physical forces might also regulate the turnover of contractile proteins at a posttranslational site of control, beating and nonbeating neonatal cardiac myocytes (NCM) were subjected to a 5% static stretch. The L-type calcium channel blocker nifedipine (12 microM) was used to inhibit contraction. Pulse-chase biosynthetic labeling experiments demonstrated that contractile arrest accelerated the loss of isotopic tracer from the total myofibrillar protein fraction, myosin heavy chain (MHC), and actin, but not desmin. Myofibrillar abnormalities developed in parallel with these metabolic changes. A 5% static load appeared to partially stabilize myofibrillar structure in nonbeating NCM and suppressed the loss of isotopic tracer from the total myofibrillar protein fraction, MHC, and actin in beating and nonbeating NCM. Contractile activity and/or a static stretch promoted the accumulation of MHC, actin, and desmin. Applying a static load to myocytes that lacked preexisting myofibrils did not promote the assembly of sarcomeres or alter protein turnover. These data indicate that the turnover of MHC and actin is correlated with the organizational state of the myofibrillar apparatus.
A Common Origin for B-1a and B-2 Lymphocytes in Clonal Pre- Hematopoietic Stem Cells (2017)

Recent evidence points to the embryonic emergence of some tissue-resident innate immune cells, such as B-1a lymphocytes, prior to and independently of hematopoietic stem cells (HSCs). However, whether the full hematopoietic repertoire of embryonic HSCs initially includes these unique lineages of innate immune cells has been difficult to assess due to lack of clonal assays that identify and assess HSC precursor (pre-HSC) potential. Here, by combining index sorting of single embryonic hemogenic precursors with in vitro HSC maturation and transplantation assays, we analyze emerging pre-HSCs at the single-cell level, revealing their unique stage-specific properties and clonal lineage potential. Remarkably, clonal pre-HSCs detected between E9.5 and E11.5 contribute to the complete B cell repertoire, including B-1a lymphocytes, revealing a previously unappreciated common precursor for all B cell lineages at the pre-HSC stage and a second embryonic origin for B-1a lymphocytes.
Tracheal antimicrobial peptide, a cysteine-rich peptide from mammalian tracheal mucosa: peptide isolation and cloning of a cDNA. (1991)

Extracts of the bovine tracheal mucosa have an abundant peptide with potent antimicrobial activity. The 38-amino acid peptide, which we have named tracheal antimicrobial peptide (TAP), was isolated by a sequential use of size-exclusion, ion-exchange, and reverse-phase chromatographic fractionations using antimicrobial activity as a functional assay. The yield was approximately 2 micrograms/g of wet mucosa. The complete peptide sequence was determined by a combination of peptide and cDNA analysis. The amino acid sequence of TAP is H-Asn-Pro-Val-Ser-Cys-Val-Arg-Asn-Lys-Gly-Ile-Cys-Val-Pro-Ile-Arg-Cys-Pr o- Gly-Ser-Met-Lys-Gln-Ile-Gly-Thr-Cys-Val-Gly-Arg-Ala-Val-Lys-Cys-Cys-Arg- Lys-Lys - OH. Mass spectral analysis of the isolated peptide was consistent with this sequence and indicated the participation of six cysteine residues in the formation of intramolecular disulfide bonds. The size, basic charge, and presence of three intramolecular disulfide bonds is similar to, but clearly distinct from, the defensins, a well-characterized class of antimicrobial peptides from mammalian circulating phagocytic cells. The putative TAP precursor is predicted to be relatively small (64 amino acids), and the mature peptide resides at the extreme carboxyl terminus and is bracketed by a short putative propeptide region and an inframe stop codon. The mRNA encoding this peptide is more abundant in the respiratory mucosa than in whole lung tissue. The purified peptide had antibacterial activity in vitro against Escherichia coli, Staphylococcus aureus, Klebsiella pneumonia, and Pseudomonas aeruginosa. In addition, the peptide was active against Candida albicans, indicating a broad spectrum of activity. This peptide appears to be, based on structure and activity, a member of a group of cysteine-rich, cationic, antimicrobial peptides found in animals, insects, and plants. The isolation of TAP from the mammalian respiratory mucosa may provide insight into our understanding of host defense of this vital tissue.
Role of SVP in the control of flowering time by ambient temperature in Arabidopsis (2007)

Plants must perceive and rapidly respond to changes in ambient temperature for their successful reproduction. Here we demonstrate that Arabidopsis SHORT VEGETATIVE PHASE (SVP) plays an important role in the response of plants to ambient temperature changes. The loss of SVP function elicited insensitivity to ambient temperature changes. SVP mediates the temperature-dependent functions of FCA and FVE within the thermosensory pathway. SVP controls flowering time by negatively regulating the expression of a floral integrator, FLOWERING LOCUS T (FT), via direct binding to the CArG motifs in the FT sequence. We propose that this is one of the molecular mechanisms that modulate flowering time under fluctuating temperature conditions.
Pseudomonas aeruginosa -Plant Root Interactions. Pathogenicity, Biofilm Formation, and Root Exudation (2004)

Pseudomonas aeruginosa is an opportunistic human pathogen capable of forming a biofilm under physiological conditions that contributes to its persistence despite long-term treatment with antibiotics. Here, we report that pathogenic P. aeruginosa strains PAO1 and PA14 are capable of infecting the roots of Arabidopsis and sweet basil (Ocimum basilicum), in vitro and in the soil, and are capable of causing plant mortality 7 d postinoculation. Before plant mortality, PAO1 and PA14 colonize the roots of Arabidopsis and sweet basil and form a biofilm as observed by scanning electron microscopy, phase contrast microscopy, and confocal scanning laser microscopy. Upon P. aeruginosa infection, sweet basil roots secrete rosmarinic acid (RA), a multifunctional caffeic acid ester that exhibits in vitro antibacterial activity against planktonic cells of both P. aeruginosa strains with a minimum inhibitory concentration of 3 microg mL(-1). However, in our studies RA did not attain minimum inhibitory concentration levels in sweet basil's root exudates before P. aeruginosa formed a biofilm that resisted the microbicidal effects of RA and ultimately caused plant mortality. We further demonstrated that P. aeruginosa biofilms were resistant to RA treatment under in vivo and in vitro conditions. In contrast, induction of RA secretion by sweet basil roots and exogenous supplementation of Arabidopsis root exudates with RA before infection conferred resistance to P. aeruginosa. Under the latter conditions, confocal scanning laser microscopy revealed large clusters of dead P. aeruginosa on the root surface of Arabidopsis and sweet basil, and biofilm formation was not observed. Studies with quorum-sensing mutants PAO210 (DeltarhlI), PAO214 (DeltalasI), and PAO216 (DeltalasI DeltarhlI) demonstrated that all of the strains were pathogenic to Arabidopsis, which does not naturally secrete RA as a root exudate. However, PAO214 was the only pathogenic strain toward sweet basil, and PAO214 biofilm appeared comparable with biofilms formed by wild-type strains of P. aeruginosa. Our results collectively suggest that upon root colonization, P. aeruginosa forms a biofilm that confers resistance against root-secreted antibiotics.
Abstract 174: Role of Cardiomyocyte-Localized Nuclear Factor (NF)-κB in Diet-Induced Diabetic Cardiomyopathy (2014)

Role of Inflammatory signaling in the development of obesity- and type 2 diabetes (T2D)-associated cardiomyopathy remains unclear. We hypothesized that cardiomyocyte-specific inflammatory activation, independent of systemic inflammation, is sufficient for the genesis of diabetic cardiomyopathy. Wild-type (WT) and transgenic (Tg) C57BL/6 mice with myocyte-restricted overexpression of phosphorylation-resistant IκBα (IκBαS32A,S36A) were fed a high fat (HFD, 45% kcal fat) or control diet (CD, 10% kcal fat) for 28 weeks to induce obesity and T2D. These Tg mice exhibit attenuated NF-kB activation, a central regulator of inflammation. After 28 weeks of feeding, WT HFD mice exhibited increased body weight, hyperglycemia, hyperinsulinemia, insulin resistance, and glucose intolerance. In contrast, although HFD-fed Tg mice exhibited significantly (p &lt; 0.05) increased body weight, the mice still maintained normal fasting blood glucose, insulin levels, and insulin sensitivity compared to CD Tg mice, indicating absence of overt T2D. Echocardiography revealed that both HFD-fed WT and Tg mice developed concentric left ventricular (LV) hypertrophy with increased septal and posterior wall thickness, decreased LV end-diastolic diameter and had unchanged LV ejection fraction suggesting development of LV hypertrophy in both strains regardless of the severity of the metabolic disorder. Analysis of mononuclear phagocyte cell profiles revealed similar trends in WT and IκB Tg mice. HFD fed mice had higher levels of pro-inflammatory (CD11b+Ly6chi) and anti-inflammatory (CD11b+Ly6clo) monocytes in the blood, heart, spleen and adipose tissue compared to CD fed mice. Analysis of antigen presenting cells indicated that HFD fed mice in both genotypes had significantly increased levels of both classical (CD11c+CD45R–) and plasmacytoid (CD11cintCD45R+) dendritic cells in blood, heart, spleen and adipose tissues compared to respective CD fed mice. Thus, we conclude that cardiomyocyte inflammation is central to the development of metabolic abnormalities related to obesity, whereas neither cardiomyocyte-specific nor systemic insulin resistance is required for the development of the hypertrophic cardiomyopathic phenotype.
Regulated hypothermia in the hypothyroid rat induced by administration of propylthiouracil (1997)

Propylthiouracil (PTU), an antithyroidal drug that reduces serum L-thyroxine (T4) and 3,5,3'-triiodothyronine (T3), is presumed to lower core temperature (T0) by impairing metabolic thermogenesis. However, it is not understood why PTU-treated animals cannot use behavioral and other thermoeffectors to maintain normal Tc. Male rats were administered PTU in drinking water (0.05 mg/ml) while the following parameters were measured: 1) Tc and motor activity (MA) recorded by radiotelemetry for 24 h at ambient temperatures (Ta) of 10-30 degrees C; 2) selected Ta, MA, and Tc in a temperature gradient; and 3) Tc, MA, and grooming behavior during exposure to heat stress (TH = 34.5 degrees C) for 2 h. PTU reduced serum levels of T4, and T3 by 95 and 60%, respectively. Tc decreased after 3 days of PTU treatment; a 0.5 degree C decrease in Tc persisted throughout the PTU treatment. PTU rats exposed to Ta of 10-30 degrees C maintained a consistent hypothermic Tc during the light phase; however, a deficit in the stability of Tc at night was noted during exposure to 10 degrees C. In the temperature gradient, PTU rats selected warmer Ta, but their Tc was maintained at the same hypothermic levels as observed at fixed Ta values of 15-30 degrees C. Heat stress caused Tc of control rats to increase to 39 degrees C, whereas Tc of the PTU rats was maintained below 38 degrees C. The regulation of Tc at hypothermic levels over a wide range of Ta values and when rats were housed in a temperature gradient indicates that chronic PTU induces a state of regulated hypothermia.
Disruption of microtubules in living cells by tyrphostin AG-1714 (2000)

Tyrphostin AG-1714 and several related molecules with the general structure of nitro-benzene malononitrile (BMN) disrupt microtubules in a large variety of cultured cells. This process can be inhibited by the stabilization of microtubules with taxol or by pretreatment of the cells with pervanadate, which inhibits tyrosine phosphatases and increases the overall levels of phosphotyrosine in cells. Unlike other microtubule-disrupting drugs such as nocodazole or colchicine, tyrphostin AG-1714 does not interfere with microtubule polymerization or stability in vitro, suggesting that the effect of this tyrphostin on microtubules is indirect. These results imply an involvement of protein tyrosine phosphorylation in the regulation of overall microtubule dynamics. Tyrphostins of AG-1714 type could thus be powerful tools for the identification of such microtubule regulatory pathways.
Backtracking intrusions (2003)

Analyzing intrusions today is an arduous, largely manual task because system administrators lack the information and tools needed to understand easily the sequence of steps that occurred in an attack. The goal of BackTracker is to identify automatically potential sequences of steps that occurred in an intrusion. Starting with a single detection point (e.g., a suspicious file), BackTracker identifies files and processes that could have affected that detection point and displays chains of events in a dependency graph. We use BackTracker to analyze several real attacks against computers that we set up as honeypots. In each case, BackTracker is able to highlight effectively the entry point used to gain access to the system and the sequence of steps from that entry point to the point at which we noticed the intrusion. The logging required to support BackTracker added 9% overhead in running time and generated 1.2 GB per day of log data for an operating-system intensive workload.
Temporally Scalable Visual SLAM using a Reduced Pose Graph (2012)

In this paper, we demonstrate a system for temporally scalable visual SLAM using a reduced pose graph representation. Unlike previous visual SLAM approaches that maintain static keyframes, our approach uses new measurements to continually improve the map, yet achieves efficiency by avoiding adding redundant frames and not using marginalization to reduce the graph. To evaluate our approach, we present results using an online binocular visual SLAM system that uses place recognition for both robustness and multi-session operation. Additionally, to enable large-scale indoor mapping, our system automatically detects elevator rides based on accelerometer data. We demonstrate long-term mapping in a large multi-floor building, using approximately nine hours of data collected over the course of six months. Our results illustrate the capability of our visual SLAM system to map a large are over extended period of time.
Oxygen Sensing, Hypoxia-Inducible Factor-1 and the Regulation of Mammalian Gene Expression (1998)

A great many aspects of the anatomy and physiology of large animals are constrained by the need to match oxygen supply to cellular metabolism and appear likely to involve the regulation of gene expression by oxygen. Some insight into possible underlying mechanisms has been provided by studies of erythropoietin, a haemopoietic growth factor which stimulates red cell production in response to hypoxia. Studies of hypoxia-inducible cis-acting sequences from the erythropoietin gene have led to the recognition of a widespread transcriptional response to hypoxia based on the activation of a DNA-binding complex termed hypoxia-inducible factor-1 (HIF-1). Perturbation of the transcriptional response by particular transition metal ions, iron chelators and certain redox-active agents have suggested a specific oxygen sensing mechanism, perhaps involving a haem protein in a flavoprotein/cytochrome system. In addition to erythropoietin, HIF-1-responsive genes include examples with functions in cellular energy metabolism, iron metabolism, catecholamine metabolism, vasomotor control and angiogenesis, suggesting an important role in the coordination of oxygen supply and cellular metabolism. In support of this, we have demonstrated an important role for HIF-1 in tumour angiogenesis. HIF-1 itself consists of a heterodimer of two basic-helix-loop-helix proteins of the PAS family, termed HIF-1alpha and HIF-1beta, although other closely related members of this family may also contribute to the response to hypoxia. We have fused domains of HIF-1 genes to heterologous transcription factors to assay for regulatory function. These experiments have defined several domains in HIF-1alpha which can independently confer the hypoxia-inducible property, and they suggest a mechanism of HIF-1 activation in which post-translational activation/derepression of HIF-1alpha is amplified by changes in HIF-1alpha abundance most probably arising from suppression of proteolytic breakdown. Pursuit of the mechanism(s) underlying these processes should ultimately lead to better definition of the oxygen-sensing process.
BIOBIBLIOMETRICS: INFORMATION RETRIEVAL AND VISUALIZATION FROM CO-OCCURRENCES OF GENE NAMES IN MEDLINE ABSTRACTS (1999)

Successful information retrieval from biomedical literature databases is becoming increasingly difficult. We have developed a prototype system for retrieving and visualizing information from literature and genomic databases using gene names. The premise of our work is that, if two genes have a related biological function, the co-occurrence of two gene names (or aliases of those genes) within the biomedical literature is more likely. From a collection of Medline documents, we have extracted the number of co-occurrences of every pair of Saccharomyces cerevisiae genes. The query is automatically conflated to include gene aliases as well. In addition, the retrieved document set can be filtered by the user with a MeSH term. From this co-occurrence data we construct a matrix that contains dissimilarity measurements of every pair of genes, based on their joint and individual occurrence statistics. A graph is generated from this matrix, with node and edge inclusion being determined by a user-defined threshold. Nodes of the graph represent genes, while edge lengths are a function of the occurrence of the two genes within the literature. Nodes can be hypertext-linked to sequence databases, while edges are linked to those Medline documents that generated them. The system is a tool for efficiently exploring the biomedical information landscape and may act as a inference network.
Hypercapnia and Ventilatory Periodicity in Obstructive Sleep Apnea Syndrome (2002)

Prevention of acute hypercapnia during obstructive events in obstructive sleep apnea requires a balance between carbon dioxide (CO(2)) loading during the event and CO(2) unloading in the interevent period. Earlier studies have demonstrated that acute CO(2) retention may occur despite high interevent ventilation when the interevent duration is short relative to the duration of the preceding event. The present study examines the relationship between apnea and interapnea durations and relates this assessment of ventilatory periodicity to the degree of chronic hypercapnia in subjects with severe sleep apnea. A total of 18 subjects with sleep apnea (> 40 apnea/hour; chronic awake Pa(CO2) 36-62 mm Hg) and without underlying lung disease underwent polysomnography. For each event, apnea duration, interapnea duration, and apnea/interapnea duration ratio were determined. No relationship was observed between chronic Pa(CO2) and mean apnea or interapnea duration (p > 0.1). However, Pa(CO2) was directly related to apnea/interapnea duration ratio (r = 0.48; p < 0.05) such that with increasing chronic hypercapnia the interapnea duration shortens relative to the apnea duration. The present study suggests that control of the interapnea ventilatory duration relative to the duration of the preceding apnea, is an important component of the integrated ventilatory response to CO(2) loading during apnea and may contribute toward the development and/or maintenance of chronic hypercapnia in obstructive sleep apnea/hypopnea syndrome.
Direct metallation of thienopyrimidines using a mixed lithium–cadmium base and antitumor activity of functionalized derivatives (2009)

A series of thieno[2,3-d]- and thieno[3,2-d]pyrimidines have been easily synthesized using as key step a deproto-cadmiation-trapping sequence. Some of the compounds thus synthesized were screened for anticancer (cytotoxic) activities, and (S)-2-(6-iodo-2-phenylthieno[2,3-d]pyrimidin-4-ylamino)-3-phenylpropanoic acid proved to have a significant activity towards liver, human breast and cervix carcinoma cell lines.
Highly Enantioselective Phenylacetylene Addition to Benzaldehyde Catalyzed by Chiral Tridentate Ligand (2004)

Development of new or improved methods for the asymmetric preparation of chiral propargylic alcohols has gained considerable significance during the past years because they are useful building blocks for the synthesis of many biologically active compounds and natural products.[1] A series of chiral tridentate ligands were conveniently synthesized from amino acids with good yields (Scheme 1).[2] A preliminary study of the enantioselective alkynylation of benzaldehyde catalyzed by this chiral tridentate ligand was carried out and up to 83% ee of chiral propargyl alcohols was obtained (Table 1 ). A further investigation of the tridentate ligand is currently underway.……