gebhart/patrepeval huggingface dataset:
Evaluation of Gas-Phase Rearrangement and Competing Fragmentation Reactions on Protein Phosphorylation Site Assignment Using Collision Induced Dissociation-MS/MS and MS<sup>3</sup> (2008)

The development of strategies directed toward comprehensive analysis of the phosphoproteome have undoubtedly been facilitated by recent advances in the application of ion trap tandem mass spectrometry-based techniques for routine phosphopeptide identification. However, when multiple potential sites of phosphorylation exist within a phosphorylated peptide sequence, unambiguous characterization of the site of phosphorylation remains a significant challenge. Here, the gas-phase fragmentation reactions of a series of 33 synthetic phospho-serine, -threonine, and -tyrosine peptides containing multiple potential phosphorylation sites have been examined using collision induced dissociation (CID) and multistage tandem mass spectrometry (MS/MS and MS(3)) in a linear quadrupole ion trap. From this study, 15 of the peptides (45%) gave rise to product ions that were formed following initial transfer of a phosphate group from the phosphorylated residue to an unmodified hydroxyl-containing amino acid residue upon CID-MS/MS. The propensity for this rearrangement was found to be highly dependent on the precursor ion charge state and amino acid composition (i.e, proton mobility) of the peptide and was observed predominantly for peptides under "nonmobile" or "partially mobile" protonation conditions. The observation of these rearrangement reactions and/or the lack of product ions that provided definitive evidence for the correct site of phosphorylation, limited the ability to unambiguously assign the correct site of phosphorylation to only 12 of the 33 peptides (36%). Furthermore, the observation of competing fragmentation reactions for the neutral loss of 98 Da from these precursor ions (i.e., the loss of H(3)PO(4) versus the combined losses of HPO(3) and H(2)O) indicates that CID-MS(3) of [M + nH - 98](n+) ions may not be used for unambiguous phosphorylation site localization.
High-Definition Fiber Tractography of the Human Brain (2012)

Our HDFT approach provides an accurate reconstruction of white matter fiber tracts with unprecedented detail in both the normal and pathological human brain. Further studies to validate the clinical findings are needed.
GLP-1 receptor stimulation depresses heart rate variability and inhibits neurotransmission to cardiac vagal neurons (2010)

Glucagon-like peptide 1 (GLP-1) is an incretin hormone released from the gut in response to food intake. Whereas GLP-1 acts in the periphery to inhibit glucagon secretion and stimulate insulin release, it also acts in the central nervous system to mediate autonomic control of feeding, body temperature, and cardiovascular function. Because of its role as an incretin hormone, GLP-1 receptor analogs are used as a treatment for type 2 diabetes. Central or peripheral administration of GLP-1 increases blood pressure and heart rate, possibly by activating brainstem autonomic nuclei and increasing vagus nerve activity. However, the mechanism(s) by which GLP-1 receptor stimulation affects cardiovascular function are unknown. We used the long-lasting GLP-1 receptor agonist Exendin-4 (Ex-4) to test the hypothesis that GLP-1 signalling modulates central parasympathetic control of heart rate.
The <i>trans</i>‐sialidase from the african trypanosome <i>Trypanosoma brucei</i> (2002)

Trypanosoma brucei is the cause of the diseases known as sleeping sickness in humans (T. brucei ssp. gambiense and ssp. rhodesiense) and ngana in domestic animals (T. brucei brucei) in Africa. Procyclic trypomastigotes, the tsetse vector stage, express a surface-bound trans-sialidase that transfers sialic acid to the glycosylphosphatidylinositol anchor of procyclin, a surface glycoprotein covering the parasite surface. Trans-sialidase is a unique enzyme expressed by a few trypanosomatids that allows them to scavenge sialic acid from sialylated compounds present in the infected host. The only enzyme extensively characterized is that of the American trypanosome T. cruzi (TcTS). In this work we identified and characterized the gene encoding the trans-sialidase from T. brucei brucei (TbTS). TbTS genes are present at a small copy number, at variance with American trypanosomes where a large gene family is present. The recombinant TbTS protein has both sialidase and trans-sialidase activity, but it is about 10 times more efficient in transferring than in hydrolysing sialic acid. Its N-terminus contains a region of 372 amino acids that is 45% identical to the catalytic domain of TcTS and contains the relevant residues required for catalysis. The enzymatic activity of mutants at key positions involved in the transfer reaction revealed that the catalytic sites of TcTS and TbTS are likely to be similar, but are not identical. As in the case of TcTS and TrSA, the substitution of a conserved tryptophanyl residue changed the substrate specificity rendering a mutant protein capable of hydrolysing both alpha-(2,3) and alpha-(2,6)-linked sialoconjugates.
Towards a new isolation abstraction for OSGi (2008)

The Open Service Gateway Initiative (OSGi) specification defines a dynamic Java-based service oriented architecture for networked environments such as home service gateways. To provide isolation between different services, it relies on the Java class loading mechanism. While class loaders have many advantages beside isolation, they are poor in protecting the system against malicious or buggy services. In this paper, we propose a new approach for service isolation. It is based on the Java isolate technology, without a task-oriented architecture. Our approach is more tailored to service-oriented architectures and in particular offers a complete isolation abstraction to the OSGi platform. It is currently under development, hence we do not provide in this paper any technical details nor results.
A simplified stochastic model for the aeronautical mobile radio channel (2003)

The aeronautical mobile radio channel is analyzed. A stochastic model for the channel is proposed in terms of the transmission coefficient. The power spectrum and the correlation functions are derived for cases of practical interest. The model is useful for predicting the error rate performance of digital modulation techniques. The results from a flight test showed the validity of the proposed model.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Finding resource-release omission faults in Linux (2011)

The management of the releasing of allocated resources is a continual problem in ensuring the robustness of systems code. Missing resource-releasing operations lead to memory leaks and deadlocks. A number of approaches have been proposed to detect such problems, but they often have a high rate of false positives, or focus only on commonly used functions. In this paper we observe that resource-releasing operations are often found in error-handling code, and that the choice of resource-releasing operation may depend on the context in which it is to be used. We propose an approach to finding resource-release omission faults in C code that takes into account these issues. We use our approach to find over 100 faults in the drivers directory of Linux 2.6.34, with a false positive rate of only 16%, well below the 30% that has been found to be acceptable to developers.
Food additives handbook (1990)

Provides data on some 1,350 food additives, including direct and indirect additives, packaging materials, pesticides, and selected animal drugs. Each additive is covered in a separate alphabetical entry which features physical properties, usage information, occupational restrictions, and toxicologic
Chemical recognition in terahertz time-domain spectroscopy and imaging (2005)

In this paper, we present an overview of chemical recognition with ultrashort THz pulses. We describe the experimental technique and demonstrate how signals for chemical recognition of substances in sealed containers can be obtained, based on the broadband absorption spectra of the substances. We then discuss chemical recognition in combination with THz imaging and show that certain groups of biological substances may give rise to characteristic recognition signals. Finally, we explore the power of numerical prediction of absorption spectra of molecular crystals and illuminate some of the challenges facing state-of-the-art computational chemistry software.
Henri Schœn. — Le Théâtre alsacien chez Noiriel à Strasbourg et Le Théâtre populaire en Alsace. — Fischbacher (1904)

Besson J. Henri Schœn. — Le Théâtre alsacien chez Noiriel à Strasbourg et Le Théâtre populaire en Alsace. — Fischbacher. In: Revue internationale de l'enseignement, tome 48, Juillet-Décembre 1904. pp. 188-189.
Vitamin E deficiency and lipoperoxidation during adult respiratory distress syndrome (1990)

Vitamin E (Vit E) is an important component of the lung's defense against oxidant injury. The aim of this study was to determine a) if adult respiratory distress syndrome (ARDS) was associated with a decrease in Vit E plasma level linked to an enhancement of plasma lipoperoxidation, and b) if this Vit E deficiency might be explained by malnutrition and/or a consumption defect. Vit E, lipoperoxides (LP), total lipids, and fatty acid plasma levels were measured in 12 patients with ARDS (PaO2 less than or equal to 60 Torr with FIO2 0.6 on mechanical ventilation). At the onset of ARDS (T0), the decrease in Vit E plasma level was significant (p less than .001) 7.73 +/- 0.54 (n = 12) vs. 11.46 +/- 0.55 mg/L (n = 7) in the control group (healthy subjects breathing room air). A significant (p less than .05) increase in LP was simultaneously observed (4.12 +/- 0.35 [n = 12] vs. 2.94 +/- 0.30 nmol/ml [n = 17]) in the control group. At T0, LP were inversely correlated with Vit E plasma levels (r = .78, p less than .01). Vit E deficiency was associated with low levels of total plasma lipids (3.68 +/- 0.25 g/L) and plasma cholesterol (0.97 +/- 0.07 g/L). Thus, the Vit E/total lipids ratio (2.18 +/- 0.17 mg/g) was always above the accepted normal limit value for this ratio (0.8 mg/g).(ABSTRACT TRUNCATED AT 250 WORDS)
Chiral Relay: A Novel Strategy for the Control and Amplification of Enantioselectivity in Chiral Lewis Acid Promoted Reactions (2002)

Chiral Lewis acid catalysis has emerged as one of the premiere method to control stereochemistry. Much effort has gone into the design of superior ligands with increasing steric extension to shield distant reactive sites. We report here an alternative and complementary approach based on a "chiral relay". This strategy focuses on the improved design of achiral templates which may relay and amplify the stereochemistry from ligands. The essence of this strategy is that the chiral Lewis acid would effectively convert an achiral template into a chiral non-racemic template. This approach combines the advantages of enantioselective catalysis (substoichiometric amount of the chiral inducer) with the ones of chiral auxiliary control (efficient and predictable stereocontrol).
Cryogels: Freezing unveiled by thawing (2010)

Cryogels are interconnected supermacroporous gels prepared at sub-zero temperatures having applications in various research fields. The process of cryogelation is ideally thought to take place via following steps: phase separation with ice-crystal formation, cross-linking and polymerization followed by thawing of ice-crystals to form an interconnected porous cryogel network. This phenomenon mostly thought as a theoretical concept has now been revealed here in practical terms via data generated by micro-computed tomography (Micro CT). Micro CT is mainly used for characterizing the gel materials in terms of their physical properties like pore size, porosity, strut size, etc., whereas this work has pioneered its role in elucidating the process of cryogel formation.
SodERF3, a Novel Sugarcane Ethylene Responsive Factor (ERF), Enhances Salt and Drought Tolerance when Overexpressed in Tobacco Plants (2008)

The molecular signals and pathways that govern biotic and abiotic stress responses in sugarcane are poorly understood. Here we describe SodERF3, a sugarcane (Saccharum officinarum L. cv Ja60-5) cDNA that encodes a 201-amino acid DNA-binding protein that acts as a transcriptional regulator of the ethylene responsive factor (ERF) superfamily. Like other ERF transcription factors, the SodERF3 protein binds to the GCC box, and its deduced amino acid sequence contains an N-terminal putative nuclear localization signal (NLS). In addition, a C-terminal short hydrophobic region that is highly homologous to an ERF-associated amphiphilic repression-like motif, typical for class II ERFs, was found. Northern and Western blot analysis showed that SodERF3 is induced by ethylene. In addition, SodERF3 is induced by ABA, salt stress and wounding. Greenhouse-grown transgenic tobacco plants (Nicotiana tabacum L. cv. SR1) expressing SodERF3 were found to display increased tolerance to drought and osmotic stress.
Protection of Mice from Lethal Influenza: Evidence that Defective Interfering Virus Modulates the Immune Response and Not Virus Multiplication (1986)

Summary Intranasal administration of defective interfering (DI) influenza virus (A/WSN) ensured the survival of 80% of C3H mice otherwise lethally infected with WSN by the intranasal route, whereas a control group which received β-propiolactone-inactivated DI virus in place of DI virus died at 7.4 days post-infection. DI virus-treated mice developed significantly less lung consolidation than controls although qualitatively the cellular pathology in the two groups was indistinguishable. Surprisingly, in view of the accepted mode of action of DI virus interference, multiplication of infectious virus in the lung, production of viral haemagglutinin (HA) antigen and neuraminidase, and the distribution and amount of viral antigen in cells as shown by immune labelling were unaffected by the presence of active DI virus. Furthermore, assays of lung extracts showed that DI virus was not stimulating significantly greater amounts of interferon than the control inactivated DI virus. An alternative explanation arises from the fact that the pathology of influenza in inbred mice is immune (T lymphocyte)-mediated. Thus, since there is no evidence that DI virus affects virus multiplication we suggest that DI virus is responsible for ameliorating the damaging host responses. Another aspect of the immune response modulated by DI virus was the enhancement of local haemagglutination-inhibiting (HI) antibody in the lung, with peak increases of up to 10-fold over the relevant controls being demonstrated at 5 days after infection. This antibody was presumably complexed to HA antigen in the lung as activity was only demonstrated after elution at low pH. It had no detectable neutralizing activity (< 10% HI: neutralization ratio of convalescent serum) which accounts for the coexistence of local antibody and virus infectivity. Mice infected with virus alone or which received β-propiolactone-inactivated DI virus in addition to a lethal dose of WSN did not develop significant amounts of lung antibody. No differences were seen in serum HI titres. The increased level of antibody could not be attributed to the presence of greater amounts of HA antigen in lungs of mice treated with DI virus, as ELISA showed no significant difference from control preparations. The possibility that the two modulated immune responses are linked through HI antibody blocking access of T cells to cell membrane-borne HA antigen is discussed.
Congenital Club Foot in Children Younger than 24 Months: Decancelous Cuboid Combined with Selective Soft Tissue Release (2012)

Purpose: To evaluate 2 surgical prosedures in treatment of congenital clubfeet in children younger than 24 months. Materials and methods: Data were analyzed on 319 patients (448 feet) from July 1990 to December 2005. Clinical and classification for all patients according to Diméglio. Operated patients were devided into two group: Group1, selective soft tissue release; and Group 2, selective soft tissue release combined with cuboid decancelation. Surgical result were classified according to McKay’s system. Results: There were 103 females (32.3%) and 216 males (67.7%) in this study. There were 192 patients (268 feet) in group 1, 127 patients (180 feet) in group 2. Bilateral involvement was found in 129 patients (40.4%), only the left foot affected in 65 patients (20.4%), and only the right in 125 patients (39.2%). According to the classification of Diméglio Grade II was seen in 32.4%, Grade III in 53,1%, and Grade IV in 14.5%. Postoperatively, in group 1, we got excellent result in 29.1%, good result in 49.2%, fair result in 18.3%, and poor result in 3.4%. In group 2, we attained excellent result in 50.6%, good result in 42.2%, fair result in 6.1% and poor result in 1.1%. The good to excellent result in group 2 was significantly higher in group 1 with p = 0.000042. There was no failure in both groups. Residual adduction of forefoot in frontal plane was seen in 78.0% of group 1, and 10.6% of group 2, which was also statistically significant with p ~ 0. Conclusion: Generally speaking, the procedure of selective soft tissue releases combined with cuboid decancelation showed an outstanding result with good to excellent result of 92.8%. Surgical procedure is simple, safe, and applicable for all patients with clubfeet’s deformyties.
A Model for Multiphase (Gas-Water-Oil) Stratified Flow in Horizontal Pipelines (1994)

ABSTRACT A mechanistic model for gas-liquid-liquid systems has been developed. Given the superficial velocities of the constituent phases and their physical properties, and the pipe diameter the corresponding oil and water film thicknesses in three phase stratified flow canbe predicted. Experimental data has been obtained for gas velocities upto 7 m/s. The model predictions agree well with the experimental data.
Chronic activation of the innate immune system may underlie the metabolic syndrome (2001)

Better understanding of the role of the innate immune system in these diseases may lead to important advances in the prediction and management of diabetes and cardiovascular disease.
Sensitivity of Escherichia coli to Viral Nucleic Acid VIII. Idiosyncrasy of Ca2+-dependent Competence for DNA* (1974)

Using øA replicative-form DNA (RF), the properties of the calcium-dependent trans-fection system were investigated in detail. Calcium ions seem to induce preferential uptake of double-stranded DNA by the treated bacteria, rather than causing nonspecific or irreversible increase in the cellular permeability. In this system, Mg2+ was ineffective as a substitute for Ca2+. Transfection does not take place when cells suitably pretreated with Ca2+ are mixed with DNA in media deficient in the cation. In 50mM CaCl2, viral DNA can infect competent cells at 0°C. The yield of transfectants decreased markedly if the Ca2+-treated bacteria and DNA were mixed at temperatures, higher than 20°C and plated directly. Efficient transfection, however, occurred when DNA-cell mixtures preincubated at higher temperatures were plated after quenching at 0°C. Cells pretreated with EDTA did not develop any competence upon subsequent Ca2+ treatment, suggesting possible involvement of surface lipopolysaccharide and/or lipoprotein in the interaction with DNA. Dialyzed supernatant obtained from EDTA-cell mixture inhibited the transfection. The Ca2+-dependent transfection is inhibited by low concentrations of phosphate and is very sensitive to ionic detergents such as. cetyltrimethylammonium bromide or sodium dodecyl sulfate. Double-stranded hetero-logous DNA considerably inhibits RF infection, while the inhibitory effect of single-stranded DNA or RNA is relatively small. The infection occurs in the presence of certain metabolic inhibitors such as dinitrophenol or sodium azide. These results suggest that the Ca2+-dependent uptake of DNA is physicochemical or at least energy-independent. The competence level of bacterial mutants deficient in phospholipase A was as high as that of wild-type cells. The effect of culture conditions such as growth phase or temperature was also examined. Based on these results, the mechanism of Ca2+-dependent competence was discussed with particular reference to liquid crystallization of the cell envelope lipids.
Biotic and Abiotic Disappearance of Four PAH Compounds from Flooded Soil under Various Redox Conditions (1992)

Biotic and abiotic disappearance, mainly in terms of biodegradation and volatilisation respectively, of flooded soil contaminated with acenaphthene, acenaphthylene, fluorene and anthracene, was studied in erlenmeyer flasks and in bench-scale bioreactors. The erlenmeyer experiments were conducted under four different redox conditions. Disappearance kinetics followed zero order. Under aerobic and denitrifying environments, biodegradation of all four compounds occurred; the rates observed ranged from 0.38 to 0.53 ppm/day for the aerobic environment and from 0.29 to 0.35 ppm/day for the denitrifying one. However, no significant biodegradation occurred under the sulphate-reducing nor methanogenic environments. Aerobic abiotic losses were very significant; the ratio of the volatilisation to the biodegradation rates ranged from 2.4 to 3.6. The ratio of the aerobic to the denitrifying volatilisation rates ranged from 5.0 to 10.1. In the light of these results, the denitrifying environment was chosen for a further experiment to investigate the performance of a bench-scale bioreactor. Results showed that by enlarging the scale of the bioreactor approximately 8 times and simultaneously reducing the mixing intensity of the soil/water system, the biodegradation rates remained virtually unchanged. This study suggests that the denitrifying environment could play an important role in the development of an effective, economical and environmentally safe decontamination technology for treating PAH-contaminated soils.
THz local oscillator technology (2004)

The last decade has seen a number of technological advancements that have now made it possible to implement fully solid state local oscillator chains up to 2 THz. These chains are composed of cascaded planar multiplier stages that are pumped with W-band high power sources. The high power W-band sources are achieved by power combining MMIC amplifiers and can provide in access of 150 mW with about 10% bandwidth. Planar diode technology has also enabled novel circuit topologies that can take advantage of the high input power and demonstrate significant efficiencies well into the THz range. Cascaded chains to 1.9 THz have now been demonstrated with enough output power to successfully pump hot-electron bolometer mixers in this frequency range. An overview of the current State-of-the-Art of the local oscillator technology will be presented along with highlighting future trends and challenges.
Das stufenweise erfolgende Vorgehen bei der Projektabwicklung mit Hilfe der 6-Stufen-Methode der Systemplanung (1976)

Die bisherigen Ausführungen zeigen schon, daß die Formulierung der Planungsaufgabe keinesfalls einfach ist, vor allem deshalb nicht, weil in einem sehr frühen Stadium von Schätzungen und Richtwerten ausgegangen werden muß.