gebhart/patrepeval huggingface dataset:
Computational and Mass-Spectrometry-Based Workflow for the Discovery and Validation of Missing Human Proteins: Application to Chromosomes 2 and 14 (2015)

In the framework of the C-HPP, our Franco-Swiss consortium has adopted chromosomes 2 and 14, coding for a total of 382 missing proteins (proteins for which evidence is lacking at protein level). Over the last 4 years, the French proteomics infrastructure has collected high-quality data sets from 40 human samples, including a series of rarely studied cell lines, tissue types, and sample preparations. Here we described a step-by-step strategy based on the use of bioinformatics screening and subsequent mass spectrometry (MS)-based validation to identify what were up to now missing proteins in these data sets. Screening database search results (85,326 dat files) identified 58 of the missing proteins (36 on chromosome 2 and 22 on chromosome 14) by 83 unique peptides following the latest release of neXtProt (2014-09-19). PSMs corresponding to these peptides were thoroughly examined by applying two different MS-based criteria: peptide-level false discovery rate calculation and expert PSM quality assessment. Synthetic peptides were then produced and used to generate reference MS/MS spectra. A spectral similarity score was then calculated for each pair of reference-endogenous spectra and used as a third criterion for missing protein validation. Finally, LC-SRM assays were developed to target proteotypic peptides from four of the missing proteins detected in tissue/cell samples, which were still available and for which sample preparation could be reproduced. These LC-SRM assays unambiguously detected the endogenous unique peptide for three of the proteins. For two of these, identification was confirmed by additional proteotypic peptides. We concluded that of the initial set of 58 proteins detected by the bioinformatics screen, the consecutive MS-based validation criteria led to propose the identification of 13 of these proteins (8 on chromosome 2 and 5 on chromosome 14) that passed at least two of the three MS-based criteria. Thus, a rigorous step-by-step approach combining bioinformatics screening and MS-based validation assays is particularly suitable to obtain protein-level evidence for proteins previously considered as missing. All MS/MS data have been deposited in ProteomeXchange under identifier PXD002131.
The Fast Radio Burst FRB 20201124A in a star forming region: constraints to the progenitor and multiwavelength counterparts (2021)

We present the results of a multiwavelength campaign of FRB 20201124A, the third closest repeating fast radio burst recently localized in a nearby (z=0.0978) galaxy. Deep VLA observations led to the detection of quiescent radio emission, also marginally visible in X-rays with Chandra. Imaging at 22 GHz allowed us to resolve the source on a scale of $\gtrsim$ 1 arcsec and locate it at the position of the FRB, within an error of 0.2 arcsec. EVN and e-MERLIN observations sampled small angular scales, from 2 to 100 mas, providing tight upper limits on the presence of a compact source and evidence for diffuse radio emission. We argue that this emission is associated with enhanced star formation activity in the proximity of the FRB, corresponding to a star formation rate of $\approx 10\ {\rm M}_\odot {\rm yr}^{-1}$. The surface star formation rate at the location of FRB 20201124A is two orders of magnitude larger than typically observed in other precisely localized FRBs. Such a high SFR is indicative of this FRB source being a new-born magnetar produced from a SN explosion of a massive star progenitor. Upper limits to the X-ray counterparts of 49 radio bursts observed in our simultaneous FAST, SRT and Chandra campaign are consistent with a magnetar scenario.
S131021 Study on the mechanism elucidation of the bactericidal effect by laser beam irradiation : Measurement of dynamic stress induced by Nd:YAG laser beam irradiation (2012)

In this paper, the measurement of dynamic stress generated in the Ti0_2 suspension induced by Nd:YAG laser beam irradiation is proposed. The dynamic stress generated in the Ti0_2 suspension by using elastic wave propagation in the cylindrical long bar made of aluminum alloy is measured. The laser induced stress intensity is evaluated from the dynamic strain measured by small semiconductor strain gauges. As a result, the dynamic stress induced by laser beam irradiation is depended on powder type and particle diameter. When the peak power is P = 4 kW, the dynamic stress generated in the TiO_2 suspension with a particle size of 0.02 um reached the maximal value, and it was 1100 Pa.
Prevalence of Escherichia coli strains with localized, diffuse, and aggregative adherence to HeLa cells in infants with diarrhea and matched controls (1989)

To determine the possible role of Escherichia coli strains with three different patterns of adherence to HeLa cells in causing diarrhea in infants in São Paulo, Brazil, we studied stool specimens from 100 infants up to 1 year of age with acute diarrheal illnesses and 100 age-matched control infants without recent diarrhea. E. coli with localized adherence to HeLa cells was much more common in patients (23%) than in controls (2%) (P less than 0.0001) and was detected more frequently than rotavirus (19%) was in patients, even though the study was conducted during the coldest months of the year. Most (80%) of the E. coli colonies with localized adherence were of traditional enteropathogenic E. coli serotypes. Little difference was found between patients and controls in the rate of isolation of E. coli with diffuse adherence (31 and 32%, respectively) or aggregative adherence (10 and 8%, respectively). A genetic probe used to detect a plasmid-mediated adhesin which confers expression of localized adherence proved to be 100% sensitive and 99.9% specific in detecting E. coli with localized adherence to HeLa cells. Although E. coli strains with localized adherence have now been shown to be enteric pathogens in several parts of the world, the role of strains showing diffuse adherence and aggregative adherence is still uncertain.
Asphaltenes Precipitation from Crude Oil and Hydrocarbon Media (2006)

The asphaltenes precipitation onset and the precipitation yield were determined for four different crude oil samples. The results confirm that crude oil samples presenting low precipitation onsets effectively present instability and depositional problems in field operations, whereas those with a high onset are stable and do not present separation or precipitation in production operations. It was also confirmed that, as reported in the literature, the onset increased and the amount of solids separated decreased with the molecular weight of the alkane used to induce the precipitation. The same methodology was extended to asphaltenes, resins, and asphaltenes/resins mixtures dissolved in toluene using n-heptane and the ethyl alcohol as nonsolvents to evaluate the influence of the resins fraction on asphaltenes stabilization. The results analyzed using the Hildebrand solubility parameter point out for asphaltenes and resins being a continuum or family of complex molecules with a variation in molecular weight and polarity rather than two fractions containing chemically different compounds. This observation seems to be corroborated by the FTIR results that show similar spectra for asphaltenes separated using different solvents and for the resins fraction.
Flow Cytometry-Assisted Cloning of Specific Sequence Motifs from Complex 16S rRNA Gene Libraries (2004)

A flow cytometry method was developed for rapid screening and recovery of cloned DNA containing common sequence motifs. This approach, termed fluorescence-activated cell sorting-assisted cloning, was used to recover sequences affiliated with a unique lineage within the Bacteroidetes not abundant in a clone library of environmental 16S rRNA genes.
Design of variable loop gains of dual-loop DPLL (1997)

An approach to the derivation of variable loop gain sequences of dual-loop digital phase-locked loop (DPLL) is developed based on some modifications of the Kalman filtering formulation. It is shown that optimal loop gain sequences which are independent of measurement noise statistics can be obtained under a deterministic source model. Computer simulation results demonstrate that the adaptive dual-loop DPLL designed by using the proposed method is more robust to noise variations than the adaptive DPLL of Driessen (see ibid., vol.47, p.673-75, 1994).
Interés del menor y derecho a la educación. Autor: Miguel Ángel Asensio Sánchez (2018)

espanolInteres del menor y derecho a la educacion de Miguel Angel Asensio Sanchez, supone una reflexion juridica sobre la minoria de edad y los derechos fundamentales, siendo un tema complejo, no en lo referente a la titularidad de los derechos sino a su ejercicio y, en concreto, a cual es la capacidad necesaria o exigida para el ejercicio autonomo de los derechos por un menor de edad. Se plantea el grado de autonomia del menor como individuo frente a sus padres o tutores legales, siendo esta autonomia una de las cuestiones fundamentales planteadas en la Ley Organica de Proteccion Jurisdiccional del Menor LO 1/1996, de 15 de enero. Abordando el autor cuestiones como si el ejercicio de los derechos educativos integrantes de la libertad de ensenanza debe perseguir como finalidad propia el interes del menor, o por el contrario, este debe entenderse unicamente como limite del ejercicio de estos derechos v EnglishIn this work, the author Miguel Angel Asensio Sanchez, makes a legal reflection of the minority of age and fundamental rights, being a complex issue, not in relation to the entitlement of rights but to their exercise and, specifically, to what is the necessary or required capacity for the autonomous exercise of rights by a minor. The degree of autonomy of the minor as an individual is considered in relation to their parents or legal guardians, this autonomy being one of the fundamental issues raised in the Organic Law of Jurisdictional Protection of Minors LO 1/1996, of January 15. Considering the author issues as if the exercise of educational rights that are part of the freedom of education must pursue the child's interest as its own purpose, or on the contrary, it should be understood only as a limit to the exercise of these rights. In short, this work, which is structured in six chapters, involves an evaluative reflection on the condition of the child as a subject with rights and its concretion in the educational system.
Preparation and Characterisation of Li‐Al‐glycine Layered Double Hydroxides (LDHs)‐Polymer Nanocomposites (2005)

Abstract LiAl‐Layered Double Hydroxides, containing glycinate anions, have been prepared using LiAlO 2 . The glycine containing LDHs were then exfoliated in chloroform. Dispersions of approximately 0.03 g of the LDH in 15 ml of the solvent were possible. Nanocomposites using the exfoliated LiAl‐glycine LDH and polyethyleneglycol were prepared by adding appropriate amounts of polymer to the LDH‐chloroform dispersion. The clay‐polymer nanocomposites were then characterised using powder X‐ray diffraction. The thermal and mechanical properties of the composites are reported. The results suggest that composites containing individual (exfoliated) LDH layers were obtained with the mechanical and thermal properties of the composites noticeably superior to those of the parent polymer.
Co-Simulation and Validation of Advanced Building Controls with VOLTTRONTM and EnergyPlusTM (2017)

This paper describes a streamlined building controls development process using the VOLTTRONTM platform. The paper introduces a new software agent that enables co-simulation with EnergyPlusTM and accelerates the development process from concept to commissioning. With this new co-simulation capability in VOLTTRON, building control developers have a method to easily design, test, validate, and deploy building applications on a single platform. The paper describes the implementation of the software agent and concludes with a case-study.
Expression, purification, crystallization and preliminary X-ray crystallographic analysis of Zucchini fromDrosophila melanogaster (2012)

PIWI-interacting RNAs (piRNAs) bind PIWI proteins and silence transposons to maintain the genomic integrity of germ cells. Zucchini (Zuc), a phospholipase D superfamily member, is conserved among animals and is implicated in piRNA biogenesis. However, the underlying mechanism by which Zuc participates in piRNA biogenesis remains elusive. Drosophila melanogaster Zuc (DmZuc) was expressed in Escherichia coli, purified and crystallized. X-ray diffraction data were collected to 1.75 Å resolution. The crystal belonged to space group P2(1), with unit-cell parameters a=55.0, b=71.2, c=56.3 Å, β=107.9°.
Strategies in the surgical treatment of type A aortic arch dissection. (2013)

Aortic dissection involving the ascending aorta is a lethal condition, with mortality approaching 60% if surgical intervention is not performed early (1).

Stanford type A acute aortic dissection involves the ascending aorta, aortic arch and a variable extent of the descending thoracic aorta. Identification and resection of the primary intimal tear with re-approximation of the intima and adventitia remains the surgical principle of repair. Despite using this approach, a residual dissection flap persists in the arch and descending thoracic aorta in 64-90% of patients (2-5). This can lead to distal malperfusion in the acute setting (6), with a risk of aneurysm formation and rupture over the long term (7).

Despite the advancement of cardiac surgery techniques, employment of modern cerebral protection strategies, myocardial protection, and aortic graft development, the surgical mortality of these operations, even in centers with a specific interest in aortic surgery, is in the range of 25% (8). In the modern era of cardiac surgery, it is rare to undertake a “common” operation with a mortality of 25% and this serves as a challenge for the cardiac surgery community to improve. In order to reduce this high operative mortality, one first needs to understand the contributing factors.
Molecular Dynamics Simulation of a Polymer Melt with a Nanoscopic Particle (2002)

We perform molecular dynamics simulations of a bead−spring polymer melt surrounding a nanoscopic particle. We explore the effect of the polymer/nanoparticle interactions, surface-to-volume ratio, and boundary conditions on both the structure and dynamics of the polymer melt. We find that the chains near the nanoparticle surface are elongated and flattened and that this effect is independent of the interaction for the range of interactions we study. We show that the glass transition temperature Tg of the melt can be shifted to either higher or lower temperatures by tuning the interactions between polymer and nanoparticle. A gradual change of the polymer dynamics approaching the nanoparticle surface causes the change in the glass transition. The magnitude of the shift is exaggerated by increasing fraction of surface monomers in the system. These behaviors support a “many-layer”-based interpretation of the dynamics. Our findings appear applicable to systems in which surface interactions dominate, including both traditional and nanofilled polymer melts, as well as systems with markedly different geometries, such as ultrathin polymer films. In particular, we show how our results might be compared with those obtained from experimental studies of “bound” polymer.
A purple acidophilic di-ferric DNA ligase from Ferroplasma (2008)

We describe here an extraordinary purple-colored DNA ligase, LigFa, from the acidophilic ferrous iron-oxidizing archaeon Ferroplasma acidiphilum, a di-ferric enzyme with an extremely low pH activity optimum. Unlike any other DNA ligase studied to date, LigFa contains two Fe(3+)-tyrosinate centers and lacks any requirement for either Mg(2+) or K(+) for activity. DNA ligases from closest phylogenetic and ecophysiological relatives have normal pH optima (6.0-7.5), lack iron, and require Mg(2+)/K(+) for activity. Ferric iron retention is pH-dependent, with release resulting in partial protein unfolding and loss of activity. Reduction of the Fe(3+) to Fe(2+) results in an 80% decrease in DNA substrate binding and an increase in the pH activity optimum to 5.0. DNA binding induces significant conformational change around the iron site(s), suggesting that the ferric irons of LigFa act both as structure organizing and stabilizing elements and as Lewis acids facilitating DNA binding at low pH.
Tricyclic Antidepressants-Reply (1979)

<h3>In Reply.—</h3> Dr Cohen-Cole interprets our use of the term "neurotic" as an endorsement of a diagnostic and classification system. We use the terms "neurotic," "reactive," and "minor depressive syndrome" because we believe that they are more easily recognized by nonpsychiatric practitioners than a technical nomenclature that is not only unadopted but is also rapidly evolving and whose intricacies may produce as many problems as solutions. For example, Dr Cohen-Cole invokes the term "major depressive episode." To our knowledge, this term appears nowhere in the<i>Diagnostic and Statistical Manual of Mental Disorders, III</i>. The term "depressive episode" is used to refer to a depressive syndrome that is basically identical to the syndrome we described in the article and the previous paragraph. In the manual, the word "major" is only used to refer to one type of serious depressive episode, a "major depressive disorder," which may occur as a single episode
Antibody Engineering for Optimized Immunotherapy in Alzheimer's Disease (2018)

There are nearly 50 million people with Alzheimer's disease (AD) worldwide and currently no disease modifying treatment is available. AD is characterized by deposits of Amyloid-β (Aβ), neurofibrillary tangles, and neuroinflammation, and several drug discovery programmes studies have focussed on Aβ as therapeutic target. Active immunization and passive immunization against Aβ leads to the clearance of deposits in humans and transgenic mice expressing human Aβ but have failed to improve memory loss. This review will discuss the possible explanations for the lack of efficacy of Aβ immunotherapy, including the role of a pro-inflammatory response and subsequent vascular side effects, the binding site of therapeutic antibodies and the timing of the treatment. We further discuss how antibodies can be engineered for improved efficacy.
Characteristics Comparison of a Conventional and Modified Spoke-Type Ferrite Magnet Motor for Traction Drives of Low-Speed Electric Vehicles (2013)

Rare-earth magnets have been widely employed for traction drive motors of hybrid and electric vehicles (EVs) due to high energy density. Nevertheless, the magnets have critical problems such as unstable supply and high cost. Recently, in order to solve the problems, a variety of motors not using rare-earth materials have been reviewed, such as an induction motor, a switched reluctance motor, and a spoke-type ferrite magnet motor (FMM). In this paper, a modified spoke-type FMM with a novel rotor configuration was presented for a traction motor of low-speed EVs. The characteristics of the modified spoke-type FMM are numerically compared with a conventional spoke-type FMM at the same design condition. Finally, the modified spoke-type FMM is fabricated and tested in order to verify its performance and feasibility.
On the Roles and Regulation of Chondroitin Sulfate and Heparan Sulfate in Zebrafish Pharyngeal Cartilage Morphogenesis (2012)

The present study addresses the roles of heparan sulfate (HS) proteoglycans and chondroitin sulfate (CS) proteoglycans in the development of zebrafish pharyngeal cartilage structures. uxs1 and b3gat3 mutants, predicted to have impaired biosynthesis of both HS and CS because of defective formation of the common proteoglycan linkage tetrasaccharide were analyzed along with ext2 and extl3 mutants, predicted to have defective HS polymerization. Notably, the effects on HS and CS biosynthesis in the respective mutant strains were shown to differ from what had been hypothesized. In uxs1 and b3gat3 mutant larvae, biosynthesis of CS was shown to be virtually abolished, whereas these mutants still were capable of synthesizing 50% of the HS produced in control larvae. extl3 and ext2 mutants on the other hand were shown to synthesize reduced amounts of hypersulfated HS. Further, extl3 mutants produced higher levels of CS than control larvae, whereas morpholino-mediated suppression of csgalnact1/csgalnact2 resulted in increased HS biosynthesis. Thus, the balance of the Extl3 and Csgalnact1/Csgalnact2 proteins influences the HS/CS ratio. A characterization of the pharyngeal cartilage element morphologies in the single mutant strains, as well as in ext2;uxs1 double mutants, was conducted. A correlation between HS and CS production and phenotypes was found, such that impaired HS biosynthesis was shown to affect chondrocyte intercalation, whereas impaired CS biosynthesis inhibited formation of the extracellular matrix surrounding chondrocytes.
Serum Free Cortisol Fraction in Healthy and Septic Neonatal Foals (2011)

Serum free cortisol is impacted by age and illness in the horse. There is no advantage to measuring free over total cortisol in septic foals.
Effect of Ca incorporation on the dielectric nonlinear behavior of (Ba, Ca)TiO3 multi layer ceramic capacitors (2014)

The difference in the dielectric nonlinearity was investigated by contrasting BaTiO3 and (Ba0.925Ca0.075)TiO3 multilayer ceramic capacitors utilizing the first order reversal curve (FORC) distribution based on the Preisach model. Ca incorporation caused a decrease of the dielectric constants in the low field but little differences in the high field region resulting in a steep ac field dependence, which became more significant with the decrease of temperature. Such behavior can be correlated with a decrease of the reversible and an increase of the irreversible FORC distribution near origin by Ca incorporation. These results suggest that Ca incorporation, which is known to cause the asymmetric off-center displacement at Ba-site, has the role of weakly pinning centers that increase the portion of irreversible domain walls that are immobile at low field but can contribute to polarization beyond a threshold field.
Comparison of a Low-Fat Diet to a Low-Carbohydrate Diet on Weight Loss, Body Composition, and Risk Factors for Diabetes and Cardiovascular Disease in Free-Living, Overweight Men and Women (2004)

Overweight and obese men and women (24-61 yr of age) were recruited into a randomized trial to compare the effects of a low-fat (LF) vs. a low-carbohydrate (LC) diet on weight loss. Thirty-one subjects completed all 10 wk of the diet intervention (retention, 78%). Subjects on the LF diet consumed an average of 17.8% of energy from fat, compared with their habitual intake of 36.4%, and had a resulting energy restriction of 2540 kJ/d. Subjects on the LC diet consumed an average of 15.4% carbohydrate, compared with habitual intakes of about 50% carbohydrate, and had a resulting energy restriction of 3195 kJ/d. Both groups of subjects had significant weight loss over the 10 wk of diet intervention and nearly identical improvements in body weight and fat mass. LF subjects lost an average of 6.8 kg and had a decrease in body mass index of 2.2 kg/m2, compared with a loss of 7.0 kg and decrease in body mass index of 2.1 kg/m2 in the LC subjects. The LF group better preserved lean body mass when compared with the LC group; however, only the LC group had a significant decrease in circulating insulin concentrations. Group results indicated that the diets were equally effective in reducing systolic blood pressure by about 10 mm Hg and diastolic pressure by 5 mm Hg and decreasing plasminogen activator inhibitor-1 bioactivity. Blood beta-hydroxybutyrate concentrations were increased in the LC only, at the 2- and 4-wk time points. These data suggest that energy restriction achieved by a very LC diet is equally effective as a LF diet strategy for weight loss and decreasing body fat in overweight and obese adults.