Miracle-dz/UniFAR-FTUs huggingface dataset:
A functional classification scheme for beta-lactamases and its correlation with molecular structure

A classification scheme for b-lactamases based on functional characteristics is presented. Three major groups of enzymes are defined by their substrate and inhibitor profiles: group 1 cephalosporinases that are not well inhibited by clavulanic acid; group 2 penicillinases, cephalosporinases, and broadspectrum b-lactamases that are generally inhibited by active site-directed b-lactamase inhibitors; and the group 3 metallob-lactamases that hydrolyze penicillins, cephalosporins, and carbapenems and that are poorly inhibited by almost all b-lactam-containing molecules. Functional characteristics have been correlated with molecular structure in a dendrogram for those enzymes with known amino acid sequences. b-Lactamases (EC 3.5.2.6) have been designated by the Nomenclature Committee of the International Union of Biochemistry as ‘‘enzymes hydrolysing amides, amidines and other CON bonds . separated on the basis of the substrate: . cyclic amides’’ (323). These enzymes are the major cause of bacterial resistance to b-lactam antibiotics and have been the subject of extensive microbiological, biochemical, and genetic investigations. Investigators have described more than 190 unique bacterial proteins with the ability to interact with the variety of b-lactam-containing molecules that can serve as sub-
A communication micro-kernel for implementing object-oriented programming on closely coupled distributed architectures

Within the framework of distributed object-oriented programming, this paper illustrates the main features of a communication micro-kernel able to perform, in a transparent way, both local and remote communications among objects located on a network of closely coupled microcomputers. The communication micro-kernel allows one to address an object by specifying its virtual location, which usually corresponds to a set of microcomputers considered as a whole. By default, an object is allowed to migrate within the bounds of a given virtual location; hence, any migration activity may occur without overloading the network with broadcast messages. As a high-level environment, a non-standard CLOS-like interpreter, enhanced with message-passing capabilities, has been defined and used to test the communication micro-kernel. Due to the virtualization capabilities provided by such an environment, both an application and the network where the application is intended to be run can be decomposed into several layers and then merged together, thus making it possible to meet hardware and software requirements at a suitable level of abstraction. We believe that the described communication micro-kernel will turn out to be very useful in building adaptive systems and in improving their load-balancing by dynamically performing object/method migration. © 1999 John Wiley & Sons, Ltd.
Calsequestrin content and SERCA determine normal and maximal Ca2+ storage levels in sarcoplasmic reticulum of fast‐ and slow‐twitch fibres of rat

Whilst calsequestrin (CSQ) is widely recognized as the primary Ca2+ buffer in the sarcoplasmic reticulum (SR) in skeletal muscle fibres, its total buffering capacity and importance have come into question. This study quantified the absolute amount of CSQ isoform 1 (CSQ1, the primary isoform) present in rat extensor digitorum longus (EDL) and soleus fibres, and related this to their endogenous and maximal SR Ca2+ content. Using Western blotting, the entire constituents of minute samples of muscle homogenates or segments of individual muscle fibres were compared with known amounts of purified CSQ1. The fidelity of the analysis was proven by examining the relative signal intensity when mixing muscle samples and purified CSQ1. The CSQ1 contents of EDL fibres, almost exclusively type II fibres, and soleus type I fibres [SOL (I)] were, respectively, 36 ± 2 and 10 ± 1 μmol (l fibre volume)−1, quantitatively accounting for the maximal SR Ca2+ content of each. Soleus type II [SOL (II)] fibres (∼20% of soleus fibres) had an intermediate amount of CSQ1. Every SOL (I) fibre examined also contained some CSQ isoform 2 (CSQ2), which was absent in every EDL and other type II fibre except for trace amounts in one case. Every EDL and other type II fibre had a high density of SERCA1, the fast‐twitch muscle sarco(endo)plasmic reticulum Ca2+‐ATPase isoform, whereas there was virtually no SERCA1 in any SOL (I) fibre. Maximal SR Ca2+ content measured in skinned fibres increased with CSQ1 content, and the ratio of endogenous to maximal Ca2+ content was inversely correlated with CSQ1 content. The relative SR Ca2+ content that could be maintained in resting cytoplasmic conditions was found to be much lower in EDL fibres than in SOL (I) fibres (∼20 versus >60%). Leakage of Ca2+ from the SR in EDL fibres could be substantially reduced with a SR Ca2+ pump blocker and increased by adding creatine to buffer cytoplasmic [ADP] at a higher level, both results indicating that at least part of the Ca2+ leakage occurred through SERCA. It is concluded that CSQ1 plays an important role in EDL muscle fibres by providing a large total pool of releasable Ca2+ in the SR whilst maintaining free [Ca2+] in the SR at sufficiently low levels that Ca2+ leakage through the high density of SERCA1 pumps does not metabolically compromise muscle function.
Comfort and Energy Efficiency Recommendations for Net Zero Energy Buildings

A major advantage of the Net Zero Energy Building (Net ZEB) approach is claimed to be the absence of energy performance indicators, hence avoiding the need to set internationally agreed limits. Nevertheless, if the rationale is to endorse the design of environmentally friendly buildings that promote sustainable development, then reasonably strict requirements on energy efficiency should be satisfied while providing high levels of indoor environmental quality and consequent users comfort. Otherwise, the risk is that poorly designed buildings could achieve the definition of Net ZEB simply by means of oversized generation systems. The purpose of this paper is to provide an overview of existing international standards and/or design best practices based on comfort and energy efficiency requirements that can be taken as general recommendations for the design of Net ZEBs.
Progress on the Development of the Nb3Sn 11T Dipole for the High Luminosity Upgrade of LHC

The high-luminosity large hadron collider (LHC) project at CERN entered into the production phase in October 2015 after the completion of the design study phase. In the meantime, the development of the 11 T dipole needed for the upgrade of the collimation system of the machine made significant progress with very good performance of the first two-in-one magnet model of 2-m length made at CERN. The 11 T dipole, which is more powerful than the current main dipoles of LHC, can be made shorter with an equivalent integrated field. This will allow creating space for the installation of additional collimators in specific locations of the dispersion suppressor regions. Following tests carried out during heavy ions runs of LHC in the end of 2015, and a more recent review of the project budget, the installation plan for the 11 T dipole was revised. Consequently, one 11 T dipole full assembly containing two 11 T dipoles of 5.5-m length will be installed on either side of interaction point 7. These two units shall be installed during the long shutdown 2 in years 2019–2020. After a brief reminder on the design features of the magnet, this paper describes the current status of the development activities, in particular the short model programme and the construction of the first full scale prototype at CERN. Critical operations such as the reaction treatment and the coil impregnation are discussed, the quench performance tests results of the two-in-one model are reviewed and finally, the plan toward the production for the long shut down 2 is described.
Spatial Stimulus-Response Compatibility and Coding of Tactile Motor Events: Influence of Distance between Stimulated and Responding Body Parts, Spatial Complexity of the Task and Sex of Subject

We studied spatial stimulus-response compatibility in the somatosensory modality by instructing 16 men and 16 women to press a key using the left or the right thumb in response to a nonnoxious electric stimulation delivered either to the left or to the right little finger or, in different blocks, to the left or to the right malleolar region. The task was performed in compatible (stimulus and key-response on the same side of the corporeal midline) and in incompatible conditions (stimulus and key-response on opposite sides of the corporeal midline). In Exp. 1 subjects were tested while keeping their limbs in anatomic position; in Exp. 2 subjects performed the task while keeping the left upper and lower limbs on the right side and the right limbs on the left side of the bodily midline (crossed position). The compatibility effect was observed in both experiments and was higher for stimuli delivered to the little finger than to the malleolar region. This suggests that the cost of inhibiting compatible responses is maximal when stimulated and responding body parts are contiguous. Moreover, in the spatially most demanding task (Exp. 2) men outperformed women for both speed and accuracy suggesting a sex-related specialisation in the spatial processing of somatosensory information.
The Calcium Antagonist Nisoldipine Improves the Functional Recovery of Reperfused Myocardium Only When Given Before Ischemia

Summary: It is unclear whether the protective effects of calcium antagonists on reperfused myocardium are secondary to increased blood flow during ischemia (anti-ischemic action) or reperfusion (Gregg phenomenon), or are mediated through altered calcium kinetics in ischemic or reperfused myocardium. To study the effect of the calcium antagonist nisoldipine on the functional recovery of stunned myocardium, 32 enflurane-anesthetized dogs were subjected to 15 min of occlusion of the left circumflex coronary artery and subsequent 4 h of reperfusion. Eight dogs served as placebo controls (group I), and eight dogs received nisoldipine (5 μ.g/kg i.v.) before occlusion (group II), eight dogs at 10 min of occlusion (group III), and eight dogs at 4 min of reperfusion (group IV). The mean aortic pressure was kept constant with an intra-aortic balloon, and the heart rate did not change. In group I, posterior systolic wall thickening (WT, sonomicrome-try) decreased from 18.3 ± 2.4% (mean ± SD) during control conditions to - 3.0 ± 2.0% at 13 min of occlusion. At 10 min of reperfusion, WT was 1.7 ± 3.9% and did not recover further (-1.2 ± 3.7% at 4 h of reperfusion). Posterior transmural blood flow (BF, colored microspheres) decreased from 1.42 ± 0.43 ml/min/g during control con- ditions to 0.26 ± 0.08 ml/min/g at 13 min of occlusion. BF was 2.07 ±0.93 ml/min/g at 10 min and 0.95 ± 0.31 ml/ min/g at 4 h of reperfusion. In groups III and IV, the WT and BF were not different from those in group I throughout the experimental protocol. In group II, however, the WT, although similar to the WT of group I before and during ischemia, recovered from 2.7 ± 4.3% at 10 min to 11.8 ± 6.0% at 4 h of reperfusion (p < 0.05 vs. groups I, HI, and IV). The BF in group II decreased from 2.52 ± 0.66 ml/min/g after administration of nisoldipine to 0.22 ± 0.14 ml/min g at 13 min of occlusion. The BF was 1.31 ± 0.51 ml/min/g at 10 min and 1.33 ± 0.43 ml/min/g at 4 h of reperfusion. Nisoldipine exerts no beneficial effect when given immediately before or after the onset of reperfusion. The improved functional recovery of reperfused myocardium in dogs pretreated with nisoldipine cannot be attributed to an increased regional myocardial blood flow during ischemia or reperfusion. The better myocardial recovery, therefore, appears to be related to an attenuated myocardial calcium overload during the first few minutes of ischemia.
Detroit en 1880: espace et ségrégation

Observer les formes des concentrations ethniques et sociales dans les villes des États-Unis revient à examiner certains traits essentiels de l'histoire urbaine. Car ce sont l'expérience ethnique, les conflits raciaux et les clivages sociaux qui se conjuguent pour produire la ségrégation caractéristique des villes américaines : quartier irlandais du North End de Boston, quartiers allemands de Milwaukee, petite Italie autour de Mulberry Street, East Side juif de Manhattan, ou la ville chinoise de San Francisco avant le tremblement de terre. Ces quartiers, agrégats momentanés ou stables, ont des frontières mouvantes et changent de configuration au rythme de l'arrivée de nouveaux immigrants et du développement urbain. L'exploitation des données de Détroit en 1880, que je présente ici, a pour but de décrire l'hétérogénéité urbaine, de déceler les différentes formes de regroupement et de déterminer l'origine, ethnique ou sociale, de la ségrégation spatiale.
Esophagogastric Junction pressure morphology: comparison between a station pull‐through and real‐time 3D‐HRM representation

Esophagogastric junction (EGJ) competence is the fundamental defense against reflux making it of great clinical significance. However, characterizing EGJ competence with conventional manometric methodologies has been confounded by its anatomic and physiological complexity. Recent technological advances in miniaturization and electronics have led to the development of a novel device that may overcome these challenges.
Gastro-entérites en milieux des réfugiés au Tchad

Les refugies et deplaces de guerre sont des personnes vulnerables. C’est pourquoi, nous avons entrepris une etude des gastro-enterites dans leurs milieux au Sud et a l’Est du Tchad. Cette etude a concerne 53 patients dans les camps du Sud dont 28,30% sont des enfants de 0 a 5 ans. Elle a ete couplee d’une enquete sur l’etat nutritionnel de 205 refugies dans les deux zones. L’isolement et l’identification des enteropathogenes dans les selles ont ete realises au laboratoire de l’Hopital General de Reference Nationale (HGRN), en utilisant les milieux Hektoen, Mueller-Hinton, EMB, Saboraud Chloramphenicol et la galerie API® 20 E. La microscopie, les tests de filamentation et biochimiques ont permis de caracteriser et de determiner les taux des infestations parasitaires, fongiques et d’infections bacteriennes qui sont respectivement de 18,86%, 11,32% et 24,52%. La caracterisation de la sensibilite des agents bacteriens Salmonella, Shigella et Escherichia coli a montre une resistance de 85% aux beta-lactamines. En revanche, 98% des germes sont sensibles aux fluoroquinolones. Cette etude nous a permis non seulement de connaitre les caracteristiques des diarrhees liees a l’etat nutritionnel des refugies, mais egalement, de mettre en evidence une antibiotherapie efficace permettant la mise en place d’un programme de prevention contre les maladies diarrheiques et d’amelioration de leur etat nutritionnel dans les milieux confines. L’amelioration de l’etat nutritionnel des enfants pourrait comporter : la distribution reguliere et complete des aliments riches en vitamines ; l’extension des programmes d’alimentation d’appoint et le logement adequat pour les refugies. Mots cles: Diarrhee, enteropathogenes, nutritionnel, antibiotique, HGRN.
Clinical impact of sirolimus‐eluting stent in ST‐segment elevation myocardial infarction: A meta‐analysis of randomized clinical trials

Objectives: To evaluate outcome of patients undergoing sirolimus‐eluting stent (SES) as compared to bare‐metal stent (BMS) implantation during primary angioplasty for ST‐segment elevation myocardial infarction (STEMI). Background: The role of SES in primary percutaneous coronary intervention setting is still debated. Methods: We searched Medline, EMBASE, CENTRAL, scientific session abstracts, and relevant Websites for studies in any language, from the inception of each database until October 2008. Only randomized clinical trials with a mean follow‐up period >6 months and sample size >100 patients were included. Primary endpoint for efficacy was target‐vessel revascularization (TVR) and primary endpoint for safety was stent thrombosis. Secondary endpoints were cardiac death and recurrent myocardial infarction (MI). Results: Six trials were included in the meta‐analysis, including 2,381 patients (1,192 randomized to SES and 1,189 to BMS). Up to 12‐month follow‐up, TVR was significantly lower in patients treated with SES as compared to patients treated with BMS (4.53% vs. 12.53%, respectively; odds ratio [OR] 0.33; 95% confidence interval [CI] 0.24–0.46; P < 0.00001). There were no significant differences in the incidence of stent thrombosis (3.02% vs. 3.70%, OR = 0.81 [95% CI, 0.52–1.27], P = 0.81), cardiac death (2.77% vs. 3.28%, OR = 0.84 [95% CI, 0.52–1.35], P = 0.47), and recurrent MI (2.94% vs. 4.04%, OR = 0.71 [95% CI, 0.45–1.11], P = 0.13) between the two groups. Conclusion: SES significantly reduces TVR rates as compared to BMS in STEMI patients up to 1 year follow‐up. Further studies with larger population and longer follow‐up time are needed to confirm our findings. © 2009 Wiley‐Liss, Inc.
Alcohol sensitivity moderates the indirect associations between impulsive traits, impaired control over drinking, and drinking outcomes.

OBJECTIVE The purpose of this study was to examine impaired control over drinking behavior as a mediator of unique pathways from impulsive traits to alcohol outcomes in young adults. We also sought to investigate the moderating influence of self-reported sensitivity to alcohol on these pathways. METHOD Young adult heavy drinkers (N = 172; 82 women) recruited from the community completed self-report measures of impulsive traits (positive urgency, negative urgency, sensation seeking), alcohol sensitivity (Self-Rating of the Effects of Alcohol scale), impaired control over drinking, and alcohol use and problems. Multiple-groups path analysis was used to analyze the data. RESULTS Path coefficients between urgency and impaired control were larger for individuals with lower versus higher self-reported sensitivity to alcohol. The same was true for the association between impaired control and alcohol problems. For participants lower on alcohol sensitivity, significant indirect paths were observed from both positive and negative urgency to all alcohol outcomes (quantity, frequency, and problems) mediated via impaired control. For participants higher on alcohol sensitivity, only the paths from negative urgency (but not positive urgency) to the three alcohol outcomes via impaired control were statistically significant. Sensation seeking was not uniquely associated with impaired control. CONCLUSIONS The findings indicate that relatively low sensitivity to the pharmacological effects of alcohol may strengthen the association between urgency--especially positive urgency--and impaired control, supporting the notion that personality and level of response to alcohol may interact to increase risk for impaired control over drinking.
Thousands of Rab GTPases for the Cell Biologist

Rab proteins are small GTPases that act as essential regulators of vesicular trafficking. 44 subfamilies are known in humans, performing specific sets of functions at distinct subcellular localisations and tissues. Rab function is conserved even amongst distant orthologs. Hence, the annotation of Rabs yields functional predictions about the cell biology of trafficking. So far, annotating Rabs has been a laborious manual task not feasible for current and future genomic output of deep sequencing technologies. We developed, validated and benchmarked the Rabifier, an automated bioinformatic pipeline for the identification and classification of Rabs, which achieves up to 90% classification accuracy. We cataloged roughly 8.000 Rabs from 247 genomes covering the entire eukaryotic tree. The full Rab database and a web tool implementing the pipeline are publicly available at www.RabDB. org. For the first time, we describe and analyse the evolution of Rabs in a dataset covering the whole eukaryotic phylogeny. We found a highly dynamic family undergoing frequent taxon-specific expansions and losses. We dated the origin of human subfamilies using phylogenetic profiling, which enlarged the Rab repertoire of the Last Eukaryotic Common Ancestor with Rab14, 32 and RabL4. Furthermore, a detailed analysis of the Choanoflagellate Monosiga brevicollis Rab family pinpointed the changes that accompanied the emergence of Metazoan multicellularity, mainly an important expansion and specialisation of the secretory pathway. Lastly, we experimentally establish tissue specificity in expression of mouse Rabs and show that neo-functionalisation best explains the emergence of new human Rab subfamilies. With the Rabifier and RabDB, we provide tools that easily allows non-bioinformaticians to integrate thousands of Rabs in their analyses. RabDB is designed to enable the cell biology community to keep pace with the increasing number of fully-sequenced genomes and change the scale at which we perform comparative analysis in cell biology.
Soy isoflavones improve systemic arterial compliance but not plasma lipids in menopausal and perimenopausal women.

The possibility that the heightened cardiovascular risk associated with the menopause, which is said to be ameliorated by soybeans, can be reduced with soy isoflavones was tested in 21 women. Although several were perimenopausal, all have been included. A placebo-controlled crossover trial tested the effects of 80-mg daily isoflavones (45 mg genistein) over 5- to 10-week periods. Systemic arterial compliance (arterial elasticity), which declined with age in this group, improved 26% (P < .001) compared with placebo. Arterial pressure and plasma lipids were unaffected. The vasodilatory capacity of the microcirculation was measured in nine women; high acetylcholine-mediated dilation in the forearm vasculature was similar with active and placebo treatments. LDL oxidizability measured in vitro was unchanged. Thus, one important measure of arterial health, systemic arterial compliance, was significantly improved in perimenopausal and menopausal women taking soy isoflavones to about the same extent as is achieved with conventional hormone replacement therapy.
Orientational order parameters in liquid crystals: a comparative study of x-ray diffraction and polarized Raman spectroscopy results.

The orientational order parameters and in the nematic liquid crystal 4-pentyl-4'-cyanobipheny (5CB) have been determined by means of the two completely different techniques: polarized Raman spectroscopy and x-ray scattering. In particular, the values of and obtained using two different Raman methods, proposed by Jen [J. Chem. Phys 66, 4635 (1977)] and Jones [J. Mol. Struct. 708, 145 (2004)], respectively, are compared with the results of x-ray measurements. A good agreement between the experimental values of and and the results of the Humphries-James-Luckhurst mean field theory has been found whenever they were determined using either x-ray measurement or following the Jen method. In addition, a study of the influence of the intensity of the exiting laser source on the apparent values of the order parameters has been performed. Therefore, it was found that the discrepancies of the value of determined following Jen and Jones could be determined by nonlinear effects.