Miracle-dz/UniFAR-FTUs huggingface dataset:
MHC studies in nonmodel vertebrates: what have we learned about natural selection in 15 years?

Abstract Elucidating how natural selection promotes local adaptation in interaction with migration, genetic drift and mutation is a central aim of evolutionary biology. While several conceptual and practical limitations are still restraining our ability to study these processes at the DNA level, genes of the major histocompatibility complex (MHC) offer several assets that make them unique candidates for this purpose. Yet, it is unclear what general conclusions can be drawn after 15 years of empirical research that documented MHC diversity in the wild. The general objective of this review is to complement earlier literature syntheses on this topic by focusing on MHC studies other than humans and mice. This review first revealed a strong taxonomic bias, whereby many more studies of MHC diversity in natural populations have dealt with mammals than all other vertebrate classes combined. Secondly, it confirmed that positive selection has a determinant role in shaping patterns of nucleotide diversity in MHC genes in all vertebrates studied. Yet, future tests of positive selection would greatly benefit from making better use of the increasing number of models potentially offering more statistical rigour and higher resolution in detecting the effect and form of selection. Thirdly, studies that compared patterns of MHC diversity within and among natural populations with neutral expectations have reported higher population differentiation at MHC than expected either under neutrality or simple models of balancing selection. Fourthly, several studies showed that MHC‐dependent mate preference and kin recognition may provide selective factors maintaining polymorphism in wild outbred populations. However, they also showed that such reproductive mechanisms are complex and context‐based. Fifthly, several studies provided evidence that MHC may significantly influence fitness, either by affecting reproductive success or progeny survival to pathogens infections. Overall, the evidence is compelling that the MHC currently represents the best system available in vertebrates to investigate how natural selection can promote local adaptation at the gene level despite the counteracting actions of migration and genetic drift. We conclude this review by proposing several directions where future research is needed.
A 40-to-44Gb/s 3× Oversampling CMOS CDR/1:16 DEMUX

A 3times oversampling CDR and 1:16 DEMUX occupies 0.8 times 1.8mm2 in a 90nm CMOS process. The chip operates at 40 to 44Gb/s and dissipates 0.91W. Input data is sampled using a 24-phase distributed VCO and a digital CDR recovers 16 bits and a 2.5GHz clock from 48 demultiplexed samples spanning 16UI. Conformance to the ITU G.8251 jitter tolerance mask (BER <10-12 with a 231 - 1 PRBS source) is demonstrated.
Mechanisms of Liver Injury. I. TNF-α-induced liver injury: role of IKK, JNK, and ROS pathways

TNF-α activates several intracellular pathways to regulate inflammation, cell death, and proliferation. In the liver, TNF-α is not only a mediator of hepatotoxicity but also contributes to the restoration of functional liver mass by driving hepatocyte proliferation and liver regeneration. This review summarizes recent advances in TNF-α signaling mechanisms that demonstrate how the IKK, ROS, and JNK pathways interact with each other to regulate hepatocyte apoptosis and proliferation. Activation of these pathways is causatively linked to liver injury induced by concanavalin A, TNF-α, and ischemia-reperfusion and to liver regeneration and hepatocarcinogenesis. In light of recent findings, pharmacological inhibitors of JNK and IKK and antioxidants may be promising new tools for the treatment of hepatitis, ischemia-reperfusion injury, and hepatocellular carcinoma.
Démonétiser l'identité numérique

De tous les « biens informationnels », les donnees qui decrivent notre identite, nos opinions, nos affinites, sont les plus precieux. A nos yeux, bien sur, mais aux yeux des marchands qui nous traquent aussi. Michel Arnaud explique comment soustraire notre identite numerique a l’indiscretion commerciale, tout en menageant la possibilite d’un usage social maitrise.
Hybridization of the marine seaweeds, Fucus serratus and Fucus evanescens (Heterokontophyta: Phaeophyceae) in a 100-year-old zone of secondary contact

Historically, the intertidal seaweeds Fucus serratus (Fs) and Fucus evanescens (Fe) were sympatric only along the western coast of Norway. In the mid-1890s, Fe (monoecious) was accidentally introduced into the Oslofjord. Putative hybridization with the endemic Fs (dioecious) was observed in Oslofjord by 1977 and in the Kattegat and western Baltic Seas by 1998. At Blushøj, Denmark (Kattegat Sea) putative Fs × Fe hybrids were present only when densities of Fe and Fs exceeded 14 and 2 m⊃-2, respectively. All of the 58 putative hybrids that were collected in 1999 were dioecious and intermediate in morphology. Essentially all (57 out of 58) were reproductively mature, but the oogonia possessed fewer and more variably sized eggs than either parent. Examination of each parental species and putative hybrids with nuclear, mitochondrial and chloroplast molecular markers confirmed the occurrence of hybridization. Furthermore, all of the hybrids possessed Fe-type chloroplasts and mitochondria, indicating that only the Fe egg × Fs sperm pairing was successful in the field. The reciprocal cross of Fs egg×Fe sperm was absent in the field and significantly less successful in laboratory crossings. Asymmetrical hybridization has also been reported for several species of plants and animals.
Attributable mortality of ventilator-associated pneumonia: a reappraisal using causal analysis.

RATIONALE Measuring the attributable mortality of ventilator-associated pneumonia (VAP) is challenging and prone to different forms of bias. Studies addressing this issue have produced variable and controversial results. OBJECTIVES We estimate the attributable mortality of VAP in a large multicenter cohort using statistical methods from the field of causal inference. METHODS Patients (n = 4,479) from the longitudinal prospective (1997-2008) French multicenter Outcomerea database were included if they stayed in the intensive care unit (ICU) for at least 2 days and received mechanical ventilation (MV) within 48 hours after ICU admission. A competing risk survival analysis, treating ICU discharge as a competing risk for ICU mortality, was conducted using a marginal structural modeling approach to adjust for time-varying confounding by disease severity. MEASUREMENTS AND MAIN RESULTS Six hundred eighty-five (15.3%) patients acquired at least one episode of VAP. We estimated that 4.4% (95% confidence interval, 1.6-7.0%) of the deaths in the ICU on Day 30 and 5.9% (95% confidence interval, 2.5-9.1%) on Day 60 are attributable to VAP. With an observed ICU mortality of 23.3% on Day 30 and 25.6% on Day 60, this corresponds to an ICU mortality attributable to VAP of about 1% on Day 30 and 1.5% on Day 60. CONCLUSIONS Our study on the attributable mortality of VAP is the first that simultaneously accounts for the time of acquiring VAP, informative loss to follow-up after ICU discharge, and the existence of complex feedback relations between VAP and the evolution of disease severity. In contrast to the majority of previous reports, we detected a relatively limited attributable ICU mortality of VAP.
First metrological applications of the PTB 1 V Josephson arbitrary waveform synthesizer

We report on the first two applications in metrology of the PTB 1 V Josephson waveform synthesizer. First, a direct comparison with the ac quantum voltmeter was carried out. The result at 250 Hz was (+3.5 ± 11.7) ×10-9 (k = 1). In addition, we have performed ac-dc transfer measurements with a thermal converter. A transconductance amplifier was used to provide the current required by the thermal converter. Preliminary results indicate differences for the frequency range from 125 Hz and 750 Hz below 1 ×10-6 with a type A uncertainty of 0.3 ×10-6(k = 1).
Short-term training, muscle glycogen, and cycle endurance.

The objective of this study was to test the hypothesis that the increased glycogen concentration found in the working muscles following short-term training would result in an increase in endurance performance. Endurance performance was examined in 8 active but untrained males who cycled until fatigue at 65% VO2max prior to and following 3 consecutive days of training. Training consisted of cycling for 2 hrs a day at the same power output used in the prolonged fatigue trials. A 39% increase in cycle time, from 103 +/- 7.7 to 143 +/- 14 min (p < 0.05), was observed following training. At fatigue prior to training, glycogen concentration in the vastus lateralis muscle was depleted by 75% (317 +/- 17 to 78.8 +/- 32 mmol.glucosyl units .kg-1 d.w). Following training, glycogen concentration at a comparable work time was 2.3 times higher. The elevated glycogen level following training was due both to higher glycogen at rest and during exercise. The energy cost of the activity as measured by the VO2 at selected intervals was unchanged with training. No change (p > 0.05) in exercise time was observed in a control group who were subjected to similar exercise protocols approximately 1 to 2 weeks apart. It is concluded that short-term training at least in untrained individuals (VO2max averaging 43.6 +/- 2.9 ml.kg-1.min-1) substantially elevates submaximal exercise tolerance and that the increase in resistance to fatigue is related to the elevated availability of glycogen.
The Effects of Intrathecal Tramadol on Spinal Somatosensory-Evoked Potentials and Motor-Evoked Responses in Rats

Tramadol has been proven to exert a local anesthetic-type effect on peripheral nerves in both clinical and laboratory studies. In this study, we evaluated the effects of tramadol on sensory and motor neural conduction when administered intrathecally in the rat. Tramadol (0, 1, or 2 mg) was administered through an intrathecal catheter. Spinal somatosensory-evoked potentials (SSEPs) were recorded at the thoracolumbar junction after stimulation of the sciatic nerve. An evoked compound muscle action potential (CMAP) was recorded in the intrinsic muscles of the foot in response to electric stimulation of the lower thoracic (T1213) interspinous space. Both SSEP and CMAP were obtained before drug application as the pretreatment baseline and at 5, 15, and 30 min after treatment, and at 30- or 60-min intervals thereafter for another 4.5 h. SSEP was averaged from 20 responses, whereas CMAP was obtained from a single stimulation. Reproducible SSEPs and CMAP were consistently recorded in all rats. Intrathecal tramadol dose-dependently reduced the amplitude and delayed the latency in both SSEPs and CMAP. Generally, the suppressive effects occurred immediately after injection and recovered over 2 h. Combined administration with 20 &mgr;g of intrathecal naloxone did not attenuate the inhibition of spinal SSEPs. We conclude that intrathecal tramadol causes a dose-related suppressive effect on both sensory and motor neural conduction in the spinal cord.
Topological data analysis and applications

Topological data analysis is interested in problems relating to nonlinear systems, large scale data and development of more accurate models, that contribute to a high level research. In the study of time-series data we can identify problems that focus aspects of that nature, with applications to digital disease detection, gene expression, viral evolution, etc. In particular, it describes the qualitative aspects of the data, focusing the topological features with longest lifetimes. To encode the latter, it uses novel mathematical methods that can provide diagrams which are a clear and practical tool that allow us the detection of outliers and to capture the dynamics of the system. In this paper we review this methodology and discuss several applications that can lead to new perspectives to modelling and simulation in system behaviour.
Differential function of nitric oxide in murine antigen-induced arthritis.

BACKGROUND The aim of our study was to investigate the role of inducible nitric oxide synthase (iNOS)-derived nitric oxide (NO) production in different stages of murine antigen-induced arthritis (AiA). METHODS Clinical, histological and microcirculatory parameters (measured by intravital fluorescence microscopy) were assessed in the knee joint during acute and chronic AiA after inhibition of iNOS with L-N(6)-(1-iminoethyl)lysine (L-NIL). Plasma concentrations of and were evaluated by the Griess reaction and the expression of iNOS, P- and E-selectin, intercellular adhesion molecule 1 (ICAM-1) and vascular cell adhesion molecule 1 (VCAM-1) by immunohistochemistry. RESULTS In both stages of the disease, plasma concentrations of and were increased and iNOS was expressed. In the acute phase, swelling, leucocyte adhesion, leucocyte infiltration and expression of adhesion molecules were increased in arthritic animals treated with L-NIL in comparison with untreated arthritic animals. In the chronic phase, no change in the disease parameters could be detected after L-NIL treatment. CONCLUSION Increased NO production induced by iNOS during the acute phase of AiA can be regarded as a protective response in the prevention of further leucocytic infiltration and joint destruction, whereas it seems to play a subordinate role in chronic AiA.
EFFECT OF COLD ISCHEMIA TIME ON THE EARLY OUTCOME OF HUMAN HEPATIC ALLOGRAFTS PRESERVED WITH UW SOLUTION

Five hundred ninety-three cadaveric livers were used for primary liver transplantation between October 24, 1987, and May 19, 1989. The grafts were procured with a combined method, using in situ cooling with cold electrolyte solution and backtable flushing with UW solution. The mean cold-ischemia time was 12.8 (range 2.4–34.7) hr. The cases were divided into 5 groups according to the cold-ischemia time: group 1: <10 hr (n=223); group 2:10–14 hr (n=188); group 3:15–19 hr (n=101); group 4: 20–24 hr (n=52); and group 5: ≥25 hr (n=29). There was no difference between the 5 groups in 1-year patient survival, highest SGOT in first week after operation, and SGOT and total bilirubin during the first month after operation. However, with a logistic regression model, the retransplantation rate (P=0.001) and primary nonfunction rate (P=0.006) significantly rose as cold-ischemia time increased, meaning that the equivalency of patient survival was increasingly dependent on aggressive retransplantation.
Effect of growth hormone treatment on the healing of left colonic anastomoses in protein‐malnourished rats

Malnutrition is known to affect wound healing but it is not known with certainty whether or not postoperative hyperalimentation can reverse this defect. The present study was designed to examine the effects of recombinant human growth hormone (hGH) on left colonic anastomoses in malnourished rats.
The biogenesis of lysosomes.

Article de synthese sur les lysosomes: biogenese, definition, role biologique. Les enzymes lysosomales sont decrites ainsi que leur role dans l'exo et l'endocytose. La structure et le biogenese de la membrane lysosomale sont etudiees
Effects of Extensive and Poor Gastrointestinal Metabolism on the Pharmacodynamics of Pravastatin

The enhanced nonenzymatic isomerization of pravastatin to SQ 31,906, a relatively inactive metabolite, has been demonstrated to occur on exposure to gastric acidity in humans. However, the effect of gastric metabolism on the pharmacodynamics of pravastatin has not been studied. In addition, it was hypothesized that some individuals may be more extensive gastric metabolizers than others. Sixteen men received 4 weeks of oral therapy with pravastatin 10 mg after a 6‐week drug washout diet run‐in period. Pharmacokinetic and pharmacodynamic parameters were determined after 8 hours of serum sampling on the final day of therapy. Patients with a metabolic ratio for area under the concentration‐time curve (AUC0–8 of pravastatin/AUC0–8 of SQ 31,906) of less than 1.6 had a significantly lower reduction in total and low‐density lipoprotein (LDL) cholesterol compared with those with a ratio > 1.6. An enteric formulation of pravastatin should increase the bioavailability of pravastatin and enhanced lipid‐lowering efficacy.
Extensive vascular occlusions as initial presentations of systemic lupus erythematosis. A case report and review of literature

Abstract Widespread arterial and venous thrombosis is a very rare initial presentation of systemic lupus erythematosus (SLE). We report a case with extensive vascular occlusion as the initial manifestation of SLE. Although these cases have high morbidity and mortality, yet our patient recovered with minimal complications.
E-campaigning on Twitter: The effectiveness of distributive promises and negative campaign in the 2013 Italian election

Recent studies investigated the effect of e-campaigning on the electoral performance. However, little attention has been paid to the content of e-campaigning. Given that political parties broadcast minute-by-minute the campaign messages on social media, this comprehensive and unmediated information can be useful to evaluate the impact of different electoral strategies. Accordingly, this article examines the electoral campaign for the 2013 Italian general election to assess the effectiveness of positive and negative campaigning messages, measured through content analysis of information published on the official Twitter accounts of Italian parties. We evaluate their impact on the share of unsolicited voting intentions expressed on Twitter, measured through an innovative technique of sentiment analysis. Our results show that negative campaign has positive effects and its impact is stronger when the attacker is meanwhile under attack. Conversely, we only find a circumstantial effect of positive campaign related to clientelistic and distributive appeals.
Fault identification for Lipschitz nonlinear systems

Fault identification for a class of nonlinear systems is considered, where the nonlinear term in the system satisfies local Lipschitz conditions. Under some fault detectability conditions are satisfied, the system is first decomposed into two subsystems, where one is coupled with and another is decoupled from faults. One asymptotic state observer is then designed for the fault-coupled subsystem, in which a fictitious input is introduced to assure the state observer is asymptotic sable. It is proven that the actuator faults would be reconstructed from the fictitious input under steady state. Both stability analysis of the state observer and fault identification scheme design is given in a constructive manner and finally such a procedure is equivalent to solving a set of linear matrix inequalities.
Social Network Analysis of European Project Consortia to Reveal Impact of Technology-Enhanced Learning Projects

The European Commission (EC) has spent hundreds of millions of euros on collaborative Technology Enhanced Learning (TEL) projects in recent years. Consequently the EC is interested in the impact generated by those projects. Spawning sustained collaboration ties can be interpreted as one aspect of project impact. In this paper we present a novel way of analyzing this latent impact of TEL projects by applying social network analysis on the projects' collaboration structures. Our analysis includes TEL projects funded under FP6, FP7 and eContentplus, and identifies central projects and strong, sustained organizational collaboration ties.
Cytotoxicity and apoptosis induced by silver nanoparticles in human liver HepG2 cells in different dispersion media

Silver nanoparticles (Ag NPs) have been widely used in medical and healthcare products owing to their unique antibacterial activities. However, their safety for humans and the environment has not yet been established. This study evaluated the cellular proliferation and apoptosis of Ag NPs suspended in different solvents using human liver HepG2 cells. The ionization of Ag NPs in different dispersion media [deionized water, phosphate‐buffered saline (PBS), saline and cell culture] was measured using an Ag ion selective electrode. The MTT assay was used to examine the cell proliferation activities. The effects of Ag NPs on cell cycle, induction of apoptosis, production of reactive oxygen species (ROS) and mitochondrial membrane potential (MMP) were analyzed using flow cytometry. The degree of Ag NPs ionization differed with dispersion media, with the concentrations of silver ions in deionized water being the highest in all suspensions. Ag NPs could inhibit the viability of HepG2 cells in a time‐ and concentration‐dependent manner. Ag NPs (40, 80 and 160 µg ml−1) exposure could cause cell‐cycle arrest in the G2/M phase, significantly increasing the apoptosis rate and ROS generation, and decreasing the MMP in HepG2 cells more sensitive to deionized water than in cell culture. These results suggested that the cellular toxicological mechanism of Ag NPs might be related to the oxidative stress of cells by the generation of ROS, leading to mitochondria injury and induction of apoptosis. It also implies that it is important to assess the physicochemical properties of NPs in the media where the biological toxicity tests are performed. Copyright © 2015 John Wiley & Sons, Ltd.
Evaluation of urban lake evolution using Google Earth Engine - A case study of Wuhan, China

In recent decades, urban lakes have been constantly evolutionalized because of rapid urbanization, which may bring severe ecological and environmental consequences. Global satellite data that are accessible through Google Earth Engine are valuable for large-scale evaluation of the evolution of the urban lakes. This study introduced the evaluation of lakes in Wuhan area in China using Google Earth Engine. 23 major lakes in this city are analyzed using classification, morphological operators, and a water index model. All the analysis were done in Google Earth Engine. The result shows that the total surface areas of these major lakes in Wuhan had significantly decreased from1991 to 2013. This case also clearly show that Google Earth Engine could significantly facilitate the scientific discovery process by enabling fast batch analysis of large volume of satellite data without downloading and analyzing them locally.
New insights on schwann cell development

In the peripheral nervous system, Schwann cells are glial cells that are in intimate contact with axons throughout development. Schwann cells generate the insulating myelin sheath and provide vital trophic support to the neurons that they ensheathe. Schwann cell precursors arise from neural crest progenitor cells, and a highly ordered developmental sequence controls the progression of these cells to become mature myelinating or nonmyelinating Schwann cells. Here, we discuss both seminal discoveries and recent advances in our understanding of the molecular mechanisms that drive Schwann cell development and myelination with a focus on cell–cell and cell–matrix signaling events. GLIA 2015;63:1376–1393
Human NAD +-dependent Mitochondrial Malic Enzyme cDNA

Mitochondrial NAD+-dependent malic enzyme (EC 1.1.1.40) is expressed in rapidly proliferating cells and tumor cells, where it is probably linked to the conversion of amino acid carbon to pyruvate. In this paper, we report the cDNA cloning, amino acid sequence, and expression in Escherichia coli of functional human NAD+-dependent mitochondrial malic enzyme. The cDNA is 1,923 base pairs long and contains an open reading frame coding for a 584-amino acid protein. The molecular mass is 65.4 kDa for the unprocessed precursor protein. Comparison of the amino acid sequence of the human protein with the published NADP+-dependent mammalian cytosolic or plant chloroplast malic enzymes reveals highly conserved regions interrupted with long stretches of amino acids without significant homology. Expression of the processed protein in E. coli yielded an enzyme with the same kinetic and allosteric properties as malic enzyme purified from human cells.