Miracle-dz/UniFAR-FTUs huggingface dataset:
BodyMass Index Is an Important Determinant of Methylation Biomarkers in Women of Reproductive Ages 1 , 2

B vitamin deficiencies lead to moderate hyperhomocysteinemia, which has been associated with health and disease. However, concomitant derangements in cellular methylation, reflected by altered plasma S-adenosylmethionine (SAM) or S-adenosylhomocysteine (SAH) concentrations, may be the primary cause. Therefore, we identified determinants of homocysteine, SAM, and SAH concentrations in 336 women, aged 20–48 y, as part of a large study focusing on risk factors for reproductive disorders. Blood was obtained to determine plasma SAM, SAH, and total homocysteine (tHcy), serum vitamin B-12 and folate, RBC folate concentrations, and the related single nucleotide polymorphisms 5,10methylenetetrahydrofolate reductase (MTHFR) 677C. T and 1298A. C, methionine synthase reductase (MTRR) 66A. G, and nicotinamide N-methyltransferase IVS1–151G . A. Questionnaires provided information on demographics, lifestyles, and nutrient intakes. Correlation coefficients were calculated andmultivariable associationswere assessedwith a general linear model. Serum folate was positively correlated with SAM concentrations (r = 0.159; P = 0.004). Folate and vitamin B-12 were not correlated with SAH concentrations or the SAM:SAH ratio but were inversely correlated with tHcy concentrations (serum folate r = 20.324; RBC folate r = 20.294; vitamin B-12 r = 20.307; P , 0.01). From the multivariable analysis, BMI was the strongest determinant of SAM (standardized b = 19.145; P , 0.001) and SAH concentrations (standardized b = 3.241; P = 0.010). MTHFR 677TT (standardized b = 0.195; P = 0.001), B vitamin supplement use (standardized b = 20.156; P , 0.001) and dietary protein intake (standardized b = 20.011; P , 0.001) were the strongest determinants of tHcy concentrations. Thus, the determinants of SAM and SAH differ from those of tHcy concentrations. Given that BMI was a strong determinant of SAM concentrations, it should be included in future studies on cellular methylation. J. Nutr. 139: 2315–2321, 2009.
What Geriatricians Should Know About the Werner Syndrome

Geriatricians want to know the extent to which inborn genetic variations influence health span and life span in their patients. Current research on this subject is largely confined to the very basic issues of identifying, mapping, and cloning relevant genes and of investigating their modes of action. Here we summarize the status of such basic research on a gene (WRN), null mutations at which cause a striking seg‐mental propertied syndrome, the Werner syndrome (WS). The views of clinicians and basic scientists concerning the significance of WRN gene action for normal aging are polarized. Some regard it as the most important aging gene and refer to the syndrome explicitly as one of premature aging. Others regard WS as an entirely inappropriate model for aging because WS exhibits many clinical and cell biological discordances with normal aging. Moreover, WS has a major impact on reproductive fitness and, hence, does not escape the forces of natural selection. By contrast, senescent phenotypes of normal (usual) aging can be defined as those that do escape the forces of natural selection. We here give a more balanced view. Work has only just begun on the potential significance of a range of variants at the WS locus, including “leaky” mutations, heterozygosity for null mutations, and polymorphisms, some of which may indeed escape the force of natural selection and thus contribute to the burden of illness in old age. We are also at a very early stage of knowledge concerning genes coding for WRN interacting proteins, variations at which may also be of significance for gerontology and geriatric medicine. J Am Geriatr Soc 47:1136–1144,1999.
New Ionic Liquid for the Dissolution of Lignin

This work aims to develop a new ionic liquid, used as an aprotic green a solvent, to dissolve kraft lignin from black liquor. The kraft lignin was extracted through precipitation with carbon dioxide at atmospheric pressure. 1,8-Diazabicyclo[5.4. 0]undec-7-ene-based ionic liquids were obtained by quaternization of the nitrogen atom with a hydrogen atom or an alkyl chain. The yields of the synthesis of the ionic liquids varied between 76 and 80%. Dissolving experiments were carried out using the lignin isolated from the black liquor of a kraft process. Up to 20% (w/w) of the lignin can be dissolved in butyl-1,8 diazabicyclo[5.4. 0] undec-7-enium chloride ([DBUC4]+Cl-]), hexyl-1,8 diazabicyclo[5.4. 0] undec-7-enium chloride [DBUC6]+[Cl-], and octyl-1,8 diazabicyclo[5.4. 0] undec-7-enium chloride [DBUC8]+[Cl-]. The time it takes to dissolve the lignin in these three liquids shows that its solubility is influenced mostly by the nature of the cations. The lignin solubility was reduced in relation to the increased length of the grafted carbon chain. The thermogravimetric analysis (TGA) showed these liquids can be used as lignin solvents from room temperature up to 300 °C (onset of degradation). Steric exclusion chromatography showed a slight decrease (6%) in the molecular weight of the lignin dissolved in these ionic liquids.
Prevalence Of Anti-EBV Antibodies in Adult Patients with

Background: Nasopharyngeal carcinoma (NPC) is a nonlymphomatous squamous cell carcinoma (SCC) that occurs in the epithelial lining of the nasopharynx. Viral, geographic, and ethnic factors are responsible for its multifactorial futures. Previous studies have showed the role of Epstein-Barr virus (EBV) in the pathogenesis of NPC but no study has been conducted on the Iranian population to assess the etiology of NPC and to investigate the role of EBV in carcinogenesis of nasopharyngeal carcinoma. Methods: We collected 87 paraffin wax embedded blocks of NPC (n=34) and Laryngeal SCC patients (n=53) operated in Isfahan Hospitals during 2003-2007 from the archives of the department of pathology and then sera of patients were provided. We measured the titers of early antigen (anti-EA) and Epstein-Barr virus nuclear antigen (anti-EBNA) antibodies by means of ELISA method in sera of patients. Results: Our data showed a significant association between elevated titer of these antibodies and the presence of NPC (P value =0.016 for anti-EBNA and 0.001 for anti-EA antibodies); however, we did not find such a relationship about Laryngeal SCC.
Dot immunobinding assay for detection of human immunodeficiency virus-associated antigens

The detection of human immunodeficiency virus (HIV)-associated antigens was simplified by the application of dot immunobinding on a nitrocellulose matrix. Antigens were detected by applying the polyethylene glycol-precipitated supernatants of experimentally infected cultures directly onto nitrocellulose strips and sequentially incubating the strips with an anti-HIV antiserum and an alkaline phosphatase-conjugated, species-specific antiserum. The immune reaction was developed by adding the precipitable substrate indoyl phosphate. The dot immunobinding assay was nearly as sensitive as the reverse transcriptase assay in detecting HIV antigens in experimentally infected peripheral blood mononuclear cells, as well as in a T-cell line. The technique was also useful in the in vitro evaluation of antiviral agents. The dot immunobinding assay is a simple and sensitive technique that is useful in the detection of HIV antigens in studies of viral pathogenesis.
S-Palmitoylation of γ-Secretase Subunits Nicastrin and APH-1*

Proteolytic processing of amyloid precursor protein (APP) by β- and γ-secretases generates β-amyloid (Aβ) peptides, which accumulate in the brains of individuals affected by Alzheimer disease. Detergent-resistant membrane microdomains (DRM) rich in cholesterol and sphingolipid, termed lipid rafts, have been implicated in Aβ production. Previously, we and others reported that the four integral subunits of the γ-secretase associate with DRM. In this study we investigated the mechanisms underlying DRM association of γ-secretase subunits. We report that in cultured cells and in brain the γ-secretase subunits nicastrin and APH-1 undergo S-palmitoylation, the post-translational covalent attachment of the long chain fatty acid palmitate common in lipid raft-associated proteins. By mutagenesis we show that nicastrin is S-palmitoylated at Cys689, and APH-1 is S-palmitoylated at Cys182 and Cys245. S-Palmitoylation-defective nicastrin and APH-1 form stable γ-secretase complexes when expressed in knock-out fibroblasts lacking wild type subunits, suggesting that S-palmitoylation is not essential for γ-secretase assembly. Nevertheless, fractionation studies show that S-palmitoylation contributes to DRM association of nicastrin and APH-1. Moreover, pulse-chase analyses reveal that S-palmitoylation is important for nascent polypeptide stability of both proteins. Co-expression of S-palmitoylation-deficient nicastrin and APH-1 in cultured cells neither affects Aβ40, Aβ42, and AICD production, nor intramembrane processing of Notch and N-cadherin. Our findings suggest that S-palmitoylation plays a role in stability and raft localization of nicastrin and APH-1, but does not directly modulate γ-secretase processing of APP and other substrates.
Méthodes exactes et approchées par partition en cliques de graphes. (Exact and approximation methods by clique partition of graphs)

Cette these se deroule au sein du projet ToDo (Time versus Optimality in discrete Optimization ANR 09-EMER-010) finance par l'Agence Nationale de la Recherche. Nous nous interessons a la resolution exacte et approchee de deux problemes de graphes. Dans un souci de compromis entre la duree d'execution et la qualite des solutions, nous proposons une nouvelle approche par partition en cliques qui a pour but (1) de resoudre de maniere rapide des problemes exacts et (2) de garantir la qualite des resultats trouves par des algorithmes d'approximation. Nous avons combine notre approche avec des techniques de filtrage et une heuristique de liste. Afin de completer ces travaux theoriques, nous avons implemente et compare nos algorithmes avec ceux existant dans la litterature. Dans un premier temps, nous avons traite le probleme de l'independant dominant de taille minimum. Nous resolvons de maniere exacte ce probleme et demontrons qu'il existe des graphes particuliers dans lesquels le probleme est 2-approximable. Dans un second temps nous resolvons par un algorithme exact et un algorithme d'approximation le probleme du vertex cover et du vertex cover connexe. Puis a la fin de cette these, nous avons etendu nos travaux aux problemes proches, dans des graphes comprenant des conflits entre les sommets.
A 5 $\mu$ W/Channel Spectral Analysis IC for Chronic Bidirectional Brain–Machine Interfaces

This paper describes an amplification and spectral processing IC for extracting key bioelectrical signals, or ldquobiomarkersrdquo, which are expressed in the brain's field potentials. The intent is to explore using these biomarkers to drive prosthetic actuators or titrate therapy devices such as a deep-brain neurostimulator. The prototype IC uses 5 muW/channel to resolve signals on the order of 1 muVrms. The four channels on the device provide independent spectral analysis from DC to 1 kHz, with variable bandwidth and power filtering characteristics. The noise floor and flexible spectral processing support a broad range of potential applications including sleep staging, Parkinson's disease, detection of movement intention for neuroprosthesis, and detection of high frequency ldquofast ripplesrdquo for exploring seizure prediction. To fully demonstrate the IC's functionality, we include results from a prototype ldquoclosed-looprdquo neurostimulator implementing adaptive titration of therapy based on measured field potential activity.
Exploring passenger assessments of bus service quality using Bayesian networks

Studies on public transit have emphasized the role of passenger satisfaction with service quality in travel choice decisions and indicated that satisfaction depends on various service attributes. Few studies have, however, systematically examined the underlying relationships among service attributes to assess their influence on passenger overall satisfaction. Therefore, to contribute to this rapidly-emerging literature, this paper applies Bayesian networks to quantify the influence of each service aspect on passenger overall satisfaction with regular bus service quality. This analysis involved 609 passengers who participated in a 2013 regular bus service survey in Nanjing, China. The derived Bayesian network shows the relationships among service attributes and passenger overall satisfaction graphically. In particular, service aspects such as running on schedule, acceptable waiting time, available seats, clean onboard environment, pleasant environment at stations, convenient design for transfers, and air-conditioning were the key determinants of overall satisfaction with bus service.
Thinning, stacking, and TSV proximity effects for Poly and High-K/Metal Gate CMOS devices in an advanced 3D integration process

An advanced 3D integration process featuring through silicon via (TSV) and chip-on-wafer (CoW) technologies has been demonstrated. Using this 3D process, Poly and High-K/Metal Gate (HKMG) CMOS wafers have been successfully thinned and stacked, showing little to no degradation in the process. The effect of TSV induced mechanical stress on ΔIdsat for HKMG is found to be smaller as compared to Poly Gate devices for the same channel length (ΔIdsat ratio of HKMG to Poly is ~0.3 and ~0.5 for PMOS and NMOS, respectively). In addition, we show that ΔIdsat for HKMG device is proportional to TSV diameter square, independent of TSV orientation, device polarity, and device distance from TSV.
CD11c+ Cells Are Required for Antigen-Induced Increase of Mast Cells in the Lung

Patients with allergic asthma have more lung mast cells, which likely worsens the symptoms. In experimental asthma, CD11c+ cells have to be present during the challenge phase for several features of allergic inflammation to occur. Whether CD11c+ cells play a role for Ag-induced increases of lung mast cells is unknown. In this study, we used diphtheria toxin treatment of sensitized CD11c-diphtheria toxin receptor transgenic mice to deplete CD11c+ cells. We demonstrate that recruitment of mast cell progenitors to the lung is substantially reduced when CD11c+ cells are depleted during the challenge phase. This correlated with an impaired induction of endothelial VCAM-1 and led to a significantly reduced number of mature mast cells 1 wk after challenge. Collectively, these data suggest that Ag challenge stimulates CD11c+ cells to produce cytokines and/or chemokines required for VCAM-1 upregulation on the lung endothelium, which in turn is crucial for the Ag-induced mast cell progenitor recruitment and the increase in mast cell numbers.
The PYHIN protein family as mediators of host defenses

Summary: The innate immune response is the first line of defense against infection and relies on the ability of immune cells to detect the presence of infection through germline‐encoded pattern recognition receptors. These include the Toll‐like receptors, the retinoic acid inducible gene‐like receptors, the nucleotide oligomerization domain‐like receptors, and a number of DNA‐sensing molecules. Members of the PYHIN protein family have recently emerged as sensors of microbial DNA. PYHIN proteins bind microbial DNA and form caspase‐1‐activating inflammasomes (AIM2) or drive type I IFN gene transcription (IFI16). Here, we review these discoveries and highlight the emerging role of the PYHIN protein family in mammalian host defenses.
ATTRIBUTIONS TO LOW GROUP EFFORT CAN MAKE YOU FEEL BETTER : THE DISTINCT ROLES OF IN-GROUP IDENTIFICATION , LEGITIMACY OF INTERGROUP STATUS , AND CONTROLLABILITY PERCEPTIONS

One experiment investigates the process whereby attributing to low group effort the social status of an in-group that is perceived as being illegitimately low can spare group members the unpleasant affective consequences of a threat to one’s social identity. Specifically, this is the case because such attributions increase the perception that in-group failings can be controlled and, thus, are unlikely to recur. In turn, this ameliorates individuals’ subsequent affect. However, this only occurs to strongly but not weakly group-identified individuals. These findings point to a fairness-based account of coping with social identity threat through biased effort attributions: perceived low effort on the part of the in-group may suggest factors potentially within group control in the future (as opposed to the less controllable low ability), which may in turn suggest that the in-group does not deserve the self-threatening low-status.
Feature selection and analysis of single lateral damper fault based on SVM-RFE with correlation bias reduction

Targeting the characteristics of high-speed train vibration signals of single lateral damper fault, a novel method based on support vector machine recursive feature elimination with correlation bias reduction(SVM-RFE+CBR) is applied to diagnose fault. In this paper, the SVM-RFE and SVM-RFE+CBR algorithms are introduced in detail. In fault diagnosis for single lateral damper, the whole vehicle feature space of each working condition is constructed in sequence, and the fault identification experiments and the fault location experiments are also carried out on datasets which contain 24*58-dimensional features. Owing to there are plenty of highly correlated features, the SVM-RFE+CBR outperforms the original SVM-RFE algorithm and other typical feature selection approaches during all experiments. Not only does it obtains the highest classification accuracy of feature selection but also it achieves the considerable stability index in this special case. Furthermore, an new strategy is studied to improve the stability of this method. By statistically analyzing the ranked features, some useful conclusions can be obtained, which will be helpful during the actual application.
Synthesis of Polypyrrole Using Ferric Chloride (FeCl3) as Oxidant Together with Some Dopants for Use in Gas Sensors

Polypyrrole (Ppy) was synthesized using Ferric Chloride (FeCl3) as oxidant. The ratio of monomer to oxidant was 1:2.4. The polymerization was carried out at 5。 C. Attempts were made to increase the electrical conduc-tivity by using various dopants viz. Lithium per Chlorate (LiClO4), para-Toluene Sulfonate (p-TS) and Nap-thalene Sulfonic acid (NSA). The materials were characterized using FTIR, X-Ray diffraction and SEM. The electrical conductivity was measured by two probe method and was found to be in the range of 10-3 to 10-2 S/cm. Thin films of these preparations were casted on the interdigited electrodes to study the detection of gases such as ammonia and LPG. It was found that for the pure Ppy and one doped with LiClO4, when ammonia gas was allowed to flow in, there was a sudden increase in the current, which decreased rapidly when gas was stopped. This behavior is in contradiction to that observed in earlier investigations where Ppy was prepared by electrochemical method. However when Ppy doped with p-TS and NSA were used, the trend was reversed. Similarly it was noted that for pure Ppy and one doped with LiClO4, p-TS and NSA there was an increase in the current when LPG gas was brought in. However the response to LPG was somewhat low as compared ammonia gas.
From Plasmids to Protection: A Review of DNA Vaccines Against Infectious Diseases

The field of DNA vaccine development began over 16 years ago with the observation that plasmid DNA could be injected into and expressed in vivo and drive adaptive immune responses. Since then, there has been great interest in developing this technology to create a new generation of vaccines with the ability to elicit both humoral and cellular immune responses from an inherently innocuous injection. However, DNA vaccines have yet to proceed past phase I/II clinical trials in humans – primarily due to a desire to induce more potent immune responses. This review will examine how DNA vaccines function to induce an immune response and how this information might be useful in future vaccine design.
Inhibitors of Deubiquitinating Enzymes Block HIV-1 Replication and Augment the Presentation of Gag-Derived MHC-I Epitopes

In recent years it has been well established that two major constituent parts of the ubiquitin proteasome system (UPS)—the proteasome holoenzymes and a number of ubiquitin ligases—play a crucial role, not only in virus replication but also in the regulation of the immunogenicity of human immunodeficiency virus type 1 (HIV-1). However, the role in HIV-1 replication of the third major component, the deubiquitinating enzymes (DUBs), has remained largely unknown. In this study, we show that the DUB-inhibitors (DIs) P22077 and PR-619, specific for the DUBs USP7 and USP47, impair Gag processing and thereby reduce the infectivity of released virions without affecting viral protease activity. Furthermore, the replication capacity of X4- and R5-tropic HIV-1NL4-3 in human lymphatic tissue is decreased upon treatment with these inhibitors without affecting cell viability. Most strikingly, combinatory treatment with DIs and proteasome inhibitors synergistically blocks virus replication at concentrations where mono-treatment was ineffective, indicating that DIs can boost the therapeutic effect of proteasome inhibitors. In addition, P22077 and PR-619 increase the polyubiquitination of Gag and thus its entry into the UPS and the major histocompatibility complex (MHC)-I pathway. In summary, our data point towards a model in which specific inhibitors of DUBs not only interfere with virus spread but also increase the immune recognition of HIV-1 expressing cells.
Asymmetrical reproductive character displacement in the house mouse

Our study addressed reproductive character displacement between two subspecies of the house mouse, Mus musculus musculus and Mus musculus domesticus that hybridize in Europe along a zone where selection against hybridization is known to occur. Based on a multi‐population approach, we investigated spatial patterns of divergence of mate preference in the two taxa. Mate preference was significantly higher in the contact zone than in allopatry in both subspecies, suggesting that reproductive character displacement occurs. Moreover, patterns of preference were stronger in M. m. musculus than in M. m. domesticus, indicating an asymmetrical divergence between the two. In the context of selection against hybridization, our results may provide empirical support for the hypothesis of reinforcement in a parapatric hybrid zone. We discuss factors that could explain the asymmetrical pattern of divergence and the possible impact of a unimodal structure on the maintenance of premating divergence between the two subspecies.
REGIONAL, CELLULAR AND SUBCELLULAR DISTRIBUTION OF CALCIUM‐ACTIVATED CYCLIC NUCLEOTIDE PHOSPHODIESTERASE AND CALCIUM‐DEPENDENT REGULATOR IN PORCINE BRAIN 1

Abstract— Cyclic nucleotide phosphodiesterase activity (calcium‐dependent and calcium‐independent) and CDR (calcium‐dependent regulator protein of phosphodiesterase) are present in all ten brain regions examined, with the specific activity of both being highest in areas predominating in grey matter and lowest in areas consisting largely of white matter. Fractionation of cerebral cortex into neuronal and glial perikarya shows that cyclic nucleotide phosphodiesterase and CDR are present at approximately equal levels in both cell types. Subcellular fractionation reveals that calcium‐sensitive enzyme specific activity, as well as CDR are highly localized in the 100,000 g supernatant fraction. Regional, cellular and subcellular distribution studies indicate that the distribution of CDR closely parallels the distribution of enzyme specific activity, suggesting that the levels of cyclic nucleotide phosphodiesterase and CDR may be synchronized.