Miracle-dz/UniFAR-FTUs huggingface dataset:
Crystal structure and substrate specificity of the β‐ketoacyl‐acyl carrier protein synthase III (FabH) from Staphylococcus aureus

β‐Ketoacyl‐ACP synthase III (FabH), an essential enzyme for bacterial viability, catalyzes the initiation of fatty acid elongation by condensing malonyl‐ACP with acetyl‐CoA. We have determined the crystal structure of FabH from Staphylococcus aureus, a Gram‐positive human pathogen, to 2 Å resolution. Although the overall structure of S. aureus FabH is similar to that of Escherichia coli FabH, the primer binding pocket in S. aureus FabH is significantly larger than that present in E. coli FabH. The structural differences, which agree with kinetic parameters, provide explanation for the observed varying substrate specificity for E. coli and S. aureus FabH. The rank order of activity of S. aureus FabH with various acyl‐CoA primers was as follows: isobutyryl‐ > hexanoyl‐ > butyryl‐ > isovaleryl‐ >> acetyl‐CoA. The availability of crystal structure may aid in designing potent, selective inhibitors of S. aureus FabH.
The potential implementation of green infrastructure assessment using high-resolution National Agriculture Imagery Program data for sustainable hazard mitigation

ABSTRACT As green infrastructure gets its attention in hazard mitigation, it is necessary to improve general understanding on what makes green infrastructure important for hazard and resiliency research. To better understand how green infrastructure fits with more traditional notions of structural and nonstructural mitigation, this study examines the relationship between green infrastructure and ‘structural and nonstructural’ mitigation approaches for hazard mitigation. Also, this study discusses a new measurement of locational aspects and spatial patterns of green infrastructure by utilizing high-resolution data in urban areas, and its potential implementation in hazard mitigation. Compared to previous research using land-use land-cover datasets, the normalized difference vegetation index (NDVI) utilizing National Agriculture Imagery Program dataset provides an ability to capture green infrastructure in greater detail. A visual comparison suggests that the NDVI data are able to capture and identify more types of ‘green’ land uses in Harris County. The total green infrastructure percentages for Harris County, Texas, based on 1-m high resolution were found to be 61.5% of the area, compared to the 51.5% based on the National Land Cover Database. This study provides support for utilizing high-resolution data to establish guidelines for green infrastructure’s spatial characteristics and sustainable hazard mitigation. The outcomes of this study will be helpful in the strategic planning and implementation of green infrastructure in urban areas with hazard issues.
XRCC1 Arg399Gln gene polymorphism and hepatocellular carcinoma risk in the Chinese Han population: a meta-analysis.

PURPOSE Numerous studies have evaluated the association between XRCC1 Arg399Gln gene polymorphism and hepatocellular carcinoma risk in the Chinese Han population. However, the results have been inconsistent. We therefore here examined whether the XRCC1 Arg399Gln gene polymorphism confers hepatocellular carcinoma risk by conducting a meta-analysis. METHODS PubMed, Google scholar and China National Knowledge Infrastructure databases were searched for eligible articles in English and Chinese that were published before April 2012. RESULTS 6 studies involving 1,246 patients with hepatocellular carcinoma and 1,953 controls were included. The association between XRCC1 Arg399Gln gene polymorphism and hepatocellular carcinoma in the Chinese Han population was significant under GG vs AA (OR = 1.48, 95% CI = 1.13 to 1.94). Limiting the analysis to the studies with controls in the Hardy-Weinberg equilibrium, the results were persistent and robust. CONCLUSIONS In the Chinese Han population, the XRCC1 Arg399Gln gene polymorphism is associated with an increased hepatocellular carcinoma risk.
Pour une grande mobilisation nationale de tous les acteurs pour la promotion de la nutrition en France. Eléments de bilan du PNNS (2001-2005) et propositions de nouvelles stratégies pour le PNNS2 (2006-2008)

Ce rapport a ete redige a la demande de Mr Xavier Bertrand, Ministre de la Sante et desSolidarites. Il vise, d’une part, a donner des elements de bilan tant quantitatif que qualitatif duPNNS 2001-2005, et, d’autre part, a proposer des recommandations pour la mise en place denouvelles strategies pour la suite du PNNS2 (2006-2008). Ce rapport a ete construit en quatre parties :1. un rappel sur le PNNS 2001-2004,2. un bilan qualitatif des differentes actions developpees, au niveau national, depuis 2001,date du debut du programme,3. les evaluations de certaines actions specifiques, en terme de processus, sans prejuger del’impact des actions sur les objectifs nutritionnels definis dans le PNNS. Cetteevaluation quantitative ne sera possible qu’apres la realisation de l’etude nationalenutrition-sante (ENNS) programmee pour 2006,4. des propositions d’actions concretes pour le PNNS2 s’appuyant sur l’experience duPNNS 2001-2005, les travaux menes dans differents pays et les progres desconnaissances scientifiques des dernieres annees, sur les differents rapports publiesdans le champ de la nutrition de sante publique, en France, en Europe et en Ameriquedu Nord et sur la concertation des multiples acteurs concernes (institutionnels,scientifiques, acteurs economiques, consommateurs,.). Les objectifs nutritionnelsprioritaires restent ceux definis dans le PNNS 2001-2005 et inscrits dans la loi de SantePublique du 9 aout 2004. Les propositions concretes faites dans ce rapport visent dont apermettre d’atteindre les objectifs fixes. Elles visent, d’une facon generale, a assurer lapromotion de la nutrition pour ameliorer l’etat de sante de la population generale etreduire le risque de maladies chroniques (notamment les maladies cardiovasculaires etles cancers), et, d’une facon specifique, reduire le risque et prendre en chargeefficacement les problemes d’obesite (notamment l’obesite infantile) et de denutrition(notamment des sujets âges).
Risk stratification schemes, anticoagulation use and outcomes: the risk–treatment paradox in patients with newly diagnosed non-valvular atrial fibrillation

Objective To examine whether warfarin use and outcomes differ across CHADS2 and CHA2DS2-VASc risk strata for non-valvular atrial fibrillation (NVAF). Design Population-based cohort study using linked administrative databases in Alberta, Canada. Setting Inpatient and outpatient. Patients 42 834 consecutive patients ≥20 years of age with newly diagnosed NVAF. Main outcome measures Cerebrovascular events and/or mortality in the first year after diagnosis. Results Of 42 834 NVAF patients, 22.7% were low risk on the CHADS2 risk score (0), 27.5% were intermediate risk (1), and 49.8% were high risk (≥2). The CHA2DS2-VASc risk score reclassified 16 722 patients such that 7.8% were defined low risk, 13.8% intermediate risk and 78.4% high risk. Of the elderly cohort (≥65 years) with definite NVAF visits (at least two encounters 30 days apart, n=8780), 49% were taking warfarin within 90 days of diagnosis. Warfarin use did not differ across risk strata using either the CHADS2 (p for trend=0.85) or CHA2DS2-VASC (p=0.35). In multivariable adjusted analyses, warfarin use was associated with substantially lower rates of death or cerebrovascular events for patients with CHADS2 scores of 1 (OR 0.52, 95% CI 0.41 to 0.67) or ≥2 (OR 0.61, 95% CI 0.53 to 0.71), or CHA2DS2-VASc scores of ≥2 (OR 0.60, 95% CI 0.53 to 0.68). Conclusions In elderly patients with NVAF and elevated CHADS2 or CHA2DS2-VASC scores, warfarin users exhibited lower rates of cerebrovascular events and mortality. However, warfarin use did not differ across risk strata, another example of the risk–treatment paradox in cardiovascular disease.
Heterologous C-terminal sequences disrupt transcriptional activation and oncogenesis by p59v-rel

Members of the NF-kappa B/rel family of transcription factors are regulated through a trans association with members of a family of inhibitor proteins, collectively known as I kappa B proteins, that contain five to eight copies of a 33-amino-acid repeat sequence (ankyrin repeat). Certain NF-kappa B/rel proteins are also regulated by cis-acting ankyrin repeat-containing domains. The C terminus of p105NF-kappa B, the precursor of the 50-kDa subunit of NF-kappa B, contains a series of ankyrin repeats; proteolytic removal of this ankyrin domain is necessary for the manifestation of sequence-specific DNA binding and nuclear translocation of the N-terminal product. To investigate the structural requirements important for regulation of different NF-kappa B/rel family members by polypeptides containing ankyrin repeat domains, we have constructed a p59v-rel:p105NF-kappa B chimeric protein (p110v-rel-ank). The presence of C-terminal p105NF-kappa B-derived sequences in p110v-rel-ank inhibited nuclear translocation, sequence-specific DNA binding, pp40I kappa B-alpha association, and oncogenic transformation. Sequential truncation of the C-terminal ankyrin domain of p110v-rel-ank resulted in the restoration of nuclear translocation, DNA binding, and pp40I kappa B-alpha association but did not restore the oncogenic properties of p59v-rel. The presence of 67 C-terminal p105NF-kappa B-derived amino acids was sufficient to inhibit both transcriptional activation and oncogenic transformation by p59v-rel. These results support a model in which activation of gene expression by p59v-rel is required for its ability to induce oncogenic transformation.
An Electrostatically Actuated Stacked-Electrode MEMS Relay With a Levering and Torsional Spring for Power Applications

This paper reports on a novel electrostatically actuated microelectromechanical systems (MEMS) relay for use in power-switching applications. It features a levering and torsional spring to enhance the stand-off voltage and contact endurance by means of an active-opening scheme. The proposed relay is based on a unique stacked-electrode structure and a soft insulating layer under the contact material that make it possible to obtain extremely low contact resistance, resulting in high current driving capability and reliable contact endurance. The fabricated relay demonstrated actuation voltages under 40 V, a switching time of 230 μs, and a maximum stand-off voltage of 360 V, which is the highest level among electrostatically actuated MEMS relays reported to date. The contact resistance was under 5 mΩ at 40 V of applied voltage, and more than 1 A could be carried. The contact reliability in a hot-switching condition was investigated for various dc current levels. At a current of 10 mA, the relay operated for more than 107 cycles before the test was stopped. In addition, the permanent contact stiction during switching operation at a 200-mA current level was overcome with a pull-off (active-opening) voltage of 90 V by the levering and torsional spring. Using this healing process, a device that failed at about 104 switching cycles in the 200-mA hot-switching mode was revived and reoperated with negligible contact resistance variation, lasting up to 4.9 ×105 cycles, constituting an order-of-magnitude enhancement in the lifetime even after failure.
Dual DNA binding specificity of a petal epidermis‐specific MYB transcription factor (MYB.Ph3) from Petunia hybrida.

The MYB.Ph3 protein recognized two DNA sequences that resemble the two known types of MYB DNA binding site: consensus I (MBSI), aaaAaaC(G/C)‐GTTA, and consensus II (MBSII), aaaAGTTAGTTA. Optimal MBSI was recognized by animal c‐MYB and not by Am305 from Antirrhinum, whereas MBSII showed the reverse behaviour. Different constraints on MYB.Ph3 binding to the two classes of sequences were demonstrated. DNA binding studies with mutated MBSI and MBSII and hydroxyl radical footprinting analysis, pointed to the N‐terminal MYB repeat (R2) as the most involved in determining the dual DNA binding specificity of MYB.Ph3 and supported the idea that binding to MBSI and MBSII does not involve alternative orientations of the two repeats of MYB.Ph3. Minimal promoters containing either MBSI and MBSII were activated to the same extent by MYB.Ph3 in yeast, indicating that both types of binding site can be functionally equivalent. MYB.Ph3 binding sites are present in the promoter of flavonoid biosynthetic genes, such as the Petunia chsJ gene, which was transcriptionally activated by MYB.Ph3 in tobacco protoplasts. MYB.Ph3 was immunolocalized in the epidermal cell layer of petals, where flavonoid biosynthetic genes are actively expressed. This strongly suggests a role for MYB.Ph3 in the regulation of flavonoid biosynthesis.
Exercise Training and Energy Expenditure following Weight Loss.

PURPOSE This study aims to determine the effects of aerobic or resistance training on activity-related energy expenditure (AEE; kcal·d(-1)) and physical activity index (activity-related time equivalent (ARTE)) following weight loss. It was hypothesized that weight loss without exercise training would be accompanied by decreases in AEE, ARTE, and nontraining physical activity energy expenditure (nonexercise activity thermogenesis (NEAT)) and that exercise training would prevent decreases in free-living energy expenditure. METHODS One hundred forty premenopausal women had an average weight loss of 25 lb during a diet (800 kcal·d(-1)) of furnished food. One group aerobically trained 3 times per week (40 min·d(-1)), another group resistance-trained 3 times per week (10 exercises/2 sets × 10 repetitions), and the third group did not exercise. Dual-energy x-ray absorptiometry was used to measure body composition, indirect calorimetry was used to measure resting energy expenditure (REE) and walking energy expenditure, and doubly labeled water was used to measure total energy expenditure (TEE). AEE, ARTE, and nontraining physical activity energy expenditure (NEAT) were calculated. RESULTS TEE, REE, and NEAT all decreased following weight loss for the no-exercise group, but not for aerobic and resistance trainers. Only REE decreased in the two exercise groups. Resistance trainers increased ARTE. HR and oxygen uptake while walking on the flat and up a grade were consistently related to TEE, AEE, NEAT, and ARTE. CONCLUSIONS Exercise training prevents a decrease in energy expenditure, including free-living energy expenditure separate from exercise training, following weight loss. Resistance training increases physical activity, whereas economy/ease of walking is associated with increased TEE, AEE, NEAT, and ARTE.
Recombinant human thioredoxin-1 becomes oxidized in circulation and suppresses bleomycin-induced neutrophil recruitment in the rat airway

Thioredoxin-1 (TRX) is a redox-active protein with anti-inflammatory effects. This study investigated the optimal delivery method and the mechanisms of recombinant human TRX (rhTRX) to suppress neutrophil recruitment in a rat bleomycin (BLM)-induced sustained acute lung injury model. In male Wister rats intratracheally administered with 0.125 mg/kg BLM, 8 mg/kg/day rhTRX was intravenously administered on days 3–6 using one of three protocols: daily bolus injection, 3 h daily infusion or continuous infusion for 96 h. Only the continuous-infusion of rhTRX significantly reduced the neutrophil infiltration compared with the other two methods. The BLM-induced down-regulation of l-selectin expression on circulating neutrophils was inhibited by rhTRX. Oxidized rhTRX showed a comparable effect with reduced rhTRX and rhTRX incubated with plasma or circulating in plasma was more than 99% oxidized. These results suggest that rhTRX becomes oxidized in circulation and continuous infusion of rhTRX suppresses neutrophil recruitment in the airway.
Combined accelerometer and EMG analysis to differentiate essential tremor from Parkinson's disease

In this study, we intended to differentiate patients with essential tremor (ET) from tremor dominant Parkinson disease (PD). Accelerometer and electromyographic signals of hand movement from standardized upper extremity movement tests (resting, holding, carrying weight) were extracted from 13 PD and 11 ET patients. The signals were filtered to remove noise and non-tremor high frequency components. A set of statistical features was then extracted from the discrete wavelet transformation of the signals. Principal component analysis was utilized to reduce dimensionality of the feature space. Classification was performed using support vector machines. We evaluated the proposed method using leave one out cross validation and we report overall accuracy of the classification. With this method, it was possible to discriminate 12/13 PD patients from 8/11 patients with ET with an overall accuracy of 83%. In order to individualize this finding for clinical application we generated a posterior probability for the test result of each patient and compared the misclassified patients, or low probability scores to available clinical follow up information for individual cases. This non-standardized post hoc analysis revealed that not only the technical accuracy but also the clinical accuracy limited the overall classification rate. We show that, in addition to the successful isolation of diagnostic features, longitudinal and larger sized validation is needed in order to prove clinical applicability.
Key-frame extraction for object-based video segmentation

We propose a coherent approach to extract key-frames within a video shot for object-based video segmentation. A unified feature space is first constructed to represent video frames and visual objects simultaneously in a joint spatio-temporal domain, and key-frame extraction is formulated as a feature selection process that aims to maximize the cluster divergence of video objects by selecting an optimal set of key-frames. Specifically, two different criteria are used to achieve joint key-frame extraction and object segmentation. One criterion recommends key-frame extraction that leads to the maximum pairwise interclass divergence between objects in the feature space. The other aims at maximizing the marginal divergence of objects in each frame. Simulations with both synthetic and real video data manifest the efficiency and robustness of the proposed methods.
Robust model predictive control for LPV systems with delayed state using relaxation matrices

This paper proposes a model predictive control (MPC) algorithm for Linear Parameter Varying (LPV) systems with unknown bounded delay, subject to input constraints. To deal with the delay, an optimization problem is formulated by applying the equivalence property. Sufficient conditions are derived in terms of linear matrix inequalities (LMIs) using relaxation matrices, satisfying the terminal inequality. The proposed MPC algorithm with the conditions guarantees the asymptotic stability of the closed-loop system. A numerical example is presented to illustrate the effectiveness of the proposed method.
A simple method for power system stability analysis with multiple time delays

There exist significant time delays in the data of phasor measurement unit (PMU) and wide-area measurement system (WAMS). To properly evaluate the impact of time delay is very important for power system online stability assessment and controller design. In this paper, the maximum delayed time that power system can sustain without losing its stability is denoted as its delay margin. From the viewpoint of Lyapunov stability, when a dynamic system is critical stable at a given equilibrium point, there must exist critical eigenvalue on the imaginary axis. This paper presents a simple method to determine such critical eigenvalue by tracing eigenvalue loci of a transformation matrix. Then the critical eigenvalue is used to determine the delay margin of power system. Comparing with previous approaches, such as Lyapunov function/functional method, LMI method, root clustering paradigm method, the presented method can locate the exact delay margin with no conservativeness and with less computation burden. Moreover, it can be easily applied to the stability analysis of bulk power system with multiple time delays. Finally, single machine and infinite bus system (SMIB) and WSCC 3-generator-9-bus system are employed to validate its effectiveness.
Human Bocavirus: Passenger or Pathogen in Acute Respiratory Tract Infections?

SUMMARY Human bocavirus (HBoV) is a newly identified virus tentatively assigned to the family Parvoviridae, subfamily Parvovirinae, genus Bocavirus. HBoV was first described in 2005 and has since been detected in respiratory tract secretions worldwide. Herein we review the literature on HBoV and discuss the biology and potential clinical impact of this virus. Most studies have been PCR based and performed on patients with acute respiratory symptoms, from whom HBoV was detected in 2 to 19% of the samples. HBoV-positive samples have been derived mainly from infants and young children. HBoV DNA has also been detected in the blood of patients with respiratory tract infection and in fecal samples of patients with diarrhea with or without concomitant respiratory symptoms. A characteristic feature of HBoV studies is the high frequency of coinciding detections, or codetections, with other viruses. Available data nevertheless indicate a statistical association between HBoV and acute respiratory tract disease. We present a model incorporating these somewhat contradictory findings and suggest that primary HBoV infection causes respiratory tract symptoms which can be followed by prolonged low-level virus shedding in the respiratory tract. Detection of the virus in this phase will be facilitated by other infections, either simply via increased sample cell count or via reactivation of HBoV, leading to an increased detection frequency of HBoV during other virus infections. We conclude that the majority of available HBoV studies are limited by the sole use of PCR diagnostics on respiratory tract secretions, addressing virus prevalence but not disease association. The ability to detect primary infection through the development of improved diagnostic methods will be of great importance for future studies seeking to assign a role for HBoV in causing respiratory illnesses.
A Protease-Independent Function for SPPL3 in NFAT Activation

ABSTRACT The signal peptide peptidase (SPP)-related intramembrane aspartyl proteases are a homologous group of polytopic membrane proteins, some of which function in innate or adaptive immunity by cleaving proteins involved in antigen presentation or intracellular signaling. Signal peptide peptidase-like 3 (SPPL3) is a poorly characterized endoplasmic reticulum (ER)-localized member of this family, with no validated cellular substrates. We report here the isolation of SPPL3 in a screen for activators of NFAT, a transcription factor that controls lymphocyte development and function. We find that SPPL3 is required downstream of T cell receptor engagement for maximal Ca2+ influx and NFAT activation. Surprisingly, the proteolytic activity of SPPL3 is not required for its role in this pathway. SPPL3 enhances the signal-induced association of stromal interaction molecule 1 (STIM1) and Orai1 and is even required for the full activity of constitutively active STIM1 variants that bind Orai1 independently of ER Ca2+ release. SPPL3 associates with STIM1 through at least two independent domains, the transmembrane region and the CRAC activation domain (CAD), and can promote the association of the STIM1 CAD with Orai1. Our results assign a function in lymphocyte signaling to SPPL3 and highlight the emerging importance of nonproteolytic functions for members of the intramembrane aspartyl protease family.