Miracle-dz/UniFAR-FTUs huggingface dataset:
The arginine finger of the Bloom syndrome protein: its structural organization and its role in energy coupling

RecQ family helicases are essential in maintaining chromosomal DNA stability and integrity. Despite extensive studies, the mechanisms of these enzymes are still poorly understood. Crystal structures of many helicases reveal a highly conserved arginine residue located near the γ-phosphate of ATP. This residue is widely recognized as an arginine finger, and may sense ATP binding and hydrolysis, and transmit conformational changes. We investigated the existence and role of the arginine finger in the Bloom syndrome protein (BLM), a RecQ family helicase, in ATP hydrolysis and energy coupling. Our studies by combination of structural modelling, site-directed mutagenesis and biochemical and biophysical approaches, demonstrate that mutations of residues interacting with the γ-phosphate of ATP or surrounding the ATP-binding sites result in severe impairment in the ATPase activity of BLM. These mutations also impair BLM's DNA-unwinding activities, but do not affect its ATP and DNA-binding abilities. These data allow us to identify R982 as the residue that functions as a BLM arginine finger. Our findings further indicate how the arginine finger is precisely positioned by the conserved motifs with respect to the γ-phosphate.
Cytoplasmic Unsaturated Free Fatty Acids Inhibit Atp-Dependent Gating of the G Protein–Gated K+ Channel

This study reports the identification of an endogenous inhibitor of the G protein–gated (KACh) channel and its effect on the KACh channel kinetics. In the presence of acetylcholine in the pipette, KACh channels in inside-out atrial patches were activated by applying GTP to the cytoplasmic side of the membrane. In these patches, addition of physiological concentration of intracellular ATP (4 mM) upregulated KACh channel activity approximately fivefold and induced long-lived openings. However, such ATP-dependent gating is normally not observed in cell-attached patches, indicating that an endogenous substance that inhibits the ATP effect is present in the cell. We searched for such an inhibitor in the cell. ATP-dependent gating of the KACh channel was inhibited by the addition of the cytosolic fraction of rat atrial or brain tissues. The lipid component of the cytosolic fraction was found to contain the inhibitory activity. To identify the lipid inhibitor, we tested the effect of ∼40 different lipid molecules. Among the lipids tested, only unsaturated free fatty acids such as oleic, linoleic, and arachidonic acids (0.2–2 μM) reversibly inhibited the ATP-dependent gating of native KACh channels in atrial cells and hippocampal neurons, and of recombinant KACh channels (GIRK1/4 and GIRK1/2) expressed in oocytes. Unsaturated free fatty acids also inhibited phosphatidylinositol-4,5-bisphosphate (PIP2)-induced changes in KACh channel kinetics but were ineffective against ATP-activated background K1 channels and PIP2-activated KATP channels. These results show that during agonist-induced activation, unsaturated free fatty acids in the cytoplasm help to keep the cardiac and neuronal KACh channels downregulated by antagonizing their ATP-dependent gating. The opposing effects of ATP and free fatty acids represent a novel regulatory mechanism for the G protein–gated K+ channel.
Effects of Straw Incorporation on Soil Organic Matter and Soil Water-Stable Aggregates Content in Semiarid Regions of Northwest China

The soil degradation caused by conventional tillage in rain-fed areas of northwest China is known to reduce the water–use efficiency and crop yield because of reduced soil porosity and the decreased availability of soil water and nutrients. Thus, we investigated the effects of straw incorporation on soil aggregates with different straw incorporation rates in semiarid areas of southern Ningxia for a three-year period (2008–2010). Four treatments were tested: (i) no straw incorporation (CK); (ii) incorporation of maize straw at a low rate of 4 500 kg ha−1 (L); (iii) incorporation of maize straw at a medium rate of 9000 kg ha−1 (M); (iv) incorporation of maize straw at a high rate of 13 500 kg ha−1 (H). The results in the final year of treatments (2010) showed that the mean soil organic carbon storage of the 0–60 cm soil layers were significantly (P<0.05) increased with H, M, and L, by 21.40%, 20.38% and 8.21% compared with CK, respectively. Straw incorporation increased >0.25 mm water-stable macroaggregates level, geometric mean diameter, mean weight diameter and the aggregate stability, which were ranked in order of increasing straw incorporation rates: H/M > L > CK. Straw incorporation significantly (P<0.05) reduced the fractal dimension in the 0–40 cm soil layers compared with CK. Our results suggest that straw incorporation is an effective practice for improving the soil aggregate structure and stability.
Wearables Can Afford: Light-weight Indoor Positioning with Visible Light

Visible Light Positioning (VLP) provides a promising means to achieve indoor localization with sub-meter accuracy. We observe that the Visible Light Communication (VLC) methods in existing VLP systems rely on intensity-based modulation, and thus they require a high pulse rate to prevent flickering. However, the high pulse rate adds an unnecessary and heavy burden to receiving devices. To eliminate this burden, we propose the polarization-based modulation, which is flicker-free, to enable a low pulse rate VLC. In this way, we make VLP light-weight enough even for resource-constrained wearable devices, e.g. smart glasses. Moreover, the polarization-based VLC can be applied to any illuminating light sources, thereby eliminating the dependency on LED. This paper presents the VLP system PIXEL, which realizes our idea. In PIXEL, we develop three techniques, each of which addresses a design challenge: 1) a novel color-based modulation scheme to handle users? mobility, 2) an adaptive downsampling algorithm to tackle the uneven sampling problem of wearables? low-cost camera and 3) a computational optimization method for the positioning algorithm to enable real-time processing. We implement PIXEL? s hardware using commodity components and develop a software program for both smartphone and Google glass. Our experiments based on the prototype show that PIXEL can provide accurate realtime VLP for wearables and smartphones with camera resolution as coarse as 60 pixel x 80 pixel and CPU frequency as low as 300MHz.
Diagnosis of Arrhythmogenic Right Ventricular Cardiomyopathy/Dysplasia: Proposed Modification of the Task Force Criteria

Background— In 1994, an International Task Force proposed criteria for the clinical diagnosis of arrhythmogenic right ventricular cardiomyopathy/dysplasia (ARVC/D) that facilitated recognition and interpretation of the frequently nonspecific clinical features of ARVC/D. This enabled confirmatory clinical diagnosis in index cases through exclusion of phenocopies and provided a standard on which clinical research and genetic studies could be based. Structural, histological, electrocardiographic, arrhythmic, and familial features of the disease were incorporated into the criteria, subdivided into major and minor categories according to the specificity of their association with ARVC/D. At that time, clinical experience with ARVC/D was dominated by symptomatic index cases and sudden cardiac death victims—the overt or severe end of the disease spectrum. Consequently, the 1994 criteria were highly specific but lacked sensitivity for early and familial disease. Methods and Results— Revision of the diagnostic criteria provides guidance on the role of emerging diagnostic modalities and advances in the genetics of ARVC/D. The criteria have been modified to incorporate new knowledge and technology to improve diagnostic sensitivity, but with the important requisite of maintaining diagnostic specificity. The approach of classifying structural, histological, electrocardiographic, arrhythmic, and genetic features of the disease as major and minor criteria has been maintained. In this modification of the Task Force criteria, quantitative criteria are proposed and abnormalities are defined on the basis of comparison with normal subject data. Conclusions— The present modifications of the Task Force Criteria represent a working framework to improve the diagnosis and management of this condition. Clinical Trial Registration— URL: http://www.clinicaltrials. gov. Unique identifier: NCT00024505.
Huntington's disease in venezuela: 7 years of follow‐up on symptomatic and asymptomatic individuals

Persons symptomatic and at risk for Huntington's disease (HD) from a large extended family in the state of Zulia, Venezuela, have been followed prospectively for 7 years. Between 1981 and 1988, 593 people were examined, of whom 128 had symptomatic HD and 171 persons at risk had examination abnormalities that were insufficient to meet criteria for diagnosis. The remaining 294 had normal examinations. Abnormalities of saccadic eye movement and slowness of rapid alternating movements were the most common abnormalities found in at‐risk individuals. Thirty persons who did not meet criteria for diagnosis at their first examination have subsequently been diagnosed with symptomatic HD. Their average age at diagnosis was 33.5 ± 8.3 (SD) years. The likelihood of developing symptomatic HD within 3 years was 3% for those persons with normal first examinations, 23% for those with mildly abnormal first examinations, and 60% for those with highly abnormal first examinations. The rate of disease progression in early symptomatic cases were 1.4 ± 0.1 (SEM) points per year on the Shoulson‐Fahn functional capacity scale. Paternal or maternal inheritance did not appear to affect the rate of progression in this group of individuals. The data suggest that there is not a discrete age of onset but rather a prolonged period of time during which symptoms unfold.
Malaria Household Knowledge and Behavior in Equatorial Guinea: Lessons to Be Learned

Background: Malaria continues to be a major public health problem in Equatorial Guinea, despite the control efforts made since 1990s. Upcoming control interventions should incorporate the behavioral and social aspects of malaria, for which is essential to have base-line and context-specific information. Methods: A retrospective study was carried out to analyze the major outcomes of three cross-sectional surveys on malaria-related knowledge and behavior, conducted in Equatorial Guinea in 1996, 2001 and 2007. Results were described using frequencies, and major outcomes were compared between regions through logistic regression analysis adjusting by socio-economic and individual-related factors. Results: The knowledge towards malaria was overall better in 2001 than in 1996 in rural Bioko, and the attitudes and practices concerning malaria treatment and prevention were more correct in Bioko Island than in mainland Equatorial Guinea in 2001. Results in the 2007 survey, showed limited knowledge but appropriate practices related to the management of children with clinical malaria in Bata. Conclusion: Equatorial Guinea is a small but heterogenic country, with population showing distinct perception of malaria and its public health impact across regions. National malaria control strategies should have this diversity into account and sensitization campaigns should be tailored to context-specific misconceptions and different epidemiological patterns identified.
Anti-Starvation Channel Assignment With Global Conflict Set Selection in IEEE 802.11 WMNs

Channel assignment algorithms play a critical role in the performance of IEEE 802.11 wireless mesh network by allocating channels and regulating interference between channels. In a channel assignment algorithm, the strategy used to compute a conflict set is crucial because it directly determines the allocation of channels to a given link. This paper investigates the fairness and prevention of flow starvation due to different strategies in selecting conflict sets in a channel assignment algorithm. We apply five different conflict set selection strategies to a vanilla channel assignment algorithm and compare the resulting network performance of each strategy. Our findings show that none of these conflict set selection strategies prevent flow starvation and achieve poor fairness as they only consider "local channel conflict" and lack the consideration of "global channel conflict". We propose a new conflict set selection for channel assignment algorithms called anti-starvation channel assignment (ASCA). Our proposed algorithm considers both local and global conflict to alleviate flow starvation and improves fairness by 62% (with respect to the fairness index) compared with the best result from existing conflict set selection strategies. To the best of our knowledge, the proposed ASCA is the first one to analyse channel assignment algorithms using the concept of local and global conflict sets.
MACS: A Quest for the Most Massive Galaxy Clusters in the Universe

We describe the design and current status of a new X-ray cluster survey aimed at the compilation of a statistically complete sample of very X-ray luminous (and thus, by inference, massive), distant clusters of galaxies. The primary goal of the Massive Cluster Survey (MACS) is to increase the number of known massive clusters at z > 0.3 from a handful to hundreds. Upon completion of the survey, the MACS cluster sample will greatly improve our ability to study quantitatively the physical and cosmological parameters driving cluster evolution at redshifts and luminosities poorly sampled by all existing surveys. To achieve these goals, we apply an X-ray flux and X-ray hardness ratio cut to select distant cluster candidates from the ROSAT Bright Source Catalogue. Starting from a list of more than 5000 X-ray sources within the survey area of 22,735 deg2, we use positional cross-correlations with public catalogs of Galactic and extragalactic objects, reference to Automated Plate Measuring Machine (APM) colors, visual inspection of Digitized Sky Survey images, extensive CCD imaging, and finally spectroscopic observations with the University of Hawaii's 2.2 m and the Keck 10 m telescopes to compile the final cluster sample. We discuss in detail the X-ray selection procedure and the resulting selection function and present model predictions for the number of distant clusters expected to emerge from MACS. At the time of this writing the MACS cluster sample comprises 101 spectroscopically confirmed clusters at 0.3 ≤ z ≤ 0.6; more than two-thirds of these are new discoveries. Our preliminary sample is already 15 times larger than that of the EMSS in the same redshift and X-ray luminosity range.
Treatment should be considered a competing risk when predicting natural conception in subfertile women.

BACKGROUND Prediction of natural conception in subfertile couples can help to differentiate between couples who should have immediate treatment and couples who can aim for natural conception for some time. Natural conception rates are often estimated using standard techniques such as Kaplan-Meier or Cox proportional hazard models. These estimates can be biased by incorrect handling of data from women who start assisted reproductive technology therapy before the end of the follow-up period. This paper discusses the validity and the impact of the assumption of non-informative censoring as used in the Kaplan-Meier and Cox models. METHODS In a cohort of 5360 subfertile couples with suspected tubal pathology, the probability of natural conception and the prognostic value of additional tests for tubal pathology were estimated using traditional methods and with a competing risks analysis. RESULTS The estimated probability of natural conception within 3 years was almost 2-fold higher when assuming non-informative censoring compared with the competing risks model, 41 versus 22%. The prognostic value of tests was more conservative using the competing risks model than with the traditional methods, the fecundity rate ratio for Chlamydia antibody testing was 0.72 versus 0.67, for hysterosalpingography, 0.83 versus 0.71 and for diagnostic laparoscopy, 0.89 versus 0.74. CONCLUSIONS Given the improbable validity of the non-informative censoring assumption, the predictions of natural conception and of the prognostic value of tests are likely to be overestimated by the traditional analytic methods. We suggest the use of competing risks models as an alternative, more conservative, form of analysis when predicting natural conception and evaluating prognostic fertility tests.
A Theory of the IMF for Star Formation in Molecular Clouds

We present models for the initial mass function (IMF) for stars forming within molecular clouds. These models use the idea that stars determine their own masses through the action of powerful stellar outflows. This concept allows us to calculate a semi-empirical mass formula (SEMF), which provides the transformation between initial conditions in molecular clouds and the final masses of forming stars. For a particular SEMF, a given distribution of initial conditions predicts a corresponding IMF. We consider several different descriptions for the distribution of initial conditions in star forming molecular clouds. We first consider the limiting case in which only one physical variable -- the effective sound speed -- determines the initial conditions. In this limit, we use observed scaling laws to determine the distribution of sound speed and the SEMF to convert this distribution into an IMF. We next consider the opposite limit in which many different independent physical variables play a role in determining stellar masses. In this limit, the central limit theorem shows that the IMF approaches a log-normal form. Realistic star forming regions contain an intermediate number of relevant variables; we thus consider intermediate cases between the two limits. Our results show that this picture of star formation and the IMF naturally produces stellar mass distributions that are roughly consistent with observations. This paper thus provides a calculational framework to construct theoretical models of the IMF.
Shape optimizing load balancing for MPI-parallel adaptive numerical simulations

Load balancing is important for the efficient execution of numerical simulations on parallel computers. In particular when the simulation domain changes over time, the mapping of computational tasks to processors needs to be modified accordingly. Most state-of-the-art libraries addressing this problem are based on graph repartitioning with a parallel variant of the Kernighan-Lin (KL) heuristic. The KL approach has a number of drawbacks, including the optimized metric and solutions with undesirable properties. Here we further explore the promising diffusion-based multilevel graph partitioning algorithm DibaP. We describe the evolution of the algorithm and report on its MPI implementation PDibaP for parallelism with distributed memory. PDibaP is targeted at small to medium scale parallelism with dozens of processors. The presented experiments use graph sequences that imitate adaptive numerical simulations. They demonstrate the applicability and quality of PDibaP for load balancing by repartitioning on this scale. Compared to the faster ParMETIS, PDibaP’s solutions often have partitions with fewer external edges and a smaller communication volume in an underlying numerical simulation.
Even Supermoms Get the Blues: Employment, Gender Attitudes, and Depression

This study examines how gender attitudes moderate the relationship between employment and depressive symptoms using data from the 1987 to 2006 waves of the National Longitudinal Survey of Youth 1979 Cohort. Results indicate that at age 40, the association of employment with reduced symptoms of depression is greatest for mothers who had previously expressed support for traditional gender roles. This finding was robust to controls for prior depressive symptoms. In contrast, the association of employment and depressive symptoms at age 40 does not vary by earlier gender attitudes among childless women. Results suggest that in light of women’s disproportionate share of domestic responsibilities and limited employer supports for parents, skepticism over mothers’ ability to “do it all” may mitigate the stress of work-family role strain and allow mothers with more traditional gender attitudes to receive greater protection against depressive symptoms from employment.
Evidence for Rapidly Spinning Black Holes in Quasars

It has long been believed that accretion onto supermassive black holes powers quasars, but there are still relatively few observational constraints on the spins of the black holes. We address this problem by estimating the average radiative efficiencies of a large sample of quasars selected from the Sloan Digital Sky Survey, by combining their luminosity function and their black hole mass function. Over the redshift interval 0.4 < z < 2.1, we find that quasars have average radiative efficiencies of ~30%-35%, strongly suggesting that their black holes are rotating very rapidly, with specific angular momentum a ≈ 1, a value that remains roughly constant with redshift. The average radiative efficiency could be reduced by a factor of ~2, depending on the adopted zero point for the black hole mass scale. The inferred large spins and their lack of significant evolution are in agreement with the predictions of recent semianalytical models of hierarchical galaxy formation if black holes gain most of their mass through accretion.
Fluticasone propionate compared with budesonide: a double-blind trial in asthmatic children using powder devices at a dosage of 400 microg x day(-1).

The aim of this study was to compare fluticasone propionate (FP) with budesonide (BUD) at a dose of 400 microg x day(-1) in the treatment of children with asthma. Two hundred and twenty nine children with mild-to-moderate asthma, currently receiving 200-400 microg x day(-1) of inhaled corticosteroid, were randomized to receive either 400 microg x day(-1) of FP from the Diskhaler (registered trade mark of the Glaxo Group of Companies) or 400 microg x day(-1) of BUD from the Turbuhaler (registered trade mark of Astra Pharmaceuticals Ltd) for 8 weeks, in a parallel-group, double-blind, double-dummy study. Primary efficacy was assessed by measurement of daily peak expiratory flow (PEF). In addition, pulmonary function tests were performed at each clinic visit and a self-administered patient-centred questionnaire was completed by one parent of each patient at the start and end of study treatment. Mean morning PEF increased following treatment both with FP and BUD, but was significantly higher following treatment with FP during Weeks 1-4 (p=0.015) and Weeks 1-8 (p=0.019). Similar results were found for mean evening PEF and percentage predicted morning and evening PEF. Children receiving FP experienced significantly less disruption in their physical activities (i.e. sports, games) because of their asthma compared to children treated with BUD (p=0.03). Mean cortisol levels increased in both groups, but the increase was significantly higher in the FP group at 4 weeks (p=0.022). Serum and urine markers of bone formation and resorption changed very little and showed no consistent pattern of change. Fluticasone propionate at a dosage of 400 microg x day(-1) from the Diskhaler provided a more rapid and greater improvement in lung function in children with mild-to-moderate asthma than BUD 400 microg day(-1) from the Turbuhaler. Both treatments were well-tolerated, with a similar safety profile.