Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic Diversity and Population Structure of the Major Peanut (Arachis hypogaea L.) Cultivars Grown in China by SSR Markers

One hundred and forty-six highly polymorphic simple sequence repeat (SSR) markers were used to assess the genetic diversity and population structure of 196 peanut (Arachis Hypogaea L.) cultivars which had been extensively planted in different regions in China. These SSR markers amplified 440 polymorphic bands with an average of 2.99, and the average gene diversity index was 0.11. Eighty-six rare alleles with a frequency of less than 1% were identified in these cultivars. The largest Fst or genetic distance was found between the cultivars that adapted to the south regions and those to the north regions in China. A neighbor-joining tree of cultivars adapted to different ecological regions was constructed based on pairwise Nei’s genetic distances, which showed a significant difference between cultivars from the south and the north regions. A model-based population structure analysis divided these peanut cultivars into five subpopulations (P1a, P1b, P2, P3a and P3b). P1a and P1b included most the cultivars from the southern provinces including Guangdong, Guangxi and Fujian. P2 population consisted of the cultivars from Hubei province and parts from Shandong and Henan. P3a and P3b had cultivars from the northern provinces including Shandong, Anhui, Henan, Hebei, Jiangsu and the Yangtze River region including Sichuan province. The cluster analysis, PCoA and PCA based on the marker genotypes, revealed five distinct clusters for the entire population that were related to their germplasm regions. The results indicated that there were obvious genetic variations between cultivars from the south and the north, and there were distinct genetic differentiation among individual cultivars from the south and the north. Taken together, these results provided a molecular basis for understanding genetic diversity of Chinese peanut cultivars.
Recent results of high-resolution wireless indoor positioning based on IEEE 802.11ac

This contribution addresses the problem of highly resolving the propagation time difference of arrival (TDOA) associated with signals in multipath communication channels for wireless indoor positioning. The Unitary Matrix Pencil (UMP) algorithm is enhanced and applied in a new way to estimate the propagation time delays from the estimated space channel frequency response (S-CFR) using MIMO-OFDM systems. The performance of using wideband orthogonal multicarrier signals and multiple antennas for wireless positioning are presented. A non-iterative least square (LS) estimator is also presented to estimate the mobile unit (MU) coordinates based on the TDOA observations. Experimental results using the emerging IEEE 802.11ac standard show that accuracy in the range of two cm can be achieved for two-dimensional (2-D) wireless indoor positioning.
Low-overhead diskless checkpoint for hybrid computing systems

As the size of new supercomputers scales to tens of thousands of sockets, the mean time between failures (MTBF) is decreasing to just several hours and long executions need some kind of fault tolerance method to survive failures. Checkpoint\Restart is a popular technique used for this purpose; but writing the state of a big scientific application to remote storage will become prohibitively expensive in the near future. Diskless checkpoint was proposed as a solution to avoid the I/O bottleneck of disk-based checkpoint. However, the complex time-consuming encoding techniques hinder its scalability. At the same time, heterogeneous computing is becoming more and more popular in high performance computing (HPC), with new clusters combining CPUs and graphic processing units (GPUs). However, hybrid applications cannot always use all the resources available on the nodes, leaving some idle resources suc h us GPUs or CPU cores. In this work, we propose a hybrid diskless checkpoint (HDC) technique for GPU-accelerated clusters, that can checkpoint CPU/GPU applications, does not require spare nodes and can tolerate up to 50% of process failures with a low, sometimes negligible, checkpoint overhead.
Imputation-based Assessment of Next Generation Rare Exome Variant Arrays

A striking finding from recent large-scale sequencing efforts is that the vast majority of variants in the human genome are rare and found within single populations or lineages. These observations hold important implications for the design of the next round of disease variant discovery efforts-if genetic variants that influence disease risk follow the same trend, then we expect to see population-specific disease associations that require large sample sizes for detection. To address this challenge, and due to the still prohibitive cost of sequencing large cohorts, researchers have developed a new generation of low-cost genotyping arrays that assay rare variation previously identified from large exome sequencing studies. Genotyping approaches rely not only on directly observing variants, but also on phasing and imputation methods that use publicly available reference panels to infer unobserved variants in a study cohort. Rare variant exome arrays are intentionally enriched for variants likely to be disease causing, and here we assay the ability of the first commercially available rare exome variant array (the Illumina Infinium HumanExome BeadChip) to also tag other potentially damaging variants not molecularly assayed. Using full sequence data from chromosome 22 from the phase I 1000 Genomes Project, we evaluate three methods for imputation (BEAGLE, MaCH-Admix, and SHAPEIT2/IMPUTE2) with the rare exome variant array under varied study panel sizes, reference panel sizes, and LD structures via population differences. We find that imputation is more accurate across both the genome and exome for common variant arrays than the next generation array for all allele frequencies, including rare alleles. We also find that imputation is the least accurate in African populations, and accuracy is substantially improved for rare variants when the same population is included in the reference panel. Depending on the goals of GWAS researchers, our results will aid budget decisions by helping determine whether money is best spent sequencing the genomes of smaller sample sizes, genotyping larger sample sizes with rare and/or common variant arrays and imputing SNPs, or some combination of the two.
10-Gbps, 5.3-mW Optical Transmitter and Receiver Circuits in 40-nm CMOS

We describe transmitter and receiver circuits for a 10-Gbps single-ended optical link in a 40-nm CMOS technology. The circuits are bonded using low-parasitic micro-solder bumps to silicon photonic devices on a 130-nm SOI platform. The transmitter drives oval resonant ring modulators with a 2-V swing and employs static thermal tuners to compensate for optical device process variations. The receiver is based on a transimpedance amplifier (TIA) with 4-kΩ gain and designed for an input power of - 15 dBm, a photodiode responsivity of 0.7 A/W, and an input extinction ratio of 6 dB. It employs a pair of interleaved clocked sense-amplifiers for voltage slicing and uses a DLL with phase adjustment for centering the clock in the data eye. Periodic calibration allows for adjustment of both voltage and timing margins. At 10 Gbps, the transmitter extinction ratio exceeds 7 dB and, excluding thermal tuning and laser power, it consumes 1.35 mW. At the same datarate, the receiver consumes 3.95 mW. On-chip PRBS generators and checkers with 231-1 sequences confirm operation at a BER better than 10-12.
Impact of Steatosis on Long-Term Histological Outcome in Chronic Hepatitis C after Antiviral Therapy

Background/Aims Steatosis is recognized as a cofactor influencing the presence and progression of fibrosis in chronic hepatitis C. It has been reported that antiviral therapy may reduce the progression of fibrosis and leads to regression in chronic hepatitis C patients achieving a sustained virological response (SVR). Whether steatosis might affect the long-term histological outcome of antiviral therapy remains unclear. Methods One-hundred and sixty-one consecutive patients (genotype 1, n=76; genotype 2, n=73) receiving interferon-α2b and ribavirin were analysed. Ninety patients had paired biopsies with a mean interval of 29.1 ±7.1 months. Results Variables associated with baseline steatosis were higher body mass index (≥25, P=0.002) and higher fibrosis stage (≥2, P=0.019). Neither the presence nor the severity of steatosis was associated with SVR. Evaluation of paired biopsies showed no different distribution of steatosis evolution between patients with and without SVR (P=0.374). Among patients achieving a SVR, there was a significant difference in fibrosis changes between those with grade 0 or 1 steatosis and with grade 2 or 3 steatosis at post-treatment biopsy (-0.6 ±1.2 vs 0.3 ±1.3, P=0.041), whereas changes in histological activity index did not differ (-3.7 ±2.6 vs -4.0 ±2.9, P=0.740). Stepwise logistic regression analysis showed that SVR (odds ratio [OR]: 16.33, P=0.004) and grade 0 or 1 post-treatment steatosis (OR: 12.82, P=0.018) were independently associated with fibrosis regression. Conclusions In patients with chronic hepatitis C, steatosis not only correlates with advanced fibrosis at baseline but also affects fibrosis regression after antiviral therapy.
Are neck pain scales and questionnaires compatible with the international classification of functioning, disability and health? A systematic review

Purpose. To identify neck-pain-specific questionnaires and scales that measure functioning and disability and assess whether their contents are comparable to the international classification of functioning, disability and health (ICF). Methods. A systematic search was conducted in LILACS, MEDLINE, CINAHL, and SPORTSDISCUS databases, identifying questionnaires and scales used to assess neck-related functioning and disability from 1966 to November 2007. Each item of each scale or questionnaire was extracted and classified according to the ICF categories. Results. The databases yielded a total of 888 articles, of which seven questionnaires were identified and included in the review. A total of 74 items were analyzed, 27 linked to body function, 46 to activities and participation, 1 to environmental factors, and 5 to non-classified items. While the pain disability index tends to focus on limitations to body functions, the functional rating index and the Copenhagen neck functional disability scale appear to be limited to measuring activity. Three questionnaires (the neck Bournemouth Questionnaire, the neck disability index, and the neck pain and disability scale) have demonstrated a well-balanced distribution of items across the ICF components. Conclusion. Most identified questionnaires reflect limitations or restrictions in one component only. These results provide valuable information on the content quality of these questionnaires for health-care providers and researchers.
Variability-driven buffer insertion considering correlations

In this work, we investigate the buffer insertion problem under process variations. Sub 100-nm fabrication process causes significant variations on many design parameters. We propose a probabilistic buffer insertion method assuming variations on both interconnect and buffer parameters and consider their correlations due to common sources of variation. Our proposed method is compatible with the more accurate DSM wire-delay model, as well as the Elmore delay model. In addition, a probabilistic pruning criterion is proposed to evaluate potential solutions, while considering their correlations. Experimental results demonstrate that considering correlations using the more accurate DSM delay model results in meeting the timing constraint with an average probability of 0.63. However probabilistic buffer insertion ignoring correlations and deterministic methods, meet the timing constraint with an average probability of 0.25 and 0.19 respectively.
Interventions for children at risk of developing antisocial personality disorder

p o l i c y r e s e a r c h b u r e a u m e s s a g e s p o l i c y r e s e a r c h u r e a u This selective review considers what is known from international research about the effectiveness of interventions for children and young people whose conduct disorders place them at risk of developing persistent and intractable patterns of problem behaviour in adult life. Commissioned to inform policy discussions preceding the launch of the British Government's Social Exclusion Task Force, it includes detailed assessments of six highly promising parenting and family support programmes: The Incredible Years, Triple P, Nurse-Family Partnership, Multisystemic Therapy, Multidimensional Treatment Foster Care and Functional Family Therapy. The conclusions, which will be of interest to a wide range of policy makers and practitioners working with troubled children, young people and families, consider the key ingredients of effective interventions and their implications for services in the UK. p o l i c y r e s e a r c h b u r e a u m e s s a g e s p o l i c y r e s e a r c h u r e a u This selective review considers what is known from international research about the effectiveness of interventions for children and young people whose conduct disorders place them at risk of developing persistent and intractable patterns of problem behaviour in adult life. Commissioned to inform policy discussions preceding the launch of the British Government's Social Exclusion Task Force, it includes detailed assessments of six highly promising parenting and family support programmes: The Incredible Years, Triple P, Nurse-Family Partnership, Multisystemic Therapy, Multidimensional Treatment Foster Care and Functional Family Therapy. The conclusions, which will be of interest to a wide range of policy makers and practitioners working with troubled children, young people and families, consider the key ingredients of effective interventions and their implications for services in the UK. This review of interventions for children at risk of antisocial personality disorder was commissioned by the Department of Health and the Prime Minister's Strategy Unit in 2006.
MULLER'S RATCHET AND THE ADVANTAGE OF SEX IN THE RNA VIRUS ϟ6

Population genetic models have shown that if genetic drift is strong and the rate of deleterious mutations is high, Muller's ratchet provides an advantage to sex. A previous study tested for the possibility that Muller's ratchet could work in RNA viruses, which are known to have very high mutation rates. Muller's ratchet was found to operate when lineages of the RNA bacteriophage φ6 were subjected to intensified genetic drift. The study did not determine, however, whether sex is advantageous to these viruses. We have examined whether sex can reverse the effects of Muller's ratchet by crossing nine φ6 lineages that were subjected to the ratchet in Chao's study. To determine whether there was a net advantage to sex, we analyzed the effect of crossing three lineages to all other lineages. Crossing increased significantly the fitness of two lineages, but it did not significantly affect the fitness of the third lineage. We argue that the minimal advantage of sex to these nine lineages is small, but positive. These results provide a possible scenario for the evolution of sex in an RNA phage like φ6.
Suicide and Suicidal Ideation Among Bhutanese Refugees — United States, 2009–2012

During the period February 2009-February 2012, the Office of Refugee Resettlement of the U.S. Department of Health and Human Services reported 16 suicides among the approximately 57,000 Bhutanese refugees who had resettled in the United States since 2008. In 2012, the office requested assistance from CDC and the Massachusetts Department of Public Health's Refugee Health Technical Assistance Center to identify risk factors that might be associated with suicidal ideation among Bhutanese refugees. In collaboration with the Massachusetts refugee health center, CDC conducted a survey of randomly selected Bhutanese refugees in four U.S. states with large populations of resettled refugees. The results indicated significant associations between ever having expressed suicidal ideation and current self-reported symptoms of mental health disorder (e.g., anxiety, depression, or posttraumatic stress disorder) and postmigration difficulties (e.g., family conflict or inability to find work). The findings highlight the need for development of culturally appropriate community-based interventions for suicide prevention and standard procedures for monitoring and reporting suicides and suicide attempts in the Bhutanese refugee population.
Using word confidence measure for OOV words detection in a spontaneous spoken dialog system

Developing a real-life spoken dialogue system must face with many practical issues, where the out-of-vocabulary (OOV) words problem is one of the key difficulties. This paper presents the OOV detection mechanism based on the word confidence scoring developed for the d-Ear Attendant system, a spontaneous spoken dialogue system. In the d-Ear Attendant system, an explicit filler model is originally used to detect the presence of OOV words [1]. Although this approach has a satisfactory OOV detection rate, it badly degrades the accuracy of in-vocabulary (IV) detection by 4.4% absolutely (from 97% to 92.6%). Such the degradation will not be acceptable in a practical system. By using a few commonly used acoustic confidence features and some new context confidence features, our confidence measure method not only is able to detect the word level speech recognition errors, but also has a good ability for OOV words detection with an acceptable false alarm rate. For example, with a false rejection rate of 2.5%, the false acceptance rate of 26% is achieved.
Polycomb Group Genes Psc and Su(z)2 Maintain Somatic Stem Cell Identity and Activity in Drosophila

Adult stem cells are essential for the proper function of many tissues, yet the mechanisms that maintain the proper identity and regulate proliferative capacity in stem cell lineages are not well understood. Polycomb group (PcG) proteins are transcriptional repressors that have recently emerged as important regulators of stem cell maintenance and differentiation. Here we describe the role of Polycomb Repressive Complex 1 (PRC1) genes Posterior sex combs (Psc) and Suppressor of zeste two (Su(z)2) in restricting the proliferation and maintaining the identity of the Cyst Stem Cell (CySC) lineage in the Drosophila testis. In contrast, Psc and Su(z)2 seem to be dispensable for both germline stem cell (GSC) maintenance and germ cell development. We show that loss of Psc and Su(z)2 function in the CySC lineage results in the formation of aggregates of mutant cells that proliferate abnormally, and display abnormal somatic identity correlated with derepression of the Hox gene Abdominal-B. Furthermore, we show that tumorigenesis in the CySC lineage interferes non-cell autonomously with maintenance of GSCs most likely by displacing them from their niche.
Eph/ephrin interactions modulate muscle satellite cell motility and patterning

During development and regeneration, directed migration of cells, including neural crest cells, endothelial cells, axonal growth cones and many types of adult stem cells, to specific areas distant from their origin is necessary for their function. We have recently shown that adult skeletal muscle stem cells (satellite cells), once activated by isolation or injury, are a highly motile population with the potential to respond to multiple guidance cues, based on their expression of classical guidance receptors. We show here that, in vivo, differentiated and regenerating myofibers dynamically express a subset of ephrin guidance ligands, as well as Eph receptors. This expression has previously only been examined in the context of muscle-nerve interactions; however, we propose that it might also play a role in satellite cell-mediated muscle repair. Therefore, we investigated whether Eph-ephrin signaling would produce changes in satellite cell directional motility. Using a classical ephrin ‘stripe’ assay, we found that satellite cells respond to a subset of ephrins with repulsive behavior in vitro; patterning of differentiating myotubes is also parallel to ephrin stripes. This behavior can be replicated in a heterologous in vivo system, the hindbrain of the developing quail, in which neural crest cells are directed in streams to the branchial arches and to the forelimb of the developing quail, where presumptive limb myoblasts emigrate from the somite. We hypothesize that guidance signaling might impact multiple steps in muscle regeneration, including escape from the niche, directed migration to sites of injury, cell-cell interactions among satellite cell progeny, and differentiation and patterning of regenerated muscle.
Healing notes : singing for well-being in an African bank

In 2005, Dr Steve Booysen - then Group Chief Executive of the Absa Group - initiated an internal choir festival as a platform for social interaction and teambuilding of staff across all cultures, age groups and post levels in the bank. Towards the end of 2005, based on the widely held perception that the effects of the project had exceeded all expectations, it was decided to repeat the initiative, which has since become an annual event. To date, Absa has invested, and continues to invest, millions of rands in their choir project - confirmation that choir participation offers valuable benefits to the ordinary employee. This paper uses data from an investigation into the ‘extra-musical benefits of this project to reflect on the value of the 2005-2008 Absa choir project for building social capital and strengthening individuals’ sense of coherence (SOC) through singing together.
Longitudinal brain metabolic changes from amnestic Mild Cognitive Impairment to Alzheimer's disease

A sensitive marker for monitoring progression of early Alzheimer's disease would help to develop and test new therapeutic strategies. The present study is aimed at investigating brain metabolism changes over time, as a potential monitoring marker, in patients with amnestic mild cognitive impairment, according to their clinical outcome (converters or non-converters), and in relation to their cognitive decline. Seventeen amnestic mild cognitive impairment patients underwent magnetic resonance imaging and 18FDG-positron emission tomography scans both at inclusion and 18 months later. Baseline and follow-up positron emission tomography data were corrected for partial volume effects and spatially normalized using magnetic resonance imaging data, scaled to the vermis and compared using SPM2. 'PET-PAC' maps reflecting metabolic per cent annual changes were created for correlation analyses with cognitive decline. In the whole sample, the greatest metabolic decrease concerned the posterior cingulate-precuneus area. Converters had significantly greater metabolic decrease than non-converters in two ventro-medial prefrontal areas, the subgenual (BA25) and anterior cingulate (BA24/32). PET-PAC in BA25 and BA24/32 combined allowed complete between-group discrimination. BA25 PET-PAC significantly correlated with both cognitive decline and PET-PAC in the hippocampal region and temporal pole, while BA24/32 PET-PAC correlated with posterior cingulate PET-PAC. Finally, the metabolic change in BA8/9/10 was inversely related to that in BA25 and showed relative increase with cognitive decline, suggesting that compensatory processes may occur in this dorso-medial prefrontal region. The observed ventro-medial prefrontal disruption is likely to reflect disconnection from the hippocampus, both indirectly through the cingulum bundle and posterior cingulate cortex for BA24/32, and directly through the uncinate fasciculus for BA25. Altogether, our findings emphasize the potential of 18FDG-positron emission tomography for monitoring early Alzheimer's disease progression.