Miracle-dz/UniFAR-FTUs huggingface dataset:
Hierarchical File Systems Are Dead

For over forty years, we have assumed hierarchical file system namespaces. These namespaces were a rudimentary attempt at simple organization. As users have begun to interact with increasing amounts of data and are increasingly demanding search capability, such a simple hierarchical model has outlasted its usefulness. For this reason, we should design file systems whose organizations map to the ways we access and manipulate data now. We present a new file system architecture in which we replace the hierarchical namespace with a tagged, search-based one.
Buruli-Ulcer Induced Disability in Ghana: A Study at Apromase in the Ashanti Region

Objectives. To describe trends and category of disabilities caused by Buruli ulcer disease. Design. This retrospective study was set up to quantify information on the disability trends caused by Buruli ulcer (BU) using data on patients attending BU and chronic ulcer clinics from 2004 to 2009, at Global Evangelical Mission Hospital, Apromase. Methods. Data was retrieved from the WHO BU1 form, case registry book, surgical theatre register, and BU patients' records book of the hospital. Disability was measured as the incapability of patients to perform one or more daily activities due to his/her state of BU disease before treatment. Results. A total of 336 positive BU cases comprising 181 males (53.9%) were recorded of which 113 (33.6%) cases of disabilities were identified. A mean age of 52.5 (±1.32) years was recorded. For the trend of disabilities, the year 2009 recorded the highest (N = 34, 31.0%). The lesions were mostly located at the lower limbs (N = 65, 57.5%) region of the patients. Lesions with diameter >15 cm were the major (59.3%) category of lesions. Conclusion. Trend of disability reveals proportional increase over the years from 2004 to 2009. Contracture at the knee and ankle joints was the commonest disability recorded.
Phage Morphology Recapitulates Phylogeny: The Comparative Genomics of a New Group of Myoviruses

Among dsDNA tailed bacteriophages (Caudovirales), members of the Myoviridae family have the most sophisticated virion design that includes a complex contractile tail structure. The Myoviridae generally have larger genomes than the other phage families. Relatively few “dwarf” myoviruses, those with a genome size of less than 50 kb such as those of the Mu group, have been analyzed in extenso. Here we report on the genome sequencing and morphological characterization of a new group of such phages that infect a diverse range of Proteobacteria, namely Aeromonas salmonicida phage 56, Vibrio cholerae phages 138 and CP-T1, Bdellovibrio phage φ1422, and Pectobacterium carotovorum phage ZF40. This group of dwarf myoviruses shares an identical virion morphology, characterized by usually short contractile tails, and have genome sizes of approximately 45 kb. Although their genome sequences are variable in their lysogeny, replication, and host adaption modules, presumably reflecting differing lifestyles and hosts, their structural and morphogenesis modules have been evolutionarily constrained by their virion morphology. Comparative genomic analysis reveals that these phages, along with related prophage genomes, form a new coherent group within the Myoviridae. The results presented in this communication support the hypothesis that the diversity of phages may be more structured than generally believed and that the innumerable phages in the biosphere all belong to discrete lineages or families.
Fully Convolutional Crowd Counting on Highly Congested Scenes

In this paper we advance the state-of-the-art for crowd counting in high density scenes by further exploring the idea of a fully convolutional crowd counting model introduced by (Zhang et al., 2016). Producing an accurate and robust crowd count estimator using computer vision techniques has attracted significant research interest in recent years. Applications for crowd counting systems exist in many diverse areas including city planning, retail, and of course general public safety. Developing a highly generalised counting model that can be deployed in any surveillance scenario with any camera perspective is the key objective for research in this area. Techniques developed in the past have generally performed poorly in highly congested scenes with several thousands of people in frame (Rodriguez et al., 2011). Our approach, influenced by the work of (Zhang et al., 2016), consists of the following contributions: (1) A training set augmentation scheme that minimises redundancy among training samples to improve model generalisation and overall counting performance; (2) a deep, single column, fully convolutional network (FCN) architecture; (3) a multi-scale averaging step during inference. The developed technique can analyse images of any resolution or aspect ratio and achieves state-of-the-art counting performance on the Shanghaitech Part B and UCF CC 50 datasets as well as competitive performance on Shanghaitech Part A.
Performance and Diagnostic Evaluation of Ozone Predictions by the Eta-Community Multiscale Air Quality Forecast System during the 2002 New England Air Quality Study

Abstract A real-time air quality forecasting system (Eta-Community Multiscale Air Quality [CMAQ] model suite) has been developed by linking the National Centers for Environmental Estimation Eta model to the U.S. Environmental Protection Agency (EPA) CMAQ model. This work presents results from the application of the Eta-CMAQ modeling system for forecasting ozone (O3) over the Northeastern United States during the 2002 New England Air Quality Study (NEAQS). Spatial and temporal performance of the Eta-CMAQ model for O3 was evaluated by comparison with observations from the EPA Air Quality System (AQS) network. This study also examines the ability of the model to simulate the processes governing the distributions of tropospheric O3 on the basis of the intensive datasets obtained at the four Atmospheric Investigation, Regional Modeling, Analysis, and Estimation (AIRMAP) and Harvard Forest (HF) surface sites. The episode analysis reveals that the model captured the buildup of O3 concentrations over the northeastern domain from August 11 and reproduced the spatial distributions of observed O3 very well for the daytime (8:00 p.m.) of both August 8 and 12 with most of normalized mean bias (NMB) within [H11006]20%. The model reproduced 53.3% of the observed hourly O3 within a factor of 1.5 with NMB of 29.7% and normalized mean error of 46.9% at the 342 AQS sites.The comparison of modeled and observed lidar O3 vertical profiles shows that whereas the model reproduced the observed vertical structure, it tended to overestimate at higher altitude. The model reproduced 64 –77% of observed NO2 photolysis rate values within a factor of 1.5 at the AIRMAP sites. At the HF site, comparison of modeled and observed O3/nitrogen oxide (NOx) ratios suggests that the site is mainly under strongly NOx-sensitive conditions (>53%). It was found that the modeled lower limits of the O3 production efficiency values (inferred from O3-CO correlation) are close to the observations.
Neighborhood Physical Disorder and Psychological Distress

Although research documents a link between neighborhood physical disorder and psychological distress, we know little about the extent to which this association varies by age. Utilizing the person–environment fit model and drawing on data from the fourth wave of the Americans’ Changing Lives Survey, we examine the extent to which age influences the association between perceptions of neighborhood physical disorder and psychological distress, as measured by depressive symptoms. We employ both continuous and categorical measures of age to test for a potential moderating effect. Overall findings based on linear regression analyses reveal that the mental distress resulting from the perception of physically deteriorating neighborhood declines with age. Stated otherwise, we find that the psychological distress associated with the perception of neighborhood physical disorder is far less pronounced for the young-old (60 years and above) and late-old (70 years and above) adults as compared with their young middle-aged (40–49 years) and late middle-aged (50–59 years) counterparts.
Domain and Function: A Dual-Space Model of Semantic Relations and Compositions

Given appropriate representations of the semantic relations between carpenter and wood and between mason and stone (for example, vectors in a vector space model), a suitable algorithm should be able to recognize that these relations are highly similar (carpenter is to wood as mason is to stone; the relations are analogous). Likewise, with representations of dog, house, and kennel, an algorithm should be able to recognize that the semantic composition of dog and house, dog house, is highly similar to kennel (dog house and kennel are synonymous). It seems that these two tasks, recognizing relations and compositions, are closely connected. However, up to now, the best models for relations are significantly different from the best models for compositions. In this paper, we introduce a dual-space model that unifies these two tasks. This model matches the performance of the best previous models for relations and compositions. The dual-space model consists of a space for measuring domain similarity and a space for measuring function similarity. Carpenter and wood share the same domain, the domain of carpentry. Mason and stone share the same domain, the domain of masonry. Carpenter and mason share the same function, the function of artisans. Wood and stone share the same function, the function of materials. In the composition dog house, kennel has some domain overlap with both dog and house (the domains of pets and buildings). The function of kennel is similar to the function of house (the function of shelters). By combining domain and function similarities in various ways, we can model relations, compositions, and other aspects of semantics.
The acute transverse strain response of the patellar tendon to quadriceps exercise.

INTRODUCTION The human patellar tendon is highly adaptive to changes in habitual loading, but little is known about its acute mechanical response to exercise. This research evaluated the immediate transverse strain response of the patellar tendon to a bout of resistive quadriceps exercise. METHODS Twelve healthy adult males (mean age, 34.0 ± 12.1 yr; height, 1.75 ± 0.09 m; and weight, 76.7 ± 12.3 kg) free of knee pain participated in the research. A 10- to 5-MHz linear array transducer was used to acquire standardized sagittal sonograms of the right patellar tendon immediately before and after 90 repetitions of a double-leg parallel-squat exercise performed against a resistance of 175% bodyweight. Tendon thickness was determined 20-mm distal to the pole of the patellar, and transverse Hencky strain was calculated as the natural log of the ratio of post- to preexercise tendon thickness and expressed as a percentage. Measures of tendon echotexture (echogenicity and entropy) were also calculated from subsequent grayscale profiles. RESULTS Quadriceps exercise resulted in an immediate decrease in patellar tendon thickness (P < 0.05), equating to a transverse strain of -22.5% ± 3.4% and was accompanied by increased tendon echogenicity (P < 0.05) and decreased entropy (P < 0.05). The transverse strain response of the patellar tendon was significantly correlated with both tendon echogenicity (r = -0.58, P < 0.05) and entropy after exercise (r = 0.73, P < 0.05), whereas older age was associated with greater entropy of the patellar tendon before exercise (r = 0.79, P < 0.05) and a reduced transverse strain response (r = 0.61, P < 0.05) after exercise. CONCLUSIONS This study is the first to show that quadriceps exercise invokes structural alignment and fluid movement within the matrix that are manifested by changes in echotexture and transverse strain in the patellar tendon.
Early intervention in bipolar disorder, part I: clinical and imaging findings

The concept of prevention is not new to psychiatry and has long been recognized in general medicine. Recent evidence has highlighted that early pharmacological and psychosocial treatment dramatically ameliorates poor prognosis and outcome for individuals with psychotic disorders, reducing conversion rates to full‐blown illness and decreasing symptom severity. Nevertheless, despite the many recent advances in our thinking about early intervention, the need for early intervention in bipolar disorder (BPD) is an area that has been relatively neglected.
Vulnerability assessment of the global water erosion tendency: Vegetation greening can partly offset increasing rainfall stress

Global water erosion is a grave threat to the sustainability of agriculture. Regional climate change may aggravate the threat of erosion, whereas global vegetation greening (an increasing trend in vegetation cover) may act as a mitigation to the threat. On the basis of the Revised Universal Soil Loss Equation, we assessed the vulnerability of the global water erosion during 1982–2015. A contribution index was built to describe the influences of rainfall erosivity and cover management on global water erosion vulnerability changes during 1982–2015. The research objective was to explore the spatial pattern of global water erosion vulnerability change in recent decades and to identify the factor that has contributed most to the vulnerability change, and three main results were obtained. (a) The global water erosion vulnerability increased over 51% of the surface during 1982–2015, and the surface with significant decreasing trends only accounted for 12% of the middle and highly sensitive areas. (b) Rainfall erosivity contributed more than cover management for absolute value except in the Amazon, Congo Basin, and Southeast Asia, whereas the contribution of cover management was increasing. (c) Vegetation greening can partly offset the stress caused by climate change. The global water erosion vulnerability decreased more than increased in sensitive area. Consequently, enhancing the vegetation growth in the highly sensitive water erosion region could reduce the erosion threat at large scale.
Exploring the RING-Catalyzed Ubiquitin Transfer Mechanism by MD and QM/MM Calculations

Ubiquitylation is a universal mechanism for controlling cellular functions. A large family of ubiquitin E3 ligases (E3) mediates Ubiquitin (Ub) modification. To facilitate Ub transfer, RING E3 ligases bind both the substrate and ubiquitin E2 conjugating enzyme (E2) linked to Ub via a thioester bond to form a catalytic complex. The mechanism of Ub transfer catalyzed by RING E3 remains elusive. By employing a combined computational approach including molecular modeling, molecular dynamics (MD) simulations, and quantum mechanics/molecular mechanics (QM/MM) calculations, we characterized this catalytic mechanism in detail. The three-dimensional model of dimeric RING E3 ligase RNF4 RING, E2 ligase UbcH5A, Ub and the substrate SUMO2 shows close contact between the substrate and Ub transfer catalytic center. Deprotonation of the substrate lysine by D117 on UbcH5A occurs with almost no energy barrier as calculated by MD and QM/MM calculations. Then, the side chain of the activated lysine gets close to the thioester bond via a conformation change. The Ub transfer pathway begins with a nucleophilic addition that forms an oxyanion intermediate of a 4.23 kcal/mol energy barrier followed by nucleophilic elimination, resulting in a Ub modified substrate by a 5.65 kcal/mol energy barrier. These results provide insight into the mechanism of RING-catalyzed Ub transfer guiding the discovery of Ub system inhibitors.
Genetic and environmental influences on prolactin secretion during wake and during sleep.

To delineate the contributions of genetic and environmental factors in the regulation of human prolactin (PRL) secretion, the 24-h profile of plasma PRL was obtained at 15-min intervals in 10 pairs of monozygotic and 10 pairs of dizygotic twins. Sleep was monitored polygraphically. PRL secretory rates were derived from plasma concentrations by deconvolution. Diurnal (24-h) variations were quantified by a regression curve to define nadir, acrophase, and amplitude. Pulses of PRL secretion were identified using a computerized algorithm. A procedure specifically developed for twin studies was used to partition the variance into genetic and environmental contributions. Significant genetic effects were identified for daytime PRL concentrations, rhythm amplitude, and overall waveshape of the daily PRL profile. In contrast, environmental effects were dominant for mean concentrations during sleep, total secretory output during sleep, overall 24-h concentrations, and total 24-h secretion. However, when interindividual variations in sleep fragmentation were taken into account, the estimates of genetic variance for PRL concentrations and secretion during sleep approached statistical significance. Significant genetic influences were identified for slow-wave sleep (SWS). Because SWS is associated with increased nocturnal PRL secretion, it is possible that genetic effects on PRL secretion during sleep reflect genetic influences on SWS. In conclusion, genetic factors determine partially both the basal daytime concentrations of PRL and the temporal organization of PRL secretion over the 24-h cycle in normal young men.
Assessment of Quality of Health Care in Jimma Zone, Southwest Ethiopia

Background Quality of care is an important aspect of health care delivery system that is given a priority. Quality is a multidimensional concept that has been defined in various ways. Variation in quality of care between different health care facilities is thought to reflect differences in efficiency and other organizational factors. There was no adequate study related to quality of health care in Jimma zone. Therefore, the objective of this study was to assess quality of health care in Jimma zone. Methods A cross sectional quantitative study design was employed to assess the quality of care with respect to structure, care process and customer satisfaction involving 640 patients and 96 care providers in Jimma zone, southwest Ethiopia. Data were collected using an interview questionnaire and observation checklist devised by the investigators. Results The study showed that, on average, the studied institutions fulfilled 153(70.4%) of the health human power need. They also fulfilled 86(62.8%) of major equipment requirement against the national standard. The composite average satisfaction level of patients was 89.1% and that of the care providers was 86.7%. Nevertheless, the respect given to patients by care providers was rated as poor. A significant proportion, 39(48.2%) of the care providers were assessed as low performance. Conclusions Majority of study subjects rated the overall quality of care as “good”. However the observation revealed that the human aspect of care was “poor”. In addition, the health institutions were facing shortage of human and material resources. Thus it was recommended that the responsible bodies at the 3 levels should take actions for improving institutional capacity and performance of care providers in order to improve quality of care.
Does warm weather climate affect eating disorder pathology?

OBJECTIVE The aim of this study was to examine whether residing in a year-round warm weather climate is related to eating disorder pathology. METHOD College females from a southeastern and a northeastern region of the United States were compared on body mass index, the Bulimia Test-Revised, the Body Shape Questionnaire, and the Body Image Avoidance Questionnaire. RESULTS Females residing in the southeastern region were of significantly lower body weight, engaged in more frequent bulimic behaviors (e.g., bingeing and inappropriate compensatory behaviors), and displayed significantly greater concern regarding their body shape compared with the females residing in the northeastern region. DISCUSSION Findings obtained in this study indicate that residing in a warm weather climate may produce a heightened risk for development of eating disorder pathology.
DNA diversity and population admixture in Anatolia.

The Turkic language was introduced in Anatolia at the start of this millennium, by nomadic Turkmen groups from Central Asia. Whether that cultural transition also had significant population-genetics consequences is not fully understood. Three nuclear microsatellite loci, the hypervariable region I of the mitochondrial genome, six microsatellite loci of the Y chromosome, and one Alu insertion (YAP) were amplified and typed in 118 individuals from four populations of Anatolia. For each locus, the number of chromosomes considered varied between 51-200. Genetic variation was large within samples, and much less so between them. The contribution of Central Asian genes to the current Anatolian gene pool was quantified using three different methods, considering for comparison populations of Mediterranean Europe, and Turkic-speaking populations of Central Asia. The most reliable estimates suggest roughly 30% Central Asian admixture for both mitochondrial and Y-chromosome loci. That (admittedly approximate) figure is compatible both with a substantial immigration accompanying the arrival of the Turkmen armies (which is not historically documented), and with continuous gene flow from Asia into Anatolia, at a rate of 1% for 40 generations. Because a military invasion is expected to more deeply affect the male gene pool, similar estimates of admixture for female- and male-transmitted traits are easier to reconcile with continuous migratory contacts between Anatolia and its Asian neighbors, perhaps facilitated by the disappearance of a linguistic barrier between them.
Words matter: increasing the implementation of clinical guidelines

Objectives: To determine whether writing clinical guideline recommendations in behaviourally specified “plain English” language increases the likelihood of their implementation by service users (patients). Design: Randomised controlled trial in which participants received either the original text of the National Institute for Clinical Excellence (NICE) public guidelines for the management of schizophrenia or a behaviourally specified text with the same content. Setting: Mental health service user networks and voluntary sector organisations within two inner London boroughs. Participants: Eighty four mental health service users recruited by post or face to face contact at service user meetings. Intervention: The section of the NICE public guidelines for schizophrenia concerning psychological and pharmacological treatments was rewritten to improve style and behavioural specificity by applying evidence-based and psychologically informed principles of good written communication. Outcome measures: Cognitive predictors of behaviour, as specified by the evidence based theory of planned behaviour, constituted the primary outcome as it was not possible to measure the actual behaviour of guideline implementation. The predictors were behavioural intentions to implement the guidelines, attitudes towards implementation, and perceived behavioural control over implementation. Satisfaction with the guidelines and perceived comprehension were also measured. Results: Behaviourally specified “plain English” guidelines led to stronger intentions to implement the guidelines, more positive attitudes towards them, and greater perceived behavioural control over using them. There was no difference in satisfaction or perceived comprehension. Conclusions: Writing guidelines with high behavioural specificity in conjunction with the use of “plain English” may be a simple and effective method of increasing their implementation. Evaluation with a behavioural outcome is now needed.