Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterizing Software Developers by Perceptions of Productivity

Understanding developer productivity is important to deliver software on time and at reasonable cost. Yet, there are numerous definitions of productivity and, as previous research found, productivity means different things to different developers. In this paper, we analyze the variation in productivity perceptions based on an online survey with 413 professional software devel-opers at Microsoft. Through a cluster analysis, we identify and describe six groups of developers with similar perceptions of productivity: social, lone, focused, balanced, leading, and goal-oriented developers. We argue why personalized recommendations for improving software developers' work is important and discuss design implications of these clusters for tools to support developers' productivity.
Early Diffusion-Weighted Imaging and Perfusion-Weighted Imaging Lesion Volumes Forecast Final Infarct Size in DEFUSE 2

Background and Purpose— It is hypothesized that early diffusion-weighted imaging (DWI) lesions accurately estimate the size of the irreversibly injured core and thresholded perfusion-weighted imaging (PWI) lesions (time to maximum of tissue residue function [Tmax] >6 seconds) approximate the volume of critically hypoperfused tissue. With incomplete reperfusion, the union of baseline DWI and posttreatment PWI is hypothesized to predict infarct volume. Methods— This is a substudy of Diffusion and Perfusion Imaging Evaluation for Understanding Stroke Evolution Study 2 (DEFUSE 2); all patients with technically adequate MRI scans at 3 time points were included. Baseline DWI and early follow-up PWI lesion volumes were determined by the RAPID software program. Final infarct volumes were assessed with 5-day fluid-attenuated inversion recovery and were corrected for edema. Reperfusion was defined on the basis of the reduction in PWI lesion volume between baseline and early follow-up MRI. DWI and PWI volumes were correlated with final infarct volumes. Results— Seventy-three patients were eligible. Twenty-six patients with >90% reperfusion show a high correlation between early DWI volume and final infarct volume (r=0.95; P<0.001). Nine patients with <10% reperfusion have a high correlation between baseline PWI (Tmax >6 seconds) volume and final infarct volume (r=0.86; P=0.002). Using all 73 patients, the union of baseline DWI and early follow-up PWI is highly correlated with final infarct volume (r=0.94; P<0.001). The median absolute difference between observed and predicted final volumes is 15 mL (interquartile range, 5.5–30.2). Conclusions— Baseline DWI and early follow-up PWI (Tmax >6 seconds) volumes provide a reasonable approximation of final infarct volume after endovascular therapy.
Laforin, a Dual Specificity Phosphatase Involved in Lafora Disease, Is Present Mainly as Monomeric Form with Full Phosphatase Activity

Lafora Disease (LD) is a fatal neurodegenerative epileptic disorder that presents as a neurological deterioration with the accumulation of insoluble, intracellular, hyperphosphorylated carbohydrates called Lafora bodies (LBs). LD is caused by mutations in either the gene encoding laforin or malin. Laforin contains a dual specificity phosphatase domain and a carbohydrate-binding module, and is a member of the recently described family of glucan phosphatases. In the current study, we investigated the functional and physiological relevance of laforin dimerization. We purified recombinant human laforin and subjected the monomer and dimer fractions to denaturing gel electrophoresis, mass spectrometry, phosphatase assays, protein-protein interaction assays, and glucan binding assays. Our results demonstrate that laforin prevalently exists as a monomer with a small dimer fraction both in vitro and in vivo. Of mechanistic importance, laforin monomer and dimer possess equal phosphatase activity, and they both associate with malin and bind glucans to a similar extent. However, we found differences between the two states' ability to interact simultaneously with malin and carbohydrates. Furthermore, we tested other members of the glucan phosphatase family. Cumulatively, our data suggest that laforin monomer is the dominant form of the protein and that it contains phosphatase activity.
Online tomato inspection using x-ray radiographies and 3-dimensional shape models

A method is proposed that fits a 3-dimensional shape model (SM) on X-ray radiographies of tomatoes on a conveyor belt to allow for inspection of internal tomato quality using X-ray. For the training of the SM a set of computed tomography (CT) scans is used. From these scans, the surfaces of the fruits are extracted. Corresponding points on all these surfaces are located after which the variation in position of every point can be determined using principal component analysis (PCA). The result of this process is a mean shape with various modes of variation, which represent the variability of the shape. Any shape can then be reconstructed through a linear combination of the mean shape and its modes of variation. During runtime, the contour of every tomato is extracted onto which the SM is fitted. This allows us to accurately estimate tomato volume and 3-dimensional shape, and assess the presence of defects and other unwanted properties from X-ray radiographies in an online application. Results are promising, but show that improvement can be made by simulating radiographs from the shape model and fitting these directly to the measured radiograph.
Reduction in cardiovascular risk using a proactive multifactorial intervention is consistent among patients residing in Pacific Asian and non-Pacific asian regions: a cRUcial trial subanalysis

Background: Few trials have compared different approaches to cardiovascular disease prevention among Pacific Asian (PA) populations. The Cluster Randomized Usual Care versus Caduet Investigation Assessing Long-term-risk (CRUCIAL) trial demonstrated that a proactive multifactorial intervention (PMI) approach (based on single-pill amlodipine/atorvastatin) resulted in a greater reduction in calculated Framingham 10-year coronary heart disease (CHD) risk compared with usual care (UC) among hypertensive patients with additional risk factors. One-third of CRUCIAL patients resided in the PA region. The aim of this subanalysis was to compare two approaches to cardiovascular risk factor management (PMI versus UC) among patients residing in PA and non-PA regions. Methods: This subanalysis of the CRUCIAL trial compared treatment-related changes in calculated CHD risk among patients residing in PA and non-PA regions. Sensitivity analyses were conducted among men and women and those with and without diabetes. Results: Overall, 448 patients (31.6%) resided in the PA region and 969 patients (68.4%) resided in non-PA regions. The PMI approach was more effective in reducing calculated CHD risk versus UC in both PA ( − 37.1% versus − 3.5%; P , 0.001) and non-PA regions ( − 31.1% versus − 4.2%; P , 0.001); region interaction P = 0.131. PA patients had slightly greater reductions in total cholesterol compared with non-PA patients. PA patients without diabetes had slightly greater reductions in CHD risk compared with non-PA patients. Treatment effects were similar in men and women and those with diabetes. Conclusion: The PMI approach was more effective in reducing calculated Framingham 10-year CHD risk compared with UC among men and women with and without diabetes residing in the PA and non-PA region.
Persistence of the mitochondrial permeability transition in the absence of subunit c of human ATP synthase

Significance Cellular powerhouses called mitochondria generate fuel known as adenosine triphosphate, or ATP, to sustain complex life. The capacity of mitochondria to do so depends on a supply of energy from oxidation of energy-rich compounds in foodstuffs to generate a chemical potential difference for hydrogen ions, called the proton motive force (pmf), across the inner mitochondrial membrane. Disruption of this membrane dissipates the pmf, and the cells die for lack of fuel. This event happens, for example, when the concentration of calcium ions inside human mitochondria is increased. The mitochondria respond by opening a pore, water enters, and the mitochondria swell and burst. The molecular identity of the pore is disputed, and we have disproved one proposal. The permeability transition in human mitochondria refers to the opening of a nonspecific channel, known as the permeability transition pore (PTP), in the inner membrane. Opening can be triggered by calcium ions, leading to swelling of the organelle, disruption of the inner membrane, and ATP synthesis, followed by cell death. Recent proposals suggest that the pore is associated with the ATP synthase complex and specifically with the ring of c-subunits that constitute the membrane domain of the enzyme’s rotor. The c-subunit is produced from three nuclear genes, ATP5G1, ATP5G2, and ATP5G3, encoding identical copies of the mature protein with different mitochondrial-targeting sequences that are removed during their import into the organelle. To investigate the involvement of the c-subunit in the PTP, we generated a clonal cell, HAP1-A12, from near-haploid human cells, in which ATP5G1, ATP5G2, and ATP5G3 were disrupted. The HAP1-A12 cells are incapable of producing the c-subunit, but they preserve the characteristic properties of the PTP. Therefore, the c-subunit does not provide the PTP. The mitochondria in HAP1-A12 cells assemble a vestigial ATP synthase, with intact F1-catalytic and peripheral stalk domains and the supernumerary subunits e, f, and g, but lacking membrane subunits ATP6 and ATP8. The same vestigial complex plus associated c-subunits was characterized from human 143B ρ0 cells, which cannot make the subunits ATP6 and ATP8, but retain the PTP. Therefore, none of the membrane subunits of the ATP synthase that are involved directly in transmembrane proton translocation is involved in forming the PTP.
Petri Nets Models for Analysis and Control of Public Bicycle-Sharing Systems

Public Bicycle-Sharing Systems (PBSS), also known as self-service public bicycle systems, are available in numerous big cities in the world (Velib' in Paris, Bicing in Barcelona, Call-aBicycle in Munich, OyBicycle in London, etc.). Since its inception, Bicycle-sharing programs have grown worldwide. There are now programs in Europe, North America, South America, Asia, and Australia. A still growing list of cities which provides such green public transportation mode can be found at the Bicycle-sharing world map (http://Bikesharing.blogspot.com) as shown in Figure 1. As a good complementary to other urban transportation modes, bicycle use entails a number of benefits including environmental, mobility and economic benefits. The public bicycle sharing systems are especially useful for short-distance city transport trips and to face many public transport problems, including growing traffic congestion, pollution, greater car dependency, buses caught in city congestion, and ageing transport infrastructure.
The exploding gradient problem demystified - definition, prevalence, impact, origin, tradeoffs, and solutions

Whereas it is believed that techniques such as Adam, batch normalization and, more recently, SeLU nonlinearities "solve" the exploding gradient problem, we show that this is not the case in general and that in a range of popular MLP architectures, exploding gradients exist and that they limit the depth to which networks can be effectively trained, both in theory and in practice. We explain why exploding gradients occur and highlight the *collapsing domain problem*, which can arise in architectures that avoid exploding gradients. ResNets have significantly lower gradients and thus can circumvent the exploding gradient problem, enabling the effective training of much deeper networks. We show this is a direct consequence of the Pythagorean equation. By noticing that *any neural network is a residual network*, we devise the *residual trick*, which reveals that introducing skip connections simplifies the network mathematically, and that this simplicity may be the major cause for their success.
Baduanjin Exercise for Stroke Rehabilitation: A Systematic Review with Meta-Analysis of Randomized Controlled Trials

Objective: The purpose of this review was to objectively evaluate the effects of Baduanjin exercise on rehabilitative outcomes in stroke patients. Methods: Both Chinese and English electronic databases were searched for potentially relevant trials. Two review authors independently screened eligible trials against the inclusion criteria, extracted data, and assessed the methodological quality by using the revised PEDro scale. Meta-analysis was only performed for balance function. Results: In total, there were eight randomized controlled trials selected in this systematic review. The aggregated result of four trials has shown a significant benefit in favor of Baduanjin on balance function (Hedges’ g = 2.39, 95% CI 2.14 to 2.65, p < 0.001, I2 = 61.54). Additionally, Baduanjin exercise effectively improved sensorimotor function of lower extremities and ability of daily activities as well as reduced depressive level, leading to improved quality of life. Conclusion: Baduanjin exercise as an adjunctive and safe method may be conducive to help stroke patients achieve the best possible short-term outcome and should be integrated with mainstream rehabilitation programs. More rigorous randomized controlled trials with long-term intervention periods among a large sample size of stroke patients are needed to draw a firm conclusion regarding the rehabilitative effects for this population.
Task Embeddings: Learning Query Embeddings using Task Context

Continuous space word embedding have been shown to be highly effective in many information retrieval tasks. Embedding representation models make use of local information available in immediately surrounding words to project nearby context words closer in the embedding space. With rising multi-tasking nature of web search sessions, users often try to accomplish different tasks in a single search session. Consequently, the search context gets polluted with queries from different unrelated tasks which renders the context heterogeneous. In this work, we hypothesize that task information provides better context for IR systems to learn from. We propose a novel task context embedding architecture to learn representation of queries in low-dimensional space by leveraging their task context information from historical search logs using neural embedding models. In addition to qualitative analysis, we empirically demonstrate the benefit of leveraging task context to learn query representations.
The Hybrid Digital Tree: A New Indexing Technique for Large String Databases

There is an increasing demand for efficient indexing techniques to support queries on large string databases. In this paper, a hybrid RAM/disk-based index structure, called the Hybrid Digital tree (HD-tree), is proposed. The HD-tree keeps internal nodes in the RAM to minimize the number of disk I/Os, while maintaining leaf nodes on the disk to maximize the capability of the tree for indexing large databases. Experimental results using real data have shown that the HD-tree outperformed the Prefix B-tree for prefix and substring searches. In particular, for distinctive random queries in the experiments, the average number of disk I/Os was reduced by a factor of two to three, while the running time was reduced in an order of magnitude.
The significance of fullerene electron acceptors in organic solar cell photo-oxidation

Stability of organic solar cells requires development before their commercialisation is possible. This review will give a brief overview of organic solar cells and their stability, before focussing on the photochemical stability of the active layer. The photo-oxidation of the donor polymers will be looked at first which has been studied quite extensively and then fullerene electron acceptors, such as widely used phenyl-C61-butyric acid methyl ester, which has been considerably less studied. It has been shown that oxidation of the fullerene cage on phenyl-C61-butyric acid methyl ester results in oxides with a deeper lowest unoccupied molecular orbital (LUMO) level than the fresh electron acceptor. These oxides act as electron traps, leading to deterioration of the blend photoconductivity. The significance of fullerene photo-oxidation on device stability has been indirectly shown via research on: photoconductivity; organic solar cells made with an oxidised fullerene derivative and organic field effect transistors. Techniques that could be developed to increase photochemical stability of fullerene electron acceptor resistance to photo-oxidation include: reducing its LUMO level; increasing its crystallinity or aggregation and changing its chemical structure. Improving the photochemical stability of organic solar cells would move us one step closer to a more accessible solar power.
Cytogenomic Abnormalities and Dosage-Sensitive Mechanisms for Intellectual and Developmental Disabilities

Within each human cell, double strand DNA molecules are packed into 22 pairs of autosomes numbered from 1 to 22 and one pair of sex chromosomes denoted as XX for female and XY for male. Every human chromosome has a centromere to guide its segregation through cell cycles and a telomere at each end to protect its integrity. Chromosomes play important roles in gene expression regulation, DNA replication and cell division. Abnormalities involving the number and the structure of each chromosome or a segment within a chromosome are known to introduce functional disturbance and cause genetic diseases.
Parenting Stress and Resilience in Parents of Children With Autism Spectrum Disorder (ASD) in Southeast Asia: A Systematic Review

Background: This paper aimed to review the literature on the factors associated with parenting stress and resilience among parents of children with autism spectrum disorder (ASD) in the South East Asia (SEA) region. Methods: An extensive search of articles in multiple online databases (PsycNET, ProQuest, PudMed, EMBASE, CINAHL, Web of Science, and Google Scholar) resulted in 28 papers that met the inclusion criteria (i.e., conducted in the SEA region, specific to ASD only, published in a peer-reviewed journal, full text in English). Studies found were conducted in the following countries: Brunei, n = 1; Indonesia, n = 2; Malaysia, n = 12; Philippines, n = 5; Singapore, n = 5, Thailand, n = 2; and Vietnam, n = 1, but none from Cambodia, East Timor, Laos, and Myanmar were identified. Results: Across the studies, six main factors were found to be associated with parenting stress: social support, severity of autism symptoms, financial difficulty, parents' perception and understanding toward ASD, parents' anxiety and worries about their child's future, and religious beliefs. These six factors could also be categorized as either a source of parenting stress or a coping strategy/resilience mechanism that may attenuate parenting stress. Conclusion: The findings suggest that greater support services in Western countries may underlie the cultural differences observed in the SEA region. Limitations in the current review were identified. The limited number of studies yielded from the search suggests a need for expanded research on ASD and parenting stress, coping, and resilience in the SEA region especially in Cambodia, East Timor, Laos, and Myanmar. The identified stress and resilience factors may serve as sociocultural markers for clinicians, psychologists, and other professionals to consider when supporting parents of children with ASD.
Cocoa and health: a decade of research

It has been over 10 years since the first mention in a medical journal about cocoa and chocolate as potential sources of antioxidants for health. During this time, cocoa has been found to improve antioxidant status, reduce inflammation and correlate with reduced heart disease risk; with these results, and its popularity, it has received wide coverage in the press. However, after 10 years of research, what is known about the potential health benefits of cocoa and what are the important next steps in understanding this decadent source of antioxidants?
Large-scale intrinsic functional connectivity and attention in schizophrenia

It has been well-established that sustained attention and executive functioning are core deficits in schizophrenia (SZ). Growing evidence suggests that such attentional impairments may reflect disruptions in dominant intrinsic networks (INs). Functional network connectivity (FNC), described as the dependency between multiple INs, has revealed dysfunction among key INs in people with SZ. The objective of the current study was to test the hypothesis that SCZ would exhibit less specialized cognitive processing and therefore decreased FNC between dominant INs, and that any disruptions in FNC would predict neuropsychological profiles of attention. Methods: Thirty-five patients with SZ and thirty-three healthy controls (HC) were recruited for this study. Five minutes of eyes-closed resting-state fMRI (3T Trio scanner) was obtained for each participant. Resting-state scans were decomposed into 75 components using a group ICA suite (GIFT), and the FNC between all pair-wise components were obtained for each subject using the FNC toolbox. Participants were assessed using the Conners’ CPT II and
Breathing-Based Meditation Decreases Posttraumatic Stress Disorder Symptoms in U.S. Military Veterans: A Randomized Controlled Longitudinal Study

Given the limited success of conventional treatments for veterans with posttraumatic stress disorder (PTSD), investigations of alternative approaches are warranted. We examined the effects of a breathing-based meditation intervention, Sudarshan Kriya yoga, on PTSD outcome variables in U.S. male veterans of the Iraq or Afghanistan war. We randomly assigned 21 veterans to an active (n = 11) or waitlist control (n = 10) group. Laboratory measures of eye-blink startle and respiration rate were obtained before and after the intervention, as were self-report symptom measures; the latter were also obtained 1 month and 1 year later. The active group showed reductions in PTSD scores, d = 1.16, 95% CI [0.20, 2.04], anxiety symptoms, and respiration rate, but the control group did not. Reductions in startle correlated with reductions in hyperarousal symptoms immediately postintervention (r =. 93, p <. 001) and at 1-year follow-up (r =. 77, p =. 025). This longitudinal intervention study suggests there may be clinical utility for Sudarshan Kriya yoga for PTSD.
Formation of quinol co-crystals with hydrogen-bond acceptors.

The crystal structures of eight new co-crystals of quinol with pyrazine, piperazine, morpholine, pyridine, piperidine, 4,4'-bipyridine, N-methylmorpholine and N,N'-dimethylpiperazine are reported. Quinol forms 1:1 co-crystals with pyrazine, piperazine and N,N'-dimethylpiperazine, but 1:2 co-crystals with morpholine, 4,4'-bipyridine, N-methylmorpholine, pyridine and piperidine. This difference can be rationalized in most cases by the presence of, respectively, two or one strong hydrogen-bond acceptor(s) in the guest molecule. The exception to this generalization is 4,4'-bipyridine, which forms a 1:2 co-crystal, possibly to optimize crystal packing. All structures are dominated by hydrogen bonding between quinol and the guest molecules. A doubly bridging motif, which connects pairs of quinol and guest molecules via NH.O or CH.O interactions, is present in all but the sterically hindered N,N'-dimethylpiperazine and N-methylmorpholine co-crystals.