Miracle-dz/UniFAR-FTUs huggingface dataset:
An empirical investigation of code completion usage by professional software developers

Code completion is a widely used feature of modern integrated development environments. This study examines the ways in which code completion is used by professional software developers, as well as their actions when code completion doesn’t offer the expected results. We observe that code completion is used with the intention of writing code faster and more correctly, that a large fraction of the code completions are not accepted by the users and that users often used code completion as a debugging tool: when the suggestions are not useful or not expected they are seen as a indicator that there is an error in the program.
Myocardial Inflammation, Cellular Death, and Viral Detection in Sudden Infant Death Caused by SIDS, Suffocation, or Myocarditis

The significance of minor myocardial inflammatory infiltrates and viral detection in SIDS is controversial. We retrospectively compared the demographic profiles, myocardial inflammation, cardiomyocyte necrosis, and myocardial virus detection in infants who died of SIDS in a safe sleep environment, accidental suffocation, or myocarditis. Formalin-fixed, paraffin-embedded myocardial sections were semiquantitatively assessed for CD3 lymphocytes and CD68 macrophages using immunohistochemistry and for cardiomyocyte cell death in H&E-stained sections. Enteroviruses and adenoviruses were searched for using PCR technology. The means of lymphocytes, macrophages, and necrotic cardiomyocytes were not statistically different in SIDS and suffocation cases. Enterovirus, not otherwise specified, was detected in one suffocation case and was the only virus detected in the three groups. Very mild myocardial lymphocyte and macrophage infiltration and scattered necrotic cardiomyocytes in SIDS are not pathologic, but may occur after the developing heart is exposed to environmental pathogens, including viruses.
Blogging : Indexing and Registering the Change in Science 2 . 0

Increasing public interest in science information in a digital and 2.0 science era promotes a dramatically, rapid and deep change in science itself. The emergence and expansion of new technologies and internet-based tools is leading to new means to improve scientific methodology and communication, assessment, promotion and certification. It allows methods of acquisition, manipulation and storage, generating vast quantities of data that can further facilitate the research process. It also improves access to scientific results through information sharing and discussion. Content previously restricted only to specialists is now available to a wider audience. This context requires new management systems to make scientific knowledge more accessible and useable, including new measures to evaluate the reach of scientific information. The new science and research quality measures are strongly related to the new online technologies and services based in social media. Tools such as blogs, social bookmarks and online reference managers, Twitter and others offer alternative, transparent and more comprehensive information about the active interest, usage and reach of scientific publications. Another of these new filters is the Research Blogging platform, which was created in 2007 and now has over 1,230 active blogs, with over 26,960 entries posted about peer-reviewed research on subjects ranging from Anthropology to Zoology. This study takes a closer look at RB, in order to get insights into its contribution to the rapidly changing landscape of scientific communication. Citation: Fausto S, Machado FA, Bento LFJ, Iamarino A, Nahas TR, et al. (2012) Research Blogging: Indexing and Registering the Change in Science 2.0. PLoS ONE 7(12): e50109. doi:10.1371/journal.pone. 0050109 Editor: Matjaz Perc, University of Maribor, Slovenia Received January 28, 2012; Accepted October 18, 2012; Published December 12, 2012 Copyright: 2012 Fausto et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: The authors have no support or funding to report. Competing Interests: The authors have read the journal’s policy and have the following conflicts: co-authors Atila Iamarino, Luiz Bento and Tatiana R. Nahas are administrators for Portuguese version of Research Blogging, which is owned and operated by Seed Media Group, LLC (Seed). They are not employed and do not receive any payment for this work, as per Research Blogging policies. By the time of this paper submission, David S. Munger used to be an administrator at the English version of the site, but he is not related to Research Blogging anymore. There are no further patents, products in development or marketed products to declare. This does not alter the authors’ adherence to all the PLOS ONE policies on sharing data and materials, as detailed online in the guide for authors. * E-mail: sifausto@usp.br
Biased Contribution Index: A Simpler Mechanism to Maintain Fairness in Peer to Peer Network

To maintain fairness, in the terms of resources shared by an individual peer, a proper incentive policy is required in a peer to peer network. This letter proposes, a simpler mechanism to rank the peers based on their resource contributions to the network. This mechanism will suppress the free riders from downloading the resources from the network. Contributions of the peers are biased in such a way that it can balance the download and upload amount of resources at each peer. This mechanism can be implemented in a distributed system and it converges much faster than the other existing approaches.
A single institution experience on 314 newly diagnosed advanced Hodgkin lymphoma patients: the role of ABVD in daily practice

Based on the results of clinical trials, there is no global consensus on the optimal first‐line therapy for patients with advanced Hodgkin lymphoma (HL) with both ABVD and BEACOPP currently being used. However, the results of clinical trials are usually better than those in daily practice. We thus describe here our experience on 314 advanced classical HL patients treated with ABVD at the Clinical Center of Serbia and associated centers between 1997 and 2008. The median follow‐up for all patients was 91 months; the estimated 5‐yr event‐free survival was 62% and the 5‐yr overall survival (OS) 76%. Multivariate Cox regression analysis revealed that patients with IPS ≥ 3 and extranodal disease involving more than one site have a poorer outcome. The data presented here show on overall improvement in outcome as compared to more previous data and illustrate the problems of treating advanced stage HL outside the setting of a clinical trial.
Patients with nodding syndrome in Uganda improve with symptomatic treatment: a cross-sectional study

Objectives Nodding syndrome (NS) is a poorly understood neurological disorder affecting thousands of children in Africa. In March 2012, we introduced a treatment intervention that aimed to provide symptomatic relief. This intervention included sodium valproate for seizures, management of behaviour and emotional difficulties, nutritional therapy and physical rehabilitation. We assessed the clinical and functional outcomes of this intervention after 12 months of implementation. Design This was a cross-sectional study of a cohort of patients with NS receiving the specified intervention. We abstracted preintervention features from records and compared these with the current clinical status. We performed similar assessments on a cohort of patients with other convulsive epilepsies (OCE) and compared the outcomes of the two groups. Participants Participants were patients with WHO-defined NS and patients with OCE attending the same centres. Outcome measures The primary outcome was the proportion of patients with seizure freedom (≥1 month without seizures). Secondary outcome measures included a reduction in seizure frequency, resolution of behaviour and emotional difficulties, and independence in basic self-care. Results Patients with NS had had a longer duration of symptoms (median 5 (IQR 3, 6) years) compared with those with OCE (4 (IQR 2, 6) years), p<0.001. The intervention resulted in marked improvements in both groups; compared to the preintervention state, 121/484 (25%) patients with NS achieved seizure freedom and there was a >70% reduction in seizure frequency; behaviour and emotional difficulties resolved in 194/327 (59%) patients; 193/484 (40%) patients had enrolled in school including 17.7% who had earlier withdrawn due to severe seizures, and over 80% had achieved independence in basic self-care. These improvements were, however, less than that in patients with OCE of whom 243/476 (51.1%) patients were seizure free and in whom the seizure frequency had reduced by 86%. Conclusions Ugandan children with NS show substantial clinical and functional improvements with symptomatic treatments suggesting that NS is probably a reversible encephalopathy.
Critical Care Needs in Patients with Diffusion-Weighted Imaging Negative MRI after tPA - Does One Size Fit All?

Background and Purpose Patients who receive intravenous (IV) tissue plasminogen activator (tPA) for ischemic stroke are currently monitored in an intensive care unit (ICU) or a comparable stroke unit for at least 24 hours due to the high frequency of neurological exams and vital sign checks. The present study evaluates ICU needs in patients with diffusion-weighted imaging (DWI) negative MRI after IV tPA. Methods A retrospective chart review was performed for 209 patients who received IV tPA for acute stroke. Data on stroke risk factors, physiologic parameters, stroke severity, MRI characteristics, and final diagnosis were collected. The timing and nature of ICU interventions, if needed, was recorded. Multivariable logistic regression was used to determine factors associated with subsequent ICU needs. Results Patients with cerebral infarct on MRI after tPA had over 9 times higher odds of requiring ICU care compared to patients with DWI negative MRI (OR 9.2, 95% CI 2.49–34.15). All DWI negative patients requiring ICU care did so by the end of tPA infusion (p = 0.006). Among patients with DWI negative MRI, need for ICU interventions was associated with higher NIH Stroke Scale (NIHSS) scores (p<0.001), uncontrolled hypertension (p<0.001), seizure at onset (p = 0.002), and reduced estimated glomerular filtration rate (eGFR) (p = 0.010). Conclusions Only a small number of DWI negative patients required ICU care. In patients without critical care needs by the end of thrombolysis, post-tPA MRI may be considered for triaging DWI negative patients to a less resource intense monitoring environment.
Analyzing oscillators using multitime PDEs

Oscillators are often difficult to analyze or simulate, because they generate waveforms that can span a range of widely separated time scales. We present a general oscillator formulation that separates slow and fast dynamics without approximations, and captures amplitude and frequency modulation in a natural and compact manner. To handle frequency-modulation effectively, we make use of a novel concept, warped time, within a multitime partial differential equation framework. The equations incorporate an explicit time-varying frequency variable that matches intuitive notions of changing frequency in a frequency-modulated signal. The formulation is useful for both hand analysis and numerical simulation.
Moving Stimuli Are Less Effectively Masked Using Traditional Continuous Flash Suppression (CFS) Compared to a Moving Mondrian Mask (MMM): A Test Case for Feature-Selective Suppression and Retinotopic Adaptation

Continuous flash suppression (CFS) is a powerful interocular suppression technique, which is often described as an effective means to reliably suppress stimuli from visual awareness. Suppression through CFS has been assumed to depend upon a reduction in (retinotopically specific) neural adaptation caused by the continual updating of the contents of the visual input to one eye. In this study, we started from the observation that suppressing a moving stimulus through CFS appeared to be more effective when using a mask that was actually more prone to retinotopically specific neural adaptation, but in which the properties of the mask were more similar to those of the to-be-suppressed stimulus. In two experiments, we find that using a moving Mondrian mask (i.e., one that includes motion) is more effective in suppressing a moving stimulus than a regular CFS mask. The observed pattern of results cannot be explained by a simple simulation that computes the degree of retinotopically specific neural adaptation over time, suggesting that this kind of neural adaptation does not play a large role in predicting the differences between conditions in this context. We also find some evidence consistent with the idea that the most effective CFS mask is the one that matches the properties (speed) of the suppressed stimulus. These results question the general importance of retinotopically specific neural adaptation in CFS, and potentially help to explain an implicit trend in the literature to adapt one’s CFS mask to match one’s to-be-suppressed stimuli. Finally, the results should help to guide the methodological development of future research where continuous suppression of moving stimuli is desired.
Safety of quadrivalent human papillomavirus vaccine administered routinely to females.

OBJECTIVE To assess the safety of the quadrivalent human papillomavirus vaccine (HPV4) in females following routine administration. DESIGN In a cohort of vaccinated females, we compared the risk of emergency department visits and hospitalizations during the interval soon after vaccination with risk during a comparison interval more remote from vaccination. SETTING Kaiser Permanente in California. PARTICIPANTS All females who received the HPV4 vaccine. MAIN EXPOSURE One or more doses of HPV4 between August 2006 and March 2008. MAIN OUTCOME MEASURES Outcomes were emergency department visits and hospitalizations, grouped into predefined diagnostic categories. Within diagnostic groups, we used odds ratios (ORs) to estimate whether each subject had any outcome in postvaccination risk intervals (days 1-60, days 1-14, and day 0), compared with a control interval distant in time from vaccination. RESULTS One hundred eighty-nine thousand six hundred twenty-nine females received at least 1 dose and 44 001 received 3 HPV4 doses. Fifty categories had significantly elevated ORs during at least 1 risk interval. Medical record review revealed that most diagnoses were present before vaccination or diagnostic workups were initiated at the vaccine visit. Only skin infections during days 1 to 14 (OR, 1.8; 95% CI, 1.3-2.4) and syncope on day of vaccination (OR, 6.0; 95% CI, 3.9-9.2) were noted by an independent Safety Review Committee as likely associations with HPV4. CONCLUSIONS The quadrivalent human papillomavirus vaccine was associated with same-day syncope and skin infections in the 2 weeks after vaccination. This study did not detect evidence of new safety concerns among females 9 to 26 years of age secondary to vaccination with HPV4.
Ephemeral adaptation: the use of gradual onset to improve menu selection performance

We introduce ephemeral adaptation, a new adaptive GUI technique that improves performance by reducing visual search time while maintaining spatial consistency. Ephemeral adaptive interfaces employ gradual onset to draw the user's attention to predicted items: adaptively predicted items appear abruptly when the menu is opened, but non-predicted items fade in gradually. To demonstrate the benefit of ephemeral adaptation we conducted two experiments with a total of 48 users to show: (1) that ephemeral adaptive menus are faster than static menus when accuracy is high, and are not significantly slower when it is low and (2) that ephemeral adaptive menus are also faster than adaptive highlighting. While we focused on user-adaptive GUIs, ephemeral adaptation should be applicable to a broad range of visually complex tasks.
Comparison of OP-1 Putty (rhBMP-7) to Iliac Crest Autograft for Posterolateral Lumbar Arthrodesis: A Minimum 2-Year Follow-up Pilot Study

Study Design. A prospective, randomized, controlled, multicenter clinical study. Objective. To compare the safety and clinical and radiographic outcomes of OP-1 (BMP-7) Putty to autogenous iliac crest bone graft in a population of patients undergoing laminectomy and posterolateral fusion for symptomatic lumbar stenosis associated with degenerative spondylolisthesis. Summary of Background Data. Although the existing preclinical and clinical data suggest that OP-1 is able to achieve osteoinduction and clinical fusion in a variety of situations, the efficacy of this recombinant protein in a clinical spine fusion population has not been fully elucidated. This study directly compares the efficacy and safety of OP-1 putty to autograft bone for arthrodesis in patients with symptomatic stenosis in association with degenerative spondylolisthesis. Methods. Thirty-six patients with degenerative lumbar spondylolisthesis and symptoms of neurogenic claudication underwent laminectomy, bilateral medial facetectomy, and posterolateral fusion using either iliac crest autograft or OP-1 Putty. Oswestry scores and SF-36 questionnaires were used to determine the clinical response to treatment. Independent, blinded neuroradiologists reviewed both static and dynamic radiographs to determine the fusion status. Successful fusion was declared whenthe presence of continuous bridging bone between the transverse processes was observed and less than 5° of angular motion and 2 mm of translational movement was measured using digital calipers. Results. Efficacy data were tabulated for 27 patients at the 24-month time point and an additional 4 patients (without evaluable 24-month results) at the 36-month time point. One patient was not evaluable for radiology, so the data reflect clinical information for 31 patients and radiology for 30 patients. Clinical success, defined as a 20% improvement in the preoperative Oswestry score, was achieved by 17 of 20 (85%) OP-1 Putty patients and 7 of 11 (64%) autograft patients. A successful posterolateral fusion was achieved in 11 of 20 (55%) OP-1 Putty patients and 4 of 10 (40%) autograft patients. SF-36 scores showed similar clinical improvement in both groups. No systemic toxicity, ectopic bone formation, recurrent stenosis, or other adverse events specifically related to the use of the OP-1 Putty implant were observed. Conclusion. This study represents the first clinical trial to demonstrate the safety and similarity of OP-1 Putty as a replacement for autogenous bone graft in the posterolateral fusion environment with a minimum of 2-year follow-up. OP-1 Putty was able to achieve osteoinduction leading to a radiographically solid fusion in the absence of autogenous iliac crest bone graft in 55% of the patients at 24 and 36 months. These results compare favorably to the historical fusion rates reported for uninstrumented arthrodesis in this challenging clinical scenario.
Plitidepsin Has a Safe Cardiac Profile: A Comprehensive Analysis

Plitidepsin is a cyclic depsipeptide of marine origin in clinical development in cancer patients. Previously, some depsipeptides have been linked to increased cardiac toxicity. Clinical databases were searched for cardiac adverse events (CAEs) that occurred in clinical trials with the single-agent plitidepsin. Demographic, clinical and pharmacological variables were explored by univariate and multivariate logistic regression analysis. Forty-six of 578 treated patients (8.0%) had at least one CAE (11 patients (1.9%) with plitidepsin-related CAEs), none with fatal outcome as a direct consequence. The more frequent CAEs were rhythm abnormalities (n = 31; 5.4%), mostly atrial fibrillation/flutter (n = 15; 2.6%). Of note, life-threatening ventricular arrhythmias did not occur. Myocardial injury events (n = 17; 3.0%) included possible ischemic-related and non-ischemic events. Other events (miscellaneous, n = 6; 1.0%) were not related to plitidepsin. Significant associations were found with prostate or pancreas cancer primary diagnosis (p = 0.0017), known baseline cardiac risk factors (p = 0.0072), myalgia present at baseline (p = 0.0140), hemoglobin levels lower than 10 g/dL (p = 0.0208) and grade ≥2 hypokalemia (p = 0.0095). Treatment-related variables (plitidepsin dose, number of cycles, schedule and/or total cumulative dose) were not associated. Electrocardiograms performed before and after plitidepsin administration (n = 136) detected no relevant effect on QTc interval. None of the pharmacokinetic parameters analyzed had a significant impact on the probability of developing a CAE. In conclusion, the most frequent CAE type was atrial fibrillation/atrial flutter, although its frequency was not different to that reported in the age-matched healthy population, while other CAEs types were rare. No dose-cumulative pattern was observed, and no treatment-related variables were associated with CAEs. Relevant risk factors identified were related to the patient’s condition and/or to disease-related characteristics rather than to drug exposure. Therefore, the current analysis supports a safe cardiac risk profile for single-agent plitidepsin in cancer patients.
Heritability of and mortality prediction with a longevity phenotype: the healthy aging index.

BACKGROUND Longevity-associated genes may modulate risk for age-related diseases and survival. The Healthy Aging Index (HAI) may be a subphenotype of longevity, which can be constructed in many studies for genetic analysis. We investigated the HAI's association with survival in the Cardiovascular Health Study and heritability in the Long Life Family Study. METHODS The HAI includes systolic blood pressure, pulmonary vital capacity, creatinine, fasting glucose, and Modified Mini-Mental Status Examination score, each scored 0, 1, or 2 using approximate tertiles and summed from 0 (healthy) to 10 (unhealthy). In Cardiovascular Health Study, the association with mortality and accuracy predicting death were determined with Cox proportional hazards analysis and c-statistics, respectively. In Long Life Family Study, heritability was determined with a variance component-based family analysis using a polygenic model. RESULTS Cardiovascular Health Study participants with unhealthier index scores (7-10) had 2.62-fold (95% confidence interval: 2.22, 3.10) greater mortality than participants with healthier scores (0-2). The HAI alone predicted death moderately well (c-statistic = 0.643, 95% confidence interval: 0.626, 0.661, p < .0001) and slightly worse than age alone (c-statistic = 0.700, 95% confidence interval: 0.684, 0.717, p < .0001; p < .0001 for comparison of c-statistics). Prediction increased significantly with adjustment for demographics, health behaviors, and clinical comorbidities (c-statistic = 0.780, 95% confidence interval: 0.765, 0.794, p < .0001). In Long Life Family Study, the heritability of the HAI was 0.295 (p < .0001) overall, 0.387 (p < .0001) in probands, and 0.238 (p = .0004) in offspring. CONCLUSION The HAI should be investigated further as a candidate phenotype for uncovering longevity-associated genes in humans.