Miracle-dz/UniFAR-FTUs huggingface dataset:
"Automatically Assessing Code Understandability" Reanalyzed: Combined Metrics Matter

Previous research shows that developers spend most of their time understanding code. Despite the importance of code understandability for maintenance-related activities, an objective measure of it remains an elusive goal. Recently, Scalabrino et al. reported on an experiment with 46 Java developers designed to evaluate metrics for code understandability. The authors collected and analyzed data on more than a hundred features describing the code snippets, the developers' experience, and the developers' performance on a quiz designed to assess understanding. They concluded that none of the metrics considered can individually capture understandability. Expecting that understandability is better captured by a combination of multiple features, we present a reanalysis of the data from the Scalabrino et al. study, in which we use different statistical modeling techniques. Our models suggest that some computed features of code, such as those arising from syntactic structure and documentation, have a small but significant correlation with understandability. Further, we construct a binary classifier of understandability based on various interpretable code features, which has a small amount of discriminating power. Our encouraging results, based on a small data set, suggest that a useful metric of understandability could feasibly be created, but more data is needed.
Effect of Negative Pressure Wound Therapy vs Standard Wound Management on 12-Month Disability Among Adults With Severe Open Fracture of the Lower Limb: The WOLLF Randomized Clinical Trial

Importance Open fractures of the lower limb occur when a broken bone penetrates the skin. There can be major complications from these fractures, which can be life-changing. Objectives To assess the disability, rate of deep infection, and quality of life in patients with severe open fracture of the lower limb treated with negative pressure wound therapy (NPWT) vs standard wound management after the first surgical debridement of the wound. Design, Setting, and Participants Multicenter randomized trial performed in the UK Major Trauma Network, recruiting 460 patients aged 16 years or older with a severe open fracture of the lower limb from July 2012 through December 2015. Final outcome data were collected through November 2016. Exclusions were presentation more than 72 hours after injury and inability to complete questionnaires. Interventions NPWT (n = 226) in which an open-cell solid foam or gauze was placed over the surface of the wound and connected to a suction pump, creating a partial vacuum over the dressing, vs standard dressings not involving application of negative pressure (n = 234). Main Outcomes and Measures Disability Rating Index score (range, 0 [no disability] to 100 [completely disabled]) at 12 months was the primary outcome measure, with a minimal clinically important difference of 8 points. Secondary outcomes were complications including deep infection and quality of life (score ranged from 1 [best possible] to −0.59 [worst possible]; minimal clinically important difference, 0.08) collected at 3, 6, 9, and 12 months. Results Among 460 patients who were randomized (mean age, 45.3 years; 74% men), 88% (374/427) of available study participants completed the trial. There were no statistically significant differences in the patients’ Disability Rating Index score at 12 months (mean score, 45.5 in the NPWT group vs 42.4 in the standard dressing group; mean difference, −3.9 [95% CI, −8.9 to 1.2]; P = .13), in the number of deep surgical site infections (16 [7.1%] in the NPWT group vs 19 [8.1%] in the standard dressing group; difference, 1.0% [95% CI, −4.2% to 6.3%]; P = .64), or in quality of life between groups (difference in EuroQol 5-dimensions questionnaire, 0.02 [95% CI, −0.05 to 0.08]; Short Form–12 Physical Component Score, 0.5 [95% CI, −3.1 to 4.1] and Mental Health Component Score, −0.4 [95% CI, −2.2 to 1.4]). Conclusions and Relevance Among patients with severe open fracture of the lower limb, use of NPWT compared with standard wound dressing did not improve self-rated disability at 12 months. The findings do not support this treatment for severe open fractures. Trial Registration isrctn.org Identifier: ISRCTN33756652
Extracorporeal shock wave therapy for the healing and management of venous leg ulcers.

BACKGROUND Leg ulcers are chronic wounds of the lower leg, caused by poor blood flow, that can take a long time to heal. The pooling of blood in the veins can damage the skin and surrounding tissues, causing an ulcer to form. Venous leg ulcers are associated with impaired quality of life, reduced mobility, pain, stress and loss of dignity. The standard treatment for venous leg ulcers is compression bandages or stockings. Shock wave therapy may aid the healing of these wounds through the promotion of angiogenesis (the formation and development of blood vessels) and reduction of inflammation, though this process is poorly understood at present. OBJECTIVES To assess the effects of extracorporeal shock wave therapy on the healing and management of venous leg ulceration. SEARCH METHODS In April 2018 we searched the Cochrane Wounds Specialised Register; the Cochrane Central Register of Controlled Trials (CENTRAL); Ovid MEDLINE (including In-Process & Other Non-Indexed Citations); Ovid Embase and EBSCO CINAHL Plus. We also searched clinical trials registries for ongoing and unpublished studies, and scanned reference lists of relevant included studies as well as reviews, meta-analyses and health technology reports to identify additional studies. We applied no restrictions with respect to language, date of publication or study setting. SELECTION CRITERIA We considered all published and unpublished randomised controlled trials (RCTs) assessing the effectiveness of extracorporeal shock wave therapy in the healing and management of venous leg ulceration. DATA COLLECTION AND ANALYSIS Two review authors independently performed study selection. We planned that two review authors would also assess the risk of bias of included studies, extract study data and rate the certainty of the evidence using GRADE. MAIN RESULTS We found no RCTs that met the inclusion criteria for this review. AUTHORS' CONCLUSIONS We found no RCTs assessing the effectiveness of extracorporeal shock wave therapy in the healing and management of venous leg ulceration. The lack of high-quality evidence in this area highlights a gap in research and may serve to justify the need for further research and evidence to provide guidance concerning the use of this treatment option for this condition. Future trials should be of clear design and include concomitant use of the current best practice treatment, multilayer compression therapy. Recruitment should aspire to best represent patients seen in clinical practice and patient-related outcome measures should be included in study design.
Deep Learning for Electromyographic Hand Gesture Signal Classification Using Transfer Learning

In recent years, deep learning algorithms have become increasingly more prominent for their unparalleled ability to automatically learn discriminant features from large amounts of data. However, within the field of electromyography-based gesture recognition, deep learning algorithms are seldom employed as they require an unreasonable amount of effort from a single person, to generate tens of thousands of examples. This paper’s hypothesis is that general, informative features can be learned from the large amounts of data generated by aggregating the signals of multiple users, thus reducing the recording burden while enhancing gesture recognition. Consequently, this paper proposes applying transfer learning on aggregated data from multiple users while leveraging the capacity of deep learning algorithms to learn discriminant features from large datasets. Two datasets comprised 19 and 17 able-bodied participants, respectively (the first one is employed for pre-training), were recorded for this work, using the Myo armband. A third Myo armband dataset was taken from the NinaPro database and is comprised ten able-bodied participants. Three different deep learning networks employing three different modalities as input (raw EMG, spectrograms, and continuous wavelet transform (CWT)) are tested on the second and third dataset. The proposed transfer learning scheme is shown to systematically and significantly enhance the performance for all three networks on the two datasets, achieving an offline accuracy of 98.31% for 7 gestures over 17 participants for the CWT-based ConvNet and 68.98% for 18 gestures over 10 participants for the raw EMG-based ConvNet. Finally, a use-case study employing eight able-bodied participants suggests that real-time feedback allows users to adapt their muscle activation strategy which reduces the degradation in accuracy normally experienced over time.
Label-Free Quantitative Proteomics Identifies Novel Plasma Biomarkers for Distinguishing Pulmonary Tuberculosis and Latent Infection

The lack of effective differential diagnostic methods for active tuberculosis (TB) and latent infection (LTBI) is still an obstacle for TB control. Furthermore, the molecular mechanism behind the progression from LTBI to active TB has been not elucidated. Therefore, we performed label-free quantitative proteomics to identify plasma biomarkers for discriminating pulmonary TB (PTB) from LTBI. A total of 31 overlapping proteins with significant difference in expression level were identified in PTB patients (n = 15), compared with LTBI individuals (n = 15) and healthy controls (HCs, n = 15). Eight differentially expressed proteins were verified using western blot analysis, which was 100% consistent with the proteomics results. Statistically significant differences of six proteins were further validated in the PTB group compared with the LTBI and HC groups in the training set (n = 240), using ELISA. Classification and regression tree (CART) analysis was employed to determine the ideal protein combination for discriminating PTB from LTBI and HC. A diagnostic model consisting of alpha-1-antichymotrypsin (ACT), alpha-1-acid glycoprotein 1 (AGP1), and E-cadherin (CDH1) was established and presented a sensitivity of 81.2% (69/85) and a specificity of 95.2% (80/84) in discriminating PTB from LTBI, and a sensitivity of 81.2% (69/85) and a specificity of 90.1% (64/81) in discriminating PTB from HCs. Additional validation was performed by evaluating the diagnostic model in blind testing set (n = 113), which yielded a sensitivity of 75.0% (21/28) and specificity of 96.1% (25/26) in PTB vs. LTBI, 75.0% (21/28) and 92.3% (24/26) in PTB vs. HCs, and 75.0% (21/28) and 81.8% (27/33) in PTB vs. lung cancer (LC), respectively. This study obtained the plasma proteomic profiles of different M.TB infection statuses, which contribute to a better understanding of the pathogenesis involved in the transition from latent infection to TB activation and provide new potential diagnostic biomarkers for distinguishing PTB and LTBI.
Tillage intensity and pasture in rotation effectively shape soil microbial communities at a landscape scale

Soil microorganisms are essential to agroecosystem functioning and services. Yet, we still lack information on which farming practices can effectively shape the soil microbial communities. The aim of this study was to identify the farming practices, which are most effective at positively or negatively modifying bacterial and fungal diversity while considering the soil environmental variation at a landscape scale. A long‐term research study catchment (12 km2) representative of intensive mixed farming (livestock and crop) in Western Europe was investigated using a regular grid for soil sampling (n = 186). Farming systems on this landscape scale were described in terms of crop rotation, use of fertilizer, soil tillage, pesticides treatments, and liming. Molecular microbial biomass was estimated by soil DNA recovery. Bacterial and fungal communities were analyzed by 16S and 18S rRNA gene pyrosequencing. Microbial biomass was significantly stimulated by the presence of pasture during the crop rotation since temporary and permanent pastures, as compared to annual crops, increased the soil microbial biomass by +23% and +93% respectively. While soil properties (mainly pH) explained much of the variation in bacterial diversity, soil tillage seemed to be the most influential among the farming practices. A 2.4% increase in bacterial richness was observed along our gradient of soil tillage intensity. In contrast, farming practices were the predominant drivers of fungal diversity, which was mainly determined by the presence of pastures during the crop rotation. Compared to annual crops, temporary and permanent pastures increased soil fungal richness by +10% and +14.5%, respectively. Altogether, our landscape‐scale investigation allows the identification of farming practices that can effectively shape the soil microbial abundance and diversity, with the goal to improve agricultural soil management and soil ecological integrity.
The Effects of Temperament on Depression According to the Schema Model: A Scoping Review

Background: Recent studies have shown that not every depressed patient responds to Cognitive Behavioral Therapy, and some of those who do relapse upon termination. Due to its dual focus on the past and present, Schema Model (SM) represents a promising alternative model to understand depression. However, studies examining SM often operationalize the same construct differently, resulting in inconsistent evidence of change. There is no known review clarifying (1) how best to assess schema constructs; and (2) the relevant pathways to depression, without which, the empirical basis for SM cannot be examined. Methods: A scoping review was conducted in accordance to PRISMA guidelines to map evidence of the relationship between constructs of SM and depression, and measures used to assess the constructs. 2463 articles were identified with 49 primary research studies included. This paper is a subset of the scoping review and focuses on the five studies examining effects of temperament on depression. Results: Two models were used to operationalize temperament: The Five Factor Model (FFM) and the Psychobiological Model of Personality (PBM). The variables of neuroticism and harm avoidance were positively associated with depressive symptoms while self-directedness and cooperativeness were negative associated with depressive symptoms. Conclusion: The FFM is more suited to operationalize temperament in studies of SM and depression due to its theoretical compatibility with SM, established psychometric properties of its measures, and widespread use among studies of SM. Out of the five factors in the FFM, only neuroticism exerts direct and indirect effects on depression. These findings are limited by homogeneous sampling, hence future research studies should consider extending it to adult clinical samples. Nevertheless, this review represents a first step in the systematic examination of the empirical basis of SM and a contribution to treatment innovation and practice for depression.
MicroRNA-145-3p suppresses proliferation and promotes apotosis and autophagy of osteosarcoma cell by targeting HDAC4

Abstract Studies have shown that miR-145-3p functions as a tumor suppressor and is associated with tumor growth and metastasis. This study intends to uncover the mechanism of a tumor suppressor of miR-145-3p. The expressions of miR-194 in osteosarcoma cell lines and tissues were monitored by real-time PCR. The proliferation ability was examined by MTT assay. The apoptosis and autophagy of cells were monitored by flow cytometry and microcopy, respectively. The regulation of miR-145-3p on HDAC4 was determined by luciferase assays and western blot assay. The results showed that miR-145-3p was significantly reduced in the osteosarcoma compared with the normal bone tissue. Overexpression of miR-145-3p significantly attenuated the proliferation and induced the apoptosis and autophagy of osteosarcoma cells. Furthermore, we demonstrated that miR-145-3p has inhibited the malignant behavior of osteosarcoma by down-regulating HDAC4 expression. These findings suggested that miR-145-3p may act as a tumor suppressor in osteosarcoma. MiR-145-3p/HDAC4 may be a novel therapeutic target in treatment of osteosarcoma.
Magnesium Potassium Phosphate Compound for Immobilization of Radioactive Waste Containing Actinide and Rare Earth Elements

The problem of effective immobilization of liquid radioactive waste (LRW) is key to the successful development of nuclear energy. The possibility of using the magnesium potassium phosphate (MKP) compound for LRW immobilization on the example of nitric acid solutions containing actinides and rare earth elements (REE), including high level waste (HLW) surrogate solution, is considered in the research work. Under the study of phase composition and structure of the MKP compounds that is obtained by the XRD and SEM methods, it was established that the compounds are composed of crystalline phases—analogues of natural phosphate minerals (struvite, metaankoleite). The hydrolytic stability of the compounds was determined according to the semi-dynamic test GOST R 52126-2003. Low leaching rates of radionuclides from the compound are established, including a differential leaching rate of 239Pu and 241Am—3.5 × 10−7 and 5.3 × 10−7 g/(cm2∙day). As a result of the research work, it was concluded that the MKP compound is promising for LRW immobilization and can become an alternative material combining the advantages of easy implementation of the technology, like cementation and the high physical and chemical stability corresponding to a glass-like compound.
Switching from reference infliximab to CT-P13 in patients with inflammatory bowel disease: results of a multicenter study after 12 months.

BACKGROUND AND AIMS infliximab has changed the natural history of inﬂammatory bowel disease (IBD). The advent of biosimilar treatments such as CT-P13 will hopefully improve the availability of biological therapies. Data with regard to drug switching are currently limited. The objective of the study was to assess the effectiveness and safety of switching from the reference product (RP), infliximab, to CT-P13 in patients with IBD. METHODS this was a multicenter prospective observational study in patients with Crohn's disease (CD) and ulcerative colitis (UC). All patients had switched from infliximab RP (Remicade®) to CT-P13 treatment and were followed up for 12 months. The efficacy endpoint was the change in clinical remission assessed at 0 and 12 months, according to the Harvey-Bradshaw score and partial Mayo score for patients with CD and UC, respectively. Adverse events were monitored and recorded throughout the study. RESULTS a total of 167 patients (116 CD/51 UC) were included; 88.8% (103/116) of patients with CD were in remission at the time of the drug switch and 69.7% were in remission at 12 months. The Harvey-Bradshaw (HB) score significantly changed at 12 months (p = 0.001); 84.3% (43/51) of patients with UC were in remission at the time of the drug switch and 76.7% were in remission at 12 months. No significant changes in the median partial Mayo score (p = 0.87) were observed at 12 months. Serious adverse events related to medication were reported in 12/167 (7.2%) cases. CONCLUSION switching from infliximab RP to CT-P13 is safe and effective at 12 months. The loss of efficacy at 12 months was 15.7%.
Long-Term Follow-Up of Acute Hepatitis B: New Insights in Its Natural History and Implications for Antiviral Treatment

Acute hepatitis B infection (AHB) is still a common viral acute hepatitis worldwide. As vaccination, antiviral treatment, and immigration are bound to affect the epidemiological landscape of HBV infections, and some of its aspects need to be investigated: (1) the circulation of vaccine escape mutants and of primary drug resistant strains; (2) the change in HBV genotype prevalence; and (3) the clinical implications of AHB and the probability of chronification. The serological, virological, and clinical parameters of 75 patients, acutely infected by HBV, were gathered for a retrospective study. Long-term follow up, either to complete seroconversion or for up to five years, was possible for 44 patients. Sequence analysis of the reverse transcriptase/HBsAg and precore regions was performed to investigate the molecular epidemiology and pathogenesis of recent infections by HBV. Genotype distribution in AHB in Italian patients was radically different from that of chronic infections, with a dramatic increase of extra-European genotypes (A1, F), suggesting that a proportion of AHBs are currently related to imported strains. None of the documented infections occurred in vaccinated individuals, while HBsAg variants (potentially vaccine escape variants) were rare and less prevalent than in chronic infections. No drug resistant strains were observed. Spontaneous viral clearance occurred in all but three cases. Time to viral clearance was inversely proportional to liver damage, but HBsAg titer on day 28 and, better still, HBsAg decay from day 0 to day 28 after admission, were the best predictors of chronification. They are, thus, potentially useful to guide antiviral treatment to prevent chronic evolution.
CO2 and O2 dynamics in leaves of aquatic plants with C3 or CAM photosynthesis – application of a novel CO2 microsensor

Background and Aims Leaf tissue CO2 partial pressure (pCO2) shows contrasting dynamics over a diurnal cycle in C3 and Crassulacean Acid Metabolism (CAM) plants. However, simultaneous and continuous monitoring of pCO2 and pO2 in C3 and CAM plants under the same conditions was lacking. Our aim was to use a new CO2 microsensor and an existing O2 microsensor for non-destructive measurements of leaf pCO2 and pO2 dynamics to compare a C3 and a CAM plant in an aquatic environment. Methods A new amperometric CO2 microsensor and an O2 microsensor elucidated with high temporal resolution the dynamics in leaf pCO2 and pO2 during light-dark cycles for C3Lobelia dortmanna and CAM Littorella uniflora aquatic plants. Underwater photosynthesis, dark respiration, tissue malate concentrations and sediment CO2 and O2 were also measured. Key Results During the dark period, for the C3 plant, pCO2 increased to approx. 3.5 kPa, whereas for the CAM plant CO2 was mostly below 0.05 kPa owing to CO2 sequestration into malate. Upon darkness, the CAM plant had an initial peak in pCO2 (approx. 0.16 kPa) which then declined to a quasi-steady state for several hours and then pCO2 increased towards the end of the dark period. The C3 plant became severely hypoxic late in the dark period, whereas the CAM plant with greater cuticle permeability did not. Upon illumination, leaf pCO2 declined and pO2 increased, although aspects of these dynamics also differed between the two plants. Conclusions The continuous measurements of pCO2 and pO2 highlighted the contrasting tissue gas compositions in submerged C3 and CAM plants. The CAM leaf pCO2 dynamics indicate an initial lag in CO2 sequestration to malate, which after several hours of malate synthesis then slows. Like the use of O2 microsensors to resolve questions related to plant aeration, deployment of the new CO2 microsensor will benefit plant ecophysiology research.