Miracle-dz/UniFAR-FTUs huggingface dataset:
Multiple-components weights model for cross-project software defect prediction

Software defect prediction (SDP) technology is receiving widely attention and most of SDP models are trained on data from the same project. However, at an early phase of the software lifecycle, there are little to no within-project training data to learn an available supervised defect-prediction model. Thus, cross-project defect prediction (CPDP), which is learning a defect predictor for a target project by using labelled data from a source project, has shown promising value in SDP. To better perform the CPDP, most current studies focus on filtering instances or selecting features to weaken the impact of irrelevant cross-project data. Instead, the authors propose a novel multiple-components weights (MCWs) learning model to analyse the varying auxiliary power of multiple components in a source project to construct a more precise ensemble classifiers for a target project. By combining the MCW model with kernel mean matching algorithm, their proposed approach adjusts the source-instance weights and source-component weights to jointly alleviate the negative impacts of irrelevant cross-project data. They conducted comprehensive experiments by employing 15 real-world datasets to demonstrate the advantages and effectiveness of their proposed approach.
Trabecular Bone Structural Variation in the Proximal Sacrum Among Primates

The sacrum occupies a functionally important anatomical position as part of the pelvic girdle and vertebral column. Sacral orientation and external morphology in modern humans are distinct from those in other primates and compatible with the demands of habitual bipedal locomotion. Among nonhuman primates, however, how sacral anatomy relates to positional behaviors is less clear. As an alternative to evaluation of the sacrum's external morphology, this study assesses if the sacrum's internal morphology (i.e., trabecular bone) differs among extant primates. The primary hypothesis tested is that trabecular bone parameters with established functional relevance will differ in the first sacral vertebra (S1) among extant primates that vary in positional behaviors. Results for analyses of individual variables demonstrate that bone volume fraction, degree of anisotropy, trabecular number, and size‐corrected trabecular thickness differ among primates grouped by positional behaviors to some extent, but not always in ways consistent with functional expectations. When examined as a suite, these trabecular parameters distinguish obligate bipeds from other positional behavior groups; and, the latter three trabecular bone variables further distinguish knuckle‐walking terrestrial quadrupeds from manual suspensor‐brachiators, vertical clingers and leapers, and arboreal quadrupeds, as well as between arboreal and terrestrial quadrupeds. As in other regions of the skeleton in modern humans, trabecular bone in S1 exhibits distinctively low bone volume fraction. Results from this study of extant primate S1 trabecular bone structural variation provide a functional context for interpretations concerning the positional behaviors of extinct primates based on internal sacral morphology. Anat Rec, 302:1354–1371, 2019. © 2018 Wiley Periodicals, Inc.
Identification of Rickettsial Infections (Rickettsia sp. TH2014) in Ctenocephalides orientis Fleas (Siphonaptera: Pulicidae)

Abstract Rickettsia felis (Rickettsiales: Rickettsiaceae) is an emergent human pathogen that causes febrile illnesses in various parts of the world. This study describes the identification and growth characteristics of a R. felis-like organism (designated as Rickettsia sp. TH2014) cultured from Ctenocephalides orientis fleas in rural Malaysia. In this study, culturing of rickettsiae from filtered triturated flea lysates was performed in Aedes albopictus C6/36 cells. Cytopathic effects were observed from one of the samples 4 d post-inoculation. Electron microscopy revealed actively replicating intracytosolic coccobacillary organisms in the rickettsia-infected cells. Sequence analysis of amplified citrate synthase (gltA) gene fragment shows complete match of the rickettsia with Rickettsia sp. Rf31 in Southeast Asia, and ‘Candidatus Rickettsia senegalensis' strain PU01-02 in Africa. The whole-genome sequence of Rickettsia sp. TH2014 was determined and assembled. The estimated genome size and guanine + cytosine content of the rickettsia are 1.37 Mb and 32.9%, respectively. The high values of average nucleotide identity and tetra-nucleotide signature correlation index obtained from pairwise genome comparison study suggest the identification of the rickettsia as R. felis.The whole-genome single-nucleotide polymorphism analysis demonstrates close genetic relatedness of the rickettsia with R. felis and Rickettsia asemboensis. However, based on sequence analyses of rickettsial genes (16S rDNA, gltA, ompB, and sca4), Rickettsia sp. TH2014 is found to be distinct from R. felis and R. asemboensis.The sequence analyses reveal that Rickettsia sp.TH2014 is highly similar to ‘Ca. Rickettsia senegalensis' detected in fleas from Africa, Asia, and North America. Further investigation to provide insights on pathogenic potential and transmission dynamics of the rickettsia is warranted.
PARS PLANA VITRECTOMY FOR THE TREATMENT OF TRACTIONAL AND DEGENERATIVE LAMELLAR MACULAR HOLES: Functional and Anatomical Results.

PURPOSE Functional and anatomical outcomes of vitrectomy with membrane peeling were compared in tractional lamellar macular holes (LMH)/macular pseudoholes (MPH) versus degenerative LMH. METHODS This multicenter retrospective study enrolled patients with a minimum follow-up of 6 months. The association of spectral domain optical coherence tomography parameters with preoperative and postoperative best-corrected visual acuity was analyzed. RESULTS Seventy-seven (74.8%) tractional LMH/MPH and 26 (25.2%) degenerative LMH were included. Preoperative best-corrected visual acuity was better in tractional LMH/MPH (0.39 ± 0.2 logarithm of the minimal angle of resolution, 20/50 Snellen equivalent) than degenerative LMH (0.56 ± 0.2 logarithm of the minimal angle of resolution, 20/66 Snellen equivalent; P < 0.001). Premacular membranes were found in all tractional LMH/MPH, whereas LMH-associated epiretinal proliferation (LHEP) was present in all degenerative LMH. Primary anatomical success was achieved in 97/103 eyes (94.2%), with foveal restoration occurring earlier in degenerative LMH (1.6 ± 2.3 vs. 3.3 ± 3.6 months; P = 0.025). Best-corrected visual acuity improved in both tractional LMH/MPH and degenerative LMH (P < 0.001 and P = 0.012, respectively) but was better in tractional LMH/MPH (P = 0.001). CONCLUSION The presence of premacular membranes and absence of LMH-associated epiretinal proliferation in all tractional LMH/MPH further distinguishes this from degenerative LMH. Best-corrected visual acuity improved in both subgroups but more so in tractional LMH/MPH. Complete anatomical restoration of foveal microanatomy was rare in degenerative LMH, reflecting significant morphological and pathophysiological differences between the two lesions.
Homotransfer FRET Reporters for Live Cell Imaging

Förster resonance energy transfer (FRET) between fluorophores of the same species was recognized in the early to mid-1900s, well before modern heterotransfer applications. Recently, homotransfer FRET principles have re-emerged in biosensors that incorporate genetically encoded fluorescent proteins. Homotransfer offers distinct advantages over the standard heterotransfer FRET method, some of which are related to the use of fluorescence polarization microscopy to quantify FRET between two fluorophores of identical color. These include enhanced signal-to-noise, greater compatibility with other optical sensors and modulators, and new design strategies based upon the clustering or dimerization of singly-labeled sensors. Here, we discuss the theoretical basis for measuring homotransfer using polarization microscopy, procedures for data collection and processing, and we review the existing genetically-encoded homotransfer biosensors.
Hnrnpab regulates neural cell motility through transcription of Eps8

Cell migration requires a complicated network of structural and regulatory proteins. Changes in cellular motility can impact migration as a result of cell-type or developmental stage regulated expression of critical motility genes. Hnrnpab is a conserved RNA-binding protein found as two isoforms produced by alternative splicing. Its expression is enriched in the subventricular zone (SVZ) and the rostral migratory stream within the brain, suggesting possible support of the migration of neural progenitor cells in this region. Here we show that the migration of cells from the SVZ of developing Hnrnpab−/− mouse brains is impaired. An RNA-seq analysis to identify Hnrnpab-dependent cell motility genes led us to Eps8, and in agreement with the change in cell motility, we show that Eps8 is decreased in Hnrnpab−/− SVZ tissue. We scrutinized the motility of Hnrnpab−/− cells and confirmed that the decreases in both cell motility and Eps8 are restored by ectopically coexpressing both alternatively spliced Hnrnpab isoforms, therefore these variants are surprisingly nonredundant for cell motility. Our results support a model where both Hnrnpab isoforms work in concert to regulate Eps8 transcription in the mouse SVZ to promote the normal migration of neural cells during CNS development.
Omitted variable bias in GLMs of neural spiking activity

Generalized linear models (GLMs) have a wide range of applications in systems neuroscience describing the encoding of stimulus and behavioral variables as well as the dynamics of single neurons. However, in any given experiment, many variables that impact neural activity are not observed or not modeled. Here we demonstrate, in both theory and practice, how these omitted variables can result in biased parameter estimates for the effects that are included. In three case studies, we estimate tuning functions for common experiments in motor cortex, hippocampus, and visual cortex. We find that including traditionally omitted variables changes estimates of the original parameters and that modulation originally attributed to one variable is reduced after new variables are included. In GLMs describing single-neuron dynamics, we then demonstrate how post-spike history effects can also be biased by omitted variables. Here we find that omitted variable bias can lead to mistaken conclusions about the stability of single neuron firing. Omitted variable bias can appear in any model with confounders – where omitted variables modulate neural activity and the effects of the omitted variables covary with the included effects. Understanding how and to what extent omitted variable bias affects parameter estimates is likely to be important for interpreting the parameters and predictions of many neural encoding models.
Association between clinically probable REM sleep behavior disorder and tetanus in dogs

Background Abnormal sleep behavior has been reported in 5 dogs during recovery from tetanus. Hypothesis REM sleep behavior disorder (RBD) is a more common consequence of tetanus than previously reported in veterinary literature and easily confused for epileptic seizures. Animals Sixty‐one client‐owned dogs diagnosed with tetanus at 2 UK referral centers. Methods A retrospective review of medical records was combined with a questionnaire sent to owners of surviving dogs, to identify cases that developed clinically probable RBD and determine its clinical progression and effect on quality of life of affected dogs and their owners. Descriptive statistical evaluation was performed. Results Eleven dogs (18%) died or were euthanized before discharge. At least 46% surviving dogs developed abnormal “dream enactment” clinically consistent with RBD. Twitching, running, and vocalization were new sleep behaviors in 53, 80, and 60% of affected dogs. Clinically probable RBD was described as violent or “nightmare”‐like in 36% affected dogs, and like an epileptic seizure in 40% affected dogs. When trialed, antiepileptic medications were ineffective. Onset occurred before discharge in 25% cases. For dogs that developed clinically probable RBD postdischarge, onset occurred within 2 weeks of discharge in 77% dogs. Clinically probable RBD did not worsen in severity or frequency in any dog, and spontaneously resolved within 6 months in 43% cases. Conclusions and Clinical Importance Clinically probable RBD is a common sequel to canine tetanus with many clinical similarities to epileptic seizure activity. Owners should be made aware of its potential development and care taken to avoid misdiagnosis with epileptic seizure activity.
Statistical Mechanics Treatment of the Broadened Snoek Relaxation Peak in Ternary Niobium–Vanadium–Oxygen Alloys

The Snoek relaxation profiles for ternary Niobium–Vanadium–Oxygen systems were analyzed by an embedded-cell model of statistical mechanics treatment. The relaxation characteristic and broadening mechanism were systematically discussed and some conflicting interpretations in the early research were clarified. The complicated Snoek spectrums of the Nb–V–O system can be resolved into a series of effective elementary Debye peaks, which result from the transitions of interstitial oxygen atoms between adjacent octahedral sites. The relaxation parameters of each elementary peak can be determined by element species and atomic arrangements within the corresponding embedded octahedron. The Snoek relaxation characteristic in Nb–V–O systems mainly depends on the sites distributions and the transitions status of the interstitial oxygen atoms, which are controlled by the site-dependence energies and the transition probabilities, respectively.
Roles of orf60a and orf61 in Development of Bacteriophages λ and Φ24B

The exo-xis region of lambdoid bacteriophage genomes contains several established and potential genes that are evolutionarily conserved, but not essential for phage propagation under laboratory conditions. Nevertheless, deletion or overexpression of either the whole exo-xis region and important regulatory elements can significantly influence the regulation of phage development. This report defines specific roles for orf60a and orf61 in bacteriophage λ and Φ24B, a specific Shiga toxin-converting phage with clinical relevance. We observed that mutant phages bearing deletions of orf60a and orf61 impaired two central aspects of phage development: the lysis-versus-lysogenization decision and prophage induction. These effects were more pronounced for phage Φ24B than for λ. Surprisingly, adsorption of phage Φ24B on Escherichia coli host cells was less efficient in the absence of either orf60a or orf61. We conclude that these open reading frames (ORFs) play important, but not essential, roles in the regulation of lambdoid phage development. Although phages can propagate without these ORFs in nutrient media, we suggest that they may be involved in the regulatory network, ensuring optimization of phage development under various environmental conditions.
A comparison of supraglottic devices in pediatric patients

Background When managing patients with a difficult airway, supraglottic airways (SGAs) have been used as rescue devices or to serve as a conduit for endotracheal intubation. The current study compares various clinical outcomes, including the bronchoscopic view of the glottis when using 2 SGAs, the Air-Q® laryngeal mask airway (LMA) and the i-gel® SGA, in pediatric patients. Methods Patients ≤18 years of age were prospectively randomized to receive either the Air-Q® LMA or the i-gel® SGA. Following SGA placement, a flexible fiberoptic bronchoscope was inserted through the SGA to visualize the glottis. Time taken to obtain the bronchoscopic view and place the SGA, and the ability to seal the airway at 20 cmH2O were compared. The bronchoscopic view obtained was graded as follows: 1) glottic aperture seen completely; 2) glottic aperture seen partially with visual obstruction <50%; 3) glottic aperture seen, but visual obstruction >50%; and 4) glottic aperture not seen. Results Fifty patients were enrolled and 48 (22/26 male/female) were included in the analysis. Median age was 13 years (IQR: 7, 16) and median weight was 49 kg (IQR: 25, 70). The Air-Q® LMA and i-gel® SGA groups did not differ in device placement time (median of 19 vs 21 seconds; 95% CI of difference in medians: − 2 to 7; P=0.331), the time to achieve fiberoptic view of the glottis (median of 25 vs 21 seconds; 95% CI of difference: − 9 to 8; P=0.489) or the grade of the bronchoscopic view of the airway. Eight Air-Q® and 6 i-gel® supraglottic devices sealed the airway at 20 cmH2O. Discussion The time required for successful placement of the SGA, the time required for bronchoscopic view, and the quality of bronchoscopic view through the Air-Q® LMA and the i-gel® SGA did not differ.
Predicting Engagement With Online Walking Promotion Among Metropolitan and Rural Cancer Survivors.

BACKGROUND Physical activity has numerous associated benefits for cancer survivors. Compared with their urban counterparts, rural Australians experience a health disadvantage, including poorer survival rate after diagnosis of cancer. OBJECTIVE The aims of this study were to test the effectiveness of an online 12-week walking intervention designed for cancer survivors and explore region-specific psychological predictors of behavior change. METHODS This was a quasi-randomized controlled trial of an online resource designed according to Social Cognitive Theory and Self-determination Theory, based on individualized goal setting. Measures of habitual walking, motivation, and self-efficacy were taken at baseline, postintervention, and 3-month follow-up in an intervention group (n = 46) and active control group (n = 45). The control group was provided a pedometer but did not have access to the online program. RESULTS An increase in steps/day at 12 weeks was observed in both groups, with a larger increase in the intervention group; these increases were not sustained at the 3-month follow-up. Psychological predictors of maintained change in steps per day (motivation, barrier self-efficacy, and relapse self-efficacy) did not differ between metropolitan and rural participants. Changes in steps per day among intervention participants were predicted by changes in relapse self-efficacy and barrier self-efficacy. CONCLUSIONS The intervention was successful in increasing physical activity postintervention; however, changes were not maintained at follow-up. There were no region-specific predictors of engagement in the intervention. IMPLICATIONS FOR PRACTICE Nurses are seamlessly positioned to promote health interventions like walking. Nurses should reframe physical activity with patients so that relapse is seen as common and possibly inevitable when adopting a regular physical activity habit.
Rates of immune cell infiltration in patients with triple-negative breast cancer by molecular subtype

In patients with triple-negative breast cancer (TNBC), tumor-infiltrating lymphocytes (TILs) are associated with improved survival. Lehmann et al. identified 4 molecular subtypes of TNBC [basal-like (BL) 1, BL2, mesenchymal (M), and luminal androgen receptor (LAR)], and an immunomodulatory (IM) gene expression signature indicates the presence of TILs and modifies these subtypes. The association between TNBC subtype and TILs is not known. Also, the association between inflammatory breast cancer (IBC) and the presence of TILs is not known. Therefore, we studied the IM subtype distribution among different TNBC subtypes. We retrospectively analyzed patients with TNBC from the World IBC Consortium dataset. The molecular subtype and the IM signature [positive (IM+) or negative (IM-)] were analyzed. Fisher’s exact test was used to analyze the distribution of positivity for the IM signature according to the TNBC molecular subtype and IBC status. There were 88 patients with TNBC in the dataset, and among them 39 patients (44%) had IBC and 49 (56%) had non-IBC. The frequency of IM+ cases differed by TNBC subtype (p = 0.001). The frequency of IM+ cases by subtype was as follows: BL1, 48% (14/29); BL2, 30% (3/10); LAR, 18% (3/17); and M, 0% (0/21) (in 11 patients, the subtype could not be determined). The frequency of IM+ cases did not differ between patients with IBC and non-IBC (23% and 33%, respectively; p = 0.35). In conclusion, the IM signature representing the underlying molecular correlate of TILs in the tumor may differ by TNBC subtype but not by IBC status.
Steric Effect of Antioxidant Diels-Alder-Type Adducts: A Comparison of Sanggenon C with Sanggenon D

Sanggenons C and D are two Diels-Alder-type adducts from Chinese crude drug Sang-bai-pi. Structurally, both sanggenons construct stereoisomers. In the study, they were comparatively determined using four antioxidant assays, including ferric ion reducing antioxidant power (FRAP) assay, Cu2+-reducing assay, 1,1-diphenyl-2-picryl-hydrazl (DPPH•)-scavenging assay, and 2,2′-azino-bis (3-ethylbenzo-thiazoline-6-sulfonic acid radical (ABTS•+)-scavenging assay. Their Fe2+-binding reactions were explored using UV-Vis spectra. Finally, their cytoprotective effects were evaluated using flow cytometry. In electron transfer (ET)-based FRAP and Cu2+-reducing assays, sanggenon D was found to have lower IC50 values than sanggenon C; however, in multi-pathway-based DPPH•-scavenging and ABTS•+-scavenging assays, sanggenon C possessed lower IC50 values than sanggenon D. UV-Vis spectra suggested that sanggenon C generated a bathochromic-shift (286 nm → 302 nm) and displayed stronger UV absorption than sanggenon D. In flow cytometry, sanggenon C and sanggenon D, respectively, exhibited 31.1% and 42.0% early apoptosis-percentages towards oxidative-stressed mesenchymal stem cells (MSCs). In conclusion, both sanggenons may undergo multiple pathways (e.g., ET and Fe2+-binding) to protect MSCs against oxidative stress. In the mere ET aspect, sanggenon D possesses a higher level than sanggenon C, while in multi-pathway-based radical-scavenging, Fe2+-binding, and cytoprotection aspects, sanggenon C is more active than sanggenon D. These discrepancies can conclusively be attributed to the steric effect.
Prevention and Control of Non-communicable Diseases in Iranian Population: Life Style Promotion Project Phase II: Study Protocol

Background: The Lifestyle Promotion Project (LPP) is a long-term community-based project for prevention and control of non-communicable diseases (NCDs). In this project, the healthy lifestyle promotion plan will be implemented by the health policy agenda of East Azerbaijan Province, Iran. Methods: The study design included two phases: phase I was a cross-sectional prevalence study of NCDs and the associated risk factors implemented from Feb 2014 to Apr 2014. Phase II is a prospective follow-up study currently ongoing. The healthy lifestyle promotion intervention consists of five core strategic plans. These programs was implemented by the health policy agenda of East Azerbaijan Province. Overall, 3000 participants aged 15–65 yr were enrolled to evaluate the impact of healthy lifestyle interventions in phase II of project. Results: The experience of the LPP in Iran may support the idea that a well-organized, fully evidence-based, and well-developed community-based program could be affordable to prevent non-communicable disorders in developing countries. Conclusion: The results of this survey will be presented as research articles and reports for policy makers.