Miracle-dz/UniFAR-FTUs huggingface dataset:
Convolutional Neural Networks over Control Flow Graphs for Software Defect Prediction

Existing defects in software components is unavoidable and leads to not only a waste of time and money but also many serious consequences. To build predictive models, previous studies focus on manually extracting features or using tree representations of programs, and exploiting different machine learning algorithms. However, the performance of the models is not high since the existing features and tree structures often fail to capture the semantics of programs. To explore deeply programs’ semantics, this paper proposes to leverage precise graphs representing program execution flows, and deep neural networks for automatically learning defect features. Firstly, control flow graphs are constructed from the assembly instructions obtained by compiling source code; we thereafter apply multi-view multi-layer directed graph-based convolutional neural networks (DGCNNs) to learn semantic features. The experiments on four real-world datasets show that our method significantly outperforms the baselines including several other deep learning approaches.
Neodymium‐yttrium aluminum garnet laser versus pulsed dye laser in erythemato‐telangiectatic rosacea: comparison of clinical efficacy and effect on cutaneous substance (P) expression

Different laser systems are reported to be effective in treatment of telangiectasia and erythema, but comparative studies on 1064‐nm neodymium‐yttrium aluminum garnet (Nd‐YAG) laser and pulsed dye laser (PDL) in treatment of erythemato‐telangiectatic rosacea are lacking. Substance (P) is implicated in rosacea pathogenesis.
The International Journal of Biostatistics Maximum Likelihood Estimation for Semiparametric Density Ratio Model

In the statistical literature, the conditional density model specification is commonly used to study regression effects. One attractive model is the semiparametric density ratio model, under which the conditional density function is the product of an unknown baseline density function and a known parametric function containing the covariate information. This model has a natural connection with generalized linear models and is closely related to biased sampling problems. Despite the attractive features and importance of this model, most existing methods are too restrictive since they are based on multi-sample data or conditional likelihood functions. The conditional likelihood approach can eliminate the unknown baseline density but cannot estimate it. We propose efficient estimation procedures based on the nonparametric likelihood. The nonparametric likelihood approach allows for general forms of covariates and estimates the regression parameters and the baseline density simultaneously. Therefore, the nonparametric likelihood approach is more versatile than the conditional likelihood approach especially when estimation of the conditional mean or other quantities of the outcome is of interest. We show that the nonparametric maximum likelihood estimators are consistent, asymptotically normal, and asymptotically efficient. Simulation studies demonstrate that the proposed methods perform well in practical settings. A real example is used for illustration.
Immunohistochemical biomarkers for bladder cancer prognosis

Urothelial carcinoma of the bladder (UCB) is an especially complex and heterogeneous disease with a broad spectrum of histologic findings and potentially lethal behavior. Despite advances in surgical techniques, as well as intravesical and systemic therapies, up to 30% of patients with non‐muscle‐invasive UCB and 50% of patients with muscle‐invasive UCB experience disease progression, recurrence, and eventual death. Standard prognostic features, such as pathologic stage and grade, have limited ability to predict the outcomes of this heterogeneous population. Current risk‐stratification algorithms using clinical and pathologic parameters are limited in their prognostic ability. Molecular medicine holds the promise that clinical outcomes will be improved by more accurate prognostication and directing therapy towards the mechanisms and targets associated with the growth of an individual patient's tumor. Immunohistochemical analysis of biomarker expression has provided insight into the molecular pathogenesis of UCB and offers the potential for improving clinical decision making. Numerous candidate immunohistochemical biomarkers for patients with UCB have been identified, with those relating to the cell cycle and apoptosis/cell proliferation being the most extensively studied. The present review discusses the most promising immunohistochemical biomarkers. Special attention is paid to recent data from a multi‐institutional collaboration that has implemented a regulated, phased biomarker discovery and validation pathway. Because UCB tumorigenesis and progression is a process involving multiple genetic and epigenetic alterations, multiple biomarkers need to be integrated into a prognostic signature to accurately predict outcomes. There is no doubt that biomarkers will eventually guide our clinical decision making regarding follow‐up scheduling and treatment choice.
The role of cyclic nucleotides and nucleotide cyclases in plant stress responses

The cyclic nucleotides monophosphates (cNMP) and in particular adenosine 3’,5’-cyclic monophosphate (cAMP) and guanosine 3’,5’-cyclic monophosphate (cGMP) are cyclic catalytic products of adenosine 5'-triphosphate (ATP) and guanosine 5’-triphosphate (GTP) respectively. These cNMPs are universal second messengers with key roles in many and diverse physiological responses and processes in prokaryotes, and in both higher and lower eukaryotes. Cyclic AMP is arguably one of the most extensively studied second messengers in animals, lower eukaryotes and bacteria where it has critical roles in signaling the metabolic status. In bacteria, cAMP is involved in the positive regulation of the lac operon where in an environment of a low glucose, cAMP accumulates and binds to the allosteric site of the cAMP receptor protein (CRP), a transcription activator protein. Once the CRP is in its active configuration, it binds to a cis-element upstream of the lac promoter and activates transcription. At high glucose concentrations, cAMP concentration decreases and CRP disengages from the lac operon promoter (Meiklejohn & Gralla, 1985). Cyclic AMP signaling is also critical for many aspects of the development of the slime mold Dictyostelium discoideum that grows unicellularly, but develops as multicellular organism (Kimmel & Firtel, 2004; McMains et al., 2008). Cyclic AMP has a role in chemotaxis and cAMP oscillations act as intracellular feedback loops in the transcriptional regulation of many regulatory pathways. Post aggregation, cAMP-dependent signals mediate cell sorting, pattern formation, and morphogenetic changes and cAMP receptor affinity can control wave dynamics, geometry and morphogenesis (Dormann et al., 2001). In animals, cAMP can be produced e.g. by Gs-coupled activation of adenylate cyclases (ACs) which triggers a signal cascade that includes the modification of Ca2+ channels, the phosphorylation of target proteins including enzymes involved in regulating glycogen metabolism and eventually the cAMP-dependent activation of the transcription factor, cAMP response element-binding (CREB) (Bolwell, 1995; Karin & Smeal, 1992). Cyclic AMP also plays a role in excitation-
A Comprehensive Review of the Effects of Worksite Health Promotion on Health-Related Outcomes

Purpose. This article provides the foundation for a series of literature reviews that critically examine the effectiveness of worksite health promotion programs. This issue reviews the exercise, health risk appraisal, nutrition and cholesterol, and weight control literatures; a future issue will review the alcohol, HIV/AIDS, multicomponent program, seat belt, smoking, and stress management literatures. Methods. The literature search used a four-step process that included a computerized database search, a reference search, a manual search of relevant health promotion journals, and the writing of the review by a recognized expert in the area being searched. The databases were searched from 1968 through 1994 and included Medline, Aidsline, Psychological Abstracts, Combined Health Information Database, Employee Benefits Infosource, National Prevention Evaluation Research Collection, National Resource Center on Worksite Health Promotion, National Technical Information Service, and the Substance Abuse Information database. A total of 288 articles were identified by the search, not including the 37 articles in the hypertension literature. Authors of each review were requested to incorporate additional studies not identified by the search, provide a research rating for each individual article, and a rating for the overall literature for their respective area. The authors reviewed 316 studies. Findings. The overall ratings for the reviews reported in this issue were suggestive for exercise, weak for health risk appraisals, suggestive/indicative for both nutrition and cholesterol, and indicative for weight control. The ratings for the other reviews will be reported in the subsequent issue. Conclusions. Research reported in these reviews suggests the effectiveness of worksite health promotion programs, however, additional research is required to provide conclusive evidence of their impact.
Ion Channels and Transporters in Lung Function and Disease Cigarette smoke has sensory effects through nicotinic and TRPA 1 but not TRPV 1 receptors on the isolated mouse trachea and larynx

Kichko TI, Kobal G, Reeh PW. Cigarette smoke has sensory effects through nicotinic and TRPA1 but not TRPV1 receptors on the isolated mouse trachea and larynx. Am J Physiol Lung Cell Mol Physiol 309: L812–L820, 2015. First published August 21, 2015; doi:10.1152/ajplung.00164. 2015. —Cigarette smoke (CS) exposes chemosensory nerves in the airways to a multitude of chemicals, some acting through the irritant receptors TRPV1 and TRPA1 but potentially also through nicotinic acetylcholine receptors (nAChR). Our aim was to characterize the differences in sensory neuronal effects of CS, gas phase, and particulate matter as well as of typical constituents, such as nicotine and reactive carbonyls. Isolated mouse trachea and larynx were employed to measure release of calcitonin gene-related peptide (CGRP) as an index of sensory neuron activation evoked by CS, by filtered CS gas phase essentially free of nicotine, and by dilute total particulate matter (TPM) containing defined nicotine concentrations. With CS stimulation of the superfused trachea, TRPV1 null mutants showed about the same large responses as wild-type mice, whereas both TRPA1 / and double knockouts exhibited 80% reduction; the retained 20% response was abolished by mecamylamine (10 M), indicating a distinct contribution of nAChRs. These phenotypes were accentuated by using TPM to stimulate the immersed trachea; 50% of response was retained in TRPA1 / and abolished by mecamylamine. In contrast, the gas phase acted like a sheer TRPA1 agonist, consistent with its composition, among other compounds, of volatile reactive carbonyls like formaldehyde and acrolein. In the trachea, the gas phase and CS were equally effective in releasing CGRP, whereas the larynx showed much larger CS than gas phase responses. Thus nicotinic receptors contribute to the sensory effects of cigarette smoke on the trachea, which are dominated by TRPA1. How this translates to human perception affords future research.
Expressive power of recurrent neural networks

Deep neural networks are surprisingly efficient at solving practical tasks, but the theory behind this phenomenon is only starting to catch up with the practice. Numerous works show that depth is the key to this efficiency. A certain class of deep convolutional networks -- namely those that correspond to the Hierarchical Tucker (HT) tensor decomposition -- has been proven to have exponentially higher expressive power than shallow networks. I.e. a shallow network of exponential width is required to realize the same score function as computed by the deep architecture. In this paper, we prove the expressive power theorem (an exponential lower bound on the width of the equivalent shallow network) for a class of recurrent neural networks -- ones that correspond to the Tensor Train (TT) decomposition. This means that even processing an image patch by patch with an RNN can be exponentially more efficient than a (shallow) convolutional network with one hidden layer. Using theoretical results on the relation between the tensor decompositions we compare expressive powers of the HT- and TT-Networks. We also implement the recurrent TT-Networks and provide numerical evidence of their expressivity.
The Loss Surface of Deep and Wide Neural Networks

While the optimization problem behind deep neural networks is highly non-convex, it is frequently observed in practice that training deep networks seems possible without getting stuck in suboptimal points. It has been argued that this is the case as all local minima are close to being globally optimal. We show that this is (almost) true, in fact almost all local minima are globally optimal, for a fully connected network with squared loss and analytic activation function given that the number of hidden units of one layer of the network is larger than the number of training points and the network structure from this layer on is pyramidal.
The role of small-colony variants in failure to diagnose and treat biofilm infections in orthopedics

Biomaterial-related infection of joint replacements is the second most common cause of implant failure, with serious consequences. Chronically infected replacements cannot be treated without removal of the implant, as the biofilm mode of growth protects the bacteria against antibiotics. This review discusses biofilm formation on joint replacements and the important clinical phenomenon of small-colony variants (SCVs). These slow-growing phenotypic variants often remain undetected or are misdiagnosed using hospital microbiological analyses due to their unusual morphological appearance and biochemical reactions. In addition, SCVs make the infection difficult to eradicate. They often lead to recurrence since they respond poorly to standard antibiotic treatment and can sometimes survive intracellularly.
From local scenarios to national maps: a participatory framework for envisioning the future of Tanzania

Tackling societal and environmental challenges requires new approaches that connect topdown global oversight with bottom-up sub-national knowledge. We present a novel framework for participatory development of spatially-explicit scenarios at national scale that model socio-economic and environmental dynamics by reconciling local stakeholder perspectives and national spatial data. We illustrate results generated by this approach and evaluate its potential to contribute to a greater understanding of the relationship between development pathways and sustainability. Using the lens of land use and land cover changes, and engaging 240 stakeholders representing sub-national (seven forest management Zones) and the national level, we applied the framework to assess alternative development strategies in the Tanzania mainland to the year 2025 - under either a business as usual or a green development scenario. In the business as usual scenario, no productivity gain is expected, cultivated land expands by ca. 2% per year (up to 88,808 km2), with large impacts on woodlands and wetlands. Despite legal protection, encroachment of natural forest occurs along reserve borders. Additional wood demand leads to degradation (i.e. loss of tree cover and biomass) up to 80,426 km2 of wooded land. The alternative green economy scenario envisages decreasing degradation and deforestation with increasing productivity (+10%) and implementation of Payment for Ecosystem Service schemes. In this scenario, cropland expands by 44,132 km2 and the additional degradation is limited to 35,778 km2. This scenario development framework captures perspectives and knowledge across a diverse range of stakeholders and regions. Although further effort is required to extend its applicability, improve users’ equity, and reduce costs the resulting spatial outputs can be used to inform national level planning and policy implementation associated with sustainable development, especially the REDD+ climate mitigation strategy.
Comparing the gender gap in educational attainment: the impact of emancipatory contexts in 33 cohorts across 33 countries

ABSTRACT Nowadays, women outperform men in educational attainment in many countries. Still, large variation between countries remains. Emancipatory contexts in which individuals are raised might explain these differences in male–female educational attainment, both over time and across countries. This study examines individual and contextual factors that affect educational attainment of men and women for cohorts born between 1950 and 1982 across 33 countries. Possible explanations for differentiation over time and across countries relate to women’s labour market participation and an emancipatory normative climate, indicated by degree of religiosity. We employ multilevel models on data (N = 138,498) from 6 waves of the European Social Survey and the US General Social Survey (2002–2012) to test our hypotheses. Results show that a higher level of female labour market participation in early adolescence improves women’s performance in education, whereas high levels of religiosity during that phase negatively affect women’s educational attainment.
Salidroside attenuates hypoxia/reoxygenation-induced human brain vascular smooth muscle cell injury by activating the SIRT1/FOXO3α pathway

It has been reported that salidroside (SAL), a natural dietary isothiocyanate, exhibits neuroprotective roles in cerebral ischemia-reperfusion injury. However, to the best of our knowledge, its underlying protective mechanism remains unknown. Sirtuin 1 (SIRT1) is a class III histone deacetylase involved in a variety of cellular functions. SIRT1 has been identified as a mediator of cerebral ischemia and may induce neuroprotection by activating various intracellular downstream targets, such as forkhead box protein O3α (FOXO3α). Therefore, the present study aimed to investigate whether SAL protects human brain vascular smooth muscle cells (HBVSMC) against hypoxia/reoxygenation (H/R) injury, which is a cell model of cerebral ischemia-reperfusion injury, through regulating the SIRT1-activited signaling pathway. The present study revealed that H/R treatment significantly reduced the expression of SIRT1 protein in HBVSMCs. Additionally, pretreatment with SAL reversed the H/R-induced decrease in cellular viability, increased caspase-3 activity, the appearance of apoptotic cells and the apoptosis rate in HBVSMCs. SAL attenuated the H/R-induced decrease in the expression of SIRT1 and phosphorylated FOXO3α protein in HBVSMCs, suggesting that the protective role of SAL in H/R injury occurs via the SIRT1/FOXO3α pathway. Furthermore, sirtinol, a SIRT1-specific inhibitor, suppressed the inhibitory effects of SAL on H/R-induced cytotoxicity and apoptosis as indicated by the downregulation of cell viability and upregulation of caspase-3 activity and apoptosis rate induced by sirtinol treatment in HBVSMCs. The reversal effects of SAL on H/R-induced alternation of B-cell lymphoma (Bcl-2) and Bcl-2 associated X protein expression were also attenuated by sirtinol. These results suggest that SAL exhibits neuroprotective effects against H/R injury by activating the SIRT1/FOXO3α pathway, which may become a novel potential therapeutic target for the treatment of cerebral ischemic disease.
Role of commercial harbours and recreational marinas in the spread of non-indigenous fouling species

Abstract The role of commercial harbours as sink and source habitats for non-indigenous species (NIS) and the role of recreational boating for their secondary spread were investigated by analysing the fouling community of five Italian harbours and five marinas in the western Mediterranean Sea. It was first hypothesised that NIS assemblages in the recreational marinas were subsets of those occurring in commercial harbours. However, the data did not consistently support this hypothesis: the NIS pools of some marinas significantly diverged from harbours even belonging to the same coastal stretches, including NIS occurring only in marinas. This study confirms harbours as hotspots for marine NIS, but also reveals that numbers of NIS in some marinas is higher than expected, suggesting that recreational vessels effectively facilitate NIS spread. It is recommended that this vector of NIS introduction is taken into account in the future planning of sustainable development of maritime tourism in Europe.
Spectral-domain optical coherence tomographic assessment of severity of cystoid macular edema in retinopathy of prematurity.

OBJECTIVE To investigate whether the severity of cystoid macular edema (CME) in neonates who were 31 to 36 weeks' postmenstrual age, as viewed by spectral-domain optical coherence tomography (SD-OCT)imaging, predicts the severity of retinopathy of prematurity(ROP) or is related to systemic health. DESIGN Of 62 prematurely born neonates in a prospective institutional review board-approved study, 42 met the following inclusion criteria: at least 1 SD-OCT imaging session prior to 37 weeks' postmenstrual age and prior to ROP laser treatment, if a laser treatment was performed,and an ophthalmic ROP examination at or after 41 weeks' postmenstrual age, evidence of complete retinal vascularization in zone III, or documentation through telephone report of such information after transfer of care.Measures of CME severity, including central foveal thickness,retinal layer thicknesses, and foveal-to-parafoveal thickness ratio in 1 eye per subject, were compared with ROP outcomes: laser treatment, maximum plus disease,and maximum ROP stage. Systemic health factors were also correlated. RESULTS Cystoid macular edema was present in 50% of neonates. Multiple elongated cystoid structures within the inner nuclear layer were most common. The presence of CME was not associated with ROP outcomes. The central foveal thickness, the thickness of the inner retinal layers, and the foveal-to-parafoveal thickness ratio were higher in eyes that required laser treatment or that developed plus disease or ROP stage 3. Cystoid macular edema was not clearly associated with systemic factors. CONCLUSIONS Cystoid macular edema is common in premature infants screened for ROP before 37 weeks' postmenstrual age, with the most common SD-OCT phenotype ofa bulging fovea from multiple elongated cystoid spaces. Detection of CME is not associated with ROP severity; however,tomographic thickness measurements could potentially predict a higher risk of requiring laser treatment or developing plus disease or ROP stage 3. Systemic health factors are probably not related to the development of CME.
Interplay of endothelial and inducible nitric oxide synthases modulates the vascular response to ischaemia–reperfusion in the rabbit lung

Aim: Lung ischaemia–reperfusion induces nitric oxide synthesis and reactive nitrogen species, decreasing nitric oxide bioavailability. We hypothesized that in the ventilated lung, this process begins during ischaemia and intensifies with reperfusion, contributing to ischaemia–reperfusion‐induced pulmonary vasoconstriction. The aim was to determine whether ischaemia–reperfusion alters inducible and endothelial nitric oxide synthase expression/activity, reactive nitrogen species generation, and nitric oxide bioavailability, potentially affecting pulmonary perfusion.