Miracle-dz/UniFAR-FTUs huggingface dataset:
Path-Based Function Embedding and its Application to Specification Mining

Identifying the relationships among program elements is useful for program understanding, debugging, and analysis. One such relationship is synonymy. Function synonyms are functions that play a similar role in code, e.g. functions that perform initialization for different device drivers, or functions that implement different symmetric-key encryption schemes. Function synonyms are not necessarily semantically equivalent and can be syntactically dissimilar; consequently, approaches for identifying code clones or functional equivalence cannot be used to identify them. This paper presents func2vec, an algorithm that maps each function to a vector in a vector space such that function synonyms are grouped together. We compute the function embedding by training a neural network on sentences generated from random walks over an encoding of the program as a labeled pushdown system (l-PDS). We demonstrate that func2vec is effective at identifying function synonyms in the Linux kernel. Furthermore, we show how function synonyms enable mining error-handling specifications with high support in Linux file systems and drivers.
HIV transmission and retention in care among HIV-exposed children enrolled in Malawi’s prevention of mother-to-child transmission programme

Introduction: In Malawi, HIV‐infected pregnant and breastfeeding women are offered lifelong antiretroviral therapy (ART) regardless of CD4 count or clinical stage (Option B+). Their HIV‐exposed children are enrolled in the national prevention of mother‐to‐child transmission (PMTCT) programme, but many are lost to follow‐up. We estimated the cumulative incidence of vertical HIV transmission, taking loss to follow‐up into account.
Comparing planar image quality of rotating slat and parallel hole collimation: influence of system modeling

The main remaining challenge for a gamma camera is to overcome the existing trade-off between collimator spatial resolution and system sensitivity. This problem, strongly limiting the performance of parallel hole collimated gamma cameras, can be overcome by applying new collimator designs such as rotating slat (RS) collimators which have a much higher photon collection efficiency. The drawback of a RS collimated gamma camera is that, even for obtaining planar images, image reconstruction is needed, resulting in noise accumulation. However, nowadays iterative reconstruction techniques with accurate system modeling can provide better image quality. Because the impact of this modeling on image quality differs from one system to another, an objective assessment of the image quality obtained with a RS collimator is needed in comparison to classical projection images obtained using a parallel hole (PH) collimator. In this paper, a comparative study of image quality, achieved with system modeling, is presented. RS data are reconstructed to planar images using maximum likelihood expectation maximization (MLEM) with an accurate Monte Carlo derived system matrix while PH projections are deconvolved using a Monte Carlo derived point-spread function. Contrast-to-noise characteristics are used to show image quality for cold and hot spots of varying size. Influence of the object size and contrast is investigated using the optimal contrast-to-noise ratio (CNRo). For a typical phantom setup, results show that cold spot imaging is slightly better for a PH collimator. For hot spot imaging, the CNRo of the RS images is found to increase with increasing lesion diameter and lesion contrast while it decreases when background dimensions become larger. Only for very large background dimensions in combination with low contrast lesions, the use of a PH collimator could be beneficial for hot spot imaging. In all other cases, the RS collimator scores better. Finally, the simulation of a planar bone scan on a RS collimator revealed a hot spot contrast improvement up to 54% compared to a classical PH bone scan.
How Does Software Process Improvement Address Global Software Engineering?

For decades, Software Process Improvement (SPI) programs have been implemented, inter alia, to improve quality and speed of software development. To set up, guide, and carry out SPI projects, and to measure SPI state, impact, and success, a multitude of different SPI approaches and considerable experience are available. SPI addresses many aspects ranging from individual developer skills to entire organizations. It comprises for instance the optimization of specific activities in the software lifecycle as well as the creation of organization awareness and project culture. In the course of conducting a systematic mapping study on the state-of-the-art in SPI from a general perspective, we observed Global Software Engineering (GSE) becoming a topic of interest in recent years. Therefore, in this paper, we provide a detailed investigation of those papers from the overall systematic mapping study that were classified as addressing SPI in the context of GSE. From the main study's result set, a set of 30 papers dealing with GSE was selected for an in-depth analysis using the systematic review instrument to study the contributions and to develop an initial picture of how GSE is considered from the perspective of SPI. Our findings show the analyzed papers delivering a substantial discussion of cultural models and how such models can be used to better address and align SPI programs with multi-national environments. Furthermore, experience is shared discussing how agile approaches can be implemented in companies working at the global scale. Finally, success factors and barriers are studied to help companies implementing SPI in a GSE context.
Nonlinear temporal dynamics of cerebral small vessel disease

Objective: To investigate the temporal dynamics of cerebral small vessel disease (SVD) by 3 consecutive assessments over a period of 9 years, distinguishing progression from regression. Methods: Changes in SVD markers of 276 participants of the Radboud University Nijmegen Diffusion Tensor and Magnetic Resonance Imaging Cohort (RUN DMC) cohort were assessed at 3 time points over 9 years. We assessed white matter hyperintensities (WMH) volume by semiautomatic segmentation and rated lacunes and microbleeds manually. We categorized baseline WMH severity as mild, moderate, or severe according to the modified Fazekas scale. We performed mixed-effects regression analysis including a quadratic term for increasing age. Results: Mean WMH progression over 9 years was 4.7 mL (0.54 mL/y; interquartile range 0.95–5.5 mL), 20.3% of patients had incident lacunes (2.3%/y), and 18.9% had incident microbleeds (2.2%/y). WMH volume declined in 9.4% of the participants during the first follow-up interval, but only for 1 participant (0.4%) throughout the whole follow-up. Lacunes disappeared in 3.6% and microbleeds in 5.7% of the participants. WMH progression accelerated over time: including a quadratic term for increasing age during follow-up significantly improved the model (p < 0.001). SVD progression was predominantly seen in participants with moderate to severe WMH at baseline compared to those with mild WMH (odds ratio [OR] 35.5, 95% confidence interval [CI] 15.8–80.0, p < 0.001 for WMH progression; OR 5.7, 95% CI 2.8–11.2, p < 0.001 for incident lacunes; and OR 2.9, 95% CI 1.4–5.9, p = 0.003 for incident microbleeds). Conclusions: SVD progression is nonlinear, accelerating over time, and a highly dynamic process, with progression interrupted by reduction in some, in a population that on average shows progression.
Density-Based Place Clustering Using Geo-Social Network Data

Spatial clustering deals with the unsupervised grouping of places into clusters and finds important applications in urban planning and marketing. Current spatial clustering models disregard information about the people and the time who and when are related to the clustered places. In this paper, we show how the density-based clustering paradigm can be extended to apply on places which are visited by users of a geo-social network. Our model considers spatio-temporal information and the social relationships between users who visit the clustered places. After formally defining the model and the distance measure it relies on, we provide alternatives to our model and the distance measure. We evaluate the effectiveness of our model via a case study on real data; in addition, we design two quantitative measures, called social entropy and community score, to evaluate the quality of the discovered clusters. The results show that temporal-geo-social clusters have special properties and cannot be found by applying simple spatial clustering approaches and other alternatives.
Systematic challenges for future gravitational wave measurements of precessing binary black holes

The properties of precessing, coalescing binary black holes are presently inferred through comparison with two approximate models of compact binary coalescence. In this work we show that these two models often disagree substantially when binaries have modestly large spins (a ≳ 0.4) and modest mass ratios (q ≳ 2). We demonstratethese disagreements using standard figures ofmeritandthe parametersinferred for recent detections of binary black holes. By comparing to numerical relativity, we confirm that these disagreements reflect systematic errors. We provide concrete examples to demonstrate that these systematic errors can significantly impact inferences about astrophysically significant binary parameters. For the immediate future, parameter inference for binary black holes should be performed with multiple models (including numerical relativity), and carefully validated by performing inference under controlled circumstances with similar synthetic events.
Genetic polymorphisms that affect selenium status and response to selenium supplementation in United Kingdom pregnant women1

Background: Low selenium status in pregnancy has been associated with a number of adverse conditions. In nonpregnant populations, the selenium status or response to supplementation has been associated with polymorphisms in dimethylglycine dehydrogenase (DMGDH), selenoprotein P (SEPP1) and the glutathione peroxidases [cytosolic glutathione peroxidase (GPx1) and phospholipid glutathione peroxidase (GPx4)]. Objective: We hypothesized that, in pregnant women, these candidate polymorphisms would be associated with selenium status in early pregnancy, its longitudinal change, and the interindividual response to selenium supplementation at 60 μg/d. Design: With the use of stored samples and data from the United Kingdom Selenium in Pregnancy Intervention (SPRINT) study in 227 pregnant women, we carried out genetic-association studies, testing for associations between selenium status, its longitudinal change, and response to supplementation and common genetic variation in DMGDH (rs921943), SEPP1 (rs3877899 and rs7579), GPx1 (rs1050450) and GPx4 (rs713041). Selenium status was represented by the concentration of whole-blood selenium at 12 and 35 wk of gestation, the concentration of toenail selenium at 16 wk of gestation, and plasma glutathione peroxidase (GPx3) activity at 12 and 35 wk of gestation. Results: Our results showed that DMGDH rs921943 was significantly associated with the whole-blood selenium concentration at 12 wk of gestation (P = 0.032), which explained ≤2.0% of the variance. This association was replicated with the use of toenail selenium (P = 0.043). In unsupplemented women, SEPP1 rs3877899 was significantly associated with the percentage change in whole-blood selenium from 12 to 35 wk of gestation (P = 0.005), which explained 8% of the variance. In supplemented women, SEPP1 rs3877899 was significantly associated with the percentage change in GPx3 activity from 12 to 35 wk of gestation (P = 0.01), which explained 5.3% of the variance. Selenium status was not associated with GPx1, GPx4, or SEPP1 rs7579. Conclusions: In agreement with previous studies, we show that the genetic variant rs921943 in DMGDH is significantly associated with selenium status in United Kingdom pregnant women. Notably, our study shows that women who carry the SEPP1 rs3877899 A allele are better able to maintain selenium status during pregnancy, and their GPx3 activity increases more with supplementation, which suggests better protection from low selenium status. The SPRINT study was registered at www.isrctn. com as ISRCTN37927591.
TDLAS-Based Detection of Dissolved Methane in Power Transformer Oil and Field Application

Methane is one of the indicative gases in power transformer oil, and the detection of methane dissolved in oil with high accuracy is of great importance for dissolved gases analysis and fault diagnosis inside power transformers. Based on the Beer–Lambert spectral absorption law, dissolved methane detection with tunable diode laser absorption spectrum (TDLAS) is proposed in this paper for the advantages of high sensitivity and resolution. On the basis of wavelength modulation spectroscopy, a specialized TDLAS system was established. To meet the actual needs of field testing, the anti-vibration design of an integrated Herriott cell and a gas pressure (P)/temperature (T) setting are worked out. Photodetector, collimator, and Herriott cell are integrated into one component to reduce the effects of vibration. It is investigated that the temperature has little effect on the second harmonic amplitude in the range of 30 °C ~ 50 °C, and the vacuum pressure is reasonably set at about 1 kPa. Experimental results showed that the resolution of sensitivity could be reached as 6.8 mV/(<inline-formula> <tex-math notation="LaTeX">$\mu$ </tex-math></inline-formula>L/L), the maximum deviation was less than <inline-formula> <tex-math notation="LaTeX">$\pm 4~\mu$ </tex-math></inline-formula>L/L, and the response time is less than 5 min. In the end, field application was also carried out, proving it is a prospective online sensing technique to serve oil-immersed power transformers better.
Recursion or Iteration: Does it Matter What Students Choose?

Recursion and iteration are two key topics taught in introductory Computer Science. This is especially so for CS2 students, as CS2 is the course where recursion is typically taught and where control-flow concepts are solidified. When asked to solve a problem that could feasibly be solved with recursion or iteration, what do CS2 students choose to do? And how does this choice relate to the correctness of their code? This paper provides one answer to these questions through an analysis of student exam responses to a problem on finding deepest common ancestors in trees. We find that 19% of students choose to use iteration, 51% choose recursion, and 16% choose to combine both iteration and recursion. In terms of correctness, we find that students who choose iteration perform better than those who choose recursion and the combination of both. Additionally, we find concern in the number of students who seemingly do not understand what the question is asking. We end the paper with some comments on helping students choose an appropriate control-flow strategy and a discussion of this type of question on a final exam.
A Novel p53 Mutant Found in Iatrogenic Urothelial Cancers Is Dysfunctional and Can Be Rescued by a Second-site Global Suppressor Mutation*

Background: Biological consequences of novel signature mutations in the p53 gene of tumors from patients exposed to Aristolochia medicines are not yet known. Results: N131Y, a prominent Aristolochia-linked mutation, confers cancer-associated behavior to cells. Conclusion: Rare mutations in cancer genes can have profound consequences to protein function. Significance: N131Y is a candidate biomarker of Aristolochia-related disease and target for pharmacological rescue of p53 function. Exposure to herbal remedies containing the carcinogen aristolochic acid (AA) has been widespread in some regions of the world. Rare A→T TP53 mutations were recently discovered in AA-associated urothelial cancers. The near absence of these mutations among all other sequenced human tumors suggests that they could be biologically silent. There are no cell banks with established lines derived from human tumors with which to explore the influence of the novel mutants on p53 function and cellular behavior. To investigate their impact, we generated isogenic mutant clones by integrase-mediated cassette exchange at the p53 locus of platform (null) murine embryonic fibroblasts and kidney epithelial cells. Common tumor mutants (R248W, R273C) were compared with the AA-associated mutants N131Y, R249W, and Q104L. Assays of cell proliferation, migration, growth in soft agar, apoptosis, senescence, and gene expression revealed contrasting outcomes on cellular behavior following introduction of N131Y or Q104L. The N131Y mutant demonstrated a phenotype akin to common tumor mutants, whereas Q104L clone behavior resembled that of cells with wild-type p53. Wild-type p53 responses were restored in double-mutant cells harboring N131Y and N239Y, a second-site rescue mutation, suggesting that pharmaceutical reactivation of p53 function in tumors expressing N131Y could have therapeutic benefit. N131Y is likely to contribute directly to tumor phenotype and is a promising candidate biomarker of AA exposure and disease. Rare mutations thus do not necessarily point to sites where amino acid exchanges are phenotypically neutral. Encounter with mutagenic insults targeting cryptic sites can reveal specific signature hotspots.
At Immature Mossy-Fiber–CA3 Synapses, Correlated Presynaptic and Postsynaptic Activity Persistently Enhances GABA Release and Network Excitability via BDNF and cAMP-Dependent PKA

In the adult rat hippocampus, the axons of granule cells in the dentate gyrus, the mossy fibers (MF), form excitatory glutamatergic synapses with CA3 principal cells. In neonates, MF release into their targets mainly GABA, which at this developmental stage is depolarizing. Here we tested the hypothesis that, at immature MF–CA3 synapses, correlated presynaptic [single fiber-evoked GABAA-mediated postsynaptic potentials (GPSPs)] and postsynaptic activity (back propagating action potentials) may exert a critical control on synaptic efficacy. This form of plasticity, called spike-timing-dependent plasticity (STDP), is a Hebbian type form of learning extensively studied at the level of glutamatergic synapses. Depending on the relative timing, pairing postsynaptic spiking and single MF-GPSPs induced bidirectional changes in synaptic efficacy. In case of positive pairing, spike-timing-dependent-long-term potentiation (STD-LTP) was associated with a persistent increase in GPSP slope and in the probability of cell firing. The transduction pathway involved a rise of calcium in the postsynaptic cell and the combined activity of cAMP-dependent PKA (protein kinase A) and brain-derived neurotrophic factor (BDNF). Retrograde signaling via BDNF and presynaptic TrkB receptors led to a persistent increase in GABA release. In “presynaptically” silent neurons, the enhanced probability of GABA release induced by the pairing protocol, unsilenced these synapses. Shifting EGABA from the depolarizing to the hyperpolarizing direction with bumetanide failed to modify synaptic strength. Thus, STD-LTP of GPSPs provides a reliable way to convey information from granule cells to the CA3 associative network at a time when glutamatergic synapses are still poorly developed.
Simple Febrile Seizures: Are the AAP Guidelines Regarding Lumbar Puncture Being Followed?

Background: In 1996, the American Academy of Pediatrics (AAP) published a practice parameter recommending that lumbar puncture (LP) be strongly considered in infants younger than 12 months presenting with a first febrile seizure. Objective: We sought: (1) to determine if the recommendations of the AAP are being followed by pediatric emergency medicine-trained physicians at our institution; (2) to describe the rate of meningitis among patients with febrile seizure who underwent LP; and (3) to determine if there were differences in performance of LP if children were younger or pretreated with antibiotics. Methods: A retrospective chart review of patients aged 6 to 12 months presenting with first simple febrile seizure to the emergency department (ED) at Miami Children's Hospital was conducted between January 2001 and November 2005. Results: A total of 242 ED records with a discharge diagnosis including the term "febrile seizure," "seizure," or "meningitis" were identified. Of those, 56 met inclusion criteria for first simple febrile seizure. Lumbar puncture was performed in 28 patients (50%) that met inclusion criteria. Younger patients were no more likely to have LP performed than older patients (P = 0.15). Ten children (17.8%) received antibiotics before the ED visit; of these, 4 (40%) underwent LP in the ED. Children who presented with first simple febrile seizure to our institution who were pretreated with antibiotics were no more likely to have LP performed than those who were not receiving antibiotics (P = 0.48). All cerebrospinal fluid cultures were sterile. Conclusion: The AAP recommendations regarding LP in patients 6 to 12 months of age with first simple febrile seizure are not being strictly adhered to. The AAP recommendations regarding simple febrile seizures were conceived in a different epidemiologic era of disease pathology with data not representative of current prevalence and etiologic issues and need to be revisited.
The Learning Curve of Laparoscopic Colorectal Surgery in Regional Hospital

Purpose. In the early 1990s, laparoscopic colon surgery was shown to be technically feasible and was applied to managing benign and malignant colon disease. Few published discussions describe the learning curve for performing this procedure in regional hospital. Here we present our surgical experience and early outcomes for laparoscopic colorectal resection. Methods. Our laparoscopic surgical team comprised well trained colorectal surgeons without prior experience performing laparoscopic colorectal surgery. From August 2008 to January 2009, we performed 30 laparoscopic colorectal surgeries. Two equal, consecutive groups, the first 15 cases (group A) and later 15 cases (group B), were retrospectively reviewed. Patient demographics, perioperative parameters and early outcomes (i.e., operative times, blood loss, length of stay, need for technique assistance, complications, conversion to open surgery) were recorded. Surgical experience and outcomes were analyzed to document our learning curve. Results. No significant differences were found between groups in surgical procedures, gender ratios and difficulty of operative procedures. Group B had shorter operative times, earlier recovery of gastrointestinal function, less blood loss, and shorter hospital stays without significant differences. Significant differences between groups included higher ages in group B and higher incidence of calls for technical assistance in group A. The groups' complication rates were identical. Group A had the only case of conversion to open surgery. Operation times and blood loss decreased significantly after case 16. Conclusions. Laparoscopic colorectal resection can be performed safely in regional hospital. Assistance from a surgeon experienced in laparoscopic colorectal resection helped, colorectal surgeons with laparoscopic experienced (laparoscopic cholecystectomy and laparoscopic appendectomy) achieve proficiency at 16 cases.