Miracle-dz/UniFAR-FTUs huggingface dataset:
SVF: interprocedural static value-flow analysis in LLVM

This paper presents SVF, a tool that enables scalable and precise interprocedural Static Value-Flow analysis for C programs by leveraging recent advances in sparse analysis. SVF, which is fully implemented in LLVM, allows value-flow construction and pointer analysis to be performed in an iterative manner, thereby providing increasingly improved precision for both. SVF accepts points- to information generated by any pointer analysis (e.g., Andersen’s analysis) and constructs an interprocedural memory SSA form, in which the def-use chains of both top-level and address-taken variables are captured. Such value-flows can be subsequently exploited to support various forms of program analysis or enable more precise pointer analysis (e.g., flow-sensitive analysis) to be performed sparsely. By dividing a pointer analysis into three loosely coupled components: Graph, Rules and Solver, SVF provides an extensible interface for users to write their own solutions easily. SVF is publicly available at http://unsw-corg.github. io/SVF.
HE LOSS SURFACE AND EXPRESSIVITY OF DEEP CONVOLUTIONAL NEURAL NETWORKS

We analyze the expressiveness and loss surface of practical deep convolutional neural networks (CNNs) with shared weights. We show that such CNNs produce linearly independent features (and thus linearly separable) at every “wide” layer which has more neurons than the number of training samples. This condition holds e.g. for the VGG network. Furthermore, we provide for such wide CNNs necessary and sufficient conditions for global minima with zero training error. For the case where the wide layer is followed by a fully connected layer we show that almost every critical point of the empirical loss is a global minimum with zero training error. Our analysis suggests that both depth and width are equally important in deep learning. While depth brings more representational power and allows the network to learn high level features, width smoothes the optimization landscape of the loss function in the sense that a sufficiently wide CNN has a well-behaved loss surface with almost no bad local minima.
Obesity and anthropometry in spina bifida: What is the best measure

Objective: Diagnosis of obesity using traditional body mass index (BMI) using length may not be a reliable indicator of body composition in spina bifida (SB). We examine traditional and surrogate measures of adiposity in adults with SB, correlated with activity, metabolic disease, attitudes towards exercise and quality of life. Design: Adult subjects with SB underwent obesity classification using BMI by length and arm span, abdominal girth and percent trunk fat (TF) on dual energy X-ray absorptiometry (DXA). Quality of life measures, activity level and metabolic laboratory values were also reviewed. Results: Among eighteen subjects (6 male, 12 female), median age was 26.5 (range 19–37) years, with level of lesion 16.7% ≤L2, 61.1% L3-4, and 22.2% ≥L5, respectively. Median weight was 71.8 (IQR 62.4, 85.8) kg, similar between sexes (P = 0.66). With median length of 152.0 (IQR 141.8, 163.3) cm, median conventional BMI was 29.4 m/kg2, with 7 (43.8%) subjects with BMI >30. Median BMI by arm span was 30.2 m/kg2, abdominal girth of 105.5 cm, and TF 45.7%. More subjects were classified as obese using alternate measures, with 9 (56.3%) by arm span, 14 (82.4%) by abdominal girth and 15 (83.3%) by TF (P = 0.008). Reclassification of obesity from conventional BMI was significant when using TF (P = 0.03). No difference in quality of life measures, activity level and metabolic abnormalities was demonstrated between obese and non-obese subjects. Conclusions: Conventional determination of obesity using BMI by length is an insensitive marker in adults with SB. Adults with SB are more often classified as obese using TF by DXA.
IN VITRO REVERSAL OF CHLOROQUINE RESISTANCE WITH CHLOKPHENIRAMINE AGAINST AFRICAN ISOLATES

The in vitro chloroquine potentiating action of racemic chlorpheniramine was assessed by a semi-microtest against chloroquine-resistant African isolates of Plasmodium falciparum. At the chlorpheniramine concentrations of 312 and 625 nM, chloroquine resistance was reversed in 4 and 11 of 14 isolates, respectively, with a diminution of their 50% inhibitory concentration (IC50) values for chloroquine to below 100 nM. No effect was observed against the chloroquine-susceptible clone. The results of the study suggest that chlorpheniramine may be a promising chloroquine resistance modulator.
PAMAM dendrimer‐based contrast agents for MR imaging of Her‐2/neu receptors by a three‐step pretargeting approach

Pretargeting of receptors is a useful approach in molecular imaging and therapy to reduce background noise or toxicity and enhance selectivity. In this study a three‐step pretargeting approach that includes a biotinylated antibody, avidin/streptavidin, and a biotinylated imaging agent is described. A PAMAM dendrimer generation 4 (G4D)‐based MRI T1 agent biotin‐G4D‐DTPA‐Gd (bG4D‐Gd) and its sister compound with remaining free surface amine groups blocked by succinic anhydride to reduce positive charges (bG4D‐Gd‐SA) were synthesized. Limited selective enhancement in MRI was observed in a Her‐2/neu mouse tumor xenograft by this three‐step pretargeting approach that includes biotinylated trastuzumab, avidin and bG4D‐Gd, or bG4D‐Gd‐SA. However, these dendrimer‐based MRI agents with molecular weight around 29 kD reached and remained in the tumor through the enhanced permeability and retention effect. Prolonged and extensive accumulation of both bG4D‐Gd and b‐G4‐Gd‐SA in the kidneys was also observed. Magn Reson Med, 2008. © 2008 Wiley‐Liss, Inc.
Sketching for Kronecker Product Regression and P-splines

TensorSketch is an oblivious linear sketch introduced in Pagh'13 and later used in Pham, Pagh'13 in the context of SVMs for polynomial kernels. It was shown in Avron, Nguyen, Woodruff'14 that TensorSketch provides a subspace embedding, and therefore can be used for canonical correlation analysis, low rank approximation, and principal component regression for the polynomial kernel. We take TensorSketch outside of the context of polynomials kernels, and show its utility in applications in which the underlying design matrix is a Kronecker product of smaller matrices. This allows us to solve Kronecker product regression and non-negative Kronecker product regression, as well as regularized spline regression. Our main technical result is then in extending TensorSketch to other norms. That is, TensorSketch only provides input sparsity time for Kronecker product regression with respect to the $2$-norm. We show how to solve Kronecker product regression with respect to the $1$-norm in time sublinear in the time required for computing the Kronecker product, as well as for more general $p$-norms.
The nasal and gut microbiome in Parkinson's disease and idiopathic rapid eye movement sleep behavior disorder

Increasing evidence connects the gut microbiota and the onset and/or phenotype of Parkinson's disease (PD). Differences in the abundances of specific bacterial taxa have been reported in PD patients. It is, however, unknown whether these differences can be observed in individuals at high risk, for example, with idiopathic rapid eye movement sleep behavior disorder, a prodromal condition of α‐synuclein aggregation disorders including PD.
PKC activation promotes internalization of DNA-immobilized inorganic nano-crystals by clathrin-dependent endocytosis for efficient transgene expression in human lymphocytes

Leukemia and lymphoma cells are potential targets in cancer therapy for genetic manipulation either by transgene expression or silencing of endogenous gene expression. In addition, genetically engineered autologous lymphocytes expressing a chimeric antigen against a receptor overexpressed in tumor or tumor vasculature are promising cellbased therapeutics for cancer. The major hurdle to the successful implementation of these attractive approaches is the lack of a smart device for efficient transgene delivery and expression in the lymphocytes. Recently, we developed an efficient nanocarrier of carbonate apatite for intracellular delivery and release of DNA molecules, achieving very high level of transgene expression in primary as well as cancer cell lines. However, its efficacy in human T leukemia cells is comparatively low. Here, we reveal that simultaneous stimulation of human T leukemia cells by the most commonly used phorbol ester-based protein kinase C (PKC) activator and an actin filament disrupting agent dramatically enhanced carbonate apatite-mediated transgene delivery and expression in the cells by synergistically activating protein kinase C (PKC), while rapidly extruding Ca2+ of intracellularly dissolved particles through plasma membrance-associated Ca2+- ATPase. Moreover, endocytosis of the DNA-associated particles across the cell membrance was found to follow the clathrin-dependent route in both normal and activated cells. The findings thus offer significant insights for pre-clinical and clinical ex-vivo trials of cancer utilizing autologous T cells.
The interaction between two coplanar dislocation-type cracks

When crystalline solids exhibit cleavage fracture, the associated deformation processes produce wedge shaped microcracks and the criteria for their stability are of paramount importance when discussing the conditions for complete fracture of a solid. Previously, consideration has been given to the behaviour of an isolated wedge shaped crack, but little attention has been given to problems involving distributions of such cracks. The present paper examines the stability of two coplanar wedge shaped cracks, and demonstrates under what conditions interaction effects are important.
Original Cervical Cytology and Follow-up Biopsy Results in Positive High Risk Human Papillomavirus DNA Tests with High-Level Results

OBJECTIVE To ascertain Pap test and biopsy results of specimens with high level of human papillomavirus (HPv) DNA and compare atypical squamous cells of undetermined signiqicance (ASC-US) populations with HPV DNA. STUDY DESIGN Positive HPV tests with relative light unit (RLU) values > or =1000 were identified and original Pap test and follow-up biopsy results recorded. Pap test and biopsy results for ASC-US were compared to positive results with RLU <1000. RESULTS From 1892 total HPV-positive tests, 156 specimens with high RLU were identified; 145 had biopsies. The interpretations of the corresponding Pap tests were as follows: negative for intraepithelial lesion and malignancy, 3; ASC-US, 87; ASC, cannot exclude high grade squamous intraepithelial lesion, 5; low grade squamous intraepithelial lesion, 40 and high grade squamous intraepithelial lesion, 10. Biopsies showed 60 negative, 58 cervical intraepithelial neoplasia (CIN) 1 and 27 CIN 2+. In the highly positive ASCUS group, biopsy showed higher percentage of CIN 1 (33% vs. 16%) compared to the low-positive group. CONCLUSION Compared to low-positive results, high-positive results showed more abnormal Pap tests. CIN 1 was a more likely result for high-positive ASCUS. More transient infections may account for these findings. The results do not argue for different management schemes between the categories.
Therapeutic potential of flavonoids in spinal cord injury

Abstract Spinal cord injury (SCI) is a catastrophic event that can profoundly affect a patient’s life, with far-reaching social and economic effects. A consequential sequence of SCI is the significant neurological or psychological deficit, which obviously contributes to the overall burden of this condition. To date, there is no effective treatment for SCI. Therefore, developing novel therapeutic strategies for SCI is highly prioritized. Flavonoids, one of the most numerous and ubiquitous groups of plant metabolites, are the active ingredients of traditional Chinese medicine such as Scutellaria baicalensis Georgi (Huang Qin) or Ginkgo biloba (Ying Xin). Accumulated research data show that flavonoids possess a range of key pharmacological properties such as anti-inflammatory, anti-oxidant, anti-tumor, anti-viral, anti-cardiovascular disease, immunomodulatory, and neuroprotective effects. Based on this, the flavonoids show therapeutic potential for SCI diseases. In this paper, we will review the pharmacological properties of different types of flavonoids for the treatment of SCI diseases, and potential underlying biochemical mechanisms of action will also be described.
Challenges for Theory and Computation

The routinely made assumptions for simulating solid materials are briefly summarized, since they need to be critically assessed when new aspects become important, such as excited states, finite temperature, time-dependence, etc. The significantly higher computer power combined with improved experimental data open new areas for interdisciplinary research, for which new ideas and concepts are needed.
A role for the actin cytoskeleton in cell death and aging in yeast

Several determinants of aging, including metabolic capacity and genetic stability, are recognized in both yeast and humans. However, many aspects of the pathways leading to cell death remain to be elucidated. Here we report a role for the actin cytoskeleton both in cell death and in promoting longevity. We have analyzed yeast strains expressing mutants with either increased or decreased actin dynamics. We show that decreased actin dynamics causes depolarization of the mitochondrial membrane and an increase in reactive oxygen species (ROS) production, resulting in cell death. Important, however, is the demonstration that increasing actin dynamics, either by a specific actin allele or by deletion of a gene encoding the actin-bundling protein Scp1p, can increase lifespan by over 65%. Increased longevity appears to be due to these cells producing lower than wild-type levels of ROS. Homology between Scp1p and mammalian SM22/transgelin, which itself has been isolated in senescence screens, suggests a conserved mechanism linking aging to actin stability.
Transcriptional profiling of ion channel genes in Brugada syndrome and other right ventricular arrhythmogenic diseases.

AIMS Brugada syndrome is an inherited sudden-death arrhythmia syndrome. Na(+)-current dysfunction is central, but mutations in the SCN5A gene (encoding the cardiac Na(+)-channel Nav1.5) are present in only 20% of probands. This study addressed the possibility that Brugada patients display specific expression patterns for ion-channels regulating cardiac conduction, excitability, and repolarization. METHODS AND RESULTS Transcriptional profiling was performed on right-ventricular endomyocardial biopsies from 10 unrelated Brugada probands, 11 non-diseased organ-donors, seven heart-transplant recipients, 10 with arrhythmogenic right-ventricular cardiomyopathy, and nine with idiopathic right-ventricular outflow-tract tachycardia. Brugada patients showed distinct clustering differences vs. the two control and two other ventricular-tachyarrhythmia groups, including 14 of 77 genes encoding important ion-channel/ion-transporter subunits. Nav1.5 and K(+)-channels Kv4.3 and Kir3.4 were more weakly expressed, whereas the Na(+)-channel Nav2.1 and the K(+)-channel TWIK1 were more strongly expressed, in Brugada syndrome. Differences were also seen in Ca(2+)-homeostasis transcripts, including stronger expression of RYR2 and NCX1. The molecular profile of Brugada patients with SCN5A mutations did not differ from Brugada patients without SCN5A mutations. CONCLUSION Brugada patients exhibit a common ion-channel molecular expression signature, irrespective of the culprit gene. This finding has potentially important implications for our understanding of the pathophysiology of Brugada syndrome, with possible therapeutic and diagnostic consequences.
Analysis of head impacts during sub-elite hurling practice sessions

ABSTRACT The reported incidence of head and neck injuries in hurling is 0.12 per 1000 hours, but no previous research has quantified head impact characteristics in this sport. Here, a wireless accelerometer and gyroscope captured head impacts, in 20 senior club level hurling players. Peak linear and rotational acceleration and impact location were recorded during three hurling training sessions, each player participating once. A mean of 27.9 impacts (linear acceleration >10g) per player, per session were recorded; 1314 impacts during a total exposure time of 247 minutes. Only 2.6% impacts had peak linear acceleration of >70g and 6.2% had peak rotational acceleration >7900 rad/s2. There were significant differences in the number and magnitude of impacts, quantified by the accelerometer, between three training sessions of differing intensity (ŋ2 0.03–0.09, p < 0.001). This study represents a first step in quantifying head impacts during hurling, demonstrating the feasibility of this technology in the field. The sensors were able to discriminate between sessions of varying intensity. These data can be used to develop athlete monitoring protocols and may be useful in developing innovative helmet-testing standards for hurling. The potential for this technology to provide feedback has clinical utility for team medical personnel.
The Persistence of the Self over Time in Mild Cognitive Impairment and Alzheimer's Disease

Diachronic unity is the belief that, despite changes, we are the same person across the lifespan. We propose that diachronic unity is supported by the experience of remembering the self over time during episodic recall (i.e., phenomenological continuity). However, we also predict that diachronic unity is also possible when episodic memory is impaired, as long as the ability to construct life narratives from semantic memory (i.e., semantic continuity) is intact. To examine this prediction, we investigated diachronic unity in Alzheimer's Disease (AD) and amnestic mild cognitive impairment (aMCI), two conditions characterised by disrupted phenomenological continuity. If semantic continuity is also altered in these conditions, there should be an associated deterioration in diachronic unity. Participants with AD, aMCI, and healthy controls (HC) completed a self-persistence interview measuring diachronic unity (beliefs about self-persistence, explanations for stability/change). Semantic continuity was assessed with a life-story interview measuring autobiographical reasoning (self-event connections), and coherence (temporal/thematic/causal) of narratives. Our results highlight a complex relationship between semantic continuity and diachronic unity and revealed a divergence between two aspects of diachronic unity: AD/aMCI groups did not differ from HC in continuity beliefs, but AD explanations for self-persistence were less sophisticated. Semantic continuity was most impaired in AD: their narratives had fewer self-event connections (vs. HCs) and lower temporal/thematic coherence (vs. HC/aMCI), while both AD/aMCI groups had lower causal coherence. Paradoxically AD participants who scored higher on measures of beliefs in the persistence of the core self, provided less sophisticated explanations for their self-persistence and were less able to explore persistence in their life narratives. These findings support the importance of semantic continuity to diachronic unity, but suggest a more nuanced and multifaceted relationship than originally proposed in our model. In AD, diminished life narratives that retain features of cultural life scripts are sufficient for strong subjective beliefs of self-persistence, but not for sophisticated explanations about persistence. Better semantic continuity, with the ability to weave high-quality life narratives, may scaffold the capacity to understand and explain one's diachronic unity, but this produces less surety about self-persistence.
Deformable Cell Model of Tissue Growth

This paper is devoted to modelling tissue growth with a deformable cell model. Each cell represents a polygon with particles located at its vertices. Stretching, bending and pressure forces act on particles and determine their displacement. Pressure-dependent cell proliferation is considered. Various patterns of growing tissue are observed. An application of the model to tissue regeneration is illustrated. Approximate analytical models of tissue growth are developed.
Measurement Error in Performance Studies of Health Information Technology: Lessons from the Management Literature

Summary Just as researchers and clinicians struggle to pin down the benefits attendant to health information technology (IT), management scholars have long labored to identify the performance effects arising from new technologies and from other organizational innovations, namely the reorganization of work and the devolution of decision-making authority. This paper applies lessons from that literature to theorize the likely sources of measurement error that yield the weak statistical relationship between measures of health IT and various performance outcomes. In so doing, it complements the evaluation literature’s more conceptual examination of health IT’s limited performance impact. The paper focuses on seven issues, in particular, that likely bias downward the estimated performance effects of health IT. They are 1. ) negative self-selection, 2. ) omitted or unobserved variables, 3. ) mis-measured contextual variables, 4. ) mismeasured health IT variables, 5. ) lack of attention to the specific stage of the adoption-to-use continuum being examined, 6. ) too short of a time horizon, and 7. ) inappropriate units-of-analysis. The authors offer ways to counter these challenges. Looking forward more broadly, they suggest that researchers take an organizationally-grounded approach that privileges internal validity over generalizability. This focus on statistical and empirical issues in health IT-performance studies should be complemented by a focus on theoretical issues, in particular, the ways that health IT creates value and apportions it to various stakeholders.
Testing an Attachment-Based Parenting Intervention-VIPP-FC/A in Adoptive Families with Post-institutionalized Children: Do Maternal Sensitivity and Genetic Markers Count?

This study investigated the effectiveness of a newly integrated version of an intervention targeting adoptive mothers’ positive parenting for promoting children’s emotional availability, by testing the moderating role of both two maternal genetic polymorphisms (i.e., 5HTTLPR and DRD4-VNTR) and emotional availability-EA on intervention outcomes. Mothers with their children (N = 80; Mage = 42.73 years, SD = 3.79; Mage = 33.18 months, SD = 16.83 months) participated in a RCT testing the Video-Feedback Intervention to Promote Positive Parenting and Sensitive Discipline-VIPP-FC/A effectiveness. Mixed effects regression models showed a significant improvement in mother–child EA for the VIPP-intervention vs. the dummy intervention condition, with a moderating role of maternal EA on children’s outcomes. No significant moderating effect was found for the two genetic polymorphisms inquired. Children’s and mother’s outcomes obtained are discussed.