Miracle-dz/UniFAR-FTUs huggingface dataset:
Delta-Bench: Differential Benchmark for Static Analysis Security Testing Tools

Background: Static analysis security testing (SAST) tools may be evaluated using synthetic micro benchmarks and benchmarks based on real-world software. Aims: The aim of this study is to address the limitations of the existing SAST tool benchmarks: lack of vulnerability realism, uncertain ground truth, and large amount of findings not related to analyzed vulnerability. Method: We propose Delta-Bench - a novel approach for the automatic construction of benchmarks for SAST tools based on differencing vulnerable and fixed versions in Free and Open Source (FOSS) repositories. To test our approach, we used 7 state of the art SAST tools against 70 revisions of four major versions of Apache Tomcat spanning 62 distinct Common Vulnerabilities and Exposures (CVE) fixes and vulnerable files totalling over 100K lines of code as the source of ground truth vulnerabilities. Results: Our experiment allows us to draw interesting conclusions (e.g., tools perform differently due to the selected benchmark). Conclusions: Delta-Bench allows SAST tools to be automatically evaluated on the real-world historical vulnerabilities using only the findings that a tool produced for the analysed vulnerability.
A Deep Policy Inference Q-Network for Multi-Agent Systems

We present DPIQN, a deep policy inference Q-network that targets multi-agent systems composed of controllable agents, collaborators, and opponents that interact with each other. We focus on one challenging issue in such systems---modeling agents with varying strategies---and propose to employ "policy features" learned from raw observations (e.g., raw images) of collaborators and opponents by inferring their policies. DPIQN incorporates the learned policy features as a hidden vector into its own deep Q-network (DQN), such that it is able to predict better Q values for the controllable agents than the state-of-the-art deep reinforcement learning models. We further propose an enhanced version of DPIQN, called deep recurrent policy inference Q-network (DRPIQN), for handling partial observability. Both DPIQN and DRPIQN are trained by an adaptive training procedure, which adjusts the network's attention to learn the policy features and its own Q-values at different phases of the training process. We present a comprehensive analysis of DPIQN and DRPIQN, and highlight their effectiveness and generalizability in various multi-agent settings. Our models are evaluated in a classic soccer game involving both competitive and collaborative scenarios. Experimental results performed on 1 vs. 1 and 2 vs. 2 games show that DPIQN and DRPIQN demonstrate superior performance to the baseline DQN and deep recurrent Q-network (DRQN) models. We also explore scenarios in which collaborators or opponents dynamically change their policies, and show that DPIQN and DRPIQN do lead to better overall performance in terms of stability and mean scores.
Approximating complex arithmetic circuits with formal error guarantees: 32-bit multipliers accomplished

We present a novel method allowing one to approximate complex arithmetic circuits with formal guarantees on the approximation error. The method integrates in a unique way formal techniques for approximate equivalence checking into a search-based circuit optimisation algorithm. The key idea of our approach is to employ a novel search strategy that drives the search towards promptly verifiable approximate circuits. The method was implemented within the ABC tool and extensively evaluated on functional approximation of multipliers (with up to 32-bit operands) and adders (with up to 128-bit operands). Within a few hours, we constructed a high-quality Pareto set of 32-bit multipliers providing trade-offs between the circuit error and size. This is for the first time when such complex approximate circuits with formal error guarantees have been derived, which demonstrates an outstanding performance and scalability of our approach compared with existing methods that have either been applied to the approximation of multipliers limited to 8-bit operands or statistical testing has been used only. Our approach thus significantly improves capabilities of the existing methods and paves a way towards an automated design process of provably-correct circuit approximations.
Fossil and genomic evidence constrains the timing of bison arrival in North America

Significance The appearance of bison in North America is both ecologically and paleontologically significant. We analyzed mitochondrial DNA from the oldest known North American bison fossils to reveal that bison were present in northern North America by 195–135 thousand y ago, having entered from Asia via the Bering Land Bridge. After their arrival, bison quickly colonized much of the rest of the continent, where they rapidly diversified phenotypically, producing, for example, the giant long-horned morphotype Bison latifrons during the last interglaciation. The arrival of bison in North America marks one of the most successful large-mammal dispersals from Asia within the last million years, yet the timing and nature of this event remain poorly determined. Here, we used a combined paleontological and paleogenomic approach to provide a robust timeline for the entry and subsequent evolution of bison within North America. We characterized two fossil-rich localities in Canada’s Yukon and identified the oldest well-constrained bison fossil in North America, a 130,000-y-old steppe bison, Bison cf. priscus. We extracted and sequenced mitochondrial genomes from both this bison and from the remains of a recently discovered, ∼120,000-y-old giant long-horned bison, Bison latifrons, from Snowmass, Colorado. We analyzed these and 44 other bison mitogenomes with ages that span the Late Pleistocene, and identified two waves of bison dispersal into North America from Asia, the earliest of which occurred ∼195–135 thousand y ago and preceded the morphological diversification of North American bison, and the second of which occurred during the Late Pleistocene, ∼45–21 thousand y ago. This chronological arc establishes that bison first entered North America during the sea level lowstand accompanying marine isotope stage 6, rejecting earlier records of bison in North America. After their invasion, bison rapidly colonized North America during the last interglaciation, spreading from Alaska through continental North America; they have been continuously resident since then.
N-3 Polyunsaturated Fatty Acids Decrease the Protein Expression of Soluble Epoxide Hydrolase via Oxidative Stress-Induced P38 Kinase in Rat Endothelial Cells

N-3 polyunsaturated fatty acids (PUFAs) improve endothelial function. The arachidonic acid-derived metabolites (epoxyeicosatrienoic acids (EETs)) are part of the endothelial hyperpolarization factor and are vasodilators independent of nitric oxide. However, little is known regarding the regulation of EET concentration by docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) in blood vessels. Sprague-Dawley rats were fed either a control or fish oil diet for 3 weeks. Compared with the control, the fish oil diet improved acetylcholine-induced vasodilation and reduced the protein expression of soluble epoxide hydrolase (sEH), a key EET metabolic enzyme, in aortic strips. Both DHA and EPA suppressed sEH protein expression in rat aorta endothelial cells (RAECs). Furthermore, the concentration of 4-hydroxy hexenal (4-HHE), a lipid peroxidation product of n-3 PUFAs, increased in n-3 PUFA-treated RAECs. In addition, 4-HHE treatment suppressed sEH expression in RAECs, suggesting that 4-HHE (derived from n-3 PUFAs) is involved in this phenomenon. The suppression of sEH was attenuated by the p38 kinase inhibitor (SB203580) and by treatment with the antioxidant N-acetyl-L-cysteine. In conclusion, sEH expression decreased after n-3 PUFAs treatment, potentially through oxidative stress and p38 kinase. Mild oxidative stress induced by n-3 PUFAs may contribute to their cardio-protective effect.
Benzoate- and Salicylate-Tolerant Strains of Escherichia coli K-12 Lose Antibiotic Resistance during Laboratory Evolution

ABSTRACT Escherichia coli K-12 W3110 grows in the presence of membrane-permeant organic acids that can depress cytoplasmic pH and accumulate in the cytoplasm. We conducted experimental evolution by daily diluting cultures in increasing concentrations of benzoic acid (up to 20 mM) buffered at external pH 6.5, a pH at which permeant acids concentrate in the cytoplasm. By 2,000 generations, clones isolated from evolving populations showed increasing tolerance to benzoate but were sensitive to chloramphenicol and tetracycline. Sixteen clones grew to stationary phase in 20 mM benzoate, whereas the ancestral strain W3110 peaked and declined. Similar growth occurred in 10 mM salicylate. Benzoate-evolved strains grew like W3110 in the absence of benzoate, in media buffered at pH 4.8, pH 7.0, or pH 9.0, or in 20 mM acetate or sorbate at pH 6.5. Genomes of 16 strains revealed over 100 mutations, including single-nucleotide polymorphisms (SNPs), large deletions, and insertion knockouts. Most strains acquired deletions in the benzoate-induced multiple antibiotic resistance (Mar) regulon or in associated regulators such as rob and cpxA, as well as the multidrug resistance (MDR) efflux pumps emrA, emrY, and mdtA. Strains also lost or downregulated the Gad acid fitness regulon. In 5 mM benzoate or in 2 mM salicylate (2-hydroxybenzoate), most strains showed increased sensitivity to the antibiotics chloramphenicol and tetracycline; some strains were more sensitive than a marA knockout strain. Thus, our benzoate-evolved strains may reveal additional unknown drug resistance components. Benzoate or salicylate selection pressure may cause general loss of MDR genes and regulators. IMPORTANCE Benzoate is a common food preservative, and salicylate is the primary active metabolite of aspirin. In the gut microbiome, genetic adaptation to salicylate may involve loss or downregulation of inducible multidrug resistance systems. This discovery implies that aspirin therapy may modulate the human gut microbiome to favor salicylate tolerance at the expense of drug resistance. Similar aspirin-associated loss of drug resistance might occur in bacterial pathogens found in arterial plaques.
Association between problematic internet use, socio-demographic variables and obesity among European adolescents.

BACKGROUND Overweight of children and adolescents continues to be an important and alarming global public health problem. As the adolescent's time spent online has increased, problematic internet use (PIU) potentially leads to negative health consequences. This study aimed to examine the relation between PIU and overweight/obesity among adolescents in seven European countries and assess the effect of demographic and lifestyle factors recorded in the European Network for Adolescent Addictive Behaviour (EU NET ADB) survey (www.eunetadb.eu). METHODS A cross-sectional school-based survey of 14- to 17-year-old adolescents was conducted in seven European countries: Germany, Greece, Iceland, the Netherlands, Poland, Romania and Spain. Anonymous self-completed questionnaires included sociodemographic data, internet usage characteristics, school achievement, parental control and the Internet Addiction Test. Associations between overweight/obesity and potential risk factors were investigated by logistic regression analysis, allowing for the complex sample design. RESULTS The study sample consisted of 10 287 adolescents aged 14-17 years. 12.4% were overweight/obese, and 14.1% presented with dysfunctional internet behavior. Greece had the highest percentage of overweight/obese adolescents (19.8%) and the Netherlands the lowest (6.8%). Male sex [odds ratio (OR) = 2.89, 95%CI: 2.46-3.38], heavier use of social networking sites (OR = 1.26, 95%CI: 1.09-1.46) and residence in Greece (OR = 2.32, 95%CI: 1.79-2.99) or Germany (OR = 1.48, 95%CI: 1.12-1.96) were independently associated with higher risk of overweight/obesity. A greater number of siblings (OR = 0.79, 95%CI: 0.64-0.97), higher school grades (OR = 0.74, 95%CI: 0.63-0.88), higher parental education (OR = 0.89, 95%CI: 0.82-0.97) and residence in the Netherlands (OR = 0.49, 95%CI: 0.31-0.77) independently predicted lower risk of overweight/obesity. CONCLUSIONS The results indicate an association of overweight/obesity with PIU and suggest the importance of formulating preventive public health policies that target physical health, education and sedentary online lifestyle early in adolescence with special attention to boys.
Fatigue and self-care in patients with chronic heart failure

Background: Fatigue is a debilitating and highly prevalent symptom in patients with chronic heart failure (HF) possibly complicating HF self-care behaviour which is crucial for maintaining health. Aims: The purpose of this study was to examine whether general and exertion fatigue are distinctively associated with self-care in patients with chronic HF. Methods: In total, 545 outpatients with chronic HF (mean age=66.2 years; 75% male) completed measures of general fatigue (i.e. a sustained sense of exhaustion including mental efforts), exertion fatigue (i.e. fatigue directly related to physical activity), sleep problems, mood symptoms and HF self-care behaviour at baseline, 12-, and 18-month follow-up. Results: Linear mixed modelling results showed that general and exertion fatigue were significantly associated with poor HF self-care (estimate=0.10, p=0.004; estimate=0.06, p=0.01, respectively) and poor consulting behaviour (estimate=0.05, p=0.04; estimate=0.04, p=0.007, respectively) over time, independent of sleep and mood problems, and other clinical covariates. Exertion fatigue was associated with supplementary determinants. Conclusion: This is the first prospective study demonstrating that general and exertion fatigue were both associated with poor HF self-care, which could not be explained by sleep problems or mood symptoms, and was independent of clinical indicators of disease severity. Treatment of fatigue problems may improve HF self-care skills and ultimately quality of life and cardiovascular outcomes. Further research is needed to examine this potential causal relationship.
Making split fabrication synergistically secure and manufacturable

Split fabrication is a promising approach to security against attacks by untrusted foundries. While existing split fabrication methods consider the overhead of conventional objectives such as wirelength and timing, they mostly neglect manufacturability — an unavoidable challenge in nanometer technologies. Observing that security and manufacturability can be addressed in a synergistic manner, this work introduces routing techniques that can simultaneously improve both security and manufacturability in terms of either Chemical Mechanical Planarization (CMP) uniformity or Self-Aligned Double Patterning (SADP) compliance. The effectiveness of these techniques is confirmed by experiments on benchmark circuits.
Speeding up crossbar resistive memory by exploiting in-memory data patterns

Resistive Memory (ReRAM) has emerged as a promising non-volatile memory technology that may replace a significant portion of DRAM in future computer systems. ReRAM has many advantages such as high density, low standby power and good scalability. ReRAM, when adopting crossbar architecture, has the smallest 4F2 planar cell size, which is ideal for constructing dense memory with large capacity. However, crossbar cell structure suffers from large sneak leakage and IR drop on long wires. To ensure operation reliability, ReRAM writes, in particular, RESET operations, conservatively use the worst-case access latency of all cells in ReRAM arrays, which leads to significant performance degradation and dynamic energy waste. In this paper, we study the correlation between the RESET latency and the number of cells in low resistant state (LRS) along bitlines, and propose to dynamically speed up ReRAM RESET operations for the rows that have small numbers of LRS cells. We leverage the intrinsic in-memory processing capability of ReRAM crossbar and propose a low overhead runtime profiler that effectively tracks the data patterns in different bitlines. To achieve further RESET latency reduction, we employ data compression and row address dependent data layout to reduce LRS cells on bitlines. The experimental results show that, on average, our design improves system performance by 20.5% and 14.2%, and reduces memory dynamic energy by 15.7% and 7.6%, compared to the baseline and the state-of-the-art crossbar design.
High rate of colistin resistance among patients with carbapenem-resistant Klebsiella pneumoniae infection accounts for an excess of mortality.

Carbapenem-resistant Klebsiella pneumoniae (CR-KP) is becoming a common cause of healthcare-associated infection in Italy, with high morbidity and mortality. Prevalent CR-KP clones and resistance mechanisms vary between regions and over time. Therapeutic approaches and their impact on mortality have to be investigated. We performed a prospective study of patients with CR-KP isolation, hospitalized in nine hospitals of Rome, Italy, from December 2010 to May 2011, to describe the molecular epidemiology, antibiotic treatment and risk factors for mortality. Overall, 97 patients (60% male, median age 69 years) were enrolled. Strains producing blaKPC-3 were identified in 89 patients, blaVIM in three patients and blaCTX-M-15 plus porin defects in the remaining five patients. Inter-hospital spread of two major clones, ST512 and ST258, was found. Overall, 36.1% and 20.4% of strains were also resistant to colistin and tigecycline, respectively. Infection was diagnosed in 91 patients who received appropriate antibiotic treatment, combination therapy and removal of the infectious source in 73.6%, 59.3% and 28.5% of cases, respectively. Overall, 23 different antibiotic regimens were prescribed. In-hospital mortality was 25.8%. Multivariate analysis adjusted for appropriate treatment, combination therapy and infectious-source removal, showed that Charlson comorbidity score, intensive-care unit onset of infection, bacteraemia and infection due to a colistin-resistant CR-KP strain were independent risk factors for mortality. The spread of clones producing K. pneumoniae carbapenemases, mainly ST258, is currently the major cause of CR-KP infection in central Italy. We observed a high rate of resistance to colistin that is independently associated with worse outcome.
Clinical reasoning—embodied meaning-making in physiotherapy

ABSTRACT This article examines physiotherapists’ lived experience of practicing physiotherapy in primary care, focusing on clinical reasoning and decision-making in the case of a patient we call Eva. The material presented derives from a larger study involving two women participants, both with a protracted history of neck and shoulder pain. A total of eight sessions, all of them conducted by the first author, a professional physiotherapist, in his own practice room, were videotaped, after which the first author transcribed the sessions and added reflective notes. One session emerged as particularly stressful for both parties and is explored in detail in this article. In our analysis, we seek to be attentive to the experiences of physiotherapy displayed and to explore their meaning, significance and uniqueness from a phenomenological perspective. Our research reveals the complexity of integrating multiple theoretical perspectives of practice in clinical decision-making and suggests that a phenomenological perspective can provide insights into clinical encounters through its recognition of embodied knowledge. We argue that good physiotherapy practice demands tactfulness, sensitivity, and the desire to build a cooperative patient–therapist relationship. Informed by theoretical and practical knowledge from multiple disciplines, patient management can evolve and unfold beyond rehearsed routines and theoretical principles.
Circular RNA expression in basal cell carcinoma.

AIM Circular RNAs (circRNAs), are nonprotein coding RNAs consisting of a circular loop with multiple miRNA, binding sites called miRNA response elements (MREs), functioning as miRNA sponges. This study was performed to identify differentially expressed circRNAs and their MREs in basal cell carcinoma (BCC). MATERIALS & METHODS Microarray circRNA expression profiles were acquired from BCC and control followed by qRT-PCR validation. Bioinformatical target prediction revealed multiple MREs. Sequence analysis was performed concerning MRE interaction potential with the BCC miRNome. RESULTS We identified 23 upregulated and 48 downregulated circRNAs with 354 miRNA response elements capable of sequestering miRNA target sequences of the BCC miRNome. CONCLUSION The present study describes a variety of circRNAs that are potentially involved in the molecular pathogenesis of BCC.
Estimating the incidence and the economic burden of third and fourth-degree obstetric tears in the English NHS: an observational study using propensity score matching

Objective Obstetric care is a high-risk area in healthcare delivery, so it is essential to have up-to-date quantitative evidence in this area to inform policy decisions regarding these services. In light of this, the objective of this study is to investigate the incidence and economic burden of third and fourth-degree lacerations in the English National Health Service (NHS) using recent national data. Methods We used coded inpatient data from Hospital Episode Statistics (HES) for the financial years from 2010/2011 to 2013/2014 for all females that gave birth during that period in the English NHS. Using HES, we used pre-existing safety indicator algorithms to calculate the incidence of third and fourth-degree obstetric tears and employed a propensity score matching method to estimate the excess length of stay and economic burden associated with these events. Results Observed rates per 1000 inpatient episodes in 2010/2011 and 2013/2014, respectively: Patient Safety Indicator—trauma during vaginal delivery with instrument (PSI 18)=84.16 and 91.24; trauma during vaginal delivery without instrument (PSI 19)=29.78 and 33.43; trauma during caesarean delivery (PSI 20)=3.61 and 4.56. Estimated overall (all PSIs) economic burden for 2010/2011=£10.7 million and for 2013/2014=£14.5 million, expressed in 2013/2014 prices. Conclusions Despite many initiatives targeting the quality of maternity care in the NHS, the incidence of third and fourth-degree lacerations has increased during the observed period which signals that quality improvement efforts in obstetric care may not be reducing incidence rates. Our conservative estimates of the financial burden of these events appear low relative to total NHS expenditure for these years.