Miracle-dz/UniFAR-FTUs huggingface dataset:
Fault tolerant subgraph for single source reachability: generic and optimal

Let G=(V,E) be an n-vertices m-edges directed graph. Let s∈ V be any designated source vertex. We address the problem of single source reachability (SSR) from s in presence of failures of vertices/edges. We show that for every k≥ 1, there is a subgraph H of G with at most 2k n edges that preserves the reachability from s even after the failure of any k edges. Formally, given a set F of k edges, a vertex u∈ V is reachable from s in G∖ F if and only if u is reachable from s in H∖ F. We call H a k-Fault Tolerant Reachability Subgraph (k-FTRS). We prove also a matching lower bound of Ω(2kn) for such subgraphs. Our results extend to vertex failures without any extra overhead. The general construction of k-FTRS is interesting from several different perspectives. From the Graph theory perspective it reveals a separation between SSR and single source shortest paths (SSSP) in directed graphs. More specifically, in the case of SSSP in weighted directed graphs, there is a lower bound of Ω(m) even for a single edge failure. In the case of unweighted graphs there is a lower bound of Ω(n3/2) edges, again, even for a single edge failure. There is also a matching upper bound but nothing is known for two or more failures in the directed graphs. From the Algorithms perspective it implies fault tolerant solutions to other interesting problems, namely, (i) verifying if the strong connectivity of a graph is preserved after k edge or vertex failures, (ii) computing a dominator tree of a graph after k-failures. From the perspective of Techniques it makes an interesting usage of the concept of farthest min-cut which was already introduced by Ford and Fulkerson in their pioneering work on flows and cuts. We show that there is a close relationship between the farthest min-cut and the k-FTRS. We believe that our new technique is of independent interest.
Inflammasomes, hormesis, and antioxidants in neuroinflammation: Role of NRLP3 in Alzheimer disease

Alzheimer disease (AD) is a progressive neurodegenerative disorder leading to cognitive decline, neuropsychiatric symptoms, disability, caregiver burden, and premature death. It represents the most prevalent cause of dementia, and its incidence rates exponentially increase with increasing age. The number of Americans living with AD is rapidly increasing. An estimated 5.4 million Americans of all ages have AD in 2016. One in nine people aged 65 and older has AD, and by midcentury, someone in the United States will develop the disease every 33 sec. It is now accepted that neuroinflammation is a common feature of neurological disease. Inflammasomes, which are a multiprotein complex part of the innate immune system, induce inflammation in response to various stimuli, such as pathogens and stress. Inflammasomes activate proinflammatory caspases, such as caspase‐1, leading to the activation of the proinflammatory cytokines interleukin (IL)‐1b, IL‐18, and IL‐33, which promote neuroinflammation and brain pathologies. The nucleotide‐binding oligomerization domain‐like receptor family, pyrin domain‐containing‐3 (NLRP3) inflammasome is the best characterized in neurodegenerative diseases, in particular AD. Recent research suggests that NLRP3 could possibly be used in targeted therapies to alleviate neuroinflammation. Modulation of endogenous cellular defense mechanisms may be an innovative approach to therapeutic intervention in AD and other disorders associated with neuroinflammation and neurodegeneration. Herein, we introduce the hormetic dose–response concept and present possible mechanisms and applications to neuroprotection. We summarize the mechanisms involved in activation of the NLRP3 inflammasome and its role in neuroinflammation. We also address and propose the potential therapeutic utility of the nutritional antioxidants sulforaphane and hydroxytyrosol against particular signs and symptoms of AD. © 2016 Wiley Periodicals, Inc.
Adaptive Anomaly Detection in Performance Metric Streams

Continuous detection of performance anomalies such as service degradations has become critical in cloud and Internet services due to impact on quality of service and end-user experience. However, the volume and fast changing behavior of metric streams have rendered it a challenging task. Many diagnosis frameworks often rely on thresholding with stationarity or normality assumption, or on complex models requiring extensive offline training. Such techniques are known to be prone to spurious false-alarms in online settings as metric streams undergo rapid contextual changes from known baselines. Hence, we propose two unsupervised incremental techniques following a two-step strategy. First, we estimate an underlying temporal property of the stream via adaptive learning and, then we apply statistically robust control charts to recognize deviations. We evaluated our techniques by replaying over 40 time-series streams from the Yahoo! Webscope S5 datasets as well as four other traces of real Web service QoS and ISP traffic measurements. Our methods achieve high detection accuracy and few false-alarms, and better performance in general compared to an open-source package for time-series anomaly detection.
Optimal Training Length for MIMO Systems with Transmit Antenna Correlation

By maximizing a derived lower bound on the ergodic capacity, the optimal design of training length is given for Multiple-Input Multiple-Output (MIMO) systems. The channel is assumed to be flat fading in presence of spatial fading correlation only at the transmitter, which is known a priori by both ends. Different from the case of independent and identically distributed channel, the optimal training length no longer equals the number of transmit antennas but is just the same as the rank of transmit correlation matrix. The stronger the channel correlation is, the less the optimal training length is. This coincides with the fact that the accuracy of channel estimation is being improved when the channel correlation increases under equal training intervals.
A Cross-Language Study of Acoustic Predictors of Speech Intelligibility in Individuals With Parkinson's Disease.

Purpose The present study aimed to compare acoustic models of speech intelligibility in individuals with the same disease (Parkinson's disease [PD]) and presumably similar underlying neuropathologies but with different native languages (American English [AE] and Korean). Method A total of 48 speakers from the 4 speaker groups (AE speakers with PD, Korean speakers with PD, healthy English speakers, and healthy Korean speakers) were asked to read a paragraph in their native languages. Four acoustic variables were analyzed: acoustic vowel space, voice onset time contrast scores, normalized pairwise variability index, and articulation rate. Speech intelligibility scores were obtained from scaled estimates of sentences extracted from the paragraph. Results The findings indicated that the multiple regression models of speech intelligibility were different in Korean and AE, even with the same set of predictor variables and with speakers matched on speech intelligibility across languages. Analysis of the descriptive data for the acoustic variables showed the expected compression of the vowel space in speakers with PD in both languages, lower normalized pairwise variability index scores in Korean compared with AE, and no differences within or across language in articulation rate. Conclusions The results indicate that the basis of an intelligibility deficit in dysarthria is likely to depend on the native language of the speaker and listener. Additional research is required to explore other potential predictor variables, as well as additional language comparisons to pursue cross-linguistic considerations in classification and diagnosis of dysarthria types.
The Buddy Benefit: Increasing the Effectiveness of an Employee-Targeted Weight-Loss Program

It is well known that significant others (particularly romantic partners) can influence people’s weight management efforts. However, what constitutes effective support—and from which type of individual (e.g., romantic partner, family member, friend)—is unclear. Thus, framed by confirmation theory, we assessed the effectiveness and types of communication of a weight-loss “buddy” through reports of 704 individuals enrolled in a 15-week synchronous online weight-loss program. Roughly 54% of participants chose buddies; and those who did lost more weight and waist inches than those who were involved in the program without buddy support. We also found that a combination of high accepting and high challenging messages from buddies was associated with the greatest decrease in body mass index (BMI) as well as the greatest reduction in waist size. Furthermore, the support by romantic partners paralleled support by other types of buddies. Having a supportive buddy who was not a romantic partner was just as effective as turning to a romantic partner for assistance. This study underscores the important role of a buddy in supporting weight-loss program involvement and encourages individuals to consider enlisting the help of a buddy, as opposed to losing weight alone, in order to maximize weight management effectiveness.
Risk of Heparin-induced Immediate-type Hypersensitivity during Arteriovenous Fistula Placement

Heparin is commonly used to prevent clotting; however, severe hypersensitivity reactions during vascular access (VA) placement are rarely but occasionally reported. A 49-year-old man experienced a heparin-induced hypersensitivity reaction during VA placement. Severe side effects may occur even while placing the VA; therefore, we reconsidered the routine use of heparin, as the side effects are unpredictable. Physicians should be aware of the risk of heparin-induced hypersensitivity and be ready to effectively manage it during VA placement.
Diversity of Murine Norovirus Strains Isolated from Asymptomatic Mice of Different Genetic Backgrounds within a Single U.S. Research Institute

Antibody prevalence studies in laboratory mice indicate that murine norovirus (MNV) infections are common, but the natural history of these viruses has not been fully established. This study examined the extent of genetic diversity of murine noroviruses isolated from healthy laboratory mice housed in multiple animal facilities within a single, large research institute- the National Institute of Allergy and Infectious Diseases of the National Institutes of Health (NIAID-NIH) in Bethesda, Maryland, U.S. Ten distinct murine norovirus strains were isolated from various tissues and feces of asymptomatic wild type sentinel mice as well as asymptomatic immunodeficient (RAG 2−/−) mice. The NIH MNV isolates showed little cytopathic effect in permissive RAW264.7 cells in early passages, but all isolates examined could be adapted to efficient growth in cell culture by serial passage. The viruses, although closely related in genome sequence, were distinguishable from each other according to facility location, likely due to the introduction of new viruses into each facility from separate sources or vendors at different times. Our study indicates that the murine noroviruses are widespread in these animal facilities, despite rigorous guidelines for animal care and maintenance.
Utilisation of preconception care services and determinants of poor uptake among a cohort of women in Abakaliki Southeast Nigeria

Abstract Preconception care (PCC) is a preventive strategy for maternal and perinatal morbidity and mortality. This study aimed to assess the level of awareness and utilisation of PCC services. A descriptive cross-sectional survey was conducted at a teaching hospital. Interviewer-administered questionnaires were used to extract information. A total of 450 participants responded; 44.2% (190/450) were aware, 31.7% (143/450) had good knowledge, while only 10.3% (46/450) received PCC. Health care providers were the main source of information (77.9%). There was statistically significant correlation between awareness and participants’ level of education (p < .001) and residence (p < .001), as well as between utilisation and education (p < .001), and information from doctors (p < .001). There was a low level of awareness and poor utilisation of PCC, underpinning the need to scale up health education, establishment of functional PCC clinics and formulation of evidence-based guidelines to improve uptake and pregnancy outcome. Impact statement What is already known on the subject of the paper? PCC has been known in high-income countries as a prevention-based strategy, which aims at improving obstetric outcomes. However, the level of utilisation in low-income countries like Nigeria is either unknown or far too low. What do this study add? This work has provided local data on PCC; clearly indicating that the awareness and utilisation of PCC services in Abakaliki, Nigeria is very low when compared with other regions of the world, and this was influenced by the socio-demographic factors – particularly education and place of residence (for awareness), and level of education and information from health care providers (for utilisation), thus suggesting that enlightenment and improvement in social infrastructures could improve awareness, access and utilisation of PCC. What are the implications for clinical practice and/or further research? The implications of these findings in low resource settings like ours will include introducing interventions to scaling up health education, universal establishment of functional PCC units and formulation of evidence-based guidelines aimed at improving the uptake of PCC and pregnancy outcome. Further research will also be needed in future to assess the impact of such interventions and how to sustain potential benefits.
Lifestyle intervention reduces body weight and improves cardiometabolic risk factors in worksites.

BACKGROUND Worksites are potentially effective locations for obesity control because they provide opportunities for group intervention and social support. Studies are needed to identify effective interventions in these settings. OBJECTIVE We examined the effects of a multicomponent lifestyle intervention on weight loss and prevention of regain in 4 worksites (2 intervention and 2 control sites). DESIGN Overweight and obese employees (n = 133) enrolled in this pilot worksite-randomized controlled trial with a 0-6-mo weight-loss phase and a 6-12-mo structured weight-maintenance phase. The intervention combined recommendations to consume a reduced-energy, low-glycemic load, high-fiber diet with behavioral change education. Outcome measurements included changes in body weight and cardiometabolic risk factors. RESULTS The mean ± SEM weight loss was substantial in intervention participants, whereas control subjects gained weight (-8.0 ± 0.7 compared with +0.9 ± 0.5 kg, respectively; P < 0.001), and 89% of participants completed the weight-loss phase. Intervention effects were not significant at the 0.05 level but would have been at the 0.10 level (P = 0.08) in a mixed model in which the worksite nested within group was a random factor. There were also significant improvements in cardiometabolic risk factors in intervention compared with control subjects regarding fasting total cholesterol, glucose, systolic blood pressure, and diastolic blood pressure (P ≤ 0.02 for each). No significant weight regain was observed in participants who enrolled in the structured weight-maintenance program (0.5 ± 0.7 kg; P = 0.65), and overweight and obese employees in intervention worksites who were not enrolled in the weight-loss program lost weight compared with subjects in control worksites (-1.3 ± 0.5 compared with +0.7 ± 0.2 kg, respectively; P = 0.02). CONCLUSION Worksites can be effective for achieving clinically important reductions in body weight and improved cardiometabolic risk factors. This trial was registered at clinicaltrials.gov as NCT01470222.
Automated software vulnerability detection with machine learning

Thousands of security vulnerabilities are discovered in production software each year, either reported publicly to the Common Vulnerabilities and Exposures database or discovered internally in proprietary code. Vulnerabilities often manifest themselves in subtle ways that are not obvious to code reviewers or the developers themselves. With the wealth of open source code available for analysis, there is an opportunity to learn the patterns of bugs that can lead to security vulnerabilities directly from data. In this paper, we present a data-driven approach to vulnerability detection using machine learning, specifically applied to C and C++ programs. We first compile a large dataset of hundreds of thousands of open-source functions labeled with the outputs of a static analyzer. We then compare methods applied directly to source code with methods applied to artifacts extracted from the build process, finding that source-based models perform better. We also compare the application of deep neural network models with more traditional models such as random forests and find the best performance comes from combining features learned by deep models with tree-based models. Ultimately, our highest performing model achieves an area under the precision-recall curve of 0.49 and an area under the ROC curve of 0.87.
Learning Large-Scale Bayesian Networks with the sparsebn Package

Learning graphical models from data is an important problem with wide applications, ranging from genomics to the social sciences. Nowadays datasets often have upwards of thousands---sometimes tens or hundreds of thousands---of variables and far fewer samples. To meet this challenge, we have developed a new R package called sparsebn for learning the structure of large, sparse graphical models with a focus on Bayesian networks. While there are many existing software packages for this task, this package focuses on the unique setting of learning large networks from high-dimensional data, possibly with interventions. As such, the methods provided place a premium on scalability and consistency in a high-dimensional setting. Furthermore, in the presence of interventions, the methods implemented here achieve the goal of learning a causal network from data. Additionally, the sparsebn package is fully compatible with existing software packages for network analysis.
Mitigation of Quantum Dot Cytotoxicity by Microencapsulation

When CdSe/ZnS-polyethyleneimine (PEI) quantum dots (QDs) are microencapsulated in polymeric microcapsules, human fibroblasts are protected from acute cytotoxic effects. Differences in cellular morphology, uptake, and viability were assessed after treatment with either microencapsulated or unencapsulated dots. Specifically, QDs contained in microcapsules terminated with polyethylene glycol (PEG) mitigate contact with and uptake by cells, thus providing a tool to retain particle luminescence for applications such as extracellular sensing and imaging. The microcapsule serves as the “first line of defense” for containing the QDs. This enables the individual QD coating to be designed primarily to enhance the function of the biosensor.
Toxoplasma gondii GRA7-Induced TRAF6 Activation Contributes to Host Protective Immunity

ABSTRACT The intracellular parasite Toxoplasma gondii has unique dense granule antigens (GRAs) that are crucial for host infection. Emerging evidence suggests that GRA7 of T. gondii is a promising serodiagnostic marker and an effective toxoplasmosis vaccine candidate; however, little is known about the intracellular regulatory mechanisms involved in the GRA7-induced host responses. Here we show that GRA7-induced MyD88 signaling through the activation of TRAF6 and production of reactive oxygen species (ROS) is required for the induction of NF-κB-mediated proinflammatory responses by macrophages. GRA7 stimulation resulted in the rapid activation of mitogen-activated protein kinases and an early burst of ROS in macrophages in a MyD88-dependent manner. GRA7 induced a physical association between GRA7 and TRAF6 via MyD88. Remarkably, the C terminus of GRA7 (GRA7-V) was sufficient for interaction with and ubiquitination of the RING domain of TRAF6, which is capable of inflammatory cytokine production. Interestingly, the generation of ROS and TRAF6 activation are mutually dependent on GRA7/MyD88-mediated signaling in macrophages. Furthermore, mice immunized with GRA7-V showed markedly increased Th1 immune responses and protective efficacy against T. gondii infection. Collectively, these results provide novel insight into the crucial role of GRA7-TRAF6 signaling in innate immune responses.
Complete mitogenome sequencing and phylogenetic analysis of PaLi yak (Bos grunniens)

Abstract PaLi yak is a very important local breed in China; as a year-round grazing animal, it plays a very important role for the economic and native herdsmen. The PaLi yak complete mitochondrial DNA is sequenced in this study, the total length is 16,324 bp, containing 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a non-coding control region (D-loop region). The order and composition are similar to most of the other vertebrates. The base contents are: 33.72% A, 25.80% C, 13.21% G and 27.27% T; A + T (60.99%) was higher than G + C (39.01%). The phylogenetic relationships were analyzed using the complete mitogenome sequence, results showed that the genetic relationship between yak and cattle is distinct. These information provides useful data for further study on protection of genetic resources and the taxonomy of Bovinae.
Lack of Consensus in Physician Recommendations Regarding Return to Driving After Cervical Spine Surgery

Study Design. A cross-sectional study. Objective. The goal of this study is to investigate how surgeons differ in collar and narcotic use, as well as return to driving recommendations following cervical spine surgeries and the associated medico-legal ramifications of these conditions. Summary of Background Data. Restoration of quality of life is one of the main goals of cervical spine surgery. Patients frequently inquire when they may safely resume driving after cervical spine surgery. There is no consensus regarding postoperative driving restrictions. This study addresses how surgeons differ in their recommendations concerning cervical immobilization, narcotic analgesia, and suggested timeline of return to driving following cervical spine surgery. Methods. Surgeons at the Cervical Spine Research Society annual meeting completed anonymous surveys assessing postoperative patient management following fusion and nonfusion cervical spine surgeries. Results. Seventy percent of surgeons returned completed surveys (n = 71). About 80.3% were orthopedic surgeons and 94.2% completed a spine fellowship. Experienced surgeons (>15 years in practice) were more likely to let patients return to driving within 2 weeks than less experienced surgeons (47.1% vs. 24.3%, P = 0.013) for multilevel anterior discectomy and fusion (ACDF) and laminectomy with fusion procedures. There were no differences between surgeons practicing inside and outside the USA for prescribing collars or return to driving time. Cervical collars were used more for fusions than nonfusions (57.7% vs. 31.0%, P = 0.001). Surgeons reported 75.3% of patients ask when they may resume driving. For cervical fusions, 31.4% of surgeons allowed their patients to resume driving while restricting them with collars for longer durations. Furthermore, 27.5% of surgeons allowed their patients to resume driving while taking narcotics postoperatively. Conclusion. This survey-based study highlights the lack of consensus regarding patient “fitness to drive” following cervical spine surgery. The importance of establishing evidence-based guidelines is critical, as recommendations for driving in the postoperative period may have significant medical, legal, and financial implications. Level of Evidence: 5