Miracle-dz/UniFAR-FTUs huggingface dataset:
Macrophage Activation Remodeling Initiated by TLR-Triggered Prevents Chromatin Toxoplasma gondii

Macrophages infected with the opportunistic protozoan Toxoplasma gondii are unable to up-regulate many proinﬂammatory cytokine genes, including TNF (TNF- (cid:1) ), upon stimulation with LPS and other TLR ligands. In this study, we examined the inﬂuence of T. gondii on transcription factors associated with TNF- (cid:1) transcription, as well as phosphorylation and acetylation of histone H3 at distal and proximal regions of the TNF- (cid:1) promoter. During LPS stimulation, we found that Toxoplasma blocks nuclear accumulation of transcription factor c-Jun, but not that of cAMP response element-binding protein or NF- (cid:2) B. However, chromatin immunoprecipitation studies revealed that binding of all of these transcription factors to the TNF promoter was decreased by T. gondii infection. Furthermore, the parasite blocked LPS-induced Ser 10 phosphorylation and Lys 9 /Lys 14 acetylation of histone H3 molecules associated with distal and proximal regions of the TNF- (cid:1) promoter. Our results show that Toxoplasma inhibits TNF- (cid:1) transcription by interfering with chromatin remodeling events required for transcriptional activation at the TNF promoter, revealing a new mechanism by which a eukaryotic pathogen incapacitates proinﬂammatory cytokine production during infection. The Journal of Immunology, 2009, 182: 489–497.
Neural control of behavioural choice in juvenile crayfish

Natural selection leads to behavioural choices that increase the animal's fitness. The neuronal mechanisms underlying behavioural choice are still elusive and empirical evidence connecting neural circuit activation to adaptive behavioural output is sparse. We exposed foraging juvenile crayfish to approaching shadows of different velocities and found that slow-moving shadows predominantly activated a pair of giant interneurons, which mediate tail-flips that thrust the animals backwards and away from the approaching threat. Tail-flips also moved the animals farther away from an expected food source, and crayfish defaulted to freezing behaviour when faced with fast-approaching shadows. Under these conditions, tail-flipping, an ineffective and costly escape strategy was suppressed in favour of freezing, a more beneficial choice. The decision to freeze also dominated in the presence of a more desirable resource; however, the increased incentive was less effective in suppressing tail-flipping when paired with slow-moving visual stimuli that reliably evoked tail-flips in most animals. Together this suggests that crayfish make value-based decisions by weighing the costs and benefits of different behavioural options, and they select adaptive behavioural output based on the activation patterns of identifiable neural circuits.
RETHINKING THE GENETIC ARCHITECTURE OF SCHIZOPHRENIA


Background For many years, the prevailing paradigm has stated that in each individual with schizophrenia (SZ) the genetic risk is due to a combination of many genetic variants, individually of small effect. Recent empirical data are prompting a re-evaluation of this polygenic, common disease–common variant (CDCV) model. Evidence includes a lack of the expected strong positive findings from genome-wide association studies and the concurrent discovery of many different mutations that individually strongly predispose to SZ and other psychiatric disorders. This has led some to adopt a mixed model wherein some cases are caused by polygenic mechanisms and some by single mutations. This model runs counter to a substantial body of theoretical literature that had supposedly conclusively rejected Mendelian inheritance with genetic heterogeneity. Here we ask how this discrepancy between theory and data arose and propose a rationalization of the recent evidence base. Method In light of recent empirical findings, we reconsider the methods and conclusions of early theoretical analyses and the explicit assumptions underlying them. Results We show that many of these assumptions can now be seen to be false and that the model of genetic heterogeneity is consistent with observed familial recurrence risks, endophenotype studies and other population-wide parameters. Conclusions We argue for a more biologically consilient mixed model that involves interactions between disease-causing and disease-modifying variants in each individual. We consider the implications of this model for moving SZ research beyond statistical associations to pathogenic mechanisms.
Eddies: continuously adaptive query processing

In large federated and shared-nothing databases, resources can exhibit widely fluctuating characteristics. Assumptions made at the time a query is submitted will rarely hold throughout the duration of query processing. As a result, traditional static query optimization and execution techniques are ineffective in these environments. In this paper we introduce a query processing mechanism called an eddy, which continuously reorders operators in a query plan as it runs. We characterize the moments of symmetry during which pipelined joins can be easily reordered, and the synchronization barriers that require inputs from different sources to be coordinated. By combining eddies with appropriate join algorithms, we merge the optimization and execution phases of query processing, allowing each tuple to have a flexible ordering of the query operators. This flexibility is controlled by a combination of fluid dynamics and a simple learning algorithm. Our initial implementation demonstrates promising results, with eddies performing nearly as well as a static optimizer/executor in static scenarios, and providing dramatic improvements in dynamic execution environments.
Cognitive Impairment, Depression, and Cooccurrence of Both among the Elderly in Panama: Differential Associations with Multimorbidity and Functional Limitations

Cognitive impairment and depression are common mental health problems among the elderly, although few studies have examined their cooccurrence in older adults in Latin America. The purpose of this study was to examine cognitive impairment, depression, and cooccurrence of the two conditions and associated factors in a sample of older adults in Panama. This study included 304 community-dwelling elderly (≥65 years) individuals. Participants underwent a clinical interview and assessments of cognitive function by the Minimental State Examination and depressive symptoms by the Geriatric Depression Scale. Limitations in basic (BADL) and instrumental (IADL) activities in daily living and the presence of chronic illnesses were recorded. Multinomial regression analysis revealed that cooccurrence of cognitive impairment and depressive symptoms was explained by increasing age (OR: 3.2, 95% CI: 1.20, 8.30), low education (OR: 3.3, 95% CI: 1.33, 8.38), having four or more chronic conditions (OR: 11.5, 95% CI: 2.84, 46.63), and BADL limitations (OR: 5.0, 95% CI: 1.26, 19.68). Less education and limitations in BADL and IADL increased the odds of cognitive impairment alone, while less education and three or more chronic conditions increased the odds of depression alone. These findings underscore the relevance of assessing cognitive impairment in the elderly as part of a long-term approach to managing depression and vice versa.
Worst-Case Upper Bounds

There are many algorithms for testing satisfiability — how to evaluate and compare them? It is common (but still disputable) to identify the efficiency of an algorithm with its worst-case complexity. From this point of view, asymptotic upper bounds on the worst-case running time and space is a criterion for evaluation and comparison of algorithms. In this chapter we survey ideas and techniques behind satisfiability algorithms with the currently best upper bounds. We also discuss some related questions: “easy” and “hard” cases of SAT, reducibility between various restricted cases of SAT, the possibility of solving SAT in subexponential time, etc. In Section 12.1 we define terminology and notation used throughout the chapter. Section 12.2 addresses the question of which special cases of SAT are polynomial-time tractable and which ones remain NP-complete. The first nontrivial upper bounds for testing satisfiability were obtained for algorithms that solve k-SAT; such algorithms also form the core of general SAT algorithms. Section 12.3 surveys the currently fastest algorithms for k-SAT. Section 12.4 shows how to use bounds for k-SAT to obtain the currently best bounds for SAT. Section 12.5 addresses structural questions like “what else happens if k-SAT is solvable in time 〈. 〉? ”. Finally, Section 12.6 summarizes the currently best bounds for the main cases of the satisfiability problem.
User Collusion Avoidance Scheme for Privacy-Preserving Decentralized Key-Policy Attribute-Based Encryption

Decentralized attribute-based encryption (ABE) is a variant of multi-authority based ABE whereby any attribute authority (AA) can independently join and leave the system without collaborating with the existing AAs. In this paper, we propose a user collusion avoidance scheme which preserves the user's privacy when they interact with multiple authorities to obtain decryption credentials. The proposed scheme mitigates the well-known user collusion security vulnerability found in previous schemes. We show that our scheme relies on the standard complexity assumption (decisional bilienar Deffie-Hellman assumption). This is contrast to previous schemes which relies on non-standard assumption (q-decisional Diffie-Hellman inversion).
Maxwell Construction: The Hidden Bridge Between Iterative and Maximum a Posteriori Decoding

There is a fundamental relationship between belief propagation and maximum a posteriori decoding. A decoding algorithm, which is called the Maxwell decoder, is introduced and provides a constructive description of this relationship. Both the algorithm itself and the analysis of the new decoder are reminiscent of the Maxwell construction in thermodynamics. This paper investigates in detail the case of transmission over the binary erasure channel, while the extension to general binary memoryless channels is discussed in a companion paper.
The impact of the evolution of invasive surgical procedures for low back pain: a population based study of patient outcomes and hospital utilization

Background: Low back pain (LBP) is a ubiquitous health problem in Western societies, and while clinical decision making for patients requiring hospitalization for LBP has changed significantly over the past two decades, knowledge of the net impact on patient outcomes and health care utilization is lacking. The aim of this study was to evaluate the effectiveness of changes in the medical control of lumbar back pain in Western Australia in terms of the rate of patient readmission and the total bed days associated with readmissions.
Neonatal outcomes following in utero exposure to buprenorphine/naloxone or methadone

Objectives: To study neonatal outcomes following buprenorphine/naloxone and methadone exposure during pregnancy. Methods: This study is a retrospective review of clinical and demographic information of 58 infants whose mothers were treated with buprenorphine/naloxone and 92 infants whose mothers were treated with methadone for opioid dependence during pregnancy. Results: Gestational age, birth weight, prematurity, admission to neonatal intensive care unit, and length of stay were similar between both groups of infants. Neonatal abstinence syndrome occurred less frequently among infants of mothers treated with buprenorphine/naloxone than those treated with methadone (64% and 80%, respectively, p = 0.03). All infants with neonatal abstinence syndrome were treated postnatally with methadone. There was a trend toward shorter duration of treatment and lower cumulative dosages of methadone among the buprenorphine/naloxone–exposed infants. Conclusions: No apparent significant adverse neonatal outcomes were detected following treatment with either maintenance medication; however, further prospective research is necessary to examine the safety and efficacy of buprenorphine/naloxone in pregnancy and its effects on the neonate.
The Role of Men in Family Planning in the Philippines: An Assessment

Sam Clark, Jr. , Jonathan Flavier, Pilar Jimenez, Romeo Lee and Harris Solomon 1 Contractor, USAID/Ethiopia, Addis Ababa, Ethiopia 2 Chairperson, CMEN (Cooperative Movement for Encouraging NSV (No-Scalpel Vasectomy)), Quezon City, Philippines 3 Program Officer, Ford Foundation, Jakarta, Indonesia 4 Associate Professor, Behavioral Sciences Department, De La Salle University, Manila, Philippines 5 Ph.D. student, Anthropology Department, Brown University, United States
Community Treatment Orders in Toronto: The Emerging Data

Objective: Over a 4-year period in Toronto, this study aimed to compare individuals on a community treatment order (CTO) with individuals not on a CTO in terms of sociodemographic and clinical variables, hospital use, and continued engagement with health services on exit from the case management program. Hospital stay reductions from preadmission into the program to various postadmission periods were compared across the 2 groups. Methods: Descriptive statistics and tests of statistical significance (chi-square and t test) were run on regularly collected administrative data for both groups. Results: Categorical data analysis indicated the 2 groups were statistically similar on a range of sociodemographic and clinical variables. Although both groups displayed reductions in hospital use, the CTO group displayed a significantly higher reduction in cumulative days in hospital per hospital admission within both the first and second 6-month period postadmission. This same group also had significantly greater reduction in hospital admissions during the second 6-month period postadmission. The CTO group also had a significantly higher portion of individuals exiting the program within these first two 6-month periods; as well, they were less likely to exit with support such as case management or assertive community treatment and more likely to continue with ongoing medical supervision than the comparison group. Conclusion: Although we were unable to rule out regression to the mean for hospitalization reductions, the Toronto experience has shown that CTOs are helpful in assisting individuals who historically refused services to remain engaged with treatment and support services. The study also calls for broadening operational measures of outcomes for CTO studies.
Towards deep learning with spiking neurons in energy based models with contrastive Hebbian plasticity

In machine learning, error back-propagation in multi-layer neural networks (deep learning) has been impressively successful in supervised and reinforcement learning tasks. As a model for learning in the brain, however, deep learning has long been regarded as implausible, since it relies in its basic form on a non-local plasticity rule. To overcome this problem, energy-based models with local contrastive Hebbian learning were proposed and tested on a classification task with networks of rate neurons. We extended this work by implementing and testing such a model with networks of leaky integrate-and-fire neurons. Preliminary results indicate that it is possible to learn a non-linear regression task with hidden layers, spiking neurons and a local synaptic plasticity rule.
iPro54-PseKNC: a sequence-based predictor for identifying sigma-54 promoters in prokaryote with pseudo k-tuple nucleotide composition

The σ54 promoters are unique in prokaryotic genome and responsible for transcripting carbon and nitrogen-related genes. With the avalanche of genome sequences generated in the postgenomic age, it is highly desired to develop automated methods for rapidly and effectively identifying the σ54 promoters. Here, a predictor called ‘iPro54-PseKNC’ was developed. In the predictor, the samples of DNA sequences were formulated by a novel feature vector called ‘pseudo k-tuple nucleotide composition’, which was further optimized by the incremental feature selection procedure. The performance of iPro54-PseKNC was examined by the rigorous jackknife cross-validation tests on a stringent benchmark data set. As a user-friendly web-server, iPro54-PseKNC is freely accessible at http://lin.uestc. edu.cn/server/iPro54-PseKNC. For the convenience of the vast majority of experimental scientists, a step-by-step protocol guide was provided on how to use the web-server to get the desired results without the need to follow the complicated mathematics that were presented in this paper just for its integrity. Meanwhile, we also discovered through an in-depth statistical analysis that the distribution of distances between the transcription start sites and the translation initiation sites were governed by the gamma distribution, which may provide a fundamental physical principle for studying the σ54 promoters.
The Effects of the Size and Shape of Landscape Features on the Formation of Traveling Waves in Cyclic Populations

Recent field data indicate that in a number of cyclic populations, the cycles are organized spatially with the form of a periodic traveling wave. One way in which this type of wave is generated is when dispersing individuals encounter landscape features that impede movement in certain directions. In this article, we investigate the dependence of such periodic waves on ecological parameters and on the form of the landscape feature. Using a standard predator‐prey model as a prototype for a cyclic population, we calculate the speed and amplitude of waves generated by a large landscape feature. This enables us to determine parameters for which the waves are stable; in other cases, they evolve into irregular oscillations. We then undertake for the first time a detailed study of the effects of the size and shape of a landscape feature on the waves that it generates. We show that size rather than shape is the key wave‐forming property, with smaller obstacles generating waves with longer wavelength and waves from larger landscape features dominating those from smaller ones. Our results suggest that periodic traveling waves may be much more common than has previously been assumed in real ecological systems, and they enable quantitative predictions on the properties of these waves for particular cases.
Epigenetic modification of the X chromosome influences susceptibility to polycystic ovary syndrome.

CONTEXT The cause of polycystic ovary syndrome (PCOS) is unknown, although genetic and environmental influences are clearly implicated. Some genetic studies have suggested the involvement of X-linked genes in PCOS, but the influence of X chromosome inactivation (XCI) on manifestation of this disorder has not previously been examined. OBJECTIVE The objective of the study was to test the null hypothesis that XCI has no influence on clinical presentation of PCOS. DESIGN We examined patterns of XCI between sister pairs with the same genotype at a polymorphic locus on the X chromosome in families with PCOS. SETTING The study was conducted at a private practice. PARTICIPANTS PCOS was defined as hyperandrogenemia with chronic anovulation. Forty families were studied in which DNA was obtained from at least one parent, the proband, and one sister that could be accurately diagnosed as being affected or unaffected. MAIN OUTCOME MEASURE(S) Relative expression of two X-linked alleles was determined, and the ratio of one to the other represented the pattern of XCI. RESULTS The statistical odds on a different clinical presentation between sisters was approximately 29 times higher in sister pairs with different patterns of XCI, compared with sister pairs with the same pattern of XCI (odds ratio 28.9; 95% confidence interval 4.0-206; P = 0.0008). CONCLUSIONS This study provides evidence to refute the null hypothesis and propose a closer inspection of X-linked genes in PCOS, one in which both genotype and epigenotype are considered. Environmental determinants of PCOS may alter clinical presentation via epigenetic modifications, which currently remain undetected in traditional genetic analyses.
Promoting Partner Testing and Couples Testing through Secondary Distribution of HIV Self-Tests: A Randomized Clinical Trial

Background Achieving higher rates of partner HIV testing and couples testing among pregnant and postpartum women in sub-Saharan Africa is essential for the success of combination HIV prevention, including the prevention of mother-to-child transmission. We aimed to determine whether providing multiple HIV self-tests to pregnant and postpartum women for secondary distribution is more effective at promoting partner testing and couples testing than conventional strategies based on invitations to clinic-based testing. Methods and Findings We conducted a randomized trial in Kisumu, Kenya, between June 11, 2015, and January 15, 2016. Six hundred antenatal and postpartum women aged 18–39 y were randomized to an HIV self-testing (HIVST) group or a comparison group. Participants in the HIVST group were given two oral-fluid-based HIV test kits, instructed on how to use them, and encouraged to distribute a test kit to their male partner or use both kits for testing as a couple. Participants in the comparison group were given an invitation card for clinic-based HIV testing and encouraged to distribute the card to their male partner, a routine practice in many health clinics. The primary outcome was partner testing within 3 mo of enrollment. Among 570 participants analyzed, partner HIV testing was more likely in the HIVST group (90.8%, 258/284) than the comparison group (51.7%, 148/286; difference = 39.1%, 95% CI 32.4% to 45.8%, p < 0.001). Couples testing was also more likely in the HIVST group than the comparison group (75.4% versus 33.2%, difference = 42.1%, 95% CI 34.7% to 49.6%, p < 0.001). No participants reported intimate partner violence due to HIV testing. This study was limited by self-reported outcomes, a common limitation in many studies involving HIVST due to the private manner in which self-tests are meant to be used. Conclusions Provision of multiple HIV self-tests to women seeking antenatal and postpartum care was successful in promoting partner testing and couples testing. This approach warrants further consideration as countries develop HIVST policies and seek new ways to increase awareness of HIV status among men and promote couples testing. Trial Registration ClinicalTrials.gov NCT02386215.
Efficacy of Aquatic Treadmill Training on Gait Symmetry and Balance in Subacute Stroke Patients

Objective To determine the efficacy of aquatic treadmill training (ATT) as a new modality for stroke rehabilitation, by assessing changes in gait symmetry, balance function, and subjective balance confidence for the paretic and non-paretic leg in stroke patients. Methods Twenty-one subacute stroke patients participated in 15 intervention sessions of aquatic treadmill training. The Comfortable 10-Meter Walk Test (CWT), spatiotemporal gait parameters, Berg Balance Scale (BBS), and Activities-specific Balance Confidence scale (ABC) were assessed pre- and post-interventions. Results From pre- to post-intervention, statistically significant improvements were observed in the CWT (0.471±0.21 to 0.558±0.23, p<0.001), BBS (39.66±8.63 to 43.80±5.21, p<0.001), and ABC (38.39±13.46 to 46.93±12.32, p<0.001). The step-length symmetry (1.017±0.25 to 0.990±0.19, p=0.720) and overall temporal symmetry (1.404±0.36 to 1.314±0.34, p=0.218) showed improvement without statistical significance. Conclusion ATT improves the functional aspects of gait, including CWT, BBS and ABC, and spatiotemporal gait symmetry, though without statistical significance. Further studies are required to examine and compare the potential benefits of ATT as a new modality for stroke therapy, with other modalities.