Miracle-dz/UniFAR-FTUs huggingface dataset:
EPIMHC: a curated database of MHC-binding peptides for customized computational vaccinology

SUMMARY EPIMHC is a relational database of MHC-binding peptides and T cell epitopes that are observed in real proteins. Currently, the database contains 4867 distinct peptide sequences from various sources, including 84 tumor-associated antigens. The EPIMHC database is accessible through a web server that has been designed to facilitate research in computational vaccinology. Importantly, peptides resulting from a query can be selected to derive specific motif-matrices. Subsequently, these motif-matrices can be used in combination with a dynamic algorithm for predicting MHC-binding peptides from user-provided protein queries. AVAILABILITY The EPIMHC database server is hosted by the Dana-Farber Cancer Institute at the site http://immunax.dfci. harvard.edu/bioinformatics/epimhc/
Rostral Ventromedial Medulla Neurons That Project to the Spinal Cord Express Multiple Opioid Receptor Phenotypes

The rostral ventromedial medulla (RVM) forms part of a descending pathway that modulates nociceptive neurotransmission at the level of the spinal cord dorsal horn. However, the involvement of descending RVM systems in opioid analgesia are a matter of some debate. In the present study, patch-clamp recordings of RVM neurons were made from rats that had received retrograde tracer injections into the spinal cord. More than 90% of identified spinally projecting RVM neurons responded to opioid agonists. Of these neurons, 53% responded only to the μ-opioid agonist d-Ala2, N-Me-Phe4, Gly-ol5 enkephalin, 14% responded only to the κ-opioid agonist U-69593, and another group responded to both μ and κ opioids (23%). In unidentified RVM neurons, a larger proportion of neurons responded only to μ opioids (75%), with smaller proportions of κ- (4%) and μ/κ-opioid (13%) responders. These RVM slices were then immunostained for tryptophan hydroxylase (TPH), a marker of serotonergic neurons. Forty-percent of spinally projecting neurons and 11% of unidentified neurons were TPH positive. Of the TPH-positive spinally projecting neurons, there were similar proportions of μ- (33%), κ- (25%), and μ/κ-opioid (33%) responders. Most of the TPH-negative spinally projecting neurons were μ-opioid responders (67%). These findings indicate that functional opioid receptor subtypes exist on spinally projecting serotonergic and nonserotonergic RVM neurons. The proportions of μ- and κ-opioid receptors expressed differ between serotonergic and nonserotonergic neurons and between retrogradely labeled and unlabeled RVM neurons. We conclude that important roles exist for both serotonergic and nonserotonergic RVM neurons in the mediation of opioid effects.
Owner Experience and the Choice to Euthanize

The human-dog relationship has change significantly over the decades, with the dog now frequently being considered a member of the family, but it still falls to the human to grantee the dog’s well-being, both legally and morally. One of the decisions required of a dog owner is when, and if, to euthanize an animal. It has been suggested that chronic illness, financial considerations and behaviour issues may predispose a dog to euthanasia. Through the use of questionnaires administered to dog owners, this study evaluated possible connections between reported canine health issues and owner choice to euthanize. Owners were asked if they had cared for at least one dog with chronic illness, that suffered a trauma (vehicular or otherwise), had been hospitalized, if their dog had bitten a person or an animal and if they had ever euthanized a dog. Contrasting with some previous reports, no association was found between any of the issues investigated and euthanasia. It is possible that the voluntary nature of this study may have introduced a bias, attracting owners with higher educational and economical status, which may make them more reluctant to euthanize their dog. In any case, more studies are required to clarify this issue.
Variation in the perception of desired qualities of police officers among trainees and senior police officers. Insights into the process and efficacy of police training

ABSTRACT Police training is the process of imparting knowledge, skills, and values to police personnel. The study analyses a survey data on the perception of trainees and senior experienced officers regarding desired professional qualities in police officers. There is a high degree of congruence, in the assessment of values which are important for police, among the two groups. There are also differences among the two groups regarding the evaluation of the importance of interpersonal skills and human qualities. The study attempts to explain the similarities and the differences in perception by examining the conservative and innovative nature of police training, and the role of experience in developing an appreciation of human qualities. The study underlines the importance of police training as a mechanism to maintain the stability of operations in the organisation and its pivotal role in bringing about change in the police.
Status, Antimicrobial Mechanism, and Regulation of Natural Preservatives in Livestock Food Systems

This review discusses the status, antimicrobial mechanisms, application, and regulation of natural preservatives in livestock food systems. Conventional preservatives are synthetic chemical substances including nitrates/nitrites, sulfites, sodium benzoate, propyl gallate, and potassium sorbate. The use of artificial preservatives is being reconsidered because of concerns relating to headache, allergies, and cancer. As the demand for biopreservation in food systems has increased, new natural antimicrobial compounds of various origins are being developed, including plant-derived products (polyphenolics, essential oils, plant antimicrobial peptides (pAMPs)), animal-derived products (lysozymes, lactoperoxidase, lactoferrin, ovotransferrin, antimicrobial peptide (AMP), chitosan and others), and microbial metabolites (nisin, natamycin, pullulan, ε-polylysine, organic acid, and others). These natural preservatives act by inhibiting microbial cell walls/membranes, DNA/RNA replication and transcription, protein synthesis, and metabolism. Natural preservatives have been recognized for their safety; however, these substances can influence color, smell, and toxicity in large amounts while being effective as a food preservative. Therefore, to evaluate the safety and toxicity of natural preservatives, various trials including combinations of other substances or different food preservation systems, and capsulation have been performed. Natamycin and nisin are currently the only natural preservatives being regulated, and other natural preservatives will have to be legally regulated before their widespread use.
A Review of Schoolwide Positive Behavior Interventions and Supports as a Framework for Reducing Disciplinary Exclusions

Schoolwide positive behavior interventions and supports (SWPBIS) is currently implemented in more than 23,000 schools nationally and internationally. Several reviews have examined the SWPBIS evidence base, including a meta-analysis of single-case design research. However, to date, there has not been a review of group-based experimental research (e.g., randomized controlled trials [RCTs]) on the school-level effects of SWPBIS implementation to reduce disciplinary exclusion, including office discipline referrals and suspensions. Therefore, we conducted a systematic review and meta-analysis following What Works Clearinghouse procedures to investigate that relationship. We identified four group experimental studies that included disciplinary exclusion as an outcome variable; two RCTs and two quasi-experimental designs. Overall, 90 schools, including both elementary and high schools, were evaluated. A statistically significant large treatment effect (g = −.86) was found for school suspension, but no treatment effect was found for office discipline referrals. Implications for future research are discussed.
Cardiovascular and Renal Benefits of SGLT2 Inhibitors: A Narrative Review

Context Most recently developed anti-hyperglycemic drugs have offered cardiovascular and renal benefits. In this narrative review, we discuss the cardiovascular and renal benefits of novel antidiabetic drugs, sodium glucose cotransporter type 2 (SGLT2) inhibitors, in type 2 diabetes. Evidence Acquisition The literature published in PubMed, Scopus, Web of Science, Google Scholar, and Cochrane library were reviewed up to January 2019. The keywords including SGLT2 inhibitor, type 2 diabetes, cardiovascular effect, and renal effect were used in different combinations. Results Cardiovascular disease represents a large health burden in patients with diabetes. The prevention of cardiovascular events is a major concern in the treatment of patients with diabetes. Diabetes is also associated with an increased risk of adverse renal events and diabetic nephropathy is the leading cause of end-stage renal disease worldwide. SGLT2 inhibitors as new glucose-lowering agents act by inhibiting glucose reabsorption in the proximal tubule of the kidney, which is independent of insulin secretion. We reviewed the cardiovascular effects of these drugs including effects on triple MACE (major adverse cardiovascular events), myocardial infarction, heart failure, cardiovascular and all-cause mortality, and stroke, as well as renal effects including albuminuria, serum creatinine, the rate of renal replacement therapy, and renal function over time, along with the mechanisms of these effects. Conclusions Given the suboptimal glycemic and cardiovascular risk control in type 2 diabetes, novel therapies such as SGLT2 inhibitors seem to have an important clinical advantage to improve glycemic control and cardiovascular and renal outcomes.
In Search of I/O-Optimal Recovery from Disk Failures

We address the problem of minimizing the I/O needed to recover from disk failures in erasure-coded storage systems. The principal result is an algorithm that finds the optimal I/O recovery from an arbitrary number of disk failures for any XOR-based erasure code. We also describe a family of codes with high-fault tolerance and low recovery I/O, e.g. one instance tolerates up to 11 failures and recovers a lost block in 4 I/Os. While we have determined I/O optimal recovery for any given code, it remains an open problem to identify codes with the best recovery properties. We describe our ongoing efforts toward characterizing space overhead versus recovery I/O tradeoffs and generating codes that realize these bounds.
A Random Onset Model for Degradation of High-Reliability Systems

Weapons stockpiles are expected to have high reliability over time, but prudence demands regular testing to detect detrimental aging effects and maintain confidence that reliability is high. We present a model, called RADAR, in which a stockpile has high initial reliability that may begin declining at any time. RADAR provides a framework for answering questions about how confidence in continued high reliability can change as a result of reduced sampling, discovery of failed units, and information about when a unit failed. Supplemental materials (available on the Technometrics web site) provide lemmas used in the proof of Theorem 1, details of the Markov chain Monte Carlo algorithm, and additional examples.
Quality of management of oral anticoagulation as assessed by time in therapeutic INR range in elderly and younger patients with low mean years of formal education : a prospective cohort study

Background: despite the overwhelming evidence of its effectiveness, oral anticoagulation continues to be underused in the elderly, presumably due to physicians’ misconceptions when estimating bleeding risk and ability to comply with treatment. Objective: to investigate the quality of anticoagulation control among deprived elderly and younger patients. Design: prospective observational study. Setting: a public anticoagulation clinic in a developing country. Subjects: all adult patients on intended long-term (>90 days) oral anticoagulation. We studied 171 patients (79 elderly and 92 non-elderly) with a mean follow-up of 273 ± 84.9 days. Methods: the main outcome measure was the quality of anticoagulation management as measured by the time in therapeutic (TTR) international normalised ratio (INR) range. Elderly patients (≥60 years) were compared with younger patients with respect to the educational level and co-morbidities. Results: the mean number of years of formal education was 4.37 ± 3.2 years. The mean TTR was 62.50 ± 17.9% in non-elderly and 62.10 ± 16.6% in elderly (P = 0.862) subjects, despite the higher prevalence of co-morbidities in the latter group: heart failure (46.3 versus 28.6%, P= 0.042), diabetes mellitus (22.8 versus 8.7%, P = 0.011), renal failure (estimated glomerular filtration rate <50 ml/min: 38.0 versus 7.1%, P < 0.001) and polypharmacy (84.8 versus 58.7%, P < 0.001). Fifty elderly and 84 non-elderly subjects require little or no assistance in taking medications. Among them, the elderly had lower educational levels (3.42 ± 2.5 versus 5.55 ± 3.4 years of formal education, P < 0.001) and higher rates of cognitive impairment (34.0 versus 13.1%, P = 0.004), but a similar mean TTR (62.46 ± 16.1 versus 63.02 ± 17.8%, P= 0.856). The oldest (≥75 years) patients did as well as those aged ≤50 years (mean TTR: 62.54 ± 16.0 versus 62.23 ± 16.4%, respectively, P= 0.98). 375 Oral anticoagulation in elderly patients D ow naded rom http/academ ic.p.com /ageing/artictract/40/3/375/21071 by gest on 20 M arch 2019 Conclusions: good-quality management of oral anticoagulation is achievable in deprived populations attending an anticoagulation clinic. Elderly patients may experience similar quality of anticoagulation despite having higher levels of co-morbidities and polypharmacy. These results add evidence to the safety of such therapeutic interventions in the elderly.
A hierarchy of linear threshold models for the spread of political revolutions on social networks

We study a linear threshold agent-based model (ABM) for the spread of political revolutions on social networks using empirical network data. We propose new techniques for building a hierarchy of simplified ordinary differential equation (ODE) based models that aim to capture essential features of the ABM, including effects of the actual networks, and give insight in the parameter regime transitions of the ABM. We relate the ABM and the hierarchy of models to a population-level compartmental ODE model that we proposed previously for the spread of political revolutions [1], which is shown to be mathematically consistent with the proposed ABM and provides a way to analyze the global behaviour of the ABM. This consistency with the linear threshold ABM also provides further justification a posteriori for the compartmental model of [1]. Extending concepts from epidemiological modelling, we define a basic reproduction number $R_0$ for the linear threshold ABM and apply it to predict ABM behaviour on empirical networks. In small-scale numerical tests we investigate experimentally the differences in spreading behaviour that occur under the linear threshold ABM model when applied to some empirical online and offline social networks, searching for quantitative evidence that political revolutions may be facilitated by the modern online social networks of social media.
The Polymorphism P315L of Human Toll-Like Receptor 1 Impairs Innate Immune Sensing of Microbial Cell Wall Components1

As a pattern recognition receptor, TLR1 mediates innate immune responses to a variety of microbial cell wall components including bacterial lipoproteins. We have previously shown that the central region of the extracellular domain of human TLR1, comprising leucine-rich repeat (LRR) motifs 9–12, is required for the sensing of bacterial lipopeptides. In this study, we have investigated three nonsynonymous single nucleotide polymorphisms (SNPs) located in this region of TLR1 by generating these variants and examining receptor function. We have found that a variant of TLR1 based upon the SNP P315L, located in the loop of LRR motif 11 (LRR11), is greatly impaired in mediating responses to lipopeptides and a variety of other bacterial agonists for this receptor. Despite normal cell surface expression, the P315L variant also fails to bind to GD2.F4, a commonly used anti-TLR1 mAb. Although a number of amino acid substitutions at position 315 impair receptor function, the leucine substitution has the strongest deleterious effect. GD2.F4 inhibits agonist-induced activation of TLR1, supporting a crucial role for the loop of LRR11 in receptor function. These results also suggest that the P315L SNP may predispose certain individuals to infectious diseases for which the sensing of microbial cell components by TLR1 is critical to innate immune defense.
Out but in: Exploring juvenile reentry through Photovoice

ABSTRACT Previously incarcerated youth reintegrating into their communities face many challenges. This study provided visual entry into the lives of three youth through the use of Photovoice methodology. Participants included three males, two Latinos and one White non-Latino, who had successfully been reentered into their communities for at least four months. During the eight-week program, participants photographed images of importance to them in their homes and communities. These were discussed and ultimately shared through a community photo exhibit. The resulting themes, related to their perceived supports and challenges to successful reentry, are presented with implications for supporting youth in their community reintegration.
Fundamental Failures of Shape Constancy Resulting from Cortical Anisotropy

Contrary to the conventional assumption that humans perceive shapes of rigid objects as constant despite retinal-image variations caused by changes in orientation and position, we show that the depths of three-dimensional (3-D) textured shapes appear to vary when the image is rotated. In paired comparisons of static stimuli, depth amplitude was perceived to be greater at vertical than at oblique orientations. A similar oblique bias was found for simple two-dimensional (2-D) obtuse angles. Using projective geometry to link angle magnitude to the orientation flows that convey 3-D shape from texture cues, we show quantitatively that the 2-D bias predicts the 3-D bias. Our finding that perception of angular magnitude is dependent on orientation has broad implications for shape constancy because orientation flows have also been implicated in 3-D perception from reflections and shading, and contour curvature is fundamental to uncovering depth and part-structure of shapes. We examined the roles played in the observed biases by anisotropies in numbers and tuning widths of orientation-tuned cells in striate cortex as well as the distribution of oriented energy in natural scenes. An optimal stimulus decoding model for 2-D angles revealed that the narrower tuning of cells for horizontal orientations combined with cross-orientation inhibition explains the orientation-dependent angle distortion and hence the 3-D shape inconstancy. Variations in properties within neural populations can thus have direct effects on visual perceptions and need to be included in neural decoding models.
Generalized contact structures

We study integrability of generalized almost contact structures, and find conditions under which the main associated maximal isotropic vector bundles form Lie bialgebroids. These conditions differentiate the concept of generalized contact structures from a counterpart of generalized complex structures on odd‐dimensional manifolds. We name the latter strong generalized contact structures. Using a Boothby–Wang construction bridging symplectic structures and contact structures, we find examples to demonstrate that, within the category of generalized contact structures, classical contact structures have non‐trivial deformations. Using deformation theory of Lie bialgebroids, we construct new families of strong generalized contact structures on the three‐dimensional Heisenberg group and its cocompact quotients.
Recent progress in understanding minimax search

Lookahead search has been known for a long time to be effective in tackling problems which can be cast in minimax form (mainly game playing, but others include maintaining unstable balance against gravity, and business decisions). Recent results have shown that the benefit of lookahead depends on the structure inherent in the problem, and even that there exist some minimax problems for which lookahead search is DIS-advantageous. This paper reviews those results and then discusses algorithms which can be interpreted as recognising the structure of local areas of the search in order to control search expansion. Such algorithms can be orders of magnitude more cost-effective than search using alpha-beta alone.
Factors affecting quality management at the Thai national institute of health.

PURPOSE The purpose of this paper is to confirm and examine organization-related factors that could affect quality management at the Thai national reference laboratory known as National Institute of Health. DESIGN/METHODOLOGY/APPROACH The authors invited 340 laboratory staff members to complete a questionnaire that enquired about their skills, opinions, perceptions, leadership, work environment, organizational culture and organizational commitment in relation to quality management. Confirmatory factor analysis (CFA) and multiple linear regression were used to analyze the data. FINDINGS In total, 65 percent of institute members responded to the questionnaire. CFA revealed that all factors were related to quality management. Three factors, leadership, organizational commitment and work environment, significantly affected quality management, but organizational culture did not. RESEARCH LIMITATIONS/IMPLICATIONS Other data types should be collected for an in-depth understanding, i.e. focus groups or in-depth interviews. A longitudinal study could also enhance quality management understanding to see how each variable changes over time. ORIGINALITY/VALUE Analyzing quality management through confirmatory factor and regression analysis showed that the four analyzed variables are statistically significant in relation to quality management at the laboratory. Managers could apply this information to revise the current policy.
Stochastic analysis of periodic real-time systems

This paper describes a stochastic analysis method for general periodic real-time systems. The proposed method accurately computes the response time distribution of each task in the system, thus making it possible to determine the deadline miss probability of individual tasks, even for systems with maximum utilization factor greater than one. The method uniformly covers both fixed-priority scheduling (such as rate monotonic) as well as dynamic-priority scheduling (such as earliest deadline first) and can handle arbitrary relative deadlines and execution time distributions. The accuracy of the method is proven by comparing the results from the analysis with those obtained from simulations, as well as other methodologies in the literature.