Miracle-dz/UniFAR-FTUs huggingface dataset:
The complete mitogenomes of six higher termite species reconstructed from metagenomic datasets (Cornitermes sp., Cubitermes ugandensis, Microcerotermes parvus, Nasutitermes corniger, Neocapritermes taracua, and Termes hospes)

Abstract We reconstructed the complete mitochondrial genomes of six higher termite species from metagenomic datasets of their isolated hindgut compartments. The sequencing reads were retrieved and assembled with the mitochondrial-baiting and iterative-mapping algorithm (MITObim), which yielded closed mitogenomes without additional finishing efforts (average coverage ranging from 2300- to 17,000-fold). The genomes ranged from 16.1 to 17.6 kbp in size and had G+C contents between 32 and 35 mol%; each contained the same 37 genes present also in the mitochondria of other termite species. Our study substantially increases the number of termite mitogenomes available for phylogenetic studies and offers a facile strategy for identifying host species in metagenomic studies of their associated microbiota.
Effect of nitrogen pressure on structure and optical band gap of copper nitride thin films

Copper nitride (Cu 3 N) thin films were deposited on glass substrates by reactive radio frequency magnetron sputtering under different radio frequency power ( P ) and nitrogen partial pressure r ( r =N 2 /［N 2 +Ar］). The thickness, crystalline structure and surface morphology of films were characterized by profilometer, X-ray diffraction (XRD) and atomic force microscopy (AFM), respectively. The optical transmission spectrum was obtained by an ultraviolet-visible (UV-VIS) spectrophotometer and the optical band gap ( E g ) was calculated. The results suggest that the films' deposition rate increases with P and r . The surface of the films reveals a compact structure, and the grain size of Cu 3 N is about 30nm. Meanwhile, with increasing r , the grain size and optical band gap of Cu 3 N increase, of which E g ranges from 1.47 to 1.82eV, and the films' growth prefers the (111) direction at low r and the (100) direction at high r .
A pooled analysis of dietary sugar/carbohydrate intake and esophageal and gastric cardia adenocarcinoma incidence and survival in the USA.

Background During the past 40 years, esophageal/gastric cardia adenocarcinoma (EA/GCA) incidence increased in Westernized countries, but survival remained low. A parallel increase in sugar intake, which may facilitate carcinogenesis by promoting hyperglycaemia, led us to examine sugar/carbohydrate intake in association with EA/GCA incidence and survival. Methods We pooled 500 EA cases, 529 GCA cases and 2027 controls from two US population-based case-control studies with cases followed for vital status. Dietary intake, assessed by study-specific food frequency questionnaires, was harmonized and pooled to estimate 12 measures of sugar/carbohydrate intake. Multivariable-adjusted odds ratios (ORs) and hazard ratios [95% confidence intervals (CIs)] were calculated using multinomial logistic regression and Cox proportional hazards regression, respectively. Results EA incidence was increased by 51-58% in association with sucrose (ORQ5vs.Q1 = 1.51, 95% CI = 1.01-2.27), sweetened desserts/beverages (ORQ5vs.Q1 = 1.55, 95% CI = 1.06-2.27) and the dietary glycaemic index (ORQ5vs.Q1 = 1.58, 95% CI = 1.13-2.21). Body mass index (BMI) and gastro-esophageal reflux disease (GERD) modified these associations (Pmultiplicative-interaction ≤ 0.05). For associations with sucrose and sweetened desserts/beverages, respectively, the OR was elevated for BMI < 25 (ORQ4-5vs.Q1-3 = 1.79, 95% CI = 1.26-2.56 and ORQ4-5vs.Q1-3 = 1.45, 95% CI = 1.03-2.06), but not BMI ≥ 25 (ORQ4-5vs.Q1-3 = 1.05, 95% CI = 0.76-1.44 and ORQ4-5vs.Q1-3 = 0.85, 95% CI = 0.62-1.16). The EA-glycaemic index association was elevated for BMI ≥ 25 (ORQ4-5vs.Q1-3 = 1.38, 95% CI = 1.03-1.85), but not BMI < 25 (ORQ4-5vs.Q1-3 = 0.88, 95% CI = 0.62-1.24). The sucrose-EA association OR for GERD < weekly was 1.58 (95% CI = 1.16-2.14), but for GERD ≥ weekly was 1.01 (95% CI = 0.70-1.47). Sugar/carbohydrate measures were not associated with GCA incidence or EA/GCA survival. Conclusions If confirmed, limiting intake of sucrose (e.g. table sugar), sweetened desserts/beverages, and foods that contribute to a high glycaemic index, may be plausible EA risk reduction strategies.
Neutrophils kill the parasite Trichomonas vaginalis using trogocytosis

T. vaginalis, a human-infective parasite, causes the most common nonviral sexually transmitted infection (STI) worldwide and contributes to adverse inflammatory disorders. The immune response to T. vaginalis is poorly understood. Neutrophils (polymorphonuclear cells [PMNs]) are the major immune cell present at the T. vaginalis–host interface and are thought to clear T. vaginalis. However, the mechanism of PMN clearance of T. vaginalis has not been characterized. We demonstrate that human PMNs rapidly kill T. vaginalis in a dose-dependent, contact-dependent, and neutrophil extracellular trap (NET)-independent manner. In contrast to phagocytosis, we observed that PMN killing of T. vaginalis involves taking “bites” of T. vaginalis prior to parasite death, using trogocytosis to achieve pathogen killing. Both trogocytosis and parasite killing are dependent on the presence of PMN serine proteases and human serum factors. Our analyses provide the first demonstration, to our knowledge, of a mammalian phagocyte using trogocytosis for pathogen clearance and reveal a novel mechanism used by PMNs to kill a large, highly motile target.
On Integer Programming and Convolution

Integer programs with a fixed number of constraints can be solved in pseudo-polynomial time. We present a surprisingly simple algorithm and matching conditional lower bounds. Consider an IP in standard form $\max\{c^T x : A x = b, x\in \mathbb Z^n_{\ge 0}\}$, where $A\in \mathbb Z^{m\times n}, b\in \mathbb Z^m$ and $c\in \mathbb Z^n$. Let $\Delta$ be an upper bound on the absolute values in $A$. We show that this IP can be solved in time $O(m\Delta)^{2m} \cdot \log(\lVert b \rVert_\infty)$. The previous best algorithm has a running time of $n\cdot O(m\Delta)^{2m}\cdot \lVert b \rVert_1^2$. The hardness of (min, +)-convolution has been used to prove conditional lower bounds on a number of polynomially solvable problems. We show that improving our algorithm for IPs of any fixed number of constraints is equivalent to improving (min, +)-convolution. More precisely, for any fixed $m$ there exists an algorithm for solving IPs with $m$ constraints in time $O(m(\Delta + \lVert b \rVert_\infty))^{2m-\delta}$ for some $\delta > 0$, if and only if there is a truly sub-quadratic algorithm for (min, +)-convolution. For the feasibility problem, where the IP has no objective function, we improve the running time to $O(m\Delta)^{m} \log(\Delta) \log (\Delta + \lVert b \rVert_\infty)$. We also give a matching lower bound here: For every fixed $m$ and $\delta > 0$ there is no algorithm for testing feasibility of IPs with $m$ constraints in time $n^{O(1)} \cdot O(m(\Delta + \lVert b \rVert_\infty))^{m - \delta}$ unless the SETH is false.
Coronary Artery Circumferential Stress: Departure from Laplace Expectations with Aging

Normal, youthful arteries generally maintain constant radius/wall thickness ratios, with the relationship being described by the Laplace Law. Whether this relationship is maintained during aging is unclear. This study first examines the Laplace relationships in postmortem coronary arteries using a novel method to correct measurements for postmortem artifacts, uses data from the literature to provide preliminary validation, and then describes histology associated with low circumferential stress. Measurements of radius and wall thickness, taken at sites free from atheromas, were used with national population estimates of age-, gender-, and race-specific blood pressure data to calculate average circumferential stress within demographic groups. The estimated circumferential stress at ages 55-74 years was about half that at ages 18-24 years because of a disproportionate increase of wall thickness relative to artery radius at older ages, violating the expected relationships described by the Laplace Law. Arteries with low circumferential stress (estimated at sites distant from atherosclerosis) had more necrotic atheromas than arteries with high stress. At sites with low stress and intimal thickening, smooth muscle cells (SMCs) were spread apart, thereby diminishing their density within both the intima and media. Thus, older arteries displayed both low circumferential stress and abundant matrix of low cellularity microscopically. Such changes might alter SMC-matrix interactions.
The C Terminus of the Core β-Ladder Domain in Japanese Encephalitis Virus Nonstructural Protein 1 Is Flexible for Accommodation of Heterologous Epitope Fusion

ABSTRACT NS1 is the only nonstructural protein that enters the lumen of the endoplasmic reticulum (ER), where NS1 is glycosylated, forms a dimer, and is subsequently secreted during flavivirus replication as dimers or hexamers, which appear to be highly immunogenic to the infected host, as protective immunity can be elicited against homologous flavivirus infections. Here, by using a trans-complementation assay, we identified the C-terminal end of NS1 derived from Japanese encephalitis virus (JEV), which was more flexible than other regions in terms of housing foreign epitopes without a significant impact on virus replication. This mapped flexible region is located in the conserved tip of the core β-ladder domain of the multimeric NS1 structure and is also known to contain certain linear epitopes, readily triggering specific antibody responses from the host. Despite becoming attenuated, recombinant JEV with insertion of a neutralizing epitope derived from enterovirus 71 (EV71) into the C-terminal end of NS1 not only could be normally released from infected cells, but also induced dual protective immunity for the host to counteract lethal challenge with either JEV or EV71 in neonatal mice. These results indicated that the secreted multimeric NS1 of flaviviruses may serve as a natural protein carrier to render epitopes of interest more immunogenic in the C terminus of the core β-ladder domain. IMPORTANCE The positive-sense RNA genomes of mosquito-borne flaviviruses appear to be flexible in terms of accommodating extra insertions of short heterologous antigens into their virus genes. Here, we illustrate that the newly identified C terminus of the core β-ladder domain in NS1 could be readily inserted into entities such as EV71 epitopes, and the resulting NS1-epitope fusion proteins appeared to maintain normal virus replication, secretion ability, and multimeric formation from infected cells. Nonetheless, such an insertion attenuated the recombinant JEV in mice, despite having retained the brain replication ability observed in wild-type JEV. Mother dams immunized with recombinant JEV expressing EV71 epitope-NS1 fused proteins elicited neutralizing antibodies that protected the newborn mice against lethal EV71 challenge. Together, our results implied a potential application of JEV NS1 as a viral carrier protein to express a heterologous epitope to stimulate dual/multiple protective immunity concurrently against several pathogens.
Handgrip Strength and Blood Pressure in Children and Adolescents: Evidence From NHANES 2011 to 2014

BACKGROUND Previous studies have reported that handgrip strength, a measure of muscular fitness, is associated with cardiovascular risk factors. However, the association of handgrip strength with blood pressure (BP) in children has been inconsistent. We tested the association of handgrip strength with systolic and diastolic BP in children and adolescents from the National Health and Nutrition Examination Survey (NHANES) 2011-2014. METHODS The study included 3,929 participants aged 8-19 years who underwent a handgrip test. The sum of the maximum handgrip strength from both hands was used. General linear models were used to examine the associations between handgrip strength and the outcome variables. RESULTS After adjustment for age, race, sex, body mass index, and physical activities, handgrip strength was significantly and positively associated with systolic (P < 0.0001) and diastolic (P = 0.01) BP. There was an increasing trend in systolic BP as handgrip strength increased from the bottom quartile to the top quartile, with 2.1 mm Hg difference between the top and the bottom quartiles (P for trend <0.0001). Similar results were observed for diastolic BP. CONCLUSIONS Muscular fitness is positively associated with BP in children and adolescents. The implications and underlying mechanisms for these results need further examinations.
VizWiz Grand Challenge: Answering Visual Questions from Blind People

The study of algorithms to automatically answer visual questions currently is motivated by visual question answering (VQA) datasets constructed in artificial VQA settings. We propose VizWiz, the first goal-oriented VQA dataset arising from a natural VQA setting. VizWiz consists of over 31,000 visual questions originating from blind people who each took a picture using a mobile phone and recorded a spoken question about it, together with 10 crowdsourced answers per visual question. VizWiz differs from the many existing VQA datasets because (1) images are captured by blind photographers and so are often poor quality, (2) questions are spoken and so are more conversational, and (3) often visual questions cannot be answered. Evaluation of modern algorithms for answering visual questions and deciding if a visual question is answerable reveals that VizWiz is a challenging dataset. We introduce this dataset to encourage a larger community to develop more generalized algorithms that can assist blind people.
Multiplex matrix network analysis of protein complexes in the human TCR signalosome

A multiplex antibody-mediated capture technique reveals patient-specific protein complexes. Personalized signaling complexes The response of a cell to ligands that activate cell surface receptors depends on the resulting protein-protein interactions that occur. The formation of different protein complexes leads to the activation of different intracellular signaling pathways and different cellular outputs. Thus, knowing which protein-protein interactions occur can be clinically important. To analyze these complexes in patient samples, Smith et al. devised a multiplex, antibody-based method and used it to capture complexes from T cell lysates and identify binding partners by flow cytometry. Mathematical analyses of these data enabled the construction of protein-protein interaction networks and revealed the relative abundances of particular complexes between resting and stimulated cells. Application of this technique to T cells from skin biopsies identified protein complexes that differed in their relative abundance between control donors and patients with an autoimmune skin disease. This type of analysis brings basic research a step closer to personalized therapy and may be useful as a diagnostic tool. Multiprotein complexes transduce cellular signals through extensive interaction networks, but the ability to analyze these networks in cells from small clinical biopsies is limited. To address this, we applied an adaptable multiplex matrix system to physiologically relevant signaling protein complexes isolated from a cell line or from human patient samples. Focusing on the proximal T cell receptor (TCR) signalosome, we assessed 210 pairs of PiSCES (proteins in shared complexes detected by exposed surface epitopes). Upon stimulation of Jurkat cells with superantigen-loaded antigen-presenting cells, this system produced high-dimensional data that enabled visualization of network activity. A comprehensive analysis platform generated PiSCES biosignatures by applying unsupervised hierarchical clustering, principal component analysis, an adaptive nonparametric with empirical cutoff analysis, and weighted correlation network analysis. We generated PiSCES biosignatures from 4-mm skin punch biopsies from control patients or patients with the autoimmune skin disease alopecia areata. This analysis distinguished disease patients from the controls, detected enhanced basal TCR signaling in the autoimmune patients, and identified a potential signaling network signature that may be indicative of disease. Thus, generation of PiSCES biosignatures represents an approach that can provide information about the activity of protein signaling networks in samples including low-abundance primary cells from clinical biopsies.
Assessing hepatitis C spontaneous clearance and understanding associated factors—A systematic review and meta‐analysis

New advances in the treatment of hepatitis C provide high levels of sustained viral response but their expense limits availability in publicly funded health systems. The aim of this review was to estimate the proportion of patients who will spontaneously clear HCV, to identify factors that are associated with clearance and to support better targeting of directly acting antivirals. We searched Ovid EMBASE, Ovid MEDLINE and PubMed from 1 January 1994 to 30 June 2015 for studies reporting hepatitis C spontaneous clearance and/or demographic, clinical and behavioural factors associated with clearance. We undertook meta‐analyses to estimate the odds of clearance for each predictor. Forty‐three studies met the inclusion criteria, representing 20 110 individuals, and 6 of these studies included sufficient data to estimate spontaneous clearance. The proportion achieving clearance within 3, 6, 12 and 24 months following infection were, respectively, 19.8% (95% CI: 2.6%‐47.5%), 27.9% (95% CI: 17.2%‐41.8%), 36.1% (95% CI: 23.5%‐50.9%) and 37.1% (95% CI: 23.7%‐52.8%). Individuals who had not spontaneously cleared by 12 months were unlikely to do so. The likelihood of spontaneous clearance was lower in males and individuals with HIV co‐infection, the absence of HBV co‐infection, asymptomatic infection, black or nonindigenous race, nongenotype 1 infection, older age and alcohol or drug problems. This study suggests that patients continue to spontaneously clear HCV for at least 12 months following initial infection. However, injecting drug users are comparatively less likely to achieve clearance; thus, they should be considered a priority for early treatment given the continuing risks that these individuals pose for onwards transmission.
Projects as an effective lever in the Mission of Health Care and Health Services : The Case of Quebec

More and more health care systems are taking the project management route. The present article sets out the results of a literature review (who was produced with the help of ABI/INFORM GLOBAL and covers the period from 1979 to May 2017 inclusively) dealing with project management in the health sector. Consequently, this paper is not a comparative analysis of Quebec’s health systems vis-à-vis the rest of the world’s. Nor is it a theoretical analysis of project management and strategic health systems management. This paper is of interest to practitioners who must manage their health services and social services on a by-project basis because their organization has turned onto the project path. So, what does the discipline of Project Management (a discipline that sees itself as being oriented to practitioners) have to offer to practitioners in the health sector? Results of the literature review indicate that the information technology project management in health sector is the favorite topic of researchers. Furthermore, very little of the research on health sector project management is published in the project management discipline’s journals and, on the other hand, a minority of the articles reviewed make reference to the works that are published in these PM Journals. Although the present article review focuses only on articles with the key words “Health” and “Project Management”, we can conclude that if project management wishes to become a discipline associated with health, it must promote the initiation of research that clearly identifies the real issues involved in a project and its management, in relation to the primary mission of health care systems: care, health services and social services. This paper presents the importance given to project management in the health sector and the theme of health in project management. It demonstrates the lack of emphasis on project management as a lever for health care, health services and social services which is the primary mission of healthcare systems and its practitioners.
Media Exposure and Internal Migration – Evidence from Indonesia

This paper investigates the impact of television on internal migration in Indonesia. We exploit the differential introduction of private television throughout the country and the variation in signal reception due to topography to estimate the causal effect of media exposure. Our estimates reveal important long and short run effects. An increase of one standard deviation in the number of private TV channels received in the area of residence reduces future inter-provincial migration by 1.7-2.7 percentage points, and all migration (inter and intra-provincial) by 4-7.4 percentage points. Short run effects are slightly smaller, but still sizeable and statistically significant. We also show that respondents less exposed to private TV are more likely to consider themselves among the poorest groups of the society. As we discuss in a stylized model of migration choice under imperfect information, these findings are consistent with Indonesia citizens over-estimating the net gains from internal migration. JEL: J61, L82, O15
Exploring the Relationship between Housing and Health for Refugees and Asylum Seekers in South Australia: A Qualitative Study

Housing is an important social determinant of health; however, little is known about the impact of housing experiences on health and wellbeing for people from refugee and asylum-seeking backgrounds. In this paper, we outline a qualitative component of a study in South Australia examining these links. Specifically, interviews were conducted with 50 refugees and asylum seekers who were purposively sampled according to gender, continent and visa status, from a broader survey. Interviews were analysed thematically. The results indicated that housing was of central importance to health and wellbeing and impacted on health through a range of pathways including affordability, the suitability of housing in relation to physical aspects such as condition and layout, and social aspects such as safety and belonging and issues around security of tenure. Asylum seekers in particular reported that living in housing in poor condition negatively affected their health. Our research reinforces the importance of housing for both the physical and mental health for asylum seekers and refugees living in resettlement countries. Improving housing quality, affordability and tenure security all have the potential to lead to more positive health outcomes.
Integrated Tobacco Cessation Counseling in a Diabetes Self-management Training Program

Purpose The purpose of this study was to evaluate the impact of a tobacco cessation intervention using motivational interviewing on smoking cessation rates during diabetes self-management training (DSMT). Methods A randomized controlled trial was conducted with subjects recruited from an ongoing type 2 diabetes adult education program at a large diabetes center. A total of 114 subjects were randomized to intervention (n = 57; face-to-face motivational interviewing plus telephone counseling and offering of medication) or standard care (n = 57). Outcome measures included tobacco cessation rates, mean number of cigarettes smoked, A1C, weight, blood pressure, and lipids. Results Intensive intervention using motivational interviewing integrated into a standard DSMT program resulted in a trend toward greater abstinence at 3 months of follow-up in those receiving the intervention. However, this same trend was not observed at 6 months. The addition of this structured smoking cessation intervention did not negatively affect either diabetes education or other measures of diabetes management, including A1C values.