Miracle-dz/UniFAR-FTUs huggingface dataset:
Landscape‐scale genetic variation in a forest outbreak species, the mountain pine beetle (Dendroctonus ponderosae)

The mountain pine beetle Dendroctonus ponderosae is a native species currently experiencing large‐scale outbreaks in western North American pine forests. We sought to describe the pattern of genetic variation across the range of this species, to determine whether there were detectable genetic differences between D. ponderosae occupying different host trees in common localities, and to determine whether there was molecular evidence for a past demographic expansion. Using a combination of amplified fragment length polymorphism (AFLP) and mitochondrial sequencing analyses, we found evidence of genetic structuring among populations that followed a broad isolation‐by‐distance pattern. Our results suggest that the geographical pattern of gene flow follows the core distribution of the principal D. ponderosae host species, around rather than across the Great Basin and Mojave Deserts. Patterns of haplotype diversity and divergence were consistent with a range‐wide population expansion. This signal was particularly pronounced in the northern part of the species’ range, where outbreak activity is currently increasing. Using AFLP markers, we were unable to detect significant differences among groups of insects sampled from different host trees in common locations. Incidentally, we found that a large proportion of the polymorphic AFLP markers were gender‐specific, occurring only in males. While we did not include these markers in our analyses, this finding warrants further investigation.
Effects of Cold-Dry (Harmattan) and Hot-Dry Seasons on Daily Rhythms of Rectal and Body Surface Temperatures in Sheep and Goats in a Natural Tropical Environment

Studies on daily rhythmicity in livestock under natural conditions are limited, and there is mounting evidence that rhythm patterns differ between chronobiological studies conducted in the laboratory and studies conducted under pronounced natural seasonality. Here, we investigated the influence of cold-dry (harmattan) and hot-dry seasons on daily rhythmicity of rectal (RT) and body surface temperatures (BST) in indigenous sheep and goats under natural light-dark cycles. The RT and BST of the animals, and the ambient temperature (AT) and relative humidity (RH) inside the pen, were measured every three hours for a period of two days, twice on separate days during the hot-dry and the harmattan seasons, respectively. The AT and RH had minimum values of 16°C and 15% recorded during the harmattan and maximum values of 32°C and 46% recorded during the hot-dry season, respectively. A trigonometric statistical model was applied to characterize the main rhythmic parameters according to the single cosinor procedure. The result showed that RT and BST exhibited different degrees of daily rhythmicity, and their oscillatory patterns differed with the seasons (larger amplitude during the harmattan season than during the hot-dry season). The goats displayed greater (p < 0.05) amplitude of BST than the sheep in all seasons. The acrophases were restricted to the light phase of the light-dark cycle. The mesor of RT in goats was not affected by the season, but mesors of BST in both species were significantly higher (p < 0.05) during the hot-dry than the harmattan season. The goats had a more robust RT rhythm (70%) as compared to the sheep (56%). Overall, the results demonstrated that seasonal changes influenced considerably the daily rhythmicity of RT and BST in sheep and goats under natural light-dark cycle. Awareness of these changes may be useful in the improvement of diagnosis, treatment and prevention of diseases, and welfare and productivity of sheep and goats under cold-dry and hot-dry conditions.
Interleukin-2 and STAT5 in regulatory T cell development and function

Interleukin-2 and its downstream target STAT5 have effects on many aspects of immune function. This has been perhaps best documented in regulatory T cells. In this review we summarize the initial findings supporting a role for IL2 and STAT5 in regulatory T cell development and outline more recent studies describing how this critical signaling pathway entrains regulatory T cell differentiation and affects regulatory T cell function.
Cooperative Awareness at Low Vehicle Densities: How Parked Cars Can Help See through Buildings

Many safety applications in Intelligent Transportation Systems (ITS) require vehicles to be aware of the presence of nearby cars, but - especially in urban and suburban regions - buildings and other obstacles may block radio transmissions. In the literature, multi-hop relaying by neighboring cars has been demonstrated to perform well at disseminating safety broadcasts in the presence of obstacles. At night, in areas with low traffic density, or when the penetration rate of Car-2-X devices is low, however, there are likely to be too few relaying cars available. This again leads to the problem that vehicles which are not in line-of-sight frequently cannot be sensed either. To the best of our knowledge, we are the first to help overcome this problem by utilizing parked cars as relay nodes. We study the effectiveness and the necessity of this approach with the help of extensive simulative studies and real life experiments. We show how, for scenarios with few equipped cars, the utilization of parked cars proves crucial to support safety applications. When disseminating safety critical events in a realistic scenario, parked cars can increase cooperative awareness by over 40% in total.
Disrupted small-world brain network topology in pure conduct disorder

Objectives Conduct disorder (CD) is characterized by the violation of the rights of others or basic social rules and a repetitive, persistent pattern of antisocial and aggressive behaviors. A large number of functional and structural neuroimaging studies have identified widely abnormalities in specific brain regions in CD, but the alterations in the topological organization of functional networks among them remain largely unknown. Methods Resting-state functional magnetic resonance imaging was applied to investigate the intrinsic functional connectivity in 18 pure CD patients and eighteen typically developing healthy controls. We first constructed the functional networks and then examined the CD-related alteration in topology properties using graph theoretical analysis. Results Both the CD group and healthy controls exhibited small-world topology. However, the CD group showed decreased global and local efficiency. Changes in the nodal characteristics in CD group were found predominantly in the default-mode network, visual, and striatum regions. In addition, altered fronto-limbic-striatum network topology was found to have a relationship with clinical scores. Conclusions Our findings indicate the altered nodal topology of brain functional connectivity networks in CD. Significance The results provide unequivocal evidence of a topological disruption in the brain networks that suggest some possible pathophysiological mechanisms underlying CD.
Virome Assembly and Annotation: A Surprise in the Namib Desert

Sequencing, assembly, and annotation of environmental virome samples is challenging. Methodological biases and differences in species abundance result in fragmentary read coverage; sequence reconstruction is further complicated by the mosaic nature of viral genomes. In this paper, we focus on biocomputational aspects of virome analysis, emphasizing latent pitfalls in sequence annotation. Using simulated viromes that mimic environmental data challenges we assessed the performance of five assemblers (CLC-Workbench, IDBA-UD, SPAdes, RayMeta, ABySS). Individual analyses of relevant scaffold length fractions revealed shortcomings of some programs in reconstruction of viral genomes with excessive read coverage (IDBA-UD, RayMeta), and in accurate assembly of scaffolds ≥50 kb (SPAdes, RayMeta, ABySS). The CLC-Workbench assembler performed best in terms of genome recovery (including highly covered genomes) and correct reconstruction of large scaffolds; and was used to assemble a virome from a copper rich site in the Namib Desert. We found that scaffold network analysis and cluster-specific read reassembly improved reconstruction of sequences with excessive read coverage, and that strict data filtering for non-viral sequences prior to downstream analyses was essential. In this study we describe novel viral genomes identified in the Namib Desert copper site virome. Taxonomic affiliations of diverse proteins in the dataset and phylogenetic analyses of circovirus-like proteins indicated links to the marine habitat. Considering additional evidence from this dataset we hypothesize that viruses may have been carried from the Atlantic Ocean into the Namib Desert by fog and wind, highlighting the impact of the extended environment on an investigated niche in metagenome studies.
Mini Review of Integrated Care and Implications for Advanced Practice Nurse Role

Literature related to primary care and behavioral health integration initiatives is becoming abundant. The United States’ 2010 Patient Protection and Affordable Care Act included provisions encouraging increased collaboration of care for individuals with behavioral and physical health service needs in the public sector. There is relatively little known of Advanced Practice Registered Nurses’ (APRNs) roles with integrating primary and behavioral healthcare. The goal of this review article is to: (a) define integration of physical and behavioral healthcare and potential models; (b) answer the question as to what are effective evidence based models/strategies for integrating behavioral health and primary care; (c) explore the future role and innovations of APRNs in the integration of physical and behavioral healthcare. Results: The evidence- based literature is limited to three systematic reviews and six randomized controlled trials. It was difficult to generalize the data and the effective integration strategies varied from such interventions as care management to use of sertraline to depression management and to access. There were, though, implications for the integrated care advanced practice nurse to have roles inclusive of competencies, leadership, engagement, collaboration and advocacy.
In vivo 31P magnetic resonance spectroscopy of the human liver at 7 T: an initial experience

Phosphorus (31P) MRS is a powerful tool for the non‐invasive investigation of human liver metabolism. Four in vivo 31P localization approaches (single voxel image selected in vivo spectroscopy (3D‐ISIS), slab selective 1D‐ISIS, 2D chemical shift imaging (CSI), and 3D‐CSI) with different voxel volumes and acquisition times were demonstrated in nine healthy volunteers. Localization techniques provided comparable signal‐to‐noise ratios normalized for voxel volume and acquisition time differences, Cramer–Rao lower bounds (8.7 ± 3.3%1D‐ISIS, 7.6 ± 2.5%3D‐ISIS, 8.6 ± 4.2%2D‐CSI, 10.3 ± 2.7%3D‐CSI), and linewidths (50 ± 24 Hz1D‐ISIS, 34 ± 10 Hz3D‐ISIS, 33 ± 10 Hz2D‐CSI, 34 ± 11 Hz3D‐CSI).
Late marriage and the HIV epidemic in sub-Saharan Africa

The causes of large variation in the sizes of HIV epidemics among countries in sub-Saharan Africa are not well understood. Here we assess the potential roles of late age at marriage and a long period of premarital sexual activity as population risk factors, using ecological data from 33 sub-Saharan African countries and with individual-level data from Demographic and Health Surveys (DHS) in Kenya and Ghana in 2003. The ecological analysis finds a significant positive correlation between HIV prevalence and median age at first marriage, and between HIV prevalence and interval between first sexual intercourse and first marriage. The individual-level analysis shows that HIV infection per year of exposure is higher before than after first marriage. These findings support the hypothesis of a link between a high average age at marriage and a long period of premarital intercourse during which partner changes are relatively common and facilitate the spread of HIV.
Cross-layer resource allocation and scheduling in LTE systems under imperfect CSIT

3GPP LTE/LTE-A is set to become the dominant technology for 4G and Beyond 4G wireless communications. As in any MIMO-OFDMA-based system, scheduling and resource allocation algorithms play a pivotal role towards the maximisation of capacity while providing support to applications with heterogeneous QoS requirements. To this end, the transmitter is assumed to have access to channel state information (CSIT) that, in most practical situations, will not be perfect. This paper first presents an analytical framework for QoS-guaranteed cross-layer scheduling and resource allocation that takes into account the accuracy of the available CSIT and then particularizes using specifications drawn from the LTE/LTE-A standards. Simulation results are shown assessing the performance of different schedulers and power allocation policies and the impact CSIT accuracy has on them.
Gastrointestinal Blood Flow in the Dog

That the radiorubidium distribution method provides good estimates of blood flow to the gastrointestinal organs was demonstrated by comparing the arterial concentration course of the isotope with the simultaneous venous concentration for the individual organs. Blood flow to stomach, intestine and colon are accurately assessed by this method. Estimates for pancreas, gall bladder, esophagus and duodenum are probably correct. Average perfusion rates in the pentobarbital anesthetized dog are, in cc/min.g of tissue: —esophagus, 0.21; stomach, 0.51; duodenum, 0.70; small intestine, 0.72; colon, 0.82; pancreas, 0.60; and gall bladder, 0.39.
Clinical Outcomes of Drug-Eluting Stents vs. Bare-Metal Stents in Acute Myocardial Infarction Patients Under Dialysis - A Nationwide Cohort Study.

BACKGROUND Data on the cardiovascular (CV) outcomes of drug-eluting stents (DES) vs. bare-metal stents (BMS) in patients with acute myocardial infarction (AMI) under dialysis are limited. METHODSANDRESULTS We analyzed the data from 42,592 AMI patients in the Taiwan National Health Insurance Research Database between 1 January 2007 and 31 December 2011. A total of 984 AMI patients under dialysis were selected as the study cohort. We evaluated the clinical outcomes by comparing 492 subjects who had DES to 492 matched subjects who had BMS. The primary composite outcomes, which included recurrent MI, coronary revascularization and CV death, were significantly lower in the DES group than in the BMS group (41.7% vs. 47.6%, hazard ratio (HR), 0.77; 95% confidence interval (CI), 0.63-0.92, P=0.005) after mean 1.2 years. The patients who received DES had a lower risk of recurrent MI (HR, 0.63; 95% CI, 0.45-0.90), CV death (HR, 0.74; 95% CI, 0.56-0.98) and all-cause mortality (HR, 0.74; 95% CI, 0.61-0.89) than those who used BMS, but a similar risk of major bleeding (HR, 0.99; 95% CI, 0.69-1.42, P=0.952) and ischemic stroke (HR, 1.15; 95% CI, 0.66-2.01, P=0.631). CONCLUSIONS Among AMI patients on dialysis undergoing percutaneous coronary interventions, DES implantation significantly reduced the risk of recurrent MI, CV death and all-cause mortality compared with BMS implantation.
Generalized Osteopenia in Adolescent Idiopathic Scoliosis–Association With Abnormal Pubertal Growth, Bone Turnover, and Calcium Intake?

Study Design. A cross-sectional study in girls with adolescent idiopathic scoliosis (AIS) and healthy counterparts of similar age. Objectives. To study the association of bone mass with anthropometric parameters, bone turnover, and calcium intake in 621 girls with AIS, aged 11–6-years, and compare the results with 300 healthy girls of similar age. Summary of Background Data. Generalized low bone mass has been documented in AIS, yet the cause of low bone mineral density in AIS is unknown. Methods. Corrected height and arm span, bone mineral density and bone mineral content of proximal femur, lumbar spine, and distal tibia, and bone turnover markers (bone alkaline phosphatase [bALP] and deoxypyridinoline) were evaluated. Results. From age 13 years and older, the AIS group had longer anthropometric parameters (P < 0.05), generalized lower bone mass (P < 0.035), and 38.6% higher in bALP (P < 0.004) when compared with controls. A stronger inverse correlation between bALP and bone mass was noted in the AIS group. The bALP was positively correlated with bone area of tibia (P = 0.013) in the AIS group only. Deoxypyridonine of the AIS group was not different from the controls until age 15 years. The mean calcium intake of the AIS group was very low (only 361 mg/day), and calcium intake was significantly associated with bone mass in the AIS group. Low bone mass in AIS could be explained by faster anthropometric bone growth, higher bone turnover, and lower calcium intake in multiple regression analysis. Conclusions. Results from the current study showed that an abnormally faster growth rate and higher bone turnover in the patient with AIS might lead to increased bone dimensions. Calcium intake in patients with AIS was very low and likely to be insufficient for normal bone mineralization. Therefore, low bone mass in AIS may result from abnormal bone mineralization qualitatively and quantitatively and, thus, fails to catch up with increased bone growth during the peripubertal period.
Epigenetic Regulation of Endothelial Lineage Committed Genes in Pro-Angiogenic Hematopoietic and Endothelial Progenitor Cells

Rationale: Proangiogenic hematopoietic and endothelial progenitor cells (EPCs) contribute to postnatal neovascularization, but the mechanisms regulating differentiation to the endothelial lineage are unclear. Objective: To elucidate the epigenetic control of endothelial gene expression in proangiogenic cells and EPCs. Methods and Results: Here we demonstrate that the endothelial nitric oxide synthase (eNOS) promoter is epigenetically silenced in proangiogenic cells (early EPCs), CD34+ cells, and mesoangioblasts by DNA methylation and prominent repressive histone H3K27me3 marks. In order to reverse epigenetic silencing to facilitate endothelial commitment, we used 3-deazaneplanocin A, which inhibits the histone methyltransferase enhancer of zest homolog 2 and, thereby, reduces H3K27me3. 3-Deazaneplanocin A was not sufficient to increase eNOS expression, but the combination of 3-deazaneplanocin A and the histone deacetylase inhibitor Trichostatin A augmented eNOS expression, indicating that the concomitant inhibition of silencing histone modification and enhancement of activating histone modification facilitates eNOS expression. In ischemic tissue, hypoxia plays a role in recruiting progenitor cells. Therefore, we examined the effect of hypoxia on epigenetic modifications. Hypoxia modulated the balance of repressive to active histone marks and increased eNOS mRNA expression. The reduction of repressive H3K27me3 was associated with an increase of the histone demethylase Jmjd3. Silencing of Jmjd3 induced apoptosis and senescence in proangiogenic cells and inhibited hypoxia-mediated up-regulation of eNOS expression in mesoangioblasts. Conclusions: These findings provide evidence that histone modifications epigenetically control the eNOS promoter in proangiogenic cells.
Organically Grown Food Provides Health Benefits to Drosophila melanogaster

The “organic food” market is the fastest growing food sector, yet it is unclear whether organically raised food is nutritionally superior to conventionally grown food and whether consuming organic food bestows health benefits. In order to evaluate potential health benefits of organic foods, we used the well-characterized fruit fly Drosophila melanogaster as a model system. Fruit flies were raised on a diets consisting of extracts of either conventionally or organically raised produce (bananas, potatoes, raisins, soy beans). Flies were then subjected to a variety of tests designed to assess overall fly health. Flies raised on diets made from organically grown produce had greater fertility and longevity. On certain food sources, greater activity and greater stress resistance was additionally observed, suggesting that organic food bestows positive effects on fly health. Our data show that Drosophila can be used as a convenient model system to experimentally test potential health effects of dietary components. Using this system, we provide evidence that organically raised food may provide animals with tangible benefits to overall health.
Effects of Electrical Stimulation in Spastic Muscles After Stroke: Systematic Review and Meta-Analysis of Randomized Controlled Trials

Background and Purpose— Neuromuscular electric stimulation (NMES) has been used to reduce spasticity and improve range of motion in patients with stroke. However, contradictory results have been reported by clinical trials. A systematic review of randomized clinical trials was conducted to assess the effect of treatment with NMES with or without association to another therapy on spastic muscles after stroke compared with placebo or another intervention. Methods— We searched the following electronic databases (from inception to February 2015): Medline (PubMed), EMBASE, Cochrane Central Register of Controlled Trials and Physiotherapy Evidence Database (PEDro). Two independent reviewers assessed the eligibility of studies based on predefined inclusion criteria (application of electric stimulation on the lower or upper extremities, regardless of NMES dosage, and comparison with a control group which was not exposed to electric stimulation), excluding studies with <3 days of intervention. The primary outcome extracted was spasticity, assessed by the Modified Ashworth Scale, and the secondary outcome extracted was range of motion, assessed by Goniometer. Results— Of the total of 5066 titles, 29 randomized clinical trials were included with 940 subjects. NMES provided reductions in spasticity (−0.30 [95% confidence interval, −0.58 to −0.03], n=14 randomized clinical trials) and increase in range of motion when compared with control group (2.87 [95% confidence interval, 1.18–4.56], n=13 randomized clinical trials) after stroke. Conclusions— NMES combined with other intervention modalities can be considered as a treatment option that provides improvements in spasticity and range of motion in patients after stroke. Clinical Trial Registration Information— URL: http://www.crd. york.ac. uk/PROSPERO. Unique identifier: CRD42014008946.
Federal Reserve Bank of New York Staff Reports The Case for TIPS : An Examination of the Costs and Benefits

Several studies have shown that, ex-post, the issuance of Treasury Inflation-Protected Securities (TIPS) has cost U.S. taxpayers money. We propose that evaluations of the TIPS program be more comprehensive and focus on the ex-ante costs of TIPS issuance versus nominal Treasury issuance and, especially when these costs are negligible, the more difficult-to-measure benefits of the program. Our study finds that the ex-ante costs of TIPS issuance versus nominal Treasury issuance are currently about equal and that TIPS provide meaningful benefits to investors and policymakers.
The interpretation and application of Rent's rule

This paper provides a review of both Rent's rule and the placement models derived from it. It is proposed that the power-law form of Rent's rule, which predicts the number of terminals required by a group of gates for communication with the rest of the circuit, is a consequence of a statistically homogeneous circuit topology and gate placement. The term "homogeneous" is used to imply that quantities such as the average wire length per gate and the average number of terminals per gate are independent of the position within the circuit. Rent's rule is used to derive a variety of net length distribution models and the approach adopted in this paper is to factor the distribution function into the product of an occupancy probability distribution and a function which represents the number of valid net placement sites. This approach places diverse placement models under a common framework and allows the errors introduced by the modeling process to be isolated and evaluated. Models for both planar and hierarchical gate placement are presented.