Miracle-dz/UniFAR-FTUs huggingface dataset:
A Prospective Three-Year Cohort Study of the Epidemiology and Virology of Acute Respiratory Infections of Children in Rural India

Background Acute respiratory infection (ARI) is a major killer of children in developing countries. Although the frequency of ARI is similar in both developed and developing countries, mortality due to ARI is 10–50 times higher in developing countries. Viruses are common causes of ARI among such children, yet the disease burden of these infections in rural communities is unknown. Methodology/Principal Findings A prospective longitudinal study was carried out in children enrolled from two rural Indian villages at birth and followed weekly for the development of ARI, classified as upper respiratory infection, acute lower respiratory infection (ALRI), or severe ALRI. Respiratory syncytial virus (RSV), influenza, parainfluenza viruses and adenoviruses in nasopharyngeal aspirates were detected by direct fluorescent antibody testing (DFA) and, in addition, centrifugation enhanced culture for RSV was done. 281 infants enrolled in 39 months and followed until 42 months. During 440 child years of follow-up there were 1307 ARIs, including 236 ALRIs and 19 severe ALRIs. Virus specific incidence rates per 1000 child years for RSV were total ARI 234, ALRI 39, and severe ALRI 9; for influenza A total ARI 141, ALRI 39; for INF B total ARI 37; for PIV1 total ARI 23, for PIV2 total ARI 28, ALRI 5; for parainfluenza virus 3 total ARI 229, ALRI 48, and severe ALRI 5 and for adenovirus total ARI 18, ALRI 5. Repeat infections with RSV were seen in 18 children. Conclusions/Significance RSV, influenza A and parainfluenza virus 3 were important causes of ARI among children in rural communities in India. These data will be useful for vaccine design, development and implementation purposes.
Evidence of Polygenic Adaptation in the Systems Genetics of Anthropometric Traits

Many signals of natural selection have been identified in the human genome. However, except for some single-locus mechanisms, most molecular processes generating these adaptation signals are still unknown. We developed an approach that integrates datasets related to genome-wide association studies (GWAS) with information about systems biology and genetic signatures of natural selection to identify evidence of polygenic adaptation. Specifically, we focused on five anthropometric measurements: body mass index (BMI), height, waist-to-hip ratio adjusted for BMI (WHR), and waist circumference adjusted for BMI (WC), and sex differences for WHR and WC. We performed an enrichment analysis for signals of natural selection in protein interaction networks associated with anthropometric traits in European populations. The adaptation signals-enriched gene networks associated highlighted epistatic interactions in the context of polygenic selection for the investigated traits. These polygenic mechanisms indicated intriguing selective mechanisms related to the anthropometric traits: adult locomotory behavior for BMI, infection resistance for height, interplay between lipid transport and immune systems for WHR, and female-specific polygenic adaptation for WHR and WC. In conclusion, we observed evidence of polygenic adaptation in the context of systems genetics of anthropometric traits that indicates polygenic mechanisms related to the natural selection in European populations.
Moving to suburbia: ontogenetic and evolutionary consequences of life on predator‐free islands

Many species find themselves isolated from the predators with which they evolved. This situation commonly occurs with island biota, and is similar to moving from the dangerous inner‐city to the suburbs. Economic thinking tells us that we should expect costly antipredator behaviour to be lost if it is no longer beneficial. The loss of antipredator behaviour has important consequences for those seeking to translocate or reintroduce individuals from predator‐free islands back to the predator‐rich mainland, but we have neither a detailed understanding of the mechanisms of loss nor information on the time course of relaxed selection. Some antipredator behaviours are experience‐dependent: experience with predators is required for their proper performance. In these cases, antipredator behaviour is lost after only a single generation of isolation, but it should be able to be regained following exposure to predators. Other behaviours may be more `hard‐wired'. The evolutionary loss of antipredator behaviour may occur over as few as several generations, but behaviours may also persist for many thousands of years of predator‐free living.
Coboundary Lie bialgebras and commutative subalgebras of universal enveloping algebras

We solve a functional version of the problem of twist quantization of a coboundary Lie bialgebra (g, r, Z). We derive from this that the formal Poisson manifolds g and G are isomorphic, and we construct an injective algebra morphism S(g ) g ,! U(g ). When (g, r, Z) can be quantized, we construct a deformation of this morphism. In the particular case when g is quasitriangular and nondegenerate, we compare our construction with Semenov-Tian-Shansky’s construction of a commutative subalgebra of U(g ). We also show that the canonical derivation of the function ring of G is Hamiltonian.
Non‐homologous end joining‐mediated functional marker selection for DNA cloning in the yeast Kluyveromyces marxianus

The cloning of DNA fragments into vectors or host genomes has traditionally been performed using Escherichia coli with restriction enzymes and DNA ligase or homologous recombination‐based reactions. We report here a novel DNA cloning method that does not require DNA end processing or homologous recombination, but that ensures highly accurate cloning. The method exploits the efficient non‐homologous end‐joining (NHEJ) activity of the yeast Kluyveromyces marxianus and consists of a novel functional marker selection system. First, to demonstrate the applicability of NHEJ to DNA cloning, a C‐terminal‐truncated non‐functional ura3 selection marker and the truncated region were PCR‐amplified separately, mixed and directly used for the transformation. URA3+ transformants appeared on the selection plates, indicating that the two DNA fragments were correctly joined by NHEJ to generate a functional URA3 gene that had inserted into the yeast chromosome. To develop the cloning system, the shortest URA3 C‐terminal encoding sequence that could restore the function of a truncated non‐functional ura3 was determined by deletion analysis, and was included in the primers to amplify target DNAs for cloning. Transformation with PCR‐amplified target DNAs and C‐terminal truncated ura3 produced numerous transformant colonies, in which a functional URA3 gene was generated and was integrated into the chromosome with the target DNAs. Several K. marxianus circular plasmids with different selection markers were also developed for NHEJ‐based cloning and recombinant DNA construction. The one‐step DNA cloning method developed here is a relatively simple and reliable procedure among the DNA cloning systems developed to date. Copyright © 2013 John Wiley & Sons, Ltd.
Variability in the severity of colonic disease in familial adenomatous polyposis results from differences in tumour initiation rather than progression and depends relatively little on patient age

INTRODUCTION As large scale genetic analysis becomes increasingly efficient, attention is turning to problems arising from inaccurate measurement of the phenotype. We have investigated the underlying basis of variation in disease severity in the large intestine of familial adenomatous polyposis (FAP) patients. The development of objective and reproducible measures may have future use in genetic studies, such as analysis of modifier genes. METHODS We examined the ratio of adenomas to crypts from microscopic slides taken from all parts of the colon of 44 resected FAP specimens. These findings were compared with a carefully reported macroscopic polyp count. Age dependency of adenoma counts (in the period around colectomy) was also analysed. RESULTS The adenoma:crypt ratio strongly correlated with reported macroscopic polyp count (r=0.82, p<0.001) with no significant residual variation. Polyp density measured using the adenoma: crypt ratio did not vary significantly within an individual colon. Apparent visible variation in polyp density within any colon was not found at the microscopic level. There was no detectable age related increase in macroscopic adenoma count between siblings over the age range at which colectomies were performed. DISCUSSION The severity of colonic polyposis in FAP can be determined accurately by counting the adenoma:crypt ratio in sections derived from stored tissue blocks. Variation between patients—dependent on APC genotype and, probably, modifier genes—is manifest at both the microscopic and macroscopic levels. Thus variation in disease severity is more likely to result from different rates of tumour initiation than from differences in progression of microadenomas to macroscopic tumours. The absence of a detectable relationship between adenoma number and age (over the range studied) suggests that most tumours may be initiated relatively early in the patient's life, perhaps at a time of particular susceptibility.
The Stem Cell Hard Sell: Report from a Clinic's Patient Recruitment Seminar

The growing direct‐to‐consumer, stem cell clinic industry in the U.S. uses a number of strategies for patient recruitment, including self‐styled educational seminars, which may reach thousands of members of the public annually. Here I report on a first‐hand experience at such a seminar that I recently attended. Numerous specific medical claims were made at the seminar: no potential for rejection; no side effects, including no pain; proven efficacy for a variety of conditions, including in particular arthritis and pain; and U.S. Food and Drug Administration approval. I discuss the potential impact of these kinds of seminars on the public and on the stem cell field. Stem Cells Translational Medicine 2017;6:14–16
Validation of Short a Computer User Satisfaction Questionnaire to Measure IS Success in Small Business

The determination of factors that influence success in small business information systems(IS) is of obvious importance to the individuals running those businesses and to the regional economies where the businesses are located. The first step in this process is to develop models of interacting factors that contribute to success. Considerable progress has already been made in this area. DeLone and McLean (1992), for example, identified six inter-related factors that help to account for success. Their model has served as a platform for other researchers in this area (e.g., Seddon & Kiew, 1996). A second important step in this process is the development of well-validated instruments that can be used to measure the constructs making up the models. Without such instruments, it is not possible to go beyond mere speculation about possible contributors to small business IS success. The present study reports on the factorial validation of an instrument that can be used to access assess core constructs identified by previous researchers as predictors of success. The instrument also also contains a two-item measure of user satisfaction, a variable that is commonly accepted as a surrogate measure of IS success.
Predicting adverse events: detecting myocardial damage in intensive care unit (ICU) patients

Myocardial damage is known to occur relatively frequently, and although it is not often fatal it results in the patient staying in the ICU for significantly longer. Thus it is important for clinicians to detect these events. Confirmation of myocardial damage is by a biomarker (troponin), but these tests are only done at fixed time-points. Consequently it is desirable for doctors, and support systems, to detect myocardial damage from the standard parameters collected for ICU patients. We have undertaken a study with several ICU consultants to determine the conditions which generally precede a myocardial-damaging event. In fact, these knowledge acquisition sessions produced a complex model which we have realized as 2 interacting modules. Subsequently, we compared this model's predictions against the original datasets; the model when run against the test dataset resulted in a relatively high True Positive (TP) rate (75.8%). The implications of these analyses are discussed, as are a number of planned follow-up studies
Co-Production of Light p-, s- and r-Process Isotopes in the High-Entropy Wind of Type II Supernovae

Abstract We have performed large-scale nucleosynthesis calculations within the high-entropy-wind (HEW) scenario of Type II supernovae. The primary aim was to constrain the conditions for the production of the classical ‘p-only’ isotopes of the light trans-Fe elements. We find, however, that for electron fractions in the range 0.458 ≤ Y e ≤ 0.478, sizeable abundances of p-, s- and r-process nuclei between 64Zn and 98Ru are coproduced in the HEW at low entropies (S ≤ 100) by a primary charged-particle process after an α-rich freezeout. With the above Y e–S correlation, most of the predicted isotopic abundance ratios within a given element, e.g. 64Zn(p)/70Zn(r) or 92Mo(p)/94Mo(p), as well as of neighboring elements, e.g. 70Ge(s + p)/74Se(p) or 74Se(p)/78Kr(p) agree with the observed Solar-System ratios. Taking the Mo isotopic chain as a particularly challenging example, we show that our HEW model can account for the production of all 7 stable isotopes, from ‘p-only’ 92Mo, via ‘s-only’ 96Mo up to ‘r-only’ 100Mo. Furthermore, our model is able to reproduce the isotopic composition of Mo in presolar SiC X-grains.
Children on the Homefront: The Experience of Children From Military Families

OBJECTIVE: Although studies have begun to explore the impact of the current wars on child well-being, none have examined how children are doing across social, emotional, and academic domains. In this study, we describe the health and well-being of children from military families from the perspectives of the child and nondeployed parent. We also assessed the experience of deployment for children and how it varies according to deployment length and military service component. PARTICIPANTS AND METHODS. Data from a computer-assisted telephone interview with military children, aged 11 to 17 years, and nondeployed caregivers (n = 1507) were used to assess child well-being and difficulties with deployment. Multivariate regression analyses assessed the association between family characteristics, deployment histories, and child outcomes. RESULTS: After controlling for family and service-member characteristics, children in this study had more emotional difficulties compared with national samples. Older youth and girls of all ages reported significantly more school-, family-, and peer-related difficulties with parental deployment (P < .01). Length of parental deployment and poorer nondeployed caregiver mental health were significantly associated with a greater number of challenges for children both during deployment and deployed-parent reintegration (P < .01). Family characteristics (eg, living in rented housing) were also associated with difficulties with deployment. CONCLUSIONS: Families that experienced more total months of parental deployment may benefit from targeted support to deal with stressors that emerge over time. Also, families in which caregivers experience poorer mental health may benefit from programs that support the caregiver and child.
HESS upper limits for Kepler's supernova remnant

Observations of Kepler's supernova remnant (G4.5+6.8) with the H.E. S.S. telescope array in 2004 and 2005 with a total live time of 13 h are presented. Stereoscopic imaging of Cherenkov radiation from extensive air showers is used to reconstruct the energy and direction of the incident gamma rays. No evidence for a very high energy (VHE: >100 GeV) gamma-ray signal from the direction of the remnant is found. An upper limit (99% confidence level) on the energy flux in the range 230 GeV - 12.8 TeV of 8.6 x 10^{-13} erg cm^{-2} s^{-1} is obtained. In the context of an existing theoretical model for the remnant, the lack of a detectable gamma-ray flux implies a distance of at least 6.4 kpc. A corresponding upper limit for the density of the ambient matter of 0.7 cm^{-3} is derived. With this distance limit, and assuming a spectral index Gamma = 2, the total energy in accelerated protons is limited to E_p < 8.6 x 10^{49} erg. In the synchrotron/inverse Compton framework, extrapolating the power law measured by RXTE between 10 and 20 keV down in energy, the predicted gamma-ray flux from inverse Compton scattering is below the measured upper limit for magnetic field values greater than 52 muG.
Outcomes in HrHPV-positive women with low grade cervical smears and normal or low grade initial colposcopy results.

AIM To determine outcomes in HrHPV-positive women with low grade cervical smears and normal or low grade initial colposcopy biopsy results in a cohort of women over a 2-year follow-up period. BACKGROUND The revised National Cervical Screening (NCS) programme guidelines in New Zealand were implemented in October 2009. The guidelines state that women 30 years and older should undergo reflex HPV testing. If this test confirms the presence of HrHPV, women are to be referred for a colposcopic assessment. The guidelines do not mention what the follow-up period should be of women with HrHPV and normal or low grade abnormalities at colposcopy/biopsy. METHOD In this study we followed up women 30 years and older referred to Wellington Hospital from 1/10/2009 to 1/10/2011 with a LGSIL or ASC-US smear and positive HrHPV test. Those with a normal or low grade biopsy result were followed over a 2-year period to determine outcomes. RESULTS Our study found that 4% of women with initial normal biopsy results and 15.2% with initial low grade results had progressed to high grade (CIN 2/3/invasion) over a 2-year follow-up period. During the same time period, 68% of women with an initial normal biopsy and 61% with a low grade biopsy had a normal colposcopy after 2 years. Twenty-eight percent of women with normal and 24% of those with initial with low grade biopsy continued to have LG abnormalities at 2 years of follow-up. CONCLUSION Women 30 years and older who are HrHPV-positive and have low grade abnormalities at colposcopic biopsy may be followed up with a 12-month cervical smear rather than repeat colposcopy as the risk of progression to a high grade abnormality is low.
Mitochondrial and nuclear markers highlight the biodiversity of Kalotermes flavicollis (Fabricius, 1793) (Insecta, Isoptera, Kalotermitidae) in the Mediterranean area

Abstract The biodiversity of the European termite Kalotermes flavicollis is here studied through the analysis of mitochondrial (303 bp of control region and 912 bp of COI/tRNALeu/COII) and nuclear (five microsatellite and 20 Inter-SINE loci) markers on 18 colonies collected in Southern France, Corsica, Sardinia, peninsular Italy, the Balkans and Greece. Different statistical analyses (Bayesian phylogenetic analysis, parsimony network, F-statistics, PCA) were performed. Mitochondrial sequences produced an unresolved polytomy including samples from peninsular Italy, Balkans and Greece, and three main clades: southern France, Corsica-Sardinia and Portoscuso (SW Sardinia). Nuclear markers confirm these data, further highlighting a more significant divergence at the regional scale. The results obtained for the peri-Tyrrhenian area agree with major paleogeographic and paleoclimatic events that shaped the biodiversity of the local fauna. K. flavicollis biodiversity and its phylogeographic pattern are also evaluated in the light of the data available for the other native European termite taxon (genus Reticulitermes), in order to produce a more complete scenario of the Mediterranean. In the area comprised between southern France and Italy, the degree of diversity is similar; however, in the eastern area, while K. flavicollis is differentiated only at the population level, the genus Reticulitermes comprises at least six entities of specific and/or subspecific level. This discrepancy may be explained by taking into account the different evolutionary histories of the two taxa.
Reducing the Risk at Community Banks : Is It Size or Geographic Diversification that Matters ?

Most community banks face relatively high levels of credit risk because they have relatively few loan customers (idiosyncratic risk) and are not geographically diversified (local market risk). We focus on merger strategies that community banks might pursue to improve their risk-return tradeoff, identifying in the process which type of risk is more important. We find that the greatest risk-reduction benefits are achieved by increasing a community bank’s size, regardless of where the merger partner is located. We interpret this result as evidence that idiosyncratic risk dominates local market risk, especially at rural banks. Community banks face enormous pressure to grow, yet the pressure to geographically diversify is limited. As a consequence, larger community banks are likely to replace smaller community banks, but their focus on relationship lending will not disappear. Banks will be able to serve the businesses and households in their communities without being forced to acquire and manage offices distant from their community roots. JEL Code: G1, G2
Prenatally Fabricated Autologous Human Living Heart Valves Based on Amniotic Fluid–Derived Progenitor Cells as Single Cell Source

Background— A novel concept providing prenatally tissue engineered human autologous heart valves based on routinely obtained fetal amniotic fluid progenitors as single cell source is introduced. Methods and Results— Fetal human amniotic progenitors were isolated from routinely sampled amniotic fluid and sorted using CD133 magnetic beads. After expansion and differentiation, cell phenotypes of CD133− and CD133+ cells were analyzed by immunohistochemistry and flowcytometry. After characterization, CD133− derived cells were seeded onto heart valve leaflet scaffolds (n=18) fabricated from rapidly biodegradable polymers, conditioned in a pulse duplicator system, and subsequently coated with CD133+ derived cells. After in vitro maturation, opening and closing behavior of leaflets was investigated. Neo-tissues were analyzed by histology, immunohistochemistry, and scanning electron microscopy (SEM). Extracellular matrix (ECM) elements and cell numbers were quantified biochemically. Mechanical properties were assessed by tensile testing. CD133− derived cells demonstrated characteristics of mesenchymal progenitors expressing CD44 and CD105. Differentiated CD133+ cells showed features of functional endothelial cells by eNOS and CD141 expression. Engineered heart valve leaflets demonstrated endothelialized tissue formation with production of ECM elements (GAG 80%, HYP 5%, cell number 100% of native values). SEM showed intact endothelial surfaces. Opening and closing behavior was sufficient under half of systemic conditions. Conclusions— The use of amniotic fluid as single cell source is a promising low-risk approach enabling the prenatal fabrication of heart valves ready to use at birth. These living replacements with the potential of growth, remodeling, and regeneration may realize the early repair of congenital malformations.