Miracle-dz/UniFAR-FTUs huggingface dataset:
Taxonomic Status, Phylogenetic Affinities and Genetic Diversity of a Presumed Extinct Genus, Paraisometrum W.T. Wang (Gesneriaceae) from the Karst Regions of Southwest China

Background The karst regions in South China have an abundance of endemic plants that face high extinction risks. The Chinese Gesneriaceae endemic Paraisometrum mileense ( = Oreocharis mileensis), was presumed extinct for 100 years. After its re-discovery, the species has become one of five key plants selected by the Chinese forestry government to establish a new conservation category for plants with extremely small populations. For conservation purposes, we studied the phylogenetic and population genetic status of P. mileense at the three only known localities in Guangxi, Guizhou and Yunnan. Methodology/Principal Findings We collected 64 samples (52 species) of Oreocharis and 8 samples from three provinces of P. mileense and generated molecular phylogenies, and inferred that P. mileense represents a relatively isolated and derived taxonomic unit within Oreocharis. Phylogeographic results of 104 samples of 12 populations of P. mileense indicated that the populations in Yunnan have derived from those in Guangxi and Guizhou. Based on AFLP data, the populations were found to harbor low levels of genetic diversity (He = 0.118), with no apparent gradient across the species’ range, a restricted gene flow and significant isolation-by-distance with limited genetic differentiation among the populations across the three provinces (F ST = 0.207, P<0.001). The 10 populations in Yunnan were found to represent two distinct lineages residing at different altitudes and distances from villages. Conclusion/Significance The low levels of genetic diversity found in P. mileense are perhaps a consequence of severe bottlenecks in the recent past. The distribution of the genetic diversity suggests that all populations are significant for conservation. Current in situ and ex situ measures are discussed. Further conservation actions are apparently needed to fully safeguard this conservation flagship species. Our work provides a model of an integrated study for the numerous endemic species in the karst regions with extremely small populations.
Diarrhea-Associated Hospitalizations Among US Children Over 2 Rotavirus Seasons After Vaccine Introduction

OBJECTIVE: After implementation of rotavirus vaccination in 2006, large decreases in rates of severe diarrhea among US children occurred in 2007–2008. We ascertained whether these decreases were sustained in 2008–2009. METHODS: We examined hospital discharge data from a national network of pediatric hospitals and compared all-cause diarrhea-related and rotavirus-specific hospitalizations in 3 prevaccine rotavirus seasons (2003–2006) with those in 2 postvaccine seasons (2007–2008 and 2008–2009) among children <5 years of age. We defined rotavirus seasons using data from a national laboratory surveillance network. RESULTS: At 62 consistently reporting hospitals, a median of 15 645 diarrhea-related hospitalizations (range: 14 881–16 884 hospitalizations) occurred each rotavirus season among children <5 years of age in 2003–2006. Compared with this median, all-cause diarrhea-related hospitalizations decreased by 50% (n = 7760) in 2007–2008 and by 29% (n = 11 039) in 2008–2009. In 2007–2008, reductions of 47% to 55% were seen for all age groups, including vaccine-ineligible children ≥2 years of age (48%). In 2008–2009, these reductions decreased in magnitude, especially among children ≥2 years of age (17%). Decreases in 2007–2008 and 2008–2009 were similar in the Northeast and West, but decreases were smaller in 2008–2009, compared with 2007–2008, in the Midwest and South. CONCLUSIONS: Compared with prevaccine seasons, decreases in diarrhea- and rotavirus-associated hospitalizations seen in 2007–2008 were sustained in 2008–2009 but were somewhat smaller. Given the variability in diarrhea-related hospitalization trends over the 2 postvaccine seasons according to age group and region, continued surveillance is required for full assessment of the impact of rotavirus vaccination.
Variation in natural selection for growth and phlorotannins in the brown alga Fucus vesiculosus

Directional selection for plant traits associated with resistance to herbivory tends to eliminate genetic variation in such traits. On the other hand, balancing selection arising from trade‐offs between resistance and growth or spatially variable selection acts against the elimination of genetic variation. We explore both the amount of genetic variation and variability of natural selection for growth and concentration of phenolic secondary compounds, phlorotannins, in the brown alga Fucus vesiculosus. We measured variation in selection at two growing depths and two levels of nutrient availability in algae that had faced two kinds of past growing environments. Genetic variation was low for growth but high for phlorotannins. The form and strength of selection for both focal traits depended on the past growing environment of the algae. We found strong directional selection for growth rate in algae previously subjected to higher ultraviolet radiation, but not in algae previously subjected to higher nutrient availability. Stabilizing selection for growth occurred especially in the deep growing environment. Selection for phlorotannins was generally weak, but in some past‐environment–current‐environment combinations we detected either directional selection against phlorotannins or stabilizing selection. Thus, phlorotannins are not selectively neutral but affect the fitness of F. vesiculosus. In particular, there may be a fitness cost of producing phlorotannins, but the realization of such a cost varies from one environment to another. Genetic correlations between selective environments were high for growth but nonexistent for phlorotannins, emphasizing the high phenotypic plasticity of phlorotannin production. The highly heterogeneous selection, including directional, stabilizing, and spatially variable selection as well as temporal change in selection due to responses to past environmental conditions, probably maintains a high amount of genetic variation in phlorotannins. Such variation provides the potential for rapid evolutionary response of phlorotannins under directional selection.
Antimicrobial polypeptides in host defense of the respiratory tract.

The large surfaces of the respiratory tract are often the initial site of contact between microbes and their human hosts. Respiratory epithelia are coated with a thin layer of airway and alveolar secretions whose composition varies by anatomical location and in response to mechanical, chemical, and microbial stimulation. In the nose, trachea, and bronchi, the secretions are generated by airway epithelial cells, especially the goblet cells; by the submucosal glands; by transudation and transport of proteins from plasma; and by resident and recruited phagocytes — neutrophils, eosinophils, monocytes, and macrophages. In the distal airways and alveoli, Clara cells and type 2 alveolar cells are, respectively, the predominant secretory epithelial cells. As first described by Alexander Fleming nearly 80 years ago (1), respiratory secretions have microbicidal and microbistatic properties mediated by their constituent antimicrobial polypeptides. These intrinsic antimicrobial properties of respiratory secretions act in concert with the mechanical and phagocytic clearance mechanisms, described elsewhere in this Perspective series, to defend the respiratory tract against colonization or invasion by environmental microbes.
Antimicrobial resistance in swine production

Abstract Large amounts of antimicrobial agents are still being used in modern swine production in many countries around the world. This facilitates the emergence and development of antimicrobial resistance. Bacteria causing infections in swine have in several cases acquired resistance to a number of the agents most commonly used for treatment, making it difficult to predict the efficacy of different antimicrobial agents without prior susceptibility testing. This review gives an overview of recent susceptibility data from different parts of the world and discusses the importance of the development of resistance not only in the treatment of infections in swine but also taking into account the human health implications of antimicrobial resistance.
Protamine ratio and the level of histone retention in sperm selected from a density gradient preparation

Fertile males express two forms of sperm nuclear proteins, protamine 1 (P1) and protamine 2 (P2), in roughly equal quantities, whereas some infertile men have been shown to have a reduction in protamine content and an increase in the level of histones retained in mature sperm. In this study, we assessed histone and protamine levels in spermatozoa isolated from different layers of a density gradient centrifugation column to evaluate the nuclear protein content of the sperm population selected. Protamine levels were measured using acid gel electrophoresis and immunofluorescence, and the percentage of cells retaining histones was evaluated using aniline staining and immunofluorescence. Our data suggests that there is an inverse correlation between P1/P2 ratio and the level of histone expression in the different layers of the density gradient. Paradoxically, the 90% layer had a lower P1/P2 ratio, which corresponded with an increase in histone expression. It is concluded that although the sperm population selected in the 90% layer of the density gradient columns had a lower P1/P2 ratio, it was yet similar to the P1/P2 ratio observed in previously screened fertile donors.
Spatiotemporal Stochastic Modeling of IoT Enabled Cellular Networks: Scalability and Stability Analysis

The Internet of Things (IoT) is large scale by nature, which is manifested by the massive number of connected devices as well as their vast spatial existence. Cellular networks, which provide ubiquitous, reliable, and efficient wireless access, will play fundamental rule in delivering the first-mile access for the data tsunami to be generated by the IoT. However, cellular networks may have scalability problems to provide uplink connectivity to massive numbers of connected things. To characterize the scalability of cellular uplink in the context of IoT networks, this paper develops a traffic-aware spatiotemporal mathematical model for IoT devices supported by cellular uplink connectivity. The developed model is based on stochastic geometry and queueing theory to account for the traffic requirement per IoT device, the different transmission strategies, and the mutual interference between the IoT devices. To this end, the developed model is utilized to characterize the extent to which cellular networks can accommodate IoT traffic as well as to assess and compare three different transmission strategies that incorporate a combination of transmission persistency, backoff, and power-ramping. The analysis and the results clearly illustrate the scalability problem imposed by IoT on cellular network and offer insights into effective scenarios for each transmission strategy.
Patterns of referral and examination for retinopathy in pregnant women with diabetes by primary care physicians.

PURPOSE Family practice (FP), General Practice (GP) and obstetrics-gynecology (OB/GYN) physicians were surveyed to determine whether they routinely referred pregnant patients with diabetes to an ophthalmologist, looked into the patient's eyes to screen for retinopathy, and dilated the eyes for fundi examination. METHODS Hospitals providing obstetrical services were contacted to identify primary-care physicians. Physicians identified as having obstetrical privileges were surveyed by mail to determine if they were actively providing obstetrical care. Physicians who provided both obstetrical and diabetes care were mailed a survey. RESULTS Of 668 physicians surveyed, 429 responded: 224 FPS, 184 OB/GYNS and 21 GPS. A relatively small percentage (27%) of physicians in both groups routinely refer all of their pregnant patients with pre-existing diabetes to an ophthalmologist. Family practice physicians were more likely to perform an eye exam to screen for retinopathy in patients with both pre-existing and gestational diabetes than OB/GYNS (p < .0005). Only 11% of FPS and no OB/GYNS reported that they dilated the eyes when performing a fundus examination (p = .04). CONCLUSION The physicians surveyed under-utilize recommended strategies for eye care of pregnant women with pre-existing diabetes. Based upon these results, we call for a recommitment to partnership of primary-care physicians and ophthalmologists in the detection and treatment of diabetic retinopathy during pregnancy.
Tissue Compartment Analysis for Biomarker Discovery by Gene Expression Profiling

Background Although high throughput technologies for gene profiling are reliable tools, sample/tissue heterogeneity limits their outcomes when applied to identify molecular markers. Indeed, inter-sample differences in cell composition contribute to scatter the data, preventing detection of small but relevant changes in gene expression level. To date, attempts to circumvent this difficulty were based on isolation of the different cell structures constituting biological samples. As an alternate approach, we developed a tissue compartment analysis (TCA) method to assess the cell composition of tissue samples, and applied it to standardize data and to identify biomarkers. Methodology/Principal Findings TCA is based on the comparison of mRNA expression levels of specific markers of the different constitutive structures in pure isolated structures, on the one hand, and in the whole sample on the other. TCA method was here developed with human kidney samples, as an example of highly heterogeneous organ. It was validated by comparison of the data with those obtained by histo-morphometry. TCA demonstrated the extreme variety of composition of kidney samples, with abundance of specific structures varying from 5 to 95% of the whole sample. TCA permitted to accurately standardize gene expression level amongst >100 kidney biopsies, and to identify otherwise imperceptible molecular disease markers. Conclusions/Significance Because TCA does not require specific preparation of sample, it can be applied to all existing tissue or cDNA libraries or to published data sets, inasmuch specific operational compartments markers are available. In human, where the small size of tissue samples collected in clinical practice accounts for high structural diversity, TCA is well suited for the identification of molecular markers of diseases, and the follow up of identified markers in single patients for diagnosis/prognosis and evaluation of therapy efficiency. In laboratory animals, TCA will interestingly be applied to central nervous system where tissue heterogeneity is a limiting factor.
Characteristics of RIE SF6/O2/Ar Plasmas on n-Silicon Etching

In this work, highly anisotropic Si plasma etching process has been developed in reactive ion etching (RIE) reactor. The etch chemistry utilized consists of a mixture of sulphur tetra fluoride (SF6), oxygen (02) and argon (Ar). The use of nickel as masks was successfully patterned on Si by lift-off. Lines of 50 mum feature size were patterned on Si, resulting in perpendicular sidewalls and no observable undercutting. Etch rates were studied for gas compositions of SF6/O2/Ar, chamber pressures and DC bias. For chamber pressure in the range of 5 mTorr to 20 mTorr, the etch rates is found to increase with increasing dc bias, attaining a maximum rate of 2997 A/min at 20 mTorr. Surface morphology after etching is checked by atomic force microscopy and scanning electron microscopy, which show that the anisotropic of the etched surface and the smoothness of the etched surface is comparable to that of the etched.
Coordinated Pricing and Inventory in A System with Minimum and Maximum Production Constraints

Most inventory researches assume that the production level can be fluctuated arbitrarily. However, in many firms, large fluctuation in production levels may be very costly. This paper addresses the coordinated pricing and inventory control problem in a smoothing production system, in which the production level is constrained between a maximum and a minimum level in each period and the price can be adjusted dynamically. We show that the optimal policy is modifiedmodified base stock list price policy.
The effects of the psychiatric label 'borderline personality disorder' on nursing staff's perceptions and causal attributions for challenging behaviours.

OBJECTIVES The aim of the study was to investigate how the psychiatric label 'borderline personality disorder' (BPD) affected staff's perceptions and causal attributions about patients' behaviour. METHODS AND DESIGN The study utilized a within-participants questionnaire methodology and participants comprised qualified mental health nursing staff. The questionnaire contained descriptions of challenging behaviour in which the patient was described with a diagnosis of depression, schizophrenia or BPD. Participants were asked to identify a likely cause of the behaviour and then on a Likert-type scale rate attributions of internality, stability, globality and controllability. In addition they recorded their level of sympathy with the patient and their optimism for change. RESULTS Patients with a label of BPD attracted more negative responses from staff than those with a label of schizophrenia or depression. Causes of their negative behaviour were rated as more stable and they were thought to be more in control of the causes of the behaviour and the behaviour itself. Staff reported less sympathy and optimism towards patients with a diagnosis of BPD and rated their personal experiences as more negative than their experiences of working with patients with a diagnosis of depression or schizophrenia. CONCLUSIONS Staff regard patients with a BPD label to be more in control of negative behaviour than patients with a label of schizophrenia or depression. In accord with Weiner's (1985) model, attributions of control were inversely related to staff sympathy. Addressing attributions of control may provide a means to modify staff sympathy towards patients with a diagnosis of BPD and counteract their negative experiences.
Oxidation of Bilirubin Produces Compounds that Cause Prolonged Vasospasm of Rat Cerebral Vessels: A Contributor to Subarachnoid Hemorrhage–Induced Vasospasm

The authors have previously shown that bilirubin-oxidation products (BOXes) are present in CSF of subarachnoid hemorrhage patients with vasospasm, and that BOXes cause vasoconstriction in vitro. This study determined whether BOXes cause vasospasm in vivo. Identical volumes of either lysed blood or standardized amounts of BOXes were injected into the cisterna magna of adult rats. BOX injections caused 6 of 10 rats to die within 10 minutes, whereas 12 of 12 rats survived for 24 hours after blood injections. The mechanism for this significant (P ⩽ 0.01) increase in mortality was unclear. To directly test whether BOXes produced vasospasm, a cranial window technique was used. Application of 20 μL of 10-μmol/L bilirubin had little effect on the vessels. However, application of BOXes produced marked, dose-dependent small artery and arteriole vasospasm that approached a 90% decrease in diameter by 40 minutes after application in some vessels, and persisted for at least 24 hours. To determine if BOX-mediated vasospasm led to cortical injury, histology and immunocytochemistry were performed on animals that survived for 24 hours. There was a BOX-related stress protein response for HSP25 and HSP32 (HO-1) without evidence of infarction. The finding that the BOXes produce vasospasm of cerebral vessels in vivo, in conjunction with BOXes being found in CSF of vasospasm patients, supports our hypothesis that BOXes contribute to or cause cerebral vasospasm after subarachnoid hemorrhage.
Effectiveness of treatment with oral paricalcitol in patients on peritoneal dialysis: a Spanish multicenter study.

AIMS Recently, oral form of paricalcitol has allowed extension of treatment to ambulatory patients on peritoneal dialysis but few data have been published about the benefits of paricalcitol in this subgroup. A multicenter, retrospective study was carried out to increase current knowledge on the effectiveness and safety of paricalcitol in 162 peritoneal dialyzed patients with secondary hyperparathyroidism. METHODS Case histories of patients treated with paricalcitol for at least 6 months were reviewed to extract data on 12 biochemical parameters related to bone disease and health status. Changes in these parameters were described. Doses of paricalcitol and other concomitant treatments were evaluated at least every 3 months. RESULTS 99 men (61.1%) and 63 women (38.9%) with an average age of 62.07 years were included. PTH levels showed an acute decrease in the three first months (35.88%) and a global decrease at month 6 of 42.39%. A slight increase in calcium was observed (p < 0.001) but it remained between normal range values. Only 5 patients presented serum calcium over 10.2 in two consecutive measurements. No changes were found in phosphorus, calcium-phosphorus product, hemoglobin, alkaline phosphatase, GGT, albumin, PCR inflammatory markers, pH and bicarbonate. The decrease in proteinuria levels was nearly statistically significant (p = 0.061). Only 6 patients (0.36%) abandoned the treatment. CONCLUSIONS Paricalcitol therapy was well tolerated with a high effectiveness in patients on peritoneal dialysis. A slight increase in serum calcium levels was observed, although within normal ranges. No changes in other biochemical parameters related to bone disease could be associated to paricalcitol with data compiled in our study. Paricalcitol seems to have a protective effect on proteinuria levels.
Cellular Mechanisms of Long-Lasting Adaptation in Visual Cortical Neurons In Vitro

The cellular mechanisms of spike-frequency adaptation during prolonged discharges and of the slow afterhyperpolarization (AHP) that follows, as occur in vivo with contrast adaptation, were investigated with intracellular recordings of cortical neurons in slices of ferret primary visual cortex. Intracellular injection of 2 Hz sinusoidal or constant currents for 20 sec resulted in a slow (τ = 1–10 sec) spike-frequency adaptation, the degree of which varied widely among neurons. Reducing either [Ca2+]o or [Na+]o reduced the rate of spike-frequency adaptation. After the prolonged discharge was a slow (12–75 sec) AHP that was associated with an increase in membrane conductance and a rightward shift in the discharge frequency versus injected current relationship. The reversal potential of the slow AHP was sensitive to changes in [K+]o, indicating that it was mediated by a K+ current. Blockade of transmembrane Ca2+ conductances did not reduce the slow AHP. In contrast, reductions of [Na+]o reduced the slow AHP, even in the presence of pronounced Ca2+ spikes. We suggest that the activation of Na+-activated and Ca2+-activated K+ currents plays an important role in prolonged spike-frequency adaptation and therefore may contribute to contrast adaptation and other forms of adaptation in the visual system in vivo.