Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamics and ecological consequences of avian influenza virus infection in greater white-fronted geese in their winter staging areas

Recent outbreaks of highly pathogenic avian influenza (HPAI) in poultry have raised interest in the interplay between avian influenza (AI) viruses and their wild hosts. Studies linking virus ecology to host ecology are still scarce, particularly for non-duck species. Here, we link capture–resighting data of greater white-fronted geese Anser albifrons albifrons with the AI virus infection data collected during capture in The Netherlands in four consecutive winters. We ask what factors are related to AI virus prevalence and whether there are ecological consequences associated with AI virus infection in staging white-fronted geese. Mean seasonal (low pathogenic) AI virus prevalence ranged between 2.5 and 10.7 per cent, among the highest reported values for non-duck species, and occurred in distinct peaks with near-zero prevalence before and after. Throat samples had a 2.4 times higher detection frequency than cloacal samples. AI virus infection was significantly related to age and body mass in some but not other winters. AI virus infection was not related to resighting probability, nor to maximum distance travelled, which was at least 191 km during the short infectious lifespan of an AI virus. Our results suggest that transmission via the respiratory route could be an important transmission route of AI virus in this species. Near-zero prevalence upon arrival on their wintering grounds, in combination with the epidemic nature of AI virus infections in white-fronted geese, suggests that white-fronted geese are not likely to disperse Asian AI viruses from their Siberian breeding grounds to their European wintering areas.
Allocating Roadside Units in VANETs Using a Variable Neighborhood Search Strategy

In this work, we propose a GRASP+VNS algorithm for solving the allocation of Roadside Units (RSUs) in a Vehicular Network. Our main objective is to find the minimum set of RSUs to meet a Deployment Delta (ρ1,ρ2). The Deployment Delta (ρ1,ρ2) is a metric for specifying minimal communication guarantees from the infrastructure supporting the Vehicular Network. We compare GRASP+VNS to some baseline algorithms: (i) Delta-g; (ii) Delta-r and, (iii) the optimal value. Our results demonstrate that our approach requires up to 90% less Roadside Units to meet the QoS required by Deployment Delta (ρ1,ρ2) metric. Besides, different from the baseline algorithms, our approach find results that differ no more than 17% from the optimal values for all tested instances.
Understanding the challenges of COPD diagnosis and treatment Table 4 Differential treatment of chronic obstructive pulmonary disease and asthma Treatment COPD Asthma Smoking cessation

Correspondence: Len Fromer David Geffen School of Medicine at UCLA, 15525 Hamner Drive, Los Angeles, CA 90077, USA Tel +1 310 383 8168 Fax +1 310 471 5392 email mdwelby@aol.com Abstract: Chronic obstructive pulmonary disease (COPD) is characterized by airflow obstruction that is not fully reversible; symptoms include chronic cough, sputum production, and dyspnea with exertion. An estimated 50% of the 24 million adults in the USA who have COPD are thought to be misdiagnosed or undiagnosed. Factors contributing to this include a low awareness of COPD and the initial symptoms of the disease among the general population, acceptance of these symptoms as a consequence of aging or smoking, some symptomatic similarity to asthma, and failure of health care personnel to use spirometry for diagnosis. Increased familiarization with COPD diagnosis and treatment guidelines, and proactive identification of patients with increased risk of developing COPD through occupational, environmental, or lifestyle exposures, will assist in a timely, accurate diagnosis and effective treatment, which will consequently improve patient outcomes. This review addresses the issues surrounding the diagnosis and misdiagnosis of COPD, their consequences, and how COPD can be better managed within primary care, including consideration of COPD care in patient-centered medical home and chronic care models.
Machine learning in molecular classification

Chemical and biological research is facilitated by big data repositories of chemical compounds from ultra-high-throughput screening techniques, where large numbers of molecules are tested and classified based on their activities against given target. With the increasing availability of data, it is quite necessary to develop accurate and robust models to predict chemical and biological properties of novel molecules based on their structural representations of different dimensions. In this report, we will briefly review literatures of several machine learning approaches on molecular classification problem. These approaches include mining statistically significant molecular substructures, graph walk kernel, and molecular fingerprints. We will focus on recently developed methodology of mining statistically significant molecular substructures. Then, we will propose our novel method which we call atom properties enrichment kernel. The new method can incorporate huge amount of atom level properties. Finally, we will give experimental results of these methods by applying them on standard datasets.
Flare and change of psoriasis morphology during the course of treatment with tumour necrosis factor blockers

Tumour necrosis factor (TNF) blockers represent an exciting advance in the management of psoriasis. However, the safety profile of these drugs is not completely established. We present a review of the literature, and report on eight patients: two with the unexpected appearance of psoriasis, and the remaining six with exacerbation and change in morphology of their existing psoriasis, all of which occurred during treatment with the TNF blockers adalimumab, etanercept and infliximab. The two new cases, neither of whom had any personal or family history of psoriasis, developed pustular psoriasis on the palms and/or soles. The other six patients, previously diagnosed with severe chronic plaque psoriasis (four patients), generalized pustular psoriasis (one) and erythrodermic psoriasis (one), developed eruptive guttate psoriasis between 15 days and 18 months after the beginning of therapy. These patients had never before presented guttate‐type psoriatic lesions, and the lesions appeared in areas of the body that were free of psoriatic plaques at baseline.
A Heptosyltransferase Mutant of Pasteurella multocida Produces a Truncated Lipopolysaccharide Structure and Is Attenuated in Virulence

ABSTRACT Pasteurella multocida is the causative agent of fowl cholera in birds. In a previous study using signature-tagged mutagenesis, we identified a mutant, AL251, which was attenuated for virulence in mice and in the natural chicken host. Sequence analysis indicated that AL251 had an insertional inactivation of the gene waaQPM, encoding a putative heptosyl transferase, required for the addition of heptose to lipopolysaccharide (LPS) (M. Harper, J. D. Boyce, I. W. Wilkie, and B. Adler, Infect. Immun. 71:5440-5446, 2003). In the present study, using mass spectrometry and nuclear magnetic resonance, we have confirmed the identity of the enzyme encoded by waaQPM as a heptosyl transferase III and demonstrated that the predominant LPS glycoforms isolated from this mutant are severely truncated. Complementation experiments demonstrated that providing a functional waaQPM gene in trans can restore both the LPS to its full length and growth in mice to wild-type levels. Furthermore, we have shown that mutant AL251 is unable to cause fowl cholera in chickens and that the attenuation observed is not due to increased serum sensitivity.
The sixth and seventh cholera pandemics are due to independent clones separately derived from environmental, nontoxigenic, non-O1 Vibrio cholerae

The DNA sequences of the asd genes from 45 isolates of Vibrio cholerae (19 clinical O1 isolates, 2 environmental nontoxigenic O1 isolates, and 24 isolates with different non-O1 antigens) were determined. No differences were found within either sixth- or seventh-pandemic isolates; however, variation was found between the two forms and among the non-O1 isolates. O139 isolates had sequences identical to those of seventh-pandemic isolates. Phylogenetic trees with Vibrio mimicus as the outgroup suggest that the sixth-pandemic, seventh-pandemic, and U.S. Gulf isolates are three clones that have evolved independently from different lineages of environmental, nontoxigenic, non-O1 V. cholerae isolates. There is evidence for horizontal transfer of O antigen, since isolates with nearly identical asd sequences had different O antigens, and isolates with the O1 antigen did not cluster together but were found in different lineages. We also found evidence for recombination events within the asd gene of V. cholerae. V. cholerae may have a higher level of genetic exchange and a lower level of clonality than species such as Salmonella enterica and Escherichia coli.
Shotgun Proteomic Analysis of Plasma from Dairy Cattle Suffering from Footrot: Characterization of Potential Disease-Associated Factors

The plasma proteome of healthy dairy cattle and those with footrot was investigated using a shotgun LC-MS/MS approach. In total, 648 proteins were identified in healthy plasma samples, of which 234 were non-redundant proteins and 123 were high-confidence proteins; 712 proteins were identified from footrot plasma samples, of which 272 were non-redundant proteins and 138 were high-confidence proteins. The high-confidence proteins showed significant differences between healthy and footrot plasma samples in molecular weight, isoelectric points and the Gene Ontology categories. 22 proteins were found that may differentiate between the two sets of plasma proteins, of which 16 potential differential expression (PDE) proteins from footrot plasma involved in immunoglobulins, innate immune recognition molecules, acute phase proteins, regulatory proteins, and cell adhesion and cytoskeletal proteins; 6 PDE proteins from healthy plasma involved in regulatory proteins, cytoskeletal proteins and coagulation factors. Of these PDE proteins, haptoglobin, SERPINA10 protein, afamin precursor, haptoglobin precursor, apolipoprotein D, predicted peptidoglycan recognition protein L (PGRP-L) and keratan sulfate proteoglycan (KS-PG) were suggested to be potential footrot-associated factors. The PDE proteins PGRP-L and KS-PG were highlighted as potential biomarkers of footrot in cattle. The resulting protein lists and potential differentially expressed proteins may provide valuable information to increase understanding of plasma protein profiles in cattle and to assist studies of footrot-associated factors.
View Synthesis from Image and Video for Object Recognition Applications

Object recognition is one of the most important and successful applications in computer vision community. The varying appearances of the test object due to different poses or illumination conditions can make the object recognition problem very challenging. Using view synthesis techniques to generate pose-invariant or illumination-invariant images or videos of the test object is an appealing approach to alleviate the degrading recognition performance due to non-canonical views or lighting conditions. In this thesis, we first present a complete framework for better synthesis and understanding of the human pose from a limited number of available silhouette images. Pose-normalized silhouette images are generated using an active virtual camera and an image based visual hull technique, with the silhouette turning function distance being used as the pose similarity measurement. In order to overcome the inability of the shape from silhouettes method to reconstruct concave regions for human postures, a view synthesis algorithm is proposed for articulating humans using visual hull and contour-based body part segmentation. These two components improve each other for better performance through the correspondence across viewpoints built via the inner distance shape context measurement. Face recognition under varying pose is a challenging problem, especially when illumination variations are also present. We propose two algorithms to address this scenario. For a single light source, we demonstrate a pose-normalized face synthesis approach on a pixel-by-pixel basis from a single view by exploiting the bilateral symmetry of the human face. For more complicated illumination condition, the spherical harmonic representation is extended to encode pose information. An efficient method is proposed for robust face synthesis and recognition with a very compact training set. Finally, we present an end-to-end moving object verification system for airborne video, wherein a homography based view synthesis algorithm is used to simultaneously handle the object's changes in aspect angle, depression angle, and resolution. Efficient integration of spatial and temporal model matching assures the robustness of the verification step. As a byproduct, a robust two camera tracking method using homography is also proposed and demonstrated using challenging surveillance video sequences.
Impact of Coal Mine Dump Contaminated Soils on Elemental Uptake by Spinacia Oleracea (Spinach)

The elemental uptake and the growth response of Spinacia oleracea (spinach) to the soil contaminated with the South African bituminous coal mine dump soil, viz. 0%, 5%, 15%, and 25% w/w, was investigated. The contaminated soils were analyzed for pH, cation exchange capacity (CEC), soil organic matter (SOM), and concentrations of selected heavy metals. The pH, SOM, and CEC decreased with an increase in contamination indicating the acidic nature of coal mine soil and the raise in the soil binding sites. The distribution of Fe, Mn, Ni, Cd, and Pb in the in roots and leaves of the plants was determined in two stages of plant growth. Spinach showed high accumulation of Fe and increased levels of Ni and Cd with an increase in contamination. No plant growth was recorded with 25% contamination.
Two-Vector-Based Model Predictive Torque Control Without Weighting Factors for Induction Motor Drives

Conventional model predictive torque control (MPTC) suffers from weighing factor tuning work and relatively high torque ripple, due to the different units of torque and stator flux and the limited number of voltage vectors. This paper proposes an improved MPTC without the use of weighting factor. The torque and flux magnitude references are converted into an equivalent reference vector of stator flux, hence eliminating the weighting factor of stator flux in conventional MPTC. Furthermore, two voltage vectors are applied during one control period to achieve better steady-state performance. Different from prior method using an active vector and a zero vector, the selected voltage vectors may be two nonzero vectors in the proposed method, which provides more opportunities to reduce both torque and flux ripples. The durations of the selected voltage vectors are determined based on the principle of stator flux error minimization. Both simulation and experimental results are presented to validate the effectiveness of the proposed method.
Aggressive Epstein-Barr Virus-Associated, CD8+, CD30+, CD56+, Surface CD3−, Natural Killer (NK)-Like Cytotoxic T-Cell Lymphoma

We report an unusual case of aggressive natural killer (NK)-like cytotoxic T-cell lymphoma in a previously healthy immunocompetent West African male. He presented with a fever of unknown origin, subsequently developed erythematous skin nodules, generalized lymphadenopathy, and hepatosplenomegaly, and then died of multiple organ failure. A skin nodule and lymph node biopsy showed an infiltrate of pleomorphic atypical medium and large lymphoid cells with extensive necrosis and prominent apoptosis. Peripheral blood and ascites also harbored these cells, with cytology revealing irregular nuclear folding and basophilic cytoplasm, and some with azurophilic cytoplasmic granules. Flow cytometry and immunohistochemistry demonstrated the expression of CD2, CD7, CD8, CD30, CD56, and cytoplasmic but not surface CD3. In situ hybridization demonstrated Epstein-Barr virus transcripts. A monoclonal T-cell receptor &ggr; chain gene rearrangement was detected by polymerase chain reaction. This is the first reported case of an NK-like T-cell lymphoma with these unusual features, making precise classification difficult. Some features suggest an NK1.1 or NKT lymphocyte origin. Because the earliest clinical manifestation was splenomegaly and abnormal liver function, the normal cellular counterpart may be a distinct subset of NK1.1 cells normally present in hepatosplenic sinusoids. This tumor disseminated early and pursued a fulminant clinical course, thus emphasizing the importance of early recognition and diagnosis.
Disinhibition from opioid influence augments hypothalamic neuropeptide Y (NPY) gene expression and pituitary luteinizing hormone release: effects of NPY messenger ribonucleic acid antisense oligodeoxynucleotides.

It is well known that hypothalamic endogenous opioid peptides (EOP) exert an inhibitory influence on LH release, and that a restraint on this inhibitory tone triggers preovulatory LHRH and LH hypersecretion. Recent evidence suggests that hypothalamic neuropeptide Y (NPY) is an important component of the neural circuitry that participates in induction of the LH surge. We have reported previously that blockade of EOP influence by the opioid receptor antagonist, naloxone (NAL), stimulated NPY accumulation in the median eminence (ME) in association with increased LH release in estradiol-17 beta-primed ovariectomized rats. To evaluate whether a restraint on the EOP system will result in an increase in NPY synthesis, the effects of NAL infusion on preproNPY messenger RNA (mRNA) levels in the medial basal hypothalamus were studied by solution hybridization/RNase protection assay and by in situ hybridization. NAL (2 mg/0.6 ml.h) or saline (SAL, 0.6 ml/h) was infused for 3 h (1100-1400 h) via an intrajugular cannula in estradiol-17 beta-primed ovariectomized rats. In accord with previous studies, NAL infusion significantly increased plasma LH levels at 1400 h. concomitant with this activation of LH release, NPY gene expression was also augmented. As compared with initial control levels at 1100 h, preproNPY mRNA levels in the medial basal hypothalamus increased at 1400 h in SAL (106%)- and NAL (202%)-infused rats, and at this time, preproNPY mRNA levels were significantly higher in NAL-infused rats than in SAL-infused rats. In situ hybridization studies showed that NAL infusion significantly increased the preproNPY mRNA signal at 1400 h mainly in the rostral and middle regions of the arcuate nucleus (ARC) as compared with that seen at 1100 and 1400 h in SAL-infused rats. To examine further the relationship between the NAL-induced increase in LH release and increase in NPY gene expression, the effects of NPY mRNA antisense oligonucleotides (oligos) on NPY levels in the ME-ARC and on plasma LH levels were studied in NAL-infused rats. In NAL-infused rats, intracerebroventricular administration of a NPY antisense oligo (25 micrograms/rat) at 1000, 1200, and 1300 h decreased NPY levels in the ME-ARC and blocked the increase in plasma LH levels at 1500 h, whereas control missense oligos had no effect. Collectively, these results show that a decrease in opioid influence rapidly augments NPY gene expression in a subpopulation of neurons in the ARC, and support the hypothesis that a disinhibition from opioid influence acutely promotes NPY synthesis and release, which is necessary for phasic LH discharge in rats.
High urinary bisphenol A concentrations in workers and possible laboratory abnormalities

Objectives Bisphenol A (BPA) is widely used in epoxy resins in China. There are few reports on the adverse health effects of occupational exposure to BPA. This study examined associations between urinary BPA concentrations in workers and laboratory parameters for health status. Methods Spot urine checks at the end shift on Friday were used for cross-sectional analysis of BPA concentrations, and blood or urinary markers of liver function, glucose homeostasis, thyroid function and cardiovascular diseases were measured. The 28 participants were workers in two semiautomatic epoxy resin factories. Results The average urinary BPA concentration was 55.73±5.48 ng/ml (geometric mean ± geometric SD) (range 5.56–1934.85 ng/ml). After adjusting for urine creatinine (Cr), it was 31.96±4.42 μg/g Cr (geometric mean ± geometric SD) (range 4.61–1253.69 μg/g Cr). BPA feeding operators showed the highest concentrations, over 10 times those of the crushing and packing and office workers. Higher BPA concentrations were associated with clinically abnormal concentrations of FT3, FT4, TT3, TT4, thyroid-stimulating hormone, glutamic-oxaloacetic transaminase and γ-glutamyl transferase. Workers with higher BPA concentrations showed higher FT3 concentrations (linear trend: p<0.001). Bivariate correlation tests for laboratory analytes within normal limits showed FT3 to be positively associated with logged BPA concentrations, r=0.57, p=0.002. FT4 was positively associated with lactate dehydrogenase, r=0.45, p=0.020, and insulin was positively associated with thyroid-stimulating hormone with r=0.57, p=0.009. Conclusions Higher occupational BPA exposure, reflected in urinary concentrations of BPA, may be associated with thyroid hormone disruption.
ACCESS TO CONTRACEPTIVE METHODS AND PREVALENCE OF USE

Summary Survey data on contraceptive use for about 80 countries are related to measures of contraceptive access, by method, from 1999 to 2009. Cross-tabulation and correlational methods are employed, with geographic comparisons and time trends. Total prevalence of use for five modern contraceptive methods correlates well to a variety of access measures. Greater access is also accompanied by a better balance among methods for both access and use. Sub-Saharan African countries show similar patterns though at lower levels. Improved access to multiple methods is consistently associated with higher levels of contraceptive use.
Effects of type of light on mouse circadian behaviour and stress levels

Light is the principal synchronizing environmental factor for the biological clock. Light quantity (intensity), and light quality (type of light source) can have different effects. The aim of this study was to determine the effects of the type of light experienced from the time of birth on mouse growth, circadian behaviour and stress levels. We raised pigmented and albino mice under 24 h light–dark cycles of either fluorescent or white light-emitting diode (LED) light source during the suckling stage, and the animals were then exposed to various light environments after weaning and their growth rate, locomotor activity and plasma corticosterone concentration were measured. We found that the type of light the animals were exposed to did not affect the animals’ growth rates or stress levels. However, we observed significant effects on the expression of the locomotor activity rhythm under low contrast light–dark cycles in pigmented mice, and under constant light in both albino and pigmented mice. These results highlight the importance of environmental light quality (light source) on circadian behavioural rhythms, and the need for close monitoring of light environments in animal facilities.