Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of a direct live count and an improved quantitative protargol stain (QPS) in determining abundance and cell volumes of pelagic freshwater protozoa

To compare the efficiency of 2 common methods in protozooplankton ecology the protozooplankton spring community of a mesotrophic prealpine lake was investigated. A direct live count and a routinely applicable modification of a quantitative protargol stain (QPS) were evaluated with respect to their reliability in determining and quantifying pelagic freshwater ciliates and heterotrophic and mixotrophic flagellates. Cell counts of most ciliate species from field samples as well as of cultures were not significantly different when estimated by the 2 methods. The QPS allowed for detailed ciliate identification even for species not determinable by the applied direct live observation. Consequently, 60% of all determined species from field samples were identified exclusively by means of the QPS. Both flagellate and ciliate cell volumes showed high and species-specific shrinkage after the QPS, thus underestimating calculations of cell volumes. After the QPS, aloricate ciliates shrank to less than 20% of their respective live volumes, whereas the armoured Colepsspetai did not shrink significantly. Thus, drawbacks in applying average conversion factors for cell volume calculations after the QPS are discussed. Total heterotrophic and mixotrophic flagellate numbers counted by the QPS method were 37 % of the direct live counts. Based on these results the advantages and disadvantages of the 2 tested methods used in protozooplankton analysis are summarized.
Local Atopy in Childhood Adenotonsillar Hypertrophy

Background Although the cause of adenotonsillar hypertrophy remains unknown, some studies have shown that allergy may be a risk factor. Purpose This study determined the levels of allergen-specific immunoglobulin E (sIgE) in the adenotonsillar tissues of children with adenotonsillar hypertrophy and evaluated the clinical significance of local atopy in adenotonsillar tissues. Methods We measured 21 types of specific immunoglobulin E in the serum and adenotonsillar tissues of 102 children with adenotonsillar hypertrophy and compared the sensitization patterns of the serum and local tissues. The patients were divided into three groups—atopy, local atopy, and nonatopy—according to the sensitization of serum and adenotonsillar tissues, and the clinical symptoms among the groups were analyzed. Results Seventy-two (70.6%) children with adenotonsillar hypertrophy were sensitized to more than one allergen in the serum and/or adenotonsillar tissue. Thirty (29.4%) children had no IgE positivity to any allergen in both serum and adenotonsillar tissues. Fifty-five (53.9%) were sensitized to at least one allergen in the serum. Seventy (68.6%) were sensitized to at least one allergen in the adenotonsillar tissue. Seventeen (36.2%) of 47 children with specific immunoglobulin E-negative serum had specific immunoglobulin E-positive adenotonsillar tissues. The rate of specific immunoglobulin E was significantly higher in local tissues than in serum. The rate of inhalant allergen specific immunoglobulin E was significantly higher in the adenoids than in the tonsils. However, the rate of food allergen specific immunoglobulin E was significantly higher in the tonsils than adenoids. The lifetime prevalence of asthma and allergic rhinitis, recent symptoms or treatment of allergic rhinitis, and severity of nasal symptoms (rhinorrhea, sneezing, and nasal itching) were significantly higher in children with local atopy than with nonatopy. Conclusions These results confirm that allergic response may be a risk factor for adenotonsillar hypertrophy. Local allergic inflammation may play an important role in childhood adenotonsillar hypertrophy, and local atopy in adenotonsillar tissues can cause respiratory allergic symptoms in children.
Origin of the moisture feeding the Heavy Precipitating Systems over Southeastern France

Abstract. In the Northwestern Mediterranean region, large amounts of precipitation can accumulate over the coasts in less than a day. The present study aims at characterising the origin and the pathways of the moisture feeding such heavy precipitation. The ten Heavy Precipitating Events (HPEs) that occurred over the French Mediterranean region during the autumns of 2008 and 2009 are simulated with the non-hydrostatic research numerical model Meso-NH at 2.5 km, 10 km and 40 km horizontal resolution. Using eulerian on-line passive tracers, high-resolution simulations (2.5 km horizontal resolution) show that the heavy precipitating systems are fed by a south-southwesterly to easterly low-level moist flow. It is typically 1000 m deep and remains almost unchanged all along an event. This low-level feeding flow crosses the most northwestern part of the Mediterranean in 5 to 10 h. Larger-scale simulations (40 km and 10 km horizontal resolution) show that the moisture of the low-level feeding flow is provided by both evaporation of the Mediterranean Sea within the last 2 days before the HPE triggering and transport from remote sources in the lower half of the troposphere over more than 3 to 4 days. Local Mediterranean moisture is gained along the air mass low-level progress towards the Northwestern Mediterranean basin following two main branches along the Spanish coast and west of Sardinia. The Mediterranean Sea is the main moisture source when anticyclonic conditions prevail during the last 3 or 4 days before the HPE. When cyclonic conditions prevail before the HPE, the relative contribution of local and remote sources is more balanced. Remote moisture comes most of the time from the Atlantic Ocean. African tropical moisture is a less frequent but larger remote source.
Trifluoperazine induces apoptosis through the upregulation of Bax/Bcl-2 and downregulated phosphorylation of AKT in mesangial cells and improves renal function in lupus nephritis mice

The inhibition of mesangial cell (MC) proliferation has become an important therapy in preventing glomerular proliferation diseases. Trifluoperazine (TFP) has been reported to inhibit the proliferation of several types of cancer cell, however, the effects of TFP in renal proliferation diseases remain to be fully elucidated. The present study examined the effects of TFP on the proliferation of MCs and quantified cell apoptosis progression in vivo and in vitro. The effects of various TFP concentrations and treatment durations on cell proliferation and cell apoptosis in vitro were analyzed using flow cytometry in conjunction with a Cell Counting kit-8 assay. Cell proliferation in vivo was determined using hematoxylin and eosin staining and immunohistochemistry of Ki67. The expression of the two cell apoptosis-related proteins, B-cell lymphoma-2 (Bcl-2) and Bcl-2-associated X protein (Bax), were estimated using western blot analysis and immunohistochemistry in vivo and in vitro. TFP-induced phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT) signaling pathways were also estimated using western blot analysis. These results suggested that TFP inhibited MC proliferation in a dose- and time-dependent manner. It was found that TFP inhibited the abnormal proliferation of MCs, which was stimulated by 20% fetal bovine serum in vitro and in lupus MRL/lpr mice. TFP promoted cell apoptosis, downregulated the expression of Bcl-2 and upregulated the expression of Bax in a dose-dependent manner at mRNA and protein levels. In addition, TFP inhibited phosphorylated AKT, potentially leading to the suppressed activation of PI3K/AKT signaling pathways. TFP treatment significantly decreased the levels of blood urea nitrogen and serum creatinine, but had no significant effects on the body weight and liver function of the lupus mice. These results validated and reinforced the potential of TFP in the treatment of mesangial proliferative diseases.
Transactional sex and HIV: understanding the gendered structural drivers of HIV in fishing communities in Southern Malawi

In Southern Malawi, the fishing industry is highly gendered, with men carrying out the fishing and women processing, drying and selling the fish. Research has shown that individuals living in fishing communities in low‐income countries are particularly vulnerable to HIV infection. One of the key drivers of HIV in fishing communities is transactional sex. In the fishing industry this takes the form of “fish‐for‐sex” networks where female fish traders exchange sex with fishermen for access to or more favourable prices of fish. By controlling the means of production, the power dynamics in these exchanges favour men and can make it more difficult for women to negotiate safe sex.
Study on the fiber distribution in a drafting zone

Abstract This paper presents a model in a time domain to simulate the dynamic drafting process based on calculated movement time of individual fibers, and provide an approach to investigate the quantitative variation in fiber numbers in a drafting zone. The model was validated by the newly obtained experimental data of sliver irregularities and attenuation curves. The effect of parameters on the drafting process was simulated and discussed based on the experiments. It is shown that the linear density of input strand only changes the fiber number in a drafting zone, but has no effect on the dynamic drafting process; the draft ratio and fiber length have effect on the fiber distributions in a drafting zone; the slow-floating fibers are the most significant parts among them, which eventually results in the total number of fibers in a drafting zone fluctuating.
Determinants of protein hydrogen exchange studied in equine cytochrome c

The exchange of a large number of amide hydrogens in oxidized equine cytochrome c was measured by NMR and compared with structural parameters. Hydrogens known to exchange through local structural fluctuations and through larger unfolding reactions were separately considered. All hydrogens protected from exchange by factors greater than 103 are in defined H‐bonds, and almost all H‐bonded hydrogens including those at the protein surface were measured to exchange slowly. H‐exchange rates do not correlate with H‐bond strength (length) or crystallographic B factors. It appears that the transient structural fluctuation necessary to bring an exchangeable hydrogen into H‐bonding contact with the H‐exchange catalyst (OH−‐ion) involves a fairly large separation of the H‐bond donor and acceptor, several angstroms at least, and therefore depends on the relative resistance to distortion of immediately neighboring structure. Accordingly, H‐exchange by way of local fluctuational pathways tends to be very slow for hydrogens that are neighbored by tightly anchored structure and for hydrogens that are well buried. The slowing of buried hydrogens may also reflect the need for additional motions that allow solvent access once the protecting H‐bond is separated, although it is noteworthy that burial in a protein like cytochrome c does not exceed 4 Å. When local fluctuational pathways are very slow, exchange can become dominated by a different category of larger, cooperative, segmental unfolding reactions reaching up to global unfolding.
The effect of supplementation of multistrain probiotic preparation in combination with vitamins and minerals to the basal diet on the growth performance, carcass traits, and physiological response of broilers

Aim: The aim of the present study was to investigate the effect of supplementation of multistrain probiotic preparation in combination with vitamins and minerals to the broiler chicken diets on their growth performance, hematological parameters, and carcass traits. Materials and Methods: Two hundred and eighty-eight Lohmann 1-day-old broiler chicks were randomly allocated to four groups, i.e., control (without additional supplementation) and three experimental treatments where basal diet was enriched by 0.1%, 0.5%, or 1% of multistrain probiotic preparation in combination with vitamins and minerals, respectively. Blood sampling was conducted on day 28, while the selected organs and eviscerated carcasses were collected on day 42. Results: Dietary supplementation did not affect (p>0.05) the final body weight, feed intake, and feed conversion ratio of broilers. Supplementation by 0.1% and 0.5% of multistrain probiotic preparation in combination with vitamins and minerals reduced (p≤0.05) heart relative weight of broilers. Dietary supplementation tended (p=0.07) to increase the relative weight of ileum and pancreas of broilers. Supplemented birds had lower (p≤0.05) numbers of leukocytes and eosinophils compared to unsupplemented birds. There were tendencies that supplementation of multistrain probiotics in combination with vitamins and minerals resulted in lower (p=0.07) counts of lymphocytes and heterophils when compared with no supplementation. Supplementation by 0.5% of multistrain probiotics in combination with vitamins and minerals resulted in lower (p≤0.05) serum concentration of uric acid when compared with control. There was no significant effect of dietary supplementation on carcass traits, pH, and drip loss of broiler breast muscles. Conclusion: Dietary supplementation of commercial broiler feeds with 0.5% of multistrain probiotic preparation in combination with vitamins and minerals was potential to improve digestive functions and physiological status of broiler chickens.
Global characterization of copy number variants in epilepsy patients from whole genome sequencing

Epilepsy will affect nearly 3% of people at some point during their lifetime. Previous copy number variants (CNVs) studies of epilepsy have used array-based technology and were restricted to the detection of large or exonic events. In contrast, whole-genome sequencing (WGS) has the potential to more comprehensively profile CNVs but existing analytic methods suffer from limited accuracy. We show that this is in part due to the non-uniformity of read coverage, even after intra-sample normalization. To improve on this, we developed PopSV, an algorithm that uses multiple samples to control for technical variation and enables the robust detection of CNVs. Using WGS and PopSV, we performed a comprehensive characterization of CNVs in 198 individuals affected with epilepsy and 301 controls. For both large and small variants, we found an enrichment of rare exonic events in epilepsy patients, especially in genes with predicted loss-of-function intolerance. Notably, this genome-wide survey also revealed an enrichment of rare non-coding CNVs near previously known epilepsy genes. This enrichment was strongest for non-coding CNVs located within 100 Kbp of an epilepsy gene and in regions associated with changes in the gene expression, such as expression QTLs or DNase I hypersensitive sites. Finally, we report on 21 potentially damaging events that could be associated with known or new candidate epilepsy genes. Our results suggest that comprehensive sequence-based profiling of CNVs could help explain a larger fraction of epilepsy cases.
Higher Incidence Rates of Hypothyroidism and Late TSH Rise in Preterm Very-Low-Birth-Weight Infants at a Tertiary Care Center

Background/Aims: Preterm newborns with a very low birth weight (VLBW) of < 1,500 g have an atypical form of hypothyroidism with a delayed rise in TSH, necessitating a second newborn screening specimen collection. The aims of this study were to survey the compliance with second newborn screening to detect delayed TSH rise in VLBW preterm infants at a tertiary care center, and to determine the rate of atypical hypothyroidism. Methods: Retrospective review of the records of 104 preterm VLBW infants. Late TSH rise was defined as an increase in TSH concentration after 14 days of age in the presence of a normal initial screen. Results: The compliance rate was 92% for the second screening. High rates of hypothyroidism (16.3%) and of late TSH rise (4.8%) were detected. Patients with hypothyroidism had a significantly lower birth weight (p = 0.01) and longer hospital stay (p = 0.004). Patients with late versus those with early TSH rise had a significantly lower mean birth weight (851 ± 302 vs. 1,191 ± 121 g, p = 0.004). Conclusion: The rates of early and late TSH rise in this VLBW population were higher than those in the literature and could be due to the use of povidone-iodine disinfectants. The yield of a second TSH screening in this study was high indicating the need for vigilance in screening VLBW preterm infants.
BLOOD CONCENTRATIONS OF THYROID HORMONES AND LIPIDS AND HISTOLOGICAL CHANGES IN THE LIVER IN DAIRY COWS IN POSTPARTURIENT PERIOD

The triiodthyronine (T3), thyroxine (T4), glucose, free fatty acids (FFA), triacylglycerols (TAG) and total cholesterol concentrations were estimated in the blood serum and content of lipids in the liver in healthy (n=10) and ketotic (n=10) dairy cows in the postparturient period. Samples of liver and blood tissues were taken from all the cows. Pathohistoligical examination of liver tissues showed statistically significant higher (p<0.01) lipid infiltration in ketotic cows compared to healthy ones. Biochemical examination of blood serum showed significantly higher values (p<0.01) of free fatty acids in ketotic cows such as significantly lower concentrations of glucose (p<0.01), triacylglycerols (p<0.01), total cholesterol (p<0.05), triiodthyronine (p<0.05) and thyroxine (p<0.05) compared to values of these parameters in the blood serum in healthy cows. Significant increase of concentration of free fatty acids, such as positive correlation (r=0.51; p<0.05) between the free fatty acids in blood and the content of lipids in liver in ketotic cows compared to healthy ones, as well as pathohistological report, shows that during intensive lipomobilisation newly synthetized triacylglycerols accumulated in the hepatocytes.In ketotic cows hypothyroidal status is established and it can be a significant factor in the development of fatty liver.
Effect of weight reduction on respiratory function and airway reactivity in obese women.

BACKGROUND Population-based studies have documented an association between obesity and an increased prevalence of asthma in women. METHODS We prospectively studied 58 obese women with a body mass index of > 30 kg/m(2), 24 of whom had asthma, who were enrolled in an intensive 6-month weight loss program to determine whether loss of body mass would be correlated with improvements in bronchial reactivity, lung function, and disease-specific health status. RESULTS Patients lost an average of 20 kg over the 6-month period. For every 10% relative loss of weight, the FVC improved by 92 mL (p = 0.05) and the FEV(1) improved by 73 mL (p = 0.04), however, bronchial reactivity did not significantly change with weight loss (p = 0.23). Patients who lost > 13% of their pretreatment weight experienced improvements in FEV(1) (p = 0.01), FVC (p = 0.02), and total lung capacity (p = 0.05) compared to patients in the lowest quartile who failed to lose significant amounts of weight. Neither group experienced any significant change in methacholine responsiveness (p = 0.57). Patients who completed the 6-month weight loss program experienced improvements in respiratory health status, irrespective of weight loss. CONCLUSION We concluded that weight loss can improve lung function in obese women, however, the improvements appear to be independent of changes in airway reactivity.
MWC 297: a young high-mass star rotating at critical velocity

Context. MWC 297 is a nearby young massive B[e] star. The central star is attenuated by 8 mag in the optical and has a high projected rotational velocity of 350 km s −1 . Despite the wealth of published observations, the nature of this object and its circumstellar environment is not understood very well. Aims. With the present paper, we intend to shed light on the geometrical structure of the circumstellar matter that is responsible for the near- to mid-infrared flux excess. Methods. The H-band (1.6−2.0 μm), K-band (2.0−2.5 μm), and N-band (8−13 μm) brightness distribution of MWC 297 was probed with the ESO interferometric spectrographs AMBER and MIDI, mounted on the VLTI in Paranal, Chile. We obtained visibility measurements on 3 AMBER and 12 MIDI baselines, covering a wide range of spatial frequencies. Different models (parametrized circumstellar disks, a dusty halo) were invoked to fit the data, all of which fail to do so in a satisfying way. We approximated the brightness distribution in H, K ,a ndN with a geometric model consisting of three Gaussian disks with different extents and brightness temperatures. This model can account for the entire near- to mid-IR emission of MWC 297. Results. The circumstellar matter around MWC 297 is resolved on all baselines. The near- and mid-IR emission, including the silicate emission at 10 micron, emanates from a very compact region (FWHM < 1.5 AU) around the central star. Conclusions. We argue that the extinction towards the MWC 297 star+disk system is interstellar and most likely due to remnants of the natal cloud from which MWC 297 was formed. Furthermore, we argue that the circumstellar matter in the MWC 297 system is organized in a circumstellar disk, seen under moderate (i < 40 ◦ ) inclination. The disk displays no inner emission-free gap at the resolution of our interferometric observations. The low inclination of the disk implies that the already high projected rotational velocity of the star corresponds to an actual rotational velocity that exceeds the critical velocity of the star. This result shows that stars can obtain such high rotation rates at birth. We discuss the impact of this result in terms of the formation of high-mass stars and the main-sequence evolution of classical Be stars.
Preclinical and Clinical Resistance Profile of EDP-239, a Novel Hepatitis C Virus NS5A Inhibitor

ABSTRACT EDP-239, a potent and selective hepatitis C virus (HCV) nonstructural protein 5A (NS5A) inhibitor developed for the treatment of HCV infection, has been investigated in vitro and in vivo. This study sought to characterize genotypic changes in the HCV NS5A sequence of genotype 1 (GT1) replicons and to compare those changes to GT1 viral RNA mutations isolated from clinical trial patients. Resistance selection experiments in vitro using a subgenomic replicon identified resistance-associated mutations (RAMs) at GT1a NS5A amino acid positions 24, 28, 30, 31, and 93 that confer various degrees of resistance to EDP-239. Key RAMs were similarly identified in GT1b NS5A at amino acid positions 31 and 93. Mutations F36L in GT1a and A92V in GT1b do not confer resistance to EDP-239 individually but were found to enhance the resistance of GT1a K24R and GT1b Y93H. RAMs were identified in GT1 patients at baseline or after dosing with EDP-239 that were similar to those detected in vitro. Baseline RAMs identified at NS5A position 93 in GT1, or positions 28 or 30 in GT1a only, correlated with a reduced treatment response. RAMs at additional positions were also detected and may have contributed to reduced EDP-239 efficacy. The most common GT1a and GT1b RAMs found to persist up to weeks 12, 24, or 48 were those at NS5A positions 28, 30, 31, 58 (GT1a only), and 93. Those RAMs persisting at the highest frequencies up to weeks 24 or 48 were L31M and Q30H/R for GT1a and L31M and Y93H for GT1b. (This study has been registered at ClinicalTrials.gov under identifier NCT01856426.)