Miracle-dz/UniFAR-FTUs huggingface dataset:
Pooling sputum from multiple individuals for Xpert® MTB/RIF testing: a strategy for screening high-risk populations.

SETTING Symptom-based screening for tuberculosis (TB) disease is limited by poor performance of symptom screening in several key populations. We tested the hypothesis that pooling sputum from multiple individuals for Xpert(®) MTB/RIF testing would reduce the number of tests required while retaining an acceptable sensitivity, thus allowing the use of Xpert for TB screening. METHODS We compared pooling ratios that would require the least number of assays using Xpert and determined that for a population with a TB prevalence of approximately 3%, a 1:5 pooling ratio is optimal. To evaluate sensitivity, we generated pools of one specimen with known Mycobacterium tuberculosis culture positivity (smear microscopy-positive or -negative) with four culture-negative specimens. RESULTS All 20 of the pools generated from a smear- and culture-positive sputum sample were positive using Xpert. Of the 22 pools with a smear-negative, culture-positive sample, we included 17 in the analysis, of which 13 (76%) were Xpert-positive. CONCLUSIONS Pooling of sputum samples using Xpert achieved reasonable sensitivity and warrants further evaluation of the systematic screening of high TB prevalence populations.
Interactive comment on “ Remote sensing-based estimation of gross primary production in a subalpine grassland ” by M .

Dear Reviewer, Thank you for the positive evaluation of the manuscript. The manuscript has been revised, according to the Reviewer’s comments and suggestions. We have carefully considered each of them and have implemented the corresponding changes in order to improve the manuscript. We are confident to have fully answered all questions and incorporated all the recommendations in the revised paper. The Reviewer will find below the responses to the specific comments (typed in bold characters, while authors’ replies are in italics).
Density-Dependent Prevalence of Francisella tularensis in Fluctuating Vole Populations, Northwestern Spain

Tularemia in humans in northwestern Spain is associated with increases in vole populations. Prevalence of infection with Francisella tularensis in common voles increased to 33% during a vole population fluctuation. This finding confirms that voles are spillover agents for zoonotic outbreaks. Ecologic interactions associated with tularemia prevention should be considered.
The Impact of Total and Partial Inclusion or Exclusion of Active and Inactive Time Invariant Covariates in Growth Mixture Models

This article evaluates the impact of partial or total covariate inclusion or exclusion on the class enumeration performance of growth mixture models (GMMs). Study 1 examines the effect of including an inactive covariate when the population model is specified without covariates. Study 2 examines the case in which the population model is specified with 2 covariates influencing only the class membership. Study 3 examines a population model including 2 covariates influencing the class membership and the growth factors. In all studies, we contrast the accuracy of various indicators to correctly identify the number of latent classes as a function of different design conditions (sample size, mixing ratio, invariance or noninvariance of the variance-covariance matrix, class separation, and correlations between the covariates in Studies 2 and 3) and covariate specification (exclusion, partial or total inclusion as influencing class membership, partial or total inclusion as influencing class membership, and the growth factors in a class-invariant or class-varying manner). The accuracy of the indicators shows important variation across studies, indicators, design conditions, and specification of the covariates effects. However, the results suggest that the GMM class enumeration process should be conducted without covariates, and should rely mostly on the Bayesian information criterion (BIC) and consistent Akaike information criterion (CAIC) as the most reliable indicators under conditions of high class separation (as indicated by higher entropy), versus the sample size adjusted BIC or CAIC (SBIC, SCAIC) and bootstrapped likelihood ratio test (BLRT) under conditions of low class separation (indicated by lower entropy).
What can the annual 10Be solar activity reconstructions tell us about historic space weather

Context : Cosmogenic isotopes provide useful estimates of past solar magnetic activity, constraining past space climate with reasonable uncertainty. Much less is known about past space weather conditions. Recent advances in the analysis of 10 Be by (MB15) suggest that annually resolved 10 Be can be significantly affected by solar energetic particle (SEP) fluxes. This poses a problem, and presents an opportunity, as the accurate quantification of past solar magnetic activity requires the SEP effects to be determined and isolated, whilst doing so might provide a valuable record of past SEP fluxes. Aims : We compare the MB15 reconstruction of the heliospheric magnetic field (HMF), with two independent estimates of the HMF derived from sunspot records and geomagnetic variability. We aim to quantify the differences between the HMF reconstructions, and speculate on the origin of these differences. We test whether the differences between the reconstructions appear to depend on known significant space weather events. Methods : We analyse the distributions of the differences between the HMF reconstructions. We consider how the differences vary as a function of solar cycle phase, and, using a Kolmogorov-Smirnov test, we compare the distributions under the two conditions of whether or not large space weather events were known to have occurred. Results : We find that the MB15 reconstructions are generally marginally smaller in magnitude than the sunspot and geomagnetic HMF reconstructions. This bias varies as a function of solar cycle phase, and is largest in the declining phase of the solar cycle. We find that MB15's excision of the years with very large ground level enhancement (GLE) improves the agreement of the 10 Be HMF estimate with the sunspot and geomagnetic reconstructions. We find no statistical evidence that GLEs, in general, affect the MB15 reconstruction, but this analysis is limited by having too few samples. We do find evidence that the MB15 reconstructions appear statistically different in years with great geomagnetic storms.
HIV induces production of IL-18 from intestinal epithelial cells that increases intestinal permeability and microbial translocation

Interleukin-18 (IL-18) is a pleiotropic cytokine of the IL-1 family with multiple context dependent functions. We and others have shown that HIV infection is accompanied by increased circulating levels of IL-18 along with decreased levels of its antagonist, Interleukin-18 Binding Protein (IL-18BP). The infection is also accompanied by intestinal inflammation and decreased intestinal integrity as measured by intestinal permeability, regeneration and repair. However, little is known concerning the relation between high level of IL-18 associated with the viral infection and intestinal permeability. Here we demonstrate that HIV treatment increases production of IL-18 and decreases that of IL-18BP production in human intestinal epithelial cell (IEC) lines. IL-18 causes apoptosis of the IEC by activating caspase-1 and caspase-3. It induces epithelial barrier hyperpermeability by decreasing and disrupting both tight and adherens junction proteins, occludin, claudin 2 and beta-catenin. Disorganization of F-actin was also observed in the IEC that were exposed to the cytokine. Moreover IL-18 decreases transepithelial electrical resistance (TEER) in Caco-2 and increases permeability in HT29 monolayers. The cells’ treatment with IL-18 causes an increase in the expression of phosphorylated myosin II regulatory light-chain (p-MLC) and myosin light-chain kinase (MLCK), and a decrease in phosphorylated Signal Transducer and Activator of Transcription (p-STAT)-5. This increase in p-MLC is suppressed by a Rho-kinase (ROCK)-specific inhibitor. Interestingly, the levels of the cytokine correlate with those of LPS in the circulation in three different categories of HIV infected patients (HAART-naïve and HAART-treated HIV-infected individuals, and Elite controls) as well as in healthy controls. Collectively, these results suggest that the HIV-induced IL-18 plays a role in increased intestinal permeability and microbial translocation observed in HIV-infected individuals.
Diagnostic value of TREM-1 and TREM-2 expression in bronchoalveolar lavage fluid in sarcoidosis and other lung diseases.

BACKGROUND Triggering receptors expressed on myelocytes (TREM) belong to new molecules with a great role in innate immune system and inflammation. While TREM-1 is known for its pro-inflammatory activity, the TREM-2 has anti-inflammatory activity and has a great impact on granuloma formation, typical sign of sarcoidosis and other granulomatous diseases. METHODS In our study, we compared the TREM-1 and TREM-2 receptor expressions on the myeloid cell surfaces in bronchoalveolar lavage fluid in patients with pulmonary sarcoidosis (PS), other interstitial lung diseases (ILD), asthma bronchiale (AB), pneumonia, lung cancers, and Quantiferon TB positive patients. RESULTS We found increased number of all TREM variables (total number, percentage, and mean fluorescence intensity /MFI/) of TREM-1 and TREM-2 positive cells in PS and AB patients compared to the control group of patients with other ILD. In patients with pneumonia, only expression of TREM-1 receptor was increased. In ILD, AB and group of pneumonia patients, the increase of TREM-1 and TREM-2 expression was associated with an increased number of eosinophils. CONCLUSION TREM-1 and TREM-2 tests are good diagnostic tests for sarcoidosis. Their sensitivity and specificity are comparable with the currently common using test, that of CD4/CD8 ratio. The combination of both tests (CD4/CD8 ratio test together with TREM-1 and TREM-2 tests) resulted in an increased sensitivity and specificity (Tab. 7, Fig. 1, Ref. 28).
Cytotoxicity of Different Degrees of De-Acetylated Chitosan on 3T3- and Two Human Tooth Fibroblast Cell-Lines

Nowadays chitosan becomes more and more important as a drug carrier. In this study the influence of different degrees of de-acetylation of chitosan on the cytotoxicity were investigated. Materials and Methods: Chitosan (87%, 70% and 40% de-acetylated) was analysed for their cytotoxic effect on mouse Balb/c 3T3 fibroblast cells as well as two different human tooth pulp fibroblast cell-lines. The cell survival rate was determined over a 24 hour period according to the standard MTT assay. Results: The Univariate ANOVA test showed significant differences in the cell survival rates (p<0.01) amongst 87% and 70% and 40% de-acetylated chitosan products for the 3T3 as well as the two pulp fibroblast cell-lines. Significant differences were also found between both tooth cell-lines and the 3T3 cell-line at all 3 different de- acetylated chitosan levels. The 3T3 cell line was mostly affected at 40% de-acetylation. The difference between both human cell-lines was not significant. Conclusion: The lower the degree of chitosan de-acetylation the less the cell survival rate while an 87% de- acetylation degree improved the cell survival rate. Different cell lines react differently towards different degrees of de-acetylation. The relative survival rates of different cell lines changed at different degrees of de-acetylation.
Tetrahydrobiopterin and its functions

Tetrahydrobiopterin (BH4) is essential for diverse processes and is ubiquitously present in all tissues of higher organisms. It is well established as essential cofactor for various enzyme activities to activate dioxygen, and for less defined functions at the cellular level. The latter function of BH4 seems to have a dual nature, depending on the concentration of the cofactor and the cell type, between proliferative activity and trigger for apoptosis. Since BH4 (and related tetrahydropterins) can form radicals, it can act as a generator or scavenger of reactive oxygen species in cells. More characteristics are arising based on recent observations, including chaperon function reported at least for the hepatic phenylalanine hydroxylase. The BH4 cofactor is endogenously synthesized and a (genetic) deficiency in the biosynthesis or regeneration leads to neurological abnormalities, including Dopa-responsive dystonia or severe monoamine neurotransmitter depletion. However, also under normal BH4 concentrations its availability becomes limiting in various pathological situations involving endothelial dysfunction, for instance, in diabetes or coronary heart diseases. From such developments it is expected that research on cofactor function will become of even broader interest in unraveling pathophysiological connections.
Raw and Count Data Comparability of Hip-Worn ActiGraph GT3X+ and Link Accelerometers

To enable inter- and intrastudy comparisons it is important to ascertain comparability among accelerometer models. Purpose The purpose of this study was to compare raw and count data between hip-worn ActiGraph GT3X+ and GT9X Link accelerometers. Methods Adults (n = 26 (n = 15 women); age, 49.1 ± 20.0 yr) wore GT3X+ and Link accelerometers over the right hip for an 80-min protocol involving 12–21 sedentary, household, and ambulatory/exercise activities lasting 2–15 min each. For each accelerometer, mean and variance of the raw (60 Hz) data for each axis and vector magnitude (VM) were extracted in 30-s epochs. A machine learning model (Montoye 2015) was used to predict energy expenditure in METs from the raw data. Raw data were also processed into activity counts in 30-s epochs for each axis and VM, with Freedson 1998 and 2011 count-based regression models used to predict METs. Time spent in sedentary, light, moderate, and vigorous intensities was derived from predicted METs from each model. Correlations were calculated to compare raw and count data between accelerometers, and percent agreement was used to compare epoch-by-epoch activity intensity. Results For raw data, correlations for mean acceleration were 0.96 ± 0.05, 0.89 ± 0.16, 0.71 ± 0.33, and 0.80 ± 0.28, and those for variance were 0.98 ± 0.02, 0.98 ± 0.03, 0.91 ± 0.06, and 1.00 ± 0.00 in the X, Y, and Z axes and VM, respectively. For count data, corresponding correlations were 1.00 ± 0.01, 0.98 ± 0.02, 0.96 ± 0.04, and 1.00 ± 0.00, respectively. Freedson 1998 and 2011 count-based models had significantly higher percent agreement for activity intensity (95.1% ± 5.6% and 95.5% ± 4.0%) compared with the Montoye 2015 raw data model (61.5% ± 27.6%; P < 0.001). Conclusions Count data were more highly comparable than raw data between accelerometers. Data filtering and/or more robust raw data models are needed to improve raw data comparability between ActiGraph GT3X+ and Link accelerometers.
Brain Network Connectivity During Language Comprehension: Interacting Linguistic and Perceptual Subsystems

The dynamic neural processes underlying spoken language comprehension require the real-time integration of general perceptual and specialized linguistic information. We recorded combined electro- and magnetoencephalographic measurements of participants listening to spoken words varying in perceptual and linguistic complexity. Combinatorial linguistic complexity processing was consistently localized to left perisylvian cortices, whereas competition-based perceptual complexity triggered distributed activity over both hemispheres. Functional connectivity showed that linguistically complex words engaged a distributed network of oscillations in the gamma band (20–60 Hz), which only partially overlapped with the network supporting perceptual analysis. Both processes enhanced cross-talk between left temporal regions and bilateral pars orbitalis (BA47). The left-lateralized synchrony between temporal regions and pars opercularis (BA44) was specific to the linguistically complex words, suggesting a specific role of left frontotemporal cross-cortical interactions in morphosyntactic computations. Synchronizations in oscillatory dynamics reveal the transient coupling of functional networks that support specific computational processes in language comprehension.
Nutrient Optimization for the Production of Microbial Flocs in Suspended Growth Bioreactors = تحديد أفضلية المغذيات لإنتاج التجمعات الميكروبية في المفاعلات الحيوية

Four successive experiments were carried out to determine the best combination of nutrients that could be added to sea water to enhance microbes to produce biofloc. In the first experiment, four levels of Nitrogen/ Phosphorus (N/P) ratio were tried with two sets of treatments for the four levels; with and without chicken manure. The level 4:1 from the second treatment was significantly (P <0.001) higher in dry weight (DW) and crude protein (CP) than the others. The second experiment aimed to using five levels of carbon/ nitrogen (C/N) ratios. The level (16:1) differed significantly, it was the highest in DW but its CP was slightly lower (P <0.001). This level was used in the third experiment with different carbon sources. The obtained DW from the rice meal was slightly higher, in contrast, the CP of the corn meal was the highest (P <0.001). In the fourth experiment a larger scale production of biofloc units using the best carbon source were used in different water sources. DW and CP of the biofloc for both trials were weakly significant (P <0.526). The nutritional composition of microbial flocs produced showed that CP was the highest component (39%). The study suggested that microbial protein could replace fishmeal or other protein sources in fish and shrimp feeding due to its good nutritional value and appropriate aminoacid profile which make it suitable for feeding omnivorous cultured species.
Does Genotype Determine Habitat Preferences? – Studies on Forest and Field Roe Deer

The main habitat of roe deer includes the outer edges of forests and wooded steppes but this species has also adapted itself at least 100 years ago to living in open agricultural areas all year round. The presence of forest roe deer as well as field roe deer was confirmed at the turn of the 20 and 21 centuries with radio telemetry research projects. Therefore, the question arises as to how there are two roe deer populations with different habitat preferences and behaviour existing in the same areas in Europe for so many decades. Genetic differences between forest and field roe deer were examined by analyzing the polymorphism of eight microsatellite DNA loci of individuals within three regions of Poland. The fact that the individuals studied belonged to specific populations did not result in significant differences in allele and genotype frequencies. The obtained results suggest a lack of genetic differences between the forest and field roe deers. Negligible genetic differentiation is probably a consequence of the matching of individuals from both populations neighbouring each other in many areas. Moreover, some forest roe deer periodically live in agricultural territories in the summer, during the period of rut. A hypothesis was put forward that young roe deer choose their future habitat (forests or fields) by observing the behaviour of adults, especially their mothers whom they accompany in the first year of their lives. In this case, the obtained genetic resemblance for progeny can result from the field origin of their dam(s).
Challenges and confrontations in care by nurses: a study of social representations

Objetivo: analisar os desafios do cuidado de enfermagem a pessoas com HIV/Aids e seus modos de enfrentamento presentes nas representacoes sociais de enfermeiros acerca de sua propria vulnerabilidade e empoderamento. Metodo: Foram abordados por meio de entrevista semiestruturada trinta enfermeiros de um hospital publico. Realizou-se a analise de conteudo instrumentalizada pelo software NVivo 9.0 a partir dos pressupostos teorico-metodologicos das Representacoes Sociais. Resultados: os desafios se mostram ligados a dimensoes afetivas, imageticas e cognitivas da representacao, enquanto as formas de enfrentamento estao ligadas, sobretudo, a dimensoes praticas. Discussao: a vulnerabilidade se conforma pela intersecao entre fatores politico-institucionais e humano-afetivos, enquanto o empoderamento se coloca como um processo fluido de ressignificacao da atividade exercida. Conclusao: e urgente o desenvolvimento de acoes programaticas voltadas para a saude de profissionais de enfermagem que cuidam de pessoas com HIV/Aids.
Effect of growth at low pH on the cell surface properties of a typical strain of Lactobacillus casei group

Background and Objectives Although members of the Lactobacillus casei group are known to survive under acidic conditions, the underlying mechanisms of growth at acidic condition and the impact of low pH on the relative level of protein expression at the cell surface remain poorly studied. Material and Methods After confirming the taxonomy of L. casei strain GCRL 12 which was originally isolated from cheese and confirmed by 16S rRNA sequence analysis, the impact of acidic pH on growth rate was determined. Results Late log-phase cells cultured at pH 4.0 showed obvious changes in Gram staining properties while transmission electron microscopy analysis revealed evidence of structural distortions of the cell surface relative to the controls cultured at pH 6.5. When comparing cytosolic or whole cell preparations on SDS-PAGE, few changes in protein profiles were observed under the two growth conditions. However, analysis of surface protein extracted by 5M LiCl demonstrated changes in the proportions of proteins present in the molecular weight range of 10 to 80 kDa, with some proteins more dominant at pH 6.5 and other at pH 4. Conclusion These data suggest that surface proteins of this strain are associated with growth and survival at low pH. The function of these proteins is subject to further investigation.
Characterization of Rice Husk-Incorporated Recycled Thermoplastic Blend Composites

High-fiber-content composites made from rice husk (RH) (from 50 up to 80 wt%) as well as a recycled thermoplastic blend (rTPB) were fabricated using a two-step extrusion and hot/cold press molding technique. The temperature dependency of the thermal degradation and dynamic-mechanical behavior was investigated using thermogravimetric analysis (TGA) and dynamic mechanical analysis (DMA). The long-term water absorption and orthotropic swelling were analyzed following immersion in distilled, tap, and sea water for 15 weeks. Improvements in the thermal stability, storage, and loss modulus, as well as reductions in dimensional stability, were observed as the alkali content of the RH in the rTPB composites was increased. The composites immersed in sea water showed the lowest water absorption, followed by those in distilled and then tap water. The thickness dimension of the composite specimens exhibited the highest swelling values, followed by width and then length dimensions. The tensile strength and elastic modulus showed the maximum values at 70 wt% RH (21.2 MPa and 1.6 GPa, respectively). The surface morphology, interfacial adherence, and bonding between the matrix-fiber phases in the composites were characterized using a scanning electron microscope (SEM).
Hidden Markov Convolutive Mixture Model for Pitch Contour Analysis of Speech

This paper proposes a stochastic model of speech F0 contours, based on the stochastic formulation of the Fujisaki model. Our motivation for the stochastic formulation is twofold. Firstly, it allows us to derive a well-behaved algorithm for estimating the Fujisaki model parameters from a raw F0 contour. Secondly, it will open the door to incorporating the well-founded F0 contour model into various statistical speech processing problems. We quantitatively evaluated the performance of our method in terms of an Fujisaki-model parameter estimation accuracy using real speech data. Experimental results revealed that our method was superior to a state-of-the-art Fujisaki model parameter extractor.