Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of Structured Physical Activity on Inflammation and Immune Activation Profile of Antiretroviral Therapy-Experienced Children Living With HIV.

AIM To compare the markers of inflammation and immune activation in virally suppressed HIV-infected children on antiretroviral therapy, who practiced regular structured exercise comprising running and yoga to those who did not over a 2-year period. METHODS This retrospective cohort study included 72 children aged 8 to 16 years divided into 2 groups, exercisers (n = 36) and the nonexercisers (n = 36) based on their intentional physical activity. The analyses were carried out at baseline and after 2 years (Y2) for the soluble biomarkers of inflammation and immune activation (tumor necrosis factor alpha, interleukin-6, interleukin-10, interferon gamma, sCD14, and sCD163). In addition, cell-associated biomarker (CD38), lipopolysaccharides, and the gene expression of interleukin-2 and brain-derived neurotrophic factor were also measured at Y2. RESULTS Reduction in levels of sCD14 (effect size [ES], -0.6; 95% confidence interval [CI], -1.08 to -0.14), tumor necrosis factor alpha (ES, -0.7; 95% CI, -1.18 to -0.23), interferon gamma (ES, -0.7; 95% CI, -1.17 to -0.22), and interleukin-10 (ES, -0.6; 95% CI, -1.08 to -0.14) was observed among exercisers as compared with nonexercisers at Y2. In addition, CD38+ expressing CD4+ T cells were found to be lower among exercisers (P = .01) at Y2. However, the differences in levels of interleukin-6, sCD163, lipopolysaccharides, interleukin-2, and brain-derived neurotrophic factor were not significantly different among the 2 groups. CONCLUSION The study result suggests that regular structured physical activity improves the inflammatory profile of antiretroviral therapy-treated HIV-infected children.
Exterior and Internal Uniform Loading of Pt Nanoparticles on Yolk-Shell La2O3 by Acoustic Levitation Synthesis with Enhanced Photocatalytic Performance

By the deposition of noble metal nanoparticles on a metal oxide substrate with a specific micro-/nanostructure, namely, yolk-shell structure, a remarkable improvement in photocatalytic performance can be achieved by the composites. Nevertheless, noble metal nanoparticles only distribute on the surface shell of metal oxide substrates when the conventional wet-chemistry reduction approach is employed. Herein, we proposed a novel acoustic levitation synthesis of Pt nanoparticles deposited on yolk-shell La2O3. The composites not only displayed well-defined, homogeneous distribution of Pt NPs on the exterior shell of La2O3 and the interior La2O3 core, but an enhanced chemical interaction between Pt and La2O3. The unique structure not only can display improved photocatalytic degradation rate toward methyl orange, but also may show great potential in fields of hydrogen generation, environmental protection, etc. The novel acoustic levitation synthesis can supplement the methodology of synthesizing well dispersed noble metal oxides over the whole yolk-shell structure through noble metal NPs deposition method.
Transmembrane helix 6b links proton and metal release pathways and drives conformational change in an Nramp-family transition metal transporter

The natural resistance-associated macrophage protein (Nramp) family encompasses transition metal and proton cotransporters that are present in many organisms from bacteria to humans. Recent structures of Deinococcus radiodurans Nramp (DraNramp) in multiple conformations revealed the intramolecular rearrangements required for alternating access of the metal-binding site to the external or cytosolic environment. Here, using recombinant proteins and metal transport and cysteine accessibility assays, we demonstrate that two parallel cytoplasm-accessible networks of conserved hydrophilic residues in DraNramp, one lining the wide intracellular vestibule for metal release and the other forming a narrow proton transport pathway, are essential for metal transport. We further show that mutagenic or posttranslational modifications of transmembrane helix (TM) 6b, which structurally links these two pathways, impede normal conformational cycling and metal transport. TM6b contains two highly conserved histidines, His232 and His237. We found that different mutagenic perturbations of His232, just below the metal-binding site along the proton exit route, differentially affect DraNramp's conformational state, suggesting that His232 serves as a pivot point for conformational changes. In contrast, any replacement of His237, lining the metal exit route, locked the transporter in a transport-inactive outward-closed state. We conclude that these two histidines, and TM6b more broadly, help trigger the bulk rearrangement of DraNramp to the inward-open state upon metal binding and facilitate return of the empty transporter to an outward-open state upon metal release.
Disentangling the Effects of Processing Speed on the Association between Age Differences and Fluid Intelligence

Several studies have demonstrated that individual differences in processing speed fully mediate the association between age and intelligence, whereas the association between processing speed and intelligence cannot be explained by age differences. Because measures of processing speed reflect a plethora of cognitive and motivational processes, it cannot be determined which specific processes give rise to this mediation effect. This makes it hard to decide whether these processes should be conceived of as a cause or an indicator of cognitive aging. In the present study, we addressed this question by using a neurocognitive psychometrics approach to decompose the association between age differences and fluid intelligence. Reanalyzing data from two previously published datasets containing 223 participants between 18 and 61 years, we investigated whether individual differences in diffusion model parameters and in ERP latencies associated with higher-order attentional processing explained the association between age differences and fluid intelligence. We demonstrate that individual differences in the speed of non-decisional processes such as encoding, response preparation, and response execution, and individual differences in latencies of ERP components associated with higher-order cognitive processes explained the negative association between age differences and fluid intelligence. Because both parameters jointly accounted for the association between age differences and fluid intelligence, age-related differences in both parameters may reflect age-related differences in anterior brain regions associated with response planning that are prone to be affected by age-related changes. Conversely, age differences did not account for the association between processing speed and fluid intelligence. Our results suggest that the relationship between age differences and fluid intelligence is multifactorially determined.
Effects of treated wastewater on the ecotoxicity of small streams – Unravelling the contribution of chemicals causing effects

Wastewater treatment plant effluents are important point sources of micropollutants. To assess how the discharge of treated wastewater affects the ecotoxicity of small to medium-sized streams we collected water samples up- and downstream of 24 wastewater treatment plants across the Swiss Plateau and the Jura regions of Switzerland. We investigated estrogenicity, inhibition of algal photosynthetic activity (photosystem II, PSII) and growth, and acetylcholinesterase (AChE) inhibition. At four sites, we measured feeding activity of amphipods (Gammarus fossarum) in situ as well as water flea (Ceriodaphnia dubia) reproduction in water samples. Ecotoxicological endpoints were compared with results from analyses of general water quality parameters as well as a target screening of a wide range of organic micropollutants with a focus on pesticides and pharmaceuticals using liquid chromatography high-resolution tandem mass spectrometry. Measured ecotoxicological effects in stream water varied substantially among sites: 17β-estradiol equivalent concentrations (EEQbio, indicating the degree of estrogenicity) were relatively low and ranged from 0.04 to 0.85 ng/L, never exceeding a proposed effect-based trigger (EBT) value of 0.88 ng/L. Diuron equivalent (DEQbio) concentrations (indicating the degree of photosystem II inhibition in algae) ranged from 2.4 to 1576 ng/L and exceeded the EBT value (70 ng/L) in one third of the rivers studied, sometimes even upstream of the WWTP. Parathion equivalent (PtEQbio) concentrations (indicating the degree of AChE inhibition) reached relatively high values (37 to 1278 ng/L) mostly exceeding the corresponding EBT (196 ng/L PtEQbio). Decreased feeding activity by amphipods or decreased water flea reproduction downstream compared to the upstream site was observed at one of four investigated sites only. Results of the combined algae assay (PSII inhibition) correlated best with results of chemical analysis for PSII inhibiting herbicides. Estrogenicity was partly and AChE inhibition strongly underestimated based on measured steroidal estrogens respectively organophosphate and carbamate insecticides. An impact of dissolved organic carbon on results of the AChE inhibition assay was obvious. For this assay more work is required to further explore the missing correlation of bioassay data with chemical analytical data. Overall, the discharge of WWTP effluent led to increased estrogenicity, PSII and AChE inhibition downstream, irrespective of upstream land use.
The Role of Efflux Pumps and Environmental pH in Bacterial Multidrug Resistance

Background/Aim: One of the most studied bacterial resistance mechanisms is the resistance related to multidrug efflux pumps. In our study the pump activity of the Escherichia coli K-12 AG100 strain expressing the AcrAB-TolC pump system was investigated at pH 7 and pH 5 in the presence of the efflux pump inhibitor (EPI) promethazine (PMZ). Materials and Methods: The EPI activity was assessed by real-time fluorimetry. The influence of PMZ treatment on the relative expression of the pump genes acrA, acrB and their regulators marA, marB, marR, the stress genes soxS, rob, as well as the bacterial growth control genes ftsI, and sdiA were determined by RT-qPCR. Results: The EPI activity of PMZ was more effective at neutral pH. The PMZ treatment induced a significant stress response in the bacterium at acidic pH by the up-regulation of genes. Conclusion: The genetic system that regulates the activity of the main efflux pump is pH-dependent.
Vaccination with a live-attenuated small-colony variant improves the humoral and cell-mediated responses against Staphylococcus aureus

Staphylococcus aureus is known to produce persistent and chronic infections in both humans and animals. It is recognized that small-colony variants (SCVs), which produce higher levels of biofilm and that are capable of intracellular persistence, contribute to the chronicity or recurrence of infections and that this phenotype is inherent to the pathogenesis process. Prevention of S. aureus infections through vaccination has not yet met with considerable success. Some of the current vaccine formulations for S. aureus bovine mastitis consist of inactivated S. aureus bacteria, sometimes combined to E. coli J5. As such, the stimulation of cell-mediated immunity by these vaccines might not be optimal. With this in mind, we recently engineered a genetically stable double mutant SCV (ΔvraGΔhemB), which was highly attenuated in a mastitis model of infection. The present work describes the immune responses elicited in mice by various experimental vaccine compositions including the live-attenuated SCV double mutant and its inactivated form, combined or not with inactivated E. coli J5. The live-attenuated SCV was found to provoke a strong and balanced humoral response in immunized mice, as well as strong proliferation of ex-vivo stimulated splenocytes isolated from these animals. These splenocytes were also found to release high concentration of IL-17 and IFN-γ when compared to every other vaccination formulation. Inversely, the inactivated whole-cell vaccine, alone or in combination with the E. coli J5 bacterin, elicited lower antibody titers and failed to induce Th1 or Th17 cell-mediated responses in the splenocyte proliferation assay. Our results suggest that live-attenuated SCVs can trigger host immunity differently than inactivated bacteria and could represent a suitable vector for inducing strong humoral and cell-mediated immune responses, which are crucial for protection. This could represent an important improvement over existing vaccine formulations for preventing S. aureus bovine mastitis and other infections caused by this pathogen.
The temperature optima for tree seedling photosynthesis and growth depend on water inputs

Understanding how tree growth is affected by rising temperature is a key to predicting the fate of forests in future warmer climates. Increasing temperature has direct effects on plant physiology, but there are also indirect effects of increased water limitation because evaporative demand increases with temperature in many systems. In this study, we experimentally resolved the direct and indirect effects of temperature on the response of growth and photosynthesis of the widely distributed species Eucalyptus tereticornis. We grew E. tereticornis in an array of six growth temperatures from 18 to 35.5°C, spanning the climatic distribution of the species, with two watering treatments: (a) water inputs increasing with temperature to match plant demand at all temperatures (Wincr), isolating the direct effect of temperature; and (b) water inputs constant for all temperatures, matching demand for coolest grown plants (Wconst), such that water limitation increased with growth temperature. We found that constant water inputs resulted in a reduction of temperature optima for both photosynthesis and growth by ~3°C compared to increasing water inputs. Water limitation particularly reduced the total amount of leaf area displayed at Topt and intermediate growth temperatures. The reduction in photosynthesis could be attributed to lower leaf water potential and consequent stomatal closure. The reduction in growth was a result of decreased photosynthesis, reduced total leaf area display and a reduction in specific leaf area. Water availability had no effect on the response of stem and root respiration to warming, but we observed lower leaf respiration rates under constant water inputs compared to increasing water inputs at higher growth temperatures. Overall, this study demonstrates that the indirect effect of increasing water limitation strongly modifies the potential response of tree growth to rising global temperatures.
Individual and Regional Characteristics Associated with Maternal Smoking During Pregnancy in Japan: Healthy Parents and Children 21

Smoking during pregnancy causes various maternal and fetal health problems. Although there are considerable differences in maternal smoking proportions between localities, only a few studies have investigated the effects of regional characteristics on maternal smoking behavior. This study aimed to clarify the association between maternal smoking during pregnancy and individual and regional characteristics. We used data from a large nationwide birth cohort study in Japan that consisted of information on 20,267 women with children aged 3–4 months. The multilevel regression model was used to examine the association between smoking behavior during pregnancy and individual and regional characteristics. On multilevel analysis, late birth order, young age of the mother at birth, low birth weight, low economic status, husband’s smoking during pregnancy, maternal alcohol consumption during pregnancy, absence of a pregnancy counselor, and lack of participation in local events for childrearing were significantly associated with maternal smoking behavior during pregnancy at the individual level. Meanwhile, a high unemployment rate and a high number of nurseries were significantly associated with maternal smoking behavior during pregnancy at the regional level. In conclusion, we showed the relation between maternal smoking during pregnancy and the individual- and regional-level characteristics.
No inflammation? No cancer! Clear HBV early and live happily

Some individuals who are chronically infected with hep- atitis B virus (HBV) eventually lose hepatitis B surface antigen (HBsAg). Hepatocellular carcinoma (HCC) has been demonstrated to occur in a few patients after loss of HBsAg. Neither factors associated with loss of HBsAg nor the incidence of HCC thereafter have been clearly eluci- dated. We performed a prospective population-based cohort study in 1271 Alaska native persons with chronic HBV infection followed for an average of 19.6 years to determine factors associated with loss of HBsAg and risk of developing HCC thereafter. HBsAg loss occurred in 158 persons for a rate of HBsAg clearance of 0.7%/year. Older age, but not sex, was associated with clearance of HBsAg, and loss of HBsAg was not associated with any particular HBV genotypes (A-D, and F) found in this population. Participants were followed for an average of 108.9 months after HBsAg loss. Six patients, two with cirrhosis and four without, developed HCC a mean of 7.3 years after HBsAg clearance (range, 2.0-15.5 years). The incidence of HCC after clearance of HBsAg was 36.8 per 100,000 per year (95% CI 13.5-80.0) which was significantly lower than the rate in those who remained HBsAg-posi- tive (195.7 cases per 100,000 person-years of follow-up (95% CI 141.1-264.5; P < 0.001). After loss of HBsAg, HBV DNA was detected in the sera of 28 (18%) of those who cleared a median of 3.6 years after clearance. Conclusion: HCC can occur in persons with chronic hepatitis B who have lost HBsAg, even in the absence of cirrhosis. These persons should still be followed with periodic liver ultrasound to detect HCC early. 2010 European Association for the Study of the Liver. Published
Transcriptome Response to Drought, Rehydration and Re-Dehydration in Potato

Potato is an important food crop and its production is susceptible to drought. Drought stress in crop growth is usually multiple- or long-term. In this study, the drought tolerant potato landrace Jancko Sisu Yari was treated with drought stress, rehydration and re-dehydration, and RNA-seq was applied to analyze the characteristics of gene regulation during these treatments. The results showed that drought-responsive genes mainly involved photosynthesis, signal transduction, lipid metabolism, sugar metabolism, wax synthesis, cell wall regulation, osmotic adjustment. Potato also can be recovered well in the re-emergence of water through gene regulation. The recovery of rehydration mainly related to patatin, lipid metabolism, sugar metabolism, flavonoids metabolism and detoxification besides the reverse expression of the most of drought-responsive genes. The previous drought stress can produce a positive responsive ability to the subsequent drought by drought hardening. Drought hardening was not only reflected in the drought-responsive genes related to the modified structure and cell components, but also in the hardening of gene expression or the “memory” of drought-responsive genes. Abundant genes involved photosynthesis, signal transduction, sugar metabolism, protease and protease inhibitors, flavonoids metabolism, transporters and transcription factors were subject to drought hardening or memorized drought in potato.
Operating Characteristics of the Rank-Based Inverse Normal Transformation for Quantitative Trait Analysis in Genome-Wide Association Studies

Quantitative traits analyzed in Genome-Wide Association Studies (GWAS) are often non-normally distributed. For such traits, association tests based on standard linear regression are subject to reduced power and inflated type I error in finite samples. Applying the rank-based Inverse Normal Transformation (INT) to non-normally distributed traits has become common practice in GWAS. However, the different variations on INT-based association testing have not been formally defined, and guidance is lacking on when to use which approach. In this paper, we formally define and systematically compare the direct (D-INT) and indirect (I-INT) INT-based association tests. We discuss their assumptions, underlying generative models, and connections. We demonstrate that the relative powers of D-INT and I-INT depend on the underlying data generating process. Since neither approach is uniformly most powerful, we combine them into an adaptive omnibus test (O-INT). O-INT is robust to model misspecification, protects the type I error, and is well powered against a wide range of non-normally distributed traits. Extensive simulations were conducted to examine the finite sample operating characteristics of these tests. Our results demonstrate that, for non-normally distributed traits, INT-based tests outperform the standard untransformed association test (UAT), both in terms of power and type I error rate control. We apply the proposed methods to GWAS of spirometry traits in the UK Biobank. O-INT has been implemented in the R package RNOmni, which is available on CRAN.
Psychometric assessment of the Multidimensional Quality of Life Questionnaire for Persons Infected with HIV or with AIDS in a cohort of HIV-infected women

This methodological study was designed to assess the psychometric properties of a relatively new HIV-specific quality of life questionnaire, the Multidimensional Quality of Life Questionnaire for Persons Living with HIV or with AIDS (MQOL-HIV), in a cohort of Canadian, HIV-infected women. The study was prompted by an identified lack of information regarding the validity and reliability of HIV-specific quality of life (QOL) scales in populations of HIV-infected women. The specific analyses conducted were content validity, concurrent validity, internal consistency, and test-retest reliability. The study was conducted in the fall of 2001 at the Oak Tree Clinic, British Columbia's outpatient referral centre for women, children, and families living with HIV. Seven health care professionals and six patients participated in the content validity testing, which involved rating the validity of the 40 items and 10 domains of the MQOL-HIV. Eighty-five patients participated in the concurrent validity and internal consistency testing, which involved baseline completion of the MQOL-HIV and the Medical Outcomes Study HIV Health Survey (MOSHIV) during a clinic visit. Forty-three patients participated in the test-retest reliability testing, which involved completing a second MQOL-HIV two weeks after baseline. Content validity findings indicated that most of the items and all of the domains of the scale were valid for HIV-infected women, but that revision and replacement of some of the items were needed. Several important domains and aspects of domains were identified as missing from the scale. Five domains, the Summary Index, and the overall scale demonstrated strong concurrent validity when correlated with similar domains contained in the more commonly used MOS-HIV. Most of the domains demonstrated strong internal consistency and test-retest