Miracle-dz/UniFAR-FTUs huggingface dataset:
Distribution of Chlamydia trachomatis ompA genotypes in patients attending a sexually transmitted disease outpatient clinic in New Delhi, India

Background & objectives: Limited data are available on the typing of Chlamydia trachomatis in India. Serovars D to K of C. trachomatis are chiefly responsible for urogenital infections. Thus, this study was conducted to determine the distribution of C. trachomatis serovars in patients with urogenital infections and to characterize omp A gene of the detected C. trachomatis isolates by sequence analysis. Presence of other co-infections was also evaluated. Methods: Endocervical swabs were collected from 324 women and urethral swabs/urine were collected from 193 men attending the sexually transmitted diseases outpatient clinic. The samples were screened for C. trachomatis by cryptic plasmid PCR and omp A gene PCR. Genotyping was performed by PCR-restriction fragment length polymorphism (RFLP) and sequencing of the omp A gene. Samples were screened for genital mycoplasmas, Neisseria gonorrhoeae, Treponema pallidum and human immunodeficiency virus (HIV). Results: C. trachomatis was found in 15.0 per cent men and 10.8 per cent women. Serovar D was the most prevalent followed by serovars E, F, I and G. Twenty two C. trachomatis isolates were selected for omp A gene sequencing. No mixed infection was found. Variability in omp A sequences was seen in 31.8 per cent cases. Both PCR-RFLP and omp A gene sequencing showed concordant results. The presence of Ureaplasma spp. and Mycoplasma hominis was observed in 18.7 and 9.5 per cent patients, respectively. Co-infection of C. trachomatis was significantly associated with Ureaplasma urealyticum and HIV. Interpretation & conclusions: The high occurence of C. trachomatis infections warrants its screening in addition to other sexually transmitted infections namely U. urealyticum and HIV. Genotyping of the omp A gene may provide additional information for vaccine development.
Untargeted Assessment of Tumor Fractions in Plasma for Monitoring and Prognostication from Metastatic Breast Cancer Patients Undergoing Systemic Treatment

The aim of this study was to assess the prognostic and predictive value of an untargeted assessment of tumor fractions in the plasma of metastatic breast cancer patients and to compare circulating tumor DNA (ctDNA) with circulating tumor cells (CTC) and conventional tumor markers. In metastatic breast cancer patients (n = 29), tumor fractions in plasma were assessed using the untargeted mFAST-SeqS method from 127 serial blood samples. Resulting z-scores for the ctDNA were compared to tumor fractions established with the recently published ichorCNA algorithm and associated with the clinical outcome. We observed a close correlation between mFAST-SeqS z-scores and ichorCNA ctDNA quantifications. Patients with mFAST-SeqS z-scores above three (34.5%) showed significantly worse overall survival (p = 0.014) and progression-free survival (p = 0.018) compared to patients with lower values. Elevated z-score values were clearly associated with radiologically proven progression. The baseline CTC count, carcinoembryonic antigen (CEA), and cancer antigen (CA)15-5 had no prognostic impact on the outcome of patients in the analyzed cohort. This proof of principle study demonstrates the prognostic impact of ctDNA levels detected with mFAST-SeqS as a very fast and cost-effective means to assess the ctDNA fraction without prior knowledge of the genetic landscape of the tumor. Furthermore, mFAST-SeqS-based ctDNA levels provided an early means of measuring treatment response.
Associations between Indoor Air Pollution and Acute Respiratory Infections among Under-Five Children in Afghanistan: Do SES and Sex Matter?

Background: Low-income families often depend on fuels such as wood, coal, and animal dung for cooking. Such solid fuels are highly polluting and are a primary source of indoor air pollutants (IAP). We examined the association between solid fuel use (SFU) and acute respiratory infection (ARI) among under-five children in Afghanistan and the extent to which this association varies by socioeconomic status (SES) and gender. Materials and Methods: This is a cross-sectional study based on de-identified data from Afghanistan’s first standard Demographic and Health Survey (DHS) conducted in 2015. The sample consists of ever-married mothers with under-five children in the household (n = 27,565). We used mixed-effect Poisson regression models with robust error variance accounting for clustering to examine the associations between SFU and ARI among under-five children after adjusting for potential confounders. We also investigated potential effect modification by SES and sex. Additional analyses were conducted using an augmented measure of the exposure to IAP accounting for both SFU and the location of cooking/kitchen (High Exposure, Moderate, and No Exposure). Results: Around 70.2% of households reported SFU, whereas the prevalence of ARI was 17.6%. The prevalence of ARI was higher in children living in households with SFU compared to children living in households with no SFU (adjusted prevalence ratio (aPR) = 1.10; 95% CI: (0.98, 1.23)). We did not observe any effect modification by SES or child sex. When using the augmented measure of exposure incorporating the kitchen’s location, children highly exposed to IAP had a higher prevalence of ARI compared to unexposed children (aPR = 1.17; 95% CI: (1.03, 1.32)). SES modified this association with the strongest associations observed among children from the middle wealth quintile. Conclusion: The findings have significant policy implications and suggest that ARI risk in children may be reduced by ensuring there are clean cookstoves as well as clean fuels and acting on the socio-environmental pathways.
Exploratory analysis of genetic variants influencing molecular traits in cerebral cortex of suicide completers

Genetic factors have been implicated in suicidal behavior. It has been suggested that one of the roles of genetic factors in suicide could be represented by the effect of genetic variants on gene expression regulation. Alteration in the expression of genes participating in multiple biological systems in the suicidal brain has been demonstrated, so it is imperative to identify genetic variants that could influence gene expression or its regulatory mechanisms. In this study, we integrated DNA methylation, gene expression, and genotype data from the prefrontal cortex of suicides to identify genetic variants that could be factors in the regulation of gene expression, generally called quantitative trait locus (xQTLs). We identify 6,224 methylation quantitative trait loci and 2,239 expression quantitative trait loci (eQTLs) in the prefrontal cortex of suicide completers. The xQTLs identified influence the expression of genes involved in neurodevelopment and cell organization. Two of the eQTLs identified (rs8065311 and rs1019238) were previously associated with cannabis dependence, highlighting a candidate genetic variant for the increased suicide risk in subjects with substance use disorders. Our findings suggest that genetic variants may regulate gene expression in the prefrontal cortex of suicides through the modulation of promoter and enhancer activity, and to a lesser extent, binding transcription factors.
Effects of Bio-Banding upon Physical and Technical Performance during Soccer Competition: A Preliminary Analysis

Bio-banded competition has been introduced to address the variation in physical maturity within soccer. To date, no research has investigated the effect of bio-banded competition relative to chronological competition. The current study investigated the effect of bio-banding upon physical and technical performance in elite youth soccer athletes. Twenty-five male soccer athletes (11–15 years) from an English Premier League soccer academy participated in bio-banded and chronological competition, with physical and technical performance data collected for each athlete. Athletes were between 85–90% of predicted adult stature, and sub-divided into early, on-time and late developers. For early developers, significantly more short passes, significantly less dribbles and a higher rating of perceived exertion (RPE) were evident during bio-banded competition compared to chronological competition (p < 0.05). Significantly more short passes and dribbles, and significantly fewer long passes were seen for on-time developers during bio-banded competition (p < 0.05). For late developers, significantly more tackles, and significantly fewer long passes were evident during bio-banded competition (p < 0.05). No significant differences in physical performance were identified between competition formats. Results demonstrated that bio-banded competition changed the technical demand placed upon athletes compared to chronological competition, without reducing the physical demands. Bio-banded competition can be prescribed to athletes of differing maturation groups dependent upon their specific developmental needs.
Neurophysiological correlates of collective perceptual decision-making

Humans frequently coordinate with others in daily life. A recent study on perceptual decision-making showed that dyad members with similar individual performances attain a higher joint performance than the better dyad member (i.e., a collective benefit). However, little is known about the physiological basis of these results. Here, we replicate this earlier work and also investigate the neurophysiological correlates of decision-making using EEG. In a two interval forced choice task, co-actors individually indicated presence of a target stimulus with a higher contrast and then indicated their confidence on a rating scale. Viewing the individual ratings, dyads made a joint decision. Replicating earlier work, we found a positive correlation between the similarity of individual performances and collective benefit. We analyzed event related potentials (ERPs) in three phases (i.e., stimulus onset, response, and feedback) using explorative cluster mass permutation tests. At stimulus onset, ERPs were significantly linearly related to our manipulation of contrast differences, validating our manipulation of task difficulty. For individual and joint responses, we found a significant centro-parietal error-related positivity for correct versus incorrect responses, which suggests that accuracy is already evaluated at the response level. At feedback presentation, we found a significant late positive fronto-central potential elicited by incorrect joint responses, suggesting a stronger emotional response to negative as compared to positive feedback. In sum, these results demonstrate that response- and feedback-related components elicited by an error-monitoring system differentially integrate conflicting information exchanged during the joint decision-making process.
Fast photochemistry in wintertime haze: Consequences for pollution mitigation strategies.

In contrast to summer smog, the contribution of photochemistry to the formation of winter haze in northern mid-to-high latitude is generally assumed to be minor due to reduced solar UV and water vapor concentrations. Our comprehensive observations of atmospheric radicals and relevant parameters during several haze events in winter 2016 Beijing, however, reveal surprisingly high hydroxyl radical (OH) oxidation rates up to 15 ppbv/h which is comparable to the high values reported in summer photochemical smog and is 2-3 times larger than those determined in previous observations during winter in Birmingham1, Tokyo2, and New York3. The active photochemistry facilitates the production of secondary pollutants. It is mainly initiated by the photolysis of nitrous acid, ozonolysis of olefins and maintained by an extremely efficiently radical cycling process driven by nitric oxide (NO). This boosted radical recycling generates fast photochemical ozone production rates that are again comparable to those during summer photochemical smog. The formation of ozone, however, is currently masked by its efficient chemical removal by nitrogen oxides contributing to the high level of wintertime particles. The future emission regulations, such as the reduction of nitrogen oxide emissions, therefore are facing the challenge of reducing haze and avoiding an increase in ozone pollution at the same time. Efficient control strategies to mitigate winter haze in Beijing may require measures similar as implemented to avoid photochemical smog in summer.
Dietary Fat Intake and Metabolic Syndrome in Older Adults

Background: Metabolic Syndrome (MetS) is associated with higher rates of cardiovascular disease (CVD), type 2 diabetes mellitus, and cancer worldwide. Objective: To assess fat intake in older adults with or without MetS. Design: Cross-sectional nutritional survey in older adults living in the Balearic Islands (n = 477, 48% women, 55–80 years old) with no previous CVD. Methods: Assessment of fat (total fat, MUFA, PUFA, SFA, TFA, linoleic acid, α-linolenic acid, marine and non-marine ω-3 FA, animal fat and vegetable fat, cholesterol) and macronutrient intake using a validated food frequency questionnaire, and its comparison with recommendations of the US Institute of Medicine (IOM) and the Spanish Society of Community Nutrition (SENC). Results: Participants with MetS showed higher BMI, lower physical activity, higher total fat and MUFA intake, and lower intake of energy, carbohydrates, and fiber than participants without MetS. Men and women with MetS were below the Acceptable Macronutrient Distribution Range (AMDR) proposed by IOM for carbohydrates and above the AMDR for total fat and MUFAs, and women were below the AMDR proposed for α-linolenic acid (ALA) compared with participants without MetS. Conclusions: Subjects with MetS were less likely to meet IOM and SENC recommendations for fat and macronutrient intakes as compared to non-MetS subjects.
Remarkable Effect of [Li(G4)]TFSI Solvate Ionic Liquid (SIL) on the Regio- and Stereoselective Ring Opening of α-Gluco Carbasugar 1,2-Epoxides

Carba analogues of biologically relevant natural carbohydrates are promising structures for the development of future drugs endowed with enhanced hydrolytic stability. An open synthetic challenge in this field is the optimization of new methodologies for the stereo- and regioselective opening of α-gluco carbasugar 1,2-epoxides that allow for the preparation of pseudo mono- and disaccharides of great interest. Therefore, we investigated the effect of Lewis acids and solvate ionic liquids (SILs) on the epoxide ring opening of a model substrate. Of particular interest was the complete stereo- and regioselectivity, albeit limited to simple nucleophiles, toward the desired C(1) isomer that was observed using LiClO4. The results obtained with SILs were also remarkable. In particular, Li[NTf2]/tetraglyme ([Li(G4)]TFSI) was able to function as a Lewis acid and to direct the attack of the nucleophile preferentially at the pseudo anomeric position, even with a more complex and synthetically interesting nucleophile. The regioselectivity observed for LiClO4 and [Li(G4)]TFSI was tentatively ascribed to the formation of a bidentate chelating system, which changed the conformational equilibrium and ultimately permitted a trans-diaxial attack on C(1). To the best of our knowledge, we report here the first case in which SILs were successfully employed in a ring-opening process of epoxides.
Characterizing the Risk of Long-Term Opioid Utilization in Patients Undergoing Lumbar Spine Surgery.

STUDY DESIGN Single-institution retrospective cohort study. OBJECTIVE To determine whether prescribing practices at discharge are associated with opioid dependence in patients undergoing discectomy or laminectomy procedures for degenerative indications. SUMMARY OF BACKGROUND DATA Long-term opioid use in spine surgery is associated with higher healthcare utilization and worse postoperative outcomes. The impact of prescribing practices at discharge within this surgical population is poorly understood. METHODS A query of an administrative database was conducted to identify all patients undergoing discectomy or laminectomy procedures at our high volume tertiary referral center between 2007 and 2016. For patients included in the analysis, opioid prescription data on admission and discharge were manually abstracted from the electronic health record, including opioid type, frequency, route, and dose, and then converted to daily morphine equivalent dose (MED) values. We defined opioid dependence as a consecutive narcotic prescription lasting for at least 90 days within the first 12 months following the index surgical procedure. RESULTS Of the 819 total patients, 499 (60.9%) patients had an active opioid prescription before surgery. Postoperatively, 813 (99.3%) received at least one narcotic prescription within 30 days of index surgery, and 162 (19.8%) continued with sustained opioid use in the 12 months following surgery. In adjusted analysis, patients with opioid dependence had a higher incidence of preoperative depression (p = 0.012) and preoperative opioid use (p < 0.001), as well as a higher frequency of preoperative benzodiazepine prescriptions (p = 0.009), and discharge MED value exceeding 120 mg/d (p = 0.013). Postoperative opioid dependence was observed in 7.5% of previously opioid-naïve patients. CONCLUSION This is the first study to test for an association between MED values prescribed at discharge and sustained opioid use after lumbar spine surgery. In addition to previously reported risk factors, discharge prescription dose exceeding 120 mg/day is independently associated with opioid dependence following spine surgery. LEVEL OF EVIDENCE 3.
Balanced actions of protein synthesis and degradation in memory formation

Storage of long-term memory requires not only protein synthesis but also protein degradation. In this article, we overview recent publications related to this issue, stressing that the balanced actions of protein synthesis and degradation are critical for long-term memory formation. We particularly focused on the brain-derived neurotrophic factor signaling that leads to protein synthesis; proteasome- and autophagy-dependent protein degradation that removes molecular constraints; the role of Fragile X mental retardation protein in translational suppression; and epigenetic modifications that control gene expression at the genomic level. Numerous studies suggest that an imbalance between protein synthesis and degradation leads to intellectual impairment and cognitive disorders.
Performance of horizontal sub-surface flow constructed wetlands with different flow patterns using dual media for low-strength municipal wastewater: a case of pilot scale experiment in a tropical climate region

Abstract The work presented in this paper is based on the pilot study that was performed to investigate the role of flow pattern in the constructed wetlands (CWs) on the treatment performance of real low-strength municipal wastewater. Four identical pilot-scale horizontal sub-surface flow constructed wetlands (HSSF-CWs) were installed, out of which three beds were planted with a common macrophyte, whereas one was kept as a control. The distinction in the hydraulic design was baffles, vertical up-down (CW2) and side slits (CW3), and the third bed (CW1) was kept horizontal plain type (without baffles). The filter media used in all the beds was dual type, coarse and fine gravel. Monitoring was carried out to determine BOD5, COD, TSS, NH4+-N, TN, and TP concentrations at different sampling points. Results show that the baffled beds performed better compared to the non-baffled in the order of CW2 > CW3 > CW1 > Control. The highest removal efficiency was measured in the CW2 with a reduction in BOD5 (86%), COD (77%), TSS (80%), NH4+-N (59%), TN (66%), and TP (64%). The statistical method used also showed that the flow pattern has an impact on the treatment performances of the CWs.
Parental stressor exposure simultaneously conveys both adaptive and maladaptive larval phenotypes through epigenetic inheritance in the zebrafish (Danio rerio)

ABSTRACT Genomic modifications occur slowly across generations, whereas short-term epigenetic inheritance of adaptive phenotypes may be immediately beneficial to large numbers of individuals, acting as a bridge for survival when adverse environments occur. In the present study, crude oil was used as an example of an environmental stressor. Adult zebrafish (P0) were dietarily exposed for 3 weeks to no, low, medium or high concentrations of crude oil. The F1 offspring obtained from the P0 groups were then assessed for transgenerational epigenetic transfer of oil-induced phenotypes. The exposure did not alter body length, body and organ mass or condition factor in the P0 groups. However, the P0 fecundity of both sexes decreased in proportion to the amount of oil fed. The F1 larvae from each P0 were then exposed from 3 hpf to 5 dpf to oil in their ambient water. Remarkably, F1 larvae derived from oil-exposed parents, when reared in oiled water, showed a 30% enhanced survival compared with controls (P<0.001). Unexpectedly, from day 3 to 5 of exposure, F1 larvae from oil-exposed parents showed poorer survival in clean water (up to 55% decreased survival). Additionally, parental oil exposure induced bradycardia (presumably maladaptive) in F1 larvae in both clean and oiled water. We conclude that epigenetic transgenerational inheritance can lead to an immediate and simultaneous inheritance of both beneficial and maladaptive traits in a large proportion of the F1 larvae. The adaptive responses may help fish populations survive when facing transient environmental stressors. Editors' Choice: Exposure to environmental stressors may be detrimental for a population; however, it may prompt epigenetically inherited adaptive phenotypes in the offspring, acting as a bridge for survival when persistent stressors occur.
The Bateman domain of IMP dehydrogenase is a binding target for dinucleoside polyphosphates

IMP dehydrogenase (IMPDH) is an essential enzyme that catalyzes the rate-limiting step in the de novo guanine nucleotide biosynthetic pathway. Because of its involvement in the control of cell division and proliferation, IMPDH represents a therapeutic for managing several diseases, including microbial infections and cancer. IMPDH must be tightly regulated, but the molecular mechanisms responsible for its physiological regulation remain unknown. To this end, we recently reported an important role of adenine and guanine mononucleotides that bind to the regulatory Bateman domain to allosterically modulate the catalytic activity of eukaryotic IMPDHs. Here, we have used enzyme kinetics, X-ray crystallography, and small-angle X-ray scattering (SAXS) methodologies to demonstrate that adenine/guanine dinucleoside polyphosphates bind to the Bateman domain of IMPDH from the fungus Ashbya gossypii with submicromolar affinities. We found that these dinucleoside polyphosphates modulate the catalytic activity of IMPDHs in vitro by efficiently competing with the adenine/guanine mononucleotides for the allosteric sites. These results suggest that dinucleoside polyphosphates play important physiological roles in the allosteric regulation of IMPDHs by adding an additional mechanism for fine-tuning the activities of these enzymes. We propose that these findings may have important implications for the design of therapeutic strategies to inhibit IMPDHs.