Miracle-dz/UniFAR-FTUs huggingface dataset:
Chest radiograph findings in children aged 2–59 months hospitalised with community-acquired pneumonia, prior to the introduction of pneumococcal conjugate vaccine in India: a prospective multisite observational study

Objectives The current study was a hospital-based surveillance of cases hospitalised with WHO-defined community-acquired pneumonia in children aged 2–59 months, to assess the radiological abnormalities in chest X-rays and to identify the demographic and clinical correlates of specific radiological abnormalities, in residents of prespecified districts of Uttar Pradesh and Bihar, India. Design Prospective, active, hospital-based surveillance. Setting Multisite study conducted in a network of 117 secondary/tertiary care hospitals in four districts of Uttar Pradesh and Bihar, India. Participants Included were children aged 2–59 months, hospitalised with community-acquired pneumonia, residing in the project district, with duration of illness <14 days and who had not been hospitalised elsewhere for this episode nor had been recruited previously. Main outcome measure Concordant radiological abnormalities in the chest X-rays. Results From January 2015 to April 2017, 3214 cases were recruited and in 99.40% (3195/3214) chest X-rays were available, among which 88.54% (2829/3195) were interpretable. Relevant radiological abnormalities were found in 34.53% (977/2829, 95% CI 32.78 to 36.28). These were primary end point pneumonia alone or with other infiltrates in 22.44% (635/2829, 95% CI 20.90% to 23.98%) and other infiltrates in 12.09% (342/2829; 95% CI 10.88% to 13.29%). There was a statistically significant interdistrict variation in radiological abnormalities. Statistically significantly higher proportion of abnormal chest X-rays were found in girls, those with weight-for-age z-score ≤−3SD, longer duration of fever, pallor and with exposure to biomass fuel. Conclusions Among hospitalised cases of community-acquired pneumonia, almost one-third children had abnormal chest radiographs, which were higher in females, malnourished children and those with longer illnesses; and an intra-district variation was observed.
The Valuation of Recreational Use of Wetlands and the Impact of the Economic Crisis

The economic valuation of environmental resources is of great interest to society in general and to public managers in particular. It can promote more sustainable environmental policies, as it clearly shows the high economic value of natural resources. Thus, these valuation tools can provide useful evidence to support such policies by quantifying the economic value associated with the protection of such resources. However, there is an inherent difficulty in the implementation of methods to assess the economic valuation of environmental resources, mainly as a result of the absence of a market and hence a price that explains its social demand. However, both the travel cost method and the contingent valuation method used in this paper offer an approach to the economic values of the recreational services for wetlands. The aim is to analyze whether these values have been influenced by the economic crisis, so two time periods are compared separated for a decade. Results do not show an unequivocal influence between values in both periods, with different behaviors among natural areas, although with a certain tendency to increase in the decade being analyzed.
The biology of Mustelus schmitti in southern Patagonia, Argentina

The relationship of body weight and total length (L T ) of Mustelus schmitti in southern Patagonia was different between sexes. Changes in maturity stages in males appear at larger sizes in Ria Deseado specimens than in the Mar del Plata area. Mature females ranged from 795 to 913 mm while all male specimens > 759 mm L T were mature. The data suggest that mating occurs before parturition, with simultaneous ovulation. The diet of adult M. schmitti was mainly carcinophage and the diet of young-of-the-year and adults differed. The young-of-the-year use the Ria Deseado as a pupping area.
Nicotine Dependence and Factors Related to Smoking Cessation among Physicians in Estonia

Smoking withdrawal can be difficult due to nicotine dependence (ND). The study objective was to describe ND and to analyze the association between ND and factors related to smoking cessation among daily smoking physicians in Estonia. Data was collected in 2014, using cross-sectional postal survey sampling all practicing physicians (n = 5666) in Estonia, of whom 2939 responded (corrected response rate 53.1%). The study sample was restricted to daily smoking physicians (n = 171). Results of the Fagerström Test for Nicotine Dependence (FTND) were described and ND scores calculated. Logistic regression was used to determine the association of ND (at-least-moderate vs. low) with factors related to smoking cessation. Crude and fully adjusted ORs with 95% CIs were calculated. The mean FTND score was 2.8 ± 2.1. The odds of having at-least-moderate ND decreased significantly with each year postponing smoking initiation (OR = 0.82, 95% CI 0.72–0.94). After adjustment, ND was no longer associated with the desire to quit smoking and motives to quit. In conclusion, more than half of daily smoking physicians had low ND. Higher ND was associated with younger age of smoking initiation. Knowledge of ND and factors related to smoking cessation is useful in the prevention of smoking and in development of cessation counselling tailored for physicians.
The Association of Frailty With Adverse Outcomes After Multisystem Trauma: A Systematic Review and Meta-analysis

BACKGROUND: Frailty strongly predicts adverse outcomes in a variety of clinical settings; however, frailty-related trauma outcomes have not been systematically reviewed and quantitatively synthesized. Our objective was to systematically review and meta-analyze the association between frailty and outcomes (mortality-primary; complications, health resource use, and patient experience-secondary) after multisystem trauma. METHODS: After registration (CRD42018104116), we applied a peer-reviewed search strategy to MEDLINE, EMBASE, and Comprehensive Index to Nursing and Allied Health Literature (CINAHL) from inception to May 22, 2019, to identify studies that described: (1) multisystem trauma; (2) participants ≥18 years of age; (3) explicit frailty instrument application; and (4) relevant outcomes. Excluded studies included those that: (1) lacked a comparator group; (2) reported isolated injuries; and (3) reported mixed trauma and nontrauma populations. Criteria were applied independently, in duplicate to title/abstract and full-text articles. Risk of bias was assessed using the Risk of Bias in Nonrandomized Studies-of Interventions (ROBINS-I) tool. Effect measures (adjusted for prespecified confounders) were pooled using random-effects models; otherwise, narrative synthesis was used. RESULTS: Sixteen studies were included that represented 5198 participants; 9.9% of people with frailty died compared to 4.2% of people without frailty. Frailty was associated with increased mortality (adjusted odds ratio [OR], 1.53; 95% confidence interval [CI], 1.37–1.71), complications (adjusted OR, 2.32; 95% CI, 1.72–3.15), and adverse discharge (adjusted OR, 1.78; 95% CI, 1.29–2.45). Patient function, experience, and resource use outcomes were rarely reported. CONCLUSIONS: The presence of frailty is significantly associated with mortality, complications, and adverse discharge disposition after multisystem trauma. This provides important prognostic information to inform discussions with patients and families and highlights the need for trauma system optimization to meet the complex needs of older patients.
Biochemical analysis of cross‐feeding behaviour between two common gut commensals when cultivated on plant‐derived arabinogalactan

In this paper, we reveal and characterize cross‐feeding behaviour between the common gut commensal Bacteroides cellulosilyticus (Baccell) and certain bifidobacterial strains, including Bifidobacterium breve UCC2003, when grown on a medium containing Larch Wood Arabinogalactan (LW‐AG). We furthermore show that cross‐feeding is dependent on the release of β‐1,3‐galacto‐di/trisaccharides (β‐1,3‐GOS), and identified that the bga gene cluster of B. breve UCC2003 allows β‐1,3‐GOS metabolism. The product of bgaB is presumed to be responsible for the import of β‐1,3‐GOS, while the bgaA gene product, a glycoside hydrolase family 2 member, was shown to hydrolyse both β‐1,3‐galactobiose and β‐1,3‐galactotriose into galactose monomers. This study advances our understanding of strain‐specific syntrophic interactions between two glycan degraders in the human gut in the presence of AG‐type dietary polysaccharides.
The function of kin discrimination

Kin discrimination should be a tactic in the fitness strategy of individuals. Two postulates derived from inclusive fitness theory that fitness benefits toward kin are correlated with degree of relatedness and that social behavior of members of a kin group is always cooperative are refuted by analyses of the social dynamics of yellowbellied marmots. Cooperative behavior occurs predominantly between mother/ daughter and sister/sister pairs, but such pairs also compete. More distant kin are treated similarly to unrelated animals, social behavior is primarily agonistic. Patterns of space-use, matrilineal formation and organization, social dynamics, and reproductive suppression of close kin suggest that marmots attempt to maximize direct fitness.
Metabolic and Lipidomic Profiling of Vegetable Juices Fermented with Various Probiotics

Fermented vegetable juices have gained attention due to their various beneficial effects on human health. In this study, we employed gas chromatography–mass spectrometry, direct infusion-mass spectrometry, and liquid chromatography–mass spectrometry to identify useful metabolites, lipids, and carotenoids in vegetable juice (VJ) fermented with Lactobacillus plantarum HY7712, Lactobacillus plantarum HY7715, Lactobacillus helveticus HY7801, and Bifidobacterium animalis ssp. lactis HY8002. A total of 41 metabolites, 24 lipids, and 4 carotenoids were detected in the fermented and non-fermented VJ (control). The lycopene, α-carotene, and β-carotene levels were higher in VJ fermented with L. plantarum strains (HY7712 and HY7715) than in the control. Proline content was also elevated in VJ fermented with HY7715. Uracil, succinic acid, and α-carotene concentration was increased in VJ fermented with HY7801, while glycine and lycopene levels were raised in VJ fermented with HY8002. This study confirmed that each probiotic strain has distinctive characteristics and produces unique changes to metabolic profiles of VJ during fermentation. Our results suggest that probiotic-fermented VJ is a promising functional beverage that contains more beneficial metabolites and carotenoids than commercial non-fermented VJ.
Long‐term mortality in the Intermediate care after emergency abdominal surgery (InCare) trial—A post‐hoc follow‐up study

Patients undergoing emergency abdominal surgery are at high risk of post‐operative complications. Although post‐operative treatment at an intermediate care unit may improve early outcome, there is a lack of studies on the long‐term effects of such therapy. The aim of this study was to assess the long‐term effect of intermediate care versus standard surgical ward care on mortality in the Intermediate Care After Emergency Abdominal Surgery (InCare) trial.
Fluorene exposure among PAH-exposed workers is associated with epigenetic markers related to lung cancer

Objectives Exposure to high-molecular-weight polycyclic aromatic hydrocarbons (PAHs) may cause cancer in chimney sweeps and creosote-exposed workers, however, knowledge about exposure to low-molecular-weight PAHs in relation to cancer risk is limited. In this study, we aimed to investigate occupational exposure to the low-molecular-weight PAHs phenanthrene and fluorene in relation to different cancer biomarkers. Methods We recruited 151 chimney sweeps, 19 creosote-exposed workers and 152 unexposed workers (controls), all men. We measured monohydroxylated metabolites of phenanthrene and fluorene in urine using liquid chromatography coupled to tandem mass spectrometry. We measured, in peripheral blood, the cancer biomarkers telomere length and mitochondrial DNA copy number using quantitative PCR; and DNA methylation of F2RL3 and AHRR using pyrosequencing. Results Median PAH metabolite concentrations were higher among chimney sweeps (up to 3 times) and creosote-exposed workers (up to 353 times), compared with controls (p<0.001; adjusted for age and smoking). ∑OH-fluorene (sum of 2-hydroxyfluorene and 3-hydroxyfluorene) showed inverse associations with percentage DNA methylation of F2RL3 and AHRR in chimney sweeps (B (95% CI)=–2.7 (–3.9 to –1.5) for F2RL3_cg03636183, and –7.1 (–9.6 to –4.7) for AHRR_cg05575921: adjusted for age and smoking), but not in creosote-exposed workers. In addition, ∑OH-fluorene showed a 42% mediation effect on the inverse association between being a chimney sweep and DNA methylation of AHRR CpG2. Conclusions Chimney sweeps and creosote-exposed workers were occupationally exposed to low-molecular-weight PAHs. Increasing fluorene exposure, among chimney sweeps, was associated with lower DNA methylation of F2RL3 and AHRR, markers for increased lung cancer risk. These findings warrant further investigation of fluorene exposure and toxicity.
A Rat Liver Transcriptomic Point of Departure Predicts a Prospective Liver or Non-Liver Apical Point of Departure.

Identifying a toxicity point of departure (POD) is a required step in human health risk characterization of crop protection molecules, and this POD has historically been derived from apical endpoints across a battery of animal-based toxicology studies. Using rat transcriptome and apical data for 79 molecules obtained from Open TG-GATES (Toxicogenomics Project-Genomics Assisted Toxicity Evaluation System) (632 datasets), the hypothesis was tested that a short-term exposure, transcriptome-based liver biological effect POD (BEPOD) could estimate a longer-term exposure "systemic" apical endpoint POD. Apical endpoints considered were body weight, clinical observation, kidney weight and histopathology and liver weight and histopathology. A BMDExpress algorithm using Gene Ontology Biological Process gene sets was optimized to derive a liver BEPOD most predictive of a systemic apical POD. Liver BEPODs were stable from 3 hours to 29 days of exposure; the median fold difference of the 29 day BEPOD to BEPODs from earlier time points was approximately 1 (range of 0.7-1.1). Strong positive correlation (Pearson R = 0.86) and predictive accuracy (root mean square difference = 0.41) were observed between a concurrent (29 day) liver BEPOD and the systemic apical POD. Similar Pearson R and root mean square difference values were observed for comparisons between a 29 day systemic apical POD and liver BEPODs derived from 3 hours to 15 days of exposure. These data across 79 molecules suggest that a longer-term exposure study apical POD from liver and non-liver compartments can be estimated using a liver BEPOD derived from an acute or subacute exposure study.
Ethyl glucuronide, a marker of alcohol consumption, correlates with metabolic markers of oxidant stress but not with hemolysis in stored red blood cells from healthy blood donors

Red blood cell (RBC) storage in the blood bank is associated with the progressive accumulation of oxidant stress. While the mature erythrocyte is well equipped to cope with such stress, recreative habits like alcohol consumption may further exacerbate the basal level of oxidant stress and contribute to the progress of the storage lesion.
Enhancing medication adherence in older adults at two nurse practitioner–owned clinics

ABSTRACT Background: The World Health Organization identified medication adherence as the greatest opportunity to improve outcomes related to chronic disease. Adherence rates of 80% or greater, or taking medication as prescribed at least 80% of the time, can positively impact health outcomes. Local problem: A prior study at two nurse practitioner (NP)–owned family practice clinics in New Hampshire measured medication adherence among adult type-2 diabetes mellitus (DM) patients at 77% and declining over a 4-year period. Patients' hemoglobin A1c rates were stagnant despite previous initiative to improve this biomarker. Methods: Nurse practitioners were educated on provider-driven strategies to improve medication adherence in the older adult with DM, hypertension, and hyperlipidemia. A review of medical records was performed on patients for 52 weeks before seminar and 13 weeks after seminar to capture medication adherence rates and clinical biomarkers. Intervention: Pre- and postseminar data were analyzed to determine whether the seminar resulted in improved adherence and clinical outcomes. Results: Preseminar medication adherence rates exceeded evidence-based standards of 80% for each condition. Postseminar, statistically significant improved adherence rates were seen among DM patients with hypertension. Adherence worsened among hyperlipidemia patients, although this change was not statistically significant. Clinical biomarkers saw little change. Conclusions: This quality improvement project found that educating NPs on strategies to improve medication adherence can improve adherence among DM and hypertension patients. Continued education and measurement of adherence and clinical biomarkers are encouraged to capture more postseminar visits. This project adds to the growing body of knowledge about patients managed by NPs and NP-owned practices.
A response‐locking protocol to boost sensitivity for fMRI‐based neurochronometry

The timeline of brain‐wide neural activity relative to a behavioral event is crucial when decoding the neural implementation of a cognitive process. Yet, fMRI assesses neural processes indirectly via delayed and regionally variable hemodynamics. This method‐inherent temporal distortion impacts the interpretation of behavior‐linked neural timing. Here we describe a novel behavioral protocol that aims at disentangling the BOLD dynamics of the pre‐ and post‐response periods in response time tasks. We tested this response‐locking protocol in a perceptual decision‐making (random dot) task. Increasing perceptual difficulty produced expected activity increases over a broad network involving the lateral/medial prefrontal cortex and the anterior insula. However, response‐locking revealed a previously unreported functional dissociation within this network. preSMA and anterior premotor cortex (prePMV) showed post‐response activity modulations while anterior insula and anterior cingulate cortex did not. Furthermore, post‐response BOLD activity at preSMA showed a modulation in timing but not amplitude while this pattern was reversed at prePMV. These timeline dissociations with response‐locking thus revealed three functionally distinct sub‐networks in what was seemingly one shared distributed network modulated by perceptual difficulty. These findings suggest that our novel response‐locked protocol could boost the timing‐related sensitivity of fMRI.
High-yielding lines of wheat carrying Gpc-B1 adapted to Mediterranean-type environments of the south and west of Australia

Abstract. The Gpc-B1 gene from wild emmer has been proposed as a potential mechanism for improving grain protein in bread wheat without reducing grain yield. Near-isolines with and without the Gpc-B1 gene in three Australian-adapted genetic backgrounds, Gladius, Wyalkatchem and VR1128, were compared in 14 experiments across the south and west of Australia for grain yield, grain protein content and grain weight. The donor parents of Gpc-B1 were the Canadian cultivars Burnside and Somerset. One of the 14 experiments was discarded because of inadequate rust control and confounding effects of Yr36, a gene closely linked to Gpc-B1. Heading date and test weight were measured in five experiments. Across all comparisons, Gpc-B1 increased grain protein content and reduced grain weight, with a negligible effect on grain yield. Selected lines containing Gpc-B1 in a Wyalkatchem background had comparable grain yields to the elite cultivar Mace, but with significantly higher grain protein contents, slightly higher grain weights, similar heading dates and acceptable test weights. The development of agronomically acceptable lines containing Gpc-B1 was partially attributed to the removal of undesirable genes from wild emmer during the breeding of the Canadian donor parents and the use of Australian recurrent parents with high test weights.
A homozygous variant in NDUFA8 is associated with developmental delay, microcephaly, and epilepsy due to mitochondrial complex I deficiency

Mitochondrial complex I deficiency is caused by pathogenic variants in mitochondrial and nuclear genes associated with complex I structure and assembly. We report the case of a patient with NDUFA8‐related mitochondrial disease. The patient presented with developmental delay, microcephaly, and epilepsy. His fibroblasts showed apparent biochemical defects in mitochondrial complex I. Whole‐exome sequencing revealed that the patient carried a homozygous variant in NDUFA8. His fibroblasts showed a reduction in the protein expression level of not only NDUFA8, but also the other complex I subunits, consistent with assembly defects. The enzyme activity of complex I and oxygen consumption rate were restored by reintroducing wild‐typeNDUFA8 cDNA into patient fibroblasts. The functional properties of the variant in NDUFA8 were also investigated using NDUFA8 knockout cells expressing wild‐type or mutated NDUFA8 cDNA. These experiments further supported the pathogenicity of the variant in complex I assembly. This is the first report describing that the loss of NDUFA8, which has not previously been associated with mitochondrial disease, causes severe defect in the assembly of mitochondrial complex I, leading to progressive neurological and developmental abnormalities.
Outcome measurement in speech and language therapy: a digital journey

Background Evidencing the impact of speech and language therapy interventions is challenging. The UK’s professional body for speech and language therapists (SLTs) is supporting a consistent approach to outcome measurement and analysis using Therapy Outcome Measures (TOMs). Objective To develop a digital solution for collecting TOMs data, evaluate the impact of therapeutic interventions and explore contributing factors to outcome variation across clinical areas. Method Agile methodology was applied to software development. Organisations were recruited to provide data. Criteria were identified to exemplify outcome variability. Results A digital tool was developed. 21 organisations provided data on 16 356 individuals. Improvement in at least one domain of TOMs occurred in 77.1% of instances. Data for two clinical areas exemplify the tool’s effectiveness in highlighting the impact of speech and language therapy. Conclusion This established outcomes data set can be used to evaluate the impact of speech and language therapy, and explore variation in outcomes.