Miracle-dz/UniFAR-FTUs huggingface dataset:
The Genome of Mycobacterium Africanum West African 2 Reveals a Lineage-Specific Locus and Genome Erosion Common to the M. tuberculosis Complex

Background M. africanum West African 2 constitutes an ancient lineage of the M. tuberculosis complex that commonly causes human tuberculosis in West Africa and has an attenuated phenotype relative to M. tuberculosis. Methodology/Principal Findings In search of candidate genes underlying these differences, the genome of M. africanum West African 2 was sequenced using classical capillary sequencing techniques. Our findings reveal a unique sequence, RD900, that was independently lost during the evolution of two important lineages within the complex: the “modern” M. tuberculosis group and the lineage leading to M. bovis. Closely related to M. bovis and other animal strains within the M. tuberculosis complex, M. africanum West African 2 shares an abundance of pseudogenes with M. bovis but also with M. africanum West African clade 1. Comparison with other strains of the M. tuberculosis complex revealed pseudogenes events in all the known lineages pointing toward ongoing genome erosion likely due to increased genetic drift and relaxed selection linked to serial transmission-bottlenecks and an intracellular lifestyle. Conclusions/Significance The genomic differences identified between M. africanum West African 2 and the other strains of the Mycobacterium tuberculosis complex may explain its attenuated phenotype, and pave the way for targeted experiments to elucidate the phenotypic characteristic of M. africanum. Moreover, availability of the whole genome data allows for verification of conservation of targets used for the next generation of diagnostics and vaccines, in order to ensure similar efficacy in West Africa.
Thematic Roles Assigned along the Garden Path Linger

In the literature dealing with the reanalysis of garden path sentences such as While the man hunted the deer ran into the woods, it is generally assumed either that people completely repair their initial incorrect syntactic representations to yield a final interpretation whose syntactic structure is fully consistent with the input string or that the parse fails. In a series of five experiments, we explored the possibility that partial reanalyses take place. Specifically, we examined the conditions under which part of the initial incorrect analysis persists at the same time that part of the correct final analysis is constructed. In Experiments 1a and 1b, we found that both the length of the ambiguous region and the plausibility of the ultimate interpretation affected the likelihood that such sentences would be fully reanalyzed. In Experiment 2, we compared garden path sentences with non-garden path sentences and compared performance on two different types of comprehension questions. In Experiments 3a and 3b, we constructed garden path sentences using a small class of syntactically unique verbs to provide converging evidence against the position that people employ some sort of "general reasoning" or pragmatic inference when faced with syntactically difficult garden paths. The results from these experiments indicate that reanalysis of such sentences is not always complete, so that comprehenders often derive an interpretation for the full sentence in which part of the initial misanalysis persists. We conclude that the goal of language processing is not always to create an idealized structure, but rather to create a representation that is "good enough" to satisfy the comprehender that an appropriate interpretation has been obtained.
Mechanical power, thrust power and propelling efficiency: relationships with elite sprint swimming performance

ABSTRACT The purpose of this study was to explore the relationships between mechanical power, thrust power, propelling efficiency and sprint performance in elite swimmers. Mechanical power was measured in 12 elite sprint male swimmers: (1) in the laboratory, by using a whole-body swimming ergometer (W'TOT) and (2) in the pool, by measuring full tethered swimming force (FT) and maximal swimming velocity (Vmax): W'T = FT · Vmax. Propelling efficiency (ηP) was estimated based on the “paddle wheel model” at Vmax. Vmax was 2.17 ± 0.06 m · s−1, ηP was 0.39 ± 0.02, W'T was 374 ± 62 W and W'TOT was 941 ± 92 W. Vmax was better related to W'T (useful power output: R = 0.943, P < 0.001) than to W'TOT (total power output: R = 0.744, P < 0.01) and this confirms the use of the full tethered test as a valid test to assess power propulsion in sprinters and to estimate swimming performance. The ratio W'T/W'TOT (0.40 ± 0.04) represents the fraction of total mechanical power that can be utilised in water (e.g., ηP) and was indeed the same as that estimated based on the “paddle wheel model”; this supports the use of this model to estimate ηP in swimming.
Randomised, parallel-group, multicentre, multinational phase 2 study comparing edoxaban, an oral factor Xa inhibitor, with warfarin for stroke prevention in patients with atrial fibrillation

Summary The primary objective of this study was to compare the safety of four fixed-dose regimens of edoxaban with warfarin in patients with nonvalvular atrial fibrillation (AF). In this 12-week, parallel-group, multi-centre, multinational study, 1,146 patients with AF and risk of stroke were randomised to edoxaban 30 mg qd, 30 mg bid, 60 mg qd, or 60 mg bid or warfarin dose-adjusted to a target international normalised ratio of 2.0–3.0. The study was double-blind to edoxaban dose, but open-label to warfarin. Primary outcomes were occurrence of major and/or clinically relevant non-major bleeding and elevated hepatic enzymes and/or bilirubin. Mean age was 65 ± 8.7 years and 64.4% were warfarin-naïve. Whereas major plus clinically relevant non-major bleeding occurred in 3.2% of patients randomised to warfarin, the incidence of bleeding was significantly higher with the edoxaban 60 mg bid (10.6%; p=0.002) and 30 mg bid regimens (7.8%; p=0.029), but not with the edoxaban 60 mg qd (3.8%) or 30 mg qd regimens (3.0%). For the same total daily dose of 60 mg, both bleeding frequency and trough edoxaban concentrations were higher in the 30-mg bid group than in the 60-mg qd group. There were no significant differences in hepatic enzyme elevations or bilirubin values among the groups. The safety profiles of edoxaban 30 and 60 mg qd in patients with AF were similar to warfarin. In contrast, the edoxaban bid regimens were associated with more bleeding than warfarin. These results suggest that in this three-month study, edoxaban 30 or 60 mg qd are safe and well-tolerated. ClinicalTrials.gov Registration Number: NCT00504556
Decision‐making role preferences and information needs: a comparison of colorectal and breast cancer

Objective An exploratory study has been carried out to examine decision‐making role preferences and information needs for a sample of people with colorectal cancer (n=48). The work replicated a larger study carried out for women with breast cancer (n=150), and this paper compares and contrasts findings for both disease groups.
A gender-based comparison of promotion and research productivity in academic dermatology.

PURPOSE Gender disparities within academic promotion have been reported in several medical specialties. Female representationin association with research productivity has not been reported among academic dermatologists. As research productivity is a heavily weighted factor in determining promotion, we sought to determine whether gender disparities in academic rank and scholarly impact, measured by the h-index, exist in academic dermatology. METHODS In 2015, the authors determined gender and academic rank using academic dermatology department websites. H- index and publication range were determined using the Scopus database. Rank, h-index, and publication range were compared between male and female academic dermatologists. RESULTS The h-index of academic dermatologists increased with successive academic rank from Assistant Professor through Professor (p<0.001), although no significant difference existed between Chairs and Professors. Publication range also increased with each successive rank from Assistant Professor through Professor (p<0.001), with no statistical significant difference between publication range of Chairs and Professors. Overall, men had higher h-indices than female colleagues (p<0.001). This difference was maintained when controlling for academic rank among Assistant Professors, Professors, and Chairs and when controlling for publication range in years. CONCLUSION Women in academic dermatology are underrepresented among senior academic ranks. The difference in scholarly productivity between male and female academic dermatologists may contribute to this disparity. Recommendation for earlyinvolvement in research activities may help minimize this gap.
Effect of sintering profiles on the properties and ageing resistance of Y-TZP ceramic

Commercially available Y-TZP ceramic powder were fabricated under four different sintering profiles in order to investigate the effects of conventional Single-Stage Sintering (SSS) with 1 min and 2 h dwell time, respectively when compared with Two-Stage Sintering (TSS) on the physical and mechanical properties of Y-TZP. Sintering was done up to 1400oC at a ramp rate of 10oC/min. It was revealed that samples sintered via TSS yielded better properties than the SSS samples sintered at 1400oC using a dwell time of 2 hours. In the hydrothermal ageing test, TSS samples did not undergo the lowtemperature degradation via the tetragonal to monoclinic phase transformation.Nevertheless, it was found by XRD analysis that Y-TZP ceramics sintered by the SSS method using a short dwell time of 1 minute was effective in maintaining the tetragonal phase stability after 50 hours of exposure in superheated steam conditions.
The Trauma of Birth

A glass article is moulded by supplying a gob of molten glass to a mould, regulating the temperature of the mould and the time of closure of the mould so that when moulding is complete the surface viscosity of the glass is at mmost 1010.5 poises and the viscosity at the centre of the glass is at most 108 poises, rapidly transferring the article from the mould before the surface viscosity exceeds 1010.5 poises and passing it to a cooling medium where the heat transfer is regulated to cool the article to a temperature such that its surface viscosity is at least 1012.5 poises. The moulding apparatus may open and drop the moulded article into the cooling medium or a gas jet may be provided to blow the article off a support in the open mould into the cooling medium.
Physiological Effects of Visual Stimulation with Forest Imagery

This study was aimed to clarify the physiological effects of visual stimulation using forest imagery on activity of the brain and autonomic nervous system. Seventeen female university students (mean age, 21.1 ± 1.0 years) participated in the study. As an indicator of brain activity, oxyhemoglobin (oxy-Hb) concentrations were measured in the left and right prefrontal cortex using near-infrared time-resolved spectroscopy. Heart rate variability (HRV) was used as an indicator of autonomic nervous activity. The high-frequency (HF) component of HRV, which reflected parasympathetic nervous activity, and the ratio of low-frequency (LF) and high-frequency components (LF/HF), which reflected sympathetic nervous activity, were measured. Forest and city (control) images were used as visual stimuli using a large plasma display window. After sitting at rest viewing a gray background for 60 s, participants viewed two images for 90 s. During rest and visual stimulation, HRV and oxy-Hb concentration in the prefrontal cortex were continuously measured. Immediately thereafter, subjective evaluation of feelings was performed using a modified semantic differential (SD) method. The results showed that visual stimulation with forest imagery induced (1) a significant decrease in oxy-Hb concentrations in the right prefrontal cortex and (2) a significant increase in perceptions of feeling “comfortable,” “relaxed,” and “natural. ”
Influence of Culture Conditions on the Fatty Acids Composition of Green and Purple Photosynthetic Sulphur Bacteria

Within Eubacteria, photosynthetic organisms are found according to the following divisions: (i) gram-positive bacteria belonging to the family Heliobacteriaceae, (ii) green non-sulphur bacteria (also known as filamentous green bacteria) such as Chloroflexus aurantiacus, (iii) green sulphur bacteria such as Chlorobium tepidum, (iv) cyanobacteria, (v) and several genera of proteobacteria (or purple bacteria) [1].
Cost of Lifetime Immunosuppression Coverage for Kidney Transplant Recipients

On January 1, 2000, Medicare extended the coverage of immunosuppression medications from 3 years to life for elderly and disabled kidney transplant recipients. This research estimates the impact of extending this lifetime coverage to all kidney transplant recipients on Medicare's cash flows. The study finds that extending coverage to all kidney transplant recipients would have increased Medicare's net cash outflows if the coverage were extended for patients of all income levels. There is evidence that extending coverage to only patients in the lowest income quartile could have resulted in a net cost savings to Medicare.
High-Resolution Metabolomics Assessment of Military Personnel: Evaluating Analytical Strategies for Chemical Detection

Objective: The aim of this study was to maximize detection of serum metabolites with high-resolution metabolomics (HRM). Methods: Department of Defense Serum Repository (DoDSR) samples were analyzed using ultrahigh resolution mass spectrometry with three complementary chromatographic phases and four ionization modes. Chemical coverage was evaluated by number of ions detected and accurate mass matches to a human metabolomics database. Results: Individual HRM platforms provided accurate mass matches for up to 58% of the KEGG metabolite database. Combining two analytical methods increased matches to 72% and included metabolites in most major human metabolic pathways and chemical classes. Detection and feature quality varied by analytical configuration. Conclusions: Dual chromatography HRM with positive and negative electrospray ionization provides an effective generalized method for metabolic assessment of military personnel.
Implementation of a Standardized Data-Collection System for Comprehensive Appraisal of Cleft Care

Objective: Our objective is to describe the process of adapting a conceptual framework into a practical toolkit for one cleft team. Design: This is a single-arm implementation study in a single institution. Setting: Implementation took place at a mid-sized multidisciplinary clinic for patients with cleft lip and/or palate (CL/P) from urban/suburban and rural areas across North Carolina and neighboring states. Participants: Eligible participants were patients with CL/P from English-speaking families. Sixty patients entered and finished the study. Interventions: The implementation of a prospective data collection system based on the International Consortium for Health Outcomes Measurement (ICHOM) standard set of outcome measures for CL/P was accomplished in multiple stages. Patient- and clinician-reported forms and protocols for gathering data were created. Team members were trained and the system was tested; finally, the system was deployed. Main outcome measures: Success was appraised using the RE-AIM framework to assess reach, effectiveness, adoption, implementation, and maintenance. Results: Ninety-eight percent of patients and all team members agreed to participate. Ninety-four percent of required data were captured. Adaptations to friction points were made; specifically, visible reminders were affixed to charts, primary clinicians were required to assume data entry responsibility, and e-mail reminders were instituted. Development cost was US$7707; average time cost per clinician was 21 min/wk. Conclusions: Conceptual frameworks for outcomes studies must be tailored to their environments; otherwise, they cannot be practically implemented and sustained. We present this process for a cleft team using the ICHOM standard set. The process may help other teams implement the standard set or other conceptual frameworks.
Amygdala-orbitofrontal connectivity predicts alcohol use two years later: a longitudinal neuroimaging study on alcohol use in adolescence.

This study tested the relation between cortical-subcortical functional connectivity and alcohol consumption in adolescents using an accelerated longitudinal design, as well as normative developmental patterns for these measures. Participants between ages 8 and 27 completed resting-state neuroimaging scans at two time points separated by two years (N = 274 at T1, N = 231 at T2). In addition, participants between ages 12 and 27 reported on recent and lifetime alcohol use (N = 193 at T1, N = 244 at T2). Resting-state connectivity analyses focused on amygdala-orbitofrontal connectivity given prior research linking reduced coupling between these regions to alcohol use. Mixed model analyses revealed that age had a cubic relationship with alcohol use, with little to no use in childhood, steep increases in adolescence and leveling off in adulthood. No age effects were found for amygdala-OFC connectivity. Prediction analyses showed that left amygdala-orbitofrontal connectivity at the first time point predicted recent and lifetime alcohol use two years later. There was no evidence for the reversed relation, suggesting that brain connectivity measures precede explorative risk-taking behavior in adolescence, possibly because decreased subcortical-frontal connectivity biases towards more explorative or risky behavior.
Desert Tortoise (Gopherus agassizii) Dietary Specialization Decreases across a Precipitation Gradient

We studied the plant resource use between and within populations of desert tortoise (Gopherus agassizii) across a precipitation gradient in the Sonoran Desert of Arizona. The carbon and nitrogen stable isotope values in animal tissues are a reflection of the carbon and nitrogen isotope values in diet, and consequently represent a powerful tool to study animal feeding ecology. We measured the δ13C and δ15N values in the growth rings on the shells of tortoises in different populations to characterize dietary specialization and track tortoise use of isotopically distinct C4/CAM versus C3 plant resources. Plants using C3 photosynthesis are generally more nutritious than C4 plants and these trait differences can have important growth and fitness consequences for consumers. We found that dietary specialization decreases in successively drier and less vegetated sites, and that broader population niche widths are accompanied by an increase in the dietary variability between individuals. Our results highlight how individual consumer plant resource use is bounded under a varying regime of precipitation and plant productivity, lending insight into how intra-individual dietary specialization varies over a spatial scale of environmental variability.
Asthma-Related Emergency Department Visits in North Carolina, 2010–2014

BACKGROUND The purpose of this study was to compare asthma-related emergency department (ED) visit rates across North Carolina. Results from this study can inform health planning while helping public health and health care professionals in identifying geographical areas and targeting age groups to reduce the asthma burden in North Carolina. METHODS This was a retrospective data analysis between 2010 and 2014 among North Carolina patients presenting to an ED with a first or second listed diagnosis code related to asthma (ICD–9–CM, 493.xx). Data was obtained from the North Carolina Disease Event Tracking and Epidemiology Collection Tool. Annual, age-adjusted rates were standardized to the 2000 US standard population using the direct method. Repeated measures ANOVA was conducted to compare differences between mean values of asthma-related ED visit rates in regions, urbanicity, and age groups across years. RESULTS Asthma ED rates were consistently higher in the east (85.1 per 10,000) compared with other regions. While most age group ED rates fluctuated over the study period, univariate test results indicated statistical increases in ED asthma visits among the groups aged 5 to 9 years (P < .01), and 65 and over (P < .03). CONCLUSION Public health officials should recognize the disproportionate burden of asthma-related ED visits, particularly among rural and impoverished counties in the eastern portion of North Carolina when prioritizing health concerns across North Carolina.
Effectiveness of modified hyper‐CVAD chemotherapy regimen in the treatment of adult acute lymphoblastic leukemia: a retrospective experience

Several chemotherapy regimens have been developed for the treatment of acute lymphoblastic leukemia (ALL), but relapse still presents the most common obstacles to attaining long‐term survival. The hyper‐CVAD (hyperfractionated cyclophosphamide, vincristine, doxorubicin, and prednisolone)/HD MTX and Ara‐C (high‐dose methotrexate and cytarabine) chemotherapy regimen was first started in the MD Anderson Cancer Center as an intensive regimen for adult patients with ALL. The purpose of this study was to evaluate the effectiveness of a modified hyper‐CVAD protocol. We used hyper‐CVAD as consolidation/maintenance after remission induction with daunorubicin, vincristine, and prednisolone (and cyclophosphamide for T‐cell ALL only) rather than standard hyper‐CVAD in order to reduce treatment complications. This study was conducted as a retrospective review of medical records of ALL patients at 501 army hospital, Tehran, Iran, from 2005 to 2015. Three hundred and one patients underwent modified hyper‐CVAD chemotherapy regimen. Complete remission and overall survival (OS) rates were measured as primary endpoints. Two hundred and forty‐six (81.7%) reached complete remission (CR) during the first 6 months of treatment, and 55 patients (18.3%) did not reach CR. The 5‐year OS rate was 51.8% (95% CI (confidence interval): 45.1–57.8%). Modified hyper‐CVAD regimen is an efficient intensive chemotherapy regimen for consolidation/maintenance of adults with newly diagnosed ALL and has an acceptable 5‐year overall that is comparable to standard hyper‐CVAD regimen.