Miracle-dz/UniFAR-FTUs huggingface dataset:
An Efficient Phase Domain Synchronous Machine Model With Constant Equivalent Admittance Matrix

In this paper, a new synchronous machine model is developed for electromagnetic transients program type simulations. The stator circuit is expressed in the abc phase domain. The machine model is represented as a Norton equivalent with a current source in parallel with a constant Norton admittance. The machine equations are reformulated so that the computational effort required for the modeling of the machine is reduced. Test studies demonstrate the accuracy of the proposed synchronous machine model and show that the proposed model is computationally more efficient than the existing constant conductance phase domain model and voltage-behind-reactance model.
Search for proton decay into e/sup +/. pi. °

Observations were made 1570 meters of water equivalent underground with an 8000-metric-ton water Cherenkov detector. During a live time of 80 d no events consistent with the decay p.-->. e/sup +/. pi. /sup 0/ were found in a fiducial mass of 3300 metric tons. It is concluded that the limit on the lifetime for bound plus free protons divided by the e/sup +/. pi. /sup 0/ branching ratio is tau/B>6.5 x 10/sup 31/ yr; for free protons the limit is tau/B>1.9 x 10/sup 31/ yr (90% confidence). Observed cosmic-ray muons and neutrinos are compatible with expectations.
DNA methylation in people with anorexia nervosa: Epigenome-wide patterns in actively ill, long-term remitted, and healthy-eater women

Abstract Objectives Recent studies have reported altered methylation levels at disorder-relevant DNA sites in people who are ill with Anorexia Nervosa (AN) compared to findings in people with no eating disorder (ED) or in whom AN has remitted. The preceding implies state-related influences upon gene expression in people with AN. This study further examined this notion. Methods We measured genome-wide DNA methylation in 145 women with active AN, 49 showing stable one-year remission of AN, and 64 with no ED. Results Comparisons revealed 205 differentially methylated sites between active and no ED groups, and 162 differentially methylated sites between active and remitted groups (Q < 0.01). Probes tended to map onto genes relevant to psychiatric, metabolic and immune functions. Notably, several of the genes identified here as being differentially methylated in people with AN (e.g. SYNJ2, PRKAG2, STAT3, CSGALNACT1, NEGR1, NR1H3) have figured in previous studies on AN. Effects also associated illness chronicity and lower BMI with more pronounced DNA methylation alterations, and remission of AN with normalisation of DNA methylation. Conclusions Findings corroborate earlier results suggesting reversible DNA methylation alterations in AN, and point to particular genes at which epigenetic mechanisms may act to shape AN phenomenology.
Topical application of Porphyromonas gingivalis into the gingival pocket in mice leads to chronic-active infection, periodontitis and systemic inflammation

Porphyromonas gingivalis (Pg), one of the 'red-complex' perio-pathogens known to play a critical role in the development of periodontitis, has been used in various animal models to mimic human bacteria-induced periodontitis. In order to achieve a more realistic animal model of human Pg infection, the present study investigated whether repeated small-volume topical applications of Pg directly into the gingival pocket can induce local infection, including periodontitis and systemic vascular inflammation in wild-type mice. Freshly cultured Pg was topically applied directly into the gingival pocket of the second molars for 5 weeks (3 times/week). After the final application, the mice were left in cages for 4 or 8 weeks and sacrificed. The status of Pg colony formation in the pocket, gingival inflammation, alveolar bone loss, the expression levels of pro-inflammatory cytokines in the serum and aorta, the presence of anti-Pg lipopolysaccharide (LPS) and gingipain (Kpg and RgpB) antibodies in the serum, as well as the accumulation of Pg LPS and gingipain aggregates in the gingiva and arterial wall were evaluated. The topical application of Pg into the gingival pocket induced the following local and systemic pathohistological changes in mice when examined at 4 or 8 weeks after the final topical Pg application: Pg colonization in the majority of gingival pockets; increased gingival pocket depths; gingival inflammation indicated by the increased expression of TNF-α, IL-6 and IL-1β; significant loss of alveolar bone at the sites of topical Pg application; and increased levels of pro-inflammatory cytokines, such as TNF-α, IL-1β, IL-17, IL-13, KC and IFN-γ in the serum in comparison to those from mice receiving PBS. In addition, the Pg application/colonization model induced anti-Pg LPS and gingipain antibodies in serum, as well as the accumulation of Pg LPS and gingipain aggregates in the gingivae and arterial walls. To the best of our knowledge, this mouse model represents the first example of creating a more sustained local infection in the gingival tissues of wild-type mice and may prove to be useful for the investigation of the more natural and complete pathogenesis of the bacteria in the development of local oral and systemic diseases, such as atherosclerosis. It may also be useful for the determination of a treatment/prevention/efficacy model associated with Pg-induced colonization periodontitis in mice.
Incidence and prevalence of pulmonary tuberculosis among patients with type 2 diabetes mellitus: a systematic review and meta-analysis

Abstract Background The epidemic of type 2 diabetes mellitus (T2DM) poses a great challenge to pulmonary tuberculosis (PTB) control. However, the incidence and prevalence of PTB among T2DM patients has not been fully determined. This meta-analysis aimed to provide the estimation on the global incidence and prevalence of PTB among T2DM patients (T2DM-PTB). Methods Online databases including Web of Science, PubMed, China National Knowledge Infrastructure and Cochrane Library were searched for all relevant studies that reported the incidence or prevalence of T2DM-PTB through 31 January 2022. Pooled incidence and prevalence of T2DM-PTB with 95% confidence interval (CI) was estimated by the random-effect model. All statistical analyses were performed using R software. Results A total of 24 studies (14 cohort studies, 10 cross-sectional studies) were included. The pooled incidence and prevalence of T2DM-PTB were 129.89 per 100,000 person-years (95% confidence interval (CI): 97.55–172.95) and 511.19 per 100,000 (95% CI: 375.94–695.09), respectively. Subgroup analyses identified that the incidence of T2DM-PTB was significantly higher in Asia (187.20 per 100,000 person-years, 95% CI: 147.76–237.17), in countries with a high TB burden (172.04 per 100,000 person-years, 95% CI: 122.98–240.68) and in studies whose data collection ended before 2011 (219.81 per 100,000 person-years, 95% CI: 176.15–274.28), but lower in studies using International Classification of Diseases-10 codes (73.75 per 100,000 person-years, 95% CI: 40.92–132.91). The prevalence of T2DM-PTB was significantly higher in countries with a high TB burden (692.15 per 100,000, 95% CI: 468.75–1022.04), but lower in Europe (105.01 per 100,000, 95% CI: 72.55–151.98). Conclusions This systematic review and meta-analysis suggests high global incidence and prevalence of PTB among T2DM patients, underlining the necessity of more preventive interventions among T2DM patients especially in countries with a high TB-burden. Key messages A total of 24 studies (14 cohort studies, 10 cross-sectional studies) containing 2,569,451 T2DM patients were included in this meta-analysis. The pooled incidence and prevalence of T2DM-PTB are 129.89 per 100,000 person-years (95% CI: 97.55–172.95) and 511.19 per 100,000 (95% CI: 375.94–695.09) respectively. The incidence of T2DM-PTB was significantly higher in Asia, in countries with a high TB burden and in studies whose data collection ended before 2011, but lower in studies using International Classification of Diseases-10 codes. The prevalence of T2DM-PTB was significantly higher in countries with a high TB-burden, but lower in Europe.
The metabolome of Mexican cavefish shows a convergent signature highlighting sugar, antioxidant, and Ageing-Related metabolites

Insights from organisms, which have evolved natural strategies for promoting survivability under extreme environmental pressures, may help guide future research into novel approaches for enhancing human longevity. The cave-adapted Mexican tetra, Astyanax mexicanus, has attracted interest as a model system for metabolic resilience, a term we use to denote the property of maintaining health and longevity under conditions that would be highly deleterious in other organisms (Figure 1). Cave-dwelling populations of Mexican tetra exhibit elevated blood glucose, insulin resistance and hypertrophic visceral adipocytes compared to surface-dwelling counterparts. However, cavefish appear to avoid pathologies typically associated with these conditions, such as accumulation of advanced-glycation-end-products (AGEs) and chronic tissue inflammation. The metabolic strategies underlying the resilience properties of A. mexicanus cavefish, and how they relate to environmental challenges of the cave environment, are poorly understood. Here, we provide an untargeted metabolomics study of long- and short-term fasting in two A. mexicanus cave populations and one surface population. We find that, although the metabolome of cavefish bears many similarities with pathological conditions such as metabolic syndrome, cavefish also exhibit features not commonly associated with a pathological condition, and in some cases considered indicative of an overall robust metabolic condition. These include a reduction in cholesteryl esters and intermediates of protein glycation, and an increase in antioxidants and metabolites associated with hypoxia and longevity. This work suggests that certain metabolic features associated with human pathologies are either not intrinsically harmful, or can be counteracted by reciprocal adaptations. We provide a transparent pipeline for reproducing our analysis and a Shiny app for other researchers to explore and visualize our dataset.
Discrimination of cancerous from benign pigmented skin lesions based on multispectral autofluorescence lifetime imaging dermoscopy and machine learning

Abstract. Significance: Accurate early diagnosis of malignant skin lesions is critical in providing adequate and timely treatment; unfortunately, initial clinical evaluation of similar-looking benign and malignant skin lesions can result in missed diagnosis of malignant lesions and unnecessary biopsy of benign ones. Aim: To develop and validate a label-free and objective image-guided strategy for the clinical evaluation of suspicious pigmented skin lesions based on multispectral autofluorescence lifetime imaging (maFLIM) dermoscopy. Approach: We tested the hypothesis that maFLIM-derived autofluorescence global features can be used in machine-learning (ML) models to discriminate malignant from benign pigmented skin lesions. Clinical widefield maFLIM dermoscopy imaging of 41 benign and 19 malignant pigmented skin lesions from 30 patients were acquired prior to tissue biopsy sampling. Three different pools of global image-level maFLIM features were extracted: multispectral intensity, time-domain biexponential, and frequency-domain phasor features. The classification potential of each feature pool to discriminate benign versus malignant pigmented skin lesions was evaluated by training quadratic discriminant analysis (QDA) classification models and applying a leave-one-patient-out cross-validation strategy. Results: Classification performance estimates obtained after unbiased feature selection were as follows: 68% sensitivity and 80% specificity with the phasor feature pool, 84% sensitivity, and 71% specificity with the biexponential feature pool, and 84% sensitivity and 32% specificity with the intensity feature pool. Ensemble combinations of QDA models trained with phasor and biexponential features yielded sensitivity of 84% and specificity of 90%, outperforming all other models considered. Conclusions: Simple classification ML models based on time-resolved (biexponential and phasor) autofluorescence global features extracted from maFLIM dermoscopy images have the potential to provide objective discrimination of malignant from benign pigmented lesions. ML-assisted maFLIM dermoscopy could potentially assist with the clinical evaluation of suspicious lesions and the identification of those patients benefiting the most from biopsy examination.
Modeling of the electron beam induced current signal in nanowires with an axial p-n junction

A tridimensional mathematical model to calculate the electron beam induced current (EBIC) of an axial p-n nanowire junction is proposed. The effect of the electron beam and junction parameters on the distribution of charge carriers and on the collected EBIC current is reported. We demonstrate that the diffusion of charge carriers within the wire is strongly influenced by the electrical state of its lateral surface which is characterized by a parameter called surface recombination velocity (v r). When the surface recombination is weak (i.e. low v r value), the diffusion of charge carriers occurs in one dimension (1D) along the wire axis, and, in this case, the use of bulk EBIC models to extract the diffusion length (L) of charge carriers is justified. However, when the surface effects are strong (i.e. high v r values), the diffusion happens in three dimensions (3D). In this case, the EBIC profiles depend on v r value and two distinct cases can be defined. If the L is larger than the nanowire radius (r a), the EBIC profiles show a strong dependency with this parameter. This gives evidence that the recombination of generated carriers on the surface through v r is the dominant process. In this situation, a decrease of two orders of magnitude in the EBIC profiles computed with a high and a low v r value is observed in neutral regions of the junction. For the case of L smaller than r a the dependency of the EBIC profiles on the v r is weak, and the prevalent recombination mechanism is the bulk recombination process.
Tallo: A global tree allometry and crown architecture database

Data capturing multiple axes of tree size and shape, such as a tree's stem diameter, height and crown size, underpin a wide range of ecological research—from developing and testing theory on forest structure and dynamics, to estimating forest carbon stocks and their uncertainties, and integrating remote sensing imagery into forest monitoring programmes. However, these data can be surprisingly hard to come by, particularly for certain regions of the world and for specific taxonomic groups, posing a real barrier to progress in these fields. To overcome this challenge, we developed the Tallo database, a collection of 498,838 georeferenced and taxonomically standardized records of individual trees for which stem diameter, height and/or crown radius have been measured. These data were collected at 61,856 globally distributed sites, spanning all major forested and non‐forested biomes. The majority of trees in the database are identified to species (88%), and collectively Tallo includes data for 5163 species distributed across 1453 genera and 187 plant families. The database is publicly archived under a CC‐BY 4.0 licence and can be access from: https://doi.org/10.5281/zenodo.6637599. To demonstrate its value, here we present three case studies that highlight how the Tallo database can be used to address a range of theoretical and applied questions in ecology—from testing the predictions of metabolic scaling theory, to exploring the limits of tree allometric plasticity along environmental gradients and modelling global variation in maximum attainable tree height. In doing so, we provide a key resource for field ecologists, remote sensing researchers and the modelling community working together to better understand the role that trees play in regulating the terrestrial carbon cycle.
Doing Optimality Theory

Acknowledgments. Read This First! List of Abbreviations. 1. An Introduction to Optimality Theory. 1.1 How OT Began. 1.2 Why Must Constraints Be Violable? 1.3 The Nature of Constraints in OT. 1.4 Candidate Sets: OT's Gen Component. 1.5 Candidate Evaluation: OT's Eval Component. 1.6 Constraint Activity. 1.7 Differences Between Languages. 1.8 The Version of OT Discussed in This Book. 1.9 Suggestions for Further Reading. 2. How to Construct an Analysis. 2.1 Where to Begin. 2.2 How to Rank Constraints. 2.3 Working through an Analysis in Phonology. 2.4 The Limits of Ranking Arguments. 2.5 Candidates in Ranking Arguments. 2.6 Harmonic Bounding. 2.7 Constraints in Ranking Arguments. 2.8 Inputs in Ranking Arguments. 2.9 Working through an Analysis in Syntax. 2.10 Finding and Fixing Problems in an Analysis. 2.11 Constraint Ranking by Algorithm and Computer. 2.12 The Logic of Constraint Ranking and Its Uses. 3. How to Write Up an Analysis. 3.1 Introduction. 3.2 How to Organize a Paper. 3.3 How to Present an OT analysis. 3.4 The Responsibilities of Good Scholarship. 3.5 How to Write Clearly. 3.6 General Advice about Research Topics. 4. Developing New Constraints. 4.1 Introduction. 4.2 When Is It Necessary to Modify Con? 4.3 How to Discover a New Constraint. 4.4 How to Define a New Constraint. 4.5 Properties of Markedness Constraints. 4.6 Properties of Faithfulness Constraints. 4.7 Justifying Constraints. 4.8 A Classified List of Common Phonological Markedness Constraints. 5. Language Typology and Universals. 5.1 Factorial Typology. 5.2 Languages Universals and How to Explain Them in OT. 5.3 Investigating the Factorial Typology of a Constraint Set. 5.4 Using Factorial Typology to Test New Constraints. 5.5 Factorial Typology When Con Isn't Fully Known. 5.6 How to Proceed from Typology to Constraints. 6. Some Current Research Questions. 6.1 Introduction. 6.2 How Does a Language Vary? 6.3 How Is Language Acquired? 6.4 Does OT Need Derivations? 6.5 How Is Ungrammaticality Accounted For? 6.6 Is Faithfulness Enough? Afterword. References. Constraint Index. Language Index. Subject Index
Performance of Xpert MTB/RIF and Mycobacterial Culture on Multiple Specimen Types for Diagnosis of Tuberculosis Disease in Young Children and Clinical Characterization According to Standardized Research Case Definitions

Background: Tuberculosis (TB) is a leading cause of illness and death in children globally. Improved bacteriologic and clinical diagnostic approaches in children are urgently needed. Methods: In a prospective cohort study, a consecutive series of young (<5 years) children presenting with symptoms suggestive of TB and parenchymal abnormality on chest radiograph in inpatient and outpatient settings in Kisumu County, Kenya from October 2013 to August 2015 were evaluated at baseline and over 6 months. Up to 14 specimens per child were tested for the Mycobacterium tuberculosis complex by fluorescence microscopy, Xpert MTB/RIF and mycobacterial culture. Using detailed clinical characterization, cases were retrospectively classified according to standardized research case definitions and the sensitivity and specificity of microbiological tests on different specimen types were determined. Results: Among 300 young children enrolled, 266 had sufficient information to be classified according to the research clinical case definition. Of these, 36% (96/266) had TB disease; 32% (31/96) with bacteriologically confirmed intrathoracic TB. Compared to culture, the sensitivity of a single Xpert test ranged from 60 to 67% and specificity from 97.5 to 100% for different specimen types. Conclusions: Despite extensive specimen collection and laboratory testing, TB could not be bacteriologically confirmed in almost two-thirds of children with intrathoracic TB classified by research clinical case definitions. Improved diagnostic tests are needed to identify children with TB and to exclude other potential causes of illness.
Temporal changes in the proportion of Salmonella outbreaks associated with 12 food commodity groups in the United States

Abstract Using data from 20 years of Salmonella foodborne outbreaks, this study investigates significant trends in the proportion of outbreaks associated with 12 broad commodity groups. Outbreak counts are demonstrated to have a stronger trend signal than outbreak illness counts. The number of outbreaks with an identified food vehicle increased significantly between 1998 and 2000. This was followed by a 10-year period when the number of outbreaks decreased. The number of outbreaks increased significantly between 2010 and 2014 and then remained unchanged for the remainder of the study period. During the period of 1998 through 2017, the proportion of outbreaks for three commodities groups, consisting of eggs, pork and seeded vegetables, changed significantly. No significant changes were observed in the remaining nine commodity groups. Simple approximations are derived to highlight the effect of dependencies between outbreak proportions and a consumption analysis for meat and poultry is used to enhance the limited interpretability of the changes in these proportions. Given commodity-specific approaches to verifying food safety and promoting pathogen reduction, regulatory agencies benefit from analyses that elucidate illness trends attributable to the products under their jurisdiction. Results from this trend analysis can be used to inform the development and assessment of new pathogen reduction programmes in the United States.
Basic mobility, accidental falls, and lifetime physical activity among rural and urban community-dwelling older adults: a population-based study in Northern Iceland

ABSTRACT The objective of this research was to investigate late-life physical functioning and lifetime history of physical activity (PA) among older adults in rural and urban Arctic communities. Data was collected in a cross-sectional, population-based study among 65 to 92-year-old community-dwelling Icelanders (N = 175, 41% ≥75-year-old, 43% women, 40% rural). Late-life physical functioning was operationalised as: basic mobility (Timed Up and Go in seconds, TUG); fall risk (TUG≥12 sec); a fall (≥1 fall/year); and recurrent falls (≥2 falls/year). PA history was based on a self-assessment. Compared to urban participants, rural participants were more likely to have fallen recently, be at fall risk, and describe more PA history. Among urban participants, no fall in the past year was independently associated with more PA in middle adulthood; and worse basic mobility and late-life fall risk were independently associated with being in the ≥75-year-old group. Among rural participants, recurrent falls were independently associated with being a man; and better basic mobility was independently associated with more PA in late adulthood. To conclude, this evidence supports an important association between better late-life physical functioning and more mid- and late-life PA and encourages further research to understand high fall risk among older men in Arctic rural areas.