Miracle-dz/UniFAR-FTUs huggingface dataset:
Depression, Anxiety, and Cigarette Smoking Among Patients with Tuberculosis

Smoking adversely affects tuberculosis (TB) outcomes and may be associated with depression and anxiety among people diagnosed with TB in Botswana. We conducted a cross-sectional study among patients newly diagnosed with TB in Gaborone, Botswana, evaluating factors associated with self-reported cigarette smoking. We performed Poisson regression analyses with robust variance to examine whether depressive and anxiety symptoms were associated with smoking. Among 180 participants with TB enrolled from primary health clinics, depressive symptoms were reported in 47 (26.1%) participants and anxiety symptoms were reported in 85 (47.2%) participants. Overall, 45 (25.0%) participants reported current smoking. Depressive symptoms were associated with a higher prevalence of smoking (adjusted prevalence ratio [aPR]: 2.04; 95% confidence interval [CI]: 1.29–3.25) in the adjusted analysis. The association between anxiety symptoms and smoking did not reach statistical significance (aPR: 1.26; 95% CI: 0.77–2.05). Future studies should further investigate these associations when addressing TB care.
Phase-space mass bound for fermionic dark matter from dwarf spheroidal galaxies

We reconsider the lower bound on the mass of a fermionic dark matter (DM) candidate resulting from the existence of known small Dwarf Spheroidal galaxies, in the hypothesis that their DM halo is constituted by degenerate fermions, with phase-space density limited by the Pauli exclusion principle. By relaxing the common assumption that the DM halo scale radius is tied to that of the luminous stellar component and by marginalizing on the unknown stellar velocity dispersion anisotropy, we prove that observations lead to rather weak constraints on the DM mass, that could be as low as tens of eV. In this scenario, however, the DM halos would be quite large and massive, so that a bound stems from the requirement that the time of orbital decay due to dynamical friction in the hosting Milky Way DM halo is longer than their lifetime. The smallest and nearest satellites Segue I and Willman I lead to a final lower bound of $m\gtrsim100$ eV, still weaker than previous estimates but robust and independent on the model of DM formation and decoupling. We thus show that phase space constraints do not rule out the possibility of sub-keV fermionic DM.
Multi-step motion planning: application to free-climbing robots

This dissertation addresses the problem of planning the motion of a multi-limbed robot to “free-climb” vertical rock surfaces. Free-climbing relies on natural features and friction (such as holes or protrusions) rather than special fixtures or tools. It requires strength, but more importantly it requires deliberate reasoning: not only must the robot decide how to adjust its posture to reach the next feature without falling, it must plan an entire sequence of steps, where each one might have future consequences. This process of reasoning is called multi-step planning. A multi-step planning framework is presented for computing non-gaited, free-climbing motions. This framework derives from an analysis of a free-climbing robot's configuration space, which can be decomposed into constraint manifolds associated with each state of contact between the robot and its environment. An understanding of the adjacency between manifolds motivates a two-stage strategy that uses a candidate sequence of steps to direct the subsequent search for motions. Three algorithms are developed to support the framework. The first algorithm reduces the amount of time required to plan each potential step, a large number of which must be considered over an entire multi-step search. It extends the probabilistic roadmap (PRM) approach based on an analysis of the interaction between balance and the topology of closed kinematic chains. The second algorithm addresses a problem with the PRM approach, that it is unable to distinguish challenging steps (which may be critical) from impossible ones. This algorithm detects impossible steps explicitly, using automated algebraic inference and machine learning. The third algorithm provides a fast constraint checker (on which the PRM approach depends), in particular a test of balance at the initially unknown number of sampled configurations associated with each step. It is a method of incremental precomputation, fast because it takes advantage of the sample distribution. Validation with real hardware was done with a four-limbed, free-climbing robot called LEMUR (developed by the Mechanical and Robotic Technologies Group at NASA-JPL). Using the multi-step planner presented in this dissertation, LEMUR free-climbed an indoor, near-vertical surface with artificial rock features. It did so with limited control and sensing, demonstrating that planning is absolutely critical.
Virulence Potential of Escherichia coli Isolates from a Beef Farm in Puerto Rico

Sixteen Escherichia coli isolates were obtained from fecal matter from a beef farm in Puerto Rico. Isolates were whole-genome sequenced for in silico characterization, including pathotype characterization, virulence, and plasmid identification. The results of the draft genomes identified potential pathogenic E. coli strains from beef cattle in Puerto Rico. ABSTRACT Sixteen Escherichia coli isolates were obtained from fecal matter from a beef farm in Puerto Rico. Isolates were whole-genome sequenced for in silico characterization, including pathotype characterization, virulence, and plasmid identification. The results of the draft genomes identified potential pathogenic E. coli strains from beef cattle in Puerto Rico.
Colonic Epithelial Circadian Disruption Worsens Dextran Sulfate Sodium–Induced Colitis

Abstract Background Disruption of central circadian rhythms likely mediated by changes in microbiota and a decrease in gut-derived metabolites like short chain fatty acids (SCFAs) negatively impacts colonic barrier homeostasis. We aimed to explore the effects of isolated peripheral colonic circadian disruption on the colonic barrier in a mouse model of colitis and explore the mechanisms, including intestinal microbiota community structure and function. Methods Colon epithelial cell circadian rhythms were conditionally genetically disrupted in mice: TS4Cre-BMAL1lox (cBMAL1KO) with TS4Cre as control animals. Colitis was induced through 5 days of 2% dextran sulfate sodium (DSS). Disease activity index and intestinal barrier were assessed, as were fecal microbiota and metabolites. Results Colitis symptoms were worse in mice with peripheral circadian disruption (cBMAL1KO). Specifically, the disease activity index and intestinal permeability were significantly higher in circadian-disrupted mice compared with control animals (TS4Cre) (P < .05). The worsening of colitis appears to be mediated, in part, through JAK (Janus kinase)-mediated STAT3 (signal transducer and activator of transcription 3), which was significantly elevated in circadian-disrupted (cBMAL1KO) mice treated with DSS (P < .05). Circadian-disrupted (cBMAL1KO) mice also had decreased SCFA metabolite concentrations and decreased relative abundances of SCFA-producing bacteria in their stool when compared with control animals (TS4Cre). Conclusions Disruption of intestinal circadian rhythms in colonic epithelial cells promoted more severe colitis, increased inflammatory mediators (STAT3 [signal transducer and activator of transcription 3]), and decreased gut microbiota–derived SCFAs compared with DSS alone. Further investigation elucidating the molecular mechanisms behind these findings could provide novel circadian directed targets and strategies in the treatment of inflammatory bowel disease.
Effect of Selective Decontamination of the Digestive Tract on Hospital Mortality in Critically Ill Patients Receiving Mechanical Ventilation: A Randomized Clinical Trial.

Importance Whether selective decontamination of the digestive tract (SDD) reduces mortality in critically ill patients remains uncertain. Objective To determine whether SDD reduces in-hospital mortality in critically ill adults. Design, Setting, and Participants A cluster, crossover, randomized clinical trial that recruited 5982 mechanically ventilated adults from 19 intensive care units (ICUs) in Australia between April 2018 and May 2021 (final follow-up, August 2021). A contemporaneous ecological assessment recruited 8599 patients from participating ICUs between May 2017 and August 2021. Interventions ICUs were randomly assigned to adopt or not adopt a SDD strategy for 2 alternating 12-month periods, separated by a 3-month interperiod gap. Patients in the SDD group (n = 2791) received a 6-hourly application of an oral paste and administration of a gastric suspension containing colistin, tobramycin, and nystatin for the duration of mechanical ventilation, plus a 4-day course of an intravenous antibiotic with a suitable antimicrobial spectrum. Patients in the control group (n = 3191) received standard care. Main Outcomes and Measures The primary outcome was in-hospital mortality within 90 days. There were 8 secondary outcomes, including the proportion of patients with new positive blood cultures, antibiotic-resistant organisms (AROs), and Clostridioides difficile infections. For the ecological assessment, a noninferiority margin of 2% was prespecified for 3 outcomes including new cultures of AROs. Results Of 5982 patients (mean age, 58.3 years; 36.8% women) enrolled from 19 ICUs, all patients completed the trial. There were 753/2791 (27.0%) and 928/3191 (29.1%) in-hospital deaths in the SDD and standard care groups, respectively (mean difference, -1.7% [95% CI, -4.8% to 1.3%]; odds ratio, 0.91 [95% CI, 0.82-1.02]; P = .12). Of 8 prespecified secondary outcomes, 6 showed no significant differences. In the SDD vs standard care groups, 23.1% vs 34.6% had new ARO cultures (absolute difference, -11.0%; 95% CI, -14.7% to -7.3%), 5.6% vs 8.1% had new positive blood cultures (absolute difference, -1.95%; 95% CI, -3.5% to -0.4%), and 0.5% vs 0.9% had new C difficile infections (absolute difference, -0.24%; 95% CI, -0.6% to 0.1%). In 8599 patients enrolled in the ecological assessment, use of SDD was not shown to be noninferior with regard to the change in the proportion of patients who developed new AROs (-3.3% vs -1.59%; mean difference, -1.71% [1-sided 97.5% CI, -∞ to 4.31%] and 0.88% vs 0.55%; mean difference, -0.32% [1-sided 97.5% CI, -∞ to 5.47%]) in the first and second periods, respectively. Conclusions and Relevance Among critically ill patients receiving mechanical ventilation, SDD, compared with standard care without SDD, did not significantly reduce in-hospital mortality. However, the confidence interval around the effect estimate includes a clinically important benefit. Trial Registration ClinicalTrials.gov Identifier: NCT02389036.
Imp2p forms actin-dependent clusters and imparts stiffness to the contractile ring

The contractile ring must anchor to the plasma membrane and cell wall to transmit its tension. F-BAR domain containing proteins including Imp2p and Cdc15p in fission yeast are likely candidate anchoring proteins based on their mutant phenotypes. Cdc15p is a node component, links the actin bundle to the plasma membrane, recruits Bgs1p to the division plane, prevents contractile ring sliding, and contributes to the stiffness of the contractile ring. Less is known about Imp2p. We found that similarly to Cdc15p, Imp2p contributes to the stiffness of the contractile ring and assembles into protein clusters. Imp2p clusters contain approximately eight Imp2p dimers and depend on the actin network for their stability at the division plane. Importantly, Imp2p and Cdc15p reciprocally affect the amount of each other in the contractile ring, indicating that the two proteins influence each other during cytokinesis, which may partially explain their similar phenotypes.
Relationship between nurses' resilience and depression, anxiety and stress during the 2021 COVID‐19 outbreak in Taiwan

The COVID‐19 outbreak in Taiwan had a significant impact on medical services. These changes posed a threat to nurses' mental health. Resilience may protect nurses from the psychological impact of COVID‐19. This study aimed to understand nurses' resilience and its relationship with nurses' characteristics (life and work situations) and mental health (depression, anxiety and stress) during the outbreak.
Contemporary Clinical Research in the Management of Pelvic Organ Prolapse in the United States: A Systematic Review

Importance Pelvic organ prolapse (POP) can cause bothersome symptoms that negatively affect quality of life. Management strategies include observation, conservative management, and surgery. Objective The purpose of this study was to evaluate the current focus of research in POP. Study Design We queried clinicaltrials.gov, a registry of clinical research studies maintained by the U.S. National Library of Medicine, for active, recruiting, and enrolling studies involving POP. Results A total of 104 unique clinical trials were included for analysis. Investigators most commonly specialized in obstetrics and gynecology (obstetrician-gynecologists [ob-gyns]; n = 66, 57.9%); urologists numbered 5 (4.4%). The most common subspecialty was urogynecology (n = 46, 40.4%). Seventy-six percent of clinical research involved surgical intervention. The second most common field of research was diagnostic evaluation of POP (8.4%). Only 12.1% of clinical research focused on conservative measures, and 2.8% investigated medications. Objective outcome measures were used more often than subjective or mixed measures (42.3%, 22.3%, and 32.7%, respectively). The most common outcome measure was Pelvic Organ Prolapse Quantification (14.5%), followed by the mixed measure, “composite success” (8.7%). Conclusions Urologists are less involved in POP research than ob-gyns. Urogynecologists from either background are most involved. Most clinical research involves surgical management of POP, despite the fact that less than 20% of women pursue surgical correction. Despite dubious concordance with quality of life, objective outcome measures are used more often than subjective or mixed measures to assess severity of POP. Clinical research in POP should be directed to better align with the needs and preferences of patients.
Spatially resolved spectroscopy across stellar surfaces: II. High-resolution spectra across HD 209458 (G0 V)

Context. High-resolution spectroscopy across spatially resolved stellar surfaces aims at obtaining spectral-line profiles that are free from rotational broadening; the gradual changes of these profiles from disk center toward the stellar limb reveal properties of atmospheric fine structure, which are possible to model with 3D hydrodynamics. Aims. Previous such studies have only been carried out for the Sun but are now extended to other stars. In this work, profiles of photospheric spectral lines are retrieved across the disk of the planet-hosting star HD 209458 (G0 V). Methods. During exoplanet transit, stellar surface portions successively become hidden and differential spectroscopy provides spectra of small surface segments temporarily hidden behind the planet. The method was elaborated in Paper I, with observable signatures quantitatively predicted from hydrodynamic simulations. Results. From observations of HD 209458 with spectral resolution λ/ Δλ ~ 80 000, photospheric Fe I line profiles are obtained at several center-To-limb positions, reaching adequately high S/N after averaging over numerous similar lines. Conclusions. Retrieved line profiles are compared to synthetic line profiles. Hydrodynamic 3D models predict, and current observations confirm, that photospheric absorption lines become broader and shallower toward the stellar limb, reflecting that horizontal velocities in stellar granulation are greater than vertical velocities. Additional types of 3D signatures will become observable with the highest resolution spectrometers at large telescopes. (Less)
Inverse Ising inference by combining Ornstein-Zernike theory with deep learning

Inferring a generative model from data is a fundamental problem in machine learning. It is well-known that the Ising model is the maximum entropy model for binary variables which reproduces the sample mean and pairwise correlations. Learning the parameters of the Ising model from data is the challenge. We establish an analogy between the inverse Ising problem and the Ornstein-Zernike formalism in liquid state physics. Rather than analytically deriving the closure relation, we use a deep neural network to learn the closure from simulations of the Ising model. We show, using simulations as well as biochemical datasets, that the deep neural network model outperforms systematic field-theoretic expansions, is more data-efficient than the pseudolikelihood method, and can generalize well beyond the parameter regime of the training data. The neural network is able to learn from synthetic data, which can be generated with relative ease, to give accurate predictions on real world datasets.
Bioinformatic approaches for studying the microbiome of fermented food

Abstract High-throughput DNA sequencing-based approaches continue to revolutionise our understanding of microbial ecosystems, including those associated with fermented foods. Metagenomic and metatranscriptomic approaches are state-of-the-art biological profiling methods and are employed to investigate a wide variety of characteristics of microbial communities, such as taxonomic membership, gene content and the range and level at which these genes are expressed. Individual groups and consortia of researchers are utilising these approaches to produce increasingly large and complex datasets, representing vast populations of microorganisms. There is a corresponding requirement for the development and application of appropriate bioinformatic tools and pipelines to interpret this data. This review critically analyses the tools and pipelines that have been used or that could be applied to the analysis of metagenomic and metatranscriptomic data from fermented foods. In addition, we critically analyse a number of studies of fermented foods in which these tools have previously been applied, to highlight the insights that these approaches can provide.
Rat resistance to rheumatoid arthritis induction as a function of the early‐phase adrenal–pineal crosstalk

Chronic inflammatory diseases are triggered by causal stimuli that might occur long before the appearance of the symptoms. Increasing evidence suggests that these stimuli are necessary but not always sufficient to induce the diseases. The murine model of type II collagen emulsified in Freund's incomplete adjuvant (collagen‐induced arthritis) to induce rheumatoid arthritis (RA) follows this pattern as some animals do not develop the chronically inflamed phenotype. Considering that in the immune–pineal axis (IPA) theory adrenal–pineal cross‐talk adjusts early phases of inflammatory processes, we investigated whether differences in IPA activation could explain why some animals are resistant (RES) while others develop RA. We observed a similar increase in 6‐sulfatoxymelatonin (aMT6s) excretion from day 3 to 13 in both RES and RA animals, followed by a significant decrease in RA animals. This pattern of aMT6s excretion positively correlated with plasma corticosterone (CORT) in RES animals. Additionally, RA animals presented a lower aMT6s/CORT ratio than saline‐injected or RES animals. Plasmatic levels of tumour necrosis factor were similar in both groups, but interleukin (IL)‐1β and monocyte chemotactic protein 1 (MCP‐1) levels were lower in RES compared to RA animals. IL‐2 and IL‐4 were decreased in RES animals compared to saline‐injected animals. The aMT6s/CORT ratio inversely correlated with the paw thickness and the inflammatory score (levels of IL‐1β, MCP‐1, IL‐2 and IL‐4 combined). Thus, adrenocortical–pineal positive interaction is an early defence mechanism for avoiding inflammatory chronification.
Transcranial Ultrasound Imaging With Decomposition Descent Learning-Based Full Waveform Inversion

Noninvasive brain diagnosis is extremely important because of its efficiency, low cost, and painless nature in the prediction of stroke, cerebral hemorrhage, and other brain research. At present, achieving full 3-D quantitative ultrasonic imaging of the human brain is a cutting-edge challenge due to the complex structures of the human brain and the strong scattering caused by the skulls. In this article, we achieved quantitative ultrasonic imaging of inside-brain anomalies with our proposed method, the decomposition descent learning-based full waveform inversion (DDL-FWI). The proposed method adopts a linear residual decomposing technique to greatly alleviate the computation burden in fast inversion tomography (FIT) with enhanced convergence guaranteed by residual functions. Testing results in both simulation and laboratory experiments demonstrated that our method can achieve high-quality quantitative imaging of brain soft tissues and skulls even starting from homogeneous water background in 2-D, and this method is capable of reconstructing both complex brain tissues and clots in 2-D and 3-D cases using either clean or noisy signals, with a robust 3-D clot resolution as small as 18 mm and 2-D reconstruction speed in 11.20 s. Combined with advanced ultrasonic hardware, DDL-FWI can be easily trained and used for brain imaging efficiently that frees patients from harmful influences from traditional imaging techniques, e.g., ionization radiations from X-ray computed tomography (CT).
Enterococcus durans infection and diarrhea in Thoroughbred foals

Abstract Background Diarrhea remains an important cause of morbidity and mortality in neonatal foals, and correct identification of etiologic agents is essential for effective disease management. Objective To examine the association between diarrhea and detection of Enterococcus durans or other enteropathogens in neonatal foals on 1 breeding farm in Kentucky, USA. Animals Fifty‐nine Thoroughbred foals and their broodmares. Methods Prospective observational study. Study foals and broodmares were sampled and tested for E. durans and other enteropathogens during the first 10 days after foaling. The frequency of foals in which E. durans or other enteropathogens was compared between foals with or without diarrhea. Results Seven of 59 foals developed diarrhea. The frequency of foals with E. durans infection was higher in foals with diarrhea 5/7 (71%), compared to foals without diarrhea 0/51 (0%; P < .01). Detection of E. durans in foals was associated with detection of E. durans in broodmares; in 2/7 (29%) foals with diarrhea, the 2 broodmares tested positive for E. durans, and, in 51/51 (100%) foals without diarrhea, all broodmares tested negative to E. durans (P = .01). Based on the spatial and temporal distribution of foals with diarrhea, 5 of 6 additional cases of diarrhea were attributed to lateral transmission of E. durans infection. Conclusions and Clinical Importance Detection of E. durans was associated with diarrhea in foals. Implementation of enhanced biosecurity measures might mitigate disease transmission associated with E. durans infection in foals.