Miracle-dz/UniFAR-FTUs huggingface dataset:
Pyroptosis in host defence against bacterial infection

ABSTRACT Pyroptosis, a regulated form of pro-inflammatory cell death, is characterised by cell lysis and by the release of cytokines, damage- and pathogen-associated molecular patterns. It plays an important role during bacterial infection, where it can promote an inflammatory response and eliminate the replicative niche of intracellular pathogens. Recent work, using a variety of bacterial pathogens, has illuminated the versatility of pyroptosis, revealing unexpected and important concepts underlying host defence. In this Review, we overview the molecular mechanisms underlying pyroptosis and discuss their role in host defence, from the single cell to the whole organism. We focus on recent studies using three cellular microbiology paradigms – Mycobacterium tuberculosis, Salmonella Typhimurium and Shigella flexneri – that have transformed the field of pyroptosis. We compare insights discovered in tissue culture, zebrafish and mouse models, highlighting the advantages and disadvantages of using these complementary infection models to investigate pyroptosis and for modelling human infection. Moving forward, we propose that in-depth knowledge of pyroptosis obtained from complementary infection models can better inform future studies using higher vertebrates, including humans, and help develop innovative host-directed therapies to combat bacterial infection.
The effect of oral vocabulary training on reading novel complex words

Do readers benefit from their knowledge of the phonological form and meaning of stems when seeing them embedded in morphologically complex words for the first time in print? This question was addressed using a word learning paradigm. Participants were trained on novel spoken word stems and their meanings (“tump”). Following training, participants then saw the novel stems for the first time in print, either in combination with a real affix (tumpist, tumpor) or with a non-affix (tumpel, tumpain). Untrained items were also included to test whether the affix effect was modulated by the prior training of the spoken word stems. First, the complex words were embedded in meaningful sentences which participants read as their eye movements were recorded (first orthographic exposure). Second, participants were asked to read aloud and spell each individual complex novel word (second orthographic exposure). Participants spent less time fixating on words that included trained stems compared with untrained stems. However, the training effect did not change depending on whether stems were accompanied by a real affix or a non-affix. In the reading aloud and spelling tasks, there was no effect of training, suggesting that the effect of oral vocabulary training did not extend beyond the initial print exposure. The results indicate that familiarity with spoken stems influences how complex words containing those stems are processed when being read for the first time. Our findings highlight the flexibility and adaptability of the morphological processing system to novel complex words during the first print exposure.
The impact of chronic kidney disease severity on clinical outcomes after current generation drug-eluting stent implantation for left main distal bifurcation lesions: the Milan and New-Tokyo registry

Abstract Objectives. The impact of chronic kidney disease (CKD) on clinical outcomes after percutaneous coronary intervention (PCI) for unprotected left main distal bifurcation lesions (ULMD) is not fully understood in current generation drug eluting stent (cDES) era. We assessed clinical outcomes after PCI using cDES for ULMD according to CKD severity based on estimated glomerular filtration rate (eGFR). Design. We identified 720 consecutive patients who underwent PCI using cDES for ULMD at three high volume centers between January 2005 and December 2015. We divided those patients to the following five groups according to eGFR. Each group was defined as follows: no CKD (60 mL/min/1.73 m2 ≤ eGFR), mild CKD (45 ≤ eGFR < 60 mL/min/1.73 m2), moderate CKD (30 ≤ eGFR < 45 mL/min/1.73 m2), severe CKD (15 ≤ eGFR < 30 mL/min/1.73 m2) and hemodialysis (HD). The primary endpoint was target lesion failure (TLF) at 3 years. TLF was defined as a composite of cardiac death, target lesion revascularization (TLR) and myocardial infarction (MI). Results. TLF occurred more frequently in severe CKD and HD group compared with other three groups. Conclusions. The patients who have severe CKD or are on HD, were extremely associated with worse clinical outcomes after PCI for ULMD even with cDES.
A qualitative study exploring parent-daughter approaches for communicating about sex and transactional sex in Central Uganda: Implications for comprehensive sexuality education interventions.

INTRODUCTION Ugandan adolescent girls and young women are disproportionately impacted by human immunodeficiency virus, and this is largely driven by their engagement in transactional sex. Globally, parent-daughter communication about sex is associated with increased contraceptive use and delayed/decreased sexual activity, but research on parent-daughter communication about transactional sex is lacking. This paper elucidates local perspectives on, and experiences of parent-daughter communication about sex and transactional sex, to inform family-level comprehensive sexuality education interventions. METHODS We conducted a secondary, thematic analysis of 13 focus group discussions (n = 119) and 30 in-depth interviews collected between 2014 and 2015 with adolescent girls and young women aged 14+, and men and women in Kampala and Masaka. RESULTS We found that parents used three approaches to discuss sex and transactional sex with their daughters: (1) frightening their daughters into avoiding sex; (2) being "strict"; and (3) relying on mothers rather than fathers to "counsel" daughters. Mother-daughter communication about transactional sex was common, but frequently unidirectional. Adolescent girls and young women bringing home gifts sparked conversations about the risks of transactional sex, although less in poorer households. Mothers felt they lacked control over their daughters' sexual behaviors and thus restricted their movements and friendships to try to prevent them from having sex. In contrast to previous research, we found some evidence of mothers encouraging condom use and father-daughter communication about sex. CONCLUSIONS Family-level comprehensive sexuality education interventions targeting parent-daughter communication about sex could further highlight the role that fathers might play, and emphasize communication about the inequitable power dynamics in transactional sex and condom negotiation skills, while reducing fear surrounding parent-daughter communication.
Evaluation of post‐tracheostomy scars and their impact on persons' quality of life: A case‐control study

Tracheostomy is one of the more commonly performed procedures in critically ill patients under mechanical ventilation. Postoperative scarring is one of the bothersome sequelae of tracheostomies. Scars distort physical appearance, especially when found on the head and neck, which could have a negative impact on quality of life. The aim of this study was to evaluate and assess the impact of post‐tracheostomy scars on quality of life according to the tracheostomy method. A prospective, single‐center, observational, case‐control study was conducted. One hundred fifty‐six persons with a post‐tracheostomy surgical scar for more than four months were observed using the Patient and Observer Scar Assessment Scale and Dermatology Life Quality Index questionnaire. Persons were divided into two groups depending on the method of tracheostomy, and the duration of the cannulated period was considered in both groups. Statistical analyses were performed using SPSS ver. 16.0 (SPSS Inc., Chicago, IL, USA), and P values of <0.05 were considered significant. The patients who had a tracheostomic tube cannulation period of fewer than 15 days had better cosmetic results than those who had tracheostomic tubes for more than 15 days, regardless of the tracheostomy method: 6.64 ± 0.082 versus 16.15 ± 0.096 (P < 0.001) in the surgical tracheostomy group and 7.26 ± 0.211 versus 14.17 ± 0.379 (P < 0.05) in the percutaneous dilatational group. The Dermatology Life Quality Index scores had a mean value of 0.6 ± 0.01, which means that post‐tracheostomy scarring in the present study had no effect on the person's quality of life. The aesthetic outcomes of post‐tracheostomy scars after the open surgical tracheostomy technique did not significantly differ from those of the percutaneous dilatational technique in the present study. Persons with a long duration of tracheostomic tube ventilation showed worse aesthetic outcomes than those with short‐term tracheostomic cannulation, which was not dependent on the tracheostomy technique. The Dermatology Life Quality Index showed that post‐ttracheostomy scarring in the present study had no effect on the person's quality of life.
Japanese Morphophonemics: Markedness and Word Structure

The sound pattern of Japanese, with its characteristic pitch accent system and rich segmental alternations, has played an important role in modern phonology, from structuralist phonemics to current constraint-based theories. In Japanese Morphophonemics Junko Ito and Armin Mester provide the first book-length treatment of central issues in Japanese phonology from the perspective of Optimality Theory.In Optimality Theory (OT), a generative grammar (including its phonological component) is built directly on the often conflicting demands of different grammatical principles and incorporates a specific kind of optimization as the means of resolving these conflicts. OT offers a new perspective from which to view many of the processes, alternations, and generalizations that are the traditional subject matter of phonology. Using the phonology of compounds as an analytical thread, Ito and Mester revisit central aspects of the sound pattern of Japanese and submit them to the rigor of OT. In pursuing both well-known and less-explored issues in this area, they show that an optimality-theoretic approach not only provides new solutions to old puzzles but also suggests interesting new questions for both descriptive work and theoretical research.
Association Between Tinnitus and Hypertension: A Cross-Sectional Analysis of the National Health and Nutrition Examination Survey

Objective Evaluating the association between arterial hypertension and tinnitus while controlling for gender, race, diabetes, hearing loss, and depression as potential confounders. Study Design The present study employed a cross-sectional design. Setting Health interviews were conducted in the respondents’ homes. Patients Respondents represent a nationwide sample of the noninstitutionalized civilian population of the United States. A total of 5,735 adults were identified by the NHANES 2015 to 2016 questionnaires. Interventions Questionnaires were administered to each participant. Main Outcome Measures Participants’ responses regarding tinnitus, hypertension, hearing loss, depression, diabetes, and demographics were used to evaluate potential associations. Multivariate logistic regression analyses were conducted on different age groups with the presence of hypertension as the response variable. Results Participants aged 20 to 39 with tinnitus were significantly more likely to be diagnosed with hypertension (OR = 2.49; p = 0.024) after adjusting for potential confounding. No significant association between tinnitus and hypertension was found for older age groups. The diagnosis of diabetes was associated with hypertension in ages 20 to 39 (OR = 7.11; p = 0.001), 40 to 59 (OR = 3.45; p = 0.020), and 60 to 69 (OR = 3.89; p = 0.032). Conclusions Tinnitus is associated with hypertension in younger age groups of 20 to 39 years of age but not in age groups greater than 40 years. Diabetes is also associated with hypertension in individuals aged 20 to 69 years. This finding of tinnitus as a risk factor for hypertension in younger populations may inform better clinical practice and lead to earlier detection of hypertension in at-risk patients.
Accuracy and consistency of intensity-based deformable image registration in 4DCT for tumor motion estimation in liver radiotherapy planning

We investigate the accuracy of intensity-based deformable image registration (DIR) for tumor localization in liver stereotactic body radiotherapy (SBRT). We included 4DCT scans to capture the breathing motion of eight patients receiving SBRT for liver metastases within a retrospective clinical study. Each patient had three fiducial markers implanted. The liver and the tumor were delineated in the mid-ventilation phase, and their positions in the other phases were estimated with deformable image registration. We tested referenced and sequential registrations strategies. The fiducial markers were the gold standard to evaluate registration accuracy. The registration errors related to measured versus estimated fiducial markers showed a mean value less than 1.6mm. The positions of some fiducial markers appeared not stable on the 4DCT throughout the respiratory phases. Markers’ center of mass tends to be a more reliable measurement. Distance errors of tumor location based on registration versus markers center of mass were less than 2mm. There were no statistically significant differences between the reference and the sequential registration, i.e., consistency and errors were comparable to resolution errors. We demonstrated that intensity-based DIR is accurate up to resolution level for locating the tumor in the liver during breathing motion.
REVIEW ARTICLE: Wall conditioning in fusion devices and its influence on plasma performance

Proper wall conditioning has turned out to be an essential element for achieving the highest possible plasma performance in present day fusion devices. The main issues are controlling the generation of plasma impurities, liberated by plasma - surface interactions, and controlling the recycling hydrogenic fluxes. The underlying mechanisms are discussed in this paper. The paper presents a review of the different wall conditioning methods. It focuses on low-Z wall coatings (beryllium evaporation, boronization, siliconization, lithium pellet injection) and on helium glow discharge cleaning and assesses their effects on fusion plasmas. New wall conditioning concepts, compatible with steady-state magnetic fields, are discussed in view of future large devices with superconducting coils.
Safety, efficacy, and drug survival of the infliximab biosimilar CT‐P13 in post‐marketing surveillance of Japanese patients with psoriasis

Based on extrapolation of similar clinical outcomes in rheumatoid arthritis to the originator infliximab (IFX) in randomized clinical trials, the first biosimilar antibody CT‐P13 was approved for the treatment of psoriasis. To evaluate the safety, efficacy, and drug survival of CT‐P13 for psoriasis in real‐world clinical practice, prospective post‐marketing surveillance was conducted in 165 Japanese psoriasis patients. During a 1‐year follow‐up period, adverse drug reactions (ADRs) occurred in 29 patients (17.6%). Infusion reaction was the most frequent ADR (6.7%), and mild pneumonia was reported as the only case of infection. Serious ADRs were reported in two patients (1.2%): acute cholecystitis and interstitial pneumonia. The interstitial pneumonia developed after a single infusion of CT‐P13 and the patient died of respiratory failure. In naive patients to biologic therapy (n = 44), the Psoriasis Area Severity Index (PASI) decreased rapidly after the start of CT‐P13 treatment, and response rate achieving an absolute PASI score <1 was 55% at 30 weeks. The response rate was high (78%) in patients with psoriatic arthritis, and 40% and 20% in those in plaque psoriasis and pustular psoriasis, respectively. Of patients switched from IFX to CT‐P13 mainly for nonmedical reasons (n = 105), 57% had already reached PASI <1 by pretreatment with IFX and CT‐P13 maintained this status. The incidence of ADRs in this patient group was low and the drug survival rate was as high as 74%, even at 1 year, which was significantly higher than that in the naïve patient group (47%). Patients switched from other biologics for medical reasons (n = 16) responded similarly to biologic‐naïve patients, but drug survival was lower (24%). In conclusion, CT‐P13 showed excellent effectiveness as a first‐line therapy, no clinical difficulties in switching from IFX, and usefulness in patients who failed other biologics. CT‐P13 could be a cost‐effective alternative to IFX for the treatment of psoriasis.
Dynamical Signatures of Multifunnel Energy Landscapes

Multifunctional systems, such as molecular switches, exhibit multifunnel energy landscapes associated with the alternative functional states. In this contribution the multifunnel organization is decoded from dynamical signatures in the first passage time distribution between reactants and products. Characteristic relaxation rates are revealed by analyzing the kinetics as a function of the observation time scale, which scans the underlying distribution. Extracting the corresponding dynamical signatures provides direct insight into the organization of the molecular energy landscape, which will facilitate a rational design of target functionality. Examples are illustrated for multifunnel landscapes in biomolecular systems and an atomic cluster.
Needle: a fast and space-efficient prefilter for estimating the quantification of very large collections of expression experiments

Abstract Motivation The ever-growing size of sequencing data is a major bottleneck in bioinformatics as the advances of hardware development cannot keep up with the data growth. Therefore, an enormous amount of data is collected but rarely ever reused, because it is nearly impossible to find meaningful experiments in the stream of raw data. Results As a solution, we propose Needle, a fast and space-efficient index which can be built for thousands of experiments in <2 h and can estimate the quantification of a transcript in these experiments in seconds, thereby outperforming its competitors. The basic idea of the Needle index is to create multiple interleaved Bloom filters that each store a set of representative k-mers depending on their multiplicity in the raw data. This is then used to quantify the query. Availability and implementation https://github.com/seqan/needle. Supplementary information Supplementary data are available at Bioinformatics online.
Clinical indicators, nursing diagnoses, and mortality risk in critically ill patients with COVID-19: a retrospective cohort

ABSTRACT Objective: To identify clinical indicators and nursing diagnoses with the highest risk of mortality in critically ill patients with COVID-19. Method: Retrospective cohort with the population of adults and elderly people with COVID-19 from an Intensive Care Unit. Categorical variables were described using absolute and relative frequencies and risk factors for mortality using Cox regression, with a confidence interval of 95%. Results: The main clinical indicators of COVID-19 patients were dyspnea, fever, fatigue, cough, among others, and the Nursing Diagnoses at higher risk of mortality were Ineffective protection, Ineffective tissue perfusion, Contamination, Ineffective Breathing Pattern, Impaired spontaneous ventilation, Acute confusion, Frailty syndrome, Obesity, and Decreased cardiac output. It is worth mentioning that there was little information about the diagnoses of Domains 9, 10, and 12. Conclusion: This research infers the need to monitor the clinical indicators dyspnea, fever, fatigue, cough, among others, and the Nursing Diagnoses with the highest risk of mortality Ineffective protection, Ineffective tissue perfusion, Contamination, Ineffective Breathing Pattern, Impaired spontaneous ventilation in critically ill patients.
Observation of the B_{c}^{+} Meson in Pb-Pb and pp Collisions at sqrt[s_{NN}]=5.02  TeV and Measurement of its Nuclear Modification Factor.

The B_{c}^{+} meson is observed for the first time in heavy ion collisions. Data from the CMS detector are used to study the production of the B_{c}^{+} meson in lead-lead (Pb-Pb) and proton-proton (pp) collisions at a center-of-mass energy per nucleon pair of sqrt[s_{NN}]=5.02 TeV, via the B_{c}^{+}→(J/ψ→μ^{+}μ^{-})μ^{+}ν_{μ} decay. The B_{c}^{+} nuclear modification factor, derived from the Pb-Pb-to-pp ratio of production cross sections, is measured in two bins of the trimuon transverse momentum and of the Pb-Pb collision centrality. The B_{c}^{+} meson is shown to be less suppressed than quarkonia and most of the open heavy-flavor mesons, suggesting that effects of the hot and dense nuclear matter created in heavy ion collisions contribute to its production. This measurement sets forth a promising new probe of the interplay of suppression and enhancement mechanisms in the production of heavy-flavor mesons in the quark-gluon plasma.
Loss of control as a transdiagnostic feature in obesity‐related eating behaviours: A systematic review

Abstract Objective Emerging evidence suggests that loss of control (LOC) may present as a common feature across disordered eating behaviours. However, there has been limited research on the transdiagnostic nature of LOC in this area. The primary aim of this study was to systematically review disordered eating behaviours and measures of LOC in clinical and non‐clinical populations. Method Electronic searches of the relevant databases were conducted. Selected articles were screened for eligibility and assessed for methodological quality. Results Thirty‐four studies met inclusion criteria. Findings demonstrated that LOC was associated with disordered eating behaviours across bariatric populations, eating disorder populations, and community populations. Specifically, LOC was associated with binge eating (subjective and objective episodes), grazing, night eating, and emotional or stress eating. Findings also revealed that LOC was inconsistently operationalised across studies, with varied approaches to measuring the construct. Conclusion Overall, the findings from this review provide support for LOC as a transdiagnostic feature of disordered eating behaviours. Future studies should utilise robust multi‐method assessments to measure the severity of LOC, which may provide greater insight into how LOC manifests across different eating disorder presentations.