Miracle-dz/UniFAR-FTUs huggingface dataset:
In silico functional annotation of hypothetical proteins from the Bacillus paralicheniformis strain Bac84 reveals proteins with biotechnological potentials and adaptational functions to extreme environments

Members of the Bacillus genus are industrial cell factories due to their capacity to secrete significant quantities of biomolecules with industrial applications. The Bacillus paralicheniformis strain Bac84 was isolated from the Red Sea and it shares a close evolutionary relationship with Bacillus licheniformis. However, a significant number of proteins in its genome are annotated as functionally uncharacterized hypothetical proteins. Investigating these proteins’ functions may help us better understand how bacteria survive extreme environmental conditions and to find novel targets for biotechnological applications. Therefore, the purpose of our research was to functionally annotate the hypothetical proteins from the genome of B. paralicheniformis strain Bac84. We employed a structured in-silico approach incorporating numerous bioinformatics tools and databases for functional annotation, physicochemical characterization, subcellular localization, protein-protein interactions, and three-dimensional structure determination. Sequences of 414 hypothetical proteins were evaluated and we were able to successfully attribute a function to 37 hypothetical proteins. Moreover, we performed receiver operating characteristic analysis to assess the performance of various tools used in this present study. We identified 12 proteins having significant adaptational roles to unfavorable environments such as sporulation, formation of biofilm, motility, regulation of transcription, etc. Additionally, 8 proteins were predicted with biotechnological potentials such as coenzyme A biosynthesis, phenylalanine biosynthesis, rare-sugars biosynthesis, antibiotic biosynthesis, bioremediation, and others. Evaluation of the performance of the tools showed an accuracy of 98% which represented the rationality of the tools used. This work shows that this annotation strategy will make the functional characterization of unknown proteins easier and can find the target for further investigation. The knowledge of these hypothetical proteins’ potential functions aids B. paralicheniformis strain Bac84 in effectively creating a new biotechnological target. In addition, the results may also facilitate a better understanding of the survival mechanisms in harsh environmental conditions.
Race (black-white) and sex inequalities in tooth loss: A population-based study

The effect of health inequalities is determined by different socioeconomic, sex, and race conditions. This study aimed to analyze the association of tooth loss with race (defined by self-reported skin color) and sex. Based on the hypothesis that the association between tooth loss and race may be modified by sex, we also aimed to evaluate possible interactions between race and sex in association with this event, in a population-based study in the city of Campinas, Brazil. A directed acyclic graph was used to select covariates. The prevalence, of tooth loss was 19% higher in black women compared to white men (Prevalence ratio [PR]: 1.19; 95%CI: 1.05–1.34). Moreover, the prevalence of tooth loss in black women was 26% higher than in white women (PR: 1.26; 95%CI: 1.13–1.42); and, within the strata of black people, black women had 14% higher dental loss (PR: 1.14; 95%CI: 1.02–1.27) compared to black men. This study found a significant interaction between race and sex in tooth loss, with a disadvantage for black women. In addition, this work contributes to the discussion of health inequities and can support policies for the provision of universal dental care.
Perspectives of clinical pharmacists on the provision of pharmaceutical care through telepharmacy services during COVID-19 pandemic in Qatar: A focus group

Background Coronavirus disease 2019 (COVID-19) pandemic created unprecedented pressures on healthcare systems and led to the widespread adoption of telepharmacy services, a practice that was not previously established in the state of Qatar. Objective The -study aimed to explore clinical pharmacists’ (CPs) perspectives and experiences in utilizing telepharmacy for the provision of pharmaceutical care during the COVID-19 pandemic. Methods A descriptive, qualitative approach using face-to-face focus group (FG) discussions was used. CPs across Hamad Medical Corporation (HMC) were purposively invited to participate in the study. FG discussions were audio-recorded, transcribed verbatim, and validated. Transcripts were analyzed using inductive thematic analysis. Recruitment continued until a saturation point was achieved. Results We conducted five focus groups that included 23 CPs and led to seven themes. Overall, CPs reported inadequate preparedness for the practice of telepharmacy, which they perceived as challenging. The primary perceived benefits of telepharmacy were decreased infection exposure risk, improved quality of care, improved patients’ satisfaction, and enhanced workplace efficiency and productivity. The main highlighted risks of telepharmacy were related to threatened patient confidentiality, missed pharmaceutical care opportunities, and negatively impacted professional rapport with other healthcare providers; and the major perceived challenges were low digital health literacy, complex illnesses and medication regimens, lack of standardized protocols, and inadequacy of resources and cultural resistance for virtual care. Participants recommended standardization and training, resource allocation, and proper service promotion as potential facilitators of telepharmacy practice. Conclusion The current study revealed that despite perceived barriers, pharmacists identified several benefits of telepharmacy and recommended potential facilitators that should be used to integrate and sustain the practice of telepharmacy in the future. Future studies should investigate the impact of telepharmacy on clinical pharmacy interventions and patient outcomes.
Antenna phase centre calibration effects on position time-series: preliminary results

Advances in GPS error modelling and the continued effort of re-processing have considerably decreased the scatter in position estimates over the last two decades. The associated reduction of noise in derived position time-series has revealed the presence of previously undetected periodic signals. It has been shown that these signals have frequencies related to the orbits of GPS satellites. A number of potential sources for these periodicities at the draconitic frequency and its harmonics have already been suggested in the literature and include, e.g. errors in the sub-daily tidal models, multipath and unresolved integer ambiguities. Due to the geometrical relationship between an observation point and an orbiting satellite, deficiencies in the modelling of electromagnetic phase centres of receiving antennas have the potential to also contribute to the discovered periodic signals. The change from relative to absolute type mean antenna/radome calibrations within the international GNSS service (IGS) lead to a significant improvement and the use of individual calibrations could add further refinements to computed solutions. However, at this stage providing individual calibrations for all IGS stations is not feasible. Furthermore, antenna near-field electromagnetic effects might out-weight the benefits of individual calibrations once an antenna is permanently installed. In this study we investigate the differences between position estimates obtained using individual and type mean antenna/radome calibrations as used by the IGS community. We employ position time-series derived from precise point positioning (PPP) as implemented in two scientific GNSS software packages. Our results suggest that the differences in the employed calibrations propagate directly into the position estimates, affecting both sub-daily and daily results and yielding periodic variations. The sub-daily variations have periods close to half a sidereal day and one sidereal day with amplitudes of up to 10 mm in all position components. The stacked power spectra of the daily difference time-series reveal peaks at the GPS draconitic frequency and its harmonics, having the associated amplitudes of up to 1 mm. Although these results are still preliminary, they confirm that small differences between individual and type mean antenna/radome calibrations propagate into position time series and may be partly responsible for the spurious signals with draconitic frequency and its harmonics. Antenna Phase Centre Calibration Effects on Position Time-Series: Preliminary Results D. Sidorov, F.N. Teferle Geophysics Laboratory, University of Luxembourg, Luxembourg Contact: dmitry.sidorov@uni.lu Introduction Results—Sub-daily
Effect of different training frequencies on maximal strength performance and muscle hypertrophy in trained individuals—a within-subject design

Several studies comparing resistance training (RT) frequencies may have been affected by the large between-subject variability. This study aimed to compare the changes in lower limbs maximal dynamic strength (1RM) and quadriceps femoris cross-sectional area (CSA) after a RT with different weekly frequencies in strength-trained individuals using a within-subject design. Twenty-four men participated in a 9-week RT program, being randomly divided into two conditions: resistance training with equalized total training volume (RTEV) and with unequalized total training volume (RTUV). The RT protocol used the unilateral leg press 45° exercise and each subject’s lower limb executed one of the proposed frequencies (one and three times/week). All conditions effectively increased 1RM and CSA (p<0.001); however, no significant differences were observed in the values of 1RM (p = 0.454) and CSA (p = 0.310) between the RT frequencies in the RTEV and RTUV conditions. Therefore, RT performed three times a week showed similar increases in 1RM and CSA to the program performed once a week, regardless of training volume equalization. Nevertheless, when the higher RT frequency allowed the application of a greater TTV (i.e., RTUV), higher effect size (ES) values (0.51 and 0.63, 1RM and CSA, respectively) were observed for the adaptations.
Flow cytometric assessment of DNA double-strand break and repair kinetics in prediction of intrinsic radiosensitivity

Objective(s): To enhance the efficiency of radiotherapy (RT), implementation of individual-based treatment is essential. In this way, determining individual intrinsic radiosensitivity (IRS) can be useful to achieve minimal adverse effects of RT. The present study aimed to identify IRS of breast cancer (BC) patients through determination of radiation-induced DNA double-strand breaks (DSBs), repair kinetics, and acute normal tissue complications induced by RT. Materials and Methods: DSBs induction and its repair kinetics in 50 BC patients’ lymphocytes were analyzed by flow cytometric analysis of H2AX Ser-139 phosphorylation at 30 min, 3 and 24 hr after in vitro irradiation. In vivo skin dosimetry was done by GAFChromic films and acute skin toxicity was scored by radiation oncologists according to the criteria of Radiation Therapy and Oncology Group (RTOG) in all patients with similar prescribed treatment. Results: The average surface dose for patients ranged from 0.92 to 1.9 Gy and correlation analysis showed no significant relationship with weekly acute skin reactions. Formation of γH2AX after 30 min, slope of dose-response curve and repair kinetics of DSBs after 3 and 24 hr (intrinsic radiosensitivity) were significantly correlated with the RTOG scores following irradiation (clinical radiosensitivity) (r=0.48 and P-value<0.0001, r=0.72 and P-value<0.0001, r=0.48 and P-value<0.001, and finally r=0.53 and P-value<0.001, respectively; (using Pearson’s correlation test). Conclusion: Flow cytometric analysis of DNA DSBs by γH2AX measurement has the potential to be developed into a clinical predictor for identifying the overreactor patients prior to RT. Our result suggests that the slope-related quantity based on the linear pattern of the dose-response curve has the merit to predict overreactor patients with a sensitivity of 89% and a specificity of 94%.
Experimental investigation of laminar turbulent intermittency in pipe flow

In shear flows, turbulence first occurs in the form of localized structures (puffs/spots) surrounded by laminar fluid. We here investigate such spatially intermittent flows in a pipe experiment showing that turbulent puffs have a well-defined interaction distance, which sets their minimum spacing as well as the maximum observable turbulent fraction. Two methodologies are employed. Starting from a laminar flow, puffs are first created by locally injecting a jet of fluid through the pipe wall. When the perturbation is applied periodically at low frequencies, as expected, a regular sequence of puffs is observed where the puff spacing is given by the ratio of the mean flow speed to the perturbation frequency. At large frequencies however puffs are found to interact and annihilate each other. Varying the perturbation frequency, an interaction distance is determined which sets the highest possible turbulence fraction. This enables us to establish an upper bound for the friction factor in the transitional regime, which provides a well-defined link between the Blasius and the Hagen-Poiseuille friction laws. In the second set of experiments, the Reynolds number is reduced suddenly from fully turbulent to the intermittent regime. The resulting flow reorganizes itself to a sequence of constant size puffs which, unlike in Couette and Taylor–Couette flow are randomly spaced. The minimum distance between the turbulent patches is identical to the puff interaction length. The puff interaction length is found to be in agreement with the wavelength of regular stripe and spiral patterns in plane Couette and Taylor–Couette flow.
Individual differences in dissonance arousal/reduction relate to physical exercise: Testing the action-based model

Introduction The present research was designed to test predictions derived from the action-based model of cognitive dissonance theory. These predictions were that dissonance arousal would be negatively related to effective behavior, and that dissonance reduction would be positively related to effective behavior. Method Dissonance arousal and reduction were measured using an individual differences questionnaire. Effective behavior was measured as amount of physical exercise obtained from an exercise app that measures exercise using GPS (cycling kilometers over one year; Study 1) and from self-reports (number of days during the previous week; Study 2–3). Results Results suggested that individual differences in dissonance arousal relate to less exercise and that individual differences in dissonance reduction relate to more exercise. Statistically controlling for trait approach and avoidance motivation as well as satisfaction with life revealed that dissonance processes predicted exercise behavior over these traits. This pattern of results was generally consistent across the three studies. Moreover, results from Studies 2–3 suggested possible statistical mediators from the exercise commitment literature of the relationship between trait dissonance arousal/reduction and exercise behavior. Discussion and conclusion These results highlight the importance of considering dissonance processes as adaptive ones, and they suggest possible ways of increasing exercise behavior.
Hilbert Transform by Numerical Integration

Abstract : Many engineering studies require the evaluation of a Hilbert Transform of a tabular function. The function is also considered as an even function in order to conform to physical reality. A numerical procedure, incorporated into a Fortran subroutine HTRAN, has been developed to accomplish this task. The procedure has been designed to avoid the theoretical and numerical singularities and employs cubic polynomial interpolation to enhance numerical accuracy.
QUANTUM HITTING TIME ON THE COMPLETE GRAPH

Quantum walks play an important role in the area of quantum algorithms. Many interesting problems can be reduced to searching marked states in a quantum Markov chain. In this context, the notion of quantum hitting time is very important, because it quantifies the running time of the algorithms. Markov chain-based algorithms are probabilistic, therefore the calculation of the success probability is also required in the analysis of the computational complexity. Using Szegedy's definition of quantum hitting time, which is a natural extension of the definition of the classical hitting time, we present analytical expressions for the hitting time and success probability of the quantum walk on the complete graph.
On the Effective Equation of State of Dark Energy

In an effective field theory model with an ultraviolet momentum cutoff, there is a relation between the effective equation-of-state of dark energy and the ultraviolet cutoff scale. It implies that a measure of the equation of state of dark energy different from minus one, ω ≠ -1, does not rule out vacuum energy as dark energy. It also indicates an interesting possibility that precise measurements of the infrared properties of dark energy can be used to probe the ultraviolet cutoff scale of effective quantum field theory coupled to gravity. In a toy model with a vacuum energy-dominated universe with a Planck scale cutoff, the dark energy effective equation of state is weff ≈ -0.96.
Youths with asthma and their experiences of self‐management education: A systematic review of qualitative evidence

Abstract Aims To identify and synthesize the available evidence of youths with asthma and their experience of self‐management education. Design Systematic literature review of qualitative studies with meta‐synthesis of findings. Data sources We searched five databases, CINAHL Complete, Embase, MEDLINE (EBSCO) PsycINFO, ASSIA and the Global Index Medicus (formerly the WHOLIS). Initial search in September 2019 and updated in July 2020 and July 2022. Review Methods The systematic review was conducted in accordance with the JBI methodology for systematic reviews of qualitative evidence. Qualitative data were extracted, meta‐summarized and then meta‐synthesized. Results Eighteen studies were identified for inclusion in this review and three themes were identified: The theory and practice gap, contemporary health‐seeking preferences and the psychosocial impacts of living with asthma. Conclusion The needs of youths with asthma are specific and must be measurable against the change in asthma outcomes for this group. They have unmet self‐management educational needs that stakeholders, involved in their care and support, should address. Education and practice policy should focus on youth‐centric approaches. Through meaningful engagement with youths, stakeholders can identify their support needs, requirements and preferences to successfully underpin the theory and practice of self‐management education. Impact This review synthesized evidence of youths with asthma and their experiences of self‐management education, highlighting their specific self‐management information needs. The findings highlight several implications for healthcare professionals in education, practice and research. This age profile is under‐explored and further research into this population would work towards filling the theory and practice gap and highlighting the identified psychosocial issues faced by this group.
Optimisation sans dérivées sous contraintes : deux applications industrielles en ingénierie de réservoir et en calibration des moteurs

L'optimisation intervient dans de nombreuses applications IFPEN, notamment dans l'estimation de parametres de modeles numeriques a partir de donnees en geosciences ou en calibration des moteurs. Dans ces applications, on cherche a minimiser une fonction complexe, couteuse a estimer, et dont les derivees ne sont pas toujours disponibles. A ces difficultes s'ajoutent la prise en compte de contraintes non lineaires et parfois l'aspect multi-objectifs. Au cours de cette these, nous avons developpe la methode SQA (Sequential Quadradic Approximation), une extension de la methode d'optimisation sans derivees de M.J.D. Powell pour la prise en compte de contraintes a derivees connues ou non. Cette methode est basee sur la resolution de problemes d'optimisation simplifies bases sur des modeles quadratiques interpolant la fonction et les contraintes sans derivees, construits a partir d'un nombre limite d'evaluations de celles-ci. Si la resolution de ce sous-probleme ne permet pas une progression pour l'optimisation originale, de nouvelles simulations sont realisees pour tenter d'ameliorer les modeles. Les resultats de SQA sur differents benchmarks montrent son efficacite pour l'optimisation sans derivees sous contraintes. Enfin, SQA a ete applique avec succes a deux applications industrielles en ingenierie de reservoir et en calibration des moteurs. Une autre problematique majeure en optimisation etudiee dans cette these est la minimisation multi-objectifs sous contraintes. La methode evolutionnaire Multi-Objective Covariance Matrix Adaptation, adaptee a la prise en compte des contraintes, s'est revelee tres performante dans l'obtention de compromis pour la calibration des moteurs.
Neurocognitive deficits in COVID-19 patients five months after discharge from hospital

ABSTRACT This observational cohort study explored objective neurocognitive deficits in COVID-19 patients five months after discharge, and any associations with demographic factors and disease severity indicators. Medical notes of all COVID-19 patients admitted to hospital in Region Östergötland, Sweden, March-May 2020, were reviewed. After applying exclusion criteria, 433 patients were screened by telephone. Of these, 185 patients reported persistent and concerning post-COVID-19 problems, including but not restricted to cognitive functions, and were invited to a clinical evaluation. The Repeatable Battery for Assessment of Neuropsychological Status (RBANS) and Colour-Word Interference Test (CWIT) were used to assess immediate memory, visuo-spatial function, language, attention, delayed memory, and executive function. A total of 133 patients had valid test performances. Mean RBANS Global Cognition Score was 83.4, with 37% scoring below cut-off (1.5 SD). Deficits in Attention and Memory indices were most common, each affecting approximately 30% of the patients. After adjustment for sex, language, level of education and premorbid function, neurocognitive performance was positively associated with length of hospital stay, but not with the disease severity indicators WHO CPS and CRP. Findings support that comprehensive neuropsychological assessment should be performed when patients report post-COVID-19 symptoms that affect daily life.