Miracle-dz/UniFAR-FTUs huggingface dataset:
Trade-Offs between Competitive Ability and Resistance to Top-Down Control in Marine Microbes

We addressed the “kill-the-winner” hypothesis from the perspective of its principle (the competition-resistance trade-off) in marine bacterial communities incubated in situ. Our results supported the existence of competition-resistance trade-offs and the positive effect on bacterial community diversity. ABSTRACT Trade-offs between competitive ability and resistance to top-down control manifest the “kill-the-winner” hypothesis that explains how mortality caused by protists and viruses can promote bacterial diversity. However, the existence of such trade-offs has rarely been investigated in natural marine bacterial communities. To address this question, we conducted on-board dilution experiments to manipulate top-down control pressure (protists only or protists plus viruses [protists+viruses] combined) and then applied 16S rRNA gene high-throughput sequencing techniques to assess the responses of each bacterial taxon. Dilution experiments enabled us to measure the top-down-control-free growth rate as the competitive ability and top-down-control-caused mortality as the reverse of resistance to top-down control. Overall, bacterial taxa with higher top-down-control-free growth rates were accompanied by lower top-down-control-caused resistance. Furthermore, competition-resistance trade-offs were stronger and more consistent when top-down control was caused by protists+viruses combined than by protists only. When protists+viruses were diluted, the bacterial rank abundance distribution became steepened and evenness and richness were decreased. However, when protists were diluted, only richness decreased. Our results indicate the existence of competition-resistance trade-offs in marine microbes and demonstrate the positive impacts of such trade-offs on bacterial diversity. Regardless, the strength of the competition-resistance trade-offs and the impacts on bacterial diversity were contingent on whether top-down control was caused by protists+viruses combined or protists only. IMPORTANCE We addressed the “kill-the-winner” hypothesis from the perspective of its principle (the competition-resistance trade-off) in marine bacterial communities incubated in situ. Our results supported the existence of competition-resistance trade-offs and the positive effect on bacterial community diversity. The study linked theoretical expectations and complex natural systems and provided new knowledge regarding how top-down controls and competition trade-offs shaped natural bacterial communities.
A new non‐randomized response model: The parallel model

Despite certain advances for non‐randomized response (NRR) techniques in the past 6 years, the existing non‐randomized crosswise and triangular models have several limitations in practice. In this paper, I propose a new NRR model, called the parallel model with a wider application range. Asymptotical properties of the maximum likelihood estimator (and its modified version) for the proportion of interest are explored. Theoretical comparisons with the crosswise and triangular models show that the parallel model is always more efficient than the two existing NRR models for most of the possible parameter ranges. Bayesian methods for analyzing survey data from the parallel model are developed. A case study on college students' premarital sexual behavior at Wuhan and a case study on plagiarism at the University of Hong Kong are conducted and are used to illustrate the proposed methods. © 2014 The Authors. Statistica Neerlandica © 2014 VVS.
Computational prediction of interactions between Paxlovid and prescription drugs

Pfizer’s Paxlovid has recently been approved for the emergency use authorization (EUA) from the US Food and Drug Administration (FDA) for the treatment of mild-to-moderate COVID-19. Drug interactions can be a serious medical problem for COVID-19 patients with underlying medical conditions, such as hypertension and diabetes, who have likely been taking other drugs. Here, we use deep learning to predict potential drug–drug interactions between Paxlovid components (nirmatrelvir and ritonavir) and 2,248 prescription drugs for treating various diseases.
Efficacy and safety of low-dose aspirin on preventing transplant renal artery stenosis: a prospective randomized controlled trial

Abstract Background: Transplant renal artery stenosis (TRAS) is a vascular complication after kidney transplantation associated with poor outcomes. This study aimed to analyze the efficacy and safety of low-dose aspirin for preventing TRAS. Methods: After kidney transplantation, patients were enrolled from January 2018 to December 2020 in Henan Provincial People's Hospital. A total of 351 enrolled recipients were randomized to an aspirin group with low-dose intake of aspirin in addition to standard treatment (n = 178), or a control group with only standard treatment (n = 173). The patients was initially diagnosed as TRAS (id-TRAS) by Doppler ultrasound, and confirmed cases were diagnosed by DSA (c-TRAS). Results: In the aspirin and control groups, 15.7% (28/178) and 22.0% (38/173) of the recipients developed id-TRAS, respectively, with no statistical difference. However, for c-TRAS, the difference of incidence and cumulative incidence was statistically significant. The incidence of c-TRAS was lower in the aspirin group compared with the control group (2.8% [5/178] vs. 11.6% [20/173], P = 0.001). Kaplan–Meier estimates and Cox regression model identified the cumulative incidence and hazard ratio (HR) of TRAS over time in two groups, showing that recipients treated with aspirin had a significantly lower risk of c-TRAS than those who were not treated (log-rank P = 0.001, HR = 0.23, 95% confidence interval [CI]: 0.09–0.62). The levels of platelet aggregation rate (P < 0.001), cholesterol (P = 0.028), and low-density lipoprotein cholesterol (P = 0.003) in the aspirin group were decreased compared with the control group in the third-month post-transplantation. For the incidence of adverse events, there was no statistical difference. Conclusion: Clinical application of low-dose aspirin after renal transplant could prevent the development of TRAS with no significant increase in adverse effects. Trial Registration: Clinicaltrials.gov, NCT04260828.
Metabolic Alterations in Streptozotocin–nicotinamide-induced Diabetic Rats Treated with Muntingia calabura Extract via 1 H-NMR-based Metabolomics

Abstract Diabetes mellitus (DM) is a metabolic endocrine disorder caused by decreased insulin concentration or poor insulin response. Muntingia calabura (MC) has been used traditionally to reduce blood glucose levels. This study aims to support the traditional claim of MC as a functional food and blood-glucose-lowering regimen. The antidiabetic potential of MC is tested on a streptozotocin–nicotinamide (STZ-NA)-induced diabetic rat model by using the 1 H-NMR-based metabolomic approach. Serum biochemical analyses reveal that treatment with 250 mg/kg body weight (bw) standardized freeze-dried (FD) 50% ethanolic MC extract (MCE 250) shows favorable serum creatinine (37.77 ± 3.53 µM), urea (5.98 ± 0.84 mM) and glucose (7.36 ± 0.57 mM) lowering capacity, which was comparable to the standard drug, metformin. The clear separation between diabetic control (DC) and normal group in principal component analysis indicates the successful induction of diabetes in the STZ-NA-induced type 2 diabetic rat model. A total of nine biomarkers, including allantoin, glucose, methylnicotinamide, lactate, hippurate, creatine, dimethylamine, citrate and pyruvate are identified in ratsʼ urinary profile, discriminating DC and normal groups through orthogonal partial least squares-discriminant analysis. Induction of diabetes by STZ-NA is due to alteration in the tricarboxylic acid (TCA) cycle, gluconeogenesis pathway, pyruvate metabolism and nicotinate and nicotinamide metabolism. Oral treatment with MCE 250 in STZ-NA-induced diabetic rats shows improvement in the altered carbohydrate metabolism, cofactor and vitamin metabolic pathway, as well as purine and homocysteine metabolism.
Refractive errors and their effects on visual evoked potentials

In view of the increasing use of visual evoked potentials (VEP) technique in neuro-ophthalmological diagnosis, it was thought pertinent to appraise the changes brought about in VEPs in the presence of refractive error (RE) as studied by the vision researchers and neurophysiologists. The purpose of this review was to provide a comprehensive quintessence of the work carried out in this fi eld with an attempt to summarize the previous concepts, recent perspective and current notion about the value of RE in electrophysiologic testing particularly the VEP technique.
Ceres Surface Properties by High-Resolution Imaging from Earth

Direct imaging of Ceres has been performed using an adaptive optics system, developed by Laserdot (France), Paris Observatory (Meudon, France), ONERA (France), and ESO. The diffraction limit of the 3.6-m ESO telescope (La Silla, Chile) was obtained at near infrared wavelengths in the K, L ′, and M bands (0.13, 0.25, and 0.30 arcsec, respectively). Several physical parameters for Ceres are deduced from these observations. The rotation is prograde (consistent with previous observations). The pole orientation is λ = 332 ± 5° and β = 70 ± 15°, implying a low obliquity with respect to Ceres orbital plane. The estimated thermal inertia of the regolith is 3.8 ± 1.4 × 104 erg cm-2 sec-1/2K-1. The measured temperature of the warmest area is 235 ± 4 K. The value of the mean radius, 484 ± 20 km, is consistent with earlier values obtained by stellar occultation and thermal infrared photometry. No albedo variations can be detected in reflected light and the center-to-limb distribution clearly departs from a Lambertian distribution.
The challenge of dealing with non-AIDS comorbidities for people living with HIV: Perspectives and experiences of patients and healthcare providers

ABSTRACT As the cohort of People Living with HIV (PLHIV) ages, so does the spectrum and burden of non-AIDS define HIV-associated conditions (NARC). PLHIV are likely to need different and increased healthcare services. It requires health systems to adapt to this disease trend and conform to a chronic care model, which respects the distinct needs of the ageing population. In this article, we explore the lived experiences of PLHIV and their healthcare providers in managing the challenges of dealing with NARC in Arba Minch, Southern Ethiopia. This study utilises interpretative substantive methods, encompassing qualitative interviews and Focus Group Discussions. The Normalisation Practice Theory (NPT) guided the semi-structured questions concerning routine screenings and current models of HIV care for ageing individuals. The main structural challenges in providing adequate geriatric care included: (i) the lack of awareness of the risk of NARCs; (ii) the absence of blended care; (iii) an HIV-centred approach exclusive of multidisciplinary care; and (iv) financial constraints. In an era with increasing NARCs, traditional HIV care models must adapt to the emerging challenges of a ‘greying’ and growing population.
Serum levels and significance of soluble B-cell maturation antigen in childhood-onset systemic lupus erythematosus with renal involvement

Objective The aim of this study was to investigate serum levels of soluble B-cell maturation antigen (sBCMA) in childhood-onset systemic lupus erythematous (cSLE) patients with renal involvement, and to elucidate their association with clinical characteristics. Methods 116 cases of cSLE patients with renal involvement (84 females and 32 males; median age 11.6 (10.1, 12.9) years) hospitalized in Department of Pediatric Nephrology and Rheumatology, the First Affiliated Hospital, Sun Yat-sen University and 31 healthy controls (HCs) were enrolled. Serum concentrations of sBCMA were determined using enzyme-linked immunosorbent assay (ELISA). Clinical and laboratory information of cSLE patients were retrospectively analyzed. Results Serum sBCMA levels were significantly increased in primary cSLE when compared with treated cSLE patients and HCs, whereas there was no significant difference between treated cSLE patients and HCs. Patients with high disease activity displayed higher serum sBCMA levels compared with those with no or mild to moderate disease activity. Positive correlation was observed between serum sBCMA levels and systemic lupus erythematosus disease activity index-2K (SLEDAI-2K), antinuclear antibody titers, anti-double-stranded DNA titers, erythrocyte sedimentation rate, and immunoglobulin G levels, while sBCMA levels were negatively correlated with blood white blood cell count, hemoglobin, platelet count, complement C3 and C4 levels. Serum sBCMA levels decreased as disease ameliorated after treatments among 11 cases with follow-up examinations. Conclusions In cSLE patients with renal involvement, serum sBCMA levels correlated significantly with disease activity, immunological, and hematological parameters, but not with renal parameters. Our results suggest the potential and significance of serum sBCMA as a biomarker in cSLE patients.
An algebraic approach to iterative learning control

In this paper discrete-time iterative learning control (ILC) systems are analysed from an algebraic point of view. The algebraic analysis shows that an ILC synthesis problem can be considered as a tracking problem of a multi-channel step-function. Furthermore, the plant to be controlled is a static multivariable plant. Another major contribution of this paper is a general convergence theory of ILC systems in terms of their closed-loop poles. This convergence theory shows that time-variant ILC control laws should be typically used instead of time-invariant control laws in order to guarantee good transient tracking behaviour. Simulations high-light the different theoretical findings in this paper.
Development of Rat Caries-Induced Pulpitis Model for Vital Pulp Therapy

Rodent animal models for vital pulp therapy are commonly used in dental research because their tooth anatomy and cellular processes are similar to the anatomy and processes in humans. However, most studies have been conducted using uninfected sound teeth, which makes it difficult to adequately assess the inflammatory shift after vital pulp therapy. In the present study, we aimed to establish a caries-induced pulpitis model based on the conventional rat caries model and then evaluate inflammatory changes during the wound-healing process after pulp capping in a model of reversible pulpitis induced by carious infection. To establish the caries-induced pulpitis model, the pulpal inflammatory status was investigated at different stages of caries progression by immunostaining targeted to specific inflammatory biomarkers. Immunohistochemical staining revealed that both Toll-like receptor 2 and proliferating cell nuclear antigen were expressed in moderate and severe caries-stimulated pulp, indicating that an immune reaction occurred at both stages of caries progression. M2 macrophages were predominant in moderate caries-stimulated pulp, whereas M1 macrophages were predominant in the severe caries-stimulated pulp. Pulp capping in teeth with moderate caries (i.e., teeth with reversible pulpitis) led to complete tertiary dentin formation within 28 d after treatment. Impaired wound healing was observed in teeth with severe caries (i.e., teeth with irreversible pulpitis). During the wound-healing process in reversible pulpitis after pulp capping, M2 macrophages were predominant at all time points; their proliferative capacity was upregulated in the early stage of wound healing compared with healthy pulp. In conclusion, we successfully established a caries-induced pulpitis model for studies of vital pulp therapy. M2 macrophages have an important role in the early stages of the wound-healing process in reversible pulpitis.
Exploring structural features and potential lipid interactions of Pseudomonas aeruginosa type three secretion effector PemB by spectroscopic and calorimetric experiments

Type Three Secretion System (T3SS) is a sophisticated nano‐scale weapon utilized by several gram negative bacteria under stringent spatio‐temporal regulation to manipulate and evade host immune systems in order to cause infection. To the best of our knowledge, this present study is the first report where we embark upon characterizing inherent features of native type three secretion effector protein PemB through biophysical techniques. Herein, first, we demonstrate binding affinity of PemB for phosphoinositides through isothermal calorimetric titrations. Second, we shed light on its strong homo‐oligomerization propensity in aqueous solution through multiple biophysical methods. Third, we also employ several spectroscopic techniques to delineate its disordered and helical conformation. Lastly, we perform a phylogenetic analysis of this new effector to elucidate evolutionary relationship with other organisms. Taken together, our results shall surely contribute to our existing knowledge of Pseudomonas aeruginosa secretome.
The modern state of femoral, acetabular, and global offsets in total hip arthroplasty: a narrative review

Offsets in the frontal plane are important for hip function. Research on total hip arthroplasty (THA) surgery agrees that increasing femoral offset up to 5 mm could improve functional outcome measures. The literature indicates that global offset is a key parameter that physicians should restore within 5 mm during surgery and avoid decreasing. Substantiated findings on acetabular offset are lacking despite its recognized importance, and the medialization approach must be assessed in light of its shortcomings. Future research, possibly through improved measurement, unified definitions, patient-specific surgical planning, and technology-enhanced surgical control, with specific focus on acetabular offset, is needed to better understand its impact on THA outcomes.
Radiation effects on rare-earth doped optical fibers

In this paper, we reviewed our previous work concerning the responses of rare-earth (RE) doped fibers (Yb, Er and Er/Yb) to various types of radiations like γ-rays, X-rays and protons. For all these harsh environments, the main measured macroscopic radiation-induced effect is an increase of the linear attenuation of these waveguides due to the generation of point defects in the RE-doped core and silica-based cladding. To evaluate the vulnerability of this class of optical fibers for space missions, we characterize the growth and decay kinetics of their radiation-induced attenuation (RIA) during and after irradiation for various compositions. Laboratory testing reveals that this class of optical fibers is very sensitive to radiations compared to passive (RE-free) samples. As a consequence, despite the small length used for space applications, the understanding of the radiation-induced effects in this class of optical fibers becomes necessary before their integration as part of fiber-based systems like gyroscopes or communication systems. In this paper, we more particularly discussed about the relative influence of the rare-earth ions (Er3+ and/or Yb3+) and of the glass matrix dopants (Al, P, .) on the optical degradation due to radiations. This has been done by using a set of five prototype optical fibers designed by the fiber manufacturer iXFiber SAS to enlighten the role of these parameters. Additional spectroscopic tools like confocal microscopy of luminescence are also used to detect possible changes in the spectroscopy of the rare-earth ions and their consequences on the functionality of the active optical fibers.
Volar versus dorsal approach for supinator to posterior interosseous nerve transfer: An anatomical study in cadavers

Supinator to posterior interosseous nerve (SPIN) transfer allows reconstruction of finger/thumb extension and thumb abduction for low radial nerve palsy, incomplete C6 tetraplegia, and brachial plexus injury affecting C7‐T1. No study has compared dorsal versus volar approach to perform SPIN transfer. This comparison is studied in the present work, assessing supinator motor branch length and ability to achieve nerve transfer from either approach.
On the fractional parts of x / n and related sequences. II

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Direct Computation of Turbulent Boundary Layer Noise

Aerodynamic noise from a turbulent boundary layer, also known as flow noise is a fundamental topic in flow-induced noise insofar as it determines the structural response of a surface submitted to this turbulent buffeting. For example, in the automotive applications, sound waves transmitted inside the interior of the vehicle come from two contributions: the direct transfer of the acoustic radiation, and the indirect transfer by the incompressible pressure loading which can excite the vibrational modes of the structure. The first one has a low efficiency but a transfer function close to one, whereas the second is more energetic but the transfer function becomes very weak at high wavenumbers. For the flow around a A-pillar, Alam et al. have shown that the mechanism associated with structural responses to turbulent wall flow is preponderant, but no study has quantified precisely the contributions of the direct and indirect transfers, and the question whether the acoustic part should be considered remains an open question.