Miracle-dz/UniFAR-FTUs huggingface dataset:
Observational study of factors associated with morbidity and mortality from COVID-19 in Lebanon, 2020–2021

Background The COVID-19 pandemic claimed millions of lives worldwide without clear signs of abating despite several mitigation efforts and vaccination campaigns. There have been tremendous interests in understanding the etiology of the disease particularly in what makes it severe and fatal in certain patients. Studies have shown that COVID-19 patients with kidney injury on admission were more likely to develop severe disease, and acute kidney disease was associated with high mortality in COVID-19 hospitalized patients. Methods This study investigated 819 COVID-19 patients admitted between January 2020-April 2021 to the COVID-19 ward at a tertiary care center in Lebanon and evaluated their vital signs and biomarkers while probing for two main outcomes: intubation and fatality. Logistic and Cox regressions were performed to investigate the association between clinical and metabolic variables and disease outcomes, mainly intubation and mortality. Times were defined in terms of admission and discharge/fatality for COVID-19, with no other exclusions. Results Regression analysis revealed that the following are independent risk factors for both intubation and fatality respectively: diabetes (p = 0.021 and p = 0.04), being overweight (p = 0.021 and p = 0.072), chronic kidney disease (p = 0.045 and p = 0.001), and gender (p = 0.016 and p = 0.114). Further, shortness of breath (p<0.001), age (p<0.001) and being overweight (p = 0.014) associated with intubation, while fatality with shortness of breath (p<0.001) in our group of patients. Elevated level of serum creatinine was the highest factor associated with fatality (p = 0.002), while both white blood count (p<0.001) and serum glutamic-oxaloacetic transaminase levels (p<0.001) emerged as independent risk factors for intubation. Conclusions Collectively our data show that high creatinine levels were significantly associated with fatality in our COVID-19 study patients, underscoring the importance of kidney function as a main modulator of SARS-CoV-2 morbidity and favor a careful and proactive management of patients with elevated creatinine levels on admission.
MR‐Nucleomics: The study of pathological cellular processes with multinuclear magnetic resonance spectroscopy and imaging in vivo

Clinical medicine has experienced a rapid development in recent decades, during which therapies targeting specific cellular signaling pathways, or specific cell surface receptors, have been increasingly adopted. While these developments in clinical medicine call for improved precision in diagnosis and treatment monitoring, modern medical imaging methods are restricted mainly to anatomical imaging, lagging behind the requirements of precision medicine. Although positron emission tomography and single photon emission computed tomography have been used clinically for studies of metabolism, their applications have been limited by the exposure risk to ionizing radiation, the subsequent limitation in repeated and longitudinal studies, and the incapability in assessing downstream metabolism. Magnetic resonance spectroscopy (MRS) or spectroscopic imaging (MRSI) are, in theory, capable of assessing molecular activities in vivo, although they are often limited by sensitivity. Here, we review some recent developments in MRS and MRSI of multiple nuclei that have potential as molecular imaging tools in the clinic.
Open Access Articles Garner Increased Social Media Attention and Citation Rates Compared With Subscription Access Research Articles: An Altmetrics-Based Analysis

Background: To better understand the research impact on social media, alternative web-based metrics (Altmetrics) were developed. Open access (OA) publishing, which allows for widespread distribution of scientific content, has become increasingly common in the medical literature. However, the relationship between OA publishing and social media impact remains unclear. Purpose: To compare social media attention and citation rates between OA and subscription access (SA) research articles within the orthopaedic and sports medicine literature. Study Design: Cross-sectional study. Methods: Articles published as either OA or SA in 5 high-impact hybrid orthopaedic journals between January 2019 and December 2019 were analyzed. The primary outcome was the Altmetric Attention Score (AAS), a validated measure of social media attention. Secondary outcomes included citation rates, article characteristics, and the number of shares on social media. Independent t tests and chi-square analyses were used to compare outcomes between OA and SA articles. A multivariable linear regression analysis was performed to determine the association between article type and AAS while controlling for bibliometric characteristics. Results: A total of 2143 articles (246 OA articles, 11.5%; 1897 SA articles, 88.5%) were included. The mean AAS among all OA articles was 62.4 ± 184.6 (range, 0-2032), whereas the mean AAS among all SA articles was 18.4 ± 109.8 (range, 0-3425), representing a statistically significant difference (P < .001). The mean citation rate among OA articles was significantly higher (17.0 ± 22.5; range, 0-139) than that of SA articles (8.6 ± 13.4; range, 0-169) (P < .001). Multivariable linear regression analysis demonstrated that OA status (β = 15.15; P = .044), number of institutions (β = 2.13; P = .023), studies classified as epidemiological investigations (β = 107.40; P < .001), and disclosure of a conflict of interest (β = −11.18; P = .032) were significantly associated with a higher AAS. Conclusion: OA articles resulted in significantly greater AAS and citations in comparison with SA articles. Articles published through the OA option in hybrid journals as well as those with a higher number of institutions, those that disclosed a conflict of interest, and those classified as epidemiological investigations were positively associated with greater AAS in addition to a greater number of citations. The potential for more extensive research dissemination inherent in the OA option may therefore translate into greater reach and social media attention.
“It’s a 50/50 Thing You Know”: Exploring the Multileveled Intersections of Gender and Power Within the Relationships of Young South African Men and Women

ABSTRACT Efforts to advance sexual health globally require greater understandings of youth intimate relationship dynamics. Among 38 South African youth (21 women/17 men aged 21–30 from Durban and Soweto) we conducted qualitative cognitive interviews to explore how gender and power intersect to shape intimate relationship dynamics (October 2019-March 2021). Participants discussed perceptions and relevance of each of 13 items comprising the Sexual Relationship Power (SRP) scale, a widely used measure of gender equity, and the influence of SRP on youth sexual health. Data analysis was guided by constructivist grounded theory. The findings were organized using the socio-ecological model, revealing how gender and power intersected at multiple levels to influence youth intimate relationships. Key influencing factors included individual-level gender attitudes, male partner expectations, and women’s resistance to dominance; intimate relationship-level power dynamics, consent, and intimacy; family-level household configurations and parental monitoring of daughters; and societal-level traditional gender norms. At all levels, women discussed resisting power inequities through communication and rejection of inequitable relationships. While men also displayed resistance to inequitable power structures, most upheld traditional gender norms through institutional affiliation (e.g. church) and deep-rooted socialized beliefs and attitudes. Efforts to improve youth sexual health require multileveled approaches that address inequitable power dynamics.
Future Prospects and Applications

The concept of free-space optical communications was conceived shortly after the invention of lasers. Strides have been made in developing and demonstrating the technology ever since. Early experiments that targeted terrestrial point-to-point, air-to-ground, and space-to-ground links were not fully successful because the technology was immature. Most of these demonstrations were government-funded, both for civilian and military applications. The promise of laser communication, high data-rate delivery with significantly reduced aperture size for the flight terminal, led to the continued funding for the successful experiments and provided the incentive for further demonstrations. Table 7-1 presents a chronological summary of major successful laser-communication technology demonstrations [1–5] to or from air or space. Plans for additional major experiments are discussed below.
Niche width predicts extinction from climate change and vulnerability of tropical species

Climate change may be a major threat to global biodiversity, especially to tropical species. Yet, why tropical species are more vulnerable to climate change remains unclear. Tropical species are thought to have narrower physiological tolerances to temperature, and they have already experienced a higher estimated frequency of climate‐related local extinctions. These two patterns suggest that tropical species are more vulnerable to climate change because they have narrower thermal niche widths. However, no studies have tested whether species with narrower climatic niche widths for temperature have experienced more local extinctions, and if these narrower niche widths can explain the higher frequency of tropical local extinctions. Here, we test these ideas using resurvey data from 538 plant and animal species from 10 studies. We found that mean niche widths among species and the extent of climate change (increase in maximum annual temperatures) together explained most variation (>75%) in the frequency of local extinction among studies. Surprisingly, neither latitude nor occurrence in the tropics alone significantly predicted local extinction among studies, but latitude and niche widths were strongly inversely related. Niche width also significantly predicted local extinction among species, as well as among and (sometimes) within studies. Overall, niche width may offer a relatively simple and accessible predictor of the vulnerability of populations to climate change. Intriguingly, niche width has the best predictive power to explain extinction from global warming when it incorporates coldest yearly temperatures.
The triggering of starbursts in low-mass galaxies

Strong bursts of star formation in galaxies may be triggered either by internal or external mechanisms. We study the distribution and kinematics of the H I gas in the outer regions of 18 nearby starburst dwarf galaxies that have accurate star formation histories from Hubble Space Telescope observations of resolved stellar populations. We find that starburst dwarfs show a variety of H I morphologies, ranging from heavily disturbed H I distributions with major asymmetries, long filaments, and/or H I-stellar offsets to lopsided H I distributions with minor asymmetries. We quantify the outer H I asymmetry for both our sample and a control sample of typical dwarf irregulars. Starburst dwarfs have more asymmetric outer H I morphologies than typical irregulars, suggesting that some external mechanism triggered the starburst. Moreover, galaxies hosting an old burst (≳100 Myr) have more symmetric H I morphologies than galaxies hosting a young one (≲100 Myr), indicating that the former ones probably had enough time to regularize their outer H I distribution since the onset of the burst. We also investigate the nearby environment of these starburst dwarfs and find that most of them (˜80 per cent) have at least one potential perturber at a projected distance ≲200 kpc. Our results suggest that the starburst is triggered either by past interactions/mergers between gas-rich dwarfs or by direct gas infall from the intergalactic medium.
An HST/COS legacy survey of intervening Si III absorption in the extended gaseous halos of low-redshift galaxies

Aims. Doubly ionized silicon (Si iii) is a powerful tracer of diffuse ionized gas inside and outside of galaxies. It can be observed in the local Universe in ultraviolet (UV) absorption against bright extragalactic background sources. We here present an extensive study of intervening Si iii-selected absorbers and study the properties of the warm circumgalactic medium (CGM) around low-redshift ( z ≤ 0.1) galaxies. Methods. We analyzed the UV absorption spectra of 303 extragalactic background sources, as obtained with the Cosmic Origins Spectrograph (COS) on-board the Hubble Space Telescope (HST). We developed a geometrical model for the absorption-cross section of the CGM around the local galaxy population and compared the observed Si iii absorption statistics with predictions provided by the model. We also compared redshifts and positions of the absorbers with those of ~64 000 galaxies using archival galaxy-survey data to investigate the relation between intervening Si iii absorbers and the CGM. Results. Along a total redshift path of Δ z ≈ 24, we identify 69 intervening Si iii systems that all show associated absorption from other low and high ions (e.g., H i, Si ii, Si iv, C ii, C iv). We derive a bias-corrected number density of d N /d z (Si iii)= 2.5 ± 0.4 for absorbers with column densities log N (Si iii) > 12.2, which is ~3 times the number density of strong Mg ii systems at z = 0. This number density matches the expected cross section of a Si iii absorbing CGM around the local galaxy population with a mean covering fraction of ⟨ f c ⟩ = 0.69. For the majority (~60 percent) of the absorbers, we identify possible host galaxies within 300 km s -1 of the absorbers and derive impact parameters ρ Conclusions. Our study indicates that the majority of Si iii-selected absorbers in our sample trace the CGM of nearby galaxies within their virial radii at a typical covering fraction of ~70 percent. We estimate that diffuse gas in the CGM around galaxies, as traced by Si iii, contains substantially more (more than twice as much) baryonic mass than their neutral interstellar medium.
From Markov Chains to Non-Equilibrium Particle Systems

This volume presents a representative work of Chinese probabilists on probability theory and its applications in physics. Interesting results of jump Markov processes are discussed, as well as Markov interacting processes with noncompact states, including the Schlogal model taken from statistical physics. The main body of this book is self-contained and can be used in a course in stochastic processes for graduate students. The book consists of four parts. In Parts 1 and 2, the author introduces the general theory for jump processes. New contributions to the classical problems: uniqueness, recurrence and positive recurrence are studied. Then, probability metrics and coupling methods, stochastically monotonicity, reversibility, large deviations and the estimates of L squared-spectral gap are discussed. Part 3 begins with the study of equilibrium particle systems. This contains the criteria of the reversibility, the construction of Gibbs states and the particle systems on lattice fractals. The final part emphasizes the reaction-diffusion processes which come from non-equilibrium statistical physics. Topics include constructions, existence of stationary distributions, ergodicity, phase transitions and hydrodynamic limits for the processes.
A rare homozygous missense GDF2 (BMP9) mutation causing PAH in siblings: Does BMP10 status contribute?

Pulmonary arterial hypertension (PAH) is a disease characterized by pathological remodeling of the pulmonary vasculature causing elevated pulmonary artery pressures and ultimately, right ventricular failure from chronic pressure overload. Heterozygous pathogenic GDF2 (encoding bone morphogenetic protein 9 (BMP9)) variants account for some (>1%) adult PAH cases. Only three pediatric PAH cases, harboring homozygous or compound heterozygous variants, are reported to date. Ultra‐rare pathogenic GDF2 variants are reported in hereditary hemorrhagic telangiectasia and overlapping disorders characterized by telangiectasias and arteriovenous malformations (AVMs). Here, we present two siblings with PAH homozygous for a GDF2 mutation that impairs BMP9 proprotein processing and reduces growth factor domain availability. We confirm an absence of measurable plasma BMP9 whereas BMP10 levels are detectable and serum‐dependent endothelial BMP activity is evident. This contrasts with the absence of activity which we reported in two children with homozygous pathogenic GDF2 nonsense variants, one with PAH and one with pulmonary AVMs, both with telangiectasias, suggesting loss of BMP10 and endothelial BMP activity in the latter may precipitate telangiectasia development. An absence of phenotype in related heterozygous GDF2 variant carriers suggests incomplete penetrance in PAH and AVM‐related diseases, indicating that additional somatic and/or genetic modifiers may be necessary for disease precipitation.
Nonlinear Markov Processes and Kinetic Equations

A nonlinear Markov evolution is a dynamical system generated by a measure-valued ordinary differential equation with the specific feature of preserving positivity. This feature distinguishes it from general vector-valued differential equations and yields a natural link with probability, both in interpreting results and in the tools of analysis. This brilliant book, the first devoted to the area, develops this interplay between probability and analysis. After systematically presenting both analytic and probabilistic techniques, the author uses probability to obtain deeper insight into nonlinear dynamics, and analysis to tackle difficult problems in the description of random and chaotic behavior. The book addresses the most fundamental questions in the theory of nonlinear Markov processes: existence, uniqueness, constructions, approximation schemes, regularity, law of large numbers and probabilistic interpretations. Its careful exposition makes the book accessible to researchers and graduate students in stochastic and functional analysis with applications to mathematical physics and systems biology.
Vitrified Particulated Articular Cartilage for Joint Resurfacing: A Swine Model

Background: The use of particulated articular cartilage for repairing cartilage defects has been well established, but its use is currently limited by the availability and short shelf life of donor cartilage. Vitrification is an ice-free cryopreservation technology at ultralow temperatures for tissue banking. An optimized vitrification protocol has been developed for particulated articular cartilage; however, the equivalency of the long-term clinical efficacy of vitrified particulated articular cartilage compared with fresh articular cartilage has not yet been determined. Hypothesis: The repair effect of vitrified particulated cartilage from pigs would be equivalent to or better than that of fresh particulated cartilage stored at 4°C for 21 days. Study Design: Controlled laboratory study. Methods: A total of 19 pigs were randomly divided into 3 experimental groups: fresh particulated cartilage group (n = 8), vitrified particulated cartilage group (n = 8), and negative control group (no particulated cartilage in the defect; n = 3). An additional pig was used as the initial cartilage donor for the first set of surgical procedures. Pigs were euthanized after 6 months to obtain femoral condyles, and the contralateral condyle was used as the positive (no defect) control. Samples were evaluated for gross morphology using the Outerbridge and Osteoarthritis Research Society International (OARSI) scoring systems, histology (safranin O, collagen type I/II, DAPI), and chondrocyte viability using live-dead membrane integrity staining. Results: There were no infections after surgery, and all 19 pigs were followed for the duration of the study. The OARSI grades for the fresh and vitrified particulated cartilage groups were 2.44 ± 1.35 and 2.00 ± 0.80, respectively, while the negative control group was graded significantly higher at 4.83 ± 0.29. Analysis of histological and fluorescent staining demonstrated that the fresh and vitrified particulated cartilage groups had equivalent regeneration within cartilage defects, with similar cell viability and densities and expression of proteoglycans and collagen type I/II. Conclusion: The implantation of fresh or vitrified particulated cartilage resulted in the equivalent repair of focal cartilage defects when evaluated at 6 months after surgery. Clinical Relevance: The vitrification of particulated cartilage is a viable option for long-term storage for cartilage tissue banking and could greatly increase the availability of donor tissue for transplantation.
Risk factors for high‐dose methotrexate associated toxicities in patients with primary central nervous system lymphoma

Methotrexate (MTX) is an antimetabolic antitumor drug with high individual differences and may lead to severe toxicities in a considerable number of patients. This study aimed to explore the factors influencing major adverse events in patients with primary central nervous system lymphoma treated with high‐dose MTX (HD‐MTX), which could be useful in clinical practice.
Dihydropyrimidine dehydrogenase (DPD) genotype and phenotype among Danish cancer patients: prevalence and correlation between DPYD-genotype variants and P-uracil concentrations

Niels Herluf Paulsen , Camilla Qvortrup, Fie Juhl Vojdeman, Peter Plomgaard, Stig Ejdrup Andersen , Anne Ramlov, Birgitte Bertelsen, Maria Rossing, Claus Gyrup Nielsen, Elke Hoffmann-L€ ucke , Eva Greibe, Hanne Spangsberg Holm, Heidi Hvid Nielsen, Ihab Bishara Yousef Lolas, Jonna Skov Madsen , Marianne Lerbaek Bergmann, Morten Mørk, Palle B. Nielsen Fruekilde, Pernille Bøttger, Peter Clausager Petersen, Peter Henrik Nissen , Søren Feddersen , Troels K. Bergmann, Per Pfeiffer and Per Damkier Department of Clinical Pharmacology, Odense University Hospital, Odense, Denmark; Clinical Pharmacology, Pharmacy and Environmental Medicine Department of Public Health, University of Southern Denmark, Odense, Denmark; Department of Oncology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark; Department of Clinical Biochemistry, Holbaek Hospital, Holbaek, Denmark; Department of Clinical Biochemistry, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark; Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark; Clinical Pharmacology Unit, Zealand University Hospital, Roskilde, Denmark; Department of Oncology, Aarhus University Hospital, Aarhus, Denmark; Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark; Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark; Department of Clinical Biochemistry, Aalborg University Hospital, Aalborg, Denmark; Department of Clinical Biochemistry, Aarhus University Hospital, Aarhus N, Denmark; Institute for Clinical Medicine, Aarhus University of Health, Aarhus, Denmark; Department of Oncology, Odense University Hospital, Odense, Denmark; Department of Clinical Biochemistry, Zealand University Hospital, Køge, Denmark; Department of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark; Department of Biochemistry and Immunology, Lillebaelt Hospital – University Hospital of Southern Denmark, Vejle, Denmark; Department of Regional Health Research, University of Southern Denmark, Odense, Denmark; Department of Clinical Biochemistry, Odense University Hospital, Odense, Denmark; Department of Oncology, Zealand University Hospital, Roskilde, Denmark; Denmark and Institute for Clinical Medicine, Aarhus University, Aarhus, Denmark; Department of Clinical Research, University of Southern Denmark, Odense, Denmark; Department of Regional Health Research, University of Southern Denmark, Esbjerg, Denmark