Miracle-dz/UniFAR-FTUs huggingface dataset:
In vitro activity of ceftazidime/avibactam against clinical isolates of Enterobacterales and Pseudomonas aeruginosa from Middle Eastern and African countries: ATLAS global surveillance programme 2015–18

Abstract Objectives To assess the in vitro activity of ceftazidime/avibactam against a recent, 2015–18, collection of clinical isolates of Gram-negative bacilli from Middle Eastern and African countries with a focus on isolates from ICUs and with MDR and difficult-to-treat resistance (DTR) phenotypes. Methods Antimicrobial susceptibility testing of 4608 isolates of Enterobacterales (997 isolates from ICU patients) and 1358 isolates of Pseudomonas aeruginosa (374 isolates from ICU patients) was performed by CLSI broth microdilution methodology in a central laboratory. MICs were interpreted using both CLSI (2020) and EUCAST (2020) MIC breakpoints. Results Most isolates of Enterobacterales (Middle East: ICU, 99.1% susceptible, non-ICU, 99.1%; Africa: ICU, 96.9% susceptible, non-ICU, 98.3%) and P. aeruginosa (Middle East: ICU, 93.4%, non-ICU, 92.1%; Africa: ICU, 89.8%; non-ICU, 94.1%) were susceptible to ceftazidime/avibactam. Applying CLSI and EUCAST breakpoints, MDR rates were similar for Enterobacterales (27.8%–36.0% of isolates) and P. aeruginosa (25.0%–36.4%) while DTR rates were lower for Enterobacterales (1.6%–1.8%) than for P. aeruginosa (5.2%–7.4%). Percentage susceptible rates for ceftazidime/avibactam for MDR Enterobacterales were 96.8%–97.5% (Middle East) and 92.5%–94.3% (Africa) while rates for P. aeruginosa were 70.1%–80.0% (Middle East) and 69.5%–78.2% (Africa). 60.5%–65.8% (Middle East) and 38.9%–52.2% (Africa) of isolates of Enterobacterales with DTR phenotypes were ceftazidime/avibactam susceptible as were 29.2%–31.1% (Middle East) and 28.2%–35.8% (Africa) of DTR P. aeruginosa. Conclusions Overall, the isolates of Enterobacterales and P. aeruginosa tested from Middle Eastern and African countries were highly susceptible to ceftazidime/avibactam. Most MDR and many DTR isolates of Enterobacterales and P. aeruginosa were susceptible to ceftazidime/avibactam.
Racial disparities in COVID-19 pandemic cases, hospitalisations, and deaths: A systematic review and meta-analysis

Background People from racial minority groups in western countries experience disproportionate socioeconomic and structural determinants of health disadvantages. These disadvantages have led to inequalities and inequities in health care access and poorer health outcomes. We report disproportionate disparities in prevalence, hospitalisation, and deaths from COVID-19 by racial minority populations. Methods We conducted a systematic literature search of relevant databases to identify studies reporting on prevalence, hospitalisations, and deaths from COVID-19 by race groups between 01 January 2020 – 15 April 2021. We grouped race categories into Blacks, Hispanics, Whites and Others. Random effects model using the method of DerSimonian and Laird were fitted, and forest plot with respective ratio estimates and 95% confidence interval (CI) for each race category, and subgroup meta-regression analyses and the overall pooled ratio estimates for prevalence, hospitalisation and mortality rate were presented. Results Blacks experienced significantly higher burden of COVID-19: prevalence ratio 1.79 (95% confidence interval (CI) = 1.59-1.99), hospitalisation ratio 1.87 (95% CI = 1.69-2.04), mortality ratio 1.68 (95% CI = 1.52-1.83), compared to Whites: prevalence ratio 0.70 (95% CI = 0.0.64-0.77), hospitalisation ratio 0.74 (95% CI = 0.65-0.82), mortality ratio 0.82 (95% CI = 0.78-0.87). Also, Hispanics experienced a higher burden: prevalence ratio 1.78 (95% CI = 1.63-1.94), hospitalisation ratio 1.32 (95% CI = 1.08-1.55), mortality ratio 0.94 (95% CI = 0.84-1.04) compared to Whites. A higher burden was also observed for Other race groups: prevalence ratio 1.43 (95% CI = 1.19-1.67), hospitalisation ratio 1.12 (95% CI = 0.89-1.35), mortality ratio 1.06 (95% CI = 0.89-1.23) compared to Whites. The disproportionate burden among Blacks and Hispanics remained following correction for publication bias. Conclusions Blacks and Hispanics have been disproportionately affected by COVID-19. This is deeply concerning and highlights the systemically entrenched disadvantages (social, economic, and political) experienced by racial minorities in western countries; and this study underscores the need to address inequities in these communities to improve overall health outcomes.
Unraveling the effect of defects, domain size, and chemical doping on photophysics and charge transport in covalent organic frameworks†

Understanding the underlying physical mechanisms that govern charge transport in two-dimensional (2D) covalent organic frameworks (COFs) will facilitate the development of novel COF-based devices for optoelectronic and thermoelectric applications. In this context, the low-energy mid-infrared absorption contains valuable information about the structure–property relationships and the extent of intra- and inter-framework “hole” polaron delocalization in doped and undoped polymeric materials. In this study, we provide a quantitative characterization of the intricate interplay between electronic defects, domain sizes, pore volumes, chemical dopants, and three dimensional anisotropic charge migration in 2D COFs. We compare our simulations with recent experiments on doped COF films and establish the correlations between polaron coherence, conductivity, and transport signatures. By obtaining the first quantitative agreement with the measured absorption spectra of iodine doped (aza)triangulene-based COF, we highlight the fundamental differences between the underlying microstructure, spectral signatures, and transport physics of polymers and COFs. Our findings provide conclusive evidence of why iodine doped COFs exhibit lower conductivity compared to doped polythiophenes. Finally, we propose new research directions to address existing limitations and improve charge transport in COFs for applications in functional molecular electronic devices.
Tracing and testing multiple generations of contacts to COVID-19 cases: cost–benefit trade-offs

Traditional contact tracing tests the direct contacts of those who test positive. But, by the time an infected individual is tested, the infection starting from the person may have infected a chain of individuals. Hence, why should the testing stop at direct contacts, and not test secondary, tertiary contacts or even contacts further down? One deterrent in testing long chains of individuals right away may be that it substantially increases the testing load, or does it? We investigate the costs and benefits of such multi-hop contact tracing for different number of hops. Considering diverse contact networks, we show that the cost–benefit trade-off can be characterized in terms of a single measurable attribute, the initial epidemic growth rate. Once this growth rate crosses a threshold, multi-hop contact tracing substantially reduces the outbreak size compared with traditional tracing. Multi-hop even incurs a lower cost compared with the traditional tracing for a large range of values of the growth rate. The cost–benefit trade-offs can be classified into three phases depending on the value of the growth rate. The need for choosing a larger number of hops becomes greater as the growth rate increases or the environment becomes less conducive toward containing the disease.
Post-viral mental health sequelae: Systematic review and meta-analysis of prevalence proportions

Background: Mental health problems (MHP) in COVID-19 patients and survivors were anticipated already during early stages of this pandemic. We aimed to synthesize the prevalence of anxiety, depression, post-traumatic and general distress of major virus epidemics since 2002. Methods: In this systematic review and meta-analysis, we searched PubMed, PsycINFO, and Embase from 2002 until April 14, 2021 for peer-reviewed studies reporting prevalence of MHP in adults with laboratory-confirmed or suspected SARS-CoV-1, H1N1, MERS-CoV, H7N9, Ebolavirus, or SARS-CoV-2 infection. We included studies that assessed MHP with well-validated and frequently used scales. A three-level random-effects meta-analysis for dependent sizes was conducted to account for multiple outcome reporting. We pooled MHP jointly and separately for mild or moderate-to-severe severity by acute (one month), ongoing (one to three month), and post-illness phase (longer than three months). A meta-regression was conducted to test for moderating effects. PROSPERO registration: CRD42020194535. Findings: We identified 59 studies providing a total of 187 effect sizes. Range for sample size (n=14-n=1002), females (22-79%), and mean age (32-72 years). MHP prevalence was higher for mild (35.5-46.3%) compared to moderate-to-severe MPH (17.3-22.3). MHP, in general, decreased from acute to post-illness from 46.3% to 38.8% and for mild and moderate-to-severe from 22.3% to 18.8%, respectively. We found no evidence of moderating effects except for non-random sampling and H1N1 showing higher proportions. Interpretation: MHP decreased over time but were still on a substantial level at post-illness. This highlights a need for rapid access to mental health care and rehabilitation planning in affected individuals.
The development and usability testing of digital knowledge translation tools for parents of children with acute otitis media

Acute otitis media (AOM) is the most common bacterial ear infection affecting up to 80% of children before the age of three. Despite the common occurrence of the illness and the wide range of material available at clinics and online, parents are not always aware of these resources and they are often difficult to understand. We worked with parents to develop and assess the usability of a whiteboard animation video and interactive infographic for AOM in children. Parents rated the tools highly across all usability items, suggesting that creative tools developed using multi-method development processes can be useful, relevant, understandable, and will be used by the intended audience. Following the completion of the English-language products, our team culturally adapted the tools for the Pakistan context and evaluated the usability of these adapted tools. During usability testing, parents indicated that they felt the tools were useful, demonstrating that culturally adapted version of knowledge translations tools are effective in ensuring that parents could understand complex health information.
Association of Herpes simplex virus I&II infections with rs187084 SNP of TLR9 and male infertility

Since TLR9 recognises unmethylated CpG motifs in viral DNA, its polymorphisms may contribute to the susceptibility to Herpes simplex virus I&II infection. In the present study, to evaluate the role of rs187084 SNP (single nucleotide polymorphism) of TLR9 in Herpes simplex virus I&II infection and male infertility, 103 infertile and 27 fertile blood and semen samples were analysed. We assessed the micro and macro properties of semen specimens and the presence of HSV immunoglobulins. Tetra‐primer ARMS PCR was used to detect SNP and to investigate the genotype distribution of TLR9‐rs187084 SNPs, and the correlation between polymorphisms of TLR9 gene and male infertility. Moreover, the odds ratio (OR) and 95% confidence intervals were used to estimate the strength of the association. Based on our finding, a significant correlation was observed between HSV infection, agglutination and polymorphism (TT) under dominant (OR = 1.28, 95% CI = 0.94–1.75) and recessive (OR = 0.44, 95% CI = 0.21–0.94) models for the data, which was complied with Hardy–Weinberg equilibrium (HWE) (OR = 2.91, 95% CI = 1.02–8.30). The result showed a significant association between HSV IgM and agglutination in HSV infection (p < .001), and in addition, there were associations between alleles so that rs187084 SNP might be considered as a risk factor for the incidence of HSV infection.
Less need for differentiation? Intestinal length of reptiles as compared to mammals

Although relationships between intestinal morphology between trophic groups in reptiles are widely assumed and represent a cornerstone of ecomorphological narratives, few comparative approaches actually tested this hypothesis on a larger scale. We collected data on lengths of intestinal sections of 205 reptile species for which either body mass (BM), snout-vent-length (SVL) or carapax length (CL) was recorded, transforming SVL or CL into BM if the latter was not given, and analyzed scaling patterns with BM and SVL, accounting for phylogeny, comparing three trophic guilds (faunivores, omnivores, herbivores), and comparing with a mammal dataset. Length-BM relationships in reptiles were stronger for the small than the large intestine, suggesting that for the latter, additional factors might be relevant. Adding trophic level did not consistently improve model fit; only when controlling for phylogeny, models indicated a longer large intestine in herbivores, due to a corresponding pattern in lizards. Trophic level effects were highly susceptible to sample sizes, and not considered strong. Models that linked BM to intestine length had better support than models using SVL, due to the deviating body shape of snakes. At comparable BM, reptiles had shorter intestines than mammals. While the latter finding corresponds to findings of lower tissue masses for the digestive tract and other organs in reptiles as well as our understanding of differences in energetic requirements between the classes, they raise the hitherto unanswered question what it is that reptiles of similar BM have more than mammals. A lesser effect of trophic level on intestine lengths in reptiles compared to mammals may stem from lesser selective pressures on differentiation between trophic guilds, related to the generally lower food intake and different movement patterns of reptiles, which may not similarly escalate evolutionary arms races tuned to optimal agility as between mammalian predators and prey.
Evaluation of Conflicts of Interest among Systematic Review Authors on Pharmacological Therapies for Alcohol Use Disorder: A Cross-Sectional Study

Introduction and aims: The high prevalence and economic burden of alcohol use disorder (AUD) requires methodologically sound research to guide treatment decisions. Systematic reviews (SR) are fundamental to clinical decision making as they collate results of all studies for a given topic and provide summaries of the clinical evidence. Bias resulting from industry relationships can compromise the validity of SRs. Thus, we investigated financial conflicts of interests (FCOI) within SRs involving the pharmacologic treatment of AUD. Design and Methods: We conducted a systematic search of PubMed, Embase, and the Cochrane Database to retrieve SRs published between September 2016 and December 2019. Screening and data extraction were performed in duplicate, blinded fashion—collecting characteristics of the reviews including the authors’ FCOI statements. The results and discussion sections were rated as favorable or unfavorable toward the treatment drug. A stepwise method was used to identify undisclosed FCOIs for all SR authors. Results: Nineteen (of 51) authors representing 7 (of 12) SRs were found to have FCOI. Among reviews with conflicted authors, 3 of 7 (42.9%) results sections were favorable toward the treatment drug, whereas 6 of 7 (85.7%) conclusions were rated as favorable. Discussion and Conclusions: More than one-third of SR authors and nearly two-thirds of studies were found to have FCOIs. Our investigation shows that financial ties are frequent among SR authors on AUD pharmacotherapies and that discussion sections often favored the drug for which the sponsor provided payments.
Assessing Polyvictimization in a Family Justice Center: Lessons Learned From a Demonstration Project

There is a growing interest in developing comprehensive assessments that measure intimate partner violence (IPV) alongside other adverse events that correlate with IPV and compound its effects. One promising line of research in this area has focused on the impact of exposure to multiple types of victimization, i.e., polyvictimization. The purpose of this study is to examine the experience of administration of a polyvictimization tool from staff and client perspectives in order to inform future tool developments and assessment procedures. Qualitative interviews and focus groups with clients and staff from a family justice center who had experience with the assessment tool were used to identify strengths and challenges of the assessment too and inform future tool development. Findings demonstrate that an assessment tool provides the space for clients to talk about trauma and facilitate empowerment, while providing the opportunity for psychoeducation and service referrals. Concerns about the assessment tool included adverse reactions without proper framing and language, as well as shifting the emphasis from screening for adversities toward strengths, coping skills, and resilience. Implications for future measurement development and establishing best practices in polyvictimization assessment are discussed, with an emphasis on the benefits of social service agencies utilizing assessment tools.
Experimental Microkinetic Approach of the Surface Reconstruction of Cobalt Particles in Relationship with the CO/H2 Reaction on a Reduced 10% Co/Al2O3 Catalyst

The adsorption of x% CO/He (x = 1 and 2) on a reduced 10 wt % Co/Al2O3 catalyst at an adsorption temperature of 560 K > Ta > 420 K leads to the formation of a linear CO species on Co° sites (denoted LCo° species) with an infrared (IR) band at ≈2030 cm–1 at full coverage. This adsorption is associated with the formation of carbon that is implicated in the reconstruction of the surface of the cobalt particles, leading to the progressive transformation of the LCo° species into a new linear CO species on Co°C sites of the reconstructed surface with an IR band at ≈2060 cm–1. An experimental microkinetic approach of the reconstruction process via the LCo° → LCo°C transformation reveals the impact of different kinetic parameters such as the reaction temperature, the CO partial pressure, and the presence of hydrogen. During the reconstruction the coverages of the LCo° and LCo°C species remain very high (>0.95) due to their high heats of adsorption determined by the Adsorption Equilibrium Infra Red spectroscopy me.
Exploring how residential care facilities can enhance the autonomy of people with dementia and improve informal care

Background and objectives Residential care facilities (RCFs) strive to enhance autonomy for people with dementia and to enhance informal care provision, although this is difficult. This study explored how RCF staff can enhance autonomy and improve informal care by looking at the influence of interactions (contact and approachability between residents, staff members and informal caregivers) and the physical environment, including the use of technologies. Research design and methods A realist evaluation multiple-case study was conducted using document analyses, eight semi-structured interviews with staff members and relatives and 56 hours of observations of residents across two RCFs aiming to provide person-centred care. Realist logic of analysis was performed, involving Context-Mechanism-Outcome configurations. Findings The behaviour, attitudes and interactions of staff members with residents and informal caregivers appeared to contribute to the autonomy of people with dementia and enhance informal care provision. The physical environment of the RCFs and the use of technologies were less relevant to enhancing autonomy and informal care provision, although they can support staff members in providing person-centred care in daily practice. Discussion and implications The findings add to those of other studies regarding the importance of interaction between residents, staff members and informal caregivers. The findings provide insight for other RCFs on how successfully to enhance autonomy for their residents and to improve informal care provision, as well as, more broadly, how to implement person-centred care.
Spatiotemporal variability and origin of CO2 and CH4 tree stem fluxes in an upland forest

The exchange of multiple greenhouse gases (i.e., CO2 and CH4) between tree stems and the atmosphere represents a knowledge gap in the global carbon cycle. Stem CO2 and CH4 fluxes vary across time and space and are unclear, which are their individual or shared drivers. Here we measured CO2 and CH4 fluxes at different stem heights combining manual (biweekly; n = 678) and automated (hourly; n > 38,000) measurements in a temperate upland forest. All trees showed CO2 and CH4 emissions despite 20% of measurements showing net CH4 uptake. Stem CO2 fluxes presented clear seasonal trends from manual and automated measurements. Only automated measurements captured the high temporal variability of stem CH4 fluxes revealing clear seasonal trends. Despite that temporal integration, the limited number of automated chambers made stand‐level mean CH4 fluxes sensitive to “hot spots,” resulting in mean fluxes with high uncertainty. Manual measurements provided better integration of spatial variability, but their lack of temporal variability integration hindered the detection of temporal trends and stand‐level mean fluxes. These results highlight the potential bias of previous studies of stem CH4 fluxes solely based on manual or automated measurements. Stem height, temperature, and soil moisture only explained 7% and 11% of the stem CH4 flux variability compared to 42% and 81% for CO2 (manual and automated measurements, respectively). This large unexplained variability, in combination with high CH4 concentrations in the trees' heartwood, suggests that stem CH4 fluxes might be more influenced by gas transport and diffusivity through the wood than by drivers of respiratory CO2 flux, which has crucial implications for developing process‐based ecosystem models. We postulate that CH4 is likely originated within tree stems because of lack of a consistent vertical pattern in CH4 fluxes, evidence of CH4 production in wood incubations, and low CH4 concentration in the soil profile but high concentrations within the trees' heartwood.
Nonsense-Mediated RNA Decay Is a Unique Vulnerability of Cancer Cells Harboring SF3B1 or U2AF1 Mutations

This study has developed a novel NMD reporter system and identified a potential therapeutic approach of targeting the NMD pathway to treat cancer with spliceosome gene mutations. Nonsense-mediated RNA decay (NMD) is recognized as an RNA surveillance pathway that targets aberrant mRNAs with premature translation termination codons (PTC) for degradation, however, its molecular mechanisms and roles in health and disease remain incompletely understood. In this study, we developed a novel reporter system to accurately measure NMD activity in individual cells. A genome-wide CRISPR-Cas9 knockout screen using this reporter system identified novel NMD-promoting factors, including multiple components of the SF3B complex and other U2 spliceosome factors. Interestingly, cells with mutations in the spliceosome genes SF3B1 and U2AF1, which are commonly found in myelodysplastic syndrome (MDS) and cancers, have overall attenuated NMD activity. Compared with wild-type (WT) cells, SF3B1- and U2AF1-mutant cells were more sensitive to NMD inhibition, a phenotype that is accompanied by elevated DNA replication obstruction, DNA damage, and chromosomal instability. Remarkably, the sensitivity of spliceosome mutant cells to NMD inhibition was rescued by overexpression of RNase H1, which removes R-loops in the genome. Together, these findings shed new light on the functional interplay between NMD and RNA splicing and suggest a novel synthetic lethal strategy for the treatment of MDS and cancers with spliceosome mutations. Significance: This study has developed a novel NMD reporter system and identified a potential therapeutic approach of targeting the NMD pathway to treat cancer with spliceosome gene mutations. Graphical Abstract