Miracle-dz/UniFAR-FTUs huggingface dataset:
Snapshots of nascent RNA reveal cell- and stimulus-specific responses to acute kidney injury

The current strategy to detect acute injury of kidney tubular cells relies on changes in serum levels of creatinine. Yet serum creatinine (sCr) is a marker of both functional and pathological processes and does not adequately assay tubular injury. In addition, sCr may require days to reach diagnostic thresholds, yet tubular cells respond with programs of damage and repair within minutes or hours. To detect acute responses to clinically relevant stimuli, we created mice expressing Rosa26-floxed-stop uracil phosphoribosyltransferase (Uprt) and inoculated 4-thiouracil (4-TU) to tag nascent RNA at selected time points. Cre-driven 4-TU–tagged RNA was isolated from intact kidneys and demonstrated that volume depletion and ischemia induced different genetic programs in collecting ducts and intercalated cells. Even lineage-related cell types expressed different genes in response to the 2 stressors. TU tagging also demonstrated the transient nature of the responses. Because we placed Uprt in the ubiquitously active Rosa26 locus, nascent RNAs from many cell types can be tagged in vivo and their roles interrogated under various conditions. In short, 4-TU labeling identifies stimulus-specific, cell-specific, and time-dependent acute responses that are otherwise difficult to detect with other technologies and are entirely obscured when sCr is the sole metric of kidney damage.
Enhancement of growth and biomolecules (carbohydrates, proteins, and chlorophylls) of isolated Chlorella thermophila using optimization tools

Abstract The production of multiple products from microalgae is essential for economic sustainability and the knowledge of optimum cultivation conditions for high growth and biomolecule synthesis of a microalgal strain is the prerequisite for its commercial production. In this work, optimization of nutrient concentrations for the cultivation of isolated Chlorella thermophila was performed by manipulating nine nutrients with the objectives of maximization of growth, carbohydrate, protein, and chlorophyll contents. Experiments were designed and effects of the parameters were studied using Taguchi orthogonal array (TOA). Experimental results of TOA were used for modeling artificial neural networks (ANN) followed by the optimization using genetic algorithm (GA) to find global optimal solutions. Results showed an increase of 36, 88, 36, and 88% for growth, carbohydrates, proteins, and chlorophylls, respectively, at optimal combinations of parameters given by TOA. Results obtained through the ANN-GA optimization were 9, 10, and 3% more compared to the TOA for biomass, carbohydrates, and chlorophylls, respectively with experimental verification. Nitrates and bicarbonate were found to play the most pivotal role in biomass and biomolecule synthesis of the isolated microalgal strain. Results of the current investigation can be used in the industrial scale-up for the production of multiple products using the biorefinery approach.
Standardized assessment of depression symptoms in post‐acute care: A screening threshold approach

Depression symptoms have impacts on quality of life, rehabilitation and treatment adherence, and resource utilization among patients in post‐acute care (PAC) settings. The PHQ‐2 and PHQ‐9 are instruments for the assessment of depression, previously used in PAC settings, that have tradeoffs in terms of measurement depth versus respondent/assessor burden. Therefore, the present study tested a gateway version of the protocol (PHQ‐2 to 9).
COVID-19 infection and outcomes in a population-based cohort of 17 203 adults with intellectual disabilities compared with the general population

Background Adults with intellectual disabilities (ID) may be at higher risk of COVID-19 death. We compared COVID-19 infection, severe infection, mortality, case fatality and excess deaths, among adults with, and without, ID. Methods Adults with ID in Scotland’s Census, 2011, and a 5% sample of other adults, were linked to COVID-19 test results, hospitalisation data and deaths (24 January 2020–15 August 2020). We report crude rates of COVID-19 infection, severe infection (hospitalisation/death), mortality, case fatality; age-standardised, sex-standardised and deprivation-standardised severe infection and mortality ratios; and annual all-cause mortality for 2020 and 2015–2019. Findings Successful linkage of 94.9% provided data on 17 203 adults with, and 188 634 without, ID. Adults with ID had more infection (905/100 000 vs 521/100 000); severe infection (538/100 000 vs 242/100 000); mortality (258/100 000 vs 116/100 000) and case fatality (30% vs 24%). Poorer outcomes remained after standardisation: standardised severe infection ratio 2.61 (95% CI 1.81 to 3.40) and mortality ratio 3.26 (95% CI 2.19 to 4.32). These were higher at ages 55–64: 7.39 (95% CI 3.88 to 10.91) and 19.05 (95% CI 9.07 to 29.02), respectively, and in men, and less deprived neighbourhoods. All-cause mortality was slightly higher in 2020 than 2015–2019 for people with ID: standardised mortality ratio 2.50 (95% CI 2.18 to 2.82) and 2.39 (95% CI 2.28 to 2.51), respectively. Conclusion Adults with ID had more COVID-19 infections, and worse outcomes once infected, particularly adults under 65 years. Non-pharmaceutical interventions directed at formal and informal carers are essential to reduce transmission. All adults with ID should be prioritised for vaccination and boosters regardless of age.
Regret-Based Nash Equilibrium Sorting Genetic Algorithm for Combinatorial Game Theory Problems with Multiple Players

Abstract We introduce a regret-based fitness assignment strategy for evolutionary algorithms to find Nash equilibria in noncooperative simultaneous combinatorial game theory problems where it is computationally intractable to enumerate all decision options of the players involved in the game. Applications of evolutionary algorithms to non-cooperative simultaneous games have been limited due to challenges in guiding the evolutionary search toward equilibria, which are usually inferior points in the objective space. We propose a regret-based approach to select candidate decision options of the players for the next generation in a multipopulation genetic algorithm called Regret-Based Nash Equilibrium Sorting Genetic Algorithm (RNESGA). We show that RNESGA can converge to multiple Nash equilibria in a single run using two- and three- player competitive knapsack games and other games from the literature. We also show that pure payoff-based fitness assignment strategies perform poorly in three-player games.
Factors Associated With Hope and Quality of Life in Patients With Coronary Artery Disease

ABSTRACT Background Psychological resources such as hope have been suggested to affect quality of life (QoL) positively in patients with heart disease. However, little information regarding the relationship between these two constructs is available. Purpose This work was aimed at examining the factors associated with hope and QoL in patients with coronary artery disease. Methods In this descriptive work, perceived QoL and hope were assessed in 500 patients with heart disease. The information was collected using the McGill QoL Questionnaire, demographic variables, and the Herth Hope Index. The Pearson correlation test and general linear model were used to examine correlations through SPSS Version 22. Results A considerable correlation was discovered between QoL and hope (r = .337, p < .001). Multivariate analyses with regression revealed that religious beliefs and social support both had significant and positive effects on the total perceived hope of patients and that patient age had a considerable negative impact on QoL (p < .05). None of these factors had a significant impact on hope (p < .05). In addition, the total QoL had a significant and positive effect on patient feelings and thoughts, whereas the physical problems component of QoL had a significant and negative effect on hope (p < .05). Participants with higher levels of education reported more hope. Conclusions QoL relates significantly to self-perceived hope in patients. Understanding QoL and hopefulness in patients with coronary artery disease has implications for nurses and other healthcare professionals.
From Atherosclerosis to Myocardial Infarction: A Process-Oriented Model Investigating the Role of Risk Factors

Abstract Mathematical models are able to reflect biological processes and to capture epidemiologic data. Thus, they may help elucidate roles of risk factors in disease progression. We propose to account for smoking, hypertension, and dyslipidemia in a previously published process-oriented model that describes the development of atherosclerotic lesions resulting in myocardial infarction (MI). The model is sex-specific and incorporates individual heterogeneity. It was applied to population-based individual risk factors and MI rates (Cooperative Health Research in the Region of Augsburg (KORA) study) together with subclinical atherosclerotic lesion data (Pathobiological Determinants of Atherosclerosis in Youth (PDAY) study). Different model variants were evaluated, testing the association of risk factors with different disease processes. Best fits were obtained for smoking affecting a late-stage disease process, suggesting a thrombogenic role. Hypertension was mainly related to complicated, vulnerable lesions. Dyslipidemia was consistent with increasing the number of initial lesions. By accounting for heterogeneity, individual hazard ratios differ from the population average. The mean individual hazard ratio for smoking was twice the population-based hazard ratio for men and even more for women. Atherosclerotic lesion progression and MI incidence data can be related in a mathematical model to illuminate how risk factors affect different phases of this pathological process.
Determinants of the acceptance and adoption of a digital contact tracing tool during the COVID-19 pandemic in Singapore

Abstract The motivations that govern the adoption of digital contact tracing (DCT) tools are complex and not well understood. Hence, we assessed the factors influencing the acceptance and adoption of Singapore's national DCT tool – TraceTogether – during the COVID-19 pandemic. We surveyed 3943 visitors of Tan Tock Seng Hospital from July 2020 to February 2021 and stratified the analyses into three cohorts. Each cohort was stratified based on the time when significant policy interventions were introduced to increase the adoption of TraceTogether. Binary logistic regression was preceded by principal components analysis to reduce the Likert items. Respondents who ‘perceived TraceTogether as useful and necessary’ had higher likelihood of accepting it but those with ‘Concerns about personal data collected by TraceTogether’ had lower likelihood of accepting and adopting the tool. The injunctive and descriptive social norms were also positively associated with both the acceptance and adoption of the tool. Liberal individualism was mixed in the population and negatively associated with the acceptance and adoption of TraceTogether. Policy measures to increase the uptake of a national DCT bridged the digital divide and accelerated its adoption. However, good public communications are crucial to address the barriers of acceptance to improve voluntary uptake widespread adoption.
Relationship of anthropometric measurements and percent body fat mass to cardiovascular disease risk factors in adults with cerebral palsy

Adults with cerebral palsy (CP) face high morbidity from cardiovascular disease (CVD). Of concern, classic screening parameters are inconsistent in identifying CVD risk in this population. Dual‐energy x‐ray absorptiometry (DEXA), which provides direct measurements of fat mass (FM), may be an alternative screening method.
Self-reported Smell and Taste Disorders in Patients With COVID-19: A Japanese Single-center Study

Background/Aim: Smell and taste disorders are among the most common symptoms of COVID-19. However, the relationship between smell and taste disorders and systemic symptoms is not fully understood in Japan. Patients and Methods: Questionnaires were mailed to 105 of 111 COVID-19 patients who were hospitalized at our hospital between March and July 2020 in Japan. Results: A total of 74 patients (response rate: 70.5%) completed the survey. Of these, six patients (8.1%) presented with smell disorders only, 16 (21.6%) presented with taste disorders only, and 17 (23.0%) presented with both smell and taste disorders. The mean Visual Analog Scale for smell and taste was 0.5 and 20, respectively, at the time of the most severe symptoms. Conclusion: Among COVID-19 patients in Japan, smell and taste disorders are often followed by fever and may not be the first symptoms. Sense of smell is particularly impaired. These symptoms often improve, although they sometimes persist for a long time as sequelae.
A Short-Term Winner? Dramatic Increases in the Population of Mushroom Coral Lobactis scutaria (Anthozoa: Fungiidae) in Kāne‘ohe Bay, Hawai‘i from 2000 to 2018

Abstract: Globally, coral reefs have been in significant decline for several decades. In contrast, the reefs in Kāne‘ohe Bay, Hawai‘i have presented an opposite trend during the same period, showing recovery and resilience even while experiencing significant disturbances. Since the diversion of sewage outfalls from southern Kāne‘ohe Bay in the late 1970s, coral populations have made a gradual recovery despite periodic mortality from heat-induced coral bleaching, competition from native and invasive algae, and freshwater inundation during heavy rainfall events. This study repeated surveys originally performed in 2000 for the free-living, solitary, common mushroom coral Lobactis (Fungia) scutaria to investigate population stability and size structure in the north, central, and south regions of the Bay. We found significant increases of up to 538% in the density of L. scutaria in Kāne‘ohe Bay between 2000 and 2018. An increased abundance of sexual recruits was particularly noteworthy. In 2018, the population structure reflected 9.2% sexual recruits and 3.8% asexual buds compared to 2000 when sexual recruits were nearly absent (0.4% of population.) We also found a positive linear relationship between sexual recruit density and adult density. Sites on patch reefs under management actions that involved the physical removal of invasive algae and sea urchin out-planting to crop the algae showed no difference in mushroom coral densities from control sites. While the growing population of mushroom corals in Kāne‘ohe Bay, Hawai‘i provides an exemplar species for resilience and recovery, it is unclear if this short-term expansion will continue under future conditions.
Evolutionary dynamics of the severe acute respiratory syndrome coronavirus 2 genomes

Abstract The coronavirus disease 2019 (COVID-19) pandemic has caused immense losses in human lives and the global economy and posed significant challenges for global public health. As severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, has evolved, thousands of single nucleotide variants (SNVs) have been identified across the viral genome. The roles of individual SNVs in the zoonotic origin, evolution, and transmission of SARS-CoV-2 have become the focus of many studies. This review summarizes recent comparative genomic analyses of SARS-CoV-2 and related coronaviruses (SC2r-CoVs) found in non-human animals, including delineation of SARS-CoV-2 lineages based on characteristic SNVs. We also discuss the current understanding of receptor-binding domain (RBD) evolution and characteristic mutations in variants of concern (VOCs) of SARS-CoV-2, as well as possible co-evolution between RBD and its receptor, angiotensin-converting enzyme 2 (ACE2). We propose that the interplay between SARS-CoV-2 and host RNA editing mechanisms might have partially resulted in the bias in nucleotide changes during SARS-CoV-2 evolution. Finally, we outline some current challenges, including difficulty in deciphering the complicated relationship between viral pathogenicity and infectivity of different variants, and monitoring transmission of SARS-CoV-2 between humans and animals as the pandemic progresses.
Real-world study of flash glucose monitoring among adults with type 2 diabetes within the Swedish National Diabetes Register

Background The Swedish National Diabetes Register (NDR) initiated registration of the FreeStyle Libre® system and other continuous glucose monitoring (CGM) systems in June 2016. We investigated change in HbA1c for people with type 2 diabetes (T2DM) using FreeStyle Libre in Sweden. Methods We included adults with T2DM, registered in the NDR after January 1, 2014, and an index date for first use of FreeStyle Libre of June 2016 or later. Methodology was a before/after comparison of HbA1c within 6 months before the index date versus HbA1c around 6 and 12 months after the index date. Results 711 adults with T2DM using FreeStyle Libre had HbA1c measurements within the study period. Mean HbA1c was significantly reduced at 6 months (−0.50%-unit) and at 12 months (−0.52%-unit) in this group. Degree of change was negatively correlated to baseline HbA1c. Reductions in HbA1c were observed in incident users of FreeStyle Libre with T2DM who were truly naïve to CGM or had unknown prior experience of CGM, and aged 25–74 years. Conclusions This real‐world study on the Swedish NDR shows that people with T2DM using FreeStyle Libre system for 6 and 12 months significantly reduced their HbA1c.
Symbolic Violence: Conversations with Bourdieu

Michael Burawoyn lähtökohta teoksessa Symbolic Violence: Conversations with Bourdieu on 1900-luvun jälkipuolen tunnetuimman kriittisen sosiologin Pierre Bourdieun ja marxismin jännitteinen suhde. Burawoy on kalifornialaisen Berkeleyn yliopiston sosiologian professori ja marxilaisen etnografisen työprosessitutkimuksen pitkän linjan pioneeri. Hän korostaa, että suhteen tarkastelua hankaloittaa se, että Bourdieu ei juuri koskaan keskustele marxilaisten, ”näiden vihollisten, joilta hän lainasi niin paljon”, kanssa (1). 2 Silti Bourdieu avoimesti tunnustaa velkansa Marxille. Esimerkiksi teoksen Esquisse d’une théorie de la pratique (Bourdieu 1972/2001, 219) yhtenä mottona on Marxin ensimmäinen Feuerbach-teesi. Marxin vaikutus on ilmiselvä lähes jokaisella Bourdieun kirjoittamalla sivulla. Burawoyn mukaan Marx ei ole erityistapaus, sillä keskustelun puute teoreettisten kiistakumppanien kanssa kuvaa Bourdieun kirjoitustyyliä myös laajemmin: ”Läpi Bourdieun kirjoitusten [. ] sosiologit, taloustieteilijät ja filosofit menevät ja tulevat kuin nuket, jotka tyrmätään lauseella tai kahdella” (19), ilman lähdeviitteitä. Bourdieu tunnetusti vertasi sosiologiaa kamppailulajiin. Hyökkäävä asenne onkin
Diabetes mellitus and the causes of hospitalisation in people with heart failure

Introduction Diabetes mellitus (DM) is associated with increased risk of hospitalisation in people with heart failure and reduced ejection fraction (HFrEF). However, little is known about the causes of these events. Methods Prospective cohort study of 711 people with stable HFrEF. Hospitalisations were categorised by cause as: decompensated heart failure; other cardiovascular; infection or other non-cardiovascular. Rates of hospitalisation and burden of hospitalisation (percentage of follow-up time in hospital) were compared in people with and without DM. Results After a mean follow-up of 4.0 years, 1568 hospitalisations occurred in the entire cohort. DM (present in 32% [n=224]) was associated with a higher rate (mean 1.07 vs 0.78 per 100 patient-years; p<0.001) and burden (3.4 vs 2.2% of follow-up time; p<0.001) of hospitalisation. Cause-specific analyses revealed increased rate and burden of hospitalisation due to decompensated heart failure, other cardiovascular causes and infection in people with DM, whereas other non-cardiovascular causes were comparable. Infection made the largest contribution to the burden of hospitalisation in people with and without DM. Conclusions In people with HFrEF, DM is associated with a greater burden of hospitalisation due to decompensated heart failure, other cardiovascular events and infection, with infection making the largest contribution.
Survey of Distributed File System Design Choices

Decades of research on distributed file systems and storage systems exists. New researchers and engineers have a lot of literature to study, but only a comparatively small number of high-level design choices are available when creating a distributed file system. And within each aspect of the system, typically several common approaches are used. So, rather than surveying distributed file systems, this article presents a survey of important design decisions and, within those decisions, the most commonly used options. It also presents a qualitative exploration of their tradeoffs. We include several relatively recent designs and their variations that illustrate other tradeoff choices in the design space, despite being underexplored. In doing so, we provide a primer on distributed file systems, and we also show areas that are overexplored and underexplored, in the hopes of inspiring new research.
Selection and outcome of implantable cardioverter‐defibrillator patients with and without cardiac resynchronization therapy: Comparison of 4384 patients from the German Device Registry to randomized controlled trials

Registry data add important information to randomized controlled trials (RCT) on real‐life aspects of implantable cardioverter‐defibrillator (ICD) patients with and without cardiac resynchronization therapy (CRT‐D). This analysis of the prospectively conducted German Device Registry aims at comparing mortality rates, comorbidities, complication rates to results from RCT.
Increased birth rank of homosexual males: disentangling the older brother effect and sexual antagonism hypothesis

Male homosexual orientation remains a Darwinian paradox, as there is no consensus on its evolutionary (ultimate) determinants. One intriguing feature of homosexual men is their higher male birth rank compared to heterosexual men. This can be explained by two non-exclusive mechanisms: an antagonistic effect (AE), implying that more fertile women have a higher chance of having a homosexual son and to produce children with a higher mean birth rank, or a fraternal birth effect (FBOE), where each additional older brother increases the chances for a male embryo to develop a homosexual orientation due to an immunoreactivity process. However, there is no consensus on whether both FBOE and AE are present in human populations, or if only one of these mechanisms is at play with its effect mimicking the signature of the other mechanism. An additional sororal birth order effect (SBOE) has also recently been proposed. To clarify this situation, we developed theoretical and statistical tools to study FBOE and AE independently or in combination, taking into account all known sampling biases. These tools were applied on new individual data, and on various available published data (two individual datasets, and all relevant aggregated data). Support for FBOE was apparent in aggregated data, with the FBOE increasing linearly with fertility. The FBOE was also supported in two individual datasets. An SBOE is generated when sampling in presence of FBOE, suggesting that controlling for FBOE is required to avoid artefactual SBOE. AE was not supported in individual datasets, including the analysis of the extended maternal family. The evolutionary implications of these findings are discussed.