Miracle-dz/UniFAR-FTUs huggingface dataset:
The Climate and Nutritional Impact of Beef in Different Dietary Patterns in Denmark

There is public focus on the environmental impact, and in particular, the emissions of greenhouse gases (GHG), related to our food consumption. The aim of the present study was to estimate the carbon footprint (CF), land use and nutritional impact of the different beef products ready to eat in different real-life dietary patterns. Beef products accounted for 513, 560, 409 and 1023 g CO2eq per day, respectively, in the four dietary patterns (Traditional, Fast-food, Green, and High-beef). The total CFs of these diets were 4.4, 4.2, 4.3 and 5.0 kg CO2eq per day (10 MJ), respectively. The Green diet had almost the same CF as the Traditional and the Fast-food diets despite having the lowest intake of beef as well as the lowest intake of red meat in total. A theoretical substitution of beef with other animal products or legumes in each of these three diets reduced the diets’ CF by 4–12% and land use by 5–14%. As regards nutrients, both positive and negative impacts of these substitutions were found but only a few of particular nutritional importance, indicating that replacing beef with a combination of other foods without a significant effect on the nutrient profile of the diet is a potential mitigation option.
Viral dynamics and immune correlates of COVID-19 disease severity

Abstract Background Key knowledge gaps remain in the understanding of viral dynamics and immune response of SARS-CoV-2 infection. Methods We evaluated these characteristics and established their association with clinical severity in a prospective observational cohort study of 100 patients with PCR-confirmed SARS-CoV-2 infection (mean age 46 years, 56% male, 38% with comorbidities). Respiratory samples (n=74) were collected for viral culture, serum samples for measurement of IgM/IgG levels (n=30), and plasma samples for levels of inflammatory cytokines and chemokines (n=81). Disease severity was correlated with results from viral culture, serologic testing, and immune markers. Results 57 (57%) patients developed viral pneumonia, of whom 20 (20%) required supplemental oxygen including 12 (12%) invasive mechanical ventilation. Viral culture from respiratory samples was positive for 19 of 74 patients (26%). No virus was isolated when the PCR cycle threshold (Ct) value was >30 or >14 days after symptom onset. Seroconversion occurred at a median of 12.5 days (IQR 9-18) for IgM and 15.0 days (IQR 12-20) for IgG; 54/62 patients (87.1%) sampled at day 14 or later seroconverted. Severe infections were associated with earlier seroconversion and higher peak IgM and IgG levels. Levels of IP-10, HGF, IL-6, MCP-1, MIP-1α, IL-12p70, IL-18, VEGF-A, PDGF-BB and IL-1RA significantly correlated with disease severity. Conclusion We found virus viability was associated with lower PCR Ct value in early illness. A stronger antibody response was associated with disease severity. The overactive proinflammatory immune signatures offers targets for host-directed immunotherapy which should be evaluated in randomised controlled trials.
Endovascular Management of Superficial Femoral Artery Occlusion Secondary to Embolization of Celt ACD® Vascular Closure Device

Patient: Male, 70-year-old Final Diagnosis: Embolization of vascular closure device Symptoms: Claudication Medication: — Clinical Procedure: Angioplasty Specialty: Radiology Objective: Unusual clinical course Background: This report describes the endovascular management of a Celt ACD® vascular closure device (VCD) lodged in the superficial femoral artery (SFA), 1 year after its deployment. There is a paucity of evidence in the existing literature regarding the management of complications related to embolized VCD discovered months or years after its deployment. Case Report: A 70-year-old male patient, who was a heavy smoker, presented with right lower-limb intermittent claudication of 2 months’ duration. He underwent a successful left retrograde iliac artery and left SFA angioplasty 1 year ago. The right femoral pulse was normal, whereas the right popliteal pulse was absent. The right ankle-brachial index was 0.64. Doppler ultrasound showed evidence of mid-right SFA occlusion. Angiogram showed an embolized Celt ACD VCD in the right SFA causing segmental occlusion. An endovascular attempt to retrieve the embolized VCD via a snare failed, as the VCD got deeply embedded in the vessel wall. After successful balloon angioplasty, a stent was placed into the SFA with excellent angiographic and clinical outcomes. Conclusions: This case demonstrates the risk of dislodgement of the VCD and its distal embolization with a risk of late ischemia. Endovascular retrieval may be unsuccessful for chronically embolized VCD. Therefore, stent angioplasty is an acceptable option.
Vaccine targeting SIVmac251 protease cleavage sites protects macaques against vaginal infection.

After over three decades of research, an effective anti-HIV vaccine remains elusive. The recently halted HVTN702 clinical trial not only further stresses the challenge to develop an effective HIV vaccine, but also emphasizes that unconventional and novel vaccine strategies are urgently needed. Here, we report that a vaccine focusing the immune response on the sequences surrounding the 12 viral protease cleavage sites (PCSs) provided greater than 80% protection to Mauritian cynomolgus macaques (MCMs) against repeated intravaginal SIVmac251 challenges. The PCS-specific T cell responses correlated with vaccine efficacy. The PCS vaccine did not induce immune activation or inflammation known to be associated with increased susceptibility to HIV infection. Machine learning analyses revealed that the immune microenvironment generated by the PCS vaccine was predictive of vaccine efficacy. Our study demonstrates for the first time that a vaccine which targets only viral maturation, but lacks full-length Env and Gag immunogens, can prevent intravaginal infection in a stringent macaque/SIV challenge model. Targeting HIV maturation thus offers a novel approach to developing an effective HIV vaccine.
A Lineage-Specific Paralog of Oma1 Evolved into a Gene Family from Which a Suppressor of Male Sterility-Inducing Mitochondria Emerged in Plants

Abstract Cytoplasmic male sterility (MS) in plants is caused by MS-inducing mitochondria, which have emerged frequently during plant evolution. Nuclear restorer-of-fertility (Rf)genes can suppress their cognate MS-inducing mitochondria. Whereas many Rfs encode a class of RNA-binding protein, the sugar beet (Caryophyllales) Rf encodes a protein resembling Oma1, which is involved in the quality control of mitochondria. In this study, we investigated the molecular evolution of Oma1 homologs in plants. We analyzed 37 plant genomes and concluded that a single copy is the ancestral state in Caryophyllales. Among the sugar beet Oma1 homologs, the orthologous copy is located in a syntenic region that is preserved in Arabidopsis thaliana. The sugar beet Rf is a complex locus consisting of a small Oma1 homolog family (RF-Oma1 family) unique to sugar beet. The gene arrangement in the vicinity of the locus is seen in some but not all Caryophyllalean plants and is absent from Ar. thaliana. This suggests a segmental duplication rather than a whole-genome duplication as the mechanism of RF-Oma1 evolution. Of thirty-seven positively selected codons in RF-Oma1, twenty-six of these sites are located in predicted transmembrane helices. Phylogenetic network analysis indicated that homologous recombination among the RF-Oma1 members played an important role to generate protein activity related to suppression. Together, our data illustrate how an evolutionarily young Rf has emerged from a lineage-specific paralog. Interestingly, several evolutionary features are shared with the RNA-binding protein type Rfs. Hence, the evolution of the sugar beet Rf is representative of Rf evolution in general.
Long-term Effects of Calcium β-Hydroxy-β-Methylbutyrate and Vitamin D3 Supplementation on Muscular Function in Older Adults With and Without Resistance Training: A Randomized, Double-blind, Controlled Study

Abstract The primary aim of this study was to determine whether supplementation with calcium β-hydroxy-β-methylbutyrate (HMB) and vitamin D3 (D) would enhance muscle function and strength in older adults. Older adults over 60 years of age with insufficient circulating 25-hydroxy-vitamin D (25OH-D) levels were enrolled in a double-blinded controlled 12-month study. Study participants were randomly assigned to treatments consisting of: (a) Control + no exercise, (b) HMB+D + no exercise, (c) Control + exercise, and (d) HMB+D + exercise. The study evaluated 117 participants via multiple measurements over the 12 months that included body composition, strength, functionality, and questionnaires. HMB+D had a significant benefit on lean body mass within the nonexercise group at 6 months (0.44 ± 0.27 kg, HMB+D vs −0.33 ± 0.28 kg, control, p < .05). In nonexercisers, improvement in knee extension peak torque (60°/s) was significantly greater in HMB+D-supplemented participants than in the nonsupplemented group (p = .04) at 3 months, 10.9 ± 5.7 Nm and −5.2 ± 5.9 Nm, respectively. A composite functional index, integrating changes in handgrip, Get Up, and Get Up and Go measurements, was developed. HMB+D + no exercise resulted in significant increases in the functional index compared with those observed in the control + no exercise group at 3 (p = .03), 6 (p = .04), and 12 months (p = .04). Supplementation with HMB+D did not further improve the functional index within the exercising group. This study demonstrated the potential of HMB and vitamin D3 supplementation to enhance muscle strength and physical functionality in older adults, even in individuals not engaged in an exercise training program.
Vascular smooth muscle remodeling in health and disease.

In blood vessels, vascular smooth muscle cells (VSMCs) generally exist in two major phenotypes: contractile and non-contractile (synthetic). The contractile phenotype is predominant and includes quiescent or differentiated VSMCs, which function as the regulators of blood vessel diameter and blood flow. According to some literature in the field, contractile VSMCs do not switch to the non-contractile phenotype due to the activation of specific transcription factors that are considered as guardians of the contractile phenotype. However, a vast literature uses the terms remodeling and phenotype switching of contractile VSMCs interchangeably mainly based on studies dealing with atherosclerosis. The use of the terms remodeling and switching to describe changes in phenotype based on morphological criteria can be confusing. The term remodeling was first used to describe morphological changes in the heart and was soon used to describe phenotype changes of contractile VSMCs based on morphological criteria. The latter were introduced in early studies, and new molecular criteria were later added, including changes in gene expression, which could be irreversible. In this review, we will discuss the different views concerning remodeling and possible switching of contractile VSMCs to a non-contractile phenotype. We conclude that only remodeling of contractile VSMCs may take place upon vascular injury and disease.
Semi‐automated Rasch analysis using in‐plus‐out‐of‐questionnaire log likelihood

Rasch analysis is a popular statistical tool for developing and validating instruments that aim to measure human performance, attitudes and perceptions. Despite the availability of various software packages, constructing a good instrument based on Rasch analysis is still considered to be a complex, labour‐intensive task, requiring human expertise and rather subjective judgements along the way. In this paper we propose a semi‐automated method for Rasch analysis based on first principles that reduces the need for human input. To this end, we introduce a novel criterion, called in‐plus‐out‐of‐questionnaire log likelihood (IPOQ‐LL). On artificial data sets, we confirm that optimization of IPOQ‐LL leads to the desired behaviour in the case of multi‐dimensional and inhomogeneous surveys. On three publicly available real‐world data sets, our method leads to instruments that are, for all practical purposes, indistinguishable from those obtained by Rasch analysis experts through a manual procedure.
Increased Cancer Risk in Families with Pediatric Cancer Is Associated with Gender, Age, Diagnosis, and Degree of Relation to the Child

Background: Studies of cancer risk among relatives of children with cancer beyond parents and siblings are limited. We have investigated the cancer risk up to the third degree of relation in families with pediatric cancer to reveal patterns of inheritance. Methods: A single-center cohort of 757 patients with pediatric cancer was linked to the Swedish National Population Register, resulting in 16,137 relatives up to the third degree of relation. All relatives were matched to the Swedish Cancer Register, and standard incidence ratios (SIR) were calculated to define relatives at risk. Results: Children and adults up to the third degree of relation had increased cancer risk, with SIRs of 1.48 (P = 0.01) and 1.07 (P < 0.01), respectively. The SIRs for first- and third-degree adult relatives were 1.22 and 1.10, respectively, but no increased risk was observed in second-degree relatives. Male relatives had a higher risk than females, especially when related to a girl and when the child had leukemia. The risk was mainly increased for lung, prostate, and gastrointestinal cancer. When excluding 29 families of children with known pathogenic germline variants, the increased risk remained. Conclusions: Relatives to children with cancer up to third degree of relation have an increased cancer risk. Known pathogenic germline variants do not explain this increased risk. Impact: The overall increased cancer risk among relatives of children with cancer in this population-based cohort strengthens the importance of surveillance programs for families with pediatric cancer.
The Critical Role of Policy Enforcement in Achieving Health, Air Quality and Climate Benefits from India's Clean Electricity Transition.

The coal-dominated electricity system poses major challenges for India to tackle air pollution and climate change. Although the government has issued a series of clean air policies and low-carbon energy targets, a key barrier remains enforcement. Here, we quantify the importance of policy implementation in India's electricity sector using an integrated assessment method based on emissions scenarios, an air quality simulation, and a health impact assessment. We find that limited enforcement of air pollution control policies leads to worse future air quality and health damages (e.g., 14,200 to 59,000 more PM2.5-related deaths in 2040) than when energy policies are not fully enforced (8,700 to 5,900 more PM2.5-related deaths in 2040), since coal power plants with end-of-pipe controls already emit little air pollution. However, substantially more carbon will be emitted if low-carbon and clean coal policies are not successfully implemented (e.g., 400-800 million tons more CO2 in 2040). Thus, our results underscore the important role of effectively implementing existing air pollution and energy policy to simultaneously achieve air pollution, health and carbon mitigation goals in India.
Point-of-Care Platform Blood Biomarker Testing of GFAP versus S100B for Prediction of Traumatic Brain Injuries: a TRACK-TBI study.

GFAP is FDA-cleared to determine need for head CT within 12 hours after mild TBI (GCS 13-15); S100B serves this function in Europe. This Phase 1 Biomarker Cohort analysis of the multicenter, observational TRACK-TBI study compares GFAP's diagnostic performance, measured on a rapid point-of-care platform, against S100B to predict intracranial abnormalities on CT within 24 hours postinjury across the spectrum of TBI (GCS 3-15). Head CT scan performed in TBI subjects and blood was collected for all consenting subjects presenting to 18 U.S. trauma centers. Plasma was analyzed on a point-of-care device prototype assay for GFAP and serum was analyzed for S100B. In 1359 patients with TBI (GCS 3-15), mean (SD) age = 40.1 (17.0) years; 68% were male. Plasma GFAP levels were significantly higher in CT+ TBI subjects (median=1358pg/ml, IQR:472-3803) compared with CT- TBI subjects (median=116pg/ml, IQR:26-397) and compared with orthopedic trauma controls (N=122; median=13pg/ml, IQR: 7-20), p<0.001. Serum S100B levels were likewise higher in CT+ TBI subjects (median=0.17ug/l, IQR:0.09-0.38) compared with CT- TBI subjects (median=0.10ug/l, IQR:0.06-0.18), p<0.001. Receiver operating characteristics curves were generated for prediction of intracranial injury on admission CT scan; AUC for GFAP was significantly higher than for S100B in the same cohort (GFAP AUC - 0.85, 95% CI 0.83-0.87; S100B AUC - 0.67, 95% CI 0.64-0.70; p<0.001). GFAP, measured on a point-of-care platform prototype assay, has high discriminative ability to predict intracranial abnormalities on CT scan in patients with TBI across the full injury spectrum of GCS 3 -15 through 24 hours postinjury. GFAP substantially outperforms S100B.
Loss of cell–cell and cell–substrate contacts in single pancreatic β‐cells divert insulin release to intracellular vesicular compartments

Cell–cell or cell–substrate interactions are lost when cells are dissociated in culture, or during pathophysiological breakdowns, therefore impairing their structure and polarity, and affecting their function. We show that single rat β‐cells, cultured under non‐adhesive conditions, form intracytoplasmic vacuoles increasing in number and size over time. We characterized these structures and their implication in β‐cell function.
Serological and molecular epidemiology of Japanese Encephalitis in Zhejiang, China, 2015-2018

Background Shifts have occurred in the epidemiological characteristics of Japanese encephalitis (JE), extending from the molecular level to the population level. The aim of this study was to investigate the seroprevalence of JE neutralizing antibodies in healthy populations from different age groups in Zhejiang Province, and to conduct mosquito monitoring to evaluate the infection rate of Japanese encephalitis virus (JEV) among vectors, as well as the molecular characteristics of the E gene of isolated JEV strains. Methodology/Principal findings A total of 1190 sera samples were screened by a microseroneutralization test, including 429 infants (28d-11m) and 761 participants (2y-82y). For those under 1 year old, the geometric mean titers (GMTs) of the JE neutralizing antibody was 9.49 at birth and significantly declined as the age of month increased (r = -0.225, P<0.001). For those above 1-year old, seropositive proportions were higher in subjects aged 1–3 years old as well as ≥25 years old (65%-75%), and relatively lower in subjects aged between 4–25 years old (22%-55%). Four or more years after the 2nd dose of JEV-L (first dose administered at 8 months and the second at 2 years of age), the seropositive proportion decreased to 32.5%, and GMTs decreased to 8.08. A total of 87,201 mosquitoes were collected from livestock sheds in 6 surveillance sites during 2015–2018, from which 139 E gene sequences were successfully amplified. The annual infection rate according to bias-corrected maximum likelihood estimation of JEV in Culex tritaeniorhynchus was 1.56, 2.36, 5.65 and 1.77 per 1000, respectively. JEV strains isolated during 2015–2018 all belonged to Genotype I. The E gene of amplified 139 samples differed from the JEV-L vaccine strain at fourteen amino acid residues, including the eight key residues related to virulence and virus attenuation. No divergence was observed at the sites related to antigenicity. Conclusions/Significance Zhejiang Province was at a high risk of JE exposure due to relatively lower neutralizing antibody levels among the younger-aged population and higher infection rates of JEV in mosquitoes. Continuous, timely and full coverage of JE vaccination are essential, as well as the separation of human living areas and livestock shed areas. In addition, annual mosquito surveillance and periodic antibody level monitoring are important for providing evidence for improvement in JE vaccines and immunization schedules.
Return Hospital Admissions Among 1419 COVID‐19 Patients Discharged from Five U.S. Emergency Departments

Although many ED patients with known or suspected Covid-19 require hospital admission, the majority are discharged home. Concern for surges in hospital occupancy compel emergency providers to preserve inpatient resources and discern which patients benefit most from admission. Even in the absence of surge conditions, patients may prefer to recover at home if safe to do so. However, some patients with Covid-19 experience delayed decompensation.
Ecology, distribution, and predictive occurrence modeling of Palmer's chipmunk (Tamias palmeri): a high-elevation small mammal endemic to the Spring Mountains in southern Nevada, USA

Although montane sky islands surrounded by desert scrub and shrub steppe comprise a large part of the biological diversity of the Basin and Range Province of southwestern North America, comprehensive ecological and population demographic studies for high-elevation small mammals within these areas are rare. Here, we examine the ecology and population parameters of the Palmer's chipmunk (Tamias palmeri) in the Spring Mountains of southern Nevada, and present a predictive GIS-based distribution and probability of occurrence model at both home range and geographic spatial scales. Logistic regression analyses and Akaike Information Criterion model selection found variables of forest type, slope, and distance to water sources as predictive of chipmunk occurrence at the geographic scale. At the home range scale, increasing population density, decreasing overstory canopy cover, and decreasing understory canopy cover contributed to increased survival rates.
Thyroid fine-needle aspiration cytology in Taiwan: a nationwide survey and literature update

In Taiwan, thyroid fine-needle aspiration cytology is easily accessible and reliable for evaluating thyroid nodules. The sonographic pattern plays a major role and is the deciding factor for aspiration. We conducted a nationwide survey in 2017 and it revealed that 31% of laboratories had adopted The Bethesda System for Reporting Thyroid Cytopathology. There was a relatively high unsatisfactory rate (24.04%) and low rates of indeterminate diagnoses, including atypia of undetermined significance/follicular lesions of undetermined significance: 4.87%, and follicular neoplasm/suspicious for a follicular neoplasm: 0.35%. Moreover, the risks of malignancy in benign, atypia of undetermined significance, and suspicious for a follicular neoplasm were relatively high. These may reflect strict diagnostic criteria for indeterminate categories and better patient selection for surgery. Improvements in specimen sampling and continuing education programs are crucial. Newly-developed thyroid cytology technologies, such as immunocytochemistry, molecular testing, and computerized cytomorphometry, may further facilitate cytology diagnoses.