Miracle-dz/UniFAR-FTUs huggingface dataset:
Dispersal and recruitment limitation contribute differently to community assembly

The neutral theory of biodiversity has been criticized for being fragile with even slight deviations from its basic assumption of equal fitness among species. In response to this criticism, Hubbell ((2001) The Unified Neutral Theory of Biodiversity and Biogeography. Princeton, NJ: Princeton University Press) proposed that competitive exclusion can be infinitely delayed by dispersal and recruitment limitation, thus making species effectively neutral. But the theoretical foundation for this claim still remains unclear and controversial, and the effects of dispersal and recruitment limitation are often confounded, especially in field studies. This study aims to provide an affirmative theoretical answer to the question of whether dispersal limitation and recruitment limitation can separately or jointly overwhelm the effects of fitness differences among species and lead to neutral community dynamics. Computer simulations were used to investigate the effects of dispersal and recruitment limitation on delaying competitive exclusion in a homogeneous habitat in a spatially explicit context. We found that even a slight competitive asymmetry would require extremely strong dispersal and recruitment limitation for neutrality to emerge. Most importantly, when the effects of dispersal and recruitment limitation were set apart, it is found that recruitment limitation is more effective in delaying competitive exclusion, whereas dispersal limitation tends to have a stronger impact on the general shape of both species abundance distributions and species-area relationships.
Circulating Metabolites as Potential Biomarkers for Neurological Disorders—Metabolites in Neurological Disorders

There are, still, limitations to predicting the occurrence and prognosis of neurological disorders. Biomarkers are molecules that can change in different conditions, a feature that makes them potential tools to improve the diagnosis of disease, establish a prognosis, and monitor treatments. Metabolites can be used as biomarkers, and are small molecules derived from the metabolic process found in different biological media, such as tissue samples, cells, or biofluids. They can be identified using various strategies, targeted or untargeted experiments, and by different techniques, such as high-performance liquid chromatography, mass spectrometry, or nuclear magnetic resonance. In this review, we aim to discuss the current knowledge about metabolites as biomarkers for neurological disorders. We will present recent developments that show the need and the feasibility of identifying such biomarkers in different neurological disorders, as well as discuss relevant research findings in the field of metabolomics that are helping to unravel the mechanisms underlying neurological disorders. Although several relevant results have been reported in metabolomic studies in patients with neurological diseases, there is still a long way to go for the clinical use of metabolites as potential biomarkers in these disorders, and more research in the field is needed.
Interrelation between Plasma Concentrations of Vitamins C and E along the Trajectory of Ageing in Consideration of Lifestyle and Body Composition: A Longitudinal Study over Two Decades

Although the interrelation between vitamins C and E has been demonstrated on an experimental level, its impact on biomarkers in community-dwelling subjects along the trajectory of ageing has not yet been shown. The present longitudinal study investigates the determinants and interrelation of vitamins C and E plasma concentrations in 399 subjects aged ≥60 years with a median follow-up time of 12 years. Linear mixed-effects models were used to analyze the influence of age, sex, body composition, dietary intake, physical activity, smoking and supplement/drug use on plasma vitamin C, plasma α-tocopherol and α-tocopherol/total cholesterol ratio. At baseline, median plasma concentrations of vitamin C and α-tocopherol were 74 and 35 µmol/L. Absolute fat-free mass, physical activity, use of supplements, and plasma α-tocopherol were main determinants of plasma vitamin C in the course of ageing. For the α-tocopherol/total cholesterol ratio, age, use of supplements, use of lipid-modifying drugs, and plasma vitamin C were main determinants. The results reveal a stable positive interrelation between plasma concentrations of vitamins C and E along the trajectory of ageing independent of the other identified determinants. The possible regulatory mechanisms that could explain this robust positive interrelation remain to be elucidated.
Chloroquine and hydroxychloroquine for COVID‐19: Perspectives on their failure in repurposing

Non‐clinical studies suggest that chloroquine (CQ) and hydroxychloroquine (HCQ) have antiviral activities. Early clinical reports of successful HCQ‐associated reduction in viral load from small studies in COVID‐19 patients spurred a large number of national and international clinical trials to test their therapeutic potential. The objective of this review is to summarize the current evidence on the safety and efficacy of these two agents and to provide a perspective on why their repurposing has hitherto failed.
Varieties of Cognitive Profiles in Poor Readers: Evidence for a VAS-Impaired Subtype

A wide share of secondary school children does not reach the expected competence level in reading. These children could benefit from more efficient intervention responses, providing a better understanding of their cognitive weaknesses/deficits. Our aim was to explore the cognitive heterogeneity of a population of poor readers identified from a large sample of 948 sixth-grade children. We first assessed the contribution of phoneme awareness (PA), rapid automatized naming (RAN), and visual attention span (VAS) to reading performance in a subset of 281 children including poor and average readers/spellers. We show that all three skills are unique and significant predictors of reading fluency. We then restricted the analysis to participants with normal Raven’s score (IQ) and oral language skills to focus on 110 children with more specific reading difficulties. A unique VAS deficit was found in 18% of these poor readers while 20% and 15.5% showed a unique PA or RAN deficit. Children with multiple or no deficit were further identified. The overall findings provide evidence for a variety of cognitive profiles in poor readers. They suggest that, in addition to PA interventions, training programs targeting VAS might be useful for the nontrivial share of poor readers who exhibit a VAS deficit.
Conservation genetics of the critical plant genus Euphrasia L. in Britain

Recent national and international conservation legislation has led to an increased focus on 'prioritised species lists' for the allocation of conservation resources. Where the delimitation of a species is routine, this approach can be appropriate, and used to specify clear conservation targets. However, prioritised species lists become problematic when there are difficulties in species delimitation. This issue is particularly pertinent for the UK Biodiversity Action Plans where nearly half of the species on the high priority short list for conservation are taxonomically controversial. One particularly complex group accounting for the majority of these problems is Euphrasia. Interactions among several factors have been hypothesised as underlying the taxonomic complexity in the genus including breeding system shifts, hemi-parasitism, hybridisation, ploidy variation and local ecotypic adaptation. Six endemic species are currently recognised as having conservation importance in the UK but the taxonomic complexity of the group makes implementing conservation measures difficult. The goal of this thesis is to use molecular markers to evaluate taxon limits and evolutionary processes in British Euphrasia to clarify the most appropriate approach for conservation. The results show that the major reproductive barrier in the group corresponds to ploidy level, with AFLP and chloroplast data both significantly differentiated between diploid and tetraploid species, although occasional gene flow via inter-ploidal hybridisation appears to contribute towards diversification of the diploid group. The genetic data support the current species level taxonomy for the diploid but not the tetraploid species, where a considerable overlap between taxa was detected. The chioroplast data detected four discrete lineages, the distribution of these among species suggest at least three allopolyploid events in the formation of the tetraploid taxa, within which distinct ecological groups occur. Variation in the breeding system was detected at the intraand inter-specific levels and estimates of the inbreeding coefficient showed a strong correlation with flower size and support the importance of multiple shifts in breeding system as contributing towards the overall diversification within the group.
Adjuvant therapy following oesophagectomy for adenocarcinoma in patients with a positive resection margin

The role of adjuvant therapy in patients with oesophagogastric adenocarcinoma treated by neoadjuvant chemotherapy is contentious. In UK practice, surgical resection margin status is often used to classify patients for receiving adjuvant treatment. The aim of this study was to assess the survival benefit of adjuvant therapy in patients with positive (R1) resection margins.
Antimicrobial Use in Broilers Reared at Different Stocking Densities: A Retrospective Study

Simple Summary Broiler farms are authorized to house animals at different stocking densities (kg live weight/m2) provided that ammonia, carbon dioxide, temperature, and humidity levels are kept under specific limits set by European Union legislation. The role of stocking density on poultry health and welfare, and consequently on antimicrobial use, is still under debate. Herewith, we analyze veterinary prescription data for 2017 pertaining to a representative sample of Italian broiler farms that were authorized to house animals at 33 or 39 kg/m2. The prescribed amounts of antimicrobials in each farm were converted into a total of Defined Daily Doses per year, a non-dimensional unit proposed by the European Medicines Agency (EMA). No differences in terms of antimicrobial use, mortality, and feed conversion rates were noted between the two considered groups, suggesting a minor role of stocking density on animal health and welfare. Abstract According to the Directive 2007/43/EC, broiler farms can house animals up to 39 kg/m2, provided that specific environmental requirements are met. However, limited information is available about the effects of stocking density (SD) on broiler health and welfare, including the need for antimicrobial use. In this study, annual data on mortality, feed conversion rate, and antimicrobial use (AMU) are compared between broiler farms with stocking densities of 39 kg/m2 (N = 257) and 33 kg/m2 (N = 87). These farms were distributed throughout Italy and belonged to the same integrated poultry company. Antimicrobial use data were obtained from each farm and production cycle; AMU was expressed using the defined daily doses (DDD) method proposed by EMA. The annual AMU per farm was calculated as the median AMU over all cycles. Stratified analysis by sex and geographical area (Italy vs Northern Italy) showed no significant effect of stocking density on broiler mortality, feed conversion rate, and AMU. However, a higher AMU variability among farms with 39 kg/m2 stocking density vs. those with 33 kg/m2 was found. This study indicates that AMU does not apparently vary between animals reared at different stocking densities in intensive farms.
Comparative study between single versus dual trigger for poor responders in GnRH‐antagonist ICSI cycles: A randomized controlled study

To investigate whether dual triggering of final oocyte maturation with a combination of gonadotropin‐releasing hormone (GnRH) agonist and human chorionic gonadotropin (hCG) can improve the number of retrieved oocytes and clinical pregnancy rate in poor responders undergoing in vitro fertilization/intracytoplasmic sperm injection (IVF‐ICSI) cycles using a GnRH‐antagonist protocol.
İran’da Sığır ve Yaban Sığırları Semen Örneklerinde Brucella abortus ve Brucella melitensis: Kültür, Konvansiyonel ve Real-time Polimeraz Zincir Reaksiyonu Kullanılarak Mevsimsel, Yaşa Bağlı ve Bölgesel Dağılımı Üzerine İlk Klinik Çalışma

Conventional and real-time PCR assays were developed for detection and identification of Brucella species in bovine and buffalo semen samples. Totally, 91 bovine and buffalo semen samples were collected from 4 major provinces of Iran in various seasons. The animals which their semen samples were collected for this study had less than 1 year old, 1-2 years old, 2-3 years old and more than 3 years old. Samples were cultured and DNA was extracted and novel primers have been designed using the IS711 target of Brucella species for conventional PCR. Positive results of PCR have been studied for presences of Brucella abortus and Brucella melitensis. Totally, 21.56% and 14.28% of bovine and buffalo semen samples, respectively, were positive for Brucella species. Khozestan had the highest while Sistan Va Balochestan had the lowest incidences of Brucella species in studied regions. Samples which were collected in spring season had the highest rate of infection. Also, samples which were collected from less than 1 year old bovine and buffalo semen samples had the highest incidence of Brucella species. Totally, 25 (24.50%) and 4 (3.92%) bovine semen samples and 14 (15.38%) and 1 (1.09%) buffalo semen samples were positive for Brucella abortus and Brucella melitensis.
Experimental infection of domestic dogs and cats with SARS-CoV-2: Pathogenesis, transmission, and response to reexposure in cats

Significance SARS-CoV-2 is an emerging pathogen that has already had catastrophic consequences on the health and well-being of people worldwide. As a zoonotic virus, the implications for animal populations are largely unknown. This manuscript describes a pilot study in which domestic cats and dogs were assessed for their susceptibility to infection. While neither species developed clinical disease in this study, cats shed infectious virus for up to 5 d and infected naive cats via direct contact, while dogs do not appear to shed virus. Cats that were reinfected with SARS-CoV-2 mounted an effective immune response and did not become reinfected. These studies have important implications for animal health and suggest that cats may be a good model for vaccine development. The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has reached nearly every country in the world with extraordinary person-to-person transmission. The most likely original source of the virus was spillover from an animal reservoir and subsequent adaptation to humans sometime during the winter of 2019 in Wuhan Province, China. Because of its genetic similarity to SARS-CoV-1, it is probable that this novel virus has a similar host range and receptor specificity. Due to concern for human–pet transmission, we investigated the susceptibility of domestic cats and dogs to infection and potential for infected cats to transmit to naive cats. We report that cats are highly susceptible to infection, with a prolonged period of oral and nasal viral shedding that is not accompanied by clinical signs, and are capable of direct contact transmission to other cats. These studies confirm that cats are susceptible to productive SARS-CoV-2 infection, but are unlikely to develop clinical disease. Further, we document that cats developed a robust neutralizing antibody response that prevented reinfection following a second viral challenge. Conversely, we found that dogs do not shed virus following infection but do seroconvert and mount an antiviral neutralizing antibody response. There is currently no evidence that cats or dogs play a significant role in human infection; however, reverse zoonosis is possible if infected owners expose their domestic pets to the virus during acute infection. Resistance to reinfection holds promise that a vaccine strategy may protect cats and, by extension, humans.
YouTube Video Comments on Healthy Eating: Descriptive and Predictive Analysis

Background Poor nutrition and food selection lead to health issues such as obesity, cardiovascular disease, diabetes, and cancer. This study of YouTube comments aims to uncover patterns of food choices and the factors driving them, in addition to exploring the sentiments of healthy eating in networked communities. Objective The objectives of the study are to explore the determinants, motives, and barriers to healthy eating behaviors in online communities and provide insight into YouTube video commenters’ perceptions and sentiments of healthy eating through text mining techniques. Methods This paper applied text mining techniques to identify and categorize meaningful healthy eating determinants. These determinants were then incorporated into hypothetically defined constructs that reflect their thematic and sentimental nature in order to test our proposed model using a variance-based structural equation modeling procedure. Results With a dataset of 4654 comments extracted from YouTube videos in the context of Malaysia, we apply a text mining method to analyze the perceptions and behavior of healthy eating. There were 10 clusters identified with regard to food ingredients, food price, food choice, food portion, well-being, cooking, and culture in the concept of healthy eating. The structural equation modeling results show that clusters are positively associated with healthy eating with all P values less than . 001, indicating a statistical significance of the study results. People hold complex and multifaceted beliefs about healthy eating in the context of YouTube videos. Fruits and vegetables are the epitome of healthy foods. Despite having a favorable perception of healthy eating, people may not purchase commonly recognized healthy food if it has a premium price. People associate healthy eating with weight concerns. Food taste, variety, and availability are identified as reasons why Malaysians cannot act on eating healthily. Conclusions This study offers significant value to the existing literature of health-related studies by investigating the rich and diverse social media data gleaned from YouTube. This research integrated text mining analytics with predictive modeling techniques to identify thematic constructs and analyze the sentiments of healthy eating.
Interaction of Cytochrome C Oxidase with Steroid Hormones

Estradiol, testosterone and other steroid hormones inhibit cytochrome c oxidase (CcO) purified from bovine heart. The inhibition is strongly dependent on concentration of dodecyl-maltoside (DM) in the assay. The plots of Ki vs [DM] are linear for both estradiol and testosterone which may indicate an 1:1 stoichiometry competition between the hormones and the detergent. Binding of estradiol, but not of testosterone, brings about spectral shift of the oxidized CcO consistent with an effect on heme a33+. We presume that the hormones bind to CcO at the bile acid binding site described by Ferguson-Miller and collaborators. Estradiol is shown to inhibit intraprotein electron transfer between hemes a and a3. Notably, neither estradiol nor testosterone suppresses the peroxidase activity of CcO. Such a specific mode of action indicates that inhibition of CcO activity by the hormones is associated with impairing proton transfer via the K-proton channel.
Left ventricular M‐mode prediction intervals in 7651 dogs: Population‐wide and selected breed‐specific values

Abstract Background Echocardiography is a common method to measure heart size in dogs. The heart dimensions are influenced by body weight (BW) and potentially by breed. Objectives To establish BW‐dependent prediction intervals (PIs) of the left ventricular (LV) linear dimensions in a population of dogs of many breeds in multicenter environment, and to identify breeds deviating from these intervals. Dogs Seven thousand six hundred and fifty‐one dogs. Methods Retrospectively, data from heart screens conducted between 2009 and 2016 were included. Cardiac dimensional PIs were generated using allometric scaling including all nonsighthound dogs and values were compared to previously published PIs. The values measured in dogs of respective breeds, including sighthounds, were then compared to the overall nonsighthound PIs to identify deviant breeds. The interobserver‐variability of the measurements was determined using the explained residual variance. Results Prediction intervals for the nonsighthound dogs were in agreement with previously published cardiac PIs, although the upper limits of the generated PIs of our study were slightly below those currently applied (except the interventricular septum in systole and the left ventricular free wall in diastole below 10.0 kg and 15.0 kg, respectively). Values measured in the nonsighthound breed Newfoundland deviated for most dimensions. Most of the sighthound breeds analyzed had greater cardiac dimensions, with the exception of the Irish Wolfhound. Conclusion and Importance Findings of our study reinforces the value of BW‐dependent PIs for cardiac dimensions in dogs and suggest that these PIs are valid for most nonsighthound breeds, but not the sighthound breeds.
Profiling antibiotic resistance in Escherichia coli strains displaying differential antibiotic susceptibilities using Raman spectroscopy

The rapid identification of antibiotic resistant bacteria is important for public health. In the environment, bacteria are exposed to sub‐inhibitory antibiotic concentrations which has implications in the generation of multi‐drug resistant strains. To better understand these issues, Raman spectroscopy was employed coupled with partial least squares‐discriminant analysis to profile Escherichia coli strains treated with sub‐inhibitory concentrations of antibiotics. Clear differences were observed between cells treated with bacteriostatic (tetracycline and rifampicin) and bactericidal (ampicillin, ciprofloxacin, and ceftriaxone) antibiotics for 6 hr: First, atomic force microscopy revealed that bactericidal antibiotics cause extensive cell elongation whereas short filaments are observed with bacteriostatic antibiotics. Second, Raman spectral analysis revealed that bactericidal antibiotics lower nucleic acid to protein (I812/I830) and nucleic acid to lipid ratios (I1483/I1452) whereas the opposite is seen with bacteriostatic antibiotics. Third, the protein to lipid ratio (I2936/I2885 and I2936/I2850) is a Raman stress signature common to both the classes. These signatures were validated using two mutants, Δlon and ΔacrB, that exhibit relatively high and low resistance towards antibiotics, respectively. In addition, these spectral markers correlated with the emergence of phenotypic antibiotic resistance. Overall, this study demonstrates the efficacy of Raman spectroscopy to identify resistance in bacteria to sub‐lethal concentrations of antibiotics.