Miracle-dz/UniFAR-FTUs huggingface dataset:
Biases in bulk: DNA metabarcoding of marine communities and the methodology involved

With the growing anthropogenic pressure on marine ecosystems, the need for efficient monitoring of biodiversity grows stronger. DNA metabarcoding of bulk samples is increasingly being implemented in ecosystem assessments and is more cost‐efficient and less time‐consuming than monitoring based on morphology. However, before raw sequences are obtained from bulk samples, a profound number of methodological choices must be made. Here, we critically review the recent methods used for metabarcoding of marine bulk samples (including benthic, plankton and diet samples) and indicate how potential biases can be introduced throughout sampling, preprocessing, DNA extraction, marker and primer selection, PCR amplification and sequencing. From a total of 64 studies evaluated, our recommendations for best practices include to (a) consider DESS as a fixative instead of ethanol, (b) use the DNeasy PowerSoil kit for any samples containing traces of sediment, (c) not limit the marker selection to COI only, but preferably include multiple markers for higher taxonomic resolution, (d) avoid touchdown PCR profiles, (e) use a fixed annealing temperature for each primer pair when comparing across studies or institutes, (f) use a minimum of three PCR replicates, and (g) include both negative and positive controls. Although the implementation of DNA metabarcoding still faces several technical complexities, we foresee wide‐ranging advances in the near future, including improved bioinformatics for taxonomic assignment, sequencing of longer fragments and the use of whole‐genome information. Despite the bulk of biases involved in metabarcoding of bulk samples, if appropriate controls are included along the data generation process, it is clear that DNA metabarcoding provides a valuable tool in ecosystem assessments.
Anatomical templates for tissue (re)generation and beyond

Induced pluripotent stem cells (iPSCs) represent a valuable alternative to stem cells in regenerative medicine overcoming their ethical limitations, like embryo disruption. Takahashi and Yamanaka in 2006 reprogrammed, for the first time, mouse fibroblasts into iPSCs through the retroviral delivery of four reprogramming factors: Oct3/4, Sox2, c‐Myc, and Klf4. Since then, several studies started reporting the derivation of iPSC lines from animals other than rodents for translational and veterinary medicine. Here, we review the potential of using these cells for further intriguing applications, such as “cellular agriculture. ” iPSCs, indeed, can be a source of in vitro, skeletal muscle tissue, namely “cultured meat,” a product that improves animal welfare and encourages the consumption of healthier meat along with environmental preservation. Also, we report the potential of using iPSCs, obtained from endangered species, for therapeutic treatments for captive animals and for assisted reproductive technologies as well. This review offers a unique opportunity to explore the whole spectrum of iPSC applications from regenerative translational and veterinary medicine to the production of artificial meat and the preservation of currently endangered species.
Cell-Free DNA: Proceed, but with Caution.

As the interest in telehealth and remotemonitoring increases,1 many transplant practitioners have turned to donor-derived cell-free DNA (dd-cfDNA) to noninvasively monitor the immunologic status of allografts. As use of this testing grows, it is important to highlight limitations in its predictive value. There are several available dd-cfDNA tests. In kidney transplantation, one of the earliest tomarket was AlloSure (CareDx, Inc.), the results of which were published in JASN in 2017.2 Two features of the original Circulating Donor-Derived CellFree DNA in Blood for Diagnosing Acute Rejection in Kidney Transplant Recipients (DART) trial2 analysis may lead to confusion when interpreting dd-cfDNA testing. First, borderline rejections with allograft dysfunction were considered “no active rejection,” even though many centers treat these findings as acute rejection.3 Table 1 is adapted from figure 1 of the DART publication.2 When the study data are reanalyzed to reclassify patients with borderline rejection associated with graft dysfunction, there were 46 patients (43%) with rejection and 61 (57%) without rejection. The assay’s sensitivity for all rejection decreases to only 41%, with specificity of 82% and negative likelihood ratio of 0.72. As a result, the test will only have a reasonable negative predictive value when the pretest probability of rejection is very low. Second, acute cellular rejections were grouped together with antibody-mediated rejection (AMR), implying that the excellent performance of the dd-cfDNA assay in AMR also applies to acute cellular rejection. When excluding mixed rejections, only five of 30 purely cellular rejections test positive, including only half of patients with severe rejections (1B or worse). Because most kidney allograft rejections are cellular, using this test to rule out rejection will miss a significant proportion of patients.4 In our center, we diagnosed 187 kidney rejections from January 2016 to December 2019 (borderline: 82 [44%]; 1A: 33 [18%]; 1B: 28 [15%]; grade 2/3: 28 [15%]; AMR: 23 [12%]). If dd-cfDNA testing had been used to screen for immunologically quiescent patients, an overall sensitivity of 41% would have led to 110 missed rejections. All tests have limitations. Kidney allograft biopsy, the gold standard, is invasive, uncomfortable, and subject to its own difficulties with interpretation. The dd-cfDNA assay has a role in transplantation, particularly when following AMR and microvascular inflammation. However, clinicians must recognize that many patients with rejection will have reassuring dd-cfDNA results, so negative tests must be received with caution. On the basis of currently available data, negative dd-cfDNA alone should not be considered to “rule out” rejection in cases where the pretest probability of rejection is not already low.
Descriptive osteology of the endemic spined loach Cobitis linea from Iran.

The osteological characteristics of Cobitis linea is described and compared with the other Iranian members of the genus Cobitis. For this purpose, the specimens were cleared and stained with alizarin red S and alcian blue for osteological examination. Then, a detailed description of the skeletal structure of this species was provided. Despite numerous similarities among the compared species of the genus Cobitis, several differences were observed that can be considered as distinctive osteological features for C. linea. C. linea can be distinguished from the other Iranian Cobitis by presence of the contact between ventral part of the mesocoracoid and scapula, separated hyporals and having a welldeveloped process at the middle part of the frontal.
Optimising beef business performance in northern Australia: what can 30 years of commercial innovation teach us?

This paper evaluates three decades of innovation by a leading beef producer in the Barkly region of the Northern Territory. The case study represents a rare published analysis of changes in production, greenhouse gas emissions and land condition metrics for a commercial livestock business. Thirty years ago the property was under-developed and had poor livestock productivity by today’s standards. Between 1981 and 2013, the business has increased carrying capacity through water point development, and achieved a >50% increase in herd size, a 46% improvement in weaning rate, an 82% reduction in breeder mortality rate and an improvement in land condition. Annual liveweight turn-off has increased from 75 kg to 128 kg per adult equivalent (AE) carried. All of this has been achieved while using recommended stocking rates. In contrast, two additional analyses reflecting other management approaches being taken by some north Australian beef businesses resulted in poor productivity, economic, emissions and land condition outcomes. Total greenhouse gas emissions have increased on the case study property since 1981 as a result of increasing herd size. However, the intensity of emissions per tonne of liveweight sold has declined by 43% due to the improvements in livestock productivity. The potential for generating carbon revenue from this emissions intensity improvement was explored. We found that for >95% of northern beef enterprises, current project transaction costs would entirely negate carbon revenue at a carbon price of < $25 tCO2e–1. At $5 tCO2e–1, the minimum herd size needed to cover the project transaction costs would be in excess of 35 000 AE. Although substantial carbon profits appear unlikely at present, the management practices evaluated can deliver substantial economic, emissions and land condition benefits to individual businesses and the wider industry. The paper concludes that cost-effective investment to concurrently increase herd size and livestock productivity per head, in conjunction with safe stocking rate management, is a proven path to economic and environmental sustainability in the north Australian beef industry.
Loss of Consciousness is Associated with Elevated Cognitive Intra-Individual Variability Following Sports-Related Concussion

Abstract Objective: The purpose of this study was to evaluate whether loss of consciousness (LOC), retrograde amnesia (RA), and anterograde amnesia (AA) independently influence a particular aspect of post-concussion cognitive functioning—across-test intra-individual variability (IIV), or cognitive dispersion. Method: Concussed athletes (N = 111) were evaluated, on average, 6.04 days post-injury (SD = 5.90; Mdn = 4 days; Range = 1–26 days) via clinical interview and neuropsychological assessment. Primary outcomes of interest included two measures of IIV—an intra-individual standard deviation (ISD) score and a maximum discrepancy (MD) score—computed from 18 norm-referenced variables. Results: Analyses of covariance (ANCOVAs) adjusting for time since injury and sex revealed a significant effect of LOC on the ISD (p = .018, η p 2 = .051) and MD (p = .034, η p 2 = .041) scores, such that athletes with LOC displayed significantly greater IIV than athletes without LOC. In contrast, measures of IIV did not significantly differ between athletes who did and did not experience RA or AA (all p > .05). Conclusions: LOC, but not RA or AA, was associated with greater variability, or inconsistencies, in cognitive performance acutely following concussion. Though future studies are needed to verify the clinical significance of these findings, our results suggest that LOC may contribute to post-concussion cognitive dysfunction and may be a risk factor for less efficient cognitive functioning.
Changes in Vestibular/Ocular-Motor Screen Scores in Adolescents Treated With Vestibular Therapy After Concussion

This study examines interrelationships between various Vestibular/Ocular-Motor Screen items, to characterize recovery in performance in a sample of adolescents after concussion. Purpose: To examine interrelationships among Vestibular/Ocular-Motor Screen (VOMS) items and to characterize the recovery of VOMS performance in a sample of adolescents treated with vestibular physical therapy (VPT) after concussion. Methods: Seventy-seven patients with concussion and 77 participants without concussion completed the study. Adolescents with concussion received an individualized VPT intervention consisting of targeted exercises for gaze stability, postural stability, ocular-motor control, habituation, and aerobic activities. The exercises were performed during a weekly clinic visit and via a home exercise program. Results: Except for near-point convergence distance, all VOMS items were significantly interrelated. Over the course of VPT, significant improvements in VOMS performance were observed, and discharge scores were similar to scores observed in adolescents without concussion. Conclusions: The VOMS measured moderately related functions and captured changes over the course of VPT. Clinicians should consider the contextual risk of “false positive” in their interpretation of VOMS.
Mucosal delivery of ESX-1–expressing BCG strains provides superior immunity against tuberculosis in murine type 2 diabetes

Significance Tuberculosis (TB) susceptibility and disease are significantly exacerbated in people with type 2 diabetes. The underlying mechanisms are incompletely understood, and it is not known if new TB vaccine candidates will be safe and provide protection in the context of diabetes. Using a long-term diet-induced murine model of type 2 diabetes, we demonstrate that increased susceptibility to TB is caused by impaired mycobacterial recognition and killing in the diabetic lung. Importantly, we show that mucosal vaccination of diabetic mice with Bacillus Calmette–Guérin (BCG) strains expressing the ESX-1 secretion system from Mycobacterium tuberculosis can overcome this defect and provide superior immunity against TB. Our data warrant a consideration of ESX-1–containing BCG strains as effective TB vaccines in older individuals and diabetics. Tuberculosis (TB) claims 1.5 million lives per year. This situation is largely due to the low efficacy of the only licensed TB vaccine, Bacillus Calmette–Guérin (BCG) against pulmonary TB. The metabolic disease type 2 diabetes (T2D) is a risk factor for TB and the mechanisms underlying increased TB susceptibility in T2D are not well understood. Furthermore, it is unknown if new TB vaccines will provide protection in the context of T2D. Here we used a diet-induced murine model of T2D to investigate the underlying mechanisms of TB/T2D comorbidity and to evaluate the protective capacity of two experimental TB vaccines in comparison to conventional BCG. Our data reveal a distinct immune dysfunction that is associated with diminished recognition of mycobacterial antigens in T2D. More importantly, we provide compelling evidence that mucosal delivery of recombinant BCG strains expressing the Mycobacterium tuberculosis (Mtb) ESX-1 secretion system (BCG::RD1 and BCG::RD1 ESAT-6 ∆92–95) are safe and confer superior immunity against aerosol Mtb infection in the context of T2D. Our findings suggest that the remarkable anti-TB immunity by these recombinant BCG strains is achieved via augmenting the numbers and functional capacity of antigen presenting cells in the lungs of diabetic mice.
Consistent condom use among men who pay for sex in sub-Saharan Africa: Empirical evidence from Demographic and Health Surveys

Background Paying for sex has often been associated with risky sexual behavior among heterosexual men, and men who pay for sex are considered as a bridging population for sexually transmitted infections. Consistent condom use during paid sex is essential for reducing sexually transmitted infections, including HIV/AIDS. In this study, we assessed the prevalence and predictors of consistent condom use among men who pay for sex in sub-Saharan Africa. Materials and methods We pooled data from 29 sub-Saharan African countries’ Demographic and Health Surveys. A total of 3,353 men in sub-Saharan Africa who had paid for sex in the last 12 months preceding the surveys and had complete information on all the variables of interest were used in this study. The outcome variable for the study was consistent condom use for every paid sex in the last 12 months. Both bivariate and multivariable logistic regression analyses were carried out. Results were presented as adjusted odds ratios with their corresponding 95% confidence intervals. Statistical significance was declared at p< 0.05. Results Overall, the prevalence of consistent condom use during paid sex in sub-Saharan Africa was 83.96% (CI = 80.35–87.56), ranging from 48.70% in Benin to 98% in Burkina Faso. Men aged 35–44 [AOR, 1.39 CI = 1.04–1.49], men in the richest wealth quintile [AOR, 1.96 CI = 1.30–3.00], men with secondary level of education [AOR, 1.69 CI = 1.17–2.44], and men in Burkina Faso [AOR = 67.59, CI = 8.72–523.9] had higher odds of consistent condom use during paid sex, compared to men aged 15–19, those in the poorest wealth quintile, those with no formal education, and men in Benin respectively. Conversely, Muslim men had lower odds [AOR = 0.71, CI = 0.53–0.95] of using condom consistently during paid sex, compared to Christian men. Conclusion Empirical evidence from this study suggests that consistent condom use during paid sex encompasses complex social and demographic characteristics. The study also revealed that demographic characteristics such as age, wealth quintile, education, and religion were independently related to consistent condom use for paid sex among men. With sub-Saharan Africa having the highest sexual and reproductive health burden in the world, continuous application of evidence-based interventions (e.g., educational and entrepreneurial training) that account for behavioural and social vulnerabilities are required.
Validation of semiquantitative FFQ administered to adults: a systematic review

Abstract Objective: To conduct a systematic review of studies for the validation of semiquantitative FFQ (SFFQ) that assess food intake in adults. Design: The authors conducted a systematic search in PubMed for articles published as late as January 2020 in Spanish, English, French and Portuguese. Individual searches (twelve in total) paired three hyphenated and non-hyphenated variations of ‘semiquantitative food frequency questionnaire’ with both ‘validity’ and ‘validation’ using the ‘all fields’ and the ‘title/abstract’ retrieval categories. Independent extraction of articles was performed by four authors using predefined data fields. Setting: We searched for original SFFQ validation studies that analysed general diet composition (nutrients with or without food groups or energy analysis) in healthy adults, in any setting, and that also reported correlation coefficients. Participants: Healthy adults. Results: Sixty articles were included. The preferred comparison standard for validation was food records (n 37). The main correlation coefficients used were Pearson’s (n 41), and validity coefficients varied from −0·45 to 1. Most correlation coefficients were adjusted by energy (twelve studies presented only crude values). The elements mentioned most frequently were energy, macronutrients, cholesterol, SFA, PUFA, fibre, vitamin C, Ca and Fe. Conclusions: Although all these SFFQ are reported as validated, coefficients may vary across groups of foods and nutrients. Based on our findings, we suggest researchers to consult our revision before choosing a SFFQ and to review important issues about them, such as their validation, number of items, number of participants, etc. Systematic Review Registration: PROSPERO number CRD42017064716. Available at: http://www.crd. york.ac. uk/PROSPERO/display_record. asp? ID=CRD42017064716.
Relationship between postnatal days, serum Cu concentration and plasma diamine oxidase activity in Japanese Black calves

The aim of study was to investigate the relationships among serum diamine oxidase (DAO) activity, postnatal days and the plasma copper (Cu) concentration, using calves with or without diarrhea. In healthy calves, the serum DAO activity was significantly higher at 2 postnatal days than at ≥7 postnatal days, and no significant changes were observed after 7 postnatal days. In addition, no significant correlation was found between serum DAO activity and plasma Cu concentration at all postnatal days in healthy calves. Although, the serum DAO activity in 14 diarrheic calves (66.78 ± 14.37 IU/ml) was lower than that in 19 healthy calves (170.33 ± 97.83 IU/m, P<0.01), plasma Cu concentrations in all calves remained within the normal range.
Prevalence and associated factors of perceived cancer-related stigma in Japanese cancer survivors.

This study aimed to examine the prevalence and associated factors of perceived cancer-related stigma among Japanese cancer survivors. In this web-based survey involving 628 Japanese cancer survivors, perceived cancer-related stigma, quality of life (Quality of Life-Cancer Survivors Instrument), psychological distress (K6) and perceived social support (multidimensional scale of perceived social support) were evaluated. Perceived cancer-related stigma was endorsed by 61.2% of the participants. Perceived cancer-related stigma was significantly associated with quality of life (R = 0.35-0.37), psychological distress (R = 0.35) and perceived social support (R = 0.10). Logistic regression analysis demonstrated that cancer survivors at younger ages (odds ratio = 0.96), with low income (odds ratio = 2.49), with poorer performance status (odds ratio = 2.33), and with breast, urinary or gynecological cancers (odds ratio = 4.27, 4.01, 4.01, respectively) were at higher risk for perceived cancer-related stigma.
Effect of low-carbohydrate diets on cardiometabolic risk, insulin resistance, and metabolic syndrome

Purpose of review An obesity epidemic has resulted in increasing prevalence of insulin resistance, hyperinsulinemia, metabolic syndrome (MetS), and cardiovascular disease (CVD). The Diet-Heart Hypothesis posited that dietary fat is the culprit. Yet dietary fat reduction has contributed to the problem, not resolved it. The role of hyperinsulinemia, the genesis of its atherogenic dyslipidemia and systemic inflammation in CVD and its reversal is reviewed. Recent findings Overnutrition leads to weight gain and carbohydrate intolerance creating a vicious cycle of insulin resistance/hyperinsulinemia inhibiting fat utilization and encouraging fat storage leading to an atherogenic dyslipidemia characterized by hypertriglyceridemia, low HDL, and small dense LDL. The carbohydrate-insulin model better accounts for the pathogenesis of obesity, MetS, and ultimately type 2 diabetes (T2DM) and CVD. Ketogenic Diets reduce visceral obesity, increase insulin sensitivity, reverse the atherogenic dyslipidemia and the inflammatory biomarkers of overnutrition. Recent trials show very high adherence to ketogenic diet for up to 2 years in individuals with T2DM, reversing their metabolic, inflammatory and dysglycemic biomarkers as well as the 10-year estimated atherosclerotic risk. Diabetes reversal occurred in over 50% and complete remission in nearly 8%. Summary Therapeutic carbohydrate-restricted can prevent or reverse the components of MetS and T2DM.