Miracle-dz/UniFAR-FTUs huggingface dataset:
No evidence for incipient speciation by selfing in North American Arabidopsis lyrata

Self‐fertilization inherently restricts gene flow by reducing the fraction of offspring that can be produced by inter‐population matings. Therefore, mating system transitions from outcrossing to selfing could result in reproductive isolation between selfing and outcrossing lineages and provide a starting point for speciation. In newly diverged lineages, for example after a transition to selfing, further reproductive isolation can be caused by a variety of prezygotic and post‐zygotic mechanisms that operate before, during and after pollination. In animals, prezygotic barriers tend to evolve faster than post‐zygotic ones. This is not necessarily the case for plants, for which the relative importance of post‐mating, post‐fertilization and early‐acting post‐zygotic barriers has been investigated far less. To test whether post‐pollination isolation exists between populations of North American Arabidopsis lyrata that differ in breeding (self‐incompatible versus self‐compatible) and mating system (outcrossing versus selfing), we compared patterns of seed set after crosses made within populations, between populations of the same mating system and between populations with different mating systems. We found no evidence for post‐pollination isolation between plants from selfing populations (self‐compatible, low outcrossing rates) and outcrossing populations (self‐incompatible, high outcrossing rates) via either prezygotic or early‐acting post‐zygotic mechanisms. Together with the results of other studies indicating the absence of reproductive barriers acting before and during pollination, we conclude that the transition to selfing in this study system has not led to the formation of reproductive barriers between selfing and outcrossing populations of North American A. lyrata.
Associations Between Subclass Profile of IgG Response to Gluten and the Gastrointestinal and Motor Symptoms in Children With Cerebral Palsy

ABSTRACT Objective: Gastrointestinal problems are often seen in children with cerebral palsy, although the etiology and underlying mechanisms are not fully understood. Recent data point to significantly elevated levels of IgG antibody to dietary gluten in cerebral palsy independent of celiac disease, a gluten-mediated autoimmune enteropathy. We aimed to further characterize this antibody response by examining its subclass distribution and target reactivity in the context of relevant patient symptom profile. Methods: Study participants included children with cerebral palsy (n = 70) and celiac disease (n = 85), as well as unaffected controls (n = 30). Serum IgG antibody to gluten was investigated for subclass distribution, pattern of reactivity towards target proteins, and relationship with gastrointestinal symptoms and motor function. Results: The anti-gluten IgG antibody response in the cerebral palsy cohort was constituted of all 4 subclasses. In comparison with celiac disease, however, IgG1, IgG2, and IgG3 subclasses were significantly lower, whereas the IgG4 response was significantly higher in cerebral palsy. Within the cohort of cerebral palsy patients, levels of anti-gluten IgG1, IgG3, and IgG4 were greater in those with gastrointestinal symptoms, and the IgG3 subclass antibody correlated inversely with gross motor function. The anti-gluten IgG antibodies targeted a broad range of gliadin and glutenin proteins. Conclusions: These findings reveal an anti-gluten IgG subclass distribution in cerebral palsy that is significantly different from that in celiac disease. Furthermore, the observed association between IgG subclass and symptom profile is suggestive of a relationship between the immune response and disease pathophysiology that may indicate a role for defects in gut immune and barrier function in cerebral palsy.
Immunotherapy in Breast Cancer Patients: A Focus on the Use of the Currently Available Biomarkers in Oncology.

Immune checkpoint inhibitors (ICIs) have remarkably modified the way solid tumors are managed, including breast cancer. Unfortunately, only a relatively small number of breast cancer patients significantly respond to these treatments. To maximize the immunotherapy benefit in breast cancer, several efforts are currently being put forward for the identification of i) the best therapeutic strategy (i.e. ICI monotherapy or in association with chemotherapy, radiotherapy, or other drugs); ii) the optimal timing for administration (e.g. early/advanced stage of disease; adjuvant/neoadjuvant setting); iii) the most effective and reliable predictive biomarkers of response (e.g. tumor-infiltrating lymphocytes, programmed death-ligand 1, microsatellite instability associated with mismatch repair deficiency, and tumor mutational burden). This article reviews the impacts and gaps in the characterization of immune-related biomarkers raised by clinical and translational research studies with immunotherapy treatments. Particular emphasis has been put on the documented evidence of significant clinical benefits of ICI in different randomized clinical trials, along with preanalytical and analytical issues in predictive biomarkers pathological assessment.
Reassessment of predictive values of ACTH‐stimulated serum 21‐deoxycortisol and 17‐hydroxyprogesterone to identify CYP21A2 heterozygote carriers and nonclassic subjects

Heterozygotes (HZs) for 21‐hydroxylase deficiency (21OHD) are highly prevalent, ranging from 1:60 to 1:11 for classic and nonclassic (NC) forms, respectively. Detection of HZ and asymptomatic NC by CYP21A2 genotyping is valuable for genetic counselling, but costly, complex and narrowly available. Adrenocorticotropic hormone (ACTH)‐stimulated serum 17‐hydroxyprogesterone (17P) and 21‐deoxycortisol (21DF) discriminate 21OHD phenotypes effectively, notably if measured simultaneously by liquid chromatography‐tandem mass spectrometry (LC‐MS/MS).
Tau, XMAP215/Msps and Eb1 co-operate interdependently to regulate microtubule polymerisation and bundle formation in axons

The formation and maintenance of microtubules requires their polymerisation, but little is known about how this polymerisation is regulated in cells. Focussing on the essential microtubule bundles in axons of Drosophila and Xenopus neurons, we show that the plus-end scaffold Eb1, the polymerase XMAP215/Msps and the lattice-binder Tau co-operate interdependently to promote microtubule polymerisation and bundle organisation during axon development and maintenance. Eb1 and XMAP215/Msps promote each other’s localisation at polymerising microtubule plus-ends. Tau outcompetes Eb1-binding along microtubule lattices, thus preventing depletion of Eb1 tip pools. The three factors genetically interact and show shared mutant phenotypes: reductions in axon growth, comet sizes, comet numbers and comet velocities, as well as prominent deterioration of parallel microtubule bundles into disorganised curled conformations. This microtubule curling is caused by Eb1 plus-end depletion which impairs spectraplakin-mediated guidance of extending microtubules into parallel bundles. Our demonstration that Eb1, XMAP215/Msps and Tau co-operate during the regulation of microtubule polymerisation and bundle organisation, offers new conceptual explanations for developmental and degenerative axon pathologies.
Phytochemicals and quality level of food plants grown in aquaponics system.

BACKGROUND Beyond nutrition, fruits and vegetables can be considered as natural sources of bioactive molecules, whose beneficial effects on human health are widely recognised. To improve food quality, soilless growing systems could represent a good strategy for promoting sustainable food production chain, although nutritional and nutraceutical properties of their products should be deeply investigated. Main quality traits, volatile and non-volatile secondary metabolites of Solanum lycopersicum L. , Petroselinum crispum (Mill.) Fuss and Ocimun basilicum L. grown in aquaponics system and in organic farming were quantified and compared. RESULTS On fresh basis, soil-grown P. crispum and O. basilicum showed significantly higher total phenolics and antioxidant activity compared to aquaponic crops, while, on dry basis, both plants showed opposite results. Soil-grown S. lycopersicum was significantly richer in total phenolics, while aquaponic one showed a higher antioxidant activity. Aquaponics induced accumulation of resveratrol in P. crispum, rosmarinic acid and myricetin in O. basilicum, and lycopene in S. lycopersicum. Among the volatile compounds, in O. basilicum, linalool was the main constituent in both treatments, while τ-cadinol represented the second constituent in aquaponic crops. Volatile profiles of P. crispum did not differ significantly between the two cultivation methods. CONCLUSIONS The overall quality of organic and aquaponics cultures seemed to be comparable. Results showed that aquaponic farming method can be an innovative, rapid, and sustainable way for producing quality food. This article is protected by copyright. All rights reserved.
Health-Related Quality of Life, Depression, and Self-esteem in Patients With Androgenetic Alopecia: A Systematic Review and Meta-analysis.

Importance Androgenetic alopecia (AGA) is associated with trichodynia, anxiety, low self-esteem, and depression, which have implications for quality of life. However, no systematic evaluation has been performed on the association of AGA with health-related quality of life (HRQOL). Objective To systematically examine the association of AGA with HRQOL and psychiatric disorders. Data Sources Cochrane Library, PubMed, Embase, and WanFang databases were searched from inception through January 24, 2021. Study Selection Case series, case-control studies, cross-sectional studies, cohort studies, and randomized clinical trials that examined either HRQOL or psychiatric disorders in patients with AGA were included. Studies published in languages other than English and Mandarin were excluded. Data Extraction and Synthesis The Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) reporting guideline was used. The risk of bias in included studies was assessed with the Risk of Bias in Non-randomized Studies of Intervention (ROBINS-I) tool. A random-effects model meta-analysis was performed to calculate the pooled effect on HRQOL. A subgroup analysis according to sex and geographic regions was also conducted. Main Outcomes and Measures The outcome was HRQOL of patients with AGA. Results A total of 41 studies involving 7995 patients was included. The pooled Dermatology Life Quality Index score was 8.16 (95% CI, 5.62-10.71). The pooled Hair-Specific Skindex-29 score indicated moderate impairment of emotions, with the meta-analysis showing a score of 29.22 (95% CI, 24.17-34.28) in the emotion dimension. The pooled Center for Epidemiologic Studies Depression Scale score did not indicate depression, with the meta-analysis showing a score of 14.98 (95% CI, 14.28-15.68). Factors that had a direct association with HRQOL included married or coupled status and receipt of medical treatments, whereas factors that had an inverse association with HRQOL included higher self-rated hair loss severity, lower visual analog scale score, and higher educational level. Conclusions and Relevance This systematic review and meta-analysis found a significant association of AGA with moderate impairment of HRQOL and emotions, but no association was found with depressive symptoms. The findings suggest that patients with AGA may need psychological and psychosocial support.
Circulating serum vitamin D levels in relation to metabolic syndrome in children: A systematic review and dose–response meta‐analysis of epidemiologic studies

Findings from epidemiologic studies that evaluated the relationship between serum vitamin D levels and metabolic syndrome (MetS) in children were contradictory. We conducted a systematic review and meta‐analysis on the relation of serum 25(OH)D levels and MetS in children. A comprehensive search was conducted in electronic databases, up to November 2020. Eleven cross‐sectional studies that reported the link between circulating vitamin D levels and MetS in children were included in the analysis. Combining 11 effect sizes from 11 cross‐sectional studies with 22,196 participants revealed that highest versus lowest serum vitamin D concentration was significantly associated with a 50% reduced odds of MetS in children (OR: 0.50; 95%CI: 0.39, 0.64). Subgroup analysis by study location revealed decreased odds of MetS in both non‐Asian (OR: 0.45; 95%CI: 0.33, 0.63) and Asian countries (OR: 0.54; 95%CI: 0.39, 0.76) with no heterogeneity in these subgroups. When we confined the studies to those with representative populations (n = 21,611), a significant inverse association was found between highest versus lowest circulating vitamin D level and MetS (OR: 0.55; 95%CI: 0.42, 0.71). Dose–response analysis showed that each 10 ng/ml (or 25 nmol/L) in serum vitamin D was linearly related to a 12% reduced odds of MetS (OR: 0.88; 95%CI: 0.78, 0.99) in children. A nonlinear association was also detected between serum 25(OH)D and MetS. This meta‐analysis revealed that circulating vitamin D concentration was inversely associated with odds of MetS in children, in a dose–response fashion. The same finding was found in the studies with representative populations.
Comparing the Clinical Utility of Rapid Diagnostics for Treatment of Bloodstream Infections Using Desirability of Outcome Ranking Approach for the Management of Antibiotic Therapy (DOOR-MAT)

Decisions regarding which rapid diagnostic tests (RDT) for bloodstream infections to implement remains challenging given the diversity of organisms detected by different platforms. We used the desirability of outcome ranking management of antimicrobial therapy (DOOR-MAT) as a framework to compare two RDT platforms on potential desirability of antimicrobial therapy decisions. ABSTRACT Decisions regarding which rapid diagnostic test (RDT) for bloodstream infections to implement remain challenging given the diversity of organisms detected by different platforms. We used the desirability of outcome ranking management of antimicrobial therapy (DOOR-MAT) as a framework to compare two RDT platforms on potential desirability of antimicrobial therapy decisions. An observational study was performed at University of Maryland Medical System comparing Verigene blood culture (BC) to GenMark Dx ePlex blood culture ID (BCID) (research use only) panels on blood cultures from adult patients. Positive percent agreement (PPA) between each RDT platform and Vitek MS was calculated for comparison of on-panel targets. Theoretical antimicrobial decisions were made based on RDT results, taking into consideration patient parameters, antimicrobial stewardship practices, and local infectious diseases epidemiology. DOOR-MAT with a partial credit scoring system was applied to these decisions, and mean scores were compared across platforms using a paired t test. The study consisted of 160 unique patients. The Verigene BC PPA was 98.6% (95% confidence interval [CI], 95.1 to 99.8), and ePlex BCID PPA was 98% (95% CI, 94.3 to 99.6). Among the 31 organisms not on the Verigene BC panels, 61% were identified by the ePlex BCID panels. The mean (standard deviation [SD]) DOOR-MAT score for Verigene BC was 86.8 (28.5), while that for ePlex BCID was 91.9 (23.1) (P = 0.01). Both RDT platforms had high PPA for on-panel targets. The ePlex BCID was able to identify more organisms than Verigene, resulting in higher mean DOOR-MAT scores.
The association of mode of delivery and dyspareunia: a systematic review and meta-analysis

Abstract This meta-analysis aimed to examine the association between the mode of delivery and dyspareunia worldwide. Epidemiologic studies evaluating the link between the mode of delivery and dyspareunia (published up to July 2019) were included in this research. These studies were selected by searching several databases such as MEDLINE, ClinicalTraial.gov, PubMed, Web of Science, Scopus and Google Scholar and considering the list of selected articles extracted from references. Then, meta-analyses, subgroup analyses and meta-regressions of the studies were conducted to evaluate the association between the mode of delivery and dyspareunia. In this study, 23 out of 1099 articles were identified and used in the final analysis. Dyspareunia differed according to the mode of delivery although this difference was not statistically significant. In terms of the mode of delivery, a difference was found between instrumental vaginal delivery and caesarean section, but it was not significant. It seems that more studies with a larger sample size should be considered to determine the difference.
The current practices of Australian speech-language pathologists in providing communication services to children with autism spectrum disorder

Abstract Purpose Evidence-Based Practice (EBP) is fundamental to speech-language pathology practice. Australian speech-language pathologists (SLPs) who treat communication disorders in children with autism spectrum disorder (ASD) face unique challenges in implementing EBP. Challenges may include selecting an intervention from a myriad of available interventions for use within a complex population. Identification of current practices of Australian SLPs in communication service provision to children with ASD will provide a baseline for use of EBP and may guide future efforts to engage in EBP. Method A total of 109 Australian SLPs who provide communication services to children with ASD completed an online survey. Descriptive and inferential statistics were used to analyse service delivery and participant experiences of EBP. Result The most common barrier to delivering EBP was inadequate resources. The most utilised strategy was discussing evidence with colleagues. Most participants reported using therapies which did not adhere to a standard protocol, such as eclectic approaches. The majority also reported use of outcome measures which they believe adequately represent functional communication changes for their client. Conclusion Resource limitations may result in over-reliance on interventions lacking empirical support and over-reliance on subjective outcome measurement tools. Reflective practice and self-evaluation of communication services to children with ASD may support improved provision of EBP.
In Vitro Antifungal Resistance of Candida auris Isolates from Bloodstream Infections, South Africa

Candida auris is a multidrug-resistant fungal pathogen that is endemic in South African hospitals. We tested bloodstream C. auris isolates that were submitted to a reference laboratory for national laboratory-based surveillance for candidemia in 2016 and 2017. ABSTRACT Candida auris is a multidrug-resistant fungal pathogen that is endemic in South African hospitals. We tested bloodstream C. auris isolates that were submitted to a reference laboratory for national laboratory-based surveillance for candidemia in 2016 and 2017. We confirmed the species identification by phenotypic/molecular methods. We tested susceptibility to amphotericin B, anidulafungin, caspofungin, micafungin, itraconazole, posaconazole, voriconazole, fluconazole, and flucytosine using broth microdilution and Etest methods. We interpreted MICs using tentative breakpoints. We sequenced the genomes of a subset of isolates and compared them to the C. auris B8441 reference strain. Of 400 C. auris isolates, 361 (90%) were resistant to at least one antifungal agent, 339 (94%) to fluconazole alone (MICs of ≥32 µg/ml), 19 (6%) to fluconazole and amphotericin B (MICs of ≥2 µg/ml), and 1 (0.3%) to amphotericin B alone. Two (0.5%) isolates from a single patient were pan-resistant (resistant to fluconazole, amphotericin B, and echinocandins). Of 92 isolates selected for whole-genome sequencing, 77 clustered in clade III, including the pan-resistant isolates, 13 in clade I, and 2 in clade IV. Eighty-four of the isolates (91%) were resistant to at least one antifungal agent; both resistant and susceptible isolates had mutations. The common substitutions identified across the different clades were VF125AL, Y132F, K177R, N335S, and E343D in ERG11; N647T in MRR1; A651P, A657V, and S195G in TAC1b; S639P in FKS1HP1; and S58T in ERG3. Most South African C. auris isolates were resistant to azoles, although resistance to polyenes and echinocandins was less common. We observed mutations in resistance genes even in phenotypically susceptible isolates.
Elevated serum thyrotropin levels and endothelial dysfunction in a prospective hemodialysis cohort

Thyroid dysfunction is a highly prevalent yet under‐recognized complication in hemodialysis patients. In the general population, hypothyroidism has been associated with endothelial dysfunction due to impaired vasodilator synthesis and activity. Little is known about the association of serum thyrotropin (TSH), the most sensitive and specific single biochemical metric of thyroid function, with endothelial function in hemodialysis patients.
Bromelain‐based enzymatic debridement of chronic wounds: Results of a multicentre randomized controlled trial

Chronic wounds are estimated to affect over 6 million people annually in the United States with an estimated annual cost of $25 billion. Debridement represents a key step in their management and is considered a basic necessity to induce the functional process of tissue repair. However, there is an unmet need for an efficient rapid acting non‐surgical debridement agent. Bromelain‐based enzymatic debridement has been proven to provide an effective, selective and safe non‐surgical debridement in deep burns. EscharEx (MediWound Ltd, Yavne, Israel), is a bromelain‐based enzymatic debridement agent currently in development for chronic wounds. The aim of this study was to assess its safety and efficacy in chronic wounds. Seventy‐three patients suffering from a lower extremity ulcer of diabetic/venous insufficiency/post‐surgical/traumatic aetiology were enrolled in a multicentre, assessor blinded, randomized controlled trial. Patients were randomized to topical treatment by either EscharEx or its gel vehicle for up to 10 daily 4 hour applications, and then continued follow‐up for up to 6 months. The EscharEx arm achieved a significantly higher incidence of complete debridement compared to the gel vehicle arm; 55 versus 29% (p = .047), thus meeting the primary endpoint of this study. The EscharEx and gel vehicle arms achieved similar reductions in wound area, non‐viable tissue area and wound healing scores during the debridement period. There were no significant differences between the arms in the incidence of complete wound closure (41% in the EsxcharEx arm vs. 53% in the gel vehicle arm) and in the mean time to complete wound closure (70.0 ± 32.8 days in the EsxcharEx arm vs. 65.7 ± 38.4 days in gel vehicle arm). There were no significant safety issues and EscharEx demonstrated a favourable benefit to risk profile.