Miracle-dz/UniFAR-FTUs huggingface dataset:
Auxin-driven ecophysiological diversification of leaves in domesticated tomato

Heterobaric leaves have bundle sheath extensions (BSEs) that compartmentalise the parenchyma, whereas homobaric leaves do not. The presence of BSEs affects leaf hydraulics and photosynthetic rate. The tomato (Solanum lycopersicum) obscuravenosa (obv) mutant lacks BSEs. Here we identify the obv gene and the causative mutation, a non-synonymous amino acid change that disrupts a C2H2 zinc finger motif in a putative transcription factor. This mutation exists as a rare polymorphism in the natural range of wild tomatoes, but has increased in frequency in domesticated tomatoes, suggesting that the latter diversified into heterobaric and homobaric leaf types. The obv mutant displays reduced vein density, leaf hydraulic conductance and photosynthetic assimilation rate. We show that these and other effects on plant development, including changes in leaf insertion angle, leaf margin serration, minor vein density and fruit shape, are controlled by OBV via changes in auxin signalling. Loss of function of the transcriptional regulator AUXIN RESPONSE FACTOR (ARF4) also results in defective BSE development, revealing an additional component of a novel genetic module controlling aspects of leaf development important for ecological adaptation and subject to breeding selection. One sentence summary distribution of tomato heterobaric and homobaric leaves is controlled by a single-nucleotide polymorphism in an auxin-related transcription factor
Analgesic and anti-inflammatory activities of ethyl acetate and butanol fractions from Vitex polygama hydroalcoholic leaf extract

Abstract This study evaluated the analgesic and anti-inflammatory activities of Vitex polygama. Ethyl acetate and butanol fractions (10-30 mg/kg), obtained from the hydroalcoholic leaf extract, showed an antinociceptive effect in the acetic acid-induced abdominal writhing test, formalin test and modified hot plate test in mice, indicating a peripheral anti-inflammatory action. Ethyl acetate and butanol fractions were effective in inhibiting nitric oxide and TNF-α production, respectively, in RAW 264.7 macrophages. Both fractions (10-30 mg/kg) showed an acute analgesic effect in mice with vincristine-induced neuropathic pain exposed to a thermal stimulus. Through ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-UV-MS/MS) it was possible to identify seven major compounds: isoorientin, orientin, vitexin, isovitexin, O-p-hydroxybenzoyl orientin, O-caffeoyl-orientin, and di-caffeoylquinic acid. Orientin and isoorientin were isolated from ethyl acetate fraction and had their identity confirmed by nuclear magnetic resonance (NMR). Glucosyl flavones appear to be the main metabolites responsible for the anti-inflammatory and analgesic activities observed for V. polygama. Graphical Abstract
Effects of The Mitochondrial Genome on Germ Cell Fertility: A Review of The Literature

Infertility is one of the major problems faced in medicine. There are numerous factors that play a role in infertility. For example, numerous studies mention the impact of the quantity and quality of mitochondria in sexual gametes. This is a narrative review of the effects of the mitochondrial genome on fertility. We searched the PubMed, Science Direct, SID, Google Scholar, and Scopus databases for articles related to “Fertility, Infertility, Miscarriage, Mitochondria, Sperm, mtDNA, Oocytes” and other synonymous keywords from 2000 to 2020. The mitochondrial genome affects infertility in both male and female gametes; in sperm, it mainly releases free radicals. In the oocyte, a mutation in this genome can affect the amount of energy required after fertilisation, leading to gestation failure. In both cases, infertile cells have substantially less mitochondrial DNA (mtDNA) copies. The effects of mtDNA on gamete fertility occur via changes in oxidative phosphorylation and cellular energy production. Also, a reduction in the number of mtDNA copies is directly associated with sex cell infertility. Therefore, evaluation of the mitochondrial genome can be an excellent diagnostic option for couples who have children with neonatal disorders, infertile couples who seek assisted reproductive treatment, and those in whom assisted reproductive techniques have failed.
Fault-Tolerant Formation Control of Unmanned Aerial Vehicles in the Presence of Actuator Faults and Obstacles

This paper presents a leader-follower type of fault-tolerant formation control (FTFC) methodology with application to multiple unmanned aerial vehicles (UAVs) in the presence of actuator failures and potential collisions. The proposed FTFC scheme consists of both outer-loop and inner-loop controllers. First, a leader-follower control scheme with integration of a collision avoidance mechanism is designed as the outer-loop controller for guaranteeing UAVs to keep the desired formation while avoiding the approaching obstacles. Then, an active fault-tolerant control (FTC) strategy for counteracting the actuator failures and also for preventing the healthy actuators from saturation is synthesized as the inner-loop controller. Finally, a group of numerical simulations are carried out to verify the effectiveness of the proposed approach.
The Distinctive Plant and Insect Assemblages of An Experimental Forest in Northern Lower Michigan (United States)

Abstract The effects of plants on insects are not completely clear due to potential covariation of weather or location affecting both assemblages. To address this question, plant and insect assemblages were described during summer 2019 and 2020 in two different forest habitats of northern Lower Michigan. The first habitat was a hardwood forest typical of secondary succession in the region. The second was a hydric forest located ∼20 m from the hardwood forest which developed after lake sediment was deposited into a 10-ha area in the early 2000s. Reflecting this sediment deposition, soil of the hydric forest had higher water content and organic matter, and was dominated by the plant genera Solidago (Asterales: Asteraceae), Rubus (Rosales: Rosaceae), and Salix (Malpighiales: Salicaceae). In contrast, the hardwood forest had greater inorganic sediment and was dominated by Pteridium (Polypodiales: Dennstaedtiaceae), Carex (Poales: Cyperaceae), and Acer. Nearly 140,000 insect specimens were sampled using pitfall trapping, sweep netting, flight intercept trapping, ultraviolet light trapping, and yellow and blue pan trapping. The first three methods each sampled a unique insect assemblage, whereas the last three overlapped in taxa sampled. Insect assemblages of the two forests were distinct from each other using any of the six methods, with abundance of Pteridium and Salix (Sapindales: Sapindaceae) generally associating with changes in insect composition. A total of 41 insect taxa indicated the hydric forest and 14 indicated the hardwood forest. Insect richness increased with that of plants. These results demonstrate that differences in soil composition and plant assemblages associate with differences in forest insect assemblages, even of forests in very close proximity.
distAngsd: Fast and Accurate Inference of Genetic Distances for Next-Generation Sequencing Data

Abstract Commonly used methods for inferring phylogenies were designed before the emergence of high-throughput sequencing and can generally not accommodate the challenges associated with noisy, diploid sequencing data. In many applications, diploid genomes are still treated as haploid through the use of ambiguity characters; while the uncertainty in genotype calling—arising as a consequence of the sequencing technology—is ignored. In order to address this problem, we describe two new probabilistic approaches for estimating genetic distances: distAngsd-geno and distAngsd-nuc, both implemented in a software suite named distAngsd. These methods are specifically designed for next-generation sequencing data, utilize the full information from the data, and take uncertainty in genotype calling into account. Through extensive simulations, we show that these new methods are markedly more accurate and have more stable statistical behaviors than other currently available methods for estimating genetic distances—even for very low depth data with high error rates.
Promoting Survivor Safety in Immigrant Communities: Online Simulation Training for Korean American Faith Leaders

This study examined the efficacy of a short virtual case simulation for Korean American (KA) faith leaders, “Religious Leaders for Healthy Families. ” The goal of the program is to increase knowledge about intimate partner violence (IPV) and healthy intimate partner relationships, enhance self-efficacy in IPV prevention and intervention, strengthen attitudes that support their roles on IPV prevention and intervention, increase positive outcome expectations of their actions, and increase behavioral intentions and behaviors on IPV prevention and intervention. KA faith leaders from two large metropolitan areas with a high concentration of KA immigrants were invited to participate in the study (N=102). Participants completed three online assessments: baseline, a 3-month, and a 6-month follow-up. After the baseline assessment, participants were randomized to either intervention (n = 53) or control (n = 49). The intervention consisted of four online simulation modules, each taking approximately 15–20 min to complete. At the 6-month follow-up, faith leaders in the intervention group significantly increased their knowledge and self-efficacy in IPV prevention and intervention compared to the control group. Mean scores for attitudes against IPV and prevention behaviors increased from baseline to the 6-month follow-up for the intervention group more than the control group, but the differences were not statistically significant. “Religious Leaders for Healthy Families” has the potential to reduce disparities in accessing resources and services for immigrant survivors of IPV. With its ease of use, this short, free online intervention has a high potential for uptake among faith leaders. Results are promising, but the COVID-19 pandemic negatively affected the study, with participants having scarce opportunities to practice the skills learned from the intervention. A larger follow-up study that combines “Religious Leaders for Healthy Families” with a community-wide intervention that targets all community members is warranted to reach more faith leaders and community members.
Natural allelic variation of GmST05 controlling seed size and quality in soybean

Summary Seed size is one of the most important agronomic traits determining the yield of crops. Cloning the key genes controlling seed size and pyramiding their elite alleles will facilitate yield improvement. To date, few genes controlling seed size have been identified in soybean, a major crop that provides half of the plant oil and one quarter of the plant protein globally. Here, through a genome‐wide association study of over 1800 soybean accessions, we determined that natural allelic variation at GmST05 (Seed Thickness 05) predominantly controlled seed thickness and size in soybean germplasm. Further analyses suggested that the two major haplotypes of GmST05 differed significantly at the transcriptional level. Transgenic experiments demonstrated that GmST05 positively regulated seed size and influenced oil and protein contents, possibly by regulating the transcription of GmSWEET10a. Population genetic diversity analysis suggested that allelic variations of GmST05 were selected during geographical differentiation but have not been fixed. In summary, natural variation in GmST05 determines transcription levels and influences seed size and quality in soybean, making it an important gene resource for soybean molecular breeding.
Ultrasonic fragmentation for removing thick organized clots during diabetic vitrectomy – A novel technique

A 65-year-old male with proliferative diabetic retinopathy (PDR) and non-clearing vitreous hemorrhage underwent 25G pars plana vitrectomy (PPV). A large disk of thick organized blood of 5 disk diameter (DD) size was encountered in subhyaloid space. All attempts including lower cut rates to remove this disk using a 25G cutter turned futile. We used a 20G fragmatome to safely remove this hard clot from vitreous cavity in 50 s. Surgical time for removal of similar clot of 3 DD by 25G cutter in another eye was 5 min. Removal of thick clotted subhyaloid blood by ultrasonic fragmentation during diabetic vitrectomy is a safe, faster, and useful maneuver.
Exploration of health and health behaviours of undergraduate nursing students: a multi-methods study in two countries

Background Nurses play a vital role in health promotion, and there may be a link between a nurse’s own lifestyle practices and how they educate others. Supporting health and well-being in student nurses is critical given they will be educating others once registered and practicing. Objectives To explore the health and health behaviours of undergraduate nursing and midwifery students considering the demands of their profession, their public health role and their ability to be role models. Design Multi-methods study. Methods Undergraduate nursing students in the second and third years of their programme were invited to self-complete a health and health behaviour questionnaire in a Scottish and Australian Higher Education Institution. Qualitative data were collected from a convenience sample of 20 third-year nursing and midwifery students. Results Two hundred and thirty-five Scottish students and 113 Australian students, 175 (85%) and 84 (74%), respectively, completed the questionnaire. Some differences and similarities were noted across groups, in particular, perceived physical health, the prevalence of binge drinking, smoking and being overweight/obese and some dietary measures were found to be less favourable among Scottish students. There were worryingly high levels of poor mental well-being at both higher education institutions, with scores on a mental well-being scale suggesting that (82) 34.7% of Scottish students and 33 (29.6%) of Australian students were at risk of depression. Nine Scottish students and 11 Australian students were interviewed. Key contributors and barriers to healthy behaviours were noted across both groups of students in relation to lifestyle. Students perceived that certain elements of their curriculum had implications on their ability or motivation to make healthy lifestyle choices. Conclusion The poor health and health behaviours of future nurses need to be addressed in their higher education to shape resilient role models for future nursing practice. Impact Statement Priority should be given to supportive learning environments for student nurses that foster emotional support and encourage healthy lifestyles.
Radiation Research Journals Need to Stipulate Minimal Dosimetry Requirements for Publishing Research Using X-Radiation Exposures

The goal of publishing research is to enable the work to not only be disseminated, but also to be replicated. Replication may be essential for establishment of new experimental techniques or validation of novel findings. True replication, however, can only be achieved by providing the appropriate experimental details in the published literature and/or contacting the authors to obtain the required information.
Usefulness of high‐risk HPV early oncoprotein (E6 and E7) serological markers in the detection of cervical cancer: A systematic review and meta‐analysis

We reviewed the literature on the importance of selected anti‐high‐risk human papillomavirus (HR‐HPV) antibodies (namely, 16/18 and early oncoproteins E6 and E7) as potential serological markers for early detection of individuals at high risk of cervical cancer. We searched for studies in PubMed and Embase databases published from 2010 to 2020 on antibodies against HR‐HPV E6 and E7 early proteins and cervical cancer. Pooled sensitivity and specificity for HPV16 and HPV18 antibodies were calculated using a bivariate hierarchical random‐effects model. A total of 69 articles were identified; we included three studies with 1550 participants. For the three HPV16/18 E6 and E7 antibody tests, enzyme‐linked immunosorbent assay‐based assays had a sensitivity of 18% for detecting CIN2+ (95% confidence interval [CI]: 15–21) and a specificity of 96% (95% CI: 92–98), for slot‐blot, sensitivity was 28.9% (95% CI: 23.3–35.1) and specificity was 72% (95% CI: 66.6–77.0) for detecting CIN2+, and for multiplex HPV serology assay based on a glutathione S‐transferase, sensitivity was 16% (95% CI: 8.45–28.6) and specificity was 98% (95% CI: 97–99) for detecting invasive cervical cancer. HR‐HPV16/18 E6 and E7 serological markers showed high specificity, but sensitivity was suboptimal for the detection of cervical cancer in either population screening settings or as point‐of‐care screening tests.
Multiomics analysis of male infertility

Abstract Infertility affects 8–12% of couples globally, and the male factor is a primary cause in ∼50% of couples. Male infertility is a multifactorial reproductive disorder, which can be caused by paracrine and autocrine factors, hormones, genes, and epigenetic changes. Recent studies in rodents and most notably in humans using multiomics approach have yielded important insights into understanding the biology of spermatogenesis. Nonetheless, the etiology and pathogenesis of male infertility are still largely unknown. In this review, we summarized and critically evaluated findings based on the use of advanced technologies to compare normal and obstructive azoospermic versus nonobstructive azoospermic men, including whole-genome bisulfite sequencing, single-cell RNA-seq, whole-exome sequencing, and transposase-accessible chromatin using sequencing. It is obvious that the multiomics approach is the method of choice for basic research and clinical studies including clinical diagnosis of male infertility. Summary Sentence This review summarizes findings of the past 20 years published in literature listed in PubMed including our laboratory, utilizing multiomics approach to study the etiology and pathogenesis of male infertility. Graphical Abstract
Determining the Minimal Important Change of Everyday Functioning in Dementia

Background and Objectives Decline in everyday functioning is a key clinical change in Alzheimer disease and related disorders (ADRD). An important challenge remains the determination of what constitutes a clinically meaningful change in everyday functioning. We aimed to investigate this by establishing the minimal important change (MIC): the smallest amount of change that has a meaningful effect on patients' lives. We retrospectively investigated meaningful change in a memory clinic cohort. Methods In the first, qualitative part of the study, community-recruited informal caregivers of patients with ADRD and memory clinic clinicians completed a survey in which they judged various situations representing changes in everyday functioning. Their judgments of meaningful change were used to determine thresholds for MIC, both for decline and improvement, on the Amsterdam Instrumental Activities of Daily Living (IADL) Questionnaire. In the second, quantitative part, we applied these values in an independent longitudinal cohort study of unselected memory clinic patients. Results MIC thresholds were established at the average threshold of caregivers (N = 1,629; 62.4 ± 9.5 years; 77% female) and clinicians (N = 13): −2.2 points for clinically meaningful decline and +5.0 points for clinically meaningful improvement. Memory clinic patients (N = 230; 64.3 ± 7.7 years; 39% female; 60% dementia diagnosis) were followed for 1 year, 102 (45%) of whom showed a decline larger than the MIC, after a mean of 6.7 ± 3.5 months. Patients with a dementia diagnosis and more atrophy of the medial temporal lobe had larger odds (odds ratio [OR] = 3.4, 95% CI [1.5–7.8] and OR = 5.0, 95% CI [1.2–20.0], respectively) for passing the MIC threshold for decline than those with subjective cognitive complaints and no atrophy. Discussion We were able to operationalize clinically meaningful decline in IADL by determining the MIC. The usefulness of the MIC was supported by our findings from the clinical sample that nearly half of a sample of unselected memory clinic patients showed a meaningful decline in less than a year. Disease stage and medial temporal atrophy were predictors of functional decline greater than the MIC. Our findings provide guidance in interpreting changes in IADL and may help evaluate treatment effects and monitor disease progression.
Annotation Query (AnnoQ): an integrated and interactive platform for large-scale genetic variant annotation

Abstract The Annotation Query (AnnoQ) (http://annoq.org/) is designed to provide comprehensive and up-to-date functional annotations for human genetic variants. The system is supported by an annotation database with ∼39 million human variants from the Haplotype Reference Consortium (HRC) pre-annotated with sequence feature annotations by WGSA and functional annotations to Gene Ontology (GO) and pathways in PANTHER. The database operates on an optimized Elasticsearch framework to support real-time complex searches. This implementation enables users to annotate data with the most up-to-date functional annotations via simple queries instead of setting up individual tools. A web interface allows users to interactively browse the annotations, annotate variants and search variant data. Its easy-to-use interface and search capabilities are well-suited for scientists with fewer bioinformatics skills such as bench scientists and statisticians. AnnoQ also has an API for users to access and annotate the data programmatically. Packages for programming languages, such as the R package, are available for users to embed the annotation queries in their scripts. AnnoQ serves researchers with a wide range of backgrounds and research interests as an integrated annotation platform.
How to successfully classify EEG in motor imagery BCI: a metrological analysis of the state of the art

Objective. Processing strategies are analyzed with respect to the classification of electroencephalographic signals related to brain-computer interfaces (BCIs) based on motor imagery (MI). A review of literature is carried out to understand the achievements in MI classification, the most promising trends, and the challenges in replicating these results. Main focus is placed on performance by means of a rigorous metrological analysis carried out in compliance with the international vocabulary of metrology. Hence, classification accuracy and its uncertainty are considered, as well as repeatability and reproducibility. Approach. The paper works included in the review concern the classification of electroencephalographic signals in motor-imagery-based BCIs. Article search was carried out in accordance with the Preferred Reporting Items for Systematic reviews and Meta-Analyses standard and 89 studies were included. Main results. Statistically-based analyses show that brain-inspired approaches are increasingly proposed, and that these are particularly successful in discriminating against multiple classes. Notably, many proposals involve convolutional neural networks. Instead, classical machine learning approaches are still effective for binary classifications. Many proposals combine common spatial pattern, least absolute shrinkage and selection operator, and support vector machines. Regarding reported classification accuracies, performance above the upper quartile is in the 85%–100% range for the binary case and in the 83%–93% range for multi-class one. Associated uncertainties are up to 6% while repeatability for a predetermined dataset is up to 8%. Reproducibility assessment was instead prevented by lack of standardization in experiments. Significance. By relying on the analyzed studies, the reader is guided towards the development of a successful processing strategy as a crucial part of a BCI. Moreover, it is suggested that future studies should extend these approaches on data from more subjects and with custom experiments, even by investigating online operation. This would also enable the quantification of the results reproducibility.