Miracle-dz/UniFAR-FTUs huggingface dataset:
Virtual reality interventions to enhance upper limb motor improvement after a stroke: commonly used types of platform and outcomes

Abstract Introduction Virtual Reality (VR) based platforms are useful in enhancing post-stroke sub-optimal upper limb (UL) motor improvement. A variety of options are available from expensive highly customizable platforms to low cost turnkey solutions. Clinical outcomes primarily help assess the effects of VR-based platforms. These outcomes mainly quantify how much improvement has occurred. Very few outcomes characterize the type (i.e. how) of recovery. We categorized the types of VR-based platforms and outcome measures commonly used for post-stroke UL motor improvement. Methods We reviewed the published literature in English from 2000-2019. Different types of VR-based platforms were grouped into those available commercially and those developed by the various research groups. We initially classified outcomes from the retrieved studies under the appropriate International Classification of Functioning categories. Then, we divided the outcomes as those quantifying the type or extent of improvement. Results We found a total of 125 studies. Majority of the studies used commercially available platforms. A total of 42 different outcome measures were used. Seventeen different outcomes were used to assess body structure and functions as well as in activity limitations. Eight outcomes assessed the effects of contextual factors and participation restrictions. The Fugl Meyer Assessment, Wolf Motor Function Test and Stroke Impact Scale were most often used across the three categories. Of the 125 studies, 52 used outcomes characterizing the type of recovery. Although a smaller proportion, 24 studies included movement patterns outcomes. Conclusion A standardized set of outcomes can promote better comparisons between studies using different VR-based platforms for post-stroke UL motor improvement. Implications for Rehabilitation A wide variety of commercially available systems are present from expensive customizable systems to low-cost turnkey systems. The Fugl-Meyer Assessment and Wolf Motor Function Test along with the Stroke Impact Scale-Social Participation subscale were used most often across all studies as assessments of body structure and function, activity limitations and participation restriction. It is essential to include movement pattern outcomes addressing whether recovery of compensation occurs with the use of VR-based platforms.
Development and psychometric evaluation of the Birmingham Relationship Continuity Measure for acquired brain injury

ABSTRACT Objective Relationship continuity/discontinuity refers to whether a spouse/partner experiences their current relationship with someone with an acquired brain injury (ABI) as a continuation of their loving pre-injury relationship or as radically changed. The aim of this study was to adapt a questionnaire measure of continuity/discontinuity from dementia research for use in an ABI context and to evaluate the psychometric properties of this adaptation. Method The questionnaire was adapted in response to feedback from a focus group of ABI caregivers. Its psychometric properties were then evaluated in two studies involving partners of people with ABI. Results The measure showed high internal consistency (alpha = .956 in Study 1 and .963 in Study 2), test-retest reliability (intra-class correlation = .960 in Study 1) and discriminative power (Ferguson’s delta = .975 in Study 1 and .963 in Study 2). Evidence of construct validity was provided by a predicted pattern of correlations with other relationship questionnaires. Exploratory factor analysis suggested that the questionnaire is unidimensional. Discussion A valid and reliable quantitative measure of relationship continuity/discontinuity will enable more robust evaluation of suggestions about this construct that have been made in qualitative studies (e.g. that discontinuity is associated with a greater sense of caregiver burden).
HDAC1 dysregulation induces aberrant cell cycle and DNA damage in progress of TDP‐43 proteinopathies

TAR DNA‐binding protein 43 (TDP‐43) has been implicated in frontotemporal lobar degeneration with ubiquitin‐positive inclusions (FTLD‐TDP) and amyotrophic lateral sclerosis. Histone deacetylase 1 (HDAC1) is involved in DNA repair and neuroprotection in numerous neurodegenerative diseases. However, the pathological mechanisms of FTLD‐TDP underlying TDP‐43 proteinopathies are unclear, and the role of HDAC1 is also poorly understood. Here, we found that aberrant cell cycle activity and DNA damage are important pathogenic factors in FTLD‐TDP transgenic (Tg) mice, and we further identified these pathological features in the frontal cortices of patients with FTLD‐TDP. TDP‐43 proteinopathies contributed to pathogenesis by inducing cytosolic mislocalization of HDAC1 and reducing its activity. Pharmacological recovery of HDAC1 activity in FTLD‐TDP Tg mice ameliorated their cognitive and motor impairments, normalized their aberrant cell cycle activity, and attenuated their DNA damage and neuronal loss. Thus, HDAC1 deregulation is involved in the pathogenesis of TDP‐43 proteinopathies, and HDAC1 is a potential target for therapeutic interventions in FTLD‐TDP.
Distribution of Charophytes along the Swedish Coastin Relation to Salinity and Eutrophication

In Sweden, 14 out of 34 charophyte species are regularly found in the Baltic Sea. Nitella flexilis, N. opaca, N. wahlbergiana, Chara braunii, Chara globularis and C. delicatula occur mainly in freshwater, but occasionally in brackish water. Chara aspera and C. tomentosa occur in the Baltic and calcium-rich inland water. Chara connivens, C. baltica, C. horrida, C. canescens, Tolypella nidifica and Lamprothamnium papulosum are restricted to brackish water. Compared to older herbaria material, more recent charophyte records exist for the northernmost part of the coast probably due to higher intensity of investigation. In the southernmost part of the coast, however, charophytes disappeared from most of their former localities probably due to eutrophication. The importance of charophytes as bioindicators is discussed.
Cytokines of the IL‐17 family in psoriasis

Various immune cells and their messenger substances influence the development of psoriasis. Cytokines of the IL‐17 family are of particular importance. In addition to IL‐17A, which plays a central role in the pathogenesis of psoriasis, other subtypes of the IL‐17 family also have a proinflammatory effect. This review provides an up‐to‐date overview of the immunopathogenesis of psoriasis with regard to the six IL‐17 subtypes, in particular their physiological and pathogenic properties, as well as their significance for psoriasis therapy.
Weak relationships between swimming morphology and water depth in wrasses and parrotfish belie multiple selective demands on form-function evolution.

Mechanical tradeoffs in performance are predicted to sculpt macroevolutionary patterns of morphological diversity across environmental gradients. Water depth shapes the amount of wave energy organisms experience, which should result in evolutionary tradeoffs between speed and maneuverability in fish swimming morphology. Here, we tested whether morphological evolution would reflect functional tradeoffs in swimming performance in 131 species of wrasses and parrotfish (Family: Labridae) across a water depth gradient. We found that maximum water depth predicts variation in pectoral fin aspect ratio (AR) in wrasses, but not in parrotfish. Shallow-water wrasses exhibit wing-like pectoral fins that help with 'flapping', which allows more efficient swimming at faster speeds. Deeper water species, in contrast, exhibit more paddle-like pectoral fins associated with enhanced maneuverability at slower speeds. Functional morphology responds to a number of different, potentially contrasting selective pressures. Furthermore, many-to-one mapping may release some traits from selection on performance at the expense of others. As such, deciphering the signatures of mechanical tradeoffs on phenotypic evolution will require integrating multiple aspects of ecological and morphological variation. As the field of evolutionary biomechanics moves into the era of big data, we will be uniquely poised to disentangle the intrinsic and extrinsic predictors of functional diversity.
Size and colony cycle in Polistes satan, a Neotropical paper wasp (Hymenoptera Vespidae)

Recent studies report that reproductive and non-reproductive roles of individuals can be associated with body size variation and/or physiological differences in many primitively eusocial wasps. This paper investigates the effects of the season on the body size and reproductive differences in Polistes satan. In pre-emergence colonies, inseminated females are significantly larger than subordinates for most of body measurements. Season has no effect on the differences related to the body size between inseminated females and uninseminated females from post-emergence colonies. However, most morphometric variables were significantly different between uninseminated females collected in distinct periods of the year. We suggest that seasonal variation may affect uninseminated females directly reflecting a flexible developmental programme in primitively eusocial wasps.
Comparison of diversity indices applied to macrophyte incidence-based data

In this work, a recently proposed diversity index based on Patil and Taillie parametric diversity measure (or Tsallis entropy), Sq*, was applied to samples (presence-absence data) of macrophytes from the Itaipu Reservoir, Brazil. This new index was the value of the family of indices Sq for a specific evenness of a sample. Results demonstrated that the Shannon index and species richness showed expressively high correlation with the Sq*; however, the evenness had low correlation coefficients with the index Sq*, indicating that Sq* was particularly sensitive to rarity and species richness. On the other hand, the weak correlations of this index with evenness demonstrated that it was less sensitive to species relative abundances.
Transgenic potato virus Y resistance in potato : evidence for an RNA-mediated cellular response

This study was undertaken to assess the potential of transgenic RNA-mediated virus resistance in potato. Transgenes that expressed various versions of the potato virus Y (PVY) coat protein (CP) open reading frame (ORF) were constructed and expressed in potato. Plants highly resistant to PVY infection could be generated by expressing transgenes from which either mRNA and CP or only an untranslatable mRNA were made. An inverse correlation between transgene transcript accumulation and virus resistance was often noted when translatable or untranslatable versions of the PVY CP ORF were expressed. The data suggest that virus resistance is likely mediated by a host cell response. A dominant negative phenotype resulting from the transgene product competing with the viral-encoded product is not supported by the data.
Lipid Profile, Haemoglobin Level and Antioxidant Effect of Pre-treatment with Methanolic Extract of Byrsocarpus coccineus Schum. & Thonn. Leaf against Carbon Tetrachloride-Induced Injuries to Liver, Kidney and Heart of Rats

Aim: To evaluate the protective and ameliorative roles of methanolic extract of Byrsocarpus coccineus, Schum. & Thonn. leaf against acute and chronic carbon tetrachloride (CCl 4)-induced oxidative stress and Injuries to Liver, Kidney and Heart in Rats.
Integration and reanalysis of transcriptomics and methylomics data derived from blood and testis tissue of men with 47,XXY Klinefelter syndrome indicates the primary involvement of Sertoli cells in the testicular pathogenesis

Klinefelter syndrome (KS; 47,XXY) is the most common sex chromosomal anomaly and causes a multitude of symptoms. Often the most noticeable symptom is infertility caused by azoospermia with testicular histology showing hyalinization of tubules, germ cells loss, and Leydig cell hyperplasia. The germ cell loss begins early in life leading to partial hyalinization of the testis at puberty, but the mechanistic drivers behind this remain poorly understood. In this systematic review, we summarize the current knowledge on developmental changes in the cellularity of KS gonads supplemented by a comparative analysis of the fetal and adult gonadal transcriptome, and blood transcriptome and methylome of men with KS. We identified a high fraction of upregulated genes that escape X‐chromosome inactivation, thus supporting previous hypotheses that these are the main drivers of the testicular phenotype in KS. Enrichment analysis showed overrepresentation of genes from the X‐ and Y‐chromosome and testicular transcription factors. Furthermore, by re‐evaluation of recent single cell RNA‐sequencing data originating from adult KS testis, we found novel evidence that the Sertoli cell is the most affected cell type. Our results are consistent with disturbed cross‐talk between somatic and germ cells in the KS testis, and with X‐escapee genes acting as mediators.
Testing against umbrella or tree orderings for binomial proportions with an adaptation of an insect resistance case

Alternative hypotheses for order restrictions, such as umbrella or inverse umbrella (a.k.a tree) orderings, have been studied extensively in the literature, although less so when the studied response for each individual is the presence or absence of the event of interest. Two families of test statistics for solving the problem of testing against an umbrella or a tree ordering when the responses are binomial proportions are studied in this work and their asymptotic distributions are derived. A simulation study is conducted to compare the empirical power of some members of the derived families of test statistics with competing approaches. The methodology developed here was driven by an applied problem arising in stored products research where despite universal mortality in the case of doses of 1000 ppm of the insecticide phosphine, unexpected survival was noted at higher doses.
The Use of Artificial Intelligence and Deep Machine Learning in Oncologic Histopathology.

BACKGROUND Recently, there has been a momentous drive to apply advanced artificial intelligence (AI) technologies to diagnostic medicine. The introduction of AI has provided vast new opportunities to improve healthcare and has introduced a new wave of heightened precision in oncologic pathology. The impact of AI on oncologic pathology has now become apparent and its use with respect to oral oncology is still in the nascent stage. DISCUSSION A foundational overview of AI classification systems used in medicine and a review of common terminology used in machine learning and computational pathology will be presented. This paper provides a focused review on the recent advances in AI and deep learning in oncologic histopathology and oral oncology. In addition, specific emphasis on recent studies that have applied these technologies to oral cancer prognostication will also be discussed. CONCLUSION Machine and deep learning methods designed to enhance prognostication of oral cancer have been proposed with much of the work focused on prediction models on patient survival and locoregional recurrences in patients with oral squamous cell carcinomas (OSCC). Few studies have explored machine learning methods on OSCC digital histopathologic images. It is evident that further research at the whole slide image-level is needed and future collaborations with computer scientists may progress the field of oral oncology.
Observations on the Biology and Ecology of Selected Macroalgae from the Littoral of São Miguel (Azores)

Abstract The dominant benthic algal species from two sites, located on opposite coasts of the island of São Miguel, Azores (São Roque in the south and São Vicente on the north coast) were studied over a two-year period (September 1993–September 1995). From both sites monthly collections were made in the intertidal zone and in the adjacent subtidal zone down to a depth of 15 m. The algae occur under different ecological conditions, a few species being restricted to the intertidal zone (Fucus spiralis, Gelidium microdon, Jania crassa, Caulacanthus ustulatus and Chondria coerulescens), while others (Codium elisabethae, Zonaria tournefortii, Jania verrucosa and Sphaerococcus coronopifolius) were exclusively present subtidally. Other species were present at both levels. Differences were observed between the two sites. A few species (Chaetomorpha linum, Corallina elongata and Caulacanthus ustulatus) were more abundant at São Roque, their presence on the north being only sporadic or occasional. On the other hand, Fucus spiralis, Gelidium microdon, Sphaerococcus coronopifolius and Centroceras clavulatum were statistically more abundant at São Vicente. Seasonal changes were seen in the growth and/or reproduction of certain species, with many (Ulva rigida, Bryopsis hypnoides, Stypocaulon scoparium, Dictyota dichotoma, Padina pavonica, Colpomenia sinuosa, Gelidium microdon, Asparagopsis armata, Chondracanthus acicularis and Plocamium cartilagineum) having larger plants and/or higher values of biomass in spring and/or summer. With the exception of Dictyota dichotoma that was statistically more abundant in the second sampling year, no differences were observed on the species abundance between the two years. Reproductive phenology varied according to species, with many (Fucus spiralis, Ulva rigida, Gelidium microdon, Jania rubens, Sphaerococcus coronopifolius, Caulacanthus ustulatus, and Plocamium cartilagineum) having prolonged fertile periods. Some species were more seasonal in their reproduction, being fertile only over two seasons: Codium elisabethae and the tetrasporophyte of Asparagopsis armata in autumn and winter; Cystoseira abies-marina and Pterocladiella capillacea in summer and autumn; the gametophyte of Asparagopsis armata in winter and early spring. A few had a more restricted fertile period: Chaetomorpha linum and Jania verrucosa in summer; Chondracanthus acicularis in autumn.
Applications of Molecular Methods and Statistical Analyses for Discrimination of Accessions and Clones of Vetiver Grass

Because (i) origins and genealogies of vetiver grass have been poorly documented, and (ii) morphological uniformity and infrequent flowering precluded accurate identification of selected clones, an investigation was undertaken to link molecular methods with rigorous biometric analysis to discriminate accessions and clones. Successful DNA profiling is highly dependent on the reproducibility of the assay. Our ability to generate consistent results may have been a result of (i) genomic DNA quality, (ii) rigorous oligonucleotide primer selection, and (iii) DNA amplification protocol stringency. Because of the low level of replicate variability, we were able to bring a high level of resolution to the analysis of identity [. ]
Identification of the putative N-acetylglucosaminidase CseA associated with daughter cell separation in Tetragenococcus halophilus

ABSTRACT The lactic acid bacterium Tetragenococcus halophilus, which is used as a starter to brew soy sauce, comprises both cluster-forming strains and dispersed strains. The cluster-forming strains are industrially useful for obtaining clear soy sauce, because the cell clusters are trapped by filter cloth when the soy sauce mash is pressed. However, the molecular mechanism underlying cell cluster formation is unknown. Whole genome sequence analysis and subsequent target sequence analysis revealed that the cluster-forming strains commonly have functional defects in N-acetylglucosaminidase CseA, a peptidoglycan hydrolase. CseA is a multimodular protein that harbors a GH73 domain and six peptidoglycan-binding LysM domains. Recombinant CseA hydrolyzed peptidoglycan and promoted cell separation. Functional analysis of truncated CseA derivatives revealed that the LysM domains play an important role in efficient peptidoglycan degradation and cell separation. Taken together, the results of this study identify CseA as a factor that greatly affects the cluster formation in T. halophilus. GRAPHICAL ABSTRACT In Tetragenococcus halophilus, putative N-acetylglucosaminidase CseA contributes to daughter cell separation, whereas functional defects in CseA cause cell cluster formation.
CSA: A high-throughput chromosome-scale assembly pipeline for vertebrate genomes

Abstract Background Easy-to-use and fast bioinformatics pipelines for long-read assembly that go beyond the contig level to generate highly continuous chromosome-scale genomes from raw data remain scarce. Result Chromosome-Scale Assembler (CSA) is a novel computationally highly efficient bioinformatics pipeline that fills this gap. CSA integrates information from scaffolded assemblies (e.g., Hi-C or 10X Genomics) or even from diverged reference genomes into the assembly process. As CSA performs automated assembly of chromosome-sized scaffolds, we benchmark its performance against state-of-the-art reference genomes, i.e., conventionally built in a laborious fashion using multiple separate assembly tools and manual curation. CSA increases the contig lengths using scaffolding, local re-assembly, and gap closing. On certain datasets, initial contig N50 may be increased up to 4.5-fold. For smaller vertebrate genomes, chromosome-scale assemblies can be achieved within 12 h using low-cost, high-end desktop computers. Mammalian genomes can be processed within 16 h on compute-servers. Using diverged reference genomes for fish, birds, and mammals, we demonstrate that CSA calculates chromosome-scale assemblies from long-read data and genome comparisons alone. Even contig-level draft assemblies of diverged genomes are helpful for reconstructing chromosome-scale sequences. CSA is also capable of assembling ultra-long reads. Conclusions CSA can speed up and simplify chromosome-level assembly and significantly lower costs of large-scale family-level vertebrate genome projects.
Allopurinol and valproic acid improve cardiac triglyceride and Na+-K+-ATPase activity independent of circulating aldosterone in female rats with glucose intolerance

Abstract Context: Studies have shown that cardiac triglyceride accumulation and impaired Na+-K+-ATPase activity are linked to diabetes- related cardiovascular disease, particularly in women. Objectives: We hypothesised that allopurinol (ALL) and valproic acid (VPA) treatment would improve cardiac triglyceride and Na+-K+-ATPase activity independent of circulating aldosterone in Combined Oral Contraceptive (COC)-induced dysglycemia Materials and methods: Rats received COC (1.0 μg ethinylestradiol and 5.0 μg levonorgestrel; po) with or without ALL (1 mg; po) and VPA (20 mg; po) for 6 weeks. Results: COC-treatment led to impaired glucose tolerance, accumulated abdominal fat, dyslipidemia, elevated plasma MDA, PAI-1 and aldosterone levels and also reduced plasma nitric oxide bioavailability and cardiac Na+-K+-ATPase activity. However, either ALL or VPA treatment ameliorated these alterations comparably independent of elevated aldosterone level Discussion and conclusion: Our results suggest that either ALL or VPA would improve cardiac TG and Na+-K+-ATPase activity comparably in COC-treated rats, regardless of circulating aldosterone level.