Miracle-dz/UniFAR-FTUs huggingface dataset:
Autofluorescence microscopy as a label-free tool for renal histology and glomerular segmentation

Functional tissue units (FTUs) composed of multiple cells like the glomerulus in the kidney nephron play important roles in health and disease. Histological staining is often used for annotation or segmentation of FTUs, but chemical stains can introduce artefacts through experimental factors that influence analysis. Secondly, many molecular -omics techniques are incompatible with common histological stains. To enable FTU segmentation and annotation in human kidney without the need for histological staining, we detail here the use of widefield autofluorescence (AF) microscopy as a simple, label-free modality that provides detailed renal morphology comparable to periodic acid-Schiff (PAS) stained tissue in both formalin-fixed paraffin-embedded (FFPE) and fresh frozen samples and with no tissue processing beyond sectioning. We demonstrate automated deep learning-based glomerular unit recognition and segmentation on PAS and AF images of the same tissue section from 9 fresh frozen samples and 9 FFPE samples. All training comparisons were carried out using registered AF microscopy and PAS stained whole slide images originating from the same section, and the recognition models were built with the exact same training and test examples. Measures of recognition performance, such as the Dice-Sorensen coefficient, the true positive rate, and the positive predictive value differed less than 2% between standard PAS and AF microscopy for both preservation methods. These results demonstrate that AF is a potentially powerful tool to study human kidney tissue, that it can serve as a label-free source for automated and manual annotation of tissue structures.
Securing Your Relationship: Quality of Intimate Relationships During the COVID-19 Pandemic Can Be Predicted by Attachment Style

The COVID-19 pandemic along with the restrictions that were introduced within Europe starting in spring 2020 allows for the identification of predictors for relationship quality during unstable and stressful times. The present study began as strict measures were enforced in response to the rising spread of the COVID-19 virus within Austria, Poland, Spain and Czech Republic. Here, we investigated quality of romantic relationships among 313 participants as movement restrictions were implemented and subsequently phased out cross-nationally. Participants completed self-report questionnaires over a period of 7 weeks, where we predicted relationship quality and change in relationship quality using machine learning models that included a variety of potential predictors related to psychological, demographic and environmental variables. On average, our machine learning models predicted 29% (linear models) and 22% (non-linear models) of the variance with regard to relationship quality. Here, the most important predictors consisted of attachment style (anxious attachment being more influential than avoidant), age, and number of conflicts within the relationship. Interestingly, environmental factors such as the local severity of the pandemic did not exert a measurable influence with respect to predicting relationship quality. As opposed to overall relationship quality, the change in relationship quality during lockdown restrictions could not be predicted accurately by our machine learning models when utilizing our selected features. In conclusion, we demonstrate cross-culturally that attachment security is a major predictor of relationship quality during COVID-19 lockdown restrictions, whereas fear, pathogenic threat, sexual behavior, and the severity of governmental regulations did not significantly influence the accuracy of prediction.
Prolonged Active Prone Positioning in Spontaneously Breathing Non-intubated Patients With COVID-19-Associated Hypoxemic Acute Respiratory Failure With PaO2/FiO2 >150

Background: The COVID-19 pandemic has led to new approaches to manage patients outside the ICU, including prone positioning in non-intubated patients. Objectives: To report the use of prolonged active prone positioning in spontaneously breathing patients with COVID-19-associated acute respiratory failure. Spontaneously breathing vs non-invasive respiratory support for COVID19 associated acute respiratory failure. Methods: Patients with PaO2/FiO2 > 150, with lung posterior consolidations as assessed by means of lung ultrasound, and chest x-ray were studied. Under continuous pulse oximetry (SpO2) monitoring, patients maintained active prone position. A PaO2/FiO2 < 150 was considered as treatment failure and patients had to be switched to non-invasive respiratory support. Retrospectively, data of 16 patients undergoing who refused proning and underwent non-invasive respiratory support were used as controls. The primary outcome was the proportion of patients maintaining prolonged prone position and discharged home. Secondary outcomes included improvement in oxygenation, hospital length of stay, and 6-month survival. Results: Three out of 16 (18.7%) patients did not tolerate the procedure. Three more patients showed a worsening in PaO2/FiO2 to <150 and required non-invasive support, two of whom finally needing endotracheal intubation. After 72 h, 10 out of 16 (62.5%) patients improved oxygenation [PaO2/FiO2: from 194.6 (42.1) to 304.7 (79.3.2) (p < 0.001)] and were discharged home. In the control group, three out of 16 failed, required invasive ventilatory support, and died within 1 month in ICU. Thirteen were successful and discharged home. Conclusion: In non-intubated spontaneously breathing COVID-19 patients with PaO2/FiO2 >150, active prolonged prone positioning was feasible and tolerated with significant improvement in oxygenation.
Mediators in Psychological Treatments for Anxiety and Depression in Adolescents and Young People: A Protocol of a Systematic Review

Introduction Anxiety and depressive disorders are a significant problem that starts in childhood or adolescence and should be addressed early to avoid chronic mental conditions. There is strong evidence to demonstrate that psychological treatments are effective for these disorders, however, little is known on mediators and mechanisms of change of psychological treatment in adolescents and young adults. Understanding the pathways through which psychological treatments operate will facilitate more effective treatments. Aim We aim to conduct a systematic review, exploring the available evidence on mediators of psychological treatments for anxiety and depression in adolescents and young adults. Methods A systematic search has been performed on PubMed and PsycINFO databases to identify studies from inception to 23rd February 2020. Eligible studies include randomized controlled trials and trials (quasi-experimental) designs that have enrolled adolescents and young adults presenting with depression and/or anxiety and that have examined mediators of psychological treatments. A group of 20 reviewers from the COST-Action TREATme (CA16102) divided into 10 pairs independently screen studies for inclusion, extract information from the included studies, and assess the methodological quality of the included studies and the requirements for mediators. The methodological quality will be assessed by The Mixed Methods Appraisal Tool. Extracted data from the included studies will be collected and presented using a narrative approach. Discussion This systematic review will summarize and provide a comprehensive overview of the current evidence on mediators of psychological treatments for anxiety and depression for adolescents and young adults. Results will allow the identification of strategies to optimize intervention to enhance clinical outcomes. Ethics and dissemination Ethics approval is not required. Findings from this systematic review will be published in a peer-reviewed journal and disseminated at conferences and meetings. PROSPERO registration number: CRD42021234641.
Murine GRXCR1 Has a Different Function Than GRXCR2 in the Morphogenesis of Stereocilia

Mutations in human glutaredoxin domain-containing cysteine-rich protein 1 (GRXCR1) and its paralog GRXCR2 have been linked to hearing loss in humans. Although both GRXCR1 and GRXCR2 are required for the morphogenesis of stereocilia in cochlear hair cells, a fundamental question that remains unclear is whether GRXCR1 and GRXCR2 have similar functions in hair cells. Previously, we found that GRXCR2 is critical for the stereocilia morphogenesis by regulating taperin localization at the base of stereocilia. Reducing taperin expression level rescues the morphological defects of stereocilia and hearing loss in Grxcr2-deficient mice. So far, functions of GRXCR1 in mammalian hair cells are still unclear. Grxcr1-deficient hair cells have very thin stereocilia with less F-actin content inside, which is different from Grxcr2-deficient hair cells. In contrast to GRXCR2, which is concentrated at the base of stereocilia, GRXCR1 is diffusely distributed throughout the stereocilia. Notably, GRXCR1 interacts with GRXCR2. In Grxcr1-deficient hair cells, the expression level of GRXCR2 and taperin is reduced. Remarkably, different from that in Grxcr2-deficient mice, reducing taperin expression level does not rescue the morphological defects of stereocilia or hearing loss in Grxcr1-deficient mice. Thus, our findings suggest that GRXCR1 has different functions than GRXCR2 during the morphogenesis of stereocilia.
An Overview of Methods and Tools for Transfection of Eukaryotic Cells in vitro

Transfection is a powerful analytical tool enabling studies of gene products and functions in eukaryotic cells. Successful delivery of genetic material into cells depends on DNA quantity and quality, incubation time and ratio of transfection reagent to DNA, the origin, type and the passage of transfected cells, and the presence or absence of serum in the cell culture. So far a number of transfection methods that use viruses, non-viral particles or physical factors as the nucleic acids carriers have been developed. Among non-viral carriers, the cationic polymers are proposed as the most attractive ones due to the possibility of their chemical structure modification, low toxicity and immunogenicity. In this review the delivery systems as well as physical, biological and chemical methods used for eukaryotic cells transfection are described and discussed.
Impaired Cerebrovascular Reactivity in Huntington’s Disease

There is increasing evidence that impairments of cerebrovascular function and/or abnormalities of the cerebral vasculature might contribute to early neuronal cell loss in Huntington’s disease (HD). Studies in both healthy individuals as well as in patients with other neurodegenerative disorders have used an exogenous carbon dioxide (CO2) challenge in conjunction with functional magnetic resonance imaging (fMRI) to assess regional cerebrovascular reactivity (CVR). In this study, we explored potential impairments of CVR in HD. Twelve gene expanded HD individuals, including both pre-symptomatic and early symptomatic HD and eleven healthy controls were administered a gas mixture targeting a 4–8 mmHg increase in CO2 relative to the end-tidal partial pressure of CO2 (PETCO2) at rest. A Hilbert Transform analysis was used to compute the cross-correlation between the time series of regional BOLD signal changes (ΔBOLD) and increased PETCO2, and to estimate the response delay of ΔBOLD relative to PETCO2. After correcting for age, we found that the cross-correlation between the time series for regional ΔBOLD and for PETCO2 was weaker in HD subjects than in controls in several subcortical white matter regions, including the corpus callosum, subcortical white matter adjacent to rostral and caudal anterior cingulate, rostral and caudal middle frontal, insular, middle temporal, and posterior cingulate areas. In addition, greater volume of dilated perivascular space (PVS) was observed to overlap, primarily along the periphery, with the areas that showed greater ΔBOLD response delay. Our preliminary findings support that alterations in cerebrovascular function occur in HD and may be an important, not as yet considered, contributor to early neuropathology in HD.
Virtual Patient-Specific Quality Assurance of IMRT Using UNet++: Classification, Gamma Passing Rates Prediction, and Dose Difference Prediction

The dose verification in radiotherapy quality assurance (QA) is time-consuming and places a heavy workload on medical physicists. To provide a clinical tool to perform patient specific QA accurately, the UNet++ is investigated to classify failed or pass fields (the GPR lower than 85% is considered “failed” while the GPR higher than 85% is considered “pass”), predict gamma passing rates (GPR) for different gamma criteria, and predict dose difference from virtual patient-specific quality assurance in radiotherapy. UNet++ was trained and validated with 473 fields and tested with 95 fields. All plans used Portal Dosimetry for dose verification pre-treatment. Planar dose distribution of each field was used as the input for UNet++, with QA classification results, gamma passing rates of different gamma criteria, and dose difference were used as the output. In the test set, the accuracy of the classification model was 95.79%. The mean absolute error (MAE) were 0.82, 0.88, 2.11, 2.52, and the root mean squared error (RMSE) were 1.38, 1.57, 3.33, 3.72 for 3%/3mm, 3%/2 mm, 2%/3 mm, 2%/2 mm, respectively. The trend and position of the predicted dose difference were consistent with the measured dose difference. In conclusion, the Virtual QA based on UNet++ can be used to classify the field passed or not, predict gamma pass rate for different gamma criteria, and predict dose difference. The results show that UNet++ based Virtual QA is promising in quality assurance for radiotherapy.
Impaired Performance on a Cognitively-Based Instrumental Activities of Daily Living Task, the 10-Item Weekly Calendar Planning Activity, in Individuals With Stroke Undergoing Acute Inpatient Rehabilitation

Performance-based, functionally relevant, and standardized measures of cognitive-instrumental activities of daily living (C-IADL) can complement neuropsychological tests of cognitive impairment and provide valuable clinical information to inform rehabilitation planning. Existing measures have been validated in the outpatient setting. Here, we sought to evaluate a 10-item, short-form of a C-IADL measure, Weekly Calendar Planning Activity (WCPA-10), in inpatients with stroke undergoing acute rehabilitation. The specific goal was to determine if the WCPA-10 could differentiate between stroke patients undergoing acute inpatient rehabilitation and healthy control individuals. We also explored whether the WCPA-10 would identify C-IADL limitations in stroke patients screened as having intact cognition. Seventy-seven stroke inpatients undergoing rehabilitation and 77 healthy control participants completed the WCPA-10, which involves entering a list of simulated, fictional appointments into a weekly schedule while keeping track of and adhering to multiple task rules and ignoring built-in obstacles and distractions. Compared to the control group, stroke patients had significantly worse accuracy, made more errors, used fewer cognitive strategies, followed fewer rules, took more time to complete the task, and were less efficient. 83% of stroke patients were less accurate than predicted by their age, and 64% used less strategies than their age prediction. Among 28 participants who screened as having “normal” cognitive function on the Montreal Cognitive Assessment, the majority had deficits on the WCPA-10. Our results provide initial support for use of a brief C-IADL assessment, WCPA-10, for individuals with stroke undergoing inpatient rehabilitation. They indicate that stroke patients have deficits in C-IADL accuracy, efficiency, and strategy use at this stage of stroke recovery. Results highlight the need to use performance based, functional cognitive assessments, even for those who perform well on cognitive screening tools.
Assessing the Individual Interviewer Rapport-Building and Supportive Techniques of the R-NICHD Protocol

The use of the rapport-building and supportive techniques formulated by the R-NICHD protocol is intended to support children and increase the quality of their statements as well as disclosures without possessing suggestive potential. While the effectiveness of the entire R-NICHD protocol for children who have actually experienced child sexual abuse (CSA) has been supported by research, to date no study assessed the effect of each individual socio-emotional interview technique in both interviewees with and without CSA experiences. The current study aimed to address this gap in research by means of an online vignette-study, asking participants to rate the identified rapport-building and supportive techniques on the scales well-being, willingness to talk, and perceived pressure. A total of 187 participants were randomly assigned to either a hypothetical “abused” or a hypothetical “not abused” group by means of a vignette-manipulation. The results suggest that many socio-emotional interview techniques were perceived as supportive and non-suggestive, while a number of techniques were perceived as not supportive but suggestive. Few differences emerged between the hypothetical “abused” group and the hypothetical “not abused” control group. To conclude, most but not all rapport-building and supportive techniques proposed by the R-NICHD protocol had a positive effect on interviewees.
Transcriptome and Small RNA Combined Sequencing Analysis of Cold Tolerance in Non-heading Chinese Cabbage

Background Non-heading Chinese cabbage (Brassica rapa ssp. chinensis) is an important leaf vegetable grown worldwide. However, there has currently been not enough transcriptome and small RNA combined sequencing analysis of cold tolerance, which hinders further functional genomics research. Results In this study, 63.43 Gb of clean data was obtained from the transcriptome analysis. The clean data of each sample reached 6.99 Gb, and the basic percentage of Q30 was 93.68% and above. The clean reads of each sample were sequence aligned with the designated reference genome (Brassica rapa, IVFCAASv1), and the efficiency of the alignment varied from 81.54 to 87.24%. According to the comparison results, 1,860 new genes were discovered in Pak-choi, of which 1,613 were functionally annotated. Among them, 13 common differentially expressed genes were detected in all materials, including seven upregulated and six downregulated. At the same time, we used quantitative real-time PCR to confirm the changes of these gene expression levels. In addition, we sequenced miRNA of the same material. Our findings revealed a total of 34,182,333 small RNA reads, 88,604,604 kinds of small RNAs, among which the most common size was 24 nt. In all materials, the number of common differential miRNAs is eight. According to the corresponding relationship between miRNA and its target genes, we carried out Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis on the set of target genes on each group of differentially expressed miRNAs. Through the analysis, it is found that the distributions of candidate target genes in different materials are different. We not only used transcriptome sequencing and small RNA sequencing but also used experiments to prove the expression levels of differentially expressed genes that were obtained by sequencing. Sequencing combined with experiments proved the mechanism of some differential gene expression levels after low-temperature treatment. Conclusion In all, this study provides a resource for genetic and genomic research under abiotic stress in Pak-choi.
Beasts in the Garden: Human-Wildlife Coexistence in India's Past and Present

Human-wildlife encounters are characterized by a diverse array of engagements located on the continuum between the negative and the positive. In India, protracted conflict with wildlife is reflected in violence across a range of rural and urban ecologies, but is only one aspect of the multiple facets of ongoing human-non-human encounter. Within these shared spaces, there are often equally significant elements of acceptance, tolerance and reverence. Together, these are dependent on context, and can be explored via lived experiences and worldviews, and a moral economy of human-wildlife and human-human relationships. Historically, though hardly static, such relationships have been mediated by the ontological positioning of traditional societies and their embedded rules and practises. In recent years, these tenuous equilibria have been disrupted by top-down catalysts, including universalist conservation agendas percolating from the state and the global arena. This study aims to explore the changing nature of coexistence by using several historical and contemporary vignettes in relation to key species that routinely “transgress” from their primary natural habitats into the “garden” spaces of human cultivation and habitation. The study will argue that insights at the intersection of environmental history, political ecology and anthropology can improve our understanding of human-wildlife coexistence in India as well as across the world.
Reflections on Binary Sex/Gender Categorization in Magnetic Resonance Tomography and its Future Challenges

This paper examines the role of technical, methodological conditions in functional magnetic imaging (fMRI) in the production of binary sex/gender differences. The aim is to investigate the scanning process with a focus on the statistical parameter of gendered markers within the technology, in order to make visible the problems entangled in typical research routines. It is especially important to elaborate this because the computer models currently being used and Big Data studies are reproducing and reapplying outdated and rigid concepts of sex/gender differences with the goal of improving science considerably. Therefore, the paper discusses the empirical methodologies and epistemic underpinnings of differentiation through statistics, and argues that counter-counting, weighing and sizing might not help to substantiate the idea of “equality” (not only for the sex/gender category) in brain studies. In relation to the topic of this special issue, I argue that in order to develop an interdisciplinary approach to criticizing dimorphism and differentiation by groups, a wider understanding of the technical and theoretical foundations used in brain research is needed.