Hammerkjeldsen1313

Our novel pipeline quantifies expression of both TEs and genes using featureCounts and Stringtie, respectively. RepExpress then filters expressed repeats and characterizes their genomic context, enabling the identification of TEs that overlap with genes, or that may be influencing gene expression. Here, we describe RepExpress, and provide a step-by-step protocol detailing its workflow. We also discuss other TE analysis tools and their applicability to addressing different biological questions. © 2021 Wiley Periodicals LLC. Basic Protocol RepExpress workflow.Immunofluorescence labeling and microscopy offer a highly specific means to visualize proteins or other molecular species in a sample by labeling target antigens with fluorescent probes. These fluorescent probes can then be visualized using a fluorescence microscope, allowing their relative spatial relationships to be determined. Due to spectral overlap of common fluorophores, however, it can be challenging to analyze more than three antigens in a single sample with standard imaging approaches. This article describes multiplexed labeling and imaging of four target antigens through the use of a long-Stokes-shift fluorophore-a fluorophore with an unusually large gap between its excitation and emission maxima-in tandem with three conventional fluorophores. selleck kinase inhibitor This combination allows for multiplexed imaging of four antigens in a single sample with excellent spectral discrimination suitable for sensitive analyses using standard imaging hardware. Particular advantages of this approach are its flexibility in terms of target antigens and the lack of any specialized procedures, reagents, or equipment beyond the commercially available labeling reagent coupled to the long-Stokes-shift fluorophore. © 2021 Wiley Periodicals LLC. Basic Protocol 1 Four-probe immunofluorescence labeling Basic Protocol 2 Four-probe immunofluorescence imaging.Bone tissue engineering strategy involves the 3D scaffolds and appropriate cell types promoting the replacement of the damaged area. In this work, we aimed to develop a fast and reliable clinically relevant protocol for engineering viable bone grafts, using cryopreserved adipose tissue-derived mesenchymal stromal cells (MSCs) and composite 3D collagen-nano-hydroxyapatite (nanoHA) scaffolds. Xeno- and DMSO-free cryopreserved MSCs were perfusion-seeded into the biomimetic collagen/nanoHA scaffolds manufactured by cryotropic gelation and their osteoregenerative potential was assessed in vitro and in vivo. Cryopreserved MSCs retained the ability to homogenously repopulate the whole volume of the scaffolds during 7 days of post-thaw culture. Moreover, the scaffold provided a suitable microenvironment for induced osteogenic differentiation of cells, confirmed by alkaline phosphatase activity and mineralization. Implantation of collagen-nanoHA cryogels with cryopreserved MSCs accelerated woven bone tissue formation, maturation of bone trabeculae, and vascularization of femur defects in immunosuppressed rats compared to cell-free collagen-nanoHA scaffolds. The established combination of xeno-free cell culture and cryopreservation techniques together with an appropriate scaffold design and cell repopulation approach accelerated the generation of viable bone grafts.Demand for post-acute stroke and traumatic brain injury (TBI) rehabilitation outweighs resource availability. Every day, clinicians face the challenging task of deciding which patient will benefit or not from rehabilitation. The objectives of this scoping review were to map and compare factors reported by clinicians as influencing referral or admission decisions to post-acute rehabilitation for stroke and TBI patients, to identify most frequently reported factors and those perceived as most influential. We searched four major databases for articles published between 1946 and January 2021. Articles were included if they reported clinician's perceptions, investigated referral or admission decisions to post-acute rehabilitation and focused on stroke or TBI patients. Twenty articles met inclusion criteria. The International Classification of Functioning, Disability and Health framework was used to guide data extraction and summarizing. Patient-related factors most frequently reported by clinicians were patient's age, mental status prior to stroke or TBI and family support. The two latter were ranked amongst the most influential by clinicians working with stroke patients, whereas age was ranked of low importance. Organizational factors were reported to influence decisions (particularly availability of post-acute care services) as well as clinicians' characteristics (eg, knowledge). Moreover, clinicians' prediction of patient outcome ranked amongst the most important driver of referral or admission decisions by clinicians working with stroke patients. Findings highlight the complex nature of decision-making regarding patient selection for rehabilitation and provide insight on important factors frontline clinicians need to consider when having to make rapid decisions in high-pressured acute care environments. This article is protected by copyright. All rights reserved.Psychotropic drugs can induce strong metabolic adverse effects, potentially increasing morbidity and/or mortality of patients. Metabolomic profiling, by studying the levels of numerous metabolic intermediates and products in the blood, allows a more detailed examination of metabolism dysfunctions. We aimed to identify blood metabolomic markers associated with weight gain in psychiatric patients. Sixty-two patients starting a treatment known to induce weight gain were recruited. Two hundred and six selected metabolites implicated in various pathways were analyzed in plasma, at baseline and after 1 month of treatment. Additionally, 15 metabolites of the kynurenine pathway were quantified. This latter analysis was repeated in a confirmatory cohort of 24 patients. Among the 206 metabolites, a plasma metabolomic fingerprint after 1 month of treatment embedded 19 compounds from different chemical classes (amino acids, acylcarnitines, carboxylic acids, catecholamines, nucleosides, pyridine, and tetrapyrrole) potentially involved in metabolic disruption and inflammation processes. The predictive potential of such early metabolite changes on 3 months of weight evolution was then explored using a linear mixed-effects model. Of these 19 metabolites, short-term modifications of kynurenine, hexanoylcarnitine, and biliverdin, as well as kynurenine/tryptophan ratio at 1 month, were associated with 3 months weight evolution. Alterations of the kynurenine pathway were confirmed by quantification, in both exploratory and confirmatory cohorts. Our metabolomic study suggests a specific metabolic dysregulation after 1 month of treatment with psychotropic drugs known to induce weight gain. The identified metabolomic signature could contribute in the future to the prediction of weight gain in patients treated with psychotropic drugs.The Pharmacogenomics Knowledgebase (PharmGKB) is an integrated online knowledge resource for the understanding of how genetic variation contributes to variation in drug response. Our focus includes not only pharmacogenomic information useful for clinical implementation (e.g., drug dosing guidelines and annotated drug labels), but also information to catalyze scientific research and drug discovery (e.g., variant-drug annotations and drug-centered pathways). As of April 2021, the annotated content of PharmGKB spans 715 drugs, 1761 genes, 227 diseases, 165 clinical guidelines, and 784 drug labels. We have manually curated data from more than 9000 published papers to generate the content of PharmGKB. Recently, we have also implemented an automated natural language processing (NLP) tool to broaden our coverage of the pharmacogenomic literature. This article contains a basic protocol describing how to navigate the PharmGKB website to retrieve information on how genes and genetic variations affect drug efficacy and toxicity. It also includes a protocol on how to use PharmGKB to facilitate interpretation of findings for a pharmacogenomic variant genotype or metabolizer phenotype. PharmGKB is freely available at http//www.pharmgkb.org. © 2021 Wiley Periodicals LLC. Basic Protocol 1 Navigating the homepage of PharmGKB and searching by drug Basic Protocol 2 Using PharmGKB to facilitate interpretation of pharmacogenomic variant genotypes or metabolizer phenotypes.The mOTU profiler, or mOTUs for short, is a software tool that enables the profiling of microbial communities in terms of their taxonomic composition, relative abundance of metabolically active members, and diversity of strain populations. To this end, it maintains a database of single-copy phylogenetic marker gene sequences, which are used as a reference to which short read metagenomic and metatranscriptomic reads are mapped for the identification and quantification of microbial taxa. Here, we describe the most common use cases of the mOTU profiler in two basic protocols. Additional supporting protocols provide information on its installation and in-depth guidance on adjusting its settings for increasing or decreasing the stringency with which taxa are detected and quantified, as well as for customizing the output file format. Guidelines for understanding the profiling results are provided, along with additional information on unique features, methodological details, and the development history of the tool. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1 Metagenomic and metatranscriptomic mOTU profiling Basic Protocol 2 Metagenomic SNV profiling Support Protocol 1 Installing mOTUs Support Protocol 2 Profiling pipeline-step by step Support Protocol 3 The mOTUs profiling routine using advanced parameters Support Protocol 4 Metagenomic SNV calling advanced parameters.Ultraviolet (UV) organic emitters that can open up applications for future organic light-emitting diodes (OLEDs) are of great value but rarely developed. Here, we report a high-quality UV emitter with hybridized local and charge-transfer (HLCT) excited state and its application in UV OLEDs. The UV emitter, 2BuCz-CNCz, shows the features of low-lying locally excited (LE) emissive state and high-lying reverse intersystem crossing (hRISC) process, which helps to balance the color purity and exciton utilization of UV OLED. Consequently, the OLED based on 2BuCz-CNCz exhibits not only a desired narrowband UV electroluminescent (EL) at 396 nm with satisfactory color purity (CIEx, y =0.161, 0.031), but also a record-high maximum external quantum efficiency (EQE) of 10.79 % with small efficiency roll-off. The state-of-the-art device performance can inspire the design of UV emitters, and pave a way for the further development of high-performance UV OLEDs.The goal of this position paper on ventilatory support at home for children is to provide expert consensus from Australia and New Zealand on optimal care for children requiring ventilatory support at home, both non-invasive and invasive. It was compiled by members of the Thoracic Society of Australia and New Zealand (TSANZ) and the Australasian Sleep Association (ASA). This document provides recommendations to support the development of improved services for Australian and New Zealand children who require long-term ventilatory support. Issues relevant to providers of equipment and areas of research need are highlighted.