bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cytokine signaling converging onIL11in ILD fibroblasts provokes aberrant epithelial differentiation signatures
Authors: Kastlmeier Miriam T. , Rodriguez Erika Gonzalez , Cabanis Phoebe , Guenther Eva M. , König Ann-Christine , Han Lianyong , Hauck Stefanie M. , See Fenja , Asgharpour Sara , Bukas Christina , Burgstaller Gerald , Piraud Marie , Lehmann Mareike , Hatz Rudolf A. , Behr Jürgen , Stoeger Tobias , Hilgendorff Anne , Voss Carola 
Published: December 2022

AbstractInterstitial lung disease (ILD) is a heterogenous group of lung disorders where destruction and incomplete regeneration of the lung parenchyma often results in persistent architectural distortion of the pulmonary scaffold. Continuous mesenchyme-centered, disease-relevant signaling likely initiates and perpetuates the fibrotic remodeling process, specifically targeting the epithelial cell compartment, thereby destroying the gas exchange area.With the aim of identifying functionally relevant mediators of the lung mesenchymal-epithelial crosstalk that hold potential as new targets for therapeutic strategies, we developed a 3D organoid co-culture model based on human induced pluripotent stem cell-derived alveolar epithelial type 2 cells that form alveolar organoids in presence of lung fibroblasts from ILD patients as well as a control cell line (IMR-90). While organoid formation capacity and size was comparable in the presence of ILD or control lung fibroblasts, metabolic activity was significantly increased in ILD co-cultures. Alveolar organoids cultured with ILD fibroblasts further demonstrated reduced stem cell function as reflected by reducedSurfactant Protein Cgene expression together with an aberrant basaloid-prone differentiation program indicated by elevatedCadherin 2, Bone Morphogenic Protein 4andVimentintranscription.In order to screen for key mediators of the misguided mesenchymal-to-epithelial crosstalk with a focus on disease-relevant inflammatory processes, we used mass spectrometry and characterized the secretome of end stage ILD lung fibroblasts in comparison to non-chronic lung disease (CLD) patient fibroblasts. Out of the over 2000 proteins detected by this experimental approach, 47 proteins were differentially abundant comparing ILD and non-CLD fibroblast secretome.The ILD secretome profile was dominated by chemokines, includingCXCL1, CXCL3, andCXCL8, interfering with growth factor signaling orchestrated byInterleukin 11 (IL11), steering fibrogenic cell-cell communication, and proteins regulating extracellular matrix remodeling including epithelial-to-mesenchymal transition. When in turn treating alveolar organoids withIL11, we recapitulated the co-culture results obtained with primary ILD fibroblasts including changes in metabolic activity.In summary, we identified mediators likely contributing to the disease-perpetuating mesenchymal-to-epithelial crosstalk in ILD. In our alveolar organoid co-cultures, we were able to highlight the importance of fibroblast-initiated aberrant epithelial differentiation and confirmedIL11as a key player in ILD pathogenesis by unbiased ILD fibroblast secretome analysis.Abstract Figure
The utility of quantitative D-Dimer assay as a biomarker in the diagnosis and exclusion of Cerebral Venous Sinus Thrombosis
Authors: Soni Dipesh , Pannu Ashok Kumar , Saroch Atul , Bhatia Vikas , Ahluwalia Jasmina , Singh Rajveer , Jain Arihant 
Published: December 2022

AbstractThrombotic disorders are characterized by the presence of elevated levels of detectable fibrin degradation products in the blood. The utility and sensitivity of quantitative D-Dimer assay to rule out the diagnosis of deep vein thrombosis is well established. We extrapolated this principle to evaluate the utility of D-Dimer assay in exclusion of cerebral venous sinus thrombosis (CVST). CVST is an important cause of cerebrovascular accidents in young patients and the residual neurological deficits can be minimized if correct therapy, i.e., anticoagulation is instituted in a timely manner. As advanced imaging modalities that are required for the diagnosis of CVST might not be readily available everywhere, it is important to have a sensitive biomarker which can guide clinicians to rule out the diagnosis with a reasonable confidence. We evaluated the patients admitted at a tertiary care center who underwent Computed tomography (CT) Venography/Magnetic resonance (MR) Venography of the brain with the clinical suspicion of CVST. After appropriate exclusion, a quantitative D-Dimer assay was performed in patients who had CVST on CT/MR Venography and was compared with those patients who did not. Receiver operating characteristic (ROC) analysis revealed that quantitative D Dimer had poor diagnostic accuracy for the differentiation of CVST from non CVST cases (Area under the curve = 0.694), but D-Dimer levels of <300 ng/mL had a sensitivity of 90% for ruling out the diagnosis of CVST.
Mental health care in the city of Lubumbashi, Democratic Republic of the Congo: Analysis of demand, supply and operational response capacity of the health district of Tshamilemba
Authors: Mukala-Mayoyo Erick , Criel Bart , Michielsen Joris , Chuy Didier , Coppieters Yves , Chenge Faustin 
Published: December 2022

AbstractBackgroundIntegrating mental health care into the primary care system is an important policy option in the Democratic Republic of the Congo (DRC). From the perspective of the integration of mental health care in district health services, this study analyzed the existing demand and supply of mental health care in the health district of Tshamilemba, which is located in Lubumbashi, the second largest city of the DRC. We critically examined the district’s operational response capacity to address mental health.MethodsA multimethod cross-sectional exploratory study was carried out. We conducted a documentary review (including an analysis of the routine health information system) from the health district of Tshamilemba. We further organized a survey to which 591 residents responded and conducted 5 focus group discussions with 50 key stakeholders (doctors, nurses, managers, community health workers and leaders, health care users). The demand for mental health care was analyzed through the assessment of the burden of mental health problems and care-seeking behaviors. The mental health care supply available was described. Finally, the district’s operational response capacity was assessed.ResultsAnalysis of technical documents indicated that the burden of mental health problems is a major public problem in Lubumbashi. However, the proportion of mental health cases among the general patient population seen in the outpatient curative consultations in the Tshamilemba district remains very low, at an estimated 5.3%. The interviews not only pointed to a clear demand for mental health care but also indicated that there is currently hardly any offer of care available in the district. There are no dedicated psychiatric beds, nor is there a psychiatrist or psychologist available. In this context, the main source of care for people remains traditional medicine.ConclusionThe gaps in the management of mental health problems constitute a major challenge in the DRC in general and in the health district of Tshamilemba in particular. Testing the feasibility of integrating a basic package of mental health care into existing primary care services is therefore of great relevance. Such a policy may contribute to strengthening the health system and enhancing people’s access to quality mental health care.
Multi-center integrated analysis of non-coding CRISPR screens
Authors: Yao David , Tycko Josh , Oh Jin Woo , Bounds Lexi R. , Gosai Sager J. , Lataniotis Lazaros , Mackay-Smith Ava , Doughty Benjamin R. , Gabdank Idan , Schmidt Henri , Youngworth Ingrid , Andreeva Kalina , Ren Xingjie , Barrera Alejandro , Luo Yunhai , Siklenka Keith , Yardımcı Galip Gürkan ,   The ENCODE4 Consortium, Tewhey Ryan , Kundaje Anshul , Greenleaf William J. , Sabeti Pardis C. , Leslie Christina , Pritykin Yuri , Moore Jill E. , Beer Michael A. , Gersbach Charles A. , Reddy Timothy E. , Shen Yin , Engreitz Jesse M. , Bassik Michael C. , Reilly Steven K. 
Published: December 2022

AbstractThe ENCODE Consortium’s efforts to annotate non-coding,cis-regulatory elements (CREs) have advanced our understanding of gene regulatory landscapes which play a major role in health and disease. Pooled, non-coding CRISPR screens are a promising approach for systematically investigating gene regulatory mechanisms. Here, the ENCODE Functional Characterization Centers report 109 screens comprising 346,970 individual perturbations across 13.3Mb of the genome, using a variety of methods, readouts, and statistical analyses. Across 332 functionally confirmed CRE-gene links, we identify principles for screening endogenous, non-coding elements for causal regulatory mechanisms. Nearly all CREs show strong evidence of open chromatin, and targeting accessibility peak summits is a critical component of our proposed sgRNA design rules. We provide experimental guidelines to accurately detect CREs with variable, often low, transcriptional effects. We discover a previously undescribed DNA strand-bias for CRISPRi in transcribed regions with implications for screen design and analysis. Benchmarking five screen analysis tools, we find CASA produces the most conservative CRE calls and is robust to artifacts of low-specificity sgRNAs. Together, we provide an accessible data resource, predesigned sgRNAs targeting 3,275,697 ENCODE SCREEN candidate CREs, and screening guidelines to accelerate functional characterization of the non-coding genome.
Inflammatory Synovial Fibroblast Culture in 3D Systems: A Comparative Transcriptomic and Functional Study
Authors: Khan Aneesah , Dobre Oana , Wang Yilin , Sartyoungkul Thanutchaporn , Salmeron-Sanchez Manuel , Harnett Margaret H. , Pineda Miguel A. 
Published: December 2022

AbstractInflammation is essential for responding to infections and subsequent tissue healing. However, chronic unresolved inflammation can become a serious health problem, as exemplified in the joints during Rheumatoid Arthritis (RA). Why does inflammation persist in RA? The answer could lie with synovial fibroblasts, non-haemopoietic cells that can adopt a pathogenic phenotype that fuels disease progression for years. Critically, targeting local fibroblasts could stop joint inflammation without suppressing systemic immunity. Nevertheless, basic research findings have not been translated to new drugs, perhaps because non-physiological data can be inadvertently generated in 2D cultures. Thus, developing better in vitro platforms is an urgent need in biomedical research. In this work, we sought to understand how distinct 3D environments affect fibroblast-mediated inflammation. Arthritic synovial fibroblasts were expanded and cultured in 2D, 3D rigid scaffolds and engineered hydrogels. The results reveal that SFs are plastic and adopt inflammatory or remission-like phenotypes in response to their surroundings. This work identifies new directions to develop better models for drug testing, and even signposts candidate mechanisms by which to rewire destructive SFs.
ABorrelia burgdorferiLptD Homolog Facilitates Flipping of Surface Lipoproteins Through the Spirochetal Outer Membrane
Authors: He Huan , Pramanik Ankita S. , Swanson Selene K. , Johnson David K. , Florens Laurence , Zückert Wolfram R. 
Published: December 2022

SUMMARYBorreliaspirochetes are unique among diderm bacteria in their lack of lipopolysaccharide (LPS) in the outer membrane (OM) and their abundance of surface-exposed lipoproteins with major roles in transmission, virulence, and pathogenesis. Despite their importance, little is known about how surface lipoproteins are translocated through the periplasm and the OM. In this study, we characterizedBorrelia burgdorferiBB0838, a distant homolog of the OM LPS assembly protein LptD. Using a CRISPR interference approach, we showed that BB0838 is essential for cell growth. Upon BB0838 knockdown, sentinel surface lipoprotein OspA was retained in the inner leaflet of the OM, as determined by its inaccessibility toin situproteolysis but its presence in OM vesicles. The secretion, insertion and topology of theB. burgdorferiOM porin P66 remained unaffected. MudPIT quantitative mass spectrometry analysis of theB. burgdorferimembrane-associated proteome further confirmed the selective periplasmic retention of surface lipoproteins under BB0838 knockdown conditions. Alphafold Multimer modeling predicted aB. burgdorferiLptB2FGCAD complex spanning the periplasm. Together, this indicates that BB0838 facilitates the essential terminal step in a distinctive spirochetal lipoprotein secretion pathway that evolved in parallel to the LPS secretion pathway in gram-negative bacteria. Hence, BB0838/LptDBbrepresents an attractive target for novel antimicrobials.
Prefrontal Control of Innate Escape Behavior – A Neural Mechanism of Enhanced Posttraumatic Threat Detection
Authors: Ritter Ami , Habusha Shlomi , Edut Shahaf , Klavir Oded 
Published: December 2022

AbstractInnate defensive responses, while primarily instinctive, must also be flexible and highly adaptive to changes in risk assessment. As such, efficient innate escape behavior requires intricate processing to minimize reaction time while maximizing the success and adaptivity of the action. The superior colliculus (SC) is a subcortical sensorimotor integration center linking sensory threat information and escape. Adaptive changes in innate escape after learning could take a maladaptive turn after severe stress. Posttraumatic stress disorder (PTSD) is associated with long-term maladaptive changes after exposure to traumatic events, related to enhanced threat detection and reaction. Such long-term modifications are thought to involve the medial prefrontal cortex (mPFC), which is implicated in integrating learned emotional values into decisions that drive actions and behaviors. Here, in a series of experiments, we establish the crucial physiological role of specific mPFC neurons, exerting influence on the SC both directly and indirectly through the basal ganglia, in threat detection and reaction after adversity.
RecView: an interactive R application for viewing and locating recombination positions using pedigree data
Authors: Zhang Hongkai , Hansson Bengt 
Published: December 2022

AbstractRecombination generates new haplotypes and disconnects linked genes thereby increasing the efficiency of selection and the adaptive potential. Quantifying the recombination landscape,i.e., the recombination rate variation along chromosomes, is important for understanding how evolutionary processes such as selection and drift are acting on genes and chromosomes. Here, we presentRecView, an interactive R application, designed to view and locate recombination positions along chromosomes using whole-genome genotype data of a three-generation pedigree.RecViewvisualises the grandparent-of-origin of all informative alleles along each chromosome of the offspring in the pedigree. It also infers putative recombination positions with two algorithms, one based on change in the proportion of the alleles with specific grandparent-of-origin, and one on the degree of continuity of alleles with the same grandparent-of-origin, along the chromosome. Putative recombination positions are given in base pairs together with an estimated error based on the local density of informative alleles. We demonstrate the applicability ofRecViewusing sequencing data of one 120 Mb-large chromosome of one offspring (and its four grandparents and two parents) of a passerine bird, the great reed warbler (Acrocephalus arundinaceus). On this chromosome, we detected five recombination events, three on the paternal chromosome and two on the maternal chromosome with both algorithms. To evaluate how sensitive the analysis is for SNP density, we downsampled our data to 10% of the original dataset. In conclusion, we provide an easy-to-use and highly effective application for viewing and locating recombination positions along chromosomes in small pedigrees.RecViewand test data are available on GitHub (https://github.com/HKyleZhang/RecView.git).
Oral delivery of GLP-1R agonist by an engineered probiotic yeast strain has anti-obesity effects in mice
Authors: Hedin Karl Alex , Zhang Hongbin , Kruse Vibeke , Rees Vanessa Emily , Bäckhed Fredrik , Greiner Thomas U. , Vazquez-Uribe Ruben , Sommer Morten Otto Alexander 
Published: December 2022

AbstractObesity is rapidly increasing within the global population and is one of the leading causes of chronic diseases, including type 2 diabetes (T2D), non-alcoholic fatty liver disease, and cardiovascular diseases. Glucagon-like peptide-1 receptor (GLP-1R) agonists have emerged as promising therapeutic agents for treating T2D and obesity. However, the route of administration of the GLP-1R agonists is currently by injection or high oral dosages of the therapeutic combined with absorption enhancers. Oral delivery of GLP-1R agonists remains the preferred administration route due to convenience and high patient compliance. Thus, strategies to improve the oral delivery of this therapeutic are needed. In this study, we engineered the probiotic yeastSaccharomyces boulardiistrain to produce Exendin-4, a GLP-1R agonist, in the gastrointestinal tract to reduce the adverse effects of diet-induced obesity in male C57BL/6 mice. The biological efficiency of the secreted Exendin-4 fromS. boulardiiwas characterisedex vivoon isolated pancreatic islets, demonstrating induced insulin secretion. Furthermore,in vivocharacterisation of the engineered strain identified a synergistic effect of cold exposure and Sb-Exe4 by successfully inhibiting appetite and promoting body weight loss under cold exposure (8°C). In addition, the combination of cold and Sb-Exe4 improved the glucose and lipid homeostasis in the mice by increasing the circulating glucagon level and reducing the inflammatory marker TNF-α. Our results demonstrate thatS. boulardiican be genetically modified to secrete and deliver active therapeutic GLP-1R agonists in the gastrointestinal tract improving the metabolism of the host.
The circadian clock genebmal1is necessary for co-ordinated circatidal rhythms in the marine isopodEurydice pulchra(Leach)
Authors: Zhang Lin , Green Edward W. , Webster Simon G. , Hastings Michael H. , Wilcockson David C. , Kyriacou Charalambos P. 
Published: December 2022

SUMMARYCircadian clocks in terrestrial animals are encoded by molecular feedback loops involving the negative regulators PERIOD, TIMELESS or CRYPTOCHROME2 and positive transcription factors CLOCK and BMAL1/CYCLE. The molecular basis of circatidal (∼12.4 hour) or other lunar-mediated cycles (∼15 day, ∼29 day), widely expressed in coastal organisms, is unknown. Disrupting circadian clockworks does not appear to affect lunar-based rhythms suggesting a molecular independence of the two cycles. Nevertheless, pharmacological inhibition of casein kinase 1 (CK1) that targets PERIOD stability in mammals and flies, affects both circadian and circatidal phenotypes inEurydice pulchra (Ep), the speckled sea-louse. Here we show that these drug inhibitors of CK1 also affect the phosphorylation of EpCLK and EpBMAL1 and disrupt EpCLK-BMAL1-mediated transcription in Drosophila S2 cells, revealing a potential link between the positive circadian regulators and circatidal behaviour. We therefore performed dsRNAi knockdown of Epbmal1as well as the major negative regulator inEurydice, Epcry2. Epcry2and Epbmal1knockdown disruptedEurydice’s circadian phenotypes as expected but in addition, circatidal behaviour was also sensitive to Epbmal1knockdown. Thus threeEurydicenegative circadian regulators, EpCRY2, in addition to EpPER and EpTIM, do not appear to be required for the expression of circatidal behaviour, in contrast to the positive regulatorEpBMAL1. We suggest a neurogenetic model whereby the positive circadian regulators BMAL1-CLK are shared between circadian and circatidal mechanisms inEurydicebut circatidal rhythms require a novel, as yet unknown negative regulator.
Back to the Future- Unleashing your cytometer’s spectral potential
Authors: Hall Christopher , Ibrahim Hanan , Thompson Sam , Hobson Philip S , Crofts Jo-Anne , Nobes Peter , Lim Steven , Burpee Tony , Walker Rachael V 
Published: December 2022

AbstractWith the recent growth in spectral flow cytometry many laboratories are investing in new spectral flow cytometers in order to maximise the information gathered about every cell. This study hypothesised that traditional cytometers already within many laboratories may be used as spectral cytometers and have shown using a range of different cytometers that data acquired may be unmixed after acquisition.
The influence of N-methylation on the ansamers of an amatoxin: Gly5Sar-amanullin
Authors: Wenz Marius T. , Kosol Simone , Yao Guiyang , Süssmuth Roderich D. , Keller Bettina G. 
Published: December 2022

AbstractAmatoxins are strong inhibitors of RNA polymerase II, and cause cell death. Because of their cytotoxicity they are candidates for anti-cancer drugs, and understanding their structure-activity relationship is crucial. Amatoxins have a rigid bicyclic scaffold which consists of a cyclic octapeptide bridged by cysteine and tryptophan side chain forming a tryptathionine bridge. Here we show the influence of the N-methylation on the amatoxin scaffold by studying Gly5Sar-amanullin with MD simulations and NMR experiments. Since we have shown recently that the amatoxin scaffold allows for two isomeric forms (ansamers), we studied both isomers of Gly5Sar-amanullin. We found that both isomers of Gly5Sar-amanullin form two long-living conformations which is unusual for amatoxins, and that they are differently affected by the N-methylation. The natural Gly5Sar-amanullin forfeits the hydrogen bonds to Gly5 due to the N-methylation, which is expected from existing crystal structures for alpha-amanitin. Our results however indicate that this does not cause more flexibility due to a shift in the hydrogen bond pattern. In the unnatural isomer, we observe an interesting cis-trans-isomerisation of the backbone angles in Trp4 and Gly7, which is enabled by the N-methylation. We expect that our perspective on the effect of N-methylation in amatoxins could be a starting point for further SAR-studies which are urgently needed for the design of better anti-cancer agents.
Enhanced Viral Metagenomics with Lazypipe 2
Authors: Plyusnin Ilya , Vapalahti Olli , Sironen Tarja , Kant Ravi , Smura Teemu 
Published: December 2022

ABSTRACTViruses are the main agents causing emerging and re-emerging infectious diseases. It is therefore important to screen for and detect them and uncover the evolutionary processes that support their ability to jump species boundaries and establish themselves in new hosts. Metagenomic next-generation sequencing (mNGS) is a high-throughput, impartial technology that has enabled virologists to detect either known or novel, divergent viruses from clinical, animal, wildlife and environmental samples, with little a priori assumptions. mNGS is heavily dependent on bioinformatic analysis, with an emerging demand for integrated bioinformatic workflows. Here, we present Lazypipe2, an updated mNGS pipeline with, as compared to Lazypipe1, significant improvements in code stability, transparency, with added functionality and support for new software components. We also present extensive benchmarking results, including evaluation on a novel canine simulated metagenome, and precision and recall of virus detection at varying sequencing depth and low to extremely low proportion of viral genetic material. Additionally we report accuracy of virus detection with two strategies: homology searches using nucleotide or amino acid sequences. We show that Lazypipe2 with nucleotide-based annotation approaches near perfect detection of eukaryotic viruses and, in terms of accuracy, outperforms the compared pipelines. We also discuss the importance of homology searches with amino acid sequences for the detection of highly divergent novel viruses.