bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ureter single-cell and spatial mapping reveal cell types, architecture, and signaling networks
Authors: Fink Emily E. , Sona Surbhi , Tran Uyen , Desprez Pierre-Emmanuel , Bradley Matthew , Qiu Hong , Eltemamy Mohamed , Wee Alvin , Wolkov Madison , Nicolas Marlo , Min Booki , Haber Georges-Pascal , Wessely Oliver , Lee Byron H. , Ting Angela H. 
Published: December 2021

SummaryTissue engineering offers a promising treatment strategy for ureteral strictures, but its success requires an in-depth understanding of the architecture, cellular heterogeneity, and signaling pathways underlying tissue regeneration. Here we define and spatially map cell populations within the human ureter using single-cell RNA sequencing, spatial gene expression, and immunofluorescence approaches. We focused on the stromal and urothelial cell populations to enumerate distinct cell types composing the human ureter and inferred potential cell-cell communication networks underpinning the bi-directional crosstalk between these compartments. Furthermore, we analyzed and experimentally validated the importance of Sonic Hedgehog (SHH) signaling pathway in adult stem cell maintenance. The SHH-expressing basal cells supported organoid generation in vitro and accurately predicted the differentiation trajectory from basal stem cells to terminally differentiated umbrella cells. Our results highlight essential processes involved in adult ureter tissue homeostasis and provide a blueprint for guiding ureter tissue engineering.
The human RNA polymerase I structure reveals an HMG-like transcription factor docking domain specific to metazoans
Authors: Daiß Julia L. , Pilsl Michael , Straub Kristina , Bleckmann Andrea , Höcherl Mona , Heiss Florian B. , Abascal-Palacios Guillermo , Ramsay Ewan , Tlučková Katarina , Mars Jean-Clement , Bruckmann Astrid , Bernecky Carrie , Lamour Valérie , Panov Konstantin , Vannini Alessandro , Moss Tom , Engel Christoph 
Published: December 2021

AbstractTranscription of the ribosomal RNA precursor by RNA polymerase (Pol) I is a major determinant of cellular growth and dysregulation is observed in many cancer types. Here, we present the purification of human Pol I from cells carrying a genomic GFP-fusion on the largest subunit allowing the structural and functional analysis of the enzyme across species. In contrast to yeast, human Pol I carries a single-subunit stalk and in vitro transcription indicates a reduced proofreading activity. Determination of the human Pol I cryo-EM reconstruction in a close-to-native state rationalizes the effects of disease-associated mutations and uncovers an additional domain that is built into the sequence of Pol I subunit RPA1. This ‘dock II’ domain resembles a truncated HMG-box incapable of DNA-binding which may serve as a downstream-transcription factor binding platform in metazoans. Biochemical analysis and ChIP data indicate that Topoisomerase 2a can be recruited to Pol I via the domain and cooperates with the HMG-box domain containing factor UBF. These adaptations of the metazoan Pol I transcription system may allow efficient release of positive DNA supercoils accumulating downstream of the transcription bubble.
Heterogeneity and genomic loci of ubiquitous Cre reporter transgenes in zebrafish
Authors: Lalonde Robert L. , Kemmler Cassie L. , Riemslagh Fréderike W. , Aman Andrew J. , Kresoja-Rakic Jelena , Moran Hannah R. , Nieuwenhuize Susan , Parichy David M. , Burger Alexa , Mosimann Christian 
Published: December 2021

AbstractThe most-common strategy for zebrafish Cre/lox-mediated lineage labeling experiments combines ubiquitously expressed,lox-basedSwitchreporter transgenes with tissue-specific Cre or 4-OH-Tamoxifen-inducible CreERT2 driver lines. Although numerous Cre driver lines have been produced, only a few broadly expressed Switch reporters exist in zebrafish and their generation by random transgene integration has been challenging due to position-effect sensitivity of thelox-flanked recombination cassettes. Here, we compare commonly usedSwitchreporter lines for their recombination efficiency and reporter expression pattern during zebrafish development. Using different experimental setups, we show thatubi:Switchandhsp70l:Switchoutperform current generations of two additionalSwitchreporters due to favorable transgene integration sites. Our comparisons also document preferential Cre-dependent recombination ofubi:Switchandhsp70l:Switchin distinct zebrafish tissues at early developmental stages. To investigate what genomic features may influence Cre accessibility andloxrecombination efficiency in highly functionalSwitchlines, we mapped these transgenes and charted chromatin dynamics at their integration sites. Our data documents the heterogeneity amonglox-basedSwitchtransgenes towards informing suitable transgene selection for lineage labeling experiments. Our work further proposes thatubi:Switchandhsp70l:Switchdefine genomic integration sites suitable for universal transgene or switch reporter knock-in in zebrafish.
A dual-purpose real-time indicator and transcriptional integrator for calcium detection in living cells
Authors: Erdenee Elbegduuren , Ting Alice Y. 
Published: December 2021

AbstractCalcium is a ubiquitous second messenger in eukaryotes, correlated with neuronal activity and T-cell activation among other processes. Real-time calcium indicators such as GCaMP have recently been complemented by newer calcium integrators that convert transient calcium activity into stable gene expression. Here we introduce LuCID, a dual-purpose real-time calcium indicator and transcriptional calcium integrator that combines the benefits of both calcium detection technologies. We show that the calcium-dependent split luciferase component of LuCID provides real-time bioluminescence readout of calcium dynamics in cells, while the GI/FKF1 split GAL4 component of LuCID converts calcium-generated bioluminescence into stable gene expression. We also show that LuCID’s modular design enables it to also read out other cellular events such as protein-protein interactions. LuCID adds to the arsenal of tools for studying cells and cell populations that utilize calcium for signaling.
An analytical solution simulating growth of Lewy bodies
Authors: Kuznetsov Ivan A. , Kuznetsov Andrey V. 
Published: December 2021

AbstractThis paper reports a minimal model simulating the growth of a Lewy body (LB). To the best of our knowledge, this is the first model simulating Lewy body growth. The LB is assumed to consist of a central spherical core, which is composed of membrane fragments and various dysfunctional intracellular organelles, and a halo, which is composed of alpha-synuclein fibrils. Membrane fragments and alpha-synuclein monomers are assumed to be produced in the soma at constant rates. The growth of the core and the halo are simulated by the Finke-Watzky model. Analytical (closed-form) solutions describing the growth of the core and the halo are obtained. A sensitivity analysis in terms of model parameters is performed.
A Lattice Model on the Rate of DNA Hybridization
Authors: Murugan R. 
Published: December 2021

ABSTRACTWe develop a lattice model on the rate of hybridization of the complementary single-stranded DNAs (c-ssDNAs). Upon translational diffusion mediated collisions, c-ssDNAs interpenetrate each other to form correct (cc), incorrect (icc) and trap-correct contacts (tcc) inside the reaction volume. Correct contacts are those with exact registry matches which leads to nucleation and zipping. Incorrect contacts are the mismatch contacts which are less stable compared to tcc which can occur in the repetitive c-ssDNAs. Although tcc possess registry match within the repeating sequences, they are incorrect contacts in the view of the whole c-ssDNAs. The nucleation rate (kN) is directly proportional to the collision rate and the average number of correct-contacts (<ncc>) formed when both the c-ssDNAs interpenetrate each other. Detailed lattice model simulations suggest that 〈ncc〉 ∝L/VwhereLis the length of c-ssDNAs andVis the reaction volume. Further numerical analysis revealed the scaling for the average radius of gyration of c-ssDNAs (Rg) with their length as. Since the reaction space will be approximately a sphere with radius equals to 2RgandV∝L3/2, one obtains. When c-ssDNAs are nonrepetitive, then the overall renaturation rate becomes askR∝kNLand one finally obtainsin line with the experimental observations. When c-ssDNAs are repetitive with a complexity ofc, then earlier models suggested the scalingwhich breaks down atc=L. This clearly suggested the existence of at least two different pathways of renaturation in case of repetitive c-ssDNAs viz. via incorrect contacts and trap correct contacts. The trap correct contacts can lead to the formation of partial duplexes which can keep the complementary strands in the close vicinity for a prolonged timescale. This is essential for the extended 1D slithering, inchworm movements and internal displacement mechanisms which can accelerate the searching for the correct contacts. Clearly, the extent of slithering dynamics will be inversely proportional to the complexity. When the complexity is close to the length of c-ssDNAs, then the pathway via incorrect contacts will dominate. When the complexity is much lesser than the length of c-ssDNA, then pathway via trap correct contacts would be the dominating one.PACS87.10.-e; 87.14.gk; 82.39.Pj; 87.15.R-
External validation of six clinical models for prediction of unknown chronic kidney disease in a German population
Authors: Stolpe Susanne , Kowall Bernd , Zwanziger Denise , Frank Mirjam , Jöckel Karl-Heinz , Erbel Raimund , Stang Andreas 
Published: December 2021

AbstractBackgroundChronic kidney disease (CKD) is responsible for large personal health and societal burdens. Screening populations at higher risk for CKD is effective to initiate earlier treatment and decelerate disease progress. We externally validated clinical prediction models for unknown CKD that might be used in population screening.MethodsWe validated six risk models for prediction of unknown CKD using only non-invasive parameters. Validation data came from 4,185 participants of the German Heinz-Nixdorf-Recall study (HNR), drawn in 2000 from a general population aged 45-75 years. We estimated discrimination and calibration using the full model information, and calculated the diagnostic properties applying the published scoring algorithms of the models using various thresholds for the sum of scores.ResultsThe risk models used four to nine parameters. Age and hypertension were included in all models. Five out of six c-values ranged from 0.71 to 0.73, indicating fair discrimination. Positive predictive values ranged from 15% to 19%, negative predictive values were >93% using score thresholds that resulted in values for sensitivity and specificity above 60%.ConclusionsMost of the selected CKD prediction models show fair discrimination in a German general population. The estimated diagnostic properties indicate that the models are suitable for identifying persons at higher risk for unknown CKD without invasive procedures.
Infant malnutrition in low- and middle-income countries: assessment and prevalence of small and nutritionally at-risk infants aged under 6 months in 54 Demographic & Health Survey datasets
Authors: Kerac Marko , James Philip T , McGrath Marie G , Brennan Eilise , Opondo Charles , Frison Severine 
Published: December 2021

ABSTRACTBackgroundThere is increasing global focus on malnutrition in infants aged under 6 months (u6m) but evidence on how best to identify and manage at-risk individuals is sparse. Our objectives were to: explore data quality of commonly used anthropometric indicators; describe prevalence and disease burden of infant u6m malnutrition; compare wasting and underweight as measures of malnutrition by determining the strength and consistency of associations with biologically plausible risk factors.MethodsWe performed a cross-sectional secondary analysis of Demographic and Health Survey (DHS) datasets, focussing on infants u6m. We calculated underweight (low weight-for-age), wasting (low weight-for-length), stunting (low length-for-age), and concurrent wasting and stunting. We explored data quality by recording extreme (flagged, as per standard criteria) or missing values. We calculated the population-weighted prevalence of each type of malnutrition and extrapolated the burden to all low- and middle-income countries (LMICs). We explored associations between infant, maternal and household risk factors with underweight and wasting using logistic regression models.ResultsWe analysed 54 DHS surveys. Data quality in terms of refusals and missingness was similar for both weight and length. There were more extreme (flagged) values for length-based measures (6.1% flagged for weight-for-length, 4.8% for length-for-age) than for weight-for-age (1.0% flagged). Overall, 20.1% of infants (95% CI: 19.5, 20.7) were underweight, 21.3% (95% CI: 20.7, 22.3) were wasted, 17.6% (95% CI: 17.0, 18.2) were stunted, and 2.0% (95% CI: 1.8, 2.2) were concurrently wasted and stunted. This corresponds to an estimated burden in LMICs of 23.8m underweight infants, 24.5m wasted infants, 21.5m stunted infants and 2.2m concurrently wasted and stunted. Logistic regression models showed that numerous risk factors were associated with wasting and underweight. Effect sizes of risk factors tended to be stronger and more consistently associated with underweight compared to wasting.ConclusionMalnutrition in infants u6m is a major problem in LMICs. This is true whether assessed by underweight, wasting or stunting. Our data build on other evidence suggesting that underweight may be a better anthropometric case definition than wasting: data quality is better when length is not involved; biologically plausible risk factors are better reflected by an infant being underweight. Future research, ideally from intervention trials, should further explore how best to identify malnourished (small and nutritionally at-risk) infants u6m. For now, treatment programmes should note that many factors might underlie problems in this age group: services should thus consider how to address maternal health and wider social circumstances as well as caring for infants themselves.
Optimizing a High Performing Multiplex-CRISPRi P. putida Strain with Integrated Metabolomics and 13C-Metabolic Flux Analyses
Authors: Czajka Jeffrey J. , Banerjee Deepanwita , Eng Thomas , Menasalvas Javier , Yan Chunsheng , Munoz Nathalie Munoz , Poirier Brenton C. , Kim Young-Mo , Baker Scott E. , Tang Yinjie J. , Mukhopadhyay Aindrila 
Published: December 2021

AbstractMicrobial cell factory development often faces bottlenecks after initial rounds of design-build-test-learn (DBTL) cycles as engineered producers respond unpredictably to further genetic modifications. Thus, deciphering metabolic flux and correcting bottlenecks are key components of DBTL cycles. Here, a 14-gene edited Pseudomonas putida KT2440 strain for heterologous indigoidine production was examined using both 13C–metabolic flux analysis (13C–MFA) and metabolite measurements. The results indicated the conservation of the cyclic Entner-Doudoroff (ED)-EMP pathway flux, downregulation of the TCA cycle and pyruvate shunt, and glyoxylate shunt activation. At the metabolite level, the CRISPR/dCpf1-interference mediated multiplex repression decreased gluconate/2-ketogluconate secretion and altered several intracellular TCA metabolite concentrations, leading to succinate overflow. Further strain engineering based on the metabolic knowledge first employed an optimal ribosome binding site (RBS) to achieve stronger product-substrate growth coupling (1.6–fold increase). Then, deletion strains were constructed using ssDNA recombineering. Of the five strains tested, deletion of the PHA operon (ΔphaAZC-IID) resulted in a 2.2–fold increase in growth phase production compared to the optimal RBS construct. After 72 h of batch cultivation, the ΔphaAZC-IID strain had 1.5–fold and 1.8–fold increases of indigoidine titer compared to the improved RBS construct and the original strain, respectively. Overall, the findings provided actionable DBTL targets as well as insights into physiological responses and flux buffering when new recombineering tools were used for engineering P. putida KT2440.
Limited, but potentially functional translation of non-coding transcripts in the HEK293T cellular cytosol
Authors: Bogaert Annelies , Fijalkowska Daria , Staes An , Van de Steene Tessa , Demol Hans , Gevaert Kris 
Published: December 2021

AbstractRibosome profiling has revealed translation outside of canonical coding sequences (CDSs) including translation of short upstream ORFs, long non-coding RNAs, overlapping ORFs, ORFs in UTRs or ORFs in alternative reading frames. Studies combining mass spectrometry, ribosome profiling and CRISPR-based screens showed that hundreds of ORFs derived from non-coding transcripts produce (micro)proteins, while other studies failed to find evidence for such types of non-canonical translation products. Here, we attempted to discover translation products from non-coding regions by strongly reducing the complexity of the sample prior to mass spectrometric analysis. We used an extended database as the search space and applied stringent filtering of the identified peptides to find evidence for novel translation events. Theoretically, we show that our strategy facilitates the detection of translation events of transcripts from non-coding regions, but experimentally only find 19 peptides (less than 1% of all identified peptides) that might originate from such translation events. Virotrap based interactome analysis of two N-terminal proteoforms originating from non-coding regions finally showed the functional potential of these novel proteins.
Baltica: integrated splice junction usage analysis
Authors: Britto-Borges Thiago , Boehm Volker , Gehring Niels H. , Dieterich Christoph 
Published: December 2021

AbstractAlternative splicing is a tightly regulated co- and post-transcriptional process contributing to the transcriptome diversity observed in eukaryotes. Several methods for detecting differential junction usage (DJU) from RNA sequencing (RNA-seq) datasets exist. Yet, efforts to integrate the results from DJU methods are lacking. Here, we present Baltica, a framework that provides workflows for quality control, de novo transcriptome assembly with StringTie2, and currently 4 DJU methods: rMATS, JunctionSeq, Majiq, and LeafCutter. Baltica puts the results from different DJU methods into context by integrating the results at the junction level. We present Baltica using 2 datasets, one containing known artificial transcripts (SIRVs) and the second dataset of paired Illumina and Oxford Nanopore Technologies RNA-seq. The data integration allows the user to compare the performance of the tools and reveals that JunctionSeq outperforms the other methods, in terms of F1 score, for both datasets. Finally, we demonstrate for the first time that meta-classifiers trained on scores of multiple methods outperform classifiers trained on scores of a single method, emphasizing the application of our data integration approach for differential splicing identification. Baltica is available at https://github.com/dieterich-lab/Baltica under MIT license.
Direct RNA sequencing of Respiratory Syncytial Virus infected human cells generates a detailed overview of RSV polycistronic mRNA and transcript abundance
Authors: Donovan-Banfield I’ah , Hall Sophie , Gao Tianyi , Murphy Eleanor , Li Jack , Shawli Ghada T. , Hiscox Julian , Fearns Rachel , Matthews David A. 
Published: December 2021

AbstractTo characterize species of viral mRNA transcripts generated during respiratory syncytial virus (RSV) infection, human fibroblast-like MRC5 lung cells were infected with subgroup A RSV for 6, 16 and 24 hours. Total RNA was harvested and polyadenylated mRNA was enriched and sequenced by direct RNA sequencing on an Oxford nanopore device. This yielded over 150,000 direct mRNA transcript reads which were mapped to the viral genome and analysed to determine relative mRNA levels of viral genes using our in-house ORF-centric pipeline. We were also able to examine frequencies with which polycistronic readthrough mRNAs were generated and to assess the length of the polyadenylated tails for each group of transcripts. We show that there is a general but non-linear decline in gene transcript abundance across the viral genome, as predicted by the model of RSV gene transcription. However, the decline in transcript abundance is not consistent. We show that the polyadenylate tails generated by the viral polymerase are similar in length to those generated by the host cells polyadenylation machinery and broadly declined in length for most transcripts as infection progressed. Finally, we observed that the steady state abundance of transcripts with very short polyadenylate tails is much less for N, SH and G transcripts compared to NS1, NS2, P, M, F and M2 which may reflect differences in mRNA stability and/or translation rates.
Seafood festivals for local development in Italy and Sweden
Authors: Pizzichini Lucia , Andersson Tommy D. , Gregori Gian Luca 
Published: December 2021

PurposeThe paper focusses on festivals taking place in coastal regions whose central element is seafood. The purpose is to analyse the role of seafood festivals as potential tourist attractions for local development. The decision to focus on coastal areas is based on a perceived knowledge gap regarding the interactions between different sectors of the sea economy.Design/methodology/approachQualitative exploratory case studies of seafood festivals in Italy and Sweden have been performed using an analytical model. The participatory observation methodology contributed to a better understanding of the phenomenon.FindingsThe analysis shows the close relationship between seafood and tourism, and although it takes variable forms, food is a fundamental lever for maritime and coastal tourism and local development. Findings suggest that local food events can help strengthening gastronomic identities, despite there is a different articulation between tradition and marketing in the two countries.Research limitations/implicationsSince this paper represents an exploratory study of five seafood festivals, research needs to be extended and replicated before any findings can be generalized. However, the model is flexible enough to be tested in different food events.Practical implicationsFood events represent a key instrument for the integration of territorial policies in which tourism and food products might be used as strategic instruments for the development of coastal areas.Originality/valueThis paper is a first attempt to analyse and compare seafood events, contributing to filling the gap in event literature referring to coastal areas. The model introduced can be used to determine the articulation of tradition-marketing in different food events.