bluuebunny/crossref_metadata_2025_split huggingface dataset:
The baseline immunological and hygienic status of pigs impact disease severity of African swine fever
Authors: Radulovic Emilia , Mehinagic Kemal , Wüthrich Tsering , Hilty Markus , Posthaus Horst , Summerfield Artur , Ruggli Nicolas , Benarafa Charaf 
Published: April 2022

AbstractAfrican Swine Fever virus (ASFV) is a large double-enveloped DNA virus of the Asfarviridae family that causes a lethal hemorrhagic disease in domestic pigs and wild boars. Since 2007, a highly virulent genotype II strain has emerged and spread in Europe and South-East Asia, where millions of animals succumbed to the disease. Field- and laboratory-attenuated strains of ASFV cause highly variable clinical disease severity and survival, and mechanisms remain unclear. We hypothesized that the immunological and hygienic status of pigs is a determinant of ASF disease course. Here we compared the immunological profile at baseline and in response to ASFV infection in specific pathogen-free (SPF) and farm-raised Large White domestic pigs. At steady state, SPF pigs showed lower white blood cell counts and a lower basal inflammatory and antiviral transcriptomic profile compared to farm pigs associated with profound differences in gut microbiome composition. After inoculation with a highly virulent ASFV genotype II strain (Armenia 2008), severe clinical signs, viremia and pro-inflammatory cytokines appeared sooner in SPF pigs, indicating a reduced capacity to control early virus replication. In contrast, during infection with an attenuated field isolate (Estonia 2014), SPF pigs presented a milder and shorter clinical disease with full recovery, whereas farm pigs presented severe protracted disease with 50% lethality. Interestingly, farm pigs showed higher production of inflammatory cytokines, whereas SPF pigs produced more anti-inflammatory IL-1ra early after infection, and presented a stronger expansion of leukocytes in the recovery phase. Altogether, our data indicate that the hygiene-dependent innate immune status has a double-edge sword impact on immune responses in ASF pathogenesis. While the higher baseline innate immune activity helps the host in reducing initial virus replication, it promotes immunopathological cytokine responses, and delays lymphocyte proliferation after infection with an attenuated strain. Such effects should be considered for live vaccine development and vigilance.
Bleaching-resistant, near-continuous single-molecule fluorescence and FRET based on fluorogenic and transient DNA binding
Authors: Kümmerlin Mirjam , Mazumder Abhishek , Kapanidis Achillefs N. 
Published: April 2022

AbstractPhotobleaching of fluorescent probes limits the observation span of typical single-molecule fluorescence measurements and hinders observation of dynamics at long timescales. Here, we present a general strategy to circumvent photobleaching by replenishing fluorescent probes via transient binding of fluorogenic DNAs to complementary DNA strands attached to a target molecule. Our strategy allows observation of near-continuous single-molecule fluorescence for more than an hour, a timescale two orders of magnitude longer than the typical photobleaching time of single fluorophores under our conditions. Using two orthogonal sequences, we show that our method is adaptable to Förster Resonance Energy Transfer (FRET) and that can be used to study the conformational dynamics of dynamic structures, such as DNA Holliday junctions, for extended periods. By adjusting the temporal resolution and observation span, our approach should enable capturing the conformational dynamics of proteins and nucleic acids over a wide range of timescales.
scAEGAN: Unification of Single-Cell Genomics Data by Adversarial Learning of Latent Space Correspondences
Authors: Khan Sumeer Ahmad , Lehmann Robert , Martinez-de-Morentin Xabier , Ruiz Albert Malillo , Lagani Vincenzo , Kiani Narsis A. , Gomez-Cabrero David , Tegner Jesper 
Published: April 2022

ABSTRACTRecent progress in Single-Cell Genomics have produced different library protocols and techniques for profiling of one or more data modalities in individual cells. Machine learning methods have separately addressed specific integration challenges (libraries, samples, paired-unpaired data modalities). We formulate an unifying data-driven methodology addressing all these challenges. To this end, we design a hybrid architecture using an autoencoder (AE) network together with adversarial learning by a cycleGAN (cGAN) network, jointly referred to as scAEGAN. The AE learns a low-dimensional embedding of each condition, whereas the cGAN learns a non-linear mapping between the AE representations. The core insight is that the AE respects each sample’s uniqueness, whereas the cGAN exploits the distributional data similarity in the latent space. We evaluate scAEGAN using simulated data and real datasets of a single-modality (scRNA-seq), different library preparations (Fluidigm C1, CelSeq, CelSeq2, SmartSeq), and several data modalities such as paired scRNA-seq and scATAC-seq. We find that scAEGAN outperforms Seurat3 in library integration, is more robust against data sparsity, and beats Seurat 4 in integrating paired data from the same cell. Furthermore, in predicting one data modality from another, scAEGAN outperforms Babel. We conclude scAEGAN surpasses current state-of-the-art methods across several seemingly different integration challenges.
More than just hitchhikers: a survey of bacterial communities associated with diatoms originating from marine reptiles
Authors: Filek Klara , Lebbe Liesbeth , Willems Anne , Chaerle Peter , Vyverman Wim , Žižek Marta , Bosak Sunčica 
Published: April 2022

AbstractDiatoms and bacteria are known for being the first colonizers of submerged surfaces including the skin of marine reptiles. Sea turtle carapace and skin harbour diverse prokaryotic and eukaryotic microbial taxa, including several epizoic diatoms. However, the importance of diatom-bacteria associations is hardly investigated in biofilms associated with animal hosts. This study provides a detailed inventory of diatoms, bacteria, and diatom-associated bacteria originating from several loggerhead sea turtles using a combination of metabarcoding and culturing approaches. Carapace and skin samples rbcL and 16S rRNA amplicon sequencing showed a high diversity of diatoms and bacteria, respectively. Cultures of putative epizoic and non-epizoic diatom strains contained from 18 to 101 bacterial amplicon sequence variants (ASVs) and their bacterial assemblages strongly reflected those of their source host. Diatom strains allowed for enrichment and isolation of rare-in-source bacterial families such as Marinobacteraceae, Alteromonadaceae, and Alcanivoracaceae. When accounting for phylogenetic relationships between bacterial ASVs, we observed related diatom genera might retain related microbial taxa in culture, regardless of the source environment. These data provide deeper insights into several levels of sea turtle epizoic diatom and bacterial communities, and reveal the potential of epizoic biofilms as a source of novel microbes and possibly important diatom-bacteria associations.
Structural Basis of MicroRNA Biogenesis by Dicer-1 and Its Partner Protein Loqs-PB
Authors: Jouravleva Karina , Golovenko Dmitrij , Demo Gabriel , Dutcher Robert C. , Tanaka Hall Traci M. , Zamore Phillip D. , Korostelev Andrei A. 
Published: April 2022

SUMMARYIn animals and plants, Dicer enzymes collaborate with double-stranded RNA-binding proteins to convert precursor-microRNAs (pre-miRNAs) into miRNA duplexes. We report six cryo-EM structures of Drosophila Dicer-1 and its partner Loqs-PB. The structures show Dicer-1•Loqs-PB (1) before binding pre-miRNA, (2) after binding and in a catalytically competent state, (3) after nicking one arm of the pre-miRNA, (4) following complete dicing and initial product release. Our reconstructions suggest that pre-miRNA binds a rare, open conformation of the Dicer-1•Loqs-PB heterodimer, enabling conformational proofreading. The Dicer-1 dsRBD and three Loqs-PB dsRBD domains form a tight belt around the pre-miRNA, distorting the RNA helix to place the scissile phosphodiester bonds in the RNase III active sites. Pre-mRNA cleavage shifts the RNA- binding domains and tightens Dicer-1, promoting product release. Our data suggest a model for how the Dicer-1•Loqs-PB complex effects a complete cycle of pre-miRNA recognition, stepwise endonuclease cleavage, and sequential product release.
Canal number and configuration are predictors of external root morphology
Authors: Gellis Jason J. 
Published: April 2022

AbstractWithin tooth roots canals can vary in shape and configuration, and it is not uncommon for a single root to contain multiple canals. Externally, root morphology also varies, though the range of variation, and its relation to canals remains little explored. This investigation of modern human post-canine teeth uses data from computerized tomography scans of a global sample of 945 modern humans to identify the most frequent phenotypes of root and canal morphologies, and investigate how canal number, shape, and configuration relate to external root morphology. Results (1) include descriptions and definitions of root and canal morphologies, counts, and configurations; (2) indicate that certain canal counts, morphologies, and configurations can predict external morphologies; and (3) that this pattern varies in individual teeth and roots in the maxilla and mandible.
The transcriptional regulator Sin3A balances IL-17A and Foxp3 expression in primary CD4 T cells
Authors: Perucho Laura , Icardi Laura , Di Simone Elisabetta , Basso Veronica , Zornoza Amaia Vilas , Lozano Teresa , Prosper Felipe , Lasarte Juan José , Mondino Anna 
Published: April 2022

AbstractThe Sin3 transcriptional regulator homolog A (Sin3A) is the core member of a multi-protein chromatin-modifying complex known to control gene transcription via epigenetic mechanisms. Its inactivation in developing thymocytes halts T cell maturation. We and others had previously shown that Sin3A controls STAT3 transcriptional activity. Given the role of STAT3 in the differentiation of T helper 17 cells critical in inflammatory disorders and against opportunistic infections, we asked whether Sin3A could also contribute to their differentiation. To this aim, we exploited CD4-Cre and CD4-CreERT2deleter strains for conditional and inducible Sin3A deletion in CD4 cell subsets. We report that Sin3A inactivation in vivo arrested thymocyte development at the double positive stage, hindering the characterization of mature T cells. At difference, tamoxifen-inducible Sin3A deletion proved permissive for in vitro proliferation of T cells in Th17 skewing conditions and the acquisition of memory markers. Transcriptional profiling indicated that while Sin3A inactivation imprinted T cells with a mTORC1 signaling gene signature, Sin3A deficient cells lacked the expression of IL-17A, the signature Th17 cytokine. This reflected a defective induction of Il17a, and also of the Il23R and Il22 genes, which occurred in spite of proper upregulation of the lineage defining transcription factor RORγt. We found that Sin3A inactivation was paralleled by increased STAT3 phosphorylation and nuclear representation, and by higher fractions of IL-2 and FoxP3 expressing cells. Such events proved causally linked as inhibiting Foxp3 partially rescued IL-17A expression, and neutralizing IL-2 simultaneously lowered the representation of FoxP3+cells, while rescuing IL- 17A+ ones. Thus, together our data underline a previously unappreciated role for Sin3A in Th17 differentiation and the shaping of their immunoregulatory potential.StatementThis study identifies a new role for the transcriptional regulator Sin3A in the shaping of Th17 cell differentiation. Data indicate that by controlling IL-2 expression, and mTORC1 signaling, it balances IL-17A and Foxp3 levels, shaping Th17 inflammatory potentials.
A motor-based approach to induce chromosome-specific mis-segregations in human cells
Authors: Truong My Anh , Cané-Gasull Paula , de Vries Sippe G. , Nijenhuis Wilco , Wardenaar René , Kapitein Lukas C. , Foijer Floris , Lens Susanne M.A. 
Published: April 2022

AbstractVarious cancer types exhibit highly characteristic and recurrent aneuploidy patterns. The origin of these cancer type-specific karyotypes, and the extent to which they contribute to cancer progression, remains to be elucidated, partly because introducing or eliminating specific chromosomes in human cells still poses a challenge. Here, we describe a novel strategy to mis-segregate specific chromosomes at will in different human cell types. We employed Tet repressor (TetR) or nuclease dead Cas9 (dCas9) to link a plant-derived microtubule minus-end-directed kinesin (Physcomitrella patens Kinesin14VIb) to integrated Tet operon repeats and chromosome-specific endogenous repeats, respectively. By live- and fixed-cell imaging, we observed poleward movement of the targeted loci during (pro)metaphase. Kinesin14VIb-mediated pulling forces on the targeted chromosome were often counteracted by forces from kinetochore-attached microtubules. This tug of war resulted in chromosome-specific segregation errors during anaphase, and revealed that spindle forces can heavily stretch chromosomal arms. Using chromosome-specific FISH and single-cell whole genome sequencing, we established that motor-induced mis-segregations result in specific arm-level, and to a lesser extent, whole chromosome aneuploidies, after a single cell division. Our kinesin-based strategy to manipulate individual mitotic chromosomes opens up the possibility to investigate the immediate cellular responses to specific (arm level) aneuploidies in different cell types; an important step towards understanding how recurrent aneuploidy patterns arise in different cancer types.
High resolution shotgun metagenomics: the more data, the better?
Authors: Tremblay Julien , Schreiber Lars , Greer Charles W 
Published: April 2022

AbstractIn shotgun metagenomics (SM), the state of the art bioinformatic workflows are referred to as high resolution shotgun metagenomics (HRSM) and require intensive computing and disk storage resources. While the increase in data output of the latest iteration of high throughput DNA sequencing systems can allow for unprecedented sequencing depth at a minimal cost, adjustments in HRSM workflows will be needed to properly process these ever-increasing sequence datasets. One potential adaptation is to generate so-called shallow SM datasets that contain fewer sequencing data per sample as compared to the more classic high coverage sequencing. While shallow sequencing is a promising avenue for SM data analysis, detailed benchmarks using real data are lacking. In this case study, we took four public SM datasets, one massive and the others moderate in size and subsampled each dataset at various levels to mimic shallow sequencing datasets of various sequencing depths. Our results suggest that shallow SM sequencing is a viable avenue to obtain sound results regarding microbial community structures and that high depth sequencing does not bring additional elements for ecological interpretation. More specifically, results obtained by subsampling as little as 0.5M sequencing clusters per sample were similar to the results obtained with the largest subsampled dataset for the human gut and agricultural soil datasets. For the Antarctic dataset, which contained only a few samples, 4M sequencing clusters per sample was found to generate comparable results to the full dataset. One area where ultra-deep sequencing and maximizing the usage of all data was undeniably beneficial was in the generation of metagenome-assembled genomes (MAGs).Key points–Three public multi-sample shotgun metagenomic NovaSeq datasets totalling 12,389,583 and 202 Gb, respectively were analyzed at various sequencing depths to evaluate the accuracy of shallow shotgun metagenomic sequencing using a high resolution shotgun metagenomic bioinformatic workflow. A synthetic mock community of 20 bacterial genomes was also analyzed for validation purposes.–Datasets subsampled to low sequencing depths gave nearly identical ecological patterns (taxonomic and functional composition and beta-alpha-diversity) compared to high depth subsampled datasets.–Rare taxa and functions could be uncovered with high sequencing depth vs. low sequencing depth datasets, but did not affect global ecological patterns.–High sequencing depth was positively correlated with both quantity and quality of recovered metagenome-assembled genomes.
Tissue Specific Knockout of the Cardiolipin Transacylase Enzyme TAFAZZIN in Both Liver and Pancreatic Beta Cells Protects Mice From Diet-Induced Obesity
Authors: Cole Laura K. , Dolinsky Vernon W. , Hatch Grant M. 
Published: April 2022

AbstractMutations in the TAFAZZIN gene result in the X-linked genetic disease Barth Syndrome. The protein product tafazzin is a transacylase enzyme that remodels the phospholipid cardiolipin with fatty acids. Some Barth syndrome boys exhibit a lean phenotype. In addition, whole body knockdown of tafazzin in mice protects them from diet-induced obesity through increased hepatic fatty acid oxidation and reduced basal insulin secretion. We thus hypothesized that tafazzin deficiency in both the liver and beta cells of the pancreas contribute to this lean phenotype. Through a Cre-Lox approach we generated control, liver-specific, pancreatic beta cell-specific and liver and pancreatic beta cell-specific double knockout male mice. The animals were fed a high fat diet for 8 weeks and body weight, liver weight and fat pad weights determined. Liver-specific or pancreatic beta cell-specific male tafazzin knockout mice accumulated weight gain (≍40% increase in body weight) at the same rate as control animals. In contrast, the liver- and beta cell-specific double tafazzin knockout mice exhibited a reduced rate of weight gain by 8 weeks (≍26% increase in body weight) compared to control or the single tafazzin knockout animals. In addition, at 8 weeks the double tafazzin knockout mice exhibited reduced weight gain in tissues known to accumulate fat including the liver, the gonadal, inguinal and perirenal white adipose tissues and the brown adipose tissue. Thus, liver- and pancreatic beta cell-specific double tafazzin knockout male mice are protected from high fat diet induced weight gain and fat accumulation. These results may partially explain why some Barth Syndrome boys exhibit a lean phenotype.
Intention versus behaviour: integration of theories to help curb food waste among young Spanish consumers
Authors: Fraj-Andrés Elena , Herrando Carolina , Lucia-Palacios Laura , Pérez-López Raúl 
Published: April 2022

PurposeThis study aims to find the most relevant variables for understanding the gap between intention and behaviour in relation to food waste reduction among young consumers, providing a theoretical framework that reveals what theories can explain this gap.Design/methodology/approachA qualitative analysis based on two focus groups with participants aged 18–35 was developed to examine young consumers' intention–behaviour gap.FindingsThe results suggest that a combination of variables from different theories (the theory of planned behaviour, social practice theory and value-belief-norm theory) can better explain the gap, and that other variables such as emotions, price consciousness and situational factors should also be taken into consideration. The authors also find that although some situational variables tend to reduce the gap, some specific situations do the opposite.Originality/valueThe results offer a conceptual model that combines variables from diverse theoretical streams with the aim of understanding food waste among young consumers holistically, and identify new variables that had not been considered by previous research.
Convergence and compliance of corporate governance codes: a study of 11 Asian emerging economies
Authors: Tariq Yasir Bin , Ejaz Amir , Bashir Malik Fahim 
Published: April 2022

Purpose
The purpose of this paper is twofold. The first is to explore the convergence of corporate governance (CG) codes of 11 Asian emerging economies with the United Nations (UN) CG guidelines (United Nations Conference on Trade and Development ISAR benchmark). The second is to find the compliance level of firms in each country with the UN CG guidelines.

Design/methodology/approach
Based on the 2017 GDP growth rate, the top 11 emerging economies were selected. CG codes of each country were then analyzed by using content analysis to find the convergence level with the UN CG guidelines. To find the compliance level of individual firms in each sample country, a sample of the top 15 non-financial listed firms were selected from each country, and their annual reports were analyzed. The binary scoring method was used.

Findings
After analyzing the 11 national CG codes, 1 UN CG guidelines and 150 annual reports, this study found that Pakistan and Philippines CG codes have the highest level of convergence toward the outsider model recommended by UN CG guidelines, whereas China and India have the lowest compliance score. The Indian, Chinese, Malaysian and Indonesian listed firms showed more compliance toward the UN CG guidelines than their respective national CG codes.

Originality/value
By analyzing the top 11 emerging economies, and top 15 listed enterprises in each country, this study offered a combined convergence and compliance evidence at two different levels, i.e. country and firm-level. This study’s findings would be equally helpful for regulators, policymakers and investors in assessing their country’s CG codes against the international recommended best practices.
Quality certifications in the TripAdvisor era. Are they outdated?
Authors: Castro-Lopez Adrian , Caso Fernández-Pacheco Laura , Iglesias Víctor , De la Ballina Javier 
Published: April 2022

PurposeThis study aims to analyzes the effects of the consumer-generated media (CGM) boom on hotel managers’ investment behavior concerning quality signals.Design/methodology/approachSurvival analysis has been conducted, considering the permanence/dropout of the Spanish hotels in a quality certification system during the 1998–2020 period.FindingsThe number of hotels certified since 2010 has been progressively falling, pointing to a decreasing interest of the managers in these certifications. Nevertheless, this is not a generalized phenomenon: the hotel characteristics and the number and nature of reviews about them in CGM significantly affect their permanence decisions in certification systems.Practical implicationsThe findings provide several keys to optimizing investment management in quality signals considering hotel characteristics and their positioning in CGM.Originality/valueTo the best of the authors’ knowledge, this is the first study that analyses the relationship between the presence of hotels in CGM and their investments in alternative quality signals. The results will allow future investment decisions based on previous real business experiences.