bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multi-group biodiversity theory and an application to multi-species maximum sustainable yield
Authors: Sadykov A. , Farnsworth K.D. , Sadykova D. 
Published: November 2022

AbstractWe introduce the group-based approach, use it to develop a multi-group biodiversity theory, and apply it find solutions to the multi-species maximum sustainable yield problem for a mixed species fishery. The group-based approach to community ecology is intermediate between classical species-centric and more recent trait-based (species-less) approaches. It describes ecological communities as composed of conspecific groups rather than species (as in classical models) or species-less individuals (as in trait-based models), and reconsiders community structure as results of inter-group resource competition. The approach respects species affiliation and recognises the importance of trait trade-offs at the conspecific group level. It offers an alternative to both classical and trait-based approaches and, remarkably, provides a complete analytical description of the community structure in the bench-mark case of zero-sum resource redistribution.HighlightsWe introduce a group-based approach to modelling of ecological communities and develop a multi-group biodiversity theory.A classification of intergroup interactions is established, based on the type of contest (which is determined by the relative role of qualitative vs. quantitative factors) and the accounting of resource redistribution.For pure resource competition, we obtain the full analytic description of multi-group and multi-species community structure and its dynamics, including the processes of fission-fusion and invasion-extinction among groups.A principle of competitive coexistence is formulated, which explains the existence of conspecific groups as a mechanism for avoiding competitive exclusion.We apply the theory to harvesting multi-species communities (e.g., for fisheries) and derive analytic expression for total catch and approximate solutions for multi-species maximum sustainable yield (MSY).
No evidence for schistosome parasite fitness trade-offs in the intermediate and definitive host
Authors: Le Clec’h Winka , Chevalier Frédéric D. , Jutzeler Kathrin , Anderson Timothy J.C. 
Published: November 2022

ABSTRACTBackgroundThe trematode parasiteSchistosoma mansoniuses an aquatic snail intermediate and a vertebrate definitive host to complete its lifecycle. We previously showed that a key transmission trait – the number of cercariae larvae shed from infectedBiomphalaria spp. snails – varies significantly within and between different parasite populations and is genetically controlled by five loci. We investigated the hypothesis that the success of parasite genotypes showing high fitness in the intermediate snail host, may be offset by lower fitness in the definitive vertebrate host.MethodsWe investigated this trade-off hypothesis by selecting parasite progeny producing high or low number of larvae in the snail, and then comparing fitness parameters and virulence in the rodent host. We infected inbred BALB/c mice using twoSchistosoma mansoniparasite lines (high shedder (HS) and low shedder (LS) lines), isolated from F2 progeny generated by genetic crosses between SmLE (HS parent) and SmBRE (LS parent) parasites. We used the F3 progeny to infect two populations of inbredBiomphalaria glabratasnails. We then compared life history traits and virulence of these two selected parasite lines in the rodent host to understand pleiotropic effects of genes determining cercarial shedding in parasites infecting the definitive host.ResultsHS parasites shed high numbers of cercariae, which had a detrimental impact on snail physiology (measured by laccase-like activity and hemoglobin rate), regardless of the snail genetic background. In contrast, selected LS parasites shed fewer cercariae and had a lower impact on snail physiology. Similarly, HS worms have a higher reproductive fitness and produced more viable F3 miracidia larvae than LS parasites. This increase in transmission is correlated with an increase in virulence toward the rodent host, characterized by stronger hepato-splenomegaly and hepatic fibrosis.ConclusionsThese experiments revealed that schistosome parasite fitness was positively correlated in intermediate and definitive host (positive pleiotropy). Therefore, we rejected our trade-off hypothesis. We also show that our selected schistosome lines exhibit low and high shedding phenotype regardless of the intermediate snail host genetic background.
Single cell profiling reveals strain-specific differences in myeloid inflammatory potential in the rat liver
Authors: Pouyabahar Delaram , Chung Sai W. , Pezzutti Olivia I. , Perciani Catia T. , Wang Xinle , Ma Xue-Zhong , Jiang Chao , Camat Damra , Chung Trevor , Sekhon Manmeet , Manuel Justin , Chen Xu-Chun , McGilvray Ian D. , MacParland Sonya A. , Bader Gary D. 
Published: November 2022

AbstractLiver transplantation is currently the only treatment for end-stage liver disease and acute liver failure. Liver transplant rejection is among the most lethal complications of transplantation, and therapeutic development is limited by our lack of a comprehensive understanding of the cellular landscape of the liver. The laboratory rat (Rattus norvegicus), ideal in size as a model for surgical procedures, is a strong platform to study liver biology in the context of liver transplantation. Liver allograft rejection is known to be strain-specific in the rat model, although the transplantation is accepted without rejection in some strains, it leads to acute rejection in others. To shed light on the cellular landscape of the rat liver and build a foundation for strain comparison, we present a comprehensive single-cell transcriptomics map of the healthy rat liver of Lewis and Dark Agouti strains. Using a novel computational pipeline we developed to guide the detailed annotation of our rat liver atlas, we discovered that hepatic myeloid cells have strong Lewis and Dark Agouti strain-specific differences focused on inflammatory signaling pathways. We experimentally validated these strain-specific differences in myeloid inflammatory potentialin vitrousing intracellular cytokine staining. Our work provides the first examination of the multi-strain healthy rat liver by single cell transcriptomics and uncovers key insights into strain-specific differences in this valuable model animal.SummaryThe laboratory rat (Rattus norvegicus) is a standard model animal for orthotopic liver transplantation. Transplanting a liver from a Dark agouti (DA) to a Lewis (LEW) strain rat leads to transplant rejection and the reverse procedure leads to tolerance. Understanding this strain difference may help explain the cellular drivers of liver allograft rejection post-transplant. This study uses single-cell transcriptomics to better understand the complex cellular composition of the rat liver and unravels cellular and molecular sources of inter-strain hepatic variation. We generated single-cell transcriptomic maps of the livers of healthy DA and LEW rat strains and developed a novel, factor analysis-based bioinformatics pipeline to study data covariates, such as strain and batch. Using this approach, we discovered variations within hepatocyte and myeloid populations that explain how the states of these cells differ between strains in the healthy rat, which may explain why these strains respond differently to liver transplants.
Colonisation debt: when invasion history impacts current range expansion
Authors: Morel-Journel Thibaut , Haond Marjorie , Dunan Lana , Mailleret Ludovic , Vercken Elodie 
Published: November 2022

AbstractDemographic processes that occur at the local level, such as positive density dependence in growth or dispersal, are known to shape population range expansion, notably by linking carrying capacity to invasion speed. As a result of these processes, the advance of an invasion front depends both on populations in the core of the invaded area and on small populations at the edge. While the impact on velocity is easily tractable in homogeneous environment, information is lacking on how speed varies in heterogeneous environment due to density dependence. In this study, we tested the existence of a ‘colonisation debt’, which corresponds to the impact of conditions previously encountered by an invasion front on its future advances. Due to positive density dependence, invasions are expected to spread respectively slower and faster, along the gradients of increasing and decreasing carrying capacity, with stronger differences as the gradient slope increases. Using simulated invasions in a one-dimensional landscape with periodically varying carrying capacity, we confirmed the existence of the colonisation debt when density-dependent growth or dispersal was included. Additional experimental invasions using a biological model known to exhibit positive density-dependent dispersal confirmed the impact of the carrying capacity of the patch behind the invasion front on its progression, the mechanism behind the colonisation debt.
The insulating activity of theDrosophilaBX-C chromatin boundaryFub-1is parasegmentally regulated by lncRNA read-through
Authors: Ibragimov Airat , Bing Xin Yang , Shidlovskii Yulii , Levine Mike , Georgiev Pavel , Schedl Paul 
Published: November 2022

ABSTRACTThough long non-coding RNAs (lncRNAs) represent a substantial fraction of the Pol II transcripts in multicellular animals, only a few have known functions. Here we report that the blocking activity of the Bithorax complex (BX-C)Fub-1boundary is segmentally regulated by its own lncRNA. TheFub-1boundary is located between theUltrabithorax(Ubx) gene and thebxd/pbxregulatory domain, which is responsible for regulatingUbxexpression in parasegment PS6/segment A1.Fub-1consists of two hypersensitive sites,HS1andHS2. HS1is an insulator whileHS2functions primarily as a lncRNA promoter. To activateUbxexpression in PS6/A1 enhancers in thebxd/pbxdomain must be able to bypassFub-1blocking activity. We show that expression of theFub-1lncRNAs in PS6/A1 from theHS2promoter inactivatesFub-1insulating activity. Inactivation is due to readthrough as theHS2promoter must be directed towardsHS1to disrupt blocking.
Formation Of Small-World Network Containing Module Networks In Globally And Locally Coupled Map System With Changes In Global Connection With Time Delay Effects
Authors: Nakanishi Taito , Awazu Akinori 
Published: November 2022

AbstractIn this study, we performed comprehensive morphological investigations of spontaneously formed network structures among elements in coupled map systems involving global connections that change depending on the synchronicity of states of elements and spatially local connections. The model formed various hierarchical networks, some of which were classified as small-world networks containing multiple module networks, similar to the neural network of mammalian brains. Moreover, such complex networks were formed in wider parameter regions when the global connection to an element from the other element was strengthened by the synchronization between the present and past states of the former and latter elements, respectively. This study suggests that the time delay effects for connection changed among elements and local interactions promoted the self-organization of small-world networks containing module networks, such as neural networks; neural networks contain them as spike-timing-dependent plasticity and inter-neuron interaction through glial cells.
Long-term COVID-19 booster effectiveness by infection history and clinical vulnerability and immune imprinting
Authors: Chemaitelly Hiam , Ayoub Houssein H. , Tang Patrick , Coyle Peter , Yassine Hadi M. , Al Thani Asmaa A. , Al-Khatib Hebah A. , Hasan Mohammad R. , Al-Kanaani Zaina , Al-Kuwari Einas , Jeremijenko Andrew , Kaleeckal Anvar Hassan , Latif Ali Nizar , Shaik Riyazuddin Mohammad , Abdul-Rahim Hanan F. , Nasrallah Gheyath K. , Al-Kuwari Mohamed Ghaith , Butt Adeel A. , Al-Romaihi Hamad Eid , Al-Thani Mohamed H. , Al-Khal Abdullatif , Bertollini Roberto , Faust Jeremy Samuel , Abu-Raddad Laith J. 
Published: November 2022

AbstractBackgroundLong-term effectiveness of COVID-19 mRNA boosters in populations with different prior infection histories and clinical vulnerability profiles is inadequately understood.MethodsA national, matched, retrospective, target trial cohort study was conducted in Qatar to investigate effectiveness of a third mRNA (booster) dose, relative to a primary series of two doses, against SARS-CoV-2 omicron infection and against severe COVID-19. Associations were estimated using Cox proportional-hazards regression models.ResultsBooster effectiveness relative to primary series was 41.1% (95% CI: 40.0-42.1%) against infection and 80.5% (95% CI: 55.7-91.4%) against severe, critical, or fatal COVID-19, over one-year follow-up after the booster. Among persons clinically vulnerable to severe COVID-19, effectiveness was 49.7% (95% CI: 47.8-51.6%) against infection and 84.2% (95% CI: 58.8-93.9%) against severe, critical, or fatal COVID-19. Effectiveness against infection was highest at 57.1% (95% CI: 55.9-58.3%) in the first month after the booster but waned thereafter and was modest at only 14.4% (95% CI: 7.3-20.9%) by the sixth month. In the seventh month and thereafter, coincident with BA.4/BA.5 and BA.2.75* subvariant incidence, effectiveness was progressively negative reaching -20.3% (95% CI: -55.0-29.0%) after one year of follow-up. Similar levels and patterns of protection were observed irrespective of prior infection status, clinical vulnerability, or type of vaccine (BNT162b2 versus mRNA-1273).ConclusionsBoosters reduced infection and severe COVID-19, particularly among those clinically vulnerable to severe COVID-19. However, protection against infection waned after the booster, and eventually suggested an imprinting effect of compromised protection relative to the primary series. However, imprinting effects are unlikely to negate the overall public health value of booster vaccinations.
The Paxlovid Rebound Study: A Prospective Cohort Study to Evaluate Viral and Symptom Rebound Differences Between Paxlovid and Untreated COVID-19 Participants
Authors: Pandit Jay A. , Radin Jennifer M. , Chiang Danielle , Spencer Emily , Pawelek Jeff , Diwan Mira , Roumani Leila , Mina Michael 
Published: November 2022

AbstractIntroductionThe uptake of Paxlovid in individuals infected with COVID-19 has been significantly limited by concerns around the Paxlovid rebound phenomenon despite the scarcity of evidence around its epidemiology. The purpose of this study was to prospectively compare the epidemiology of Paxlovid rebound in treated and untreated participants with acute COVID-19 infectionMethodsWe designed a decentralized, digital, prospective observational study in which participants who tested positive for COVID-19 using eMed Test-to-Treat telehealth kits and were clinically eligible for Paxlovid were recruited to be evaluated for viral and symptom clearance, as well as rebound. Participants were assigned to a Paxlovid or control group based on their decision to take Paxlovid. Following initial diagnosis based on a telehealth proctored test both groups were provided 12 telehealth proctored rapid antigen home tests and asked to test on a regular frequent schedule for 16 days and answer symptom surveys. Viral rebound based on test results and COVID-19 symptom rebound based on patient reported symptoms were evaluated.ResultsViral rebound incidence was 14.2% in the Paxlovid group (n=127) and 9.3% in the control group (n=43). COVID-19 symptom rebound incidence was higher in the Paxlovid group (18.9%) compared to the control group (7.0%). There were no notable differences in viral rebound by age, gender, pre-existing conditions, or major symptom groups during the acute phase or at the 1-month interval.ConclusionThis preliminary report of our prospective study suggests that rebound after clearance of test positivity or symptom resolution is higher than previously reported. However, we observed a similar rate of rebound in both in the Paxlovid and control groups. Large studies with diverse participants and extended follow-up are needed to better understand the rebound phenomena.
Cerebellar-driven cortical dynamics enable task acquisition, switching and consolidation
Authors: Pemberton Joseph , Chadderton Paul , Costa Rui Ponte 
Published: November 2022

SummaryTo drive behavior, the cortex must bridge sensory cues with future outcomes. However, the principles by which cortical networks learn such sensory-behavioural transformations remain largely elusive. Here, we posit that the cerebellum assumes a crucial role in driving cortical dynamics, thereby enabling rapid and flexible task acquisition. We introduce a computational model of cerebellar networks which learn to drive cortical networks with task-outcome predictions. First, using sensorimotor tasks we show that cerebellar feedback in the presence of minimal cortical plasticity is suffcient for rapid task acquisition and multiple task switching. Next, we demonstrate that, when trained in working memory tasks, the cerebellum can also underlie the maintenance of cognitive-specific dynamics, explaining a range of optogenetic and behavioural observations. Finally, using our model we introduce a systems consolidation theory in which task information is gradually transferred from the cerebellum to the cortex. In summary, our findings suggest that cortico-cerebellar loops play a pivotal role in task acquisition, switching, and consolidation within the brain.
Targeting long non-coding RNANUDT6enhances smooth muscle cell survival and limits vascular disease progression
Authors: Winter Hanna , Winski Greg , Busch Albert , Chernogubova Ekaterina , Fasolo Francesca , Wu Zhiyuan , Bäcklund Alexandra , Khomtchouk Bohdan B. , Van Booven Derek J. , Sachs Nadja , Eckstein Hans-Henning , Wittig Ilka , Boon Reinier A. , Jin Hong , Maegdefessel Lars 
Published: November 2022

AbstractLong non-coding RNAs (lncRNAs) orchestrate various biological processes and regulate the development of cardiovascular diseases. Their potential therapeutic benefit to tackle disease progression has recently been extensively explored. Our study investigates the role of lncRNA Nudix Hydrolase 6 (NUDT6)and its antisense target Fibroblast Growth Factor 2 (FGF2)in two vascular pathologies: abdominal aortic aneurysms (AAA) and carotid artery disease. Using tissue samples from both diseases, we detected a substantial increase ofNUDT6, whereasFGF2was downregulated. TargetingNudt6 in vivowith antisense oligonucleotides in three murine and one porcine animal models of carotid artery disease and AAA limited disease progression. Restoration of FGF2 uponNudt6knockdown improved vessel wall morphology and fibrous cap stability. Overexpression ofNUDT6 in vitroimpaired smooth muscle cell (SMC) migration, while limiting their proliferation and augmenting apoptosis. By employing RNA pulldown followed by mass spectrometry as well as RNA immunoprecipitation, we identified Cysteine and Glycine Rich Protein 1 (CSRP1) as another directNUDT6interaction partner, regulating cell motility and SMC differentiation. Overall, the present study identifiesNUDT6as a well-conserved antisense transcript ofFGF2. NUDT6silencing triggers SMC survival and migration and could serve as a novel RNA-based therapeutic strategy in vascular diseases.
The adenomatous polyposis coli protein 3o years on
Authors: Abbott James , Näthke Inke S. 
Published: November 2022

ABSTRACTMutations in the gene encoding the Adenomatous polyposis coli protein (APC) were discovered as driver mutations in colorectal cancers almost 30 years ago. Since then, the importance of APC in normal tissue homeostasis has been confirmed in a plethora of other (model) organisms spanning a large evolutionary space. APC is a multifunctional protein, with roles as a key scaffold protein in complexes involved in diverse signalling pathways, most prominently the Wnt signalling pathway. APC is also a cytoskeletal regulator with direct and indirect links to and impacts on all three major cytoskeletal networks. Here, we interrogate the enormous depth of sequencing data now available to reveal the conservation of APC across taxonomy and relationships between different APC protein families.
The lncRNASweetheartregulates compensatory cardiac hypertrophy after myocardial injury
Authors: Rogala Sandra , Ali Tamer , Melissari Maria-Theodora , Währisch Sandra , Schuster Peggy , Sarre Alexandre , Boettger Thomas , Rogg Eva-Maria , Kaur Jaskiran , Krishnan Jaya , Dimmeler Stefanie , Ounzain Samir , Pedrazzini Thierry , Herrmann Bernhard G , Grote Phillip 
Published: November 2022

ABSTRACTAfter myocardial infarction in the adult heart the remaining, non-infarcted tissue adapts to compensate the loss of functional tissue. This adaptation requires changes in gene expression networks, which are mostly controlled by transcription regulating proteins. Long non-coding transcripts (lncRNAs) are now recognized for taking part in fine-tuning such gene programs. We identified and characterized the cardiomyocyte specific lncRNASweetheart RNA(Swhtr), an approximately 10 kb long transcript divergently expressed from the cardiac core transcription factor coding geneNkx2-5. We show thatSwhtris dispensable for normal heart development and function, but becomes essential for the tissue adaptation process after myocardial infarction. Re-expressingSwhtrfrom an exogenous locus rescues theSwhtr nullphenotype. Genes depending onSwhtrafter cardiac stress are significantly occupied, and therefore most likely regulated by NKX2-5. Our results indicate a synergistic role forSwhtrand the developmentally essential transcription factor NKX2-5 in tissue adaptation after myocardial injury.
An MR-based brain template and atlas for optical projection tomography and light sheet fluorescence microscopy
Authors: Willekens Stefanie M.A. , Morini Federico , Mediavilla Tomas , Nilsson Emma , Orädd Greger , Hahn Max , Chotiwan Nunya , Visa Montse , Berggren Per-Olof , Ilegemns Erwin , Överby Anna K. , Ahlgren Ulf , Marcellino Daniel 
Published: November 2022

AbstractOptical projection tomography (OPT) and light sheet fluorescence microscopy (LSFM) are high-resolution optical imaging techniques operating in the mm-cm range, ideally suited forex vivo3D whole mouse brain imaging. Although these techniques exhibit high sensitivity and specificity for antibody-labeled targets, the provided anatomical information remains limited. To allow anatomical mapping of fluorescent signal in whole brain, we developed a novel magnetic resonance (MR) – based template with its associated tissue priors and atlas labels, specifically designed for brains subjected to tissue processing protocols required for 3D optical imaging. We investigated the effect of tissue pre-processing and clearing on brain size and morphology and developed optimized templates for BABB/Murrays clear (OCUM) and DBE/iDISCO (iOCUM) cleared brains. By creating optical-(i)OCUM fusion images using our mapping procedure, we localized dopamine transporter and translocator protein expression and tracer innervation from the eye to the lateral geniculate nucleus of thalamus and superior colliculus. These fusion images allowed for precise anatomical identification of fluorescent signal in discrete brain areas. As such, these templates enable applications in a broad range of research areas integrating optical 3D brain imaging by providing an MR template for cleared brains.