bluuebunny/crossref_metadata_2025_split huggingface dataset:
Amplification of avian influenza viruses along poultry marketing chains in Bangladesh: a controlled field experiment
Authors: Kohnle Lisa , Das Tridip , Uddin Md. Helal , Nath Sanjib C. , Mohsin Md. Abu Shoieb , Mahmud Rashed , Biswas Paritosh K. , Hoque Md. Ahasanul , Pfeiffer Dirk U. , Fournié Guillaume 
Published: November 2023

AbstractThe prevalence of avian influenza viruses (AIVs) is commonly found to increase dramatically from farms to live bird markets (LBMs). Viral transmission dynamics along marketing chains is, however, poorly understood. To address this gap, we implemented a field experiment altering chicken supply to an LBM in Chattogram, Bangladesh. Chickens traded along altered (intervention) and conventional (control) marketing chains were tested for AIVs. Upon arrival at the LBM, the odds of detecting AIVs did not differ between control and intervention groups. However, 12 hours later, intervention group odds were lower, particularly for broiler chickens, indicating that viral shedding in LBM resulted partly from infections during transport and trade. Curtailing AIV prevalence in LBMs requires mitigating risk in marketing chain nodes preceding chickens’ delivery at LBMs.Article Summary LineThe high prevalence of avian influenza viruses in marketed chickens cannot be solely attributed to viral transmission within live bird markets but is also influenced by infections occurring prior to the chickens’ supply to these markets.
Evolution of rarity and phylogeny determine above- and belowground biomass in plant-plant interactions
Authors: Nytko Alivia G. , Senior John K. , O’Reilly-Wapstra Julianne , Schweitzer Jennifer A. , Bailey Joseph K. 
Published: November 2023

AbstractRare species are often considered inferior competitors due to occupancy of small ranges, specific habitats, and small local populations. However, the phylogenetic relatedness and rarity level of interacting species in plant-plant interactions are not often considered when predicting the competitive response of rare plants. We used a common garden of 25 species of TasmanianEucalyptus, varying in rarity to allow us to differentiate the competitive abilities of rare versus common species when grown in mixtures varying in phylogenetic relatedness and rarity. We demonstrate increased biomass production of rare plant species when interacting with genetically intermediate neighbors through synergistic non-additive effects not seen in common species. Additionally, we also find that all plants, regardless of rarity status, maintain 47% greater aboveground and 69% greater belowground biomass when interacting with common species compared to the rarest species. However, species-specific interactions with one particular common species,E. globulus, yielded a 97% increase in biomass compared to average biomass yields in other interactions, suggesting the importance ofE. globulusintegration into rare species restoration plantings. These results are important because they suggest that the evolutionary processes driving species rarity and the phylogenetic divergence of traits interact to drive ecological dynamics of plant-plant interactions in non-additive ways. Through the ecological and evolutionary consideration of performance traits, rarity, and species-specific effects, we can more accurately predict plant-plant interaction dynamics varying in rarity and relatedness across the landscape.
Intestinal cDC1s provide IL-12 dependent and independent functions required for CD4+T cell-mediated resistance toCryptosporidium
Authors: Cohn Ian S. , Wallbank Bethan A. , Haskins Breanne E. , O’Dea Keenan M. , Pardy Ryan D. , Shaw Sebastian , Merolle Maria I. , Gullicksrud Jodi A. , Christian David A. , Striepen Boris , Hunter Christopher A. 
Published: November 2023

AbstractCryptosporidiumis an enteric pathogen that is a prominent cause of diarrheal disease. Control of this infection requires CD4+T cells, though the processes that lead to T cell-mediated resistance have been difficult to assess. Here,Cryptosporidiumparasites that express MHCII-restricted model antigens were generated to dissect the early events that influence CD4+T cell priming and effector function. These studies highlight that parasite-specific CD4+T cells are primed in the draining mesenteric lymph node (mesLN) and differentiate into Th1 cells in the gut, where they mediate IFN-γ-dependent control of the infection. Although type 1 conventional dendritic cells (cDC1s) were not required for initial priming of CD4+T cells, cDC1s were required for CD4+T cell expansion and gut homing. cDC1s were also a major source of IL-12 that was not required for priming but promoted full differentiation of CD4+T cells and local production of IFN-γ. Together, these studies reveal distinct roles for cDC1s in shaping CD4+T cell responses to enteric infection: first to drive early expansion in the mesLN and second to drive effector responses in the gut.SummaryCryptosporidiumparasites that express model antigens were generated to dissect how parasite-specific CD4+T cells are primed and mediate effector functions required to control this enteric pathogen. cDC1s produced IL-12p40 and were required for early expansion and gut homing of CD4+T cells. However, IL-12p40 was only required for the development of Th1 CD4+T cell effector function in the gut.
Spatiotemporal overlap and contact rates among small Indian mongooses and free-roaming domestic dogs in Puerto Rico: Implications for rabies virus transmission
Authors: Sauvé Caroline C. , Berentsen Are R. , Gilbert Amy T. , Llanos Steven F. , Leighton Patrick A. 
Published: November 2023

AbstractSmall Indian mongooses (Urva auropunctata) are the primary terrestrial wildlife rabies reservoir on Puerto Rico, the Dominican Republic, Cuba and Grenada, where they represent a risk to public health through direct human exposure and through transmission of rabies virus to domestic animals that have close association with humans. Historically rabies virus was introduced via domestic dogs and then later shifted into mongoose populations on Puerto Rico and other islands, yet domestic dog-mongoose ecological interactions have been understudied throughout the Caribbean. In this study, we derived daily activity patterns from baited camera traps, and investigated the use of proximity and GPS tracking data acquired concomitantly from mongooses and free-ranging domestic dogs (FRDD) to characterise intra- and interspecific contacts and estimate contact rates. Our results highlight that although mongooses and FRDD are both relatively active in late afternoon, close interspecific contacts only occurred among 4% of collared mongoose-dog dyads, were infrequent (range: 0 – 0.19; median = 0 contacts per day), and were spatially restricted to road and forest edges. Mongooses were only documented to contact feral FRDD, whereas no mongoose contacts with stray FRDD were detected. The space use by stray FRDD and association to humans may play a role in limiting direct contacts with mongooses and the associated risks of rabies virus cross-species transmission. Intraspecific contacts were documented among 11% of collared mongoose-mongoose dyads, occurred at a rate ranging between 0 – 0.57 (median = 0) contacts per day, and took place within wildlands. Intraspecific contacts were documented among 30% of collared dog dyads, at rates ranging between 0 – 3.37 (median = 0) contacts per day, which was more frequent contact than observed for collared mongooses (χ2= 8.84;DF=2;P= 0.012). All dog-dog contacts occurred in proximity to human residential development and involved both stray-stray and stray-feral FRDD collared dyads. Feral FRDD may represent a rabies virus vector between mongooses and FRDD living close to humans. Home range overlap was a significant predictor of contact rates (P< 0.001) among intra- and interspecific dyads of both species and may represent a useful proxy for contact between species that also overlap in daily activity patterns. Transitional areas between wildlands and human residential development could represent hotspots for infectious disease transmission between mongooses and feral FRDDs. Characterization and quantification of contact rates in mongooses and FRDDs across the wildland-urban gradient across wet and dry seasons could help to inform animal rabies control strategies on Puerto Rico and other Caribbean islands with enzootic mongoose rabies.
A reference genome for the Andean cavefishTrichomycterus rosablanca(Siluriformes, Trichomycteridae): building genomic resources to study evolution in cave environments
Authors: Cadena Carlos Daniel , Pabón Laura , DoNascimiento Carlos , Abueg Linelle , Tiley Tatiana , O-Toole Brian , Absolon Dominic , Sims Ying , Formenti Giulio , Fedrigo Olivier , Jarvis Erich D. , Torres Mauricio 
Published: November 2023

AbstractAnimals living in caves are of broad relevance to evolutionary biologists interested in understanding the mechanisms underpinning convergent evolution. In the Eastern Andes of Colombia, populations from at least two distinct clades ofTrichomycteruscatfishes (Siluriformes) independently colonized cave environments and converged in phenotype by losing their eyes and pigmentation. We are pursuing several research questions using genomics to understand the evolutionary forces and molecular mechanisms responsible for repeated morphological changes in this system. As a foundation for such studies, here we describe a diploid, chromosome-scale, long-read reference genome forTrichomycterus rosablanca, a blind, depigmented species endemic to the karstic system of the department of Santander. The nuclear genome comprises 1Gb in 27 chromosomes, with a 40.0x HiFi long-read genome coverage having a N50 scaffold of 40.4 Mb and N50 contig of 13.1 Mb, with 96.9% (Eukaryota) and 95.4% (Actinopterygii) universal single-copy orthologs (BUSCO). This assembly provides the first reference genome for the speciose genusTrichomycterus, which will serve as a key resource for research on the genomics of phenotypic evolution.
In silico codon optimization of the variant antigen-encoding genes of diverse strains of Zika Virus
Authors: Hora Jahnvi , Panwar Vanshika , Mani Indra 
Published: November 2023

AbstractWith the recent emergence of the coronavirus pandemic, the scare for other viral pandemics is on the rise. Already having caused an epidemic in 2015-16, Zika virus (ZIKV) poses a threat for potential havoc. Thus, there is an urgent need to produce drugs and vaccines for the same as no approved vaccinations exist for the virus as of now. With the optimization of codon usage, the process of vaccine development can be accelerated and efficacy can be ensured. ZIKV genome has 3 structural genes (envelope, capsid and membrane which is obtained from pre membrane) and 7 nonstructural genes (NS1, NS2A, NS2B, NS3, NS4A, NS4B and NS5). We have used these 10 genes in 5 different strains of ZIKV for in silico DNA optimization inEscherichia coli.The mean CAI, GC% and AT% of wild-type DNA and optimized DNA of each were compared. It was observed that the CAI and GC% had increased in optimized DNA as compared to wild- type while the opposite was seen for AT%. The results show that codon optimization helps in efficient expression of proteins in the host. These could be used in the development of biotherapeutics. The ideal genes to be overexpressed in development of biotherapeutics are the membrane precursor (prM) and envelope (E) genes as the results have shown.
Multi-timescale reinforcement learning in the brain
Authors: Masset Paul , Tano Pablo , Kim HyungGoo R. , Malik Athar N. , Pouget Alexandre , Uchida Naoshige 
Published: November 2023

AbstractTo thrive in complex environments, animals and artificial agents must learn to act adaptively to maximize fitness and rewards. Such adaptive behavior can be learned through reinforcement learning1, a class of algorithms that has been successful at training artificial agents2–6and at characterizing the firing of dopamine neurons in the midbrain7–9. In classical reinforcement learning, agents discount future rewards exponentially according to a single time scale, controlled by the discount factor. Here, we explore the presence of multiple timescales in biological reinforcement learning. We first show that reinforcement agents learning at a multitude of timescales possess distinct computational benefits. Next, we report that dopamine neurons in mice performing two behavioral tasks encode reward prediction error with a diversity of discount time constants. Our model explains the heterogeneity of temporal discounting in both cue-evoked transient responses and slower timescale fluctuations known as dopamine ramps. Crucially, the measured discount factor of individual neurons is correlated across the two tasks suggesting that it is a cell-specific property. Together, our results provide a new paradigm to understand functional heterogeneity in dopamine neurons, a mechanistic basis for the empirical observation that humans and animals use non-exponential discounts in many situations10–14, and open new avenues for the design of more efficient reinforcement learning algorithms.
Characterizing Human KIF1Bß Motor Activity by Single-Molecule Motility Assays andCaenorhabtidis elegansGenetics
Authors: Iguchi Rei , Kita Tomoki , Watanabe Taisei , Chiba Kyoko , Niwa Shinsuke 
Published: November 2023

AbstractThe axonal transport of synaptic vesicle precursors relies on KIF1A and UNC-104 ortholog motors. In mammals, KIF1Bß is also responsible for the axonal transport of synaptic vesicle precursors. Mutations in KIF1A and KIF1Bß lead to a wide range of neuropathies. While previous studies have revealed the biochemical, biophysical and cell biological properties of KIF1A, and its defects in neurological disorders, the fundamental properties of KIF1Bß remain elusive. In this study, we determined the motile parameters of KIF1Bß through single-molecule motility assays. Additionally, we established simple methods for testing the axonal transport activity of human KIF1Bß usingCaenorhabditis elegansgenetics. Taking advantage of these methods, we demonstrated that these assays enable the detection of reduced KIF1Bß activities both in vitro and in vivo, that is caused by a disease-associated mutation.
The pathogenic p.N1662D SCN2A mutation reveals an essential molecular interaction for Nav1.2 channel inactivation
Authors: Berecki Géza , Tao Elaine , Howell Katherine B. , Coorg Rohini K. , Kahlig Kris , Wolff Markus , Corry Ben , Petrou Steven 
Published: November 2023

ABSTRACTMutations in the SCN2A gene encoding the Nav1.2 sodium channel can lead to neurodevelopmental disorders. We studied the N1662D variant associated with severe early-onset developmental and epileptic encephalopathy (DEE). The N1662D mutation almost completely prevented fast inactivation without affecting activation. The comparison of wild-type and N1662D channel structures suggested that the ambifunctional hydrogen bond formation between residues N1662 and Q1494 is essential for fast inactivation. Fast inactivation could also be prevented with engineered Q1494A or Q1494L Nav1.2 channel variants, whereas Q1494E or Q1494K variants resulted in incomplete inactivation and persistent current. Molecular dynamics simulations revealed a reduced affinity of the hydrophobic IFM-motif to its receptor site with N1662D and Q1494L variants relative to wild-type. These results demonstrate that the interactions between N1662 and Q1494 underpin the stability and the orientation of the inactivation gate and are essential for the development of fast inactivation. Six DEE-associated Nav1.2 variants, with mutations mapped to channel segments known to be implicated in fast inactivation were also evaluated. Remarkably, the L1657P variant also prevented fast inactivation and produced biophysical characteristics similar to N1662D, whereas the M1501V, M1501T, F1651C, P1658S, and A1659V variants resulted in biophysical properties that were consistent with gain-of-function and enhanced action potential firing of hybrid neurons in dynamic action potential clamp experiments. Paradoxically, low densities of N1662D or L1657P currents potentiated action potential firing, whereas increased densities resulted in sustained depolarization. The contribution of non-inactivating Nav1.2 channels to neuronal excitability may constitute a novel cellular mechanism in the pathogenesis ofSCN2A-related DEE.SIGNIFICANCE STATEMENTSCN2Agene-related early-onset developmental and epileptic encephalopathy (EO-DEE) is a rare and severe disorder that manifests in early infancy and childhood.SCN2Amutations affecting the fast inactivation gating mechanism can cause altered voltage dependence and incomplete inactivation of the encoded Nav1.2 channel, leading to abnormal neuronal excitability. In this biophysical and clinical study of neuronal Nav1.2 variants, we identified amino acid residues that are critical for the stability and orientation of the inactivation gate during fast inactivation. Mutations of these residues prevent fast inactivation and may lead to EO-DEE via a novel pathophysiological mechanism. The results provide novel structural insights into the molecular mechanism of Nav1.2 channel fast inactivation and inform treatment strategies forSCN2A-related EO-DEE.
Assessing the Impact of Mask Mandates on SARS-CoV-2 Transmission: A Case Study of Utah
Authors: Horn Alicia C. , Shoemaker Holly E. , Keegan Lindsay T. 
Published: November 2023

AbstractBackgroundThroughout the COVID-19 pandemic, the effectiveness of face masks mandates has been intensely debated. Many methods have been used to demonstrate mask effectiveness, including one that compares the change in reproduction number following implementing and removing face mask mandates1.MethodsUsing data from Utah, we calculated the effect of mask mandates (EFm) in each local health district from before and after three key mandates: the Salt Lake and Summit County (SLSC) mask mandates enacted; the Utah statewide mask mandate enacted; and the Utah statewide mandate was lifted.ResultsWe found that most counties had a reduction in the growth rate of cases following the mandates. There were reductions in EFmin many counties after the introduction of the SLSC mask mandates and a more widespread reduction in EFmacross the state following the statewide mandate. Lifting the mandates, many counties across the states saw an increase in EFm.ConclusionOur data show mask mandates were an effective way to reduce transmission both within the jurisdiction they were enacted and in neighboring jurisdictions. We provide evidence to support mask mandates as a way to prevent transmission to be better equipped to respond to future pandemics.
Exposure toPseudomonas spp.increasesAnopheles gambiaeinsecticide resistance in a host-dependent manner
Authors: Silva Luís M. , Acerbi Gwendoline , Amann Marine , Koella Jacob C. 
Published: November 2023

AbstractThe microbiota of mosquitoes influences many aspects of their biology, including developmental processes, mating and sexual reproduction, immune functions, and refractoriness to pathogens. Here, we considered their role in resistance against insecticides. In particular, we assessed how larval infection of a permethrin-resistant and a sensitive colony ofAnopheles gambiaeby four strains belonging to three differentPseudomonasspecies affects several life history traits and the impact of the insecticide on adult mortality. Our data showed that all fourPseudomonasstrains persisted in adults until death. The bacteria increased the likelihood that mosquitoes survived 24 hours after exposure to permethrin by up to two-fold. The impact of the bacteria depended on the bacterial strains and the mosquito colony: in the resistant colony, all bacteria increased survival by about 2-fold, while in the sensitive colony, only two of the four strains increased survival. The benefit concerning insecticide resistance came with little to no impact on the other traits (i.e., larval mortality, developmental time and adult longevity). Altogether, our results highlight the importance of considering environmental microbial exposure and mosquito microbial communities in epidemiological and vector-control studies, while also suggesting a possible role forPseudomonas spp.as a symbiont inA. gambiae.
Comprehensive profiling of L1 retrotransposons in mouse
Authors: Zhang Xuanming , Celic Ivana , Mitchell Hannah , Stuckert Sam , Vedula Lalitha , Han Jeffrey S. 
Published: November 2023

ABSTRACTL1 elements are retrotransposons currently active in mammals. Although L1s are typically silenced in most normal tissues, elevated L1 expression is associated with a variety of conditions, including cancer, aging, infertility, and neurological disease. These associations have raised interest in the mapping of human endogenousde novoL1 insertions, and a variety of methods have been developed for this purpose. Adapting these methods to mouse genomes would allow us to monitor endogenousin vivoL1 activity in controlled, experimental conditions using mouse disease models. Here we use a modified version of transposon insertion profiling, called nanoTIPseq, to selectively enrich young mouse L1s. By linking this amplification step with nanopore sequencing, we identified >95% annotated L1s from C57BL/6 genomic DNA using only 200,000 sequencing reads. In the process, we discovered 82 unannotated L1 insertions from a single C57BL/6 genome. Most of these unannotated L1s were near repetitive sequence and were not found with short-read TIPseq. We used nanoTIPseq on individual mouse breast cancer cells and were able to identify the annotated and unannotated L1s, as well as new insertions specific to individual cells, providing proof of principle for using nanoTIPseq to interrogate retrotransposition activity at the single cell levelin vivo.
Extreme distributions in the preconfigured developing brain
Authors: Chini Mattia , Hnida Marilena , Kostka Johanna K. , Chen Yu-Nan , Hanganu-Opatz Ileana L. 
Published: November 2023

AbstractIn the adult brain, structural and functional parameters, such as synaptic sizes and neuronal firing rates, follow right-skewed and heavy-tailed distributions. While this organization is thought of having significant implications, its development is still largely unknown. Here, we address this knowledge gap by investigating a large-scale dataset recorded from the prefrontal cortex (PFC) and the olfactory bulb of mice aged 4-60 postnatal days. We show that firing rates and pairwise correlations have a largely stable distribution shape over age, and that neural activity displays a small-world architecture. Moreover, early brain activity displays an oligarchical organization, i.e., neurons with high firing rates are likely to have hub-like properties. Leveraging neural network modeling, we show that analogously extremely distributed synaptic parameters are necessary to recapitulate the experimental data. Thus, functional and structural parameters in the developing brain are already extremely distributed, suggesting that this organization is preconfigured and not experience-dependent.