bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fast, multiplexable and highly efficient somatic gene deletions in adult mouse skeletal muscle fibers using AAV-CRISPR/Cas9
Authors: Thürkauf Marco , Lin Shuo , Oliveri Filippo , Grimm Dirk , Platt Randall J. , Rüegg Markus A. 
Published: February 2023

AbstractMolecular screens comparing different disease states to identify candidate genes rely on the availability of fast, reliable and multiplexable systems to interrogate genes of interest. CRISPR/Cas9- based reverse genetics is a promising method to eventually achieve this. However, such methods are sorely lacking for multi-nucleated muscle fibers, since highly efficient nuclei editing is a requisite to robustly inactive candidate genes. Here, we couple Cre-mediated skeletal muscle fiber-specific Cas9 expression with myotropic adeno-associated virus-mediated sgRNA delivery to establish a system for highly effective somatic gene mutation in mice. Using well-characterized genes, we show that local or systemic inactivation of these genes copy the phenotype of traditional gene-knockout mouse models. Thus, this proof-of-principle study establishes a method to unravel the function of individual genes or entire signaling pathways in adult skeletal muscle fibers without the cumbersome requirement of generating knockout mice.
Bovine milk glycoproteins inhibit SARS-CoV-2 and influenza virus co-infection
Authors: Yu Hanjie , Chen Wentian , Shu Jian , Wu Xin , Quan Jia , Cheng Hongwei , Bao Xiaojuan , Wu Di , Wang Xilong , Li Zheng 
Published: February 2023

AbstractThe attachment of S1 subunit of spike (S) protein to angiotensin-converting enzyme 2 (ACE2) is the first and crucial step of SARS-CoV-2 infection. Although S protein and ACE2 are heavily glycosylated, the precise roles of glycans in their interactions are still unclear. Here, we profiled the glycopatterns of S1 subunit of SARS-CoV-2 and ACE2, and found that the galactosylated glycoforms were dominant in both S1 subunit and ACE2. Interestingly, S1 subunit exhibited the property of glycan-binding protein (GBP) and adhered to the ACE2 via binding to the galactosylated glycans on the ACE2. Our earlier findings demonstrated that the sialylated glycoproteins isolated from bovine milk potently inhibit and neutralize viral activity against influenza A virus (IAV). Importantly, we proved further that the galactosylated glycans on isolated glycoproteins bind to the glycan recognition domains of S1 subunit and competitively inhibit binding of S1 subunit to ACE2 and ultimately impede the entry of SARS-CoV-2 pseudovirus into host cells. We provided a potential protein drug that could be multiple simultaneous inhibitor for coronavirus and IAV co-infection.
Modeling temporal and spatial effects on plant reproduction using observational data
Authors: Rodrigues Flávio R.O. , Freitas Cintia G. , Dambros Cristian 
Published: February 2023

Background and AimsThe persistence of a plant species at local sites depend on species ability to survive and reproduce under local conditions. Estimating environmental influence on reproduction is difficult because climatic and soil conditions have synergistic effects on flower and fruit production, and estimating these synergistic effects require tracking a large number of marked individuals. Here, we develop a statistical method that allows investigating the environmental influence on reproduction using observational data only (no marking required).MethodsWe surveyed 30 standardized permanent plots on central Amazonia for six herbaceous families of Zingiberales and Poales. The plots were surveyed for twelve consecutive months. Using the newly developed method, we estimated the effect of climatic (temporal) and edaphic (spatial) covariates on flower and fruit production.Key resultsWe demonstrate that plant reproduction can be estimated from observational data only when enough temporal and spatial data are available. By using the proposed statistical method, we show that the conversion of flowers into fruits in Amazonian monocots is highest in sandy soils, and the difference in conversion rates between sandy and clayey soils is more pronounced in wetter months.ConclusionsBy comparing the production of flowers and fruits with previously published data on species occurrence, our results suggesting that species distribution is limited primarily by species capacity to produce fruits (e.g. limited pollination) and not by the capacity to produce flowers. Due to the association of fruit production to climatic and edaphic variables, our results point to potential changes in species reproduction and distribution under future climatic regimes.
Accounting for unobserved population dynamics and aging error in close-kin mark-recapture assessments
Authors: Swenson John D. , Brooks Elizabeth N. , Kacev Dovi , Boyd Charlotte , Kinney Michael , Marcy-Quay Benjamin , Sévêque Anthony , Feldheim Kevin , Komoroske Lisa M. 
Published: February 2023

AbstractObtaining robust estimates of population abundance is a central challenge hindering the conservation and management of many threatened and exploited species. Close-kin mark-recapture (CKMR) is a genetics-based approach that has strong potential to improve monitoring of data-limited species by enabling estimates of abundance, survival, and other parameters for populations that are challenging to assess. However, CKMR models have received limited sensitivity testing under realistic population dynamics and sampling scenarios, impeding application of the method in population monitoring programs and stock assessments. Here, we use individual-based simulation to examine how unmodeled population dynamics and aging uncertainty affect the accuracy and precision of CKMR parameter estimates under different sampling strategies. We then present adapted models that correct the biases that arise from model misspecification. Our results demonstrate that a simple base-case CKMR model produces robust estimates of population abundance with stable populations that breed annually; however, if a population trend or non-annual breeding dynamics are present, or if year-specific estimates of abundance are desired, a more complex CKMR model must be constructed. In addition, we show that CKMR can generate reliable abundance estimates for adults from a variety of sampling strategies, including juvenile-focused sampling where adults are never directly observed (and aging error is minimal). Finally, we apply a CKMR model that has been adapted for population growth and intermittent breeding to two decades of genetic data from juvenile lemon sharks (Negaprion brevirostris) in Bimini, Bahamas, to demonstrate how application of CKMR to samples drawn solely from juveniles can contribute to monitoring efforts for highly mobile populations. Overall, this study expands our understanding of the biological factors and sampling decisions that cause bias in CKMR models, identifies key areas for future inquiry, and provides recommendations that can aid biologists in planning and implementing an effective CKMR study, particularly for long-lived data-limited species.
The long-term effects of genomic selection: 2. Changes in allele frequencies of causal loci and new mutations
Authors: Wientjes Yvonne C.J. , Bijma Piter , van den Heuvel Joost , Zwaan Bas J. , Vitezica Zulma G. , Calus Mario P.L. 
Published: February 2023

ABSTRACTGenomic selection has become the dominant tool for genetic improvement in livestock and plants. Therefore, its sustainability is essential for global food production. Selection changes the allelic architecture of traits to create genetic gain. It remains unknown whether the changes in allele architecture are different for genomic selection and whether they depend on the genetic architectures of traits. Here we investigate the allele frequency changes of loci and new causal mutations under fifty generations of phenotypic, pedigree, and genomic selection, for a trait controlled by either additive, additive and dominance, or additive, dominance and epistatic effects. Genomic selection resulted in slightly larger and faster changes in allele frequencies of causal loci than pedigree selection. For each locus, allele frequency change per generation was not only influenced by its statistical additive effect, but also by the linkage phase with other loci and its allele frequency. Selection fixed a large number of loci, and five times more unfavorable alleles became fixed with genomic and pedigree selection than with phenotypic selection. For pedigree selection, this was mainly a result of increased genetic drift, while genetic hitchhiking had a large effect with genomic selection. When epistasis was present, the average allele frequency change was smaller (∼15% lower) and a lower number of loci became fixed for all selection methods. We conclude that for long-term genetic improvement, it is very important to be able to minimize the impact of hitchhiking and to limit the loss of favorable alleles more that current genomic selection methods do.
Europe PMC Annotated Full-text Corpus for Gene/Proteins, Diseases and Organisms
Authors: Yang Xiao , Saha Shyamasree , Venkatesan Aravind , Tirunagari Santosh , Vartak Vid , McEntyre Johanna 
Published: February 2023

ABSTRACTNamed entity recognition (NER) is a widely used text-mining and natural language processing (NLP) sub-task. In recent years, deep learning methods have superseded traditional dictionary, and rule-based NER approaches. A high-quality dataset is essential to take full advantage of the recent deep learning advancements. While several gold standard corpora for biomedical entities in abstracts exist, only a few are based on full-text research articles. The Europe PMC literature database routinely annotates Gene/Proteins, Diseases and Organisms entities; to transition this pipeline from a dictionary-based to a machine learning-based approach, we have developed a human-annotated full-text corpus for these entities comprising 300 full-text open access research articles. Over 72,000 mentions of biomedical concepts have been identified within approximately 114,000 sentences. This article describes the corpus and details how to access and reuse this open community resource.
Dynamic Changes in Macrophage Polarization during the Resolution Phase of Periodontal Disease
Authors: Uttamani Juhi R. , Kulkarni Varun , Valverde Araceli , Naqvi Raza Ali , Nares Salvador , Naqvi Afsar R. 
Published: February 2023

AbstractPeriodontal inflammation is largely governed by infiltration of myeloid cells, in particular macrophages. Polarization of Mφ within the gingival tissues is a well-controlled axis and has considerable consequences for how Mφ participate in inflammatory and resolution (tissue repair) phases. We hypothesize that periodontal therapy may instigate a pro-resolution environment favoring M2 Mφ polarization and contribute towards resolution of inflammation post-therapy. We aimed to evaluate the markers of macrophage polarization before and after periodontal therapy. Gingival biopsies were excised from human subjects with generalized severe periodontitis, undergoing routine non-surgical therapy. A second set of biopsies were excised after 4-6 weeks to assess the impact of therapeutic resolution at the molecular level. As controls, gingival biopsies were excised from periodontally healthy subjects, undergoing crown lengthening. Total RNA was isolated from gingival biopsies to evaluate pro- and anti-inflammatory markers associated with macrophage polarization by RT-qPCR. Mean periodontal probing depths, CAL and BOP reduced significantly after therapy and corroborated with the reduced levels of periopathic bacterial transcripts after therapy. Compared to heathy and treated biopsies, higher load of Aa and Pg transcripts were observed in disease. Lower expression of M1Mφ markers (TNF-α, STAT1) were observed after therapy as compared to diseased samples. Conversely, M2Mφ markers (STAT6, IL-10) were highly expressed in post-therapy as opposed to pre-therapy, which correlated with clinical improvement. These findings corroborated with murine ligature-induced periodontitis and resolution model, comparing the respective murine Mφ polarization markers (M1 Mφ:cox2,iNOS2and M2 Mφ:tgm2andarg1). Our findings suggest that imbalance in M1 and M2 polarized macrophages by assessment of their markers can provide relevant clinical information on the successful response of periodontal therapy and can be used to target non-responders with exaggerated immune responses.
Multiple mating rescues offspring sex ratio but not productivity in a haplodiploid exposed to developmental heat stress
Authors: Costa Sofia G. , Magalhães Sara , Rodrigues Leonor R. 
Published: February 2023

Abstract

Reproduction is generally more sensitive to high temperatures than survival and arguably a better predictor of the response of populations to climate change than survival estimates. Still, how temperature simultaneously impacts male and female reproductive success, the mating system and the operational sex ratio remains an open question.

Here, we addressed how a sublethal high temperature affects the reproductive system of the haplodiploid spider mite Tetranychus urticae. Males and females maintained at 25 or 36°C during development were paired and the fertility of both sexes, their mating and remating eagerness, and the paternity of the offspring of females with different mating histories were measured.

Female and male fertility decreased at 36°C compared to 25°C, resulting in lower offspring production and a more male‐biased sex ratio, respectively, because of haplodiploidy. However, when either heat‐stressed females or females that mated with heat‐stressed males remated, there was a shift in paternity share, with more than one male contributing to the offspring. This was accompanied by reduced mating eagerness in pairs with partially sterile males and increased remating eagerness in pairs in which at least one sex was partially sterile in the first mating.

The observed temperature‐induced changes in female remating eagerness and sperm use allowed restoring the offspring sex ratio, by increasing the proportion of fertilized offspring, but did not lead to the recovery of offspring number.

The temperature‐induced changes in the mating behaviour and mating system should alter the interactions within and between the sexes, and with it the strength of sexual selection and sexual conflict in this species. Whether such changes are sufficient to prevent population extinction, despite the inability to recover offspring number, remains an open question.

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Functional traits explain both seedling and adult plant spatial patterns in gypsum annual species
Authors: Peralta Ana L. , Escudero Adrián , de la Cruz Marcelino , Sánchez Ana M. , Luzuriaga Arantzazu L. 
Published: February 2023

Abstract

Ecological processes such as seed dispersal or plant–plant interactions and environmental constraints such as climate or soil heterogeneity are known to influence establishment, and thus the spatial patterns of plant communities and populations. In this study, we hypothesized that key functional traits such as the specific leaf area (SLA), reproductive ratio (reproductive/vegetative biomass), seed mass and maximum plant height would influence the spatial patterns of individual species in annual, gypsophilous plant communities, and that these effects would be modulated by both the soil surface structure (biocrust) and climate (precipitation) conditions.

We mapped the spatial patterns of all plants found in six 1 × 1 m plots (more than 1000 individuals per plot) in both the seedling (autumn) and adult stages (spring) under two biocrust experimental conditions (intact vs. disturbed biocrust) during two consecutive years which were contrasted in term of precipitation (dry year and wet year). To assess the spatial patterns of seedlings and adults, we fitted four different spatial point pattern models (i.e. Poisson, inhomogeneous Poisson, Poisson cluster and inhomogeneous Poisson cluster processes) to each of the 242 populations of the 26 most abundant species that had more than 15 individuals per plot.

Most seedling populations exhibited clustered spatial patterns that persisted in the adult stage, which suggests that short‐distance dispersal is an adaptive trait for soil specialists such as gypsophilous plants. One‐third of the populations fitted an inhomogeneous model best but the physical structure of the biocrust was not related to them. More importantly, we found a connection between the functional strategies of species and the spatial distribution of plants. In particular, during the dry year, irrespective of the biocrust conditions, species with a high SLA and high Rep/Veg mainly exhibited clustered spatial patterns, whereas low SLA and low Rep/Veg were associated with random distributions. Species with heavy and light seed masses had random and clustered patterns, respectively. In both the dry and wet years, species with lower maximum heights had clustered patterns, whereas taller species exhibited random patterns. In addition, species with heavier seeds and greater maximum heights had the largest cluster sizes.

Our results confirm that the spatial patterns of seedlings and adult plants are significantly determined by the functional strategy of each species.

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A new dimethylsulfoniopropionate lyase of the cupin superfamily in marine bacteria
Authors: Wang Shu‐Yan , Zhang Nan , Teng Zhao‐Jie , Wang Xiao‐Di , Todd Jonathan D. , Zhang Yu‐Zhong , Cao Hai‐Yan , Li Chun‐Yang 
Published: February 2023

AbstractDimethylsulfoniopropionate (DMSP) is a marine organosulfur compound with important roles in stress protection, marine biogeochemical cycling, chemical signalling and atmospheric chemistry. Diverse marine microorganisms catabolize DMSP via DMSP lyases to generate the climate‐cooling gas and info‐chemical dimethyl sulphide. Abundant marine heterotrophs of the Roseobacter group (MRG) are well known for their ability to catabolize DMSP via diverse DMSP lyases. Here, a new DMSP lyase DddU within the MRG strain Amylibacter cionae H‐12 and other related bacteria was identified. DddU is a cupin superfamily DMSP lyase like DddL, DddQ, DddW, DddK and DddY, but shares <15% amino acid sequence identity with these enzymes. Moreover, DddU proteins forms a distinct clade from these other cupin‐containing DMSP lyases. Structural prediction and mutational analyses suggested that a conserved tyrosine residue is the key catalytic amino acid residue in DddU. Bioinformatic analysis indicated that the dddU gene, mainly from Alphaproteobacteria, is widely distributed in the Atlantic, Pacific, Indian and polar oceans. For reference, dddU is less abundant than dddP, dddQ and dddK, but much more frequent than dddW, dddY and dddL in marine environments. This study broadens our knowledge on the diversity of DMSP lyases, and enhances our understanding of marine DMSP biotransformation.
Dissolution and Deformation Characteristics of Limestones Containing Different Calcite and Dolomite Content Induced by CO2‐Water‐Rock Interaction
Authors: CHEN Bowen , LI Qi , TAN Yongsheng , ALVI Ishrat Hameed 
Published: February 2023

AbstractTo investigate the impacts of mineral composition on physical and mechanical properties of carbonate rocks, limestone specimens containing different contents in calcite and dolomite are selected to perform CO2‐water‐rock reaction experiments. The X‐ray Diffraction (XRD) and Nuclear Magnetic Resonance (NMR) are carried out to examine the change characteristics of mineral dissolution and pore structure after reaction. The core flooding experiments with Fiber Bragg gratings are implemented to examine the stress sensitivity of carbonate rocks. The results show that the limestones containing pure calcite are more susceptible to acid dissolution compared to limestone containing impure dolomite. The calcite content in pure limestone decreases as the reaction undergoes. The dissolution of dolomite leads to the formation of calcite in impure limestone. Calcite dissolution leads to the formation of macropore and flow channels in pure limestone, while the effects of impure dolomite in impure limestone results in mesopore formation. When confining pressure is lower than 12 MPa, pure limestones demonstrate higher strain sensitivity coefficients compared to impure limestone containing dolomite after reaction. When confining pressure exceeds 12 MPa, the strain sensitivity coefficients of both pure and impure limestones become almost equal.
Validation of the FASD‐Tree as a screening tool for fetal alcohol spectrum disorders
Authors: Mattson Sarah N. , Jones Kenneth Lyons , Chockalingam Ganz , Wozniak Jeffrey R. , Hyland Matthew T. , Courchesne‐Krak Natasia S. , Del Campo Miguel , Riley Edward P. ,   the CIFASD
Published: February 2023

AbstractBackgroundAs many as 80% of individuals with fetal alcohol spectrum disorders (FASD) are misdiagnosed or not diagnosed. This study tests the accuracy and validity of a web‐based screening tool (the FASD‐Tree) for identifying children and adolescents with FASD.MethodsChildren with histories of prenatal alcohol exposure (PAE) and controls (N = 302, including 224 with PAE and 78 controls) were examined for physical signs of fetal alcohol syndrome (FAS), and parents completed behavioral questionnaires. Data were entered into the FASD‐Tree, a web‐based decision tree application. The FASD‐Tree provided two outcomes: a dichotomous indicator (yes/no) and a numeric risk score (0 to 5), which have been shown separately to identify children with PAE and neurobehavioral impairment and to correlate with neurobehavioral outcomes. Overall accuracy (ACC), sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were calculated for the decision tree, risk score, and their combination. Misclassified cases were examined for systematic bias.ResultsThe FASD‐Tree was successful in accurately identifying youth with histories of PAE and the subgroup of individuals with FASD, indicating its validity as an FASD screening tool. Overall accuracy rates for FASD‐Tree components ranged from 75.0% to 84.1%, and both the decision tree outcome and risk score, and their combination, resulted in fair to good discrimination (area under the curve = 0.722 to 0.862) of youth with histories of PAE or FASD. While most participants were correctly classified, those who were misclassified differed in IQ and attention. Race, ethnicity, and sex did not affect the results.ConclusionThe FASD‐Tree is not a biomarker of PAE and does not provide definitive evidence of prenatal alcohol exposure. Rather it is an accurate and valid screening tool for FASD and can be used by clinicians who suspect that a patient has a history of PAE, even if the exposure is unknown.