bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expanding the use of reindeer foetal bone measurements for zooarchaeological applications
Authors: Discamps Emmanuel , Soulier Marie-Cécile 
Published: March 2024

AbstractWhen foetal bones are preserved in archaeological sites, they are often used to identify the seasonality of prey acquisition by past human populations and, subsequently, to discuss their lifestyle, their management of food resources, nomadic cycles, etc. To do so, zooarchaeologists use charts to estimate foetal age based on the growth of their bones. For reindeer (Rangifer tarandus), a species that was widely exploited since the Palaeolithic throughout Eurasia, existing reference data are limited and require the measurement of complete bones, a procedure that is rarely applicable to archaeological contexts in which bones are often fragmented. In this study we present a wide range of measurements (9-10 measurements per bone) taken on the humerus, radius, metacarpal, femur, tibia and metatarsal of 31 individuals housed at the Zoological Museum of the University of Oulu (Finland). With this large data set, a more accurate estimation of the time of death of reindeer foetus can be achieved using skeletal measurements, even in the case of fragmented bones. To facilitate the use of this referential, an open-access web interface (foetusmeteR) was designed in RShiny. This interface allows for the direct estimation of foetal age and season of death by entering a single skeletal measurement, as well as the possibility of estimating if two bones might correspond to the same individual using two different measurements. This new tool should help to discuss in more detail the condition of reindeer herds hunted in the past, the hunting techniques and strategies that may have been used by human groups, and allow for a more detailed reconstruction of the seasonal nomadic cycle of past societies that focused their subsistence onRangiferpopulations.
A pangenomic perspective of the Lake Malawi cichlid radiation reveals extensive structural variation driven by transposable elements
Authors: Quah Fu Xiang , Almeida Miguel Vasconcelos , Blumer Moritz , Yuan Chengwei Ulrika , Fischer Bettina , See Kirsten , Jackson Ben , Zatha Richard , Rusuwa Bosco , Turner George F. , Santos M. Emília , Svardal Hannes , Hemberg Martin , Durbin Richard , Miska Eric 
Published: March 2024

AbstractThe East African Rift Lakes, namely Lake Malawi, Victoria, and Tanganyika, host a remarkable diversity of cichlid fishes, representing one of nature’s most striking vertebrate radiations. Despite rich phenotypic diversity, single nucleotide polymorphism (SNP)-based sequencing studies have revealed little sequence divergence between cichlids, with 0.1 to 0.25% pairwise divergence within Lake Malawi. These studies were based on aligning short reads to a single linear reference genome, which ignores the contribution of larger scale structural variants (SVs). To complement existing SNP-based studies, we adopted a pangenomic approach by constructing a multiassembly graph of haplochromine cichlids in Lake Malawi. We produced six new long read genome assemblies, alongside two publicly available ones, to span most of the major eco-morphological clades in the lake. This approach not only identifies longer SVs, but also visually represents complex and nested variation. Strikingly, the SV landscape is dominated by large insertions, many exclusive to individual assemblies. From a pangenomic perspective, we observed an exceptional amount of extra sequence, totaling up to 33.1% additional bases with respect to a single cichlid genome. Approximately 4.73 to 9.86% of the cichlid assemblies were estimated to be interspecies structural variation, suggesting substantial genomic diversity underappreciated in previous SNP-based studies. While coding regions remain highly conserved, our analysis uncovers a significant contribution of SVs from transposable element (TE) insertions, especially DNA, LINE, and LTR transposons. These findings underscore the intricate interplay of evolutionary forces shaping cichlid genome diversity, including both small nucleotide mutations and large TE-derived sequence alterations.
CRISPR/Cas9 gene editing inDrosophilavia visual selection in a summer classroom
Authors: Kockel Lutz , Zhang Valentina , Wang Jenna , Gulick Clara , Laws Madeleine E. , Rajan Arjun , Lantz Nicole , Asgarova Ayla , Dai Lillian , Garcia Kristian , Kim Charlene , Li Michelle , Ordonez-Acosta Patricio , Peng Dongshen , Shull Henry , Tse Lauren , Wang Yixang , Yu Wenxin , Zhou Zee , Rankin Anne , Park Sangbin , Kim Seung K. 
Published: March 2024

AbstractCRISPR/Cas9 methods are a powerfulin vivoapproach to edit the genome ofDrosophila melanogaster. To convert existingDrosophila GAL4lines toLexAdriver lines in a secondary school classroom setting, we applied the CRISPR-based genetic approach to a collection ofGal4‘driver’ lines. The integration of theyellow+coat color marker into homology-assisted CRISPR knock-in (HACK) enabled visual selection ofGal4-to-LexAconversions using brightfield stereo-microscopy available in a broader set of standard classrooms. Here, we report the successful conversion of elevenGal4lines with expression in neuropeptide-expressing cells into corresponding, novelLexAdrivers. The conversion was confirmed byLexA-andGal4-specific GFP reporter gene expression. This curriculum was successfully implemented in a summer course running 16 hours/week for seven weeks. The modularity, flexibility, and compactness of this course should enable development of similar classes in secondary schools and undergraduate curricula, to provide opportunities for experience-based science instruction, and university-secondary school collaborations that simultaneously fulfill research needs in the community of science.
Diel Partitioning in Microbial Phosphorus Acquisition in the Sargasso Sea
Authors: Muratore Daniel , Gilbert Naomi E. , LeCleir Gary R. , Wilhelm Steven W. , Weitz Joshua S. 
Published: March 2024

AbstractThe daily cycle of photosynthetic primary production at the base of marine food webs is often limited by the availability of scarce nutrients. According to temporal niche partitioning theory, competition for scarce resources can be alleviated insofar as the intensity of nutrient uptake and assimilation activities are distributed heterogeneously across organisms over periodic input cycles. Recent analysis of community transcriptional dynamics in the nitrogen-limited subtropical North Pacific gyre revealed evidence of temporal partitioning of nitrogen uptake and assimilation between eukaryotic phytoplankton, cyanobacteria, and heterotrophic bacteria over day-night cycles. Here, we present results from a Lagrangian metatranscriptomic time series survey in the Sargasso Sea and demonstrate temporally partitioned phosphorus uptake in this phosphorus-limited environment. In the Sargasso, heterotrophic bacteria, eukaryotic phytoplankton, and cyanobacteria express genes for phosphorus assimilation during the morning, day, and dusk, respectively. These results support the generality of temporal niche partitioning as an emergent mechanism structuring uptake of limiting nutrients and facilitating coexistence of diverse microbes in open ocean ecosystems.
Mesenchymal Stromal Cell Senescence Induced byDnmt3a-Mutant Hematopoietic Cells is a Targetable Mechanism Driving Clonal Hematopoiesis and Initiation of Hematologic Malignancy
Authors: Mistry Jayna J. , Young Kira A. , Colom Díaz Patricia A. , Maestre Inés Fernández , Levine Ross L. , Trowbridge Jennifer J. 
Published: March 2024

AbstractClonal hematopoiesis (CH) can predispose to blood cancers due to enhanced fitness of mutant hematopoietic stem and progenitor cells (HSPCs), but the mechanisms driving this progression are not understood. We hypothesized that malignant progression is related to microenvironment-remodelling properties of CH-mutant HSPCs. Single-cell transcriptomic profiling of the bone marrow microenvironment inDnmt3aR878H/+mice revealed signatures of cellular senescence in mesenchymal stromal cells (MSCs).Dnmt3aR878H/+HSPCs caused MSCs to upregulate the senescence markers SA-β-gal, BCL-2, BCL-xL,Cdkn1a(p21) andCdkn2a(p16),ex vivoandin vivo. This effect was cell contact-independent and can be replicated by IL-6 or TNFα, which are produced byDnmt3aR878H/+HSPCs. Depletion of senescent MSCsin vivoreduced the fitness ofDnmt3aR878H/+hematopoietic cells and the progression of CH to myeloid neoplasms using a sequentially inducibleDnmt3a;Npm1-mutant model. Thus,Dnmt3a-mutant HSPCs reprogram their microenvironment via senescence induction, creating a self-reinforcing niche favoring fitness and malignant progression.Statement of SignificanceMesenchymal stromal cell senescence induced byDnmt3a-mutant hematopoietic stem and progenitor cells drives clonal hematopoiesis and initiation of hematologic malignancy.
Tools forCre-mediated conditional deletion of floxed alleles from developing cerebellar Purkinje cells
Authors: Jahncke Jennifer N. , Wright Kevin M. 
Published: March 2024

AbstractThe Cre-lox system is an indispensable tool in neuroscience research for targeting gene deletions to specific cellular populations. Here we assess the utility of several transgenicCrelines, along with a viral approach, for targeting cerebellar Purkinje cells. Using a combination of a fluorescent reporter line (Ai14) to indicateCre-mediated recombination and a floxedDystroglycanline (Dag1flox) we show that reporter expression does not always align precisely with loss of protein. The commonly usedPcp2Creline exhibits a gradual mosaic pattern ofCrerecombination in Purkinje cells from P7-P14, while loss of Dag1 protein is not complete until P30.Ptf1aCredrives recombination in precursor cells that give rise to GABAergic neurons in the embryonic cerebellum, including Purkinje cells and molecular layer interneurons. However, due to its transient expression in precursors,Ptf1aCreresults in stochastic loss of Dag1 protein in these neurons.NestinCre, which is often described as a “pan-neuronal”Creline for the central nervous system, does not driveCre-mediated recombination in Purkinje cells. We identify aCalb1Creline that drives efficient and complete recombination in embryonic Purkinje cells, resulting in loss of Dag1 protein before the period of synaptogenesis.AAV8-mediated delivery ofCreat P0 results in gradual transduction of Purkinje cells during the second postnatal week, with loss of Dag1 protein not reaching appreciable levels until P35. These results characterize several tools for targeting conditional deletions in cerebellar Purkinje cells at different developmental stages and illustrate the importance of validating the loss of protein following recombination.Significance StatementThe development ofCrelines for targeting gene deletions to defined cellular populations has led to important discoveries in neuroscience. As with any tool, there are inherent limitations that must be carefully considered. Here we describe severalCrelines available for targeting of cerebellar Purkinje cells at various developmental stages. We use the combination of aCre-dependent fluorescent reporter line and conditional deletion of the synaptic scaffolding molecule Dystroglycan as an example to highlight the potential disconnect between the presence of a fluorescent reporter and the loss of protein.
Overwintering performance of juvenile temperate estuarine fish
Authors: Bellotto Clara , Fowler Ashley M. , Booth David J. 
Published: March 2024

AbstractEstuaries, rich in biodiversity and economically valuable species, are increasingly threatened by climate change-induced factors that challenge fish resilience and survival. This study compared the performance of estuarine fishes between water temperatures reflecting two scenarios: current Sydney winters (16°C) and future winters under climate change (20°C), and at two food levels, for three estuarine fish species (eastern fortescue,Centropogon australis, common silverbiddy,Gerres subfasciatus,and eastern striped trumpeter,Pelates sexlineatus) Overall, as expected from metabolic theory, fish performance was generally higher at higher temperatures, with growth rates higher at 20°C forG. subfasciatusandC. australis.Bite rates and aerobic scope were generally higher at the higher temperature for all species.G. subfasciatusandP. sexlineatusexhibited increased escape responses at 20°C, withP. sexlineatusalso showing greater boldness. Boldness was positively associated with bite rates inP. sexlineatus, potentially indicating foraging advantages under future warming for this species. The order of temperature treatment (20°C then 16°C, vs 16°C then 20°C) affected boldness forG. subfasciatusand growth rate, total length, bite rate and burst speed forP. sexlineatus.Contrary to expectations, food had no effect on fish performance either directly or interacting with temperature, and all three species generally performed better at 20°C than 16°C, suggesting this study was conducted below the species’ thermal optima. Future climate change may therefore favour temperate estuarine fishes at winter temperatures, with potential benefits differing among these species.
Stacking haplotypes from the Vavilov wheat collection to accelerate breeding for multiple disease resistance
Authors: Tong Jingyang , Tarekegn Zerihun T. , Alahmad Samir , Hickey Lee T. , Periyannan Sambasivam K. , Dinglasan Eric , Hayes Ben J. 
Published: March 2024

SummaryWheat production is threatened by numerous fungal diseases, but the potential to breed for multiple disease resistance (MDR) mechanisms is yet to be explored. Here, significant global genetic correlations and underlying local genomic regions were identified in the Vavilov wheat diversity panel for six major fungal diseases, including biotrophic leaf rust (LR), yellow rust (YR), stem rust (SR), hemibiotrophic crown rot (CR), and necrotrophic tan spot (TS) and Septoria nodorum blotch (SNB). By adopting haplotype-based local genomic estimated breeding values, derived from an integrated set of 34,899 SNP and DArT markers, we established a novel haplotype catalogue for resistance to the six diseases in over 20 field experiments across Australia and Ethiopia. Haploblocks with high variances of haplotype effects in all environments were identified for three rusts and pleiotropic haploblocks were identified for at least two diseases, with four haploblocks affecting all six diseases. Through simulation we demonstrated that stacking optimal haplotypes for one disease could improve resistance substantially, but indirectly affected resistance for other five diseases, which varied depending on the genetic correlation with the non-target disease trait. On the other hand, our simulation results combining beneficial haplotypes for all diseases increased resistance to LR, YR, SR, CR, TS and SNB, by up to 48.1%, 35.2%, 29.1%, 12.8%, 18.8% and 32.8%, respectively. Overall, our results highlight the genetic potential to improve MDR in wheat. The haploblock-based catalogue with novel forms of resistance provides a useful resource to guide desirable haplotype stacking for breeding future wheat cultivars with MDR.
Acute promyelocytic leukemia with torque teno mini virus (TTMV)::RARAfusion: an approach to screening and diagnosis
Authors: Tsai Harrison K. , Sabbagh Mark F. , Montesion Meagan , Williams Erik A. , Arbini Arnaldo , Boué Daniel R. , Harris Emily M. , Wachter Franziska , Grimmett Leslie , Place Andrew E. , Lucas Fabienne , Nardi Valentina , Kim Annette S. , Brugnara Carlo , Degar Barbara , Pollard Jessica , Harris Marian H. , Bledsoe Jacob R. 
Published: March 2024

AbstractAcute promyelocytic leukemia (APL) with variantRARAtranslocation is linked to over 15 partner genes. Recent publications encompassing six cases have expanded the spectrum ofRARApartners to torque teno mini virus (TTMV). This entity is likely under-recognized due to lack of clinician and pathologist familiarity, inability to detect the fusion using routine testing modalities, and informatic challenges in its recognition within next-generation sequencing (NGS) data. We describe a clinicopathologic approach and provide necessary tools to screen and diagnose APL with TTMV::RARAusing existing clinical DNA or RNA-based NGS assays, which led to identification of four cases, all without other known cytogenetic/molecular drivers. One was identified prospectively and three retrospectively, including two from custom automated screening of multiple data sets (50,257 cases of hematopoietic malignancy, including 4809 acute myeloid leukemia (AML)/myeloid sarcoma/APL cases). Two cases presented as myeloid sarcoma, including one with multiple relapses after AML-type chemotherapy and hematopoietic stem cell transplant (HSCT). Two cases presented as leukemia, had a poor response to induction chemotherapy, but achieved remission upon re-induction (including all-trans retinoic acid (ATRA) in one case) and subsequent HSCT. Neoplastic cells demonstrated features of APL including frequent azurophilic granules and dim/absent CD34 and HLA-DR expression.RARArearrangement was not detected by karyotype or FISH. Custom analysis of NGS fusion panel data identified TTMV::RARArearrangements, and in the prospectively identified case, facilitated monitoring in sequential bone marrow samples. APL with TTMV::RARAis a rare leukemia with a high rate of treatment failure in described cases. The diagnosis should be considered in leukemias with features of APL that lack detectableRARAfusions and other drivers, and may be confirmed by appropriate NGS tests with custom informatics. Incorporation of ATRA may have a role in treatment but requires accurate recognition of the fusion for appropriate classification as APL.
Reverse Mendelian randomization separates causes from early proteomic biomarkers of glioma
Authors: Andrews Lily J , Thornton Zak A , Zheng Jie , Robinson Jamie W , Hemani Gibran , Kurian Kathreena M 
Published: March 2024

AbstractBackground/ObjectivesGlioma represents the largest entity of primary brain tumours in adults, with an overall survival of less than 20% over 5 years. Glioblastoma is the most frequent and aggressive glioma subtype. At present, there are few well-established pre-clinical predictors for glioma incidence. Due to the availability and size of prognostic studies in glioma, we utilised a Mendelian randomization framework to identify non-causal protein biomarkers which are associated with early-onset of glioma in the European population.MethodsWe generated polygenic risk scores (PRS) for glioma (n=12,496), glioblastoma (n=6,191), and non-glioblastoma (n=5,819) cases. We used reverse Mendelian randomization (MR) to examine the relationship between the genetic liability of glioma and 1,463 and 90 proteins were measured using an Olink panel (UKBB, n=35,571 and SCALLOP, n=21,758), additionally 4,907 and 2,994 aptamers were assayed using SOMAscan assays (deCODE n=35,559 and INTERVAL, n=3,301). We further performed a forward cis-MR and colocalization analysis leveraging the circulating protein markers in risk of glioma, glioblastoma and non-glioblastoma.ResultsReverse MR identified 161 unique proteins associated with the PRS of glioma, 79 proteins associated with the PRS of glioblastoma, and 11 proteins associated with the PRS of non-glioblastoma. Enrichment analyses identified a proportion of plasma proteins to be associated with the PRS of glioma to be correlated with response to external stimulus. A group of plasma proteins linked to the PRS of glioma and glioblastoma were related to the immune system process. Forward MR of the putative relationships were found to have little or no evidence of association on the causal pathway. Candidate markers ETFA, RIR1 and BT3A1 are evidenced in glioma risk.ConclusionOur findings identify a high genetic liability to glioma is associated with the immune system processes. Non-causal plasma biomarkers identified through PRS associations could indicate novel non-causal biomarkers of early glioma development.
Regional Variation in the Interpretation of Contact Precautions for Multidrug-resistant Gram-negative bacteria: a cross-sectional survey
Authors: van Veen Anneloes , de Goeij Inge , Damen Marjolein , Huijskens Elisabeth G.W. , Paltansing Sunita , van Rijn Michiel , Bentvelsen Robbert G. , Veenemans Jacobien , van der Linden Michael , Vos Margreet C. , Severin Juliëtte A. 
Published: March 2024

SummaryBackgroundContact precautions (CP) are recommended when caring for patients with carbapenemase-producing Enterobacterales (CPE), carbapenemase-producingPseudomonas aeruginosa(CPPA), and extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E).AimOur aim was to determine the interpretation of CP and associated infection prevention and control (IPC) measures in the non-ICU hospital setting for patients with CPE, CPPA or ESBL-E in 11 hospitals in the Southwest of the Netherlands.MethodsA cross-sectional survey was developed to collect information on all implemented IPC measures, including use of personal protective equipment, IPC measures for visitors, cleaning and disinfection, precautions during outpatient care and follow-up strategies. All eleven hospitals were invited to participate between November 2020 and April 2021.FindingsThe survey was filled together with each hospital. All hospitals installed isolation precautions for patients with CPE and CPPA during inpatient care and day admissions, whereas ten hospitals (90.9%) applied isolation precautions for patients with ESBL-E. Gloves and gowns were always used during physical contact with the patient in isolation. Large variations were identified in IPC measures for visitors, cleaning and disinfection products used, and precautions during outpatient care. Four hospitals (36.4%) actively followed up on CPE or CPPA patients with the aim to declare them CPE- or CPPA-negative as timely as possible, and two hospitals (20.0%) actively followed up on ESBL-E patients.ConclusionCP are interpreted differently between hospitals, leading to regional differences in IPC measures applied in clinical settings. Harmonizing infection-control policies between the hospitals could facilitate patient transfers and benefit collective efforts of preventing transmission of MDR-GNB.
LOMIA-T: A Transformer-based LOngitudinal Medical Image Analysis framework for predicting treatment response of esophageal cancer
Authors: Sun Yuchen , Li Kunwei , Chen Duanduan , Hu Yi , Zhang Shuaitong 
Published: March 2024

AbstractDeep learning models based on medical images have made significant strides in predicting treatment outcomes. However, previous methods have primarily concentrated on single time-point images, neglecting the temporal dynamics and changes inherent in longitudinal medical images. Thus, we propose a Transformer-based longitudinal image analysis framework (LOMIA-T) to contrast and fuse latent representations from pre- and post-treatment medical images for predicting treatment response. Specifically, we first design a treatment response- based contrastive loss to enhance latent representation by discerning evolutionary processes across various disease stages. Then, we integrate latent representations from pre- and post-treatment CT images using a cross-attention mechanism. Considering the redundancy in the dual-branch output features induced by the cross-attention mechanism, we propose a clinically interpretable feature fusion strategy to predict treatment response. Experimentally, the proposed framework outperforms several state-of-the-art longitudinal image analysis methods on an in-house Esophageal Squamous Cell Carcinoma (ESCC) dataset, encompassing 170 pre- and post-treatment contrast-enhanced CT image pairs from ESCC patients underwent neoadjuvant chemoradiotherapy. Ablation experiments validate the efficacy of the proposed treatment response-based contrastive loss and feature fusion strategy. The codes will be made available athttps://github.com/syc19074115/LOMIA-T.