bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic and epigenetic signatures for improved breeding of cultivated blueberry
Authors: Wang Zejia , Zhang Wanchen , Zhou Yangyan , Zhang Qiyan , Kulkarni Krishnanand P , Melmaiee Kalpalatha , Tian Youwen , Dong Mei , Gao Zhaoxu , Su Yanning , Yu Hong , Xu Guohui , Li Yadong , He Hang , Liu Qikun , Sun Haiyue 
Published: May 2024

Abstract
Blueberry belongs to the Vaccinium genus and is a highly popular fruit crop with significant economic importance. It was not until the early twentieth century that they began to be domesticated through extensive interspecific hybridization. Here, we collected 220 Vaccinium accessions from various geographical locations, including 154 from the United States, 14 from China, eight from Australia, and 29 from Europe and other countries, comprising 164 Vaccinium corymbosum, 15 Vaccinium ashei, 10 lowbush blueberries, seven half-high blueberries, and others. We present the whole-genome variation map of 220 accessions and reconstructed the hundred-year molecular history of interspecific hybridization of blueberry. We focused on the two major blueberry subgroups, the northern highbush blueberry (NHB) and southern highbush blueberry (SHB) and identified candidate genes that contribute to their distinct traits in climate adaptability and fruit quality. Our analysis unveiled the role of gene introgression from Vaccinium darrowii and V. ashei into SHB in driving the differentiation between SHB and NHB, potentially facilitating SHB’s adaptation to subtropical environments. Assisted by genome-wide association studies, our analysis suggested VcTBL44 as a pivotal gene regulator governing fruit firmness in SHB. Additionally, we conducted whole-genome bisulfite sequencing on nine NHB and 12 SHB cultivars, and characterized regions that are differentially methylated between the two subgroups. In particular, we discovered that the β-alanine metabolic pathway genes were enriched for DNA methylation changes. Our study provides high-quality genetic and epigenetic variation maps for blueberry, which offer valuable insights and resources for future blueberry breeding.
Heat-killed Lactiplantibacillus plantarum Shinshu N-07 exerts antiobesity effects in western diet-induced obese mice
Authors: Tanaka Yuna , Inaba Chihiro , Sawa Toko , Endo Katsunori , Saiki Takeru , Haga Hazuki , Niitsuma Fumie , Kawahara Takeshi , Watanabe Jun , Tanaka Sachi 
Published: May 2024

Abstract

Aims
The aim of this study was to evaluate the antiobesity effects of heat-killed Lactiplantibacillus plantarum Shinshu N-07 (N-07) isolated from fermented Brassica rapa L.

Methods and results
Male mice were divided into three groups (n = 10/group); normal diet, western diet (WD), or WD + N-07 (N-07) group and administered each diet for 56 days. The N-07 group showed significant suppression of body weight gain and epididymal fat, perirenal fat, and liver weights compared with the WD group. Higher levels of fecal total cholesterol, triglyceride (TG), and free fatty acid (FFA) were observed in the N-07 group than in the WD group. The mRNA expression of the cholesterol transporter ATP-binding cassette transporter G5 (ABCG5) was significantly increased in the small intestine of N-07-fed mice compared with WD-fed mice. Moreover, N-07 supplementation significantly increased the mRNA expression of ABCG5 and ABCG8 in Caco-2 cells. Furthermore, the TG- and FFA-removal ability of N-07 was confirmed to evaluate its soybean oil- and oleic acid-binding capacities in in vitro experiments.

Conclusions
The antiobesity effects of N-07 might be due to its ability to promote lipid excretion by regulating cholesterol transporter expression and lipid-binding ability.
Design and implementation of electronic health record-based tools to support a weight management program in primary care
Authors: Kukhareva Polina V , Weir Charlene R , Cedillo Maribel , Taft Teresa , Butler Jorie M , Rudd Elizabeth A , Zepeda Jesell , Zheutlin Emily , Kiraly Bernadette , Flynn Michael , Conroy Molly B , Kawamoto Kensaku 
Published: May 2024

Abstract

Objectives
This paper reports on a mixed methods formative evaluation to support the design and implementation of information technology (IT) tools for a primary care weight management intervention delivered through the patient portal using primary care staff as coaches.

Methods
We performed a qualitative needs assessment, designed the IT tools to support the weight management program, and developed implementation tracking metrics. Implementation tracking metrics were designed to use real world electronic health record (EHR) data.

Results
The needs assessment revealed IT requirements as well as barriers and facilitators to implementation of EHR-based weight management interventions in primary care. We developed implementation metrics for the IT tools. These metrics were used in weekly project team calls to make sure that project resources were allocated to areas of need.

Conclusion
This study identifies the important role of IT in supporting weight management through patient identification, weight and activity tracking in the patient portal, and the use of the EHR as a population management tool. An intensive multi-level implementation approach is required for successful primary care-based weight management interventions including well-designed IT tools, comprehensive involvement of clinic leadership, and implementation tracking metrics to guide the process of workflow integration. This study helps to bridge the gap between informatics and implementation by using socio-technical formative evaluation methods early in order to support the implementation of IT tools.

Trial registration
clinicaltrials.gov, NCT04420936. Registered June 9, 2020.
Mobilization With Femoral Catheters in the Burn ICU: A Retrospective Review Following Change in Practice Guidelines
Authors: O’Neil Audrey M , Boyd Allison , Rush Cassandra , Roggy David , Walroth Todd , Hartman Brett 
Published: May 2024

Abstract
Femoral catheters are commonly viewed as a barrier to Burn ICU mobility progression due to anatomical location and potential risk of complications. The purpose of this review was to examine outcomes and complication rates following implementation of femoral catheter mobilization guidelines, as well as determine safety and feasibility of mobilization with femoral catheters in place within the burn population. A retrospective review was completed on 17 patients prior to and following the implementation of new femoral catheter mobility guidelines, 34 patients total. Burn therapy notes were reviewed for burn admissions with at least 1 femoral catheter in place, including arterial, central, and dialysis catheters. Demographic data, admission statistics, line placement timelines, and active mobility achieved during therapy sessions were recorded for both the nonmobilization group (NMG) and mobilization group (MG). The 34 patients reviewed had 99 total lines placed (30 NMG, 69 MG). Change in mobility protocols for the MG resulted in more therapy sessions (n = 516 vs 281) and a significant increase in active mobility sessions (n = 83 vs 5, P &lt; .001), including 146 total mobility activities such as transitions to chairs, tilt table, sitting edge of bed, standing, active chair transfers, ambulation, and cycle ergometry. No catheter-associated adverse events occurred during active mobility sessions and no complications were associated with participation in mobility. This review supports that the presence of femoral catheters alone should not limit the progression of mobility interventions with the use of clinical judgment in specialty-trained burn therapists.
Using eDNA to play whack-a-mole with invasive species in green yard waste
Authors: Neven Lisa G , Walker William B , Gowton Chelsea , Carrillo Juli 
Published: May 2024

Abstract
As large cities begin to overrun their landfill capacities, they begin to look for alternative locations to handle the waste stream. Seeing an opportunity to bring in revenue, rural communities offer to handle municipal waste in their landfills. However, many rural communities are also places of agricultural production, which are vulnerable to attacks by invasive insect species, which could be present in green yard waste, the component of municipal waste most likely to contain agriculturally harmful insect species. We used environmental DNA (eDNA) to determine whether green yard waste could be a pathway for invasive insect species to enter and establish in the landfill-receiving agricultural community. We identified several target species that could be in green yard waste coming from Vancouver, BC, Canada, to Central Washington State, USA. We sampled green yard waste from 3 sites every 2 weeks from June to October in 2019 and 2020. DNA was extracted from the nearly 400 samples and subjected to amplification with COI barcoding primers followed by sequencing to identify target insects in the samples. Sequence analyses identified 3 species from the target list: 2 species that are pests of deciduous tree fruits and a generalist root-feeding crop pest. This eDNA technique was useful in identifying potential invasive species in green yard waste and may prove to be an important tool informing policy on the movement of biological material across borders and stemming the spread of invasive species.
The evolution of supermassive black hole mass–bulge mass relation by a semi-analytical model, ν2GC
Authors: Shimizu Tatsuki , Oogi Taira , Okamoto Takashi , Nagashima Masahiro , Enoki Motohiro 
Published: May 2024

ABSTRACT
We have investigated the redshift evolution of the relationship between supermassive black hole (SMBH) mass and host bulge mass using a semi-analytical galaxy formation model ν2GC. Our model reproduces the relation in the local universe well. We find that, at high redshift (z ≳ 3), two sequences appear in the SMBH mass–bulge mass plane. The emergence of these two sequences can be attributed to the primary triggers of the growth of the SMBHs and bulges: galaxy mergers and disc instabilities. The growth of SMBHs and bulges as a result of galaxy mergers is responsible for giving rise to the high-mass sequence, in which SMBHs are more massive for a given host bulge mass than in the low-mas sequence. Conversely, disc instabilities are accountable for the emergence of the low-mass sequence. At lower redshifts, galaxy mergers tend to become increasingly deficient in gas, resulting in a preferential increase of bulge mass without a corresponding growth in SMBH mass. This has the effect of causing galaxies in the upper sequence to shift towards the lower one on the SMBH mass–bulge mass plane. The galaxies that undergo dry mergers serve to bridge the gap between the two sequences, eventually leading to convergence into a single relation known in the local universe. Our results suggest that the observations of the SMBH mass–bulge mass relation in high redshifts can provide insight into their growth mechanisms.
redback: a Bayesian inference software package for electromagnetic transients
Authors: Sarin Nikhil , Hübner Moritz , Omand Conor M B , Setzer Christian N , Schulze Steve , Adhikari Naresh , Sagués-Carracedo Ana , Galaudage Shanika , Wallace Wendy F , Lamb Gavin P , Lin En-Tzu 
Published: May 2024

ABSTRACT
Fulfilling the rich promise of rapid advances in time-domain astronomy is only possible through confronting our observations with physical models and extracting the parameters that best describe what we see. Here, we introduce redback; a Bayesian inference software package for electromagnetic transients. redback provides an object-orientated python interface to over 12 different samplers and over 100 different models for kilonovae, supernovae, gamma-ray burst afterglows, tidal disruption events, engine-driven transients among other explosive transients. The models range in complexity from simple analytical and semi-analytical models to surrogates built upon numerical simulations accelerated via machine learning. redback also provides a simple interface for downloading and processing data from various catalogues such as Swift and FINK. The software can also serve as an engine to simulate transients for telescopes such as the Zwicky Transient Facility and Vera Rubin with realistic cadences, limiting magnitudes, and sky coverage or a hypothetical user-constructed survey or a generic transient for target-of-opportunity observations with different telescopes. As a demonstration of its capabilities, we show how redback can be used to jointly fit the spectrum and photometry of a kilonova, enabling a more powerful, holistic probe into the properties of a transient. We also showcase general examples of how redback can be used as a tool to simulate transients for realistic surveys, fit models to real, simulated, or private data, multimessenger inference with gravitational waves, and serve as an end-to-end software toolkit for parameter estimation and interpreting the nature of electromagnetic transients.
Detecting rare neutral atomic-carbon absorbers with a deep neural network
Authors: Ge Jian , Willis Kevin , Chao Kaixuan , Jan Albert , Zhao Yinan , Fang Hannah 
Published: May 2024

ABSTRACT
C i absorbers play an important role as indicators for exploring the presence of cold gas in the interstellar medium of galaxies. However, the current data base of C i absorbers is very limited due to their weak absorption feature and rarity. Here, we report results from a search of C i λλ1560, 1656 absorption lines using Mg ii absorbers as signposts with modified deep learning algorithms, which provides a very quick way to search for weak C i absorber candidates. A total of 107 C i absorbers were detected, which nearly doubles the size of previously known samples. In addition, we found 17 C i absorbers to be associated with 2175 Å dust absorbers (2DAs), i.e. about 16 per cent C i absorbers are associated with 2DAs. Comparing the average dust depletion patterns of C i absorbers with those of damped Lyman α absorbers (DLAs), Mg ii absorbers, Ca ii absorbers, and 2175 Å dust absorbers (2DAs) shows that C i absorbers generally have environments with more dust than DLAs, Mg ii, and Ca ii absorbers, but similar to dust in 2DAs. Similarity between the dust depletion pattern of C i absorbers to that of the warm disc in the Milky Way indicates that C i absorption clouds are possibly associated with disc components in distant galaxies. Therefore, C i absorbers are confirmed to be excellent probes to trace cold gas and dust in the Universe.
Boundary Effects Cause False Signals of Range Expansions in Population Genomic Data
Authors: Kemppainen Petri , Schembri Rhiannon , Momigliano Paolo 
Published: May 2024

Abstract
Studying range expansions is central for understanding genetic variation through space and time as well as for identifying refugia and biological invasions. Range expansions are characterized by serial founder events causing clines of decreasing genetic diversity away from the center of origin and asymmetries in the two-dimensional allele frequency spectra. These asymmetries, summarized by the directionality index (ψ), are sensitive to range expansions and persist for longer than clines in genetic diversity. In continuous and finite meta-populations, genetic drift tends to be stronger at the edges of the species distribution in equilibrium populations and populations undergoing range expansions alike. Such boundary effects are expected to affect geographic patterns in genetic diversity and ψ. Here we demonstrate that boundary effects cause high false positive rates in equilibrium meta-populations when testing for range expansions. In the simulations, the absolute value of ψ (|ψ|) in equilibrium data sets was proportional to the fixation index (FST). By fitting signatures of range expansions as a function of ɛ |ψ|/FST and geographic clines in ψ, strong evidence for range expansions could be detected in data from a recent rapid invasion of the cane toad, Rhinella marina, in Australia, but not in 28 previously published empirical data sets from Australian scincid lizards that were significant for the standard range expansion tests. Thus, while clinal variation in ψ is still the most sensitive statistic to range expansions, to detect true signatures of range expansions in natural populations, its magnitude needs to be considered in relation to the overall levels of genetic structuring in the data.
DORA: an interactive map for the visualization and analysis of ancient human DNA and associated data
Authors: Harris Keith D , Greenbaum Gili 
Published: May 2024

Abstract
The ability to sequence ancient genomes has revolutionized the way we study evolutionary history by providing access to the most important aspect of evolution—time. Until recently, studying human demography, ecology, biology, and history using population genomic inference relied on contemporary genomic datasets. Over the past decade, the availability of human ancient DNA (aDNA) has increased rapidly, almost doubling every year, opening the way for spatiotemporal studies of ancient human populations. However, the multidimensionality of aDNA, with genotypes having temporal, spatial and genomic coordinates, and integrating multiple sources of data, poses a challenge for developing meta-analyses pipelines. To address this challenge, we developed a publicly-available interactive tool, DORA, which integrates multiple data types, genomic and non-genomic, in a unified interface. This web-based tool enables browsing sample metadata alongside additional layers of information, such as population structure, climatic data, and unpublished samples. Users can perform analyses on genotypes of these samples, or export sample subsets for external analyses. DORA integrates analyses and visualizations in a single intuitive interface, resolving the technical issues of combining datasets from different sources and formats, and allowing researchers to focus on the scientific questions that can be addressed through analysis of aDNA datasets.
Single-molecule imaging reveals a direct role of CTCF’s zinc fingers in SA interaction and cluster-dependent RNA recruitment
Authors: Huber Jonas , Tanasie Nicoleta-Loredana , Zernia Sarah , Stigler Johannes 
Published: May 2024

Abstract
CTCF is a zinc finger protein associated with transcription regulation that also acts as a barrier factor for topologically associated domains (TADs) generated by cohesin via loop extrusion. These processes require different properties of CTCF-DNA interaction, and it is still unclear how CTCF’s structural features may modulate its diverse roles. Here, we employ single-molecule imaging to study both full-length CTCF and truncation mutants. We show that CTCF enriches at CTCF binding sites (CBSs), displaying a longer lifetime than observed previously. We demonstrate that the zinc finger domains mediate CTCF clustering and that clustering enables RNA recruitment, possibly creating a scaffold for interaction with RNA-binding proteins like cohesin's subunit SA. We further reveal a direct recruitment and an increase of SA residence time by CTCF bound at CBSs, suggesting that CTCF-SA interactions are crucial for cohesin stability on chromatin at TAD borders. Furthermore, we establish a single-molecule T7 transcription assay and show that although a transcribing polymerase can remove CTCF from CBSs, transcription is impaired. Our study shows that context-dependent nucleic acid binding determines the multifaceted CTCF roles in genome organization and transcription regulation.
ATM-mediated co-chaperone DNAJB11 phosphorylation facilitates α-synuclein folding upon DNA double-stranded breaks
Authors: Chen Huan-Yun , Liao Chia-Yu , Li Hsun , Ke Yi-Ci , Lin Chin-Hsien , Teng Shu-Chun 
Published: May 2024

Abstract
Parkinson's disease (PD) is a prevalent neurodegenerative disorder marked by the pathological accumulation of α-synuclein aggregates in dopaminergic neurons. This α-synuclein dyshomeostasis is caused by an interplay between aging, genetic and environmental factors. Aging process-related DNA damage and impaired DNA repair have recently been observed in the PD process. However, the precise neuronal response to DNA damage in PD remains largely unknown. Here, we demonstrate that double-strand breaks (DSBs) induce α-synuclein aggregation. Analysis of a large-scale proteomic analysis of ATM and ATR substrates identified a potential candidate in the HSP70 folding system responding to DNA damage. ATM phosphorylates co-chaperone DNAJB11 at threonine 188 which specifically facilitates the delivery of misfolded α-synuclein, but not tau or transthyretin protein, to the HSP70 folding system upon DSBs. Alteration of this response impairs the neurite outgrowth. Remarkably, DNAJB11 threonine 188 phosphorylation correlates with disease severity in transgenic SNCA mutant PD mice and PD patients. These findings reveal a DNA damage-responded HSP70 folding mechanism through a J-domain co-chaperone, offering a potential therapeutic target for PD.
Resistance, rebound, and recurrence regrowth patterns in pediatric low-grade glioma treated by MAPK inhibition: A modified Delphi approach to build international consensus-based definitions—International Pediatric Low-Grade Glioma Coalition
Authors: O’Hare Patricia , Cooney Tabitha , de Blank Peter , Gutmann David H , Kieran Mark , Milde Till , Fangusaro Jason , Fisher Michael , Avula Shivaram , Packer Roger , Fukuoka Kohei , Mankad Kshitij , Mueller Sabine , Waanders Angela J , Opocher Enrico , Bouffet Eric , Raabe Eric , Werle Natacha Entz , Azizi Amedeo A , Robison Nathan J , Hernáiz Driever Pablo , Russo Mark , Schouten Netteke , van Tilburg Cornelis M , Sehested Astrid , Grill Jacques , Bandopadhayay Pratiti , Kilday John-Paul , Witt Olaf , Ashley David M , Ertl-Wagner Birgit Betina , Tabori Uri , Hargrave Darren R 
Published: May 2024

Abstract
Pediatric low-grade glioma (pLGG) is the most common childhood brain tumor group. The natural history, when curative resection is not possible, is one of a chronic disease with periods of tumor stability and episodes of tumor progression. While there is a high overall survival rate, many patients experience significant and potentially lifelong morbidities. The majority of pLGGs have an underlying activation of the RAS/MAPK pathway due to mutational events, leading to the use of molecularly targeted therapies in clinical trials, with recent regulatory approval for the combination of BRAF and MEK inhibition for BRAFV600E mutated pLGG. Despite encouraging activity, tumor regrowth can occur during therapy due to drug resistance, off treatment as tumor recurrence, or as reported in some patients as a rapid rebound growth within 3 months of discontinuing targeted therapy. Definitions of these patterns of regrowth have not been well described in pLGG. For this reason, the International Pediatric Low-Grade Glioma Coalition, a global group of physicians and scientists, formed the Resistance, Rebound, and Recurrence (R3) working group to study resistance, rebound, and recurrence. A modified Delphi approach was undertaken to produce consensus-based definitions and recommendations for regrowth patterns in pLGG with specific reference to targeted therapies.