bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cryptic connectivity between hyporheic and riparian zones via winged aquatic insects revealed by DNA barcoding
Authors: Negishi JN , Alam MK , Tojo K , Nakamura F 
Published: November 2023

AbstractHow subsurface hyporheic zone (HZ) of rivers is connected to riparian zones remains largely unknown. We collected benthic macroinvertebrates and adult aquatic insects for six years, including those at 30-cm depth in the HZ to identify insect taxa having a high level of habitat affinity for HZ (HZ taxa). Adults of HZ taxa were identified with the aid of CO1 gene barcoding, and the relative abundance of HZ taxa in the riparian zone was quantified. In addition to the previously known stoneflyAlloperla ishikariana, three species of stonefly Leuctridae and one caddisfly species of Philopotamidae were identified as HZ taxa. At the annual scale, HZ taxa accounted for approximately 38% of the total aquatic insects in the family of stoneflies (Plecoptera), caddisflies (Trichoptera), and mayflies (Ephemeroptera) in abundance and 26% of biomass, with their seasonal peaks in early spring and mid-summer (60% in abundance and 47% in biomass). Few individuals of HZ taxa were found in benthic samples (<0.1%), and hyporheic samples quantified more but erroneously estimated relative abundances of adult HZ taxa, with Leuctridae and Philopotamidae being substantially underrepresented relative to their adult abundance. Cryptic biological connectivity between subsurface and riparian zones via winged HZ-taxa adults is substantial. DNA-based species identification combined with community surveys of adult HZ-taxa complementarily used with benthic data can substantially improve the effectiveness of biomonitoring programs and outcomes of habitat conservation based on more complete picture of ecosystem health.
Plant neighbors differentially alter a focal species’ biotic interactions through changes to resource allocation
Authors: Turner Sophia C. , Schweitzer Jennifer A. 
Published: November 2023

AbstractPlant resource allocation strategies are thought to be largely a consequence of changing abiotic conditions and evolutionary history. However, biotic interactions also influence how a plant allocates resources. As a result, plants mediate indirect interactions between organisms above- and belowground through resource allocation. Neighboring plants can influence plant fitness directly through competition for resources, and indirectly by altering associated community interactions (associational effects). Given the importance of community interactions for plant success, and the known ability for plant neighbors to change these interactions, the goal of this “pandemic project” was to separate inter- and intraspecific plant associations, above- and belowground, to understand how different plant neighbors alter plant resource allocation, and if this in turn alters biotic interactions. We specifically investigated associational effects on herbivory and soil microbial community interactions. To do so, we established a common garden experiment, manipulating plant neighbors and extent of interactions (aboveground only versus above- and belowground interactions, using customized pot types), and measured changes to a focal plant and its biotic interactions over two growing seasons. We found evidence of both neighbor effects and pot type, showing that neighbor interactions affect a focal plant through both above- and belowground processes, and how the focal plant is affected depends on neighbor identity. Though neighbors did not directly alter herbivory or most soil microbial interactions, they did alter the relationship between belowground microbial communities and plant function. Resource allocation responses were reduced with time, showing the importance of extending experiments beyond a single growing season, and is an important consideration when making predictions about plant responses to changing conditions. This study contributes to a growing body of work showing how the community context affects the above- and belowground interactions of a plant through plant resource allocation strategies.
From initial RNA encoding to the Standard Genetic Code
Authors: Yarus Michael 
Published: November 2023

AbstractMultiple experiments have shown that RNA binds chemically varied amino acids within specific oligoibonucleotide sequences. The smallest, simplest, and potentially most primitive RNA binding sites frequently contain conserved triplets corresponding to the Standard Genetic Code (SGC). Here, implications of such cognate coding triplets are calculated, combining them with an optimized kinetic model for SGC evolution. RNA-amino acid interactions at observed frequencies choose an SGC-like code, and, using the same mechanism, effectively resist alternative triplet assignments. Resistance to other kinds of coding is evident across varied code initiation scenarios. RNA-mediated assignments at experimental frequencies are sufficient to guide the ‘ribonucleopeotide transition’ (RNPT) to a modern code. This can account for extreme selection of the SGC among its astronomical code possibilities; very SGC-like codes are ca. 1/50 to 1/5 of codes within such a population. Nevertheless, full accounting depends on RNA affinities yet unmeasured. Such a code begins as mostly stereochemical, excludes mismatched assignments, and critically relies on properties characteristic of fusible microbes. After its RNPT in a partially assigned code, evolution accelerates definitively. Other assignment methods (adaptation, co-evolution, revised stereochemistry, LGT) likely complete the modern SGC because stable cellular intermediates with > 1 code exist, allowing compartmental code exchanges. Though initiated using chemical affinities, the 83 order-of-magnitude focus required to find a near-complete SGC among all possible codes was made by sequential evolutionary anthologies, in successive biological settings.
Replication of [AT/TA]25microsatellite sequences by human DNA polymerase δ holoenzymes is dependent on dNTP and RPA levels
Authors: Pytko Kara G. , Dannenberg Rachel L. , Eckert Kristin A. , Hedglin Mark 
Published: November 2023

ABSTRACTDifficult-to-Replicate Sequences (DiToRS) are natural impediments in the human genome that inhibit DNA replication under endogenous replication. Some of the most widely-studied DiToRS are A+T-rich, high “flexibility regions,” including long stretches of perfect [AT/TA] microsatellite repeats that have the potential to collapse into hairpin structures when in single-stranded DNA (ssDNA) form and are sites of recurrent structural variation and double-stranded DNA (dsDNA) breaks. Currently, it is unclear how these flexibility regions impact DNA replication, greatly limiting our fundamental understanding of human genome stability. To investigate replication through flexibility regions, we utilized FRET to characterize the effects of the major ssDNA-binding complex, RPA, on the structure of perfect [AT/TA]25microsatellite repeats and also re-constituted human lagging strand replication to quantitatively characterize initial encounters of pol δ holoenzymes with A+T-rich DNA template sequences. The results indicate that [AT/TA]25sequences adopt hairpin structures that are unwound by RPA and pol δ holoenzymes support dNTP incorporation through the [AT/TA]25sequences as well as an A+T-rich, non-structure forming sequence. Furthermore, the extent of dNTP incorporation is dependent on the sequence of the DNA template and the concentration of dNTPs. Importantly, the effects of RPA on the replication of [AT/TA]25sequences are dependent on the concentration of dNTPs, whereas the effects of RPA on the replication of an A+T-rich, non-structure forming sequence are independent of dNTP concentration. Collectively, these results reveal complexities in lagging strand replication and provide novel insights into how flexibility regions contribute to genome instability.
An acidophilic fungus is integral to prey digestion in a carnivorous plant
Authors: Sun Pei-Feng , Lu Min R. , Liu Yu-Ching , Lin Yu-fei , Hoh Daphne Z. , Ke Huei-Mien , Wang I-Fan , Lu Mei-Yeh Jade , Kirschner Roland , Jimmy Lin Ying-Chung , Chen Ying-Lan , Tsai Isheng Jason 
Published: November 2023

AbstractCarnivorous plant leaves, such as those of the spoon-leaved sundewDrosera spatulata, secrete mucilage which hosts microorganisms potentially aiding in prey digestion. We characterised the mucilage microbial communities and identified the acidophilic fungusAcrodontium crateriformeas the ecologically dominant species. The fungus grows and sporulates on sundew glands as its preferred acidic environment. We show that theA. crateriformehas a reduced genome similar to that of other symbiotic fungi. Based on the transcriptomes when encountering prey insects, we revealed a high degree of genes co-option in each species during fungus-plant coexistence and digestion. Expression patterns of the holobiont during digestion further revealed synergistic effects in several gene families including fungal aspartic and sedolisin peptidases, facilitating the digestion of sundew’s prey, as well as transporters and dose-dependent responses in plant genes involved in jasmonate signalling pathway. This study establishes that botanical carnivory is defined by multidimensional adaptations correlated with interspecies interactions.
Analysis and evaluation of blood screening testing strategies in Nagqu, Tibet: one of the highest cities in world
Authors: Zang Liang , Zhou Lei , Fan Yaxin , Liang Xiaohua , Duo Ji , Lin Hao , Bai Rui , Yang Mei , Dan Chao 
Published: November 2023

AbstractThe aim of this study was to evaluate the performance of blood screening strategies in Nagqu City, with a focus on serological and nucleic acid testing effectiveness. Analysis of blood donation data from 2017 to 2023 revealed a gradual increase in local blood donation rates, but the rate of unqualified donations remained higher than the national average. Serological performance verification showed good repeatability and precision, but improvements are needed in the accuracy of certain markers. Nucleic acid performance verification demonstrated excellent detection capability for low viral load HBV infections. The conclusion highlights significant progress in the screening strategies of Nagqu City, with the nucleic acid testing system showing outstanding performance. The findings provide valuable insights for blood screening in other high-altitude regions.
Comparison of gene expression in living and postmortem human brain
Authors: Collado-Torres Leonardo , Klei Lambertus , Liu Chunyu , Kleinman Joel E. , Hyde Thomas M. , Geschwind Daniel H. , Gandal Michael J. , Devlin Bernie , Weinberger Daniel R. 
Published: November 2023

AbstractMolecular mechanisms of neuropsychiatric disorders are challenging to study in human brain. For decades, the preferred model has been to study postmortem human brain samples despite the limitations they entail. A recent study generated RNA sequencing data from biopsies of prefrontal cortex from living patients with Parkinson’s Disease and compared gene expression to postmortem tissue samples, from which they found vast differences between the two. This led the authors to question the utility of postmortem human brain studies. Through re-analysis of the same data, we unexpectedly found that the living brain tissue samples were of much lower quality than the postmortem samples across multiple standard metrics. We also performed simulations that illustrate the effects of ignoring RNA degradation in differential gene expression analyses, showing the effects can be substantial and of similar magnitude to what the authors find. For these reasons, we believe the authors’ conclusions are unjustified. To the contrary, while opportunities to study gene expression in the living brain are welcome, evidence that this eclipses the value of postmortem analyses is not apparent.
Operationalized releases ofwAlbBWolbachiainAedes aegyptilead to sharp decreases in dengue incidence dependent onWolbachiafrequency
Authors: Hoffmann Ary A. , Wasi Ahmad Nazni , Wan Ming Keong , Cheong Yoon Ling , Ahmad Noor Afizah , Golding Nick , Tierney Nicholas , Jelip Jenarun , Wilson Putit Perada , Mokhtar Norhayati , Singh Sandhu Sukhvinder , Lau Sai Ming , Khairuddin Khadijah , Denim Kamilan , Mohd Rosli Norazman , Shahar Hanipah , Omar Topek , Ridhuan Ghazali Muhammad Kamarul , Mohd Zabari Nur Zatil Aqmar , Abdul Karim Mohd Arif , Saidin Mohamad Irwan , Mohd Nasir Muhammad Nizam , Aris Tahir , Sinkins Steven P 
Published: November 2023

AbstractInAedes aegyptimosquitoes, introduction of certain strains of inheritedWolbachiasymbionts results in transmission blocking of various viruses of public health importance, including dengue. This has resulted in a ‘replacement’ strategy for dengue control involving release of male and female mosquitoes, whereuponWolbachiais able to spread throughAe. aegyptipopulations to high frequency and reduces the incidence of dengue.WolbachiastrainwAlbB is an effective transmission blocker and stable at high temperatures, making it very suitable for use in hot tropical climates. Following the first trial field releases of thewAlbB strain inAe. aegyptiin Malaysia, releases ofwAlbBAe. aegyptihave for the first time become operationalized by the Malaysian health authorities. We report here on changes in dengue incidence based on a set of 20 releases sites and 76 control sites in high rise residential areas, which allows us to directly assess the impact ofWolbachiafrequency on dengue incidence. The results indicate an average reduction in dengue of 62.4% (confidence intervals 50-71%); importantly the level of suppression increased withWolbachiafrequency, with suppression of 75.8% (confidence intervals 61-87%) estimated at 100%Wolbachiafrequency. These findings emphasize the large impacts ofwAlbBWolbachiainvasions on dengue incidence in an operational setting, with the expectation that the level of dengue will further decrease as wider areas are invaded.
Cost-effective and scalable clonal hematopoiesis assay provides insight into clonal dynamics
Authors: Mack Taralynn , Vlasschaert Caitlyn , von Beck Kelly , Silver Alexander J. , Heimlich J. Brett , Poisner Hannah , Condon Henry Robert , Ulloa Jessica , Sochacki Andrew L. , Spaulding Travis P. , Kishtagari Ashwin , Bejan Cosmin A. , Xu Yaomin , Savona Michael R. , Jones Angela , Bick Alexander 
Published: November 2023

AbstractClonal hematopoiesis of indeterminate potential (CHIP) is a common age-related phenomenon that occurs when hematopoietic stem cells acquire mutations in a select set of genes commonly mutated in myeloid neoplasia which then expand clonally. Current sequencing assays to detect CHIP are not optimized for the detection of these variants and can be cost-prohibitive when applied to large cohorts or serial sequencing. Here, we present and validate a CHIP targeted sequencing assay that is affordable (∼$8/sample), accurate and highly scalable. To demonstrate the utility of this assay, we detected CHIP in a cohort of 456 individuals with DNA collected at multiple timepoints in the Vanderbilt BioVU biobank and quantified clonal expansion rates over time. A total of 101 individuals with CHIP were identified, and individual-level clonal expansion rate was calculated using the variant allele fraction (VAF) at both timepoints. Differences in clonal expansion rate by driver gene were observed, but there was also significant individual-level heterogeneity, emphasizing the multifactorial nature of clonal expansion. We further describe the mutation co-occurrence and clonal competition between multiple driver mutations.
Ophthalmic artery stenosis on three-dimensional rotational angiography: interrater agreement, prevalence, and risk factors
Authors: Diprose William K , Wang Michael T. M. , Reidy Joseph , Ma Alice , Brodie James , Steinfort Brendan 
Published: November 2023

ABSTRACTBackgroundThere is emerging interest in ophthalmic artery stenosis angioplasty for the treatment of age-related macular degeneration. Three-dimensional rotational angiography could be used intraoperatively to determine the presence and severity of ophthalmic artery stenosis. In patients who had undergone three-dimensional rotational angiography of the internal carotid artery, we aimed to assess the interrater agreement, prevalence, and risk factors for ophthalmic artery stenosis.MethodsConsecutive patients from two centers who had undergone diagnostic cerebral angiography with three-dimensional rotational angiography of the internal carotid arteries were enrolled in this study. Three-dimensional rotational angiograms were independently double read for the presence of ophthalmic artery stenosis, as defined as an ostial narrowing of at least 50% when compared to the more distal ‘normal’ ophthalmic artery. Interrater agreement for the evaluation of ophthalmic artery stenosis was assessed with the Cohen’s kappa coefficient. Univariate and multivariable logistic regression were used to identify potential predictors of OA stenosis.Results302 patients (97 men; mean±SD 57.6±13.4 years) were included in the analysis. Cohen’s kappa coefficient (95% CI) was 0.877 (0.798–0.956). Ophthalmic artery stenosis was present in 45 patients (14.9%). Multiple logistic regression demonstrated that female sex was independently associated with a higher odds of ophthalmic artery stenosis (odds ratio [OR]=2.70, 95% confidence interval [CI] 1.18-6.09, P=0.02). Smoking was a significant risk factor for ophthalmic artery stenosis (OR=2.11, 95% CI 1.10-4.06, P=0.03).ConclusionThe evaluation of ophthalmic artery stenosis on three-dimensional rotational angiography had excellent interrater agreement. Ophthalmic artery stenosis was common and was associated with smoking and female sex.
Investigating the consumption behavior of young adults using online food delivery platforms during the COVID-19 pandemic
Authors: Leung Yi Lok , Chan Ron L.H. , Chiu Dickson K.W. , Ruwen Tian 
Published: November 2023

PurposeOnline food delivery has been prevalent in recent years worldwide, especially during the COVID-19 pandemic, and people's consumption behaviors have changed significantly. This study aims to investigate the consumption behavior of young adults using online food delivery platforms during the COVID-19 pandemic and focuses on the dominant factors influencing their decision to use online food delivery platforms.Design/methodology/approachSemi-structured interviews including 14 young adults aged 18–25 living in Hong Kong were conducted to collect data about their perspectives on online food delivery platforms in five areas. This research adopted the stimulus-organism-response model (S-O-R model) to analyze how the factors influence young adult users' loyalty and satisfaction with online food delivery platforms.FindingsThematic analyses revealed that young adults were attracted to online food delivery platforms for their numerous benefits. They had a high frequency of usage and significant spending. Usability, usefulness, satisfaction and loyalty influenced young adults' behaviors on online food delivery platforms. Participants were overall satisfied with their experiences, but platforms still had room for improvement.Originality/valueFew prior studies investigated the factors affecting the consumer experience and behavioral intention of online food delivery for young adults in Asia. This study contributes to understanding young adults' experiences and problems with online food delivery platforms. It provides practical insights for system engineers and designers to improve the current services and for the governments to enhance the existing regulatory loopholes.
A checklist to publish collections as data in GLAM institutions
Authors: Candela Gustavo , Gabriëls Nele , Chambers Sally , Dobreva Milena , Ames Sarah , Ferriter Meghan , Fitzgerald Neil , Harbo Victor , Hofmann Katrine , Holownia Olga , Irollo Alba , Mahey Mahendra , Manchester Eileen , Pham Thuy-An , Potter Abigail , Van Keer Ellen 
Published: November 2023

PurposeThe purpose of this study is to offer a checklist that can be used for both creating and evaluating digital collections, which are also sometimes referred to as data sets as part of the collections as data movement, suitable for computational use.Design/methodology/approachThe checklist was built by synthesising and analysing the results of relevant research literature, articles and studies and the issues and needs obtained in an observational study. The checklist was tested and applied both as a tool for assessing a selection of digital collections made available by galleries, libraries, archives and museums (GLAM) institutions as proof of concept and as a supporting tool for creating collections as data.FindingsOver the past few years, there has been a growing interest in making available digital collections published by GLAM organisations for computational use. Based on previous work, the authors defined a methodology to build a checklist for the publication of Collections as data. The authors’ evaluation showed several examples of applications that can be useful to encourage other institutions to publish their digital collections for computational use.Originality/valueWhile some work on making available digital collections suitable for computational use exists, giving particular attention to data quality, planning and experimentation, to the best of the authors’ knowledge, none of the work to date provides an easy-to-follow and robust checklist to publish collection data sets in GLAM institutions. This checklist intends to encourage small- and medium-sized institutions to adopt the collection as data principles in daily workflows following best practices and guidelines.
Adoption of human resource sourcing strategies for managing supply chain performance during COVID-19 crisis: evidence from manufacturing companies
Authors: Akhil N.S.B , Kumar Vimal , Raj Rohit , De Tanmoy , Gangaraju Phanitha Kalyani 
Published: November 2023

PurposeEven the greatest developed countries have capitulated to the destructions imposed on the global supply systems, as the COVID-19 pandemic has revealed. The purpose of this study is to explore human resource sourcing strategies for managing supply chain performance during the COVID-19 outbreak. There are six human resource sourcing strategies such as outsourcing, near sourcing, integration, the requirement of suppliers, joint ventures and virtual enterprise that are considered to measure supply chain performance.Design/methodology/approachBased on collecting data from the potential respondents of Indian manufacturing companies, the elevation of human resource sourcing strategies to supply chain performance is measured considering the multiple regression analysis techniques.FindingsThe results of the study revealed that four of the six hypotheses have a significant and positive relationship with supply chain performance during the COVID-19 outbreak while two hypotheses are partially supported that lent good support to this study.Research limitations/implicationsIn this critical situation, this study will enable managers and practitioners to support the business in giving customers the best services on time.Originality/valueThe novelty of this study is to identify the key human resource sourcing strategies by using multiple regression analysis methods, considering the case of Indian manufacturing companies to measure their supply chain performance during the COVID-19 outbreak era.