bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systematic Review Protocol: The Effects of Theory-Based Interventions for Self-Help Practices in the Management of Mild to Moderate Depression
Authors: Khalil Asma’ , Azhar Zahir Izuan , Shuib Norley , Baker Philip , Wee Chen Xin 
Published: December 2024

AbstractBackgroundDepression is a leading global cause of disability, significantly affecting individuals’ quality of life and contributing to a substantial worldwide health burden. Self-help practices have emerged as cost-effective and scalable strategies for managing mild to moderate depression, empowering individuals to take an active role in their mental health care. Theory-based interventions, which are grounded in established psychological frameworks, provide a systematic approach to designing, implementing and evaluating these self-help practices. However, despite the growing availability of self-help interventions, their effectiveness varies, and many lack a solid theoretical foundation. Summarized evidence of the effects of theory-based interventions remains limited.ObjectivesThis systematic review aims to evaluate the effects of theory-based interventions incorporating self-help practices in reducing depressive symptoms severity among adults with mild to moderate depression.MethodsThe review will follow PRISMA guidelines and has been registered with the International Prospective Register of Systematic Reviews (PROSPERO). Randomised trials evaluating theory-based interventions, such as Cognitive Behavioral Therapy (CBT), Acceptance and Commitment Therapy (ACT), and Mindfulness-Based Interventions (MBIs), delivered via digital platforms will be included. Studies will be identified through searches of PubMed, Scopus, Web of Science, Science Direct and Cochrane bibliographic databases. Data extraction and risk of bias assessment will be conducted independently by two reviewers, focusing on study characteristics, intervention details and critical outcomes (reduction in depressive symptom severity and adverse effects).ResultsThe review will synthesize evidence on the effects and adaptability of theory-based interventions, highlighting the specific contributions of theoretical frameworks to intervention outcomes. Findings will be presented in tabular and narrative formats, identifying gaps and implications for clinical practice and future research.ConclusionThis systematic review will provide actionable insights into the design and implementation of theory-based interventions for managing mild to moderate depression. The findings aim to inform evidence-based guidelines for primary care integration, promoting accessible, scalable and effective mental health solutions globally.
Hyperspectral Segmentation of Plants in Fabricated Ecosystems
Authors: Zwart Petrus H. , Andeer Peter , Northen Trent 
Published: December 2024

AbstractHyperspectral imaging provides a powerful tool for analyzing above-ground plant characteristics in fabricated ecosystems, offering rich spectral information across diverse wavelengths. This study presents an efficient workflow for hyperspectral data segmentation and subsequent data analytics, minimizing the need for user annotation through the use of ensembles of sparse mixed-scale convolution neural networks. The segmentation process leverages the diversity of ensembles to achieve high accuracy with minimal labeled data, reducing labor-intensive annotation efforts. To further enhance robustness, we incorporate image alignment techniques to address spatial variability in the dataset. Down-stream analysis focuses on using the segmented data for processing spectral data, enabling monitoring of plant health. This approach not only provides a scalable solution for spectral segmentation but also facilitates actionable insights into plant conditions in complex, controlled environments. Our results demonstrate the utility of combining advanced machine learning techniques with hyperspectral analytics for high-throughput plant monitoring.
The decline of global pollinator biodiversity in the Anthropocene
Authors: Kallivalappil Ratheesh , Cotter Sheena C. 
Published: December 2024

AbstractPollination underlies the functioning of ecosystems globally. Therefore, the endangerment and extinction of pollinator species are predicted to trigger cascade effects with the potential to alter the demographic collapse of complex ecological networks. However, although some studies have investigated the endangerment levels of pollinator species, the lack of global-scale analyses providing a universal overview of their extinction risks remains a major pending challenge in a world where climate change is rapidly decimating biodiversity. Here, we present the first truly global study of the endangerment level of vertebrate pollinators from across the tree of life. Based on a 1,666 species dataset, we investigate the macroecological patterns of species diversity and extinction risk of bird, mammal, and reptile pollinators of the world. We found higher extinction risk for mammal relative to bird and reptile pollinators. Globally, 1 in 3 mammal pollinators are currently threatened with extinction than 1 in 12 bird and 1 in 8 reptile pollinators. The hotspots of threatened bird pollinators mostly confined to Colombia and Hawaiian Islands, whereas the hotspots of threatened mammal and reptile pollinators are confined to Madagascar and various isolated islands. Notably, the endemic pollinators are more threatened than the widespread pollinators. The increasing decline of population will alter the status of threatened pollinators in future. While highlighting the quantity of threat and decline, we also show that the evolutionary predisposition along with habitat destruction for agriculture, and exploitation for bushmeat and pet trade are combinedly eroding the vertebrate pollinators biodiversity across the world at multiple scales. We suggest special environmental priorities such as controlled land-use, legislation on hunting, collaborative efforts between various stakeholders and community outreach programmes are essential for effective conservation of vertebrate pollinators.
Long-read sequencing reveals extensive size variation and suggests evolutionary patterns of expansion in bivalve mitogenomes
Authors: Zhang Ning , Qi Lu , Xu Biyang , Kong Lingfeng , Li Qi 
Published: December 2024

AbstractBilaterian mitochondrial genomes are generally of conserved size and gene content, typically ranging from 14 to 20 kb and coding 37 genes. However, the major exception to this rule has been found in many bivalve species which allow the presence of long unassigned region (regions that are functionally unassigned). It is still unclear whether there are universal patterns to expansions across bivalves. Additionally, the prevalence of highly repetitive sequences within complex mitogenomes has prevented its complete assembly and led to its systematic omission from mitogenomic analyses. Here, leveraging the growing genomic resources in Mollusca, we devised a mitogenome assembly pipeline using long-read sequencing to characterize mitogenome features in 178 mollusk species. Comparing our assemblies with reference mitogenomes based on Sanger/short-read sequencing, we identified missing sequences, repeats and novel gene duplications and found that bivalves exhibit an exceptional diversity in mitogenome size compared to other mollusks. Subsequently, we investigated the factors potentially influencing mitogenome size, the potential functional elements and the patterns of expansion regions. Furthermore, we discussed that the possible selective pressure on mitogenome size and hypothesized that the variability of bivalve mitogenomes may be linked to innate immunity. Our findings underscore the significance of long-read sequencing in elucidating complex mitogenomes and provide new insights into the evolution of bivalve mitogenomes.
Nascent RNA profiling reveals regulation of gene transcription through productive reiterative initiation in bacteria
Authors: Sun Zhe , Huang Guozhong , Zhang Yuqiong , Wang Shuang , Kashlev Mikhail 
Published: December 2024

ABSTRACTProductive reiterative initiation, an alternative transcription process accompanying RNA slippage relative to the template DNA and RNA polymerase, results in the incorporation of additional nucleotides into transcripts. However, a comprehensive understanding of the mechanisms underlying productive reiterative initiation and its functional implications has been hindered due to the complexity of heterogenous slippage transcripts. Here, we develop and employ 5’ Terminal Native Elongating Transcript Sequencing (5’TNET-seq) to identify and quantify productive reiterative initiation events inEscherichia coli. 5’TNET-seq reveals that over 51% of promoters exhibit productive reiterative initiation. The conserved promoter – 10 region, an appropriate spacer between the –10 region and the TSS, and the transcription initiation region associated with weak RNA-DNA hybrid stability, particularly “AAA” and “TTT” trinucleotide tracts, contribute to high productive reiterative initiation. In addition, up to four nucleotides can be added in a single cycle of productive reiterative initiation. A smaller transcription bubble is observed during productive reiterative initiation, which may stabilize the transcription initiation complex to regulate gene transcription. Our results suggest that productive reiterative initiation emerges as an inherent transcription process regulating biological processes, including cell wall synthesis, independent of protein regulators.
Identification and analysis of DEGs of mouse tumor cells by integrated bioinformatics methods
Authors: Jing Xizhong , Li Baiyong , Wang Yifei 
Published: December 2024

AbstractMutations and genome instability are hallmarks of cancer. The advanced Next Generation Sequencing(NGS) technology now enables rapid and cost-effective analysis for tumoral and normal genomic translational research. In this research, mRNA sequencing was applied to get the whole transcriptome data of mouse B16F10 melanoma and CT26 colon carcinoma cells. Up regulation genes and down regulation genes were identified in tumor cells with differentially expressed genes(DEGs) analysis. The DEGs were analyzed with GO, KEGG and Reactome pathway enrichment study. Results demonstrated the DEGs and enriched pathways were mainly associated with cell proliferation and biosynthetic processing. Further, gene fusion and alternative splicing analysis reveled fusion genes and skipped exons were extensive exist within the chromosomes of tumor cells. Together, the integrated DEGs and bioinformatics analysis in this article may shed light on further research of cancer treating targets and molecular mechanisms of carcinogenesis.
Effect of Stroma-directed Drugs in Combination with Chemotherapy Against Pancreatic Cancer- a Preclinical Study
Authors: Gupta Mamta , Choi Hoon , Furth Emma E , Shaffer Sydney , Pickup Stephen , Clendenin Cynthia , Liu Fang , Cao Quy , Song Hee Kwon , Fan Yong , Duda Jeffrey , Gee James C , Karasic Thomos , Rosen Mark , O’Dwyer Peter , Zhou Rong 
Published: December 2024

AbstractCytotoxic chemotherapy plays an important role for extending the survival of patients with pancreatic ductal adenocarcinoma (PDAC). To enhance the efficacy of chemotherapy for eradicating the cancer cells, we have compared the standard care chemotherapy (combination of nab-paclitaxel, gemcitabine and cisplatin, NGC) versus NGC plus stroma-directed agents (calcipotriol and losartan, respectively) in a genetically engineered mouse model of PDAC. Over a 2-week study period, MRI was conducted to measure the tumor size and to test the sensitivity of imaging markers derived from diffusion-weighted imaging (DWI), dynamic contrast enhanced MRI (DCE) and magnetization transfer ratio (MTR) for assessing the tumor cellularity and stromal changes. Detailed immunohistochemistry and preliminary single cell RNA sequencing (scRNAseq) study were applied to tumor tissues collected upon euthanasia on day-14. Our major findings are: 1. Compared the untreated controls, NGC chemotherapy induced significant tumor growth inhibition and stromal changes including pronounced reduction of fibroblast associated protein (FAP) level accompanied by increased matrix collagen content, significantly reduced microvascular permeability revealed by DCE corroborated with reduced microvascular density. 2. Losartan+NGC significantly enhanced inhibition of tumor growth beyond NGC and increased lymphocytes infiltration in the tumor which may contribute to enhanced cancer cells eradication. 3. NGC treatment enriched the fraction of mesenchymal (M) subtype while reducing the epithelial (E) subtype of cancer cells compared to the controls, and this trend was reversed by calcipotriol+NGC. In conclusion, our study captured changes in cancer cell and tumor microenvironment in response to chemo stromal therapy versus chemotherapy alone with mechanistic insights.
Maize and wild relatives show distinct patterns of genome downsizing following polyploidy
Authors: Snodgrass Samantha J. , Woodhouse Margaret , Seetharam Arun , Stitzer Michelle , Hufford Matthew B. 
Published: December 2024

AbstractPlant genomes are smaller than expected despite the ubiquity of polyploidy due to the process of genome downsizing called fractionation. This process causes loss of DNA sequences, including genes, until genomes return to a diploid-like state, though some duplicates remain from the polyploid ancestor. Fractionation can affect the copies of ancestral diploid genomes (i.e., subgenomes) differently, resulting in one being preferentially retained and the other preferentially lost. While previous work suggested fractionation occurs shortly after a polyploidy event, few studies have been able to densely sample descendent genomes from the same whole genome duplication event. TheTripsacinaesubtribe of grasses, which includes the generaTripsacumandZeaand the economically and culturally important maize (Zea maysssp.mays), originates from an ancient allopolyploid (∼5-12 MYA). We use publicly available genome assemblies from theTripsacinaesubtribe of grasses to investigate the patterns and timing of fractionation relative to the outgroup sorghum, which does not share the allotetraploidy event. Our results show the majority of fractionation following polyploidy occurred in a common ancestor of modern species and that one subgenome is preferentially retained, in keeping with previous studies of maize. However,Tripsacumretains a greater proportion of duplicate genes (homoeologs) thanZea, potentially related to the fewer chromosomal rearrangements observed in this genus. Multiple, nested deletion events were commonly observed in alignments to a single sorghum reference exon, and some homoeologs show fractionation of different exons across genomes. Further, ∼35% of homoeologous pairs of exons show differential fractionation, where fractionation patterns differ between species. Altogether, this suggests multiple origins of fractionation for a given homoeolog may be common. We demonstrate that fractionation is a much more dynamic process in theTripsacinaethan previously predicted.
Understanding the structure and mechanics of the sheep calcaneal enthesis: a relevant animal model for tissue engineering applications
Authors: Sensini Alberto , Raimondi Luca , Malerba Albano , Peniche Silva Carlos , Zucchelli Andrea , Tits Alexandra , Ruffoni Davide , Blouin Stéphane , Hartmann Markus A. , van Griensven Martijn , Moroni Lorenzo 
Published: December 2024

AbstractTendon/enthesis injuries are a worldwide clinical problem. Along the enthesis, collagen fibrils show a progressive loss of anisotropy and an increase in mineralization reaching the bone. This causes gradients of mechanical properties. The design of scaffolds to regenerate these load-bearing tissues requires of being validatedin vivoin relevant large animal models. The sheep tendon of triceps surae muscle is an optimal animal model for this scope with limited knowledge about its structure and mechanics. We decided to understand in-depth its structure and full-field mechanics. Collagen fibrils morphology was investigated via scanning electron microscopy revealing a marked change in orientation/dimensions passing from tendon to enthesis. Backscatter electron images and nanoindentation at the enthesis/bone marked small gradients of mineralization at the mineralized fibrocartilage reaching 27%wt and indentation modulus around 17-30 GPa. The trabecular bone instead had indentation modulus around 15-22 GPa. Mechanical tensile tests with digital image correlation confirmed the typical non-linear behavior of tendons (failure strain = 8.2±1.0%; failure force = 1369±187 N) with maximum principal strains reaching mean values of εp1∼7%. The typical auxetic behavior of tendon was highlighted by the minimum principal strains (εp2∼5%), progressively dampened at the enthesis. Histology revealed that this behavior was caused by a local thickening of the epitenon. Cyclic tests showed a force loss of 21±7 % at the last cycle. These findings will be fundamental for biofabrication and clinicians interested in designing the new generation of scaffolds for enthesis regeneration.Graphical AbstractStatement of SignificanceTendon and enthesis lesions are a clinical problem. To validate scaffolds for these applications large animal models are needed. Sheep tendon of triceps surae muscle is an optimal site for this scope. However, little is known about its extracellular matrix structure and mechanical properties. This work investigates the structure and mechanics of this tissue from different points of view. Scanning electron microscopy and histology studied its extracellular matrix morphology and composition. Backscattered electron images and nanoindentation assessed gradients of mineralization and stiffness at the enthesis. Mechanical tensile and cyclic tests coupled with digital image correlation elucidated its mechanics and superficial strain distribution. These findings will be fundamental for biofabrication and clinician experts to design innovative scaffolds to regenerate the enthesis.
Contaminated water spillovers or peer effects? Determinants of disease outbreaks in shrimp farming in Vietnam
Authors: Suzuki Aya , Olivia Susan , Nam Vu Hoang , Lee Guenwoo 
Published: December 2024

AbstractDisease outbreaks are one of the major issues in the aquaculture sector and can lead to significant economic losses. Although the source of the disease is difficult to trace, understanding how it occurs is important to mitigate the problem. A crucial factor that has not received sufficient attention is the presence of spillovers among fish farmers connected by waterways. This study examines the presence of spillovers among shrimp farmers in Southern Vietnam based on primary data. In particular, it quantifies the effects of contaminated water spillovers from one farm to another and the peer effects of farming practices among neighbors. We solve the reflection problem by employing a method developed in social network analyses. The findings indicate that a farmer's practices are affected by their neighbors’ farming practices. Further, the disease outbreak in a farmer's pond is affected by those in their neighbors’ ponds, even after controlling for contextual peer effects and correlated effects. The negative effects of neighbors’ ponds on the probability of disease outbreaks in a farmer's pond may offset the positive effects of the farmer's good farming practices, suggesting the importance of considering neighboring farmers as a group when addressing the issue of disease control.
Identifying Drivers of Shrubland Biomass in Southern California
Authors: Underwood Emma C. , Molinari Nicole A. , Schrader‐Patton Charlie C. , Lesage Josephine , Excoffier Paul 
Published: December 2024

ABSTRACTAimThe drivers of shrubland biomass in the Mediterranean‐Climate Region of southern California are not well understood. We aim to fill a critical information gap for resource managers of shrub‐dominated landscapes who need to estimate shrub recovery post‐fire, track and monitor carbon storage and sequestration, and determine the tradeoff in restoration goals between prioritising carbon storage and species richness.LocationSouthern California, USA.MethodsUsing data from 143 field plots located in 11 fire scars (ranging from 1 to 12 years old), we used Linear Mixed Models to assess the contribution of temporal and environmental variables, along with post‐fire regeneration strategies of shrub species to explain patterns of aboveground shrub biomass.ResultsWe identified four key findings: (1) shrub biomass increased with time since last fire and the proportion of resprouting species, and decreased with distance to coast and solar radiation; (2) species with the ability to resprout (obligate resprouter and facultative seeders) contributed greater biomass at all post‐fire time periods and locations when compared with obligate seeders; (3) we found higher average biomass contributed by both obligate seeder and obligate resprouter species in plots closer to the coast than interior plots; and (4) fourth, we found a significant positive relationship between woody shrub species richness and biomass.ConclusionsThe findings of this study of biomass at a regional scale and using shrublands of multiple stand ages can help support natural resource management decision‐making for shrub‐dominated landscapes—including estimating biomass recovery post‐fire, quantifying carbon storage and setting goals for shrubland restoration.
DMFT‐Related Dental Plaque Scoring by Using Different Imaging Systems
Authors: Meşeli Simge , Korkut Bora , Tağtekin Dilek 
Published: December 2024

ABSTRACTObjectiveThis study aimed to compare dental plaque scores measured using clinical examination and different imaging methods.Materials and MethodsTwenty‐eight volunteers were included in the study and divided into two groups according to DMFT (D: Decayed, M: Missing, F: Filling, T: Teeth) scores (under 3 and over 10). Dental plaque on anterior labial surfaces' was scored using clinical visual examination with/without staining and different imaging systems (Digital photography, intraoral digital scanning, FluoreCam). Turesky Modified Quigley Hein Plaque Index was used for dental plaque scoring. The comparison between clinical examination and imaging dental plaque scores was analyzed using Linear Models and Bonferroni Correction (p < 0.050).ResultsIn low DMFT group, the scores in clinical examination scores with staining were similar to the scores obtained with digital camera (p = 1.000) and intraoral digital scanning plaque scores (p = 0.997). The lowest plaque score was obtained in clinical visual examination without staining (p < 0.05) while the highest score was recorded by FluoreCam in low DMFT group (p < 0.05). In both groups, the FluoreCam scores were quantitatively higher among all imaging methods.ConclusionsPlaque staining in low DMFT group may increase the efficiency of all imaging methods. Plaque staining‐guided digital imaging can be used as an alternative method to visual evaluation methods for monitoring dental plaque clinically.Clinical SignificanceDental plaque diagnosis is important in preventing caries and periodontal diseases. This study investigates the comparison of various imaging systems with clinical visual examination plaque scoring in patients with different oral hygiene status. The use of intraoral scanners might be a new option for the evaluation of oral hygiene levels and used as an alternative technique to clinical visual examinations in dental practice.