bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide characterization and expression analysis of the CINNAMYL ALCOHOL DEHYDROGENASE gene family in Triticum aestivum
Authors: Peracchi Luigi M. , Brew-Appiah Rhoda A.T. , Garland-Campbell Kimberly , Roalson Eric H. , Sanguinet Karen A. 
Published: August 2024

Abstract
Background
CINNAMYL ALCOHOL DEHYDROGENASE (CAD) catalyzes the NADPH-dependent reduction of cinnamaldehydes into cinnamyl alcohols and is a key enzyme found at the final step of the monolignol pathway. Cinnamyl alcohols and their conjugates are subsequently polymerized in the secondary cell wall to form lignin. CAD genes are typically encoded by multi-gene families and thus traditionally organized into general classifications of functional relevance.

Results
In silico analysis of the hexaploid Triticum aestivum genome revealed 47 high confidence TaCAD copies, of which three were determined to be the most significant isoforms (class I) considered bone fide CADs. Class I CADs were expressed throughout development both in RNAseq data sets as well as via qRT-PCR analysis. Of the 37 class II TaCADs identified, two groups were observed to be significantly co-expressed with class I TaCADs in developing tissue and under chitin elicitation in RNAseq data sets. These co-expressed class II TaCADs were also found to be phylogenetically unrelated to a separate clade of class II TaCADs previously reported to be an influential resistance factor to pathogenic fungal infection. Lastly, two groups were phylogenetically identified as class III TaCADs, which possess distinct conserved gene structures. However, the lack of data supporting their catalytic activity for cinnamaldehydes and their bereft transcriptional presence in lignifying tissues challenges their designation and function as CADs.

Conclusions
Taken together, our comprehensive transcriptomic analyses suggest that TaCAD genes contribute to overlapping but nonredundant functions during T. aestivum growth and development across a wide variety of agroecosystems and provide tolerance to various stressors.
A comparative analysis of ENCODE and Cistrome in the context of TF binding signal
Authors: Perna Stefano , Pinoli Pietro , Ceri Stefano , Wong Limsoon 
Published: August 2024

Abstract
Background
With the rise of publicly available genomic data repositories, it is now common for scientists to rely on computational models and preprocessed data, either as control or to discover new knowledge. However, different repositories adhere to the different principles and guidelines, and data processing plays a significant role in the quality of the resulting datasets. Two popular repositories for transcription factor binding sites data - ENCODE and Cistrome - process the same biological samples in alternative ways, and their results are not always consistent. Moreover, the output format of the processing (BED narrowPeak) exposes a feature, the signalValue, which is seldom used in consistency checks, but can offer valuable insight on the quality of the data.

Results
We provide evidence that data points with high signalValue(s) (top 25% of values) are more likely to be consistent between ENCODE and Cistrome in human cell lines K562, GM12878, and HepG2. In addition, we show that filtering according to said high values improves the quality of predictions for a machine learning algorithm that detects transcription factor interactions based only on positional information. Finally, we provide a set of practices and guidelines, based on the signalValue feature, for scientists who wish to compare and merge narrowPeaks from ENCODE and Cistrome.

Conclusions
The signalValue feature is an informative feature that can be effectively used to highlight consistent areas of overlap between different sources of TF binding sites that expose it. Its applicability extends to downstream to positional machine learning algorithms, making it a powerful tool for performance tweaking and data aggregation.
Discovery of NRG1-VII: the myeloid-derived class of NRG1
Authors: Berrocal-Rubio Miguel A , Pawer Yair David Joseph , Dinevska Marija , De Paoli-Iseppi Ricardo , Widodo Samuel S. , Gleeson Josie , Rajab Nadia , De Nardo Will , Hallab Jeannette , Li Anran , Mantamadiotis Theo , Clark Michael B. , Wells Christine A. 
Published: August 2024

AbstractThe growth factor Neuregulin-1 (NRG1) has pleiotropic roles in proliferation and differentiation of the stem cell niche in different tissues. It has been implicated in gut, brain and muscle development and repair. Six isoform classes of NRG1 and over 28 protein isoforms have been previously described. Here we report a new class of NRG1, designated NRG1-VII to denote that these NRG1 isoforms arise from a myeloid-specific transcriptional start site (TSS) previously uncharacterized. Long-read sequencing was used to identify eight high-confidence NRG1-VII transcripts. These transcripts presented major structural differences from one another, through the use of cassette exons and alternative stop codons. Expression of NRG1-VII was confirmed in primary human monocytes and tissue resident macrophages and induced pluripotent stem cell-derived macrophages (iPSC-derived macrophages). Isoform switching via cassette exon usage and alternate polyadenylation was apparent during monocyte maturation and macrophage differentiation. NRG1-VII is the major class expressed by the myeloid lineage, including tissue-resident macrophages. Analysis of public gene expression data indicates that monocytes and macrophages are a primary source of NRG1. The size and structure of class VII isoforms suggests that they may be more diffusible through tissues than other NRG1 classes. However, the specific roles of class VII variants in tissue homeostasis and repair have not yet been determined.
Neural acetylcholinesterase and monoamine oxidase deregulation during streptozotocin-induced behavioral, metabolic and redox modification in Nauphoeta cinerea
Authors: Ogunsuyi Opeyemi B. , Olagoke Olawande C. , Famutimi Mayokun E. , Olatunde Damilola M. , Souza Diogo O. G. , Oboh Ganiyu , Barbosa Nilda V. , Rocha João B.T. 
Published: August 2024

AbstractGenetic and environmental factors have been linked with neurodegeneration, especially in the elderly. Yet, efforts to impede neurodegenerative processes have at best addressed symptoms instead of underlying pathologies. The gap in the understanding of neuro-behavioral plasticity is consistent from insects to mammals, and cockroaches have been proven to be effective models for studying the toxicity mechanisms of various chemicals. We therefore used head injection of 74 and 740 nmol STZ in Nauphoeta cinerea to elucidate the mechanisms of chemical-induced neurotoxicity, as STZ is known to cross the blood-brain barrier. Neurolocomotor assessment was carried out in a new environment, while head homogenate was used to estimate metabolic, neurotransmitter and redox activities, followed by RT-qPCR validation of relevant cellular signaling. STZ treatment reduced the distance and maximum speed travelled by cockroaches, and increased glucose levels while reducing triglyceride levels in neural tissues. The activity of neurotransmitter regulators – AChE and MAO was exacerbated, with concurrent upregulation of glucose sensing and signaling, and increased mRNA levels of redox regulators and inflammation-related genes. Consequently, STZ neurotoxicity is conserved in insects, with possible implications for using N. cinerea to target the multi-faceted mechanisms of neurodegeneration and test potential anti-neurodegenerative agents.
Take-home naloxone administered in emergency settings: feasibility of intervention implementation in a cluster randomized trial
Authors: Snooks Helen A. , Jones Jenna K. , Bell Fiona B. , Benger Jonathon R. , Black Sarah L. , Dixon Simon , Edwards Adrian , Emery Helena , Evans Bridie A. , Fuller Gordon W. , Goodacre Steve , Hoskins Rebecca , Hughes Jane , John Ann , Johnston Sasha , Jones Matthew B. , Moore Chris R. , Parab Rakshita , Pilbery Richard , Sampson Fiona C. , Watkins Alan 
Published: August 2024

Abstract
Background
Opioids kill more people than any other class of drug. Naloxone is an opioid antagonist which can be distributed in kits for peer administration. We assessed the feasibility of implementing a Take-home Naloxone (THN) intervention in emergency settings, as part of designing a definitive randomised controlled trial (RCT).

Methods
We undertook a clustered RCT on sites pairing UK Emergency Departments (ED) and ambulance services. At intervention sites, we recruited emergency healthcare practitioners to supply THN to patients presenting with opioid overdose or related condition, with recruitment across 2019–2021. We assessed feasibility of intervention implementation against four predetermined progression criteria covering site sign up and staff training; identification of eligible patients; issue of THN kits and Serious Adverse Events.

Results
At two intervention sites, randomly selected from 4, 299/687 (43.5%) clinical staff were trained (ED1 = 107, AS1 = 121, ED2 = 25, AS2 = 46). Sixty THN kits were supplied to eligible patients (21.7%) (n: ED1 = 36, AS1 = 4, ED2 = 16, AS2 = 4). Across sites, kits were not issued to eligible patients on a further 164 occasions, with reasons reported including: staff forgot (n = 136), staff too busy (n = 15), and suspected intentional overdose (n = 3), no kit available (n = 2), already given by drugs nurse (n = 4), other (n = 4). Staff recorded 626 other patients as ineligible but considered for inclusion, with reasons listed as: patient admitted to hospital (n = 194), patient absconded (n = 161) already recruited (n = 64), uncooperative or abusive (n = 55), staff not trained (n = 43), reduced consciousness level (n = 41), lack of capacity (n = 35), patient in custody (n = 21), other (n = 12). No adverse events were reported.

Conclusion
Staff and patient recruitment were low and varied widely by site. This feasibility study did not meet progression criteria; a fully powered RCT is not planned.

Trial Registration
ISRCTN13232859 (Registered 16/02/2018).
Supporting treatment adherence for resilience and thriving (START): protocol for a mHealth randomized controlled trial
Authors: Davis-Ewart Leah , Atkins Lindsay , Ghanooni Delaram , Diaz José E. , Chuku Chika C. , Balise Raymond , DeVries Britt A. , Miller-Perusse Michael , Ackley III Donovan , Moskowitz Judith T. , McCollister Kathryn , Fardone Erminia , Hirshfield Sabina , Horvath Keith J. , Carrico Adam W. 
Published: August 2024

Abstract
Background
Although behavioral interventions show some promise for reducing stimulant use and achieving durable viral suppression in sexual minority men (SMM) with HIV, scalable mHealth applications are needed to optimize their reach and cost-effectiveness.

Methods
Supporting Treatment Adherence for Resilience and Thriving (START) is a randomized controlled trial (RCT) testing the efficacy and cost-effectiveness of a mHealth application that integrates evidence-based positive affect regulation skills with self-monitoring of adherence and mood. The primary outcome is detectable HIV viral load (i.e., > 300 copies/mL) from self-collected dried blood spot (DBS) specimens at 6 months. Secondary outcomes include detectable DBS viral load at 12 months, self-reported stimulant use severity, anti-retroviral therapy (ART) adherence, and positive affect over 12 months. A national sample of up to 250 SMM with HIV who screen positive for stimulant use disorder and reporting suboptimal ART adherence is being recruited via social networking applications through April of 2024. After providing informed consent, participants complete a run-in period (i.e., waiting period) including two baseline assessments with self-report measures and a self-collected DBS sample. Those who complete the run-in period are randomized to either the START mHealth application or access to a website with referrals to HIV care and substance use disorder treatment resources. Participants provide DBS samples at baseline, 6, and 12 months to measure HIV viral load as well as complete self-report measures for secondary outcomes at quarterly follow-up assessments over 12 months.

Discussion
To date, we have paid $117,500 to advertise START on social networking applications and reached 1,970 eligible participants ($59.77 per eligible participant). Although we identified this large national sample of potentially eligible SMM with HIV who screen positive for a stimulant use disorder and report suboptimal ART adherence, only one-in-four have enrolled in the RCT. The run-in period has proven to be crucial for maintaining scientific rigor and reproducibility of this RCT, such that only half of consented participants complete the required study enrollment activities and attended a randomization visit. Taken together, findings will guide adequate resource allocation to achieve randomization targets in future mHealth research SMM with HIV who use stimulants.

Trial Registration
This protocol was registered on clinicaltrials.gov (NCT05140876) on December 2, 2021.
Genomic variation in Plasmodium relictum (lineage SGS1) and its implications for avian malaria infection outcomes: insights from experimental infections and genome-wide analysis
Authors: Kalbskopf Victor , Aželytė Justė , Palinauskas Vaidas , Hellgren Olof 
Published: August 2024

Abstract
Background
The globally transmitted avian malaria parasite Plasmodium relictum (lineage SGS1) has been found to infect hundreds of different bird species with differences in infection outcomes ranging from more or less latent to potentially mortal. However, to date basic knowledge about the links between genetic differentiation and variation in infection outcome within this single malaria parasite species is lacking.

Methods
In this study, two different isolates of SGS1, obtained in the wild from two different host species, were used to investigate differences in their development in the blood and virulence in the experimentally infected canaries. Simultaneously, 258 kb of the parasite genome was screened for genetic differences using parasite mRNA and compared between experimental groups.

Results
The two isolates showed differences in development and caused mortality as well as effects on the blood parameters of their hosts. Although previous studies using single genes have shown very limited within lineage genetic diversity in the European population of SGS1, 226 SNPs were found across 322 genes, which separated the two experimental groups with a total of 23 SNPs that were fixed in either of the experimental groups. Moreover, genetic variation was found within each experimental group, hinting that each avian malaria infection harbours standing genetic variation that might be selected during each individual infection episode.

Conclusion
These results highlight extensive genetic variation within the SGS1 population that is transferred into individual infections, thus adding to the complexity of the infection dynamics seen in these host–parasite interactions. Simultaneously, the results open up the possibility of understanding how genetic variation within the parasite populations is linked to the commonly observed differences in infection outcomes, both in experimental settings and in the wild.

Graphical Abstract
Evaluating trends in damage to attractive targeted sugar baits (ATSBs) deployed during the second year of a two-year Phase III trial in Western Zambia
Authors: Kyomuhangi Irene , Yukich Joshua , Saili Kochelani , Orange Erica , Masuzyo Mundia H. , Mwenya Mwansa , Mambo Patricia , Hamainza Busiku , Wagman Joe , Miller John , Chanda Javan , Silumbe Kafula , Littrell Megan , Eisele Thomas P. , Ashton Ruth A. 
Published: August 2024

Abstract
Background
Attractive Targeted Sugar Baits (ATSBs) are a proposed new vector control tool for malaria that contain sugar and an ingestion toxicant, and are designed to attract and kill sugar-feeding mosquitoes. During a two-arm cluster randomized Phase III trial conducted in Zambia to test the efficacy of ATSB stations on malaria incidence, ATSB stations deployed on eligible household structures within intervention clusters were routinely monitored to ensure their good physical condition and high coverage. This study investigates trends in prevalence and rate of damage to ATSB stations during year 2 of the two-year trial.

Methods
The analysis was conducted using monitoring data collected in year 2, which included types of damage observed, location, and date of removal and/or replacement of ATSB stations. The study evaluated temporal trends in the prevalence of overall damage and different damage types among 68,299 ATSB stations deployed. A profile of all ATSB stations installed on each structure was constructed, and spatial analyses conducted on overall damage and different damage types observed on 18,890 structures. Mixed effects regression analyses were conducted to investigate drivers of damage to ATSB stations on these structures.

Results
Prevalence of overall damage and different damage types was temporally and spatially heterogeneous. Among damaged ATSB stations observed during monitoring, tears and mold had the highest prevalences on average, with tears maintaining above 50.0% prevalence through most of the monitoring period, while mold prevalence increased steadily during the first few months, peaking in February. Overall, 45.6% of structures had at least one damaged ATSB station, however this varied spatially across the trial site. Both structure characteristics and environmental factors significantly impacted the odds and rate of damage to ATSB stations on structures, including: ATSB stations’ level of protection from rainfall and sunshine; roof and wall material of the structure; night-time temperature; rainfall; enhanced vegetation index, and land cover.

Conclusion
Damage to ATSB stations in this setting was common and was temporally and spatially heterogeneous. This has implications on operational feasibility, sustainability, and cost of future deployment. Further research is required to understand the mechanisms of damage, and to minimize prevalence and rate of damage to ATSB stations.
Inclusion of people with disabilities in Chilean health policy: a policy analysis
Authors: Rodríguez Gatta Danae , Gutiérrez Monclus Pamela , Wilbur Jane , Hanefeld Johanna , Banks Lena Morgon , Kuper Hannah 
Published: August 2024

Abstract
Background
Around 18% of the population in Chile has disabilities. Evidence shows that this population has greater healthcare needs, yet they face barriers to accessing healthcare due to health system failures. This paper aims to assess the inclusion of people with disabilities in health policy documents and to explore the perceptions of key national stakeholders regarding the policy context, policy processes, and actors involved.

Methods
A policy content analysis was conducted of 12 health policy documents using the EquiFrame framework, adapted to assess disability inclusion. Documents were reviewed and rated on their quality of commitment against 21 core concepts of human rights in the framework. Key national stakeholders (n = 15) were interviewed, and data were thematically analysed under the Walt and Gilson Policy Analysis Triangle, using NVivo R1.

Results
Core human rights concepts of disability were mentioned at least once in nearly all health policy documents (92%). However, 50% had poor policy commitments for disability. Across policies, Prevention of health conditions was the main human rights concept reflected, while Privacy of information was the least referenced concept. Participants described a fragmented disability movement and health policy, related to a dominant biomedical model of disability. It appeared that disability was not prioritized in the health policy agenda, due to ineffective mainstreaming of disability by the Government and the limited influence and engagement of civil society in policy processes. Moreover, the limited existing policy framework on disability inclusion is not being implemented effectively. This implementation gap was attributed to lack of financing, leadership, and human resources, coupled with low monitoring of disability inclusion.

Conclusions
Improvements are needed in both the development and implementation of disability-inclusive health policies in Chile, to support the achievement of the right to healthcare for people with disabilities and ensuring that the health system truly “leaves no one behind”.
Montane evergreen forest deforestation for banana plantations decreased soil organic carbon and total nitrogen stores to alarming levels
Authors: Magalhães Tarquinio Mateus , Cossa Edna Rita Bernardo , Nhanombe Hunilcia Esperança , Mugabe Amélia David Muchanga 
Published: August 2024

AbstractForest conversion to agricultural land has been shown to deplete soil organic carbon (SOC) and soil total nitrogen (STN) stocks. However, research on how soil properties respond to forest conversion to shifting cultivation has produced conflicting results. The conflicting findings suggest that the agricultural system may influence the response of SOC and STN to forest conversion to agriculture, depending on the presence of vegetative cover throughout the year. Due to the unique characteristics of montane evergreen forests (MEF) and banana plantations (BP), SOC and STN response to MEF conversion to BP may differ from existing models. Nevertheless, research on how soil properties are affected by MEF conversion to BP is scarce globally. In order to fill this research gap, the goal of this study was to evaluate how much deforestation for BP affects SOC, STN, and soil quality by analysing these soil parameters in MEF and BP fields down to 1-m depth, using standard profile-based procedures. Contrary to the specified hypothesis that SOC and STN losses would be restricted to the upper 20-cm soil layer, SOC losses were extended to the 40-cm depth layer and STN losses to the 60-cm depth layer. The soils lost 18.56 Mg ha – 1 (37%) of SOC from the upper 20 cm and 33.15 Mg ha – 1 (37%) from the upper 40 cm, following MEF conversion to BP. In terms of STN, the upper 20, 40, and 60 cm lost 2.98 (43%), 6.62 (47%), and 8.30 Mg ha – 1 (44%), respectively. Following MEF conversion to BP, the SOC stratification ratio decreased by 49%, implying a decline in soil quality. Massive exportation of nutrients, reduced C inputs due to complete removal of the arboreal component and crop residues, the erodibility of the soils on the study area’s steep hillslopes, and the potential for banana plantations to increase throughfall kinetic energy, and splash erosion through canopy dripping are thought to be the leading causes of SOC and STN losses. More research is needed to identify the extent to which each cause influences SOC and STN losses.