bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plasma circulating extracellular vesicles indicate dysregulation of synaptic vesicle-associated signaling pathways in SHIV-infected rhesus macaque
Authors: Chandra Partha , Panner Selvam Manesh Kumar , Braun Stephen , Castorena-Gonzalez Jorge , Rutkai Ibolya , Sikka Suresh , Busija David 
Published: May 2024

Background: Recent studies point out the involvement of circulating extracellular vesicles (crEVs), in regulating neurotransmission via transferring proteins, lipids, and nucleic acids. Recently, we reported that plasma crEV proteins of either simian human immunodeficiency virus (SHIV) infected rhesus macaque or HIV-infected patient indicate a link to neuropathogenesis. Here, we tested the hypothesis that crEV proteins are indicative of dysfunction of synaptic vesicle (SV)-associated signaling pathways of SHIV-infected rhesus macaques. Methods: Plasma crEVs were isolated from SHIV-infected (SHIV-crEVs) and uninfected (CTL-crEVs) rhesus macaque and characterized by the ZetaView analyzer. Proteomic analysis of the isolated crEVs was performed using liquid chromatography/mass spectrometry (LC-MS/MS). Results: Our ZetaView analysis indicated that isolated crEVs were predominantly exosomes (particle size < 150 nm). In the LC-MS/MS study, 5,654 proteins were quantified, with 236 proteins (~ 4%) significantly differentially expressed between SHIV-crEVs and CTL-crEVs. Several SV and SV-signaling pathway associated proteins were quantified by tandem mass tags-based proteomic analysis both in SHIV-crEVs and CTL-crEVs. We observed that synaptogyrin, synaptotagmins, synaptobrevin, synaptosomal-associated proteins, syntaxin, and other SV-associated proteins were abundantly under expressed in SHIV-crEVs than in CTL-crEVs. Ingenuity Pathway Analysis demonstrated that proteins in SHIV-crEVs were involved in the deactivation of synaptogenesis, synaptic long-term protentiation/depression, and glutamate receptor signaling pathways. On the other hand, semaphorin neuronal repulsive signaling pathway and amyloid processing were activated in SHIV-crEVs. Bioinformatic analysis revealed that these proteins in SHIV-crEVs were involved in several CNS-related disorders/diseases such as abnormal morphology of synapses, motor dysfunction and movement disorder, seizure disorder, early/progressive neurological disorder, cognitive impairment, tauopathy, dementia, and Alzheimer’s disease. Conclusions: Our novel findings suggest that plasma crEVs could be an attractive noninvasive technique, which may elucidate the development of neuronal dysfunction and progression of neurological diseases. Funding: AG075988, HL148836, AG063345, AI110158, HL141143, HL168568, and the Louisiana Board of Regents Endowed Chairs for Eminent Scholars program. This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.
The laterodorsal tegmental nucleus improves breathing and sleep in a Parkinson’s disease animal model
Authors: Miranda Nicole , Oliveira Luiz , Moreira Thiago , Kalume Franck , Ramirez Jan Marino , Takakura Ana 
Published: May 2024

Parkinson's disease (PD) is a neurological disorder resulting from the degeneration of dopaminergic neurons in the substantia nigra pars compacta (SNpc). PD is characterized by classical and non-classical symptoms including respiratory instability and sleep disturbances. An important region for the control of sleep and possibly respiration is the laterodorsal tegmental nucleus (LDTg), a nucleus composed of cholinergic, glutamatergic, and GABAergic neurons. We hypothesize that stimulation of cholinergic neurons in the LDTg can lead to improvements in sleep and respiratory disturbances in a murine model of PD. Adult mice (CEUA: 6641200919 and SCRI: 18819) that express the fluorescent green protein in cholinergic cells (Chat-cre, ai6) received bilateral injections of AAV-hM3Dq-mCherry or AAV-mCherry vectors into LDTg. After ten days, the animals received nigrostriatal injections of vehicle or 6-hydroxydopamine (6-OHDA, 10 μg/μl). Eight days later, we implanted EEG and EMG electrodes. In 6-OHDA-injected mice, there was a 79% and 29% reduction in the number of dopaminergic neurons in SNpc and cholinergic neurons in LDTg, respectively. This reduction was associated with an increase in the number of apneas and a 17% and 26% reduction in respiratory frequency during non-REM (NREMs) and REM (REMs) sleep, respectively. In the same animals, there was also a decrease in wakefulness time, and an increase in total sleep time. Selective pharmacogenetic stimulation of ChAT+ neurons of the LDTg rescued the respiratory frequency during REMs and reduced the number of apneas both in NREMs and REMs in 6-OHDA mice. These results demonstrate that in this PD model the LDTg plays a significant role in respiratory changes associated with sleep regulation. FAPESP, CAPES, CNPq and NIH. This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.
Islamic Eschatology and Prophetic Register: the Divine Source of Pakistan’s Identity
Authors: Zafar Adnan 
Published: May 2024

Abstract
Despite religion’s ubiquity, its role has long been ignored by international relations scholars. One of the reasons behind ignoring religion’s influence in international politics is the anti-religion sentiments based on the theory of secularization. The belief that religion is a thing of the past has hampered the explanatory prowess of international relations scholarship. This article aims to explain how faith informs Pakistan about its divine role in international politics. It is argued that Islamic eschatology is pivotal in contouring Pakistan’s religious identity which is pivotal to how Pakistan establishes its ties with its arch-rival India. Prophetic register that exists in Pakistan act as a call to action to reform the community on religious bases. This article concludes that the role of religious prophecy must be accounted for to better explain popular religious aspirations that constrain the policy option for policymakers both at the domestic as well as international level.
Sustained response to atogepant in episodic migraine: post hoc analyses of a 12-week randomized trial and a 52-week long-term safety trial
Authors: Lipton Richard B. , Nahas Stephanie J. , Pozo-Rosich Patricia , Bilchik Tanya , McAllister Peter , Finnegan Michelle , Liu Yingyi , Chalermpalanupap Natty , Dabruzzo Brett , Dodick David W. 
Published: May 2024

Abstract
Background
Atogepant is an oral calcitonin gene–related peptide receptor antagonist approved for the preventive treatment of migraine in adults. These analyses evaluated the proportions of clinical trial participants who experienced sustained responses to atogepant over 12 or 52 weeks of treatment.

Methods
These were post hoc analyses of ADVANCE, a 12-week, double-blind, randomized trial of atogepant 10, 30, and 60 mg once daily vs. placebo for the preventive treatment of episodic migraine, and a separate open-label long-term safety (LTS) trial of atogepant 60 mg once daily over 52 weeks. The 60 mg dose of atogepant was used to detect safety issues. An initial response was defined as ≥50%, ≥75%, or 100% reduction from baseline in MMDs in month 1 for ADVANCE or quarter 1 for the LTS trial. The proportions of participants who continued to experience a response above each response-defining threshold through each subsequent month (for ADVANCE) or each quarter (for LTS) were calculated.

Results
In ADVANCE, sustained response rates during months 2 and 3 varied with dose and were as follows: 70.8–81.1% following an initial ≥50% response, 47.3–61.9% following an initial ≥75% response, and 34.8–41.7% following an initial 100% response. Of those who experienced an initial ≥75% or 100% response during month 1, more than 79% continued to experience at least a 50% response during both months 2 and 3. During the LTS trial, sustained response rates through quarters 2, 3, and 4 were 84.7% following an initial ≥50% response, 72.6% following an initial ≥75% response, and 37.8% following an initial 100% response. Of those who experienced an initial ≥75% or 100% response during quarter 1, more than 90% continued to experience at least a 50% response through quarters 2, 3, and 4.

Conclusion
Over 70% of participants who experienced an initial response with atogepant treatment had a sustained response with continued treatment.

Trial registration
ClinicalTrials.gov: NCT03777059 (submitted: December 13, 2018); NCT03700320 (submitted: September 25, 2018).
Exploring racial disparities in bladder urothelial cancer: insights into survival and genetic variations
Authors: Abubakar Sharafudeen Dahiru , Bello Zakariyya Muhammad , Gusau Sufiyanu Sani , Kabir Imam Malik 
Published: May 2024

Abstract
Background
Bladder urothelial cancer is the most common malignancy of the urinary system and the 10th most common cancer worldwide with incidence appearing to show a geographical and exposure pattern. Advances in genomic technologies provide abundant data and insight into tumors at the single-cell resolution and are usually stored in repositories like The Cancer Genome Atlas (TCGA). However, data sources for the TCGA appear to be focused on European and American populations. The extent to which genomic and survival data can be applied to populations not included in the study remains somewhat uncertain.

Methods
We explored the genomic and survival characteristics of the TCGA pan-cancer atlas of bladder urothelial cancer. We decluttered these characteristics based on racial groups and compared between and among the races and the overall dataset.

Results
Significant variations were seen in age groups especially Asians (51–60) years and Blacks (61–70) years compared to Whites and the BLCA dataset with a statistically significant difference in mean diagnosis age (p = 0.0048) between Asians and the whole dataset. Overall survival characteristics were similar but genetic features were vastly different. Significant inter-racial alterations could be seen among genes involved in different pathways, oncogenes, tumor suppressors, cytoband amplification and/or deletion, mutation count, and aneuploidy scores.

Conclusion
The TCGA pan-cancer atlas for bladder urothelial cancer adequately represents White populations only. The genomic features do not apply to Blacks and Asians. We recommend better coverage for other populations to ensure adequate data for clinicians and researchers.
A recurrent de novo missense mutation in COL1A1 causes osteogenesis imperfecta type II and preterm delivery in Normande cattle
Authors: Corbeau Julien , Grohs Cécile , Jourdain Jeanlin , Boussaha Mekki , Besnard Florian , Barbat Anne , Plassard Vincent , Rivière Julie , Hamelin Christophe , Mortier Jeremy , Boichard Didier , Guatteo Raphaël , Capitan Aurélien 
Published: May 2024

Abstract
Background
Nine male and eight female calves born to a Normande artificial insemination bull named “Ly” were referred to the French National Observatory of Bovine Abnormalities for multiple fractures, shortened gestation, and stillbirth or perinatal mortality.

Results
Using Illumina BovineSNP50 array genotypes from affected calves and 84 half-sib controls, the associated locus was mapped to a 6.5-Mb interval on chromosome 19, assuming autosomal inheritance with germline mosaicism. Subsequent comparison of the whole-genome sequences of one case and 5116 control genomes, followed by genotyping in the affected pedigree, identified a de novo missense substitution within the NC1 domain of the COL1A1 gene (Chr19 g.36,473,965G > A; p.D1412N) as unique candidate variant. Interestingly, the affected residue was completely conserved among 243 vertebrate orthologs, and the same substitution in humans has been reported to cause type II osteogenesis imperfecta (OI), a connective tissue disorder that is characterized primarily by bone deformity and fragility. Moreover, three COL1A1 mutations have been described to cause the same syndrome in cattle. Necropsy, computed tomography, radiology, and histology confirmed the diagnosis of type II OI, further supporting the causality of this variant. In addition, a detailed analysis of gestation length and perinatal mortality in 1387 offspring of Ly and more than 160,000 progeny of 63 control bulls allowed us to statistically confirm in a large pedigree the association between type II OI and preterm delivery, which is probably due to premature rupture of fetal membranes and has been reported in several isolated cases of type II OI in humans and cattle. Finally, analysis of perinatal mortality rates and segregation distortion supported a low level of germ cell mosaicism in Ly, with an estimate of 4.5% to 7.7% of mutant sperm and thus 63 to 107 affected calves born. These numbers contrast with the 17 cases reported and raise concerns about the underreporting of congenital defects to heredo-surveillance platforms, even for textbook genetic syndromes.

Conclusions
In conclusion, we describe a large animal model for a recurrent substitution in COL1A1 that is responsible for type II OI in humans. More generally, this study highlights the utility of such datasets and large half-sib families available in livestock species to characterize sporadic genetic defects.
The development of multiplex PCR assays for the rapid identification of multiple Saccostrea species, and their practical applications in restoration and aquaculture
Authors: Richardson Marina A. , Nenadic Nikolina , Wingfield Max , McDougall Carmel 
Published: May 2024

Abstract
Background
The ecology and biology of oysters (Ostreidae) across the tropics is poorly understood. Morphological plasticity and shared characteristics among oysters have resulted in the misidentification of species, creating challenges for understanding basic species-specific biological information that is required for restoration and aquaculture. Genetic barcoding has proven essential for accurate species identification and understanding species geographic ranges. To reduce the costs of molecular species identification we developed multiplex assays using the cytochrome c oxidase subunit I (COI or cox1) barcoding gene for the rapid identification of five species of oysters within the genus Saccostrea that are commonly found in Queensland, Australia: Saccostrea glomerata, Saccostrea lineage B, Saccostrea lineage F, Saccostrea lineage G, and Saccostrea spathulata (lineage J).

Results
Multiplex assays were successful in species-specific amplification of targeted species. The practical application of these primers was tested on wild spat collected from a pilot restoration project in Moreton Bay, Queensland, with identified species (S. glomerata, lineage B and lineage G) validated by Sanger sequencing. DNA sampling by extraction of oyster pallial fluid was also tested on adult oysters collected from the Noosa estuary in Queensland to assess whether oysters were able to be identified non-destructively. DNA concentrations as low as 1 ng/ μL still amplified in most cases, allowing for identification, and mortality at 6 weeks post pallial fluid collection was low (3 out of 104 sampled oysters).

Conclusion
These multiplex assays will be essential tools for species identification in future studies, and we successfully demonstrate their practical application in both restoration and aquaculture contexts in Queensland. The multiplex assays developed in this study outline easily replicable methods for the development of additional species-specific primer sets for the rapid identification of other species of Saccostrea found across the Indo-Pacific, which will be instrumental in unravelling the taxonomic ambiguities within this genus in tropical regions.
Genome sequencing and comparative genomics reveal insights into pathogenicity and evolution of Fusarium zanthoxyli, the causal agent of stem canker in prickly ash
Authors: Ruan Zhao , Jiao Jiahui , Zhao Junchi , Liu Jiaxue , Liang Chaoqiong , Yang Xia , Sun Yan , Tang Guanghui , Li Peiqin 
Published: May 2024

Abstract
Background
Fusarium zanthoxyli is a destructive pathogen causing stem canker in prickly ash, an ecologically and economically important forest tree. However, the genome lack of F. zanthoxyli has hindered research on its interaction with prickly ash and the development of precise control strategies for stem canker.

Results
In this study, we sequenced and annotated a relatively high-quality genome of F. zanthoxyli with a size of 43.39 Mb, encoding 11,316 putative genes. Pathogenicity-related factors are predicted, comprising 495 CAZymes, 217 effectors, 156 CYP450s, and 202 enzymes associated with secondary metabolism. Besides, a comparative genomics analysis revealed Fusarium and Colletotrichum diverged from a shared ancestor approximately 141.1 ~ 88.4 million years ago (MYA). Additionally, a phylogenomic investigation of 12 different phytopathogens within Fusarium indicated that F. zanthoxyli originated approximately 34.6 ~ 26.9 MYA, and events of gene expansion and contraction within them were also unveiled. Finally, utilizing conserved domain prediction, the results revealed that among the 59 unique genes, the most enriched domains were PnbA and ULP1. Among the 783 expanded genes, the most enriched domains were PKc_like kinases and those belonging to the APH_ChoK_Like family.

Conclusion
This study sheds light on the genetic basis of F. zanthoxyli’s pathogenicity and evolution which provides valuable information for future research on its molecular interactions with prickly ash and the development of effective strategies to combat stem canker.
Study on the causes of changes in colour during Hibiscus syriacus flowering based on transcriptome and metabolome analyses
Authors: Li Zhezhe , Liu Dan , Wang Dongsheng , Sun Meng , Zhang Guojun , Wu Yu , Zhang Yidan , Cheng Beibei 
Published: May 2024

Abstract
Background
The flower colour of H. syriacus ‘Qiansiban’ transitions from fuchsia to pink–purple and finally to pale purple, thereby enhancing the ornamental value of the cultivars. However, the molecular mechanism underlying this change in flower colour in H. syriacus has not been elucidated. In this study, the transcriptomic data of H. syriacus ‘Qiansiban’ at five developmental stages were analysed to investigate the impact of flavonoid components on flower colour variation. Additionally, five cDNA libraries were constructed from H. syriacus ‘Qiansiban’ during critical blooming stages, and the transcriptomes were sequenced to investigate the molecular mechanisms underlying changes in flower colouration.

Results
High-performance liquid chromatography‒mass spectrometry detected five anthocyanins in H. syriacus ‘Qiansiban’, with malvaccin-3-O-glucoside being the predominant compound in the flowers of H. syriacus at different stages, followed by petunigenin-3-O-glucoside. The levels of these five anthocyanins exhibited gradual declines throughout the flowering process. In terms of the composition and profile of flavonoids and flavonols, a total of seven flavonoids were identified: quercetin-3-glucoside, luteolin-7-O-glucoside, Santianol-7-O-glucoside, kaempferol-O-hexosyl-C-hexarbonoside, apigenin-C-diglucoside, luteolin-3,7-diglucoside, and apigenin-7-O-rutinoside. A total of 2,702 DEGs were identified based on the selected reference genome. Based on the enrichment analysis of differentially expressed genes, we identified 9 structural genes (PAL, CHS, FLS, DRF, ANS, CHI, F3H, F3’5’H, and UFGT) and 7 transcription factors (3 MYB, 4 bHLH) associated with flavonoid biosynthesis. The qRT‒PCR results were in good agreement with the high-throughput sequencing data.

Conclusion
This study will establish a fundamental basis for elucidating the mechanisms underlying alterations in the flower pigmentation of H. syriacus.
Fidelity, pragmatism and the “grey line” in between—exploring the delivery of a pragmatic physical activity randomised controlled trial—a secondary analysis
Authors: Hall Abigail J. , Goodwin Victoria A. , Clarke David J. 
Published: May 2024

Abstract
Background
Intervention fidelity in health services research has been poor with a reported lack of understanding about what constitutes pragmatic adaptation of interventions and what constitutes failure to maintain intervention fidelity. However, the challenges facing those delivering such interventions have not been thoroughly explored.
The aims of this study were to critically explore the challenges in maintaining fidelity experienced by physiotherapy staff and support workers when delivering a complex intervention for older people living with frailty.

Methods
This study is a secondary analysis of data from a process evaluation of a large randomised controlled trial (RCT). The process evaluation employed qualitative methodologies with mixed methods including a variety of data collection methods, including participant observation, semi-structured interviews and documentary analysis. Thematic analysis was used to make sense of the data.

Results
Many therapy staff felt ongoing confusion about what was acceptable to adapt and what needed to follow the protocol exactly. We found that some therapy staff were able to embrace the challenges of pragmatically adapting interventions while maintaining intervention fidelity, others stuck rigidly to the protocol and failed to adapt interventions where it was necessary.

Conclusion
It was clear that the understanding of fidelity and pragmatism was poor. While pragmatic trials are vital to replicate real world clinical practice, further guidance may need to be developed in order to guide the level of adaptation that is acceptable before fidelity is undermined.