bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effect of D-cycloserine on brain connectivity over a course of pulmonary rehabilitation
Authors: Finnegan Sarah L. , Harrison Olivia K. , Ezra Martyn , Harmer Catherine J. , Nichols Thomas E. , Rahman Najib M. , Reinecke Andrea , Pattinson Kyle T.S. 
Published: November 2023

AbstractRationaleCombining traditional therapies such as pulmonary rehabilitation with brain- targeted drugs may offer new therapeutic opportunities for the treatment of chronic breathlessness. Recent work has shown that D-cycloserine, a partial NMDA-receptor agonist which has been shown to enhance cognitive behavioural therapies, modifies the relationship between breathlessness related brain activity and breathlessness anxiety over pulmonary rehabilitation. However, whether these changes are supported by alterations to underlying brain structure remains unknown. Here we examine the effect of D-cycloserine over a course of pulmonary rehabilitation on regional brain volume and connectivity.Methods72 participants with mild-to-moderate COPD took part in a longitudinal study in parallel to their pulmonary rehabilitation course. Diffusion tensor brain imaging, self-report questionnaires and clinical measures of respiratory function were collected at three time points (before, during and after pulmonary rehabilitation). Participants were assigned to 250mg of D-cycloserine or placebo, which they were administered with on four occasions in a randomised, double-blind procedure.ResultsFollowing four sessions of pulmonary rehabilitation, improvements in breathlessness anxiety were linked with increased insula-hippocampal structural connectivity in the D-cycloserine group. No group differences were found following the completion of pulmonary rehabilitation, or in the integrity of structural connectivity.ConclusionsThe action of D-cycloserine on brain connectivity appears to be restricted to within a short time-window of its administration. This temporary boost of the brain connectivity of two key regions associated with the evaluation of unpleasantness may support the re-evaluation of breathlessness cues, illustrated improvements in breathlessness anxiety. This work highlights the relevance of targeting breathlessness expectation in pulmonary rehabilitation.
Social Network Strategies to Distribute HIV Self-testing Kits: A Global Systematic Review and Network Meta-analysis
Authors: Hu Siyue , Jing Fengshi , Fan Chengxin , Dai Yifan , Xie Yewei , Zhou Yi , Lv Hang , He Xi , Wu Dan , Tucker Joseph D. , Tang Weiming 
Published: November 2023

AbstractIntroductionSocial network strategies, in which social networks are utilized to influence individuals or communities, are increasingly being used to deliver human immunodeficiency virus (HIV) interventions to key populations. We summarized and critically assessed existing research on the effectiveness of social network strategies in promoting HIV self-testing (HIVST).MethodsUsing search terms related to social network interventions and HIVST, we searched five databases for trials published between January 1st, 2010, and June 30th, 2023. Outcomes included uptake of HIV testing, HIV seroconversion, and linkage to antiretroviral therapy (ART) or HIV Care. We used network meta-analysis to assess the uptake of HIV testing through social network strategies compared with control methods. A pairwise meta-analysis of studies with a comparison arm that reported outcomes was performed to assess relative risks (RR) and their corresponding 95% confidence intervals (CI).Results and discussionAmong the 3,745 manuscripts identified, 33 studies fulfilled the inclusion criteria, including one quasi-experimental study, 17 RCTs and 15 observational studies. Networks HIVST testing was organized by peers (distributed to known peers, 15 studies), partners (distributed to their sexual partners, 10 studies), and peer educators (distributed to unknown peers, 8 studies). The results showed that all of the three social network distribution strategies enhanced the uptake of HIV testing compared to standard facility-based testing. Among social networks, peer distribution had the highest uptake of HIV testing (79% probability, SUCRA 0.92), followed by partner distribution (72% probability, SUCRA 0.71), and peer educator distribution (66% probability, SUCRA 0.29). Pairwise meta-analysis showed that peer distribution (RR 2.29, 95% CI 1.54-3.39, 5 studies) and partner distribution (RR 1.45, 95% CI 1.05-2.02, 7 studies) also increased the probability of detecting HIV reactivity during testing within the key population when compared to the control. Linkage to ART or HIV Care remained comparable to facility-based testing across the three HIVST distribution strategies.ConclusionsNetwork-based HIVST distribution is considered effective in augmenting HIV testing rates and reaching marginalized populations compared to facility-based testing. These strategies can be integrated with the existing HIV care services, to fill the testing gap among key populations globally.PROSPERO Number: CRD42022361782
Polymer Implantable Electrode Foundry: A shared resource for manufacturing polymer-based microelectrodes for neural interfaces
Authors: Scholten Kee , Xu Huijing , Lu Zhouxiao , Jiang Wenxuan , Ortigoza-Diaz Jessica , Petrossians Artin , Orler Steven , Gallonio Rachael , Liu Xin , Song Dong , Meng Ellis 
Published: November 2023

AbstractLarge scale monitoring of neural activity at the single unit level can be achieved via electrophysiological recording using implanted microelectrodes. While neuroscience researchers have widely employed chronically implanted electrode-based interfaces for this purpose, a commonly encountered limitation is loss of highly resolved signals arising from immunological response over time. Next generation electrode-based interfaces improve longitudinal signal quality using the strategy of stabilizing the device-tissue interface with microelectrode arrays constructed from soft and flexible polymer materials. The limited availability of such polymer microelectrode arrays has restricted access to a small number of researchers able to build their own custom devices or who have developed specific collaborations with engineering researchers who can produce them. Here, a new technology resource model is introduced that seeks to widely increase access to polymer microelectrode arrays by the neuroscience research community. The Polymer Implantable Electrode (PIE) Foundry provides custom and standardized polymer microelectrode arrays as well as training and guidance on best-practices for implantation and chronic experiments.
Acinetobacter guillouiaestrain isolated from sludge capable of partially degrade polyethylene terephthalate: genomic and biochemical insights
Authors: Akhtar Naheed , Najjari Afef , Tullberg Cecilia , Awan Muhammad Siddique , Majeed Zahid , Grey Carl , Zhang Baozhong , Linares-Pastén Javier A. 
Published: November 2023

AbstractThe escalating accumulation of plastic waste in terrestrial and aquatic ecosystems profoundly threatens environmental health and biodiversity while impacting human well-being. Recently, many microorganisms capable of degrading polyethylene terephthalate (PET) have been reported, primarily sourced from terrestrial soils and marine environments. Notably, the challenge of PET pollution in aquatic environments has remained a persistent research concern. In this study, we present the isolation and characterization ofAcinetobacter guillouiaestrain I-MWF, obtained from a wastewater treatment plant in Makri, AJK, Pakistan, using molecular phylogenetic analysis based on genome sequencing. Results revealed that this strain exhibits the ability for PET powder degradation, as confirmed by HPLC/LCMS analysis. Furthermore, we conducted whole-genome sequencing using Illumina technology and bioinformatically explored this strain’s potential repertoire of lipase and esterase enzymes. Under optimized conditions of 23°C and pH 7 in mineral salt media with PET powder as the sole organic substrate,A. guillouiaeI-MWF could degrade partially. Extracellular enzymes yielded PET depolymerization products identified as mono(2- hydroxyethyl) terephthalic acid and terephthalic acid. The sequenced genome of this strain spans 4.61 Mb with a mean G + C content of 38.2%, containing 4,178 coding genes, 71 tRNA, and six rRNA genes. Although no cutinase-like enzymes were identified, our analysis unveiled a diverse array of putative lipases and three esterases, all sharing the typical α/β hydrolase fold. Additionally, comprehensive molecular modelling analysis suggested that some of the 18 identified extracellular hydrolases may be involved in polyester enzymatic depolymerization processes.
Total-evidence phylogenetic analysis resolves the evolutionary timescale of mantis shrimps (Stomatopoda) and provides insights into their molecular and morphological evolutionary rates
Authors: Van Der Wal Cara , Ahyong Shane T. , Adams Maxim W.D. , Lo Nathan , Ho Simon Y.W. 
Published: November 2023

ABSTRACTThe crustacean order Stomatopoda comprises approximately 500 species of mantis shrimps. These marine predators, common in tropical and subtropical waters, possess sophisticated visual systems and specialized hunting appendages. In this study, we infer the evolutionary relationships within Stomatopoda using a combined data set of 77 morphological characters, whole mitochondrial genomes, and three nuclear markers. Our data set includes representatives from all seven stomatopod superfamilies, including the first sequence data from Erythrosquilloidea. Using a Bayesian relaxed molecular clock with fossil-based calibration priors, we estimate that crown-group unipeltatan stomatopods appeared ∼140 (95% credible interval 201–102) million years ago in the Mesozoic. Additionally, our results support the hypothesis that specialized smashing and spearing appendages appeared early in the evolutionary history of Unipeltata. We found no evidence of a correlation between rates of morphological and molecular evolution across the phylogeny, but identified very high levels of among-lineage rate variation in the morphological characters. Our total-evidence analysis recovered evolutionary signals from both molecular and morphological data sets, demonstrating the merit in combining these sources of information for phylogenetic inference and evolutionary analysis.
A WIDESPREAD PICORNAVIRUS AFFECTS THE HAEMOCYTES OF THE NOBLE PEN SHELL (PINNA NOBILIS) LEADING TO IMMUNOSUPPRESSION
Authors: Carella Francesca , Prado Patricia , Vico Gionata De , Palić Dušan , Villari Grazia , García-March José Rafael , Tena-Medialdea José , Melendreras Emilio Cortés , Casalduero Francisca Giménez- , Sigovini Marco , Aceto Serena 
Published: November 2023

AbstractThe widespread mass mortality of the noble pen shell (Pinna nobilis) has occurred in several Mediterranean countries in the past seven years. Single-stranded RNA virus affecting immune cells and leading to immune disfunction have been widely reported in human and animal species. Here we present data linkingP. nobilismass mortality events (MMEs) to haemocyte picornavirus (PV) infection. This study was performed on 30 specimens, from wild and captive populations. We sampledP. nobilisfrom two regions of Spain, Catalonia [24 animals] and Murcia [two animals]), and one region in Italy (Venice [four animals]). The low number of analyzed specimens was due to the scarcity of remaining individuals in the Mediterranean Sea. In 100% of our samples, ultrastructure revealed the presence of a virus (20nm diameter), capable of replicating within granulocytes and hyalinocytes, leading to the accumulation of complex vesicles of different dimensions within the cytoplasm. As the PV infection progressed, dead haemocytes, infectious exosomes, and budding of extracellular vesicles were visible, along with endocytic vesicles entering other cells. The THC (total haemocyte count) values observed in both captive (eight animals) (3.5 x 104- 1.60 x105ml-1cells) and wild animals (14 samples) (1.90 - 2.42 x105ml-1cells) were lower than those reported before MMEs. Sequencing ofP. nobilis(six animals) haemocyte cDNA libraries revealed the presence of two main sequences ofPicornavirales, familyMarnaviridae. The highest number of reads belonged to animals that exhibited active replication phases and abundant viral particles from Trasmission Electron Microscopy (TEM) observations. These sequences correspond to the genusSogarnavirus- a picornavirus identified in the marine diatomChaetoceros tenuissimus(namedC. tenuissimusRNA virus type II). Real time PCR performed on the two most abundant RNA viruses previously identified byin silicoanalysis revealed positive results only for the sequences similar toC. tenuissimusRNA virus. These results may not be considered conclusive of picornavirus identification in noble pen shell haemocytes, and require further studies. Our findings suggest that picornavirus infection likely causes immunosuppression, making individuals prone to opportunistic infections which is a potential cause for the MMEs observed in the Mediterranean.
Phenogenomic resources immortalized in a panel of wild-derived strains of five species of house mice
Authors: Piálek Jaroslav , Ďureje Ľudovít , Hiadlovská Zuzana , Kreisinger Jakub , Aghová Tatiana , Bryjová Anna , Čížková Dagmar , Goüy de Bellocq Joëlle , Hejlová Helena , Janotová Kateřina , Martincová Iva , Orth Annie , Piálková Jana , Pospíšilová Iva , Rousková Ludmila , Bímová Barbora Vošlajerová , Bonhomme François , Forejt Jiří , Macholán Miloš , Klusáčková Pavla 
Published: November 2023

AbstractThe house mouse,Mus musculus, is a widely used animal model in biomedical research, with classical laboratory strains (CLS) being the most frequently employed. However, the limited genetic variability in CLS hinders their applicability in evolutionary studies. Wild-derived strains (WDS), on the other hand, provide a suitable resource for such investigations. This study quantifies genetic and phenotypic data of 101 WDS representing 5 species, 3 subspecies, and 8 natural Y consomic strains and compares them with CLS. Genetic variability was estimated using whole mtDNA sequences, thePrdm9gene, and copy number variation at two sex chromosome-linked genes. WDS exhibit a large natural variation with up to 2173 polymorphic sites in mitogenomes, whereas CLS display 92 sites. Moreover, while CLS have twoPrdm9alleles, WDS harbour 46 different alleles. Although CLS resembleM. m. domesticusandM. m. musculusWDS, they differ from them in 8 and 11 out of 15 phenotypic traits, respectively. The results suggest that WDS can be a useful tool in evolutionary studies and have great potential for medical applications.
COMPARATIVE TRANSCRIPTOMICS REVEALS THE MOLECULAR MECHANISMS OF MAIZE IN RESPONSE TO DOWNY MILDEW CAUSED BYPeronosclerospora philippinensis(WESTON) SHAW
Authors: Fernandez Edward Cedrick J. , Simon-Ada Eliza Vie M. , Mendoza Jay-Vee S. , Manohar Anand Noel C. , Gardoce Roanne R. , Laude Tonette P. , Dela Cueva Fe M. , Lantican Darlon V. 
Published: November 2023

ABSTRACTMaize is the Philippines’ second most valuable staple crop based on overall value and total area planted. Yellow maize, which is the most important type, is utilized as feed for poultry and swine. Still, local maize production is hampered by the Philippine downy mildew (DM) disease caused by the pathogenPeronosclerospora philippinensis(Weston) Shaw, causing substantial losses in maize production annually. To comprehend the underlying resistance mechanisms upon the presence of the disease, we performed an RNA-Seq comparative transcriptomics approach between mock-inoculated and DM-inoculated susceptible and resistant yellow maize inbred lines. Among the identified differentially expressed genes (DEGs), we detected 43 DEGs shared in both genotypes which may play roles in the basal defense response of maize upon DM infection. We also identified 68 DEGs exclusive to the susceptible genotype, providing insights into the molecular responses underlying successful DM disease progression in maize. Further, we detected 651 DEGs unique to the resistant genotype. This set of genes revealed that the molecular basis of DM resistance in maize is governed by multi-faceted defense strategies. These include multi-process regulations such as programmed cell death (PCD), regulatory proteins, and transcription factors involved in pathogen defense mechanisms, cell wall organization, homeostasis, and many others. Out of 694 resistant DEGs detected, we narrowed down genes of interest, particularly those highly overexpressed and associated with disease resistance found in other crops. Finally, transcriptome-wide variants and their corresponding impact on gene function were detected for further application in targeted genotyping-by-sequencing, association studies, and marker-assisted DM resistance breeding.
Assessing Risk Factors for Cognitive Decline Using Electronic Health Records: A Scoping Review
Authors: Wang Liqin , Yang Richard , Sha Ziqin , Kuraszkiewicz Anna Maria , Leonik Conrad , Zhou Li , Marshall Gad A. 
Published: November 2023

ABSTRACTBackgroundElectronic health records (EHR) provide rich, diverse, longitudinal real-world data, offering valuable opportunities to study antecedent risk factors for cognitive decline. However, the extent to which such records have been utilized to understand the risk factors of cognitive decline remains unclear.MethodsWe conducted a systematic review following PRISMA guidelines. We retrieved relevant articles published between January 1, 2010, and April 30, 2023, from PubMed, Web of Science, and CINAHL. Inclusion criteria were studies utilizing EHR to study risk factors for cognitive decline, including subjective cognitive decline, mild cognitive impairment, and dementia. Each article was screened by at least two reviewers. Data elements were manually extracted based on a predefined schema. The studied risk factors were reported.ResultsOf 1,593 articles identified, 80 research articles were selected. Seventy (87.5%) were retrospective cohort studies, 53 (66.3%) used datasets with greater than 10,000 patients, and 69 (86.3%) used EHR datasets from the United States or United Kingdom. Furthermore, 39 (48.8%) targeted medical conditions, 23 (28.8%) related to medical interventions, and 14 (17.5%) related to lifestyle, socioeconomic status, and environmental factors. The majority of studied medical conditions were associated with an elevated risk of cognitive decline, whereas medical interventions addressing these conditions often reduced the risk.ConclusionEHRs have significantly advanced our understanding of medical conditions, interventions, lifestyle, socioeconomic status, and environmental factors related to the risk of cognitive decline.HighlightsElectronic health records are increasingly analyzed to discern dementia risk factors.Eighty articles have been published and most of them were retrospective cohort studies.Most risk factors addressed were related to medical conditions and interventions.A few articles studied lifestyle, socioeconomic status, and environmental factors.
Compressed sensing expands the multiplexity of imaging mass cytometry
Authors: Hosogane Tsuyoshi , Santana Leonor Schubert , Eling Nils , Moch Holger , Bodenmiller Bernd 
Published: November 2023

AbstractThe multiplexity of current antibody-based imaging is limited by the number of reporters that can be detected simultaneously. Compressed sensing can be used to recover high-dimensional information from low-dimensional measurements when the data has a structure that allows sparse representation. Previously, in composite in situ imaging (CISI) of transcriptomic data, compressed sensing leveraged the gene co-regulation structure that allows sparse representation and recovered spatial expression of 37 RNA species with the measurement of 11 fluorescent channels. Here, we extended the compressed sensing framework to protein expression data measured by imaging mass cytometry (IMC). CISI-IMC accurately recovered spatial expression of 16 proteins from the images of 8 composite channels, which in effect expanded the current multiplexity limit of IMC by 8 channels. With this ratio, up to 80 protein markers could be compressed into currently available 40 isotope channels. Training the CISI-IMC framework using data collected on tissues from various locations in the human body enabled the decompression of composite data from a wide range of tissue types. Our work laid the foundation for much higher plex protein imaging by using CISI.
Novel DNA methylation changes in mouse lungs associated with heavy smoking
Authors: Onuzulu Chinonye Doris , Lee Samantha , Basu Sujata , Comte Jeannette , Hai Yan , Hizon Nikho , Chadha Shivam , Fauni Maria Shenna , Halayko Andrew J. , Pascoe Christopher D. , Jones Meaghan J. 
Published: November 2023

ABSTRACTSmoking is a potent cause of asthma, chronic obstructive pulmonary disease (COPD) and many other health defects, and changes in DNA methylation (DNAm) have been identified as a potential link between smoking and these health outcomes. However, most links between smoking and DNAm have been made using blood and other easily accessible tissues in humans, while evidence from more directly affected tissues such as the lungs is greatly lacking. Here, we identified DNAm patterns which are altered by smoking directly in the lungs. We used a well-established mouse model to measure the effects of heavy smoking first on lung phenotype immediately after smoking and then after a period of smoking cessation. Next, we determined whether our mouse model could recapitulate previous DNAm patterns observed in smoking humans by measuring DNAm at a candidate gene responsive to cigarette smoke (CS),Cyp1a1.Finally we carried out epigenome-wide DNAm analyses using the newly released Illumina mouse methylation microarrays. Our results recapitulate some of the phenotypes and DNAm patterns observed in human studies but reveal 32 differentially methylated genes specific to the lungs which have not been previously associated with smoking. The affected genes are known to be involved in nicotine dependency, tumorigenesis and metastasis, immune cell dysfunction, lung function decline, and COPD. This research emphasizes the need to study CS-mediated DNAm signatures in directly affected tissues like the lungs, as that may be essential in understanding mechanisms underlying CS-mediated health outcomes.