bluuebunny/crossref_metadata_2025_split huggingface dataset:
The youth of tamale metropolis: understanding energy drink consumption, perceptions and related factors
Authors: Kobik Williams , Aryee Paul Armah 
Published: July 2023

AbstractEnergy drinks have become a popular choice for young people seeking physical and cognitive boosts, with ingredients such as caffeine, taurine, and B vitamins aimed at improving academic, athletic, and alertness levels. However, the popularity of these drinks is also driven by low prices, taste, brand loyalty, and gendered marketing, with boys being more likely to consume them. Despite the supposed benefits, energy drinks have been associated with high-risk behaviours, deaths, and adverse health effects, especially related to cardiovascular risk. Meanwhile, in Ghana, the use of energy drinks is on the rise. Hence, this study aimed to examine the prevalence and consumption pattern, perception, and factors associated with ED consumption among the youth of the Tamale Metropolis. The study was cross-sectional consisting of 541 participants. The group consisted of 340 males and 201 females, between the ages of 15 and 45. A questionnaire was utilized to obtain data on the respondents’ consumption patterns and perceptions of EDs, as well as their socio-demographic characteristics. The results of the study indicated that a large percentage of the respondents, 98.7%, had consumed energy drinks before, while 78.7% currently consume them. Respondents believed that energy drinks provided additional energy (81.00%) and reduced stress (62.30%). However, they also perceived side effects such as insomnia (60.60%) and restlessness (51.40%). Although the majority of respondents (83.4%) were unaware of the classification of energy drinks and their ingredients, side effects, and benefits. Age, marital status, level of education, work intensity, EDs served at gatherings, and knowledge of EDs was significantly associated with ED consumption (p < .05). Consumption was higher among those aged 26 to 35 years, singles, individuals with no formal education, and those with high work intensity. Energy drinks were consumed by the majority of the youth. The high consumption was also associated with low knowledge levels. It is recommended that public health and nutrition professionals should engage in further advocacy efforts to improve the youth’s perception of EDs in a positive manner. In addition, lawmakers should use legislation to influence consumption rates and safeguard the health of consumers.
Decoding semantics from dynamic brain activation patterns: From trials to task in EEG/MEG source space
Authors: Magnabosco Federica , Hauk Olaf 
Published: July 2023

AbstractThe temporal dynamics within the semantic brain network and its dependence on stimulus and task parameters are still not well understood. Here, we addressed this by decoding task as well as stimulus information from source-estimated EEG/MEG data. We presented the same visual word stimuli in a lexical decision (LD) and three semantic decision (SD) tasks. The meanings of the presented words varied across five semantic categories. Source space decoding was applied over time in five ROIs in the left hemisphere (Anterior and Posterior Temporal Lobe, Inferior Frontal Gyrus, Primary Visual Areas, and Angular Gyrus) and one in the right hemisphere (Anterior Temporal Lobe). Task decoding produced sustained significant effects in all ROIs from 50-100 ms, both when categorising tasks with different semantic demands (LD-SD) as well as for similar semantic tasks (SD-SD). In contrast, semantic word category could only be decoded in lATL, rATL, PTC and IFG, between 250-500 ms. Furthermore, we compared two approaches to source space decoding: Conventional ROI-by-ROI decoding and combined-ROI decoding with back-projected activation patterns. The former produced more reliable results for word-category decoding while the latter was more informative for task-decoding. This indicates that task effects are distributed across the whole semantic network while stimulus effects are more focal. Our results demonstrate that the semantic network is widely distributed but that bilateral anterior temporal lobes together with control regions are particularly relevant for the processing of semantic information.Significance StatementMost previous decoding analyses of EEG/MEG data have focussed on decoding performance over time in sensor space. Here for the first time we compared two approaches to source space decoding in order to reveal the spatio-temporal dynamics of both task and stimulus features in the semantic brain network. This revealed that even semantic tasks with similar task demands can be decoded across the network from early latencies, despite reliable differences in their evoked responses. Furthermore, stimulus features can be decoded in both tasks but only for a subset of ROIs and following the earliest task effects. These results inform current neuroscientific models of controlled semantic cognition.
A Molecular Basis of Human Brain Connectivity
Authors: Ng Bernard , Tasaki Shinya , Greathouse Kelsey M , Walker Courtney K , Zhang Ada , Covitz Sydney , Cieslak Matt , Adamson Ashley B , Andrade Julia P , Poovey Emily H , Curtis Kendall A , Muhammad Hamad M , Seidlitz Jakob , Satterthwaite Ted , Bennett David A , Seyfried Nicholas T , Vogel Jacob , Gaiteri Chris , Herskowitz Jeremy H 
Published: July 2023

AbstractNeuroimaging is commonly used to infer human brain connectivity, but those measurements are far-removed from the molecular underpinnings at synapses. To uncover the molecular basis of human brain connectivity, we analyzed a unique cohort of 98 individuals who provided neuroimaging and genetic data contemporaneous with dendritic spine morphometric, proteomic, and gene expression data from the superior frontal and inferior temporal gyri. Through cellular contextualization of the molecular data with dendritic spine morphology, we identified hundreds of proteins related to synapses, energy metabolism, and RNA processing that explain between-individual differences in functional connectivity and structural covariation. By integrating data at the genetic, molecular, subcellular, and tissue levels, we bridged the divergent fields of molecular biology and neuroimaging to identify a molecular basis of brain connectivity.One-Sentence SummaryDendritic spine morphometry and synaptic proteins unite the divergent fields of molecular biology and neuroimaging.
The role of agentive and physical forces in the neural representation of motion events
Authors: Karakose-Akbiyik Seda , Sussman Oliver , Wurm Moritz F. , Caramazza Alfonso 
Published: July 2023

ABSTRACTHow does the brain represent information about motion events in relation to agentive and physical forces? In this study, we investigated the neural activity patterns associated with observing animated actions of agents (e.g., an agent hitting a chair) in comparison to similar movements of inanimate objects that were either shaped solely by the physics of the scene (e.g., gravity causing an object to fall down a hill and hit a chair) or initiated by agents (e.g., a visible agent causing an object to hit a chair). Using fMRI-based multivariate pattern analysis, this design allowed testing where in the brain the neural activity patterns associated with motion events change as a function of, or are invariant to, agentive versus physical forces behind them. Cross-decoding revealed a shared neural representation of animate and inanimate motion events that is invariant to agentive or physical forces in regions spanning frontoparietal and posterior temporal cortices. In contrast, the right lateral occipitotemporal cortex showed higher sensitivity to agentive events, while the left dorsal premotor cortex was more sensitive to information about inanimate object events that were solely shaped by the physics of the scene.
Cebranopadol, a novel long-acting opioid agonist with low abuse liability, to treat opioid use disorder: Preclinical evidence of efficacy
Authors: Lunerti Veronica , Shen Qianwei , Li Hongwu , Benvenuti Federica , Soverchia Laura , Narendran Rajesh , Weiss Friedbert , Cannella Nazzareno , Ciccocioppo Roberto 
Published: July 2023

AbstractThe gold standard pharmacological treatment for opioid use disorder (OUD) consists of maintenance therapy with long-acting opioid agonists such as buprenorphine and methadone. Despite these compounds having demonstrated substantial efficacy, a significant number of patients do not show optimal therapeutic responses. Moreover, the abuse liability of these medications remains a major concern. Cebranopadol, is a new, long-acting pan-opioid agonist that also activates the nociception/orphanin FQ NOP receptor. Here we used rats to explore the therapeutic potential of this agent in OUD. First, in operant intravenous self-administration experiments we compared the potential abuse liability of cebranopadol with the prototypical opioid heroin. Under a fixed ratio 1 (FR1) contingency, rats maintained responding for heroin (1, 7, 20, 60 μg/inf) to a larger extent than cebranopadol (0.03, 0.1, 0.3, 1.0, 6.0 μg/inf). When the contingency was switched to a progressive ratio (PR) reinforcement schedule, heroin maintained responding at high levels at all except the lowest dose. Conversely, in the cebranopadol groups responding decreased drastically and the break point (BP) did not differ from saline controls. Next, we demonstrated that oral administration of cebranopadol (0, 25, 50 μg/kg) significantly attenuated drug self-administration independent of heroin dose (1, 7, 20, 60 μg/inf). Cebranopadol also reduced the break point for heroin (20 μg/inf). Furthermore, in a heroin self-administration training extinction/reinstatement paradigm, pretreatment with cebranopadol significantly attenuated yohimbine stress-induced reinstatement of drug seeking. Together, these data indicate that cebranopadol has limited abuse liability compared to heroin and is highly efficacious in attenuating opioid self-administration and stress-induced reinstatement, suggesting clinical potential of this compound for OUD treatment.
Label-free differentiation of functional zones in mature mouse placenta using micro-Raman imaging
Authors: Inanc Arda , Bektas Nayce Ilayda , Kecoglu Ibrahim , Parlatan Ugur , Durkut Begum , Ucak Melike , Unlu Mehmet Burcin , Celik-Ozenci Ciler 
Published: July 2023

AbstractIn histopathology, it is highly crucial to have chemical and structural information about tissues. Additionally, the segmentation of zones within a tissue plays an important role in investigating the functions of these regions for better diagnosis and treatment. The placenta plays an important role in embryonic and fetal development and in the diagnosis of some diseases associated with its dysfunction. This study provides a label-free approach to obtain the images of mature mouse placenta together with the chemical differences between the tissue compartments using Raman spectroscopy. To generate the Raman images, spectra of placental tissue were collected using a custom-built optical setup. The pre-processed spectra were analyzed using statistical and machine learning methods to acquire the Raman maps. We found that the placental regions called decidua and the labyrinth zone are biochemically distinct from the junctional zone. Comparison and evaluation of the Raman maps with histological images of the placental tissue were performed by a histologist and they are found to be in agreement. The results of this study show that Raman spectroscopy offers the possibility of label-free monitoring of the placental tissue from mature mice while revealing important structural information about the zones at the same time.
InvasiveArgemone mexicana’s suppressive effects onPhaseolus vulgarisandZea maysgermination and growth
Authors: Ojija Fredrick 
Published: July 2023

AbstractInvasiveArgemone mexicanaplant species is invading many ecosystems in East Africa. However, there have not been many studies to assess how it affects plants. In petri dishes and pot experiments, we investigated the suppressive effects ofA. mexicanaonPhaseolus vulgarisand Zea mays germination and seedling growth. To investigate its suppressive effects on the test plant, different concentrations ofA. mexicanaleaf (AmL) crude extract were applied to the seeds and seedlings ofP. vulgarisandZ. mays. At higher concentrations (70% and 100%), the findings showed that AmL crude extract concentrations reduced the germination and growth ofP. vulgarisandZ. maysseeds. Compared to seeds that germinated at lower concentrations and in the control (0%) group, fewer seeds at higher concentrations grew. Accordingly, higher concentrations, relative to lower ones and controls, retarded seed germination. Additionally, the fresh biomass, root lengths, stem diameters, and heights ofP. vulgarisseedlings were reduced under 75% and 100% AmL concentrations, which had a negative impact on their growth vigor. Although this study shows thatP. vulgarisandZ. maysgermination and growth were inhibited byA. mexicanacrude extract, field research experiments are needed to investigate the suppressive effects of this invasive weed on other plant species. Due to its detrimental impact on plant growth, the study recommends further management ofA. mexicanato protect biodiversity. It is expected that these results will be helpful in developing policies and programs for managing invasive plants while taking into account the effects on people’s livelihoods.
Accuracy of retrospective birth location data – An analysis based on siblings
Authors: von Hinke Stephanie , Vitt Nicolai 
Published: July 2023

AbstractMany surveys ask participants to retrospectively record their location of birth. This paper examines the accuracy of such data in the UK Biobank using a sample of siblings. Comparison of reported birth locations for siblings with different age gaps allows us to estimate the probabilities of household moves and of misreported birth locations. We find an annual probability of 1.2% for household moves of one kilometre or more, suggesting that geographical mobility during childhood was low. Our results furthermore show a sizeable probability of misreporting, with 28% of birth coordinates, 16% of local districts and 6% of counties of birth being incorrectly reported. We show that such error can lead to substantial attenuation bias when investigating the impacts of location-based exposures, especially when there is little spatial correlation and limited time variation in the exposure variable. Sibling fixed effect models are shown to be particularly vulnerable to the attenuation bias.
Detection of viral infection in cell lines using ViralCellDetector
Authors: Shankar Rama , Paithankar Shreya , Gupta Suchir , Chen Bin 
Published: July 2023

ABSTRACTCell lines are commonly used in research to study biology, including gene expression regulation, cancer progression, and drug responses. However, cross-contaminations with bacteria, mycoplasma, and viruses are common issues in cell line experiments. Detection of bacteria and mycoplasma infections in cell lines is relatively easy but identifying viral infections in cell lines is difficult. Currently, there are no established methods or tools available for detecting viral infections in cell lines. To address this challenge, we developed a tool called ViralCellDetector that detects viruses through mapping RNA-seq data to a library of virus genome. Using this tool, we observed that around 10% of experiments with the MCF7 cell line were likely infected with viruses. Furthermore, to facilitate the detection of samples with unknown sources of viral infection, we identified the differentially expressed genes involved in viral infection from two different cell lines and used these genes in a machine learning approach to classify infected samples based on the host response gene expression biomarkers. Our model reclassifies the infected and non-infected samples with an AUC of 0.91 and an accuracy of 0.93. Overall, our mapping- and marker-based approaches can detect viral infections in any cell line simply based on readily accessible RNA-seq data, allowing researchers to avoid the use of unintentionally infected cell lines in their studies.
Transcriptome and translatome comparison of tissues fromArabidopsis thaliana
Authors: Vélez-Bermúdez Isabel Cristina , Lin Wen-Dar , Chou Shu-Jen , Chen Ai-Ping , Schmidt Wolfgang 
Published: July 2023

AbstractTranslation is one of the multiple complementary steps that orchestrates gene activity. In contrast to the straightforwardness of transcriptional surveys, genome-wide profiles of the translational landscape of plant cells remain technically challenging and are less well explored. Protein-coding genes are expressed at a variable degree of efficiency, resulting in pronounced discordance among the regulatory levels that govern gene activity. Ribo-Seq provides an extremely useful tool for estimating translation efficiency, but limited data sets are available for plants. Here, we provide comparative inventories of expressed and translated RNA populations, generated by mRNA sequencing (RNA-Seq) and ribosome footprinting (Ribo-Seq) of shoots and roots ofArabidopsis thalianaseedlings. Our data set provides information on the translational fitness of protein-coding mRNAs and lncRNAs that may aid in obtaining a comprehensive picture of the regulatory levels governing genes activity across the genome.
Characterization of Tumor-Associated Endothelial Cells and the Development of a Prognostic Model in Pancreatic Ductal Adenocarcinoma
Authors: Wu Jun , Liu Yang , Fu Qi , Cao Zhi , Li Xun , Ma Xiaodong 
Published: July 2023

AbstractBackgroundPancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignancy characterized by a complex tumor microenvironment. Angiogenesis is of paramount importance in the proliferation and metastasis of PDAC. However, currently, there are no well-defined biomarkers available to guide the prognosis and treatment of PDAC.ResultsIn this study, we investigated the interactions between tumor-associated endothelial cells (TAECs) and tumor cells in PDAC, and identified a specific subset of TAECs characterized by high expression of COL4A1. COL4A1+ endothelial cells interact with tumor cells through the COLLAGEN signaling pathway to promote tumor cell proliferation, migration, and invasion. We also observed activation of HOXD9 in COL4A1+ endothelial cells. Based on these findings, we developed a prognostic model called TaEMS, which accurately predicts patient prognosis. TaEMS identified high-risk patients enriched in cell cycle-related pathways and low-risk patients enriched in focal adhesions, smooth muscle regulation, and immune pathways. Moreover, high-risk patients displayed a reduced level of immune cell infiltration, indicating the presence of a “cold tumor” phenotype.ConclusionsOverall, our study uncovered an intricate crosstalk between TAECs and tumor cells in PDAC, emphasizing the role of HOXD9 and highlighting the potential of TaEMS as a prognostic biomarker for precise therapies.
Spatial Metabolome Lipidome and Glycome from a Single brain Section
Authors: Clarke Harrison A. , Ma Xin , Shedlock Cameron J. , Medina Terrymar , Hawkinson Tara R. , Wu Lei , Ribas Roberto A. , Keohane Shannon , Ravi Sakthivel , Bizon Jennifer , Burke Sara , Abisambra Jose Francisco , Merritt Matthew , Prentice Boone , Vander Kooi Craig W. , Gentry Matthew S. , Chen Li , Sun Ramon C. 
Published: July 2023

ABSTRACTMetabolites, lipids, and glycans are fundamental biomolecules involved in complex biological systems. They are metabolically channeled through a myriad of pathways and molecular processes that define the physiology and pathology of an organism. Here, we present a blueprint for the simultaneous analysis of spatial metabolome, lipidome, and glycome from a single tissue section using mass spectrometry imaging. Complimenting an original experimental protocol, our workflow includes a computational framework called Spatial Augmented Multiomics Interface (Sami) that offers multiomics integration, high dimensionality clustering, spatial anatomical mapping with matched multiomics features, and metabolic pathway enrichment to providing unprecedented insights into the spatial distribution and interaction of these biomolecules in mammalian tissue biology.
Characterization of the RofA regulon in the pandemic M1globaland emergent M1UKlineages ofStreptococcus pyogenes
Authors: Zhi Xiangyun , Vieira Ana , Huse Kristin , Martel Paulo J. , Lobkowicz Ludmila , Li Ho Kwong , Croucher Nick , Andrew Ivan , Game Laurence , Sriskandan Shiranee 
Published: July 2023

AbstractBackground & AimsThe standalone regulator RofA is a positive regulator of the pilus locus inStreptococcus pyogenes. Found in only certainemmgenotypes, RofA has been reported to regulate other virulence factors, although its role in the globally dominantemm1S. pyogenesis unclear. Given the recent emergence of a newemm1 (M1UK) toxigenic lineage that is distinguished by three non-synonymous SNPs inrofA, we characterized therofAregulon in sixemm1 strains, that are representative of the two contemporary majoremm1 lineages (M1globaland M1UK) using RNAseq analysis, and then determined the specific role of the M1UK-specificrofASNPs.ResultsDeletion ofrofAin three M1globalstrains led to altered expression of 14 genes, including six non-pilus locus genes. In M1UKstrains, deletion ofrofAled to altered expression of 16 genes, including 9 genes that were unique to M1UK. Only the pilus locus genes were common to the RofA regulons of both lineages, while transcriptomic changes varied between strains even within the same lineage. Although introduction of the 3 SNPs intorofAdid not impact gene expression in an M1globalstrain, reversal of 3 SNPs in an M1UKstrain led to an unexpected number of transcriptomic changes that in part recapitulated transcriptomic changes seen when deleting RofA in the same strain. Computational analysis predicted interactions with a key histidine residue in the PRD domain of RofA would differ between M1UKand M1global.SummaryRofA is a positive regulator of the pilus locus in allemm1 strains but effects on other genes are strain- and lineage-specific, with no clear, common DNA binding motif. The SNPs inrofAthat characterize M1UKmay impact regulation of RofA; whether they alter phosphorylation of the RofA PRD domain requires further investigation.Author summaryRofA belongs to the group of “mga-like” bacterial regulatory proteins that comprise a DNA binding domain as well as a phosphorylation domain (PRD) that is responsive to changes in sugar availability. In certainemmgenotypes ofStreptococcus pyogenes,rofAsits upstream of the pilus locus, to act as a positive regulator. The recent emergence of a SpeA exotoxin-producing sublineage ofemm1S. pyogenes, (M1UK) has focused attention on the role of RofA; M1UKand its associated sublineages are characterized by 3 non-synonymous SNPs inrofA,that include adjacent SNPs in the PRD domain. Here, we determine the impact ofrofAdeletion and the 3rofASNPs in both the widely disseminated M1globalclone and the newly emergent M1UKclone. While production of SpeA undoubtedly contributes to infection pathogenesis, the evolution of M1UKpoints to a role for metabolic regulatory rewiring in success of this lineage.