bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-cell transcriptomics reveals colonic immune perturbations during amyloid-β driven Alzheimer’s disease in mice
Authors: Makhijani Priya , Emani Rohini , Aguirre Carlos Galicia , Mu Wei-Chieh , Rane Anand , Ng Jenny Hong Yu , Valentino Taylor R. , Manwaring-Mueller Max , Tan Christopher Ryan , Du Huixun , Wu Fei , Khan Saad , Wilson Kenneth A. , Winer Shawn , Wang Chao , Mortha Arthur , Furman David , Ellerby Lisa M. , Rojas Olga L. , Andersen Julie K. , Winer Daniel A. 
Published: January 2024

AbstractThe “gut-brain axis” is emerging as an important target in Alzheimer’s disease (AD). However, immunological mechanisms underlying this axis remain poorly understood. Using single-cell RNA sequencing of the colon immune compartment in the 5XFAD amyloid-β (Aβ) mouse model, we uncovered AD-associated changes in ribosomal activity, oxidative stress, and BCR/plasma cell activity. Strikingly, levels of colon CXCR4+antibody secreting cells (ASCs) were significantly reduced. This corresponded with accumulating CXCR4+B cells and gut-specific IgA+cells in the brain and dura mater, respectively. Consistently, a chemokine ligand for CXCR4, CXCL12, was expressed at higher levels in 5XFAD glial cells and in in silico analyzed human brain studies, supporting altered neuroimmune trafficking. An inulin prebiotic fiber diet attenuated AD markers including Aβ plaques and overall frailty. These changes corresponded to an expansion of gut IgA+cells and rescued peripheral Tregslevels. Our study points to a key glia-gut axis and potential targets against AD.Study HighlightsAD is associated with altered immune parameters in the gut of5XFADmice.5XFADcolon has reduced ASCs, including CXCR4+cells with a migratory gene signature.5XFADbrain gliosis includes increased CXCL12 expression.CXCR4+B cells and gut-specific IgA+ASCs accumulate in the5XFADbrain and/or dura mater.Inulin diet attenuates AD disease parameters while boosting IgA+cell and Treglevels.
Spaceflight increases sarcoplasmic reticulum Ca2+leak and this cannot be counteracted with BuOE treatment
Authors: Braun Jessica L. , Fajardo Val A. 
Published: January 2024

AbstractSpending time in a microgravity environment is known to cause significant skeletal muscle atrophy and weakness via muscle unloading, which can be partly attributed to Ca2+dysregulation. The sarco(endo)plasmic reticulum Ca2+ATPase (SERCA) pump is responsible for bringing Ca2+from the cytosol into its storage site, the sarcoplasmic reticulum (SR), at the expense of ATP. We have recently demonstrated that, in the soleus of spaceflown mice, the Ca2+uptake ability of the SERCA pump is severely impaired and this may be attributed to increases in reactive oxygen/nitrogen species (RONS), to which SERCA is highly susceptible. The purpose of this study was therefore to investigate whether treatment with the antioxidant, MnTnBuOE-2-PyP (BuOE), could attenuate muscle atrophy and SERCA dysfunction. We received soleus muscles from the rodent research 18 mission which had male mice housed on the international space station for 35 days and treated with either saline or BuOE. Spaceflight significantly reduced the soleus:body mass ratio and significantly increased SERCA’s ionophore ratio, a measure of SR Ca2+leak, and 4-HNE content (marker of RONS), none of which could be rescued by BuOE treatment. In conclusion, we find that spaceflight induces significant soleus muscle atrophy and SR Ca2+leak that cannot be counteracted with antioxidant treatment. Future work should investigate alternative therapeutics that are specifically aimed at increasing SERCA activation or reducing Ca2+leak.HighlightsSpaceflight induces soleus muscle atrophy and increases SR Ca2+leakTreatment with the antioxidant, BuOE, was unable to attenuate the detrimental effects of spaceflight on the soleus muscleFuture work should investigate the potential benefits of SERCA activation or reducing SR Ca2+leak
From Planning Stage To FAIR Data: A Practical Metadatasheet For Biomedical Scientists
Authors: Seep Lea , Grein Stephan , Splichalova Iva , Ran Danli , Mikhael Mickel , Hildebrand Staffan , Lauterbach Mario , Hiller Karsten , Silva Ribeiro Dalila Juliana , Sieckmann Katharina , Kardinal Ronja , Huang Hao , Yu Jiangyan , Kallabis Sebastian , Behrens Janina , Till Andreas , Peeva Viktoriya , Strohmeyer Akim , Bruder Johanna , Blum Tobias , Soriano-Arroquia Ana , Tischer Dominik , Kuellmer Katharina , Li Yuanfang , Beyer Marc , Gellner Anne-Kathrin , Fromme Tobias , Wackerhage Henning , Klingenspor Martin , Fenske Wiebke K. , Scheja Ludger , Meissner Felix , Schlitzer Andreas , Mass Elvira , Wachten Dagmar , Latz Eicke , Pfeifer Alexander , Hasenauer Jan 
Published: January 2024

ABSTRACTDatasets consist of measurement data and metadata. Metadata provides context, essential for understanding and (re-)using data. Various metadata standards exist for different methods, systems and contexts. However, relevant information resides at differing stages across the data-lifecycle. Often, this information is defined and standardized only at publication stage, which can lead to data loss and workload increase.In this study, we developed Metadatasheet, a metadata standard based on interviews with members of two biomedical consortia and systematic screening of data repositories. It aligns with the data-lifecycle allowing synchronous metadata recording within Microsoft Excel, a widespread data recording software. Additionally, we provide an implementation, the Metadata Workbook, that offers user-friendly features like automation, dynamic adaption, metadata integrity checks, and export options for various metadata standards.By design and due to its extensive documentation, the proposed metadata standard simplifies recording and structuring of metadata for biomedical scientists, promoting practicality and convenience in data management. This framework can accelerate scientific progress by enhancing collaboration and knowledge transfer throughout the intermediate steps of data creation.
Embedding biomimetic vascular networks via coaxial sacrificial writing into functional tissue
Authors: Stankey Paul P. , Kroll Katharina T. , Ainscough Alexander J. , Reynolds Daniel S. , Elamine Alexander , Fichtenkort Ben T. , Uzel Sebastien G.M. , Lewis Jennifer A. 
Published: January 2024

AbstractPrinting human tissue constructs replete with biomimetic vascular networks is of growing interest for tissue and organ engineering. While it is now possible to embed perfusable channels within acellular and densely cellular matrices, they lack either the branching or multilayer architecture of native vessels. Here, we report a generalizable method for printing hierarchical branching vascular networks within soft and living matrices. We embed biomimetic vessels into granular hydrogel matrices via coaxial embedded printing (co-EMB3DP) as well as into bulk cardiac tissues via coaxial sacrificial writing into functional tissues (co-SWIFT). Each method relies on an extended core-shell printhead that promote facile interconnections between printed branching vessels. Though careful optimization of multiple core-shell inks and matrices, we show that embedded biomimetic vessels can be coaxially printed, which possess a smooth muscle cell-laden shell that surrounds perfusable lumens. Upon seeding these vessels with a confluent layer of endothelial cells, they exhibit good barrier function. As a final demonstration, we construct biomimetic vascularized cardiac tissues composed of a densely cellular matrix of cardiac spheroids derived from human induced pluripotent stem cells. Importantly, these co-SWIFT cardiac tissues mature under perfusion, beat synchronously, and exhibit a cardio-effective drug response in vitro. This advance opens new avenues for the scalable biomanufacturing of organ-specific tissues for drug testing, disease modeling, and therapeutic use.
Serological Survey in a university community after the fourth wave of COVID-19 in Senegal
Authors: Thiam Fatou , Diouara Abou Abdallah Malick , Ndiaye Clemence Stephanie Chloe Anoumba , Diouf Ibrahima , Kebe Khadim , Senghor Assane , Djoumoi Djibaba , Mbaye Mame Ndew , Diop Idy , Sane Sarbanding , Coundoul Seynabou , Tene Sophie deli , Diop Mamadou , Dieng Abdou Lahat , Ndiaye Mamadou , Sall Saidou Moustapha , Diouf Massamba , Nguer Cheikh Momar 
Published: January 2024

AbstractCross-sectional survey was conducted to assess the true extent of COVID-19 exposure among students and staff of Polytechnic High School (PHS). Random cluster sampling was carried out between May 19 and August 18, 2022, after the fourth wave of COVID-19 transmission. IgM and IgG SARS-CoV-2 antibodies were screened using WANTAI SARS-CoV-2 ELISA assays. Seroprevalence and descriptive statistics were calculated. Moreover, the associations between seropositivity and different factors (age, gender, preventive, etc.) were determined using logistic regression. A total of 637 participants were recruited, including 563 students, followed by 52 TAS officers, and 22 professors. The median age among was 21 years [18–63]. 62.0% of the participants were female, and 36.89% were male, with a male-to-female ratio = 0.59. The overall IgG and IgM seroprevalence were 92% and 6.91% respectively. We found a higher IgM seroprevalence in men than women (9.4% vs. 5.6%) and a lower IgM seroprevalence in (18-25) age group compared to (55-65) years. Low compliance with preventive measures was found with a significant IgM seroprevalence depending on non-respect of social distancing (p = 0.008). IgM seropositivity was associated with Body Mass Indice (BMI) categorized (O.R. 0.238,p= 0.043), ethnic group (O.R. 0.723,p= 0.046) and marital status (O.R. 2.399,p= 0.021). Moreover, IgG seropositivity was associated with vaccination status (O.R. 4.741,p< 0.001). Our study revealed that the majority of students and staff have already been exposed to SARS-CoV-2, which confirms the circulation of SARS-CoV-2 in PHS at the time of the survey. Our results underline the importance of seroepidemiological surveys to estimate the real impact of the COVID-19 pandemic in a community and to monitor disparities in antibody response in the population.
Towards the identification of the molecular toolkit involved in scale worm bioluminescence (Polinoidae, Annelida)
Authors: Gracia-Sancha Carlota , Conejero María , Taboada Sergio , Martín Daniel , Riesgo Ana , Holford Mandë , Verdes Aida 
Published: January 2024

AbstractBackgroundBioluminescence, or the ability of a living organism to produce light, has evolved independently in numerous taxa inhabiting a panoply of ecosystems, although it is more frequent among marine animals. Scale worms are a group of marine polynoid annelids characterized by having dorsal scales, known as elytra, capable of emitting bioluminescent light by a mostly unknown molecular mechanism that may involve a photoprotein called polynoidin. Here, we used RNA-seq data to characterize the expression of genes potentially involved in light production in the polynoid speciesHarmothoe imbricata(Linnaeus, 1767) andHarmothoe areolata(Grube, 1860) across tissues of the specimens. We also compared the transcriptomes of the selected species with other bioluminescent and non-bioluminescent polynoids, to identify shared orthologous genes potentially involved in light production. In addition, we investigated the disposition of the photocytes on the elytra using confocal microscopy and histological analyses.ResultsOur results showed a total of 16 candidate genes, 15 orthologous genes and 12 enriched GO terms potentially involved in bioluminescence, including genes related with oxidative stress, cytoskeleton, nervous system, stress response, wounding response, eye constituents and metabolic pathways. We also confirmed the presence of photocytes in both species, which appeared distributed around the elytrophore.ConclusionsAmong the genes found potentially implicated in bioluminescence we suggest that the oxidoreductase protein, peroxidasin, could be a polynoidin candidate since it appears overexpressed in the elytra of both species and it is located in the endoplasmic reticulum, where this photoprotein has been described to be found.
Sequence-function mapping of proline-rich antimicrobial peptides
Authors: Collins Jonathan , McConnell Adam , Schmitz Zachary D. , Hackel Benjamin J. 
Published: January 2024

AbstractAntimicrobial peptides (AMPs) are essential elements of natural cellular combat and candidates as antibiotic therapy. Elevated function may be needed for robust physiological performance. Yet, both pure protein design and combinatorial library discovery are hindered by the complexity of antimicrobial activity. We applied a recently developed high-throughput technique, sequence-activity mapping of AMPs via depletion (SAMP-Dep), to proline-rich AMPs. Robust self-inhibition was achieved for metalnikowin 1 (Met) and apidaecin 1b (Api). SAMP-Dep exhibited high reproducibility with correlation coefficients 0.90 and 0.92, for Met and Api, respectively, between replicates and 0.99 and 0.96 for synonymous genetic variants. Sequence-activity maps were obtained via characterization of 26,000 and 34,000 mutants of Met and Api, respectively. Both AMPs exhibit similar mutational profiles including beneficial mutations at one terminus, the C-terminus for Met and N-terminus for Api, which is consistent with their opposite binding orientations in the ribosome. While Met and Api reside with the family of proline-rich AMPs, different proline sites exhibit substantially different mutational tolerance. Within the PRP motif, proline mutation eliminates activity, whereas non-PRP prolines readily tolerate mutation. Homologous mutations are more tolerated, particularly at alternating sites on one ‘face’ of the peptide. Important and consistent epistasis was observed following the PRP domain within the segment that extends into the ribosomal exit tunnel for both peptides. Variants identified from the SAMP-Dep platform were produced and exposed toward Gram-negative species exogenously, showing either increased potency or specificity for strains tested. In addition to mapping sequence-activity space for fundamental insight and therapeutic engineering, the results advance the robustness of the SAMP-Dep platform for activity characterization.
On the role of urban tropical tree collections in carbon allocation: expanding their functions beyond cultural and biodiversity conservation
Authors: Echeverri-Salazar Edwin , Villegas Juan Camilo , Alviar-Ramírez Lía Isabel , Mora Edwin Andrés 
Published: January 2024

AbstractTrees support key processes in both natural and managed ecosystems. In highly intervened urban environments, trees have been generally associated with benefits such as air quality, microclimate regulation, and biodiversity conservation. University campuses contain diverse and well-managed tree collections that provide local functions such as education, conservation, research, and landscaping. However, little has been discussed about these collections in the general urban setting and how they relate to other urban ecosystem processes, such as carbon cycling. This is particularly evident in tropical regions where no current urban forest carbon sequestration estimations are available. In this work, we present the results of a pilot estimation of the carbon storage function of the university tree collection at the Universidad de Antioquia (Medellín, Colombia) through a bounding calculation that combines tree inventory data and allometric equations. Our results show that, on average, the university tree collection (including palms) sequesters 3.4 Mg C/ha/year (4.2x10−2Mg C/tree/year). Remarkably, our results are comparable to natural tropical forests, particularly in locations with similar climatic and biophysical conditions. When compared to other urban studies, our estimation ranges between 1.2-20.8 times larger than cities and other urban areas with similar estimations. We present a novel integrative method for estimating carbon storage and sequestration that can be widely applied in information-limited tropical contexts. We discuss how management practices of these urban forests contribute to improving their capacity to store carbon more efficiently and effectively participate in other urban ecosystem processes that derive benefits to society. More generally, our results highlight the role of universities and other similar urban tree collections (i.e. botanical gardens and urban parks) in local and regional ecosystem functions and their potential contribution to global carbon cycling.
Modulation of locomotion and motor neuron response by the cohesive effect of acute and chronic feeding states and acute d-amphetamine treatment in zebrafish larvae
Authors: Bansal Pushkar , Roitman Mitchell F. , Jung Erica E. 
Published: January 2024

AbstractAmphetamine (AMPH) increases locomotor activities in animals, and the locomotor response to AMPH is further modulated by caloric deficits such as food deprivation and restriction. The increment in locomotor activity regulated by AMPH-caloric deficit concomitance can be further modulated by varying feeding schedules (e.g. acute and chronic food deprivation and acute feeding after chronic food deprivation). However, the effects of different feeding schedules on AMPH-induced locomotor activity are yet to be explicated. Here, we have explored the stimulatory responses of acutely administered d-amphetamine in locomotion under systematically varying feeding states (fed/sated and food deprivation) and schedules (chronic and acute) in zebrafish larvae. We used wild-type and transgenic[Tg(mnx1:GCaMP5)] zebrafish larvae and measured swimming activity and spinal motor neuron activityin vivoin real-time in time-elapsed and cumulative manner pre- and post-AMPH treatment. Our results showed that locomotion and motor neuron activity increased in both chronic and acute food deprivation post-AMPH treatment cumulatively. A steady increase in locomotion was observed in acute food-deprivation compared to an immediate abrupt increase in chronic food-deprivation state. The ad libitum-fed larvae exhibited a moderate increase both in locomotion and motor neuron activity. Conversely to all other caloric states, food-sated (acute feeding after chronic food deprivation) larvae moved moderately less and exhibited a mild decrease in motor neuron activity after AMPH treatment. These results point to the importance of the feeding schedule in modulating amphetamine’s characteristic stimulatory response on behavior and motor neurons.
Characterization of the placenta-specific EnvV2-Fca soluble protein derived from endogenous retrovirus
Authors: Pramono Didik , Sugimoto Kenji , Kimura Tohru , Miyake Ariko , Nishigaki Kazuo 
Published: January 2024

AbstractEndogenous retroviruses (ERVs) are remnants of ancestral viruses in the host genome. Here, we identified the expression of a defective retroviralenvgene belonging to the ERV group V member 2 Env (EnvV2) inFelis catus(EnvV2-Fca), which was specifically detected in the placental trophoblast syncytiotrophobic layer. EnV2-Fca was expressed as a secreted protein in cultured cells. Genetic analyses indicated that EnvV2 genes are widely present in vertebrate, and are under purifying selection among carnivores, suggesting a potential benefit for the host. Notably, this study suggests that birds, bats, and rodents carrying EnvV2 may play significant roles as intermediate vectors in spreading or cross-transmitting viruses among species. Overall, our findings provide valuable insights into the evolution of ERV in vertebrate hosts.
Laboratory evaluation of the regeneration time, efficacy and wash-resistance of PermaNet® Dual (a deltamethrin-chlorfenapyr net) against susceptible and pyrethroid-resistant strains ofAnopheles gambiae
Authors: Syme Thomas , N’dombidjé Boris , Todjinou Damien , Ariori Victoria , Ngufor Corine 
Published: January 2024

AbstractPyrethroid-chlorfenapyr nets have been recommended for malaria control by the World Health Organisation (WHO) after an alpha-cypermethrin-chlorfenapyr net showed improved impact in epidemiological trials. PermaNet® Dual is a new deltamethrin-chlorfenapyr net developed by Vestergaard Sàrl to expand options to control programmes. We performed a series of laboratory studies according to WHO guidelines to assess the regeneration time, efficacy and wash-resistance of PermaNet® Dual. Regeneration time was determined by subjecting net pieces to cone bioassays and tunnel tests before and 0, 1, 2, 3, 5 and 7 days after washing. The wash-resistance of PermaNet® Dual was evaluated compared to WHO-prequalified pyrethroid-only (PermaNet® 2.0) and pyrethroid-chlorfenapyr (Interceptor® G2) nets by testing net pieces washed 0, 1, 3, 5, 10, 15 and 20 times in cone bioassays and tunnel tests. Tests were performed with susceptible and pyrethroid-resistant strains ofAnopheles gambiaeto separately assess the pyrethroid and chlorfenapyr components. Net pieces were also analysed to determine insecticide content. In regeneration time studies, the biological activity of the deltamethrin and chlorfenapyr components of PermaNet® Dual regenerated within 1 day after washing and a 1-day washing interval was adopted for wash-resistance studies. PermaNet® Dual induced high mortality (98%) and blood-feeding inhibition (98%) of the susceptible strain after 20 washes fulfilling WHO efficacy criteria in tunnel tests (≥80% mortality, ≥90% blood-feeding inhibition). Similar results were obtained with PermaNet® 2.0 (99% mortality, 99% blood-feeding inhibition) and Interceptor® G2 (99% mortality, 98% blood-feeding inhibition) washed 20 times. In wash-resistance tunnel tests against the pyrethroid-resistant strain, PermaNet® Dual washed 20 times induced high mortality (91%) and blood-feeding inhibition (73%) which was similar to Interceptor® G2 (87% mortality, 79% blood-feeding inhibition) and superior to PermaNet® 2.0 (47% mortality, 68% blood-feeding inhibition). PermaNet® Dual fulfilled WHO efficacy criteria in laboratory bioassays and showed potential to improve control of pyrethroid-resistant malaria vectors.
Development and Validation of The Activity-Based Checks (ABCs) of Pain: A Functional Pain Scale
Authors: Virgen Celina G. , Wright Robert , Renslo Bryan , Sawaf Tuleen , Moradi Hanna , Edelen Maria , Villwock Jennifer 
Published: January 2024

AbstractThe Activity-Based-Checks of Pain (ABCs) is a pain assessment tool incorporating activities of daily living and instrumental activities of daily living. Unlike widely used pain scales which are oftentimes unidimensional and highly subjective, the ABCs was designed to focus on function capabilities and limitations of patients due to pain. This study sought out to validate the factorial structure of the ABCs and assess its use in participants with chronic pain. Participants were recruited in two phases from Prolific – an online service designed to identify research participant recruitment based on study criteria. Phase one optimized the design of the ABCs, with 297 subjects selecting their preferred icon for each function and rating its understandability. The most preferred and understandable icons were then used in phase two, where 304 chronic pain participants completed the ABCs, PROMIS-29, additional PROMIS items that were analogous to the ABCs functions but not represented in the PROMIS-29, and the Brief Pain Inventory (BPI). Data was analyzed using exploratory factor analysis and confirmatory factor analysis demonstrating four factor loadings: multi-planal activities, sitting/hip flexor pain, walking/ambulation, and pain interference with lightweight unilateral activities. High internal consistency was demonstrated with all four factor loadings. Correlations between items in the ABCs, PROMIS, and BPI resulted in moderate to strong correlations demonstrating strong evidence for the validity of the ABCs as a functional pain assessment tool.