bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interest of tri-axial rubidium and helium optically pumped magnetometers for on-scalp magnetoencephalography recording of interictal epileptiform discharges
Authors: Feys Odile , Corvilain Pierre , Labyt Etienne , Mahmoudzadeh Mahdi , Routier Laura , Sculier Claudine , Holmes Niall , Brookes Matthew , Goldman Serge , Romain Rudy , Mitryukovskiy Sergey , Palacios-Laloy Agustin , Schwartz Denis , Betrouni Nacim , Derambure Philippe , Wallois Fabrice , Wens Vincent , De Tiège Xavier 
Published: October 2023

AbstractCryogenic magnetoencephalography (MEG) enhances the presurgical assessment of refractory focal epilepsy (RFE). Optically pumped magnetometers (OPMs) are cryogen-free sensors that enable on-scalp MEG recordings. Here, we investigate the interest of tri-axial OPMs (87Rb (Rb-OPM) and4He gas (He-OPM)) for the detection of interictal epileptiform discharges (IEDs).IEDs were recorded simultaneously with 4 tri-axial Rb- and 4 tri-axial He-OPMs in a child with RFE. IEDs were identified visually, isolated from magnetic background noise using independent component analysis (ICA), and the orientation of magnetic field generated by the IEDs was reconstructed at each sensor location.Most IEDs (>1,000) were detectable by both He- and Rb-OPM recordings. IEDs were isolated by ICA and the resulting magnetic field oriented mostly tangential to the scalp in Rb-OPMs and radial in He-OPMs. Likely due to differences in sensor locations, the IED amplitude was higher with Rb-OPMs.This case study shows comparable ability of Rb-OPMs and He-OPMs to detect IEDs and the substantial benefits of triaxial OPMs to detect IEDs from different sensor locations. Tri-axial OPMs allow to maximize spatial brain sampling for IEDs detection with a limited number of sensors.
District Level Variation in Hypertension Epidemiology in India and Influence of Social Determinants: National Family Health Survey-5
Authors: Gupta Rajeev , Gaur Kiran , Sharma Suresh C , Khedar Raghubir S , Dhamija Rajinder K 
Published: October 2023

ABSTRACTBACKGROUNDEnumeration of state and district-level variation in hypertension prevalence in India and to evaluate the influence of social determinants.METHODSWe used data from the Fifth National Family Health Survey (NFHS-5) from 707 districts and 825,954 participants (women 724,115, men 101,839 men) on prevalence of hypertension defined according to standard criteria. Data on multiple social determinants were also obtained from NFHS-5 report.RESULTSAge-standardized prevalence of hypertension was 22.4% (women 21.3%, men 24.0%) with the highest prevalence in women and men, respectively, in Sikkim (34.5 and 41.6%) and Punjab (31.2 and 37.7%) and lowest in Rajasthan (15.4 and 17.9%) and Ladakh (15.7 and 17.4%). Prevalence was more in western and southern Indian districts. High prevalence of hypertension in the young (<30y) was observed in northeastern and northern states. District-level hypertension prevalence correlated negatively with multi-dimensional poverty index (R2women 0.299, men 0.245) and positively with female literacy (women 0.165, men 0.134). Among women, districts with the highest availability of electricity, clean water, sanitation, clean cooking fuels, healthcare service delivery and better nutrition were associated with more hypertension on univariate and multivariate analyses (p<0.05).CONCLUSIONSThe study shows significant geographical variation in hypertension prevalence in India. Hypertension is more in men with high prevalence of premature hypertension. Better district-level development (less poverty, more literacy) and healthcare services are associated with greater hypertension prevalence in women.SUMMARY TABLEWhat is known about the topicSignificant state-level variation in hypertension prevalence in India has been reported but district-level variation is not known.Social determinants are important in hypertension but not well studied, especially in women.What this study addsThe study shows a significant district-level variation with greater hypertension prevalence in southern and western India.Hypertension among the young, <30 years, is more in less developed districts.Social determinants of hypertension in women are less poverty, more literacy and availability of healthcare services.
Rolling 2D Bioelectronic film into 1D: a Suturable Long-term Implantable Soft Microfiber
Authors: Xie Ruijie , Yu Qianhengyuan , Li Dong , Han Xu , Xu Xiaolong , Huang Jianping , Yan Wei , Zhou Xiaomeng , Deng Xinping , Tian Qiong , Li Qingsong , Li Hanfei , Zheng Hairong , Li Guanglin , Han Fei , Xu Tiantian , Liu Zhiyuan 
Published: October 2023

AbstractLong-term implantable bioelectronics can efficiently evaluate the function of the nervous system. 1D fiber-shaped devices require small surgical incisions significantly benefiting long-term biocompatibility. We report a strategy of rolling to reduce the dimension of bioelectronic devices from 2D film to 1D microfiber. The soft and stretchable multifunctional microfiber accommodates more than 60-channel longitudinally-distributed electrodes for bio-electric and -mechanical monitoring. It can be sutured into muscle with tiny incision for 8-month bio-electrical monitoring in rats. Importantly, after 13-month implantation, the fibroblast encapsulation around the fiber is negligible. Moreover, it can wander inside a brain under magnetic field. This strategy not only opens up the study of multi-channel and -function soft and stretchable fiber-shaped sensors but offers a platform for minimally-invasive implantable bioelectronics.One-Sentence SummaryThe rolling enables stretchable electrode array along one single microfiber and multimodal long-termin-vivomonitoring.
Reconstructing the Phylogeny ofCalliandrasect.Androcallis(Fabaceae): Insights from the Inclusion of Colombian Species, with a Focus on the Enigmatic TaxonCalliandra medellinensis
Authors: Arias Tatiana , Saldarriaga Juan David , Arenas-Castro Henry , Idárraga-Piedrahita Álvaro , López-Alvarez Norberto , Luque Eduardo Tovar , Torres-Morales Germán , Gonzalez Mailyn A. , Soto-Calderón Iván Darío 
Published: October 2023

ABSTRACTPhylogenetic relationships for the genusCalliandrasectionAndrocallis(Fabaceae) were reconstructed, including previously sequenced species from Central and South America and unexamined species from Colombia, one ofCalliandramain diversity centers. Here, we generated novel DNA sequences ofCalliandraspecies from Colombia for the nuclear Internal Transcribed Spacer (ITS)and the chloroplasttrnLandtrnL-Fintergenic spacer. By incorporating a broader taxonomic sampling, the relationships among main clades inAndrocalliswere clarified, providing a systematics framework in which to test evolutionary hypotheses. Phylogenetic analysis recovered five well-supported clades withinAndrocallis. Most species within each clade had similar geographical distributions and relationships between the five major clades are strongly supported for the first time. However, coreAndrocallisrelationships, including most species from Colombia sequenced here, remain unclear. A second goal of this study was to determine the taxonomic status ofCalliandra medellinensis. This enigmatic taxon emblematic of Medellín, Colombia, is found in limited numbers within the Aburrá Valley and has been proposed to be a hybrid taxon. Here,C. medellinensis,C. magdalenaeandC. haematocephalawere not monophyletic within the coreAndrocallisclade. This suggests thatC. medellinensiscould potentially be an interspecific hybrid betweenC. magdalenaeandC. haematocephala, thus challenging the taxonomic status of this species; however, more informative molecular markers should be used in future studies. Specifically, genomic studies should assess interspecific hybridization demographic models. Such insights can illuminate theC. medellinensisorigin, guiding conservation strategies and providing valuable evolutionary overviews.
Long-term engraftment of adult hematopoietic progenitors in a novel model of humanized mice
Authors: Yu Chun I , Maser Rick , Marches Florentina , Banchereau Jacques , Palucka Karolina 
Published: October 2023

AbstractPre-clinical use of humanized mice transplanted with CD34+hematopoietic progenitor cells (HPCs) is limited by insufficient engraftment with adult HPCs. Here, we developed a novel immunodeficient mice based in NOD-SCID-Il2γc-/-(NSG) mice to support long-term engraftment with human adult HPCs and tissue colonization with human myeloid cells. As both Flt3L and IL-6 are critical for many aspects of hematopoiesis, we knock-out mouseFlt3and knock-in humanIL6gene. The resulting mice showed an increase in the availability of mouse Flt3L to human cells, and a dose-dependent production of human IL-6 upon activation. Upon transplantation with low number of human HPCs from adult bone marrow, these humanized mice demonstrated a significantly higher engraftment with multilineage differentiation of human lymphoid and myeloid cells. Furthermore, higher frequencies of human lymphoid and myeloid cells were detected in tissues at one year after adult HPC transplant. Thus, these mice enable studies of human hematopoiesis and tissue colonization over time.SummaryPre-clinical use of humanized mice is limited by insufficient engraftment with adult hematopoietic progenitor cells (HPCs). Here, we developed a novel immunodeficient mice which support long-term engraftment with adult bone marrow HPCs and facilitate building autologous models for immuno-oncology studies.
Host glutathione is required forRickettsia parkerito properly septate, avoid ubiquitylation, and survive in macrophages
Authors: Sun Han , Luu Anh Phuong , Danielson Meggie , Vo Thaomy T. , Burke Thomas P. 
Published: October 2023

SummarySpotted fever groupRickettsiaobligately reside in the cytosol where they parasitize over fifty metabolites from their hosts. However, the role for metabolite acquisition in pathogenesis remains unclear. Here, we find that depletion of the abundant low molecular weight thiol glutathione led to an impaired ability ofRickettsia parkerito form plaques. Super-resolution microscopy revealed that glutathione depletion with buthionine sulfoximine (BSO) in endothelial or epithelial cells led to the formation of bacterial chains that increased in length over time. Chained bacteria had fewer actin-tails and were impeded for their ability to spread from cell to cell. Glutathione depletion also caused an increased frequency of colocalization between the bacterial surface and polyubiquitin.R. parkeriwas significantly more restricted upon glutathione depletion in primary macrophages than in epithelial cells in a mechanism that avoided activating the inflammasome and the production of type I interferon. Together, these data suggest that host glutathione is critical for rickettsial septation, actin-based motility, avoiding ubiquitylation, and survival in immune cells.
Robotic System for Organoid Assembly in a Multi-Well Microfluidic Chip
Authors: Sachs David M , Costa Kevin D 
Published: October 2023

AbstractWhile many cell culture systems are sensitive to the conditions in which cells are introduced into the system, we find that in situ differentiated tube-shaped microfluidic organoids have a particularly high sensitivity. Preliminary experiments using conventional seeding techniques revealed that biases in initial cell number and distribution dramatically impacted organoid shape and behavior downstream. Residual flows during seeding further complicated the process, dispersing cells to undesirable locations within the chip. To address this problem, a a robotic seeding system for controlling the process of inserting cells into microfluidic chips was developed. Environmental control of temperature, CO2, and humidity was implemented by modifying a commercial Arduino-controlled incubator. An eight-channel syringe pump controlled flow to eight cell dispensers, while a vertical leadscrew stage raised and lowered them, and a set of stackable flexure micromanipulators individually controlled the X and Y position of each cell dispenser. The flexure manipulators were 3D printed, driven by low-cost motors and electronics, and required little assembly and no alignment, resulting in a cheap and scalable method of controlling a dense array of micromanipulators. A dual objective microscope on a motorized gantry used an oblique lighting system to observe the seeding process, allowing for real-time interventions or passive observation of automated protocols. The robotic cell seeding system provided a platform for optimizing a sensitive process towards increasing the repeatability and physiological relevance of tube-shaped microfluidic organoids.
Finding and Following: A deep learning-based pipeline for tracking platelets during thrombus formationin vivoandex vivo
Authors: McGovern Abigail S. , Larsson Pia , Tarlac Volga , Setiabakti Natasha , Mashcool Leila Shabani , Hamilton Justin R. , Boknäs Niklas , Nunez-Iglesias Juan 
Published: October 2023

The last decade has seen increasing use of advanced imaging techniques in platelet research. However, there has been a lag in the development of image analysis methods, leaving much of the information trapped in images. Herein, we present a robust analytical pipeline for finding and following individual platelets over time in growing thrombi. Our pipeline covers four steps: detection, tracking, estimation of tracking accuracy, and quantification of platelet metrics. We detect platelets using a deep learning network for image segmentation, which we validated with proofreading by multiple experts. We then track platelets using a standard particle tracking algorithm and validate the tracks with custom image sampling — essential when following platelets within a dense thrombus. We show that our pipeline is more accurate than previously described methods. To demonstrate the utility of our analytical platform, we use it to show thatin vivothrombus formation is much faster than thatex vivo. Furthermore, plateletsin vivoexhibit less passive movement in the direction of blood flow. Our tools are free and open source and written in the popular and user-friendly Python programming language. They empower researchers to accurately find and follow platelets in fluorescence microscopy experiments.xPlain language summaryIn this paper we describe computational tools to find and follow individual platelets in blood clots recorded with fluorescence microscopy. Our tools work in a diverse range of conditions, both in living animals and in artificial flow chamber models of thrombosis. Our work uses deep learning methods to achieve excellent accuracy. We also provide tools for visualising data and estimating error rates, so you don’t have to just trust the output. Our workflow measures platelet density, shape, and speed, which we use to demonstrate differences in the kinetics of clotting in living vessels versus a synthetic environment. The tools we wrote are open source, written in the popular Python programming language, and freely available to all. We hope they will be of use to other platelet researchers.
Inhibition of Lactate Dehydrogenase A (LDH-A) by Diclofenac Sodium Induces Apoptosis in HeLa Cells by Activation of AMPK
Authors: Malla Avirup , Gupta Suvroma , Sur Runa 
Published: October 2023

AbstractCancer cells exhibit a unique metabolic preference for choosing the glycolytic pathway over oxidative phosphorylation for maintaining the tumor microenvironment. Lactate dehydrogenase-A (LDH-A) is a key enzyme that facilitates glycolysis by converting pyruvate to lactate and has been shown to be upregulated in multiple cancers due to the hypoxic tumor microenvironment. Diclofenac (DCF), a non-steroidal anti-inflammatory drug, has been shown to exhibit anti-cancer effects by interfering with the glucose metabolism pathway. However, the specific targets remain unknown. Usingin-silico, biochemical, and biophysical studies, we show that DCF binds to LDH-A adjacent to the substrate binding site and dose-dependently inhibits its activity in an allosteric manner in HeLa cells. Thus, DCF inhibits the hypoxic microenvironment and induces apoptosis-mediated cell death. DCF fails to induce cytotoxicity in LDH-A knocked-down HeLa cells, confirming that DCF renders its anti-mitotic effects via LDH-A inhibition. DCF-induced LDH-A inhibition alters pyruvate, lactate, NAD+, and ATP production in cells, and this could be a possible mechanism by which DCF inhibits glucose uptake in cancer cells. DCF-induced ATP deprivation leads to mitochondria-mediated oxidative stress, which results in DNA damage, lipid peroxidation, and apoptosis-mediated cell death. Reduction in intracellular ATP levels additionally activates AMPK, a sensor kinase, which further downregulates p-S6K, leading to apoptosis-mediated cell death. We find that in LDH-A knocked-down cells, intracellular ATP levels were depleted, resulting in the inhibition of p-S6K, implying the involvement of DCF-induced LDH-A inhibition in the activation of the AMPK/S6K signaling pathway.
Cheminformatics identification of phenolics as modulators of penicillin binding protein (PBP) 2x ofStreptococcus pneumoniaetowards interventive antibacterial therapy
Authors: Aribisala Jamiu Olaseni , S’thebe Nosipho Wendy , Sabiu Saheed 
Published: October 2023

AbstractInfections caused by multidrug-resistantStreptococcus pneumoniaeremain the leading cause of pneumonia-related deaths in children < 5 years globally, and mutations in penicillin-binding protein (PBP) 2x have been identified as the major cause of resistance in the organism to beta-lactams. Thus, the development of new modulators with enhanced binding of PBP2x is highly encouraged. In this study, phenolics, due to their reported antibacterial activities, were screened against the active site of PBP2x using structure-based pharmacophore and molecular docking techniques, and the ability of the top-hit phenolics to inhibit the active and allosteric sites of PBP2x was refined through 120 ns molecular dynamic simulation. Except for gallocatechin gallate and lysidicichin, respectively, at the active and allosteric sites of PBP2x, the top-hit phenolics had higher negative binding free energy (ΔGbind) than amoxicillin [active site (−19.23 kcal/mol), allosteric site (−33.75 Kcal/mol)]. Although silicristin had the best broad-spectrum effects at the active (−38.41 kcal/mol) and allosteric (−50.54 kcal/mol) sites of PBP2x, the high thermodynamic entropy (4.90 Å) of the resulting complex might suggest the need for its possible structural refinement for enhanced potency. Interestingly, silicristin had a predicted synthetic feasibility score of < 5 and quantum calculations using the DFT B3LYP/6-31G+ (dp) revealed that silicristin is less stable and more reactive than amoxicillin. These findings point to the possible benefits of the top-hit phenolics, and most especially silicristin, in the direct and synergistic treatment of infections caused byS. pneumoniae. Accordingly, silicristin is currently the subject of further confirmatoryin vitroresearch.
United States Marijuana Legalization and Opioid Mortality Trends Before and During the First Year of the COVID-19 Pandemic
Authors: Bleyer Archie , Barnes Brian , Finn Kenneth 
Published: October 2023

AbstractTo determine if marijuana legalization reduced opioid mortality, the U.S. opioid and fentanyl subset death trends during the 2010-2019 decade were compared in states and District of Columbia (D.C.) (jurisdictions) that had implemented marijuana legalization with states that had not. Acceleration of opioid mortality during 2020, first year of the COVID-19 pandemic, was also compared in recreational and medicinal-only legalizing jurisdictions. Joinpoint methodology was applied to Centers for Disease Control and Prevention WONDER data. Trends in legalizing jurisdictions were cumulative aggregates. The overall opioid and fentanyl death rates and percentage of opioid deaths due to fentanyl increased more during 2010-2019 in jurisdictions that legalized marijuana than in those that did not (pairwise comparison p = 0.007, 0.05, and 0.006, respectively). By 2019, the opioid and fentanyl death rates were 44% and 50% greater in the legalizing than non-legalizing jurisdictions, respectively. When the COVID-19 pandemic hit in 2020, jurisdictions that implemented recreational marijuana legalization before 2019 had significantly greater increases in both overall opioid and fentanyl death rates than jurisdictions with medicinal-only legalization. For all opioids, the mean (95% confidence interval [CI]) 2019-to-2020 increases were 46.5% (95% CI, 36.6% to 56.3%) and 29.1% (95% CI 20.2% to 37.9%), respectively (p = 0.02). For fentanyl, they were 115.6% (95% CI, 80.2% to 151.6%) and 55.4% (95% CI, 31.6% to 79.2%), respectively (p = 0.01). Marijuana legalization is correlated with worsening of the U.S. opioid epidemic, and especially during the COVID-19 pandemic with recreational legalization.
Segzoo: a turnkey system that summarizes genome annotations
Authors: Mendez Mickaël , Liu Yushan , Asenjo Ponce de León Marc , Hoffman Michael M. 
Published: October 2023

AbstractSegmentation and automated genome annotation (SAGA) techniques, such as Segway and ChromHMM, assign labels to every part of the genome, identifying similar patterns across multiple genomic input signals. Inferring biological meaning in these patterns remains challenging. Doing so requires a time-consuming process of manually downloading reference data, running multiple analysis methods, and interpreting many individual results.To simplify these tasks, we developed the turnkey system Segzoo. As input, Segzoo only requires a genome annotation file in browser extensible data (BED) format. It automatically downloads the rest of the data required for comparisons. Segzoo performs analyses using these data and summarizes results in a single visualization.Availability and ImplementationSource code for Python ≥3.7 on Linux freely available for download athttps://github.com/hoffmangroup/segzoounder the GNU General Public License (GPL) version 2. Segzoo is also available in the Bioconda package segzoo:https://anaconda.org/bioconda/segzoo.