bluuebunny/crossref_metadata_2025_split huggingface dataset:
Collective Almost Synchronization Modeling Used for Motor Imagery EEG Classification
Authors: Phuong Nguyen Thi Mai , Phan Minh Khanh , Hayashi Yoshikatsu , Baptista Murilo S. , Kondo Toshiyuki 
Published: August 2023

AbstractClassification based on feature extraction is a crucial technique to develop Brain Computer Interface (BCI) systems. The human brain can be considered as a dynamical system, and its behavior measured by EEG signals can be modeled by a group of nonlinear oscillators. Exploring the dynamical nature of EEG signals along with model based approach may improve classification accuracy in BCI. This study proposes a novel feature extraction method for the classification of Motor Imagery (MI) EEG using a dynamical network model operating in a special collective state, so called Collective Almost Synchronization (CAS). The CAS, the nonlinear oscillators set to operate in a weakly coupled regime, can be used to model an EEG. Purpose of this study is to investigate the performance of the CAS model to identify features for the classification of MI states. To achieve this goal, a linear regression method is used and linear coefficients are extracted as feature vectors. Our approach boils down to identifying patterns in the MI-EEG by associating them to the coefficients of a linear regression (or weights of an output function) constructed to model the MI-EEG signals from simulated time-series generated by a dynamical neural network. The dataset 2b from BCI Competition-IV was used to evaluate the performance of the proposed method. Results indicate that the CAS-based classification method is more robust in extracting distinguishable features from EEG signals as compared with other state-of-the-art methods. The proposed method achieved better performance on two-class MI classification. Moreover, the method developed in this study for MI classification across subjects is effective with 74.03% of the accuracy.
Hypertension Trends and Disparities over Twelve Years in a Large Health System: Leveraging the Electronic Health Records
Authors: Brush John E. , Lu Yuan , Liu Yuntian , Asher Jordan R. , Li Shu-Xia , Sawano Mitsuaki , Young Patrick , Schulz Wade L. , Anderson Mark , Burrows John S. , Krumholz Harlan M. 
Published: August 2023

AbstractBackgroundThe digital transformation of medical data enables health systems to leverage real-world data (RWD) from electronic health records (EHR) to gain actionable insights for improving hypertension care.MethodsWe performed a serial cross-sectional analysis of outpatients of a large regional health system from 2010 to 2021. Hypertension was defined by systolic blood pressure (SBP) ≥ 140 mmHg or diastolic blood pressure (DBP) ≥ 90 mmHg) or recorded treatment with anti-hypertension medications. We evaluated four methods of using blood pressure measurements in the EHR to define hypertension.The primary outcomes were age-adjusted prevalence rates and age-adjusted control rates. Secondary outcomes were age-adjusted mean SBP and DBP and age-adjusted proportion of patients with a searchable diagnosis code of hypertension in the EHR.ResultsHypertension prevalence varied depending on the definition used, ranging from 36.5% to 50.9% initially and increasing over time by approximately 5%, regardless of the definition used. Control rates ranged from 61.2% to 71.3% initially, rose during 2018-2019 and fell during 2020-2021. The proportion of patients with a hypertension diagnosis ranged from 45.5% to 60.2% initially and improved during the study period. Non-Hispanic Black patients represented 25% of our regional population and consistently had higher prevalence rates, higher mean SBP and DBP and lower control rates compared with other racial and ethnic groups.ConclusionIn a large regional health system, we leveraged the EHR to provide real-world insights. The findings largely reflected national trends but showed distinctive regional demographics and findings. The findings have provided opportunities for improvement, with prevalence increasing, a quarter of the patients not controlled, and marked disparities. This approach could be emulated by regional health systems seeking to improve hypertension care.Key PointsQuestion:Can a large regional health system leverage the electronic health record to analyze hypertension trends and disparities to drive improvement?Findings:We analyzed 1,376,325 patients over 12 years and found that age-adjusted hypertension prevalence increased by approximately 5%. Age-adjusted hypertension control rates were in the 70% range and remained stable. Non-Hispanic Black patients represented 25% of our specific regional population and had 12-14% higher hypertension prevalence rates, higher mean age-adjusted systolic and diastolic blood pressure, and lower hypertension control rates compared with other racial groups.Meaning:Real world data can provide actionable insights about hypertension and disparities in a specific region that could inform regional system strategies and initiatives for improvement.
Exploring the gut virome in fecal immunochemical test stool samples reveals novel associations with lifestyle in a large population-based study
Authors: Istvan Paula , Birkeland Einar , Avershina Ekaterina , Kværner Ane S , Bemanian Vahid , de Vos Willem M. , Rognes Torbjørn , Berstad Paula , Rounge Trine B 
Published: August 2023

ABSTRACTStool samples for fecal immunochemical tests (FIT) are collected in large numbers worldwide as part of colorectal cancer screening programs, but to our knowledge, the utility of these samples for virome studies is still unexplored. Employing FIT samples from 1034 CRCbiome participants, recruited from a Norwegian colorectal cancer screening study, we identified and annotated more than 18000 virus clusters (vOTUs), using shotgun metagenome sequencing. Only six percent of vOTUs were assigned to a known taxonomic family, withMicroviridaebeing the most prevalent viral family. Genome integration state was family-associated, and the majority of identified viruses were unintegrated. Linking individual profiles to comprehensive lifestyle and demographic data showed 17/25 of the variables to be associated with the gut virome. Physical activity, smoking, and dietary fiber consumption exhibited strong and consistent associations with both diversity and relative abundance of individual vOTUs, as well as with enrichment for auxiliary metabolic genes.We demonstrate the suitability of FIT samples for virome analysis, opening an opportunity for large-scale studies of this yet enigmatic part of the gut microbiome. The diverse viral populations and their connections to the individual lifestyle uncovered herein paves the way for further exploration of the role of the gut virome in health and disease.
Xylazine in Drug Seizure Reports and Overdose Deaths in the US, 2018-2022
Authors: Cano Manuel , Daniulaitye Raminta , Marsiglia Flavio 
Published: August 2023

AbstractXylazine is increasingly reported in street drugs and fatal overdoses in the United States (US), often in combination with synthetic opioids, yet state-level xylazine data are limited, hampering local public health responses. The present study analyzed 2018-2022 state-level data from the National Forensic Laboratory Information System (xylazine-positive reports of seized drugs analyzed by forensic laboratories), the Centers for Disease Control and Prevention (population estimates, synthetic opioid overdose mortality rates), and individual states’ medical examiner/public health agency reports (numbers of xylazine-involved overdose deaths). An ordinary least squares regression model predicted state-level synthetic opioid overdose mortality rates by xylazine seizure report rates, adjusting for US Census Region. In 2018, relatively low rates of xylazine seizure reports were observed, with 21 states reporting zero xylazine seizures. In 2022, only three states reported zero xylazine seizures, and the highest xylazine seizure report rates (per 100,000 residents) were observed in New Jersey (30.4), Rhode Island (22.7), Maryland (18.9), Virginia (15.5), New Hampshire (13.0), and Ohio (10.9). Data on 2019-2022 xylazine-involved overdose deaths were available for 21 states/DC (60 state-years), with the highest 2022 xylazine-involved overdose death rates (per 100,000 residents) in Vermont (10.5) and Connecticut (9.8). Finally, in 2021, at the state level, each additional reported xylazine seizure per 100,000 residents was associated with a 2% higher synthetic opioid overdose mortality rate (b=0.02, robust standard error=0.01;p=0.049). Overall, study results emphasize xylazine’s increasing involvement in US law enforcement drug seizure reports and overdose deaths, primarily in the East, yet also extending across the country.
Rates of SARS-CoV-2 transmission between and into California state prisons
Authors: Dubey Preeti , Hoover Christopher M. , Lu Phoebe , Blumberg Seth , Porco Travis C. , Parsons Todd L. , Worden Lee 
Published: August 2023

AbstractCorrectional institutions are a crucial hotspot amplifying SARS-CoV-2 spread and disease disparity in the U.S. In the California state prison system, multiple massive outbreaks have been caused by transmission between prisons. Correctional staff are a likely vector for transmission into the prison system from surrounding communities. We used publicly available data to estimate the magnitude of flows to and between California state prisons, estimating rates of transmission from communities to prison staff and residents, among and between residents and staff within facilities, and between staff and residents of distinct facilities in the state’s 34 prisons through March 22, 2021. We use a mechanistic model, the Hawkes process, reflecting the dynamics of SARS-CoV-2 transmission, for joint estimation of transmission rates. Using nested models for hypothesis testing, we compared the results to simplified models (i) without transmission between prisons, and (ii) with no distinction between prison staff and residents. We estimated that transmission between different facilities’ staff is a significant cause of disease spread, and that staff are a vector of transmission between resident populations and outside communities. While increased screening and vaccination of correctional staff may help reduce introductions, large-scale decarceration remains crucially needed as more limited measures are not likely to prevent large-scale disease spread.
Epidemiology of pediatric astrovirus gastroenteritis in a Nicaraguan birth cohort
Authors: Rubinstein Rebecca J , Reyes Yaoska , González Fredman , Gutiérrez Lester , Toval-Ruíz Christian , Hammond Kelli , Bode Lars , Vinjé Jan , Vilchez Samuel , Becker-Dreps Sylvia , Bucardo Filemón , Vielot Nadja A. 
Published: August 2023

AbstractBackgroundAstrovirus is a leading cause of acute gastroenteritis in children worldwide. However, few prospective studies have analyzed astrovirus in community-dwelling pediatric populations in low-and-middle-income countries.MethodsWe assessed the incidence, risk factors, clinical characteristics, genotypes, viral coinfections and seasonality of astrovirus gastroenteritis in 443 healthy Nicaraguan children born in 2017-2018, followed for 36 months. Children were recruited from maternity hospitals and birth records in an economically-diverse neighborhood of León, the second-largest city in Nicaragua. Astrovirus-positive episodes and genotypes were identified from diarrheal specimens with reverse transcription quantitative polymerase chain reaction and Sanger sequencing.ResultsOf 1708 total specimens tested, eighty children (18%) experienced at least 1 astrovirus episode, and 9 experienced repeat episodes, mostly during the rainy season (May-October). The incidence of astrovirus episodes was 7.8/100 child-years (95% CI: 6.2, 9.8). Genotype-specific incidence of astrovirus also exhibited seasonality. Median age of astrovirus episode onset was 16 months (IQR 9, 23). Initial astrovirus episodes were not associated with protection against future episodes during the age span studied. Astrovirus cases were exclusively breastfed for a shorter period than uninfected children, and the human milk oligosaccharide lacto-N-fucopentaose-I was more concentrated in mothers of these children. Home toilets appeared to protect against future astrovirus episodes (HR=0.19, 95% CI 0.04-0.91). Human astrovirus-5 episodes, comprising 15% of all typed episodes, were associated with longer diarrhea and more symptomatic rotavirus co-infections.ConclusionAstrovirus was a common cause of gastroenteritis in this cohort, and future studies should clarify the role of astrovirus genotype in clinical infection severity.
Improved dual-color GRAB sensors for monitoring dopaminergic activityin vivo
Authors: Zhuo Yizhou , Luo Bin , Yi Xinyang , Dong Hui , Wan Jinxia , Cai Ruyi , Williams John T. , Qian Tongrui , Campbell Malcolm G. , Miao Xiaolei , Li Bozhi , Wei Yu , Li Guochuan , Wang Huan , Zheng Yu , Watabe-Uchida Mitsuko , Li Yulong 
Published: August 2023

AbstractDopamine (DA) plays multiple roles in a wide range of physiological and pathological processes via a vast network of dopaminergic projections. To fully dissect the spatiotemporal dynamics of DA release in both dense and sparsely innervated brain regions, we developed a series of green and red fluorescent GPCR activation‒based DA (GRABDA) sensors using a variety of DA receptor subtypes. These sensors have high sensitivity, selectivity, and signal-to-noise properties with subsecond response kinetics and the ability to detect a wide range of DA concentrations. We then used these sensors in freely moving mice to measure both optogenetically evoked and behaviorally relevant DA release while measuring neurochemical signaling in the nucleus accumbens, amygdala, and cortex. Using these sensors, we also detected spatially resolved heterogeneous cortical DA release in mice performing various behaviors. These next-generation GRABDAsensors provide a robust set of tools for imaging dopaminergic activity under a variety of physiological and pathological conditions.
Rationally designed multimeric nanovaccines using icosahedral DNA origami for molecularly controlled display of SARS-CoV-2 receptor binding domain
Authors: Feng Qingqing , Cheng Keman , Zhang Lizhuo , Gao Xiaoyu , Liang Jie , Liu Guangna , Ma Nana , Xu Chen , Tang Ming , Chen Liting , Wang Xinwei , Ma Xuehui , Zou Jiajia , Shi Quanwei , Du Pei , Wang Qihui , Nie Guangjun , Zhao Xiao 
Published: August 2023

AbstractMultivalent antigen display on nanoparticles can enhance the immunogenicity of nanovaccines targeting viral moieties, such as the receptor binding domain (RBD) of SARS-CoV-2. However, particle morphology and size of current nanovaccines are significantly different from those of SARS-CoV-2. Additionally, surface antigen patterns are not controllable to enable the optimization of B cell activation. Herein, we employed an icosahedral DNA origami (ICO) as a display particle for SARS-CoV-2 RBD nanovaccines. The morphology and diameter of the particles were close to those of the virus (91 ± 11 nm). The surface addressability of the DNA origami permitted facile modification of the ICO surface with numerous RBD antigen clusters (ICO-RBD) to form various antigen patterns. Using anin vitroscreening system, we demonstrate that the antigen spacing, antigen copies within clusters and cluster number parameters of the surface antigen pattern all impact the ability of the nanovaccines to activate B cells. Importantly, the optimized ICO-RBD nanovaccines evoked stronger and more enduring humoral and T cell immune responses in mouse models compared to soluble RBD antigens. Our vaccines activated similar humoral immunity and slightly stronger cellular immunity compared to mRNA vaccines. These results provide reference principles for the rational design of nanovaccines and exemplify the utility of DNA origami as a display platform for vaccines against infectious disease.
Isoform-resolved genome annotation enables mapping of tissue-specific betalain regulation in amaranth
Authors: Winkler Tom S. , Vollmer Susanne K. , Dyballa-Rukes Nadine , Metzger Sabine , Stetter Markus G 
Published: August 2023

Summary• Betalains are coloring pigments produced in some families of the order Caryophyllales, where they replace anthocyanins as coloring pigments. While the betalain pathway itself is well studied, the tissue-specific regulation of the pathway remains mostly unknown.• We enhance the high-qualityAmaranthus hypochondriacusreference genome and produce a substantially more complete genome annotation, incorporating isoform details. We annotate betalain and anthocyanin pathway genes along with their regulators in amaranth and map the genetic control and tissue-specific regulation of the betalain pathway.• Our improved genome annotation allowed us to identify causal mutations that lead to a knock-out of red betacyanins in natural accessions of amaranth. We reveal the tissue-specific regulation of flower color via a previously uncharacterized MYB transcription factor,AhMYB2. Downregulation ofAhMYB2in the flower leads to reduced expression of key betalain enzyme genes and loss of red flower color.• Our improved amaranth reference genome represents the most complete genome of amaranth to date and a valuable resource for betalain and amaranth research. High similarity of the flower betalain regulatorAhMYB2to anthocyanin regulators and a partially conserved interaction motif support the co-option of anthocyanin regulators for the betalain pathway as possible reason for mutual exclusiveness of the two pigments.
Differential regulation of the proteome and phosphosproteome along the dorso-ventral axis of the earlyDrosophilaembryo
Authors: Gomez Juan Manuel , Nolte Hendrik , Vogelsang Elisabeth , Dey Bipasha , Takeda Michiko , Giudice Girolamo , Faxel Miriam , Cepraga Alina , Zinzen Robert Patrick , Krüger Marcus , Petsalaki Evangelia , Wang Yu-Chiun , Leptin Maria 
Published: August 2023

AbstractThe initially homogeneous epithelium of the earlyDrosophilaembryo differentiates into regional subpopulations with different behaviours and physical properties that are needed for morphogenesis. The factors at top of the genetic hierarchy that control these behaviours are known, but many of their targets are not. To understand how proteins work together to mediate differential cellular activities, we studied in an unbiased manner the proteomes and phosphoproteomes of the three main cell populations along the dorso-ventral axis during gastrulation using mutant embryos that represent the different populations. We detected 6111 protein groups and 6259 phosphosites of which 3399 and 3433 respectively, were differentially regulated. The changes in phosphosite abundance did not correlate with changes in host protein abundance, showing phosphorylation to be a regulatory step during gastrulation. Hierarchical clustering of protein groups and phosphosites identified clusters that contain known fate determinants such as Doc1, Sog, Snail and Twist. The recovery of the appropriate known marker proteins in each of the different mutants we used validated the approach, but also revealed that two mutations that both interfere with the dorsal fate pathway,Toll10Bandserpin27aexdo this in very different manners. Diffused network analyses within each cluster point to microtubule components as one of the main groups of regulated proteins. Functional studies on the role of microtubules provide the proof of principle that microtubules have different functions in different domains along the DV axis of the embryo.
Elephants develop wrinkles through both form and function
Authors: Schulz Andrew K. , Reveyaz Noemie , Kaufmann Lena , Ritter Cindy , Hildebrandt Thomas , Brecht Michael 
Published: August 2023

AbstractThe trunks of elephants have prominent wrinkles from their base to the very tip. But neither the obvious differences in wrinkles between elephant species nor their development have been studied before. Asian elephants have more dorsal major, meaning deep and wide, trunk wrinkles (~126 ± 25 SD) than African elephants (~83 ± 13 SD). Both species have more dorsal than ventral major trunk wrinkles and a closer wrinkle spacing distally than proximally. In Asian elephants wrinkle density is high in the ‘trunk wrapping zone’. Wrinkle numbers on the left and right sides of the distal trunk differed as a function of trunk lateralization, with frequent bending in one direction causing wrinkle formation. MicroCT-imaging and microscopy of newborn elephants’ trunks revealed a constant thickness of the putative epidermis, whereas the putative dermis shrinks in the wrinkle troughs. During fetal development wrinkle numbers double every 20 days in an early exponential phase. Later wrinkles are added slowly, but at a faster rate in Asian than African elephants. We characterize the lifelong development of trunk wrinkles in Asian and African elephants and discuss the relation of species differences in trunk wrinkle distribution and number with behavioral, environmental, genetic, and biomechanical factors.
KLP-7/Kinesin-13 orchestrates axon-dendrite checkpoints for polarized trafficking in neurons
Authors: Dey Swagata , Kumar Nitish , Feldman Jessica , Ghosh-Roy Anindya 
Published: August 2023

AbstractNeurons are compartmentalized cells with spatiotemporal distinction of anatomy and molecular repertoire. Microtubule organization in the neuron is crucial for its polarized structure and composition. Microtubule dynamics are differentially optimized in the axons and dendrites by the interplay between the microtubule-stabilizing and destabilizing factors. It is unclear how the destabilizing factors are important for developing and maintaining neuronal polarity.We investigated the function of KLP-7, a microtubule depolymerizing motor from the Kinesin-13 family, in the compartmentalization of axons and dendrites using the PVD neurons inCaenorhabditis elegans. In the absence of KLP-7, axonal proteins such as RAB-3 and SAD-1 were mislocalized to dendrites, suggesting a disruption in axon-dendrite compartmentalization. Notably, this phenomenon was independent of other depolymerizing factors like EFA-6, highlighting the specific role of KLP-7 in this process. We observed a reduced rate of microtubule polymerization and an altered polarity of microtubules in the PVD major dendrite due to the loss ofklp-7. Additionally, the deletion ofklp-7led to the formation of ectopic neurites from the cell body and the ectopic localization of UNC-44/Ankyrin-G, a protein associated with the axon initial segment (AIS), to the dendrites. Additionally, live imaging of GFP::KLP-7 revealed that KLP-7 is more dynamic in the dendrites as compared to the axon. These observations indicate that the precise dynamics of KLP-7 in neurites are crucial for maintaining distinct microtubule polymerization in the axons and dendrites, thereby influencing neuronal polarity.Our findings shed light on the pivotal role of KLP-7/Kinesin-13 in the establishment of axon-dendrite checkpoints, which in turn impact the polarized trafficking of cellular components within neurons.