bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluating the Effectiveness of Point-of-Entry UV Treatment for Cistern Water Among Households in the US Virgin Islands
Authors: Voth-Gaeddert Lee , Momberg Douglas , Brathwaite Kela , Schranck Andrew , Lemley Mandy , Libbey Stephen 
Published: October 2022

AbstractUV water treatment can be a viable option for point-of-entry applications among households utilizing private water sources. In the US Virgin Islands (USVI), the primary water source is roof-harvested rainwater, collected in large cisterns and supplied to household taps via a pump. While diversification of water sources provides increased resilience to climate change, literature suggests rainwater catchment systems are at high risk of microbial contamination. One option USVI households have is UV systems. However, limited data is available on UV system effectiveness for USVI installations while these systems can be expensive. Therefore, Love City Strong, a local NGO, piloted a multi-year UV access program which included free UV systems with prefiltration along with installation and monthly household visits for up to 12 months including water quality testing. In addition, due to the significant costs associated with the prefiltration portion of the system, a pilot study was conducted to evaluate the effectiveness of the UV systems without prefiltration.The results from the UV system access program demonstrated thatE. coliwas not detected in 95.2% of tap samples (n=271). Among samples with detectable levels ofE. coliand total coliforms, turbidity was lower compared to samples with non-detections. Field teams reported user error was often identified in association withE. colidetections (e.g., bypass was opened). Among all samples from the pilot study of UV systems without prefiltration, noE. coliwas detected (n=24). Total first-year costs for locally available UV systems with and without prefiltration ranged from $1,059-$1,645 and $927-$1,183, respectively, while operation and maintenance (O& M) costs ranged from $166-$266 and $142-$146, respectively. Given these data, UV systems may be a viable option for generating potable water; however, clear purchasing and installation protocols are needed as well as simple O&M guidelines for households to reduce user error.SynopsisPoint-of-entry UV systems were able to produce water for domestic use with no detectable E. coli in 95.2% of samples among USVI households using roof-harvested rainwater.
Macaque Brainnetome Atlas: A Multifaceted Brain Map with Parcellation, Connection, and Histology
Authors: Lu Yuheng , Cui Yue , Cao Long , Cheng Luqi , Dong Zhenwei , Wang Changshuo , Liu Youtong , Zhang Baogui , Wang Haiyan , Li Kaixin , Ma Liang , Shi Weiyang , Li Wen , Ma Yawei , Du Zongchang , Zhang Jiaqi , Xiong Hui , Luo Na , Liu Yanyan , Hou Xiaoxiao , Liu Xinyi , Sun Hongji , Wang Jiaojian , Paxinos George , Yang Zhengyi , Fan Lingzhong , Jiang Tianzi 
Published: October 2022

AbstractThe rhesus macaque (Macaca mulatta) is a crucial experimental animal that shares many genetic, brain organizational, and behavioral characteristics with humans. A macaque brain atlas that identifies anatomically and functionally distinct regions is fundamental to biomedical and evolutionary research. However, even though connectivity information is vital for understanding brain functions, a connectivity-based whole-brain atlas of the macaque has not previously been made. In this study, we created a new whole-brain map, the Macaque Brainnetome Atlas (MacBNA), based on the anatomical connectivity profiles provided by high angular and spatial resolution ex vivo diffusion MRI data. The new atlas consists of 248 cortical and 56 subcortical regions as well as their structural and functional connections. The parcellation and the diffusion-based tractography were comprehensively evaluated with multi-contrast MRI, invasive neuronal-tracing, and Nissl-stained images collected from a single subject and with open-access datasets from other cohorts. As a demonstrative application, the structural connectivity divergence between macaque and human brains was mapped using the Brainnetome atlases of those two species to uncover the genetic underpinnings of the evolutionary changes in brain structure. The resulting resource includes (1) the thoroughly delineated Macaque Brainnetome Atlas (MacBNA), (2) regional connectivity profiles, (3) the postmortem high resolution macaque diffusion and T2-weighted MRI dataset (Brainnetome-8), and (4) multi-contrast MRI, block-face, and section images collected from a single macaque. MacBNA can serve as a common reference frame for mapping multifaceted features across modalities and spatial scales and for integrative investigation and characterization of brain organization and function. Therefore, it will enrich the collaborative resource platform for nonhuman primates and facilitate translational and comparative neuroscience research.
Dynamic genome-based metabolic modeling of the predominant cellulolytic rumen bacteriumFibrobacter succinogenesS85
Authors: Fakih Ibrahim , Got Jeanne , Robles-Rodriguez Carlos Eduardo , Siegel Anne , Forano Evelyne , Muñoz-Tamayo Rafael 
Published: October 2022

AbstractFibrobacter succinogenesis a cellulolytic predominant bacterium that plays an essential role in the degradation of plant fibers in the rumen ecosystem. It converts cellulose polymers into intracellular glycogen and the fermentation metabolites succinate, acetate, and formate. We developed dynamic models ofF. succinogenesS85 metabolism on glucose, cellobiose, and cellulose on the basis of a network reconstruction done with the Automatic Reconstruction of metabolic models (AuReMe) workspace. The reconstruction was based on genome annotation, 5 templates-based orthology methods, gap-filling and manual curation. The metabolic network ofF. succinogenesS85 comprises 1565 reactions with 77% linked to 1317 genes, 1586 unique metabolites and 931 pathways. The network was reduced using the NetRed algorithm and analyzed for computation of Elementary Flux Modes (EFMs). A yield analysis was further performed to select a minimal set of macroscopic reactions for each substrate. The accuracy of the models was acceptable in simulatingF. succinogenescarbohydrate metabolism with an average coefficient of variation of the Root mean squared error of 19%. Resulting models are useful resources for investigating the metabolic capabilities ofF. succinogenesS85, including the dynamics of metabolite production. Such an approach is a key step towards the integration of omics microbial information into predictive models of the rumen metabolism.
Multi-histone ChIP-Seq Analysis with DecoDen
Authors: Narendra Tanmayee , Visonà Giovanni , de Jesus Cardona Crhistian , Schweikert Gabriele 
Published: October 2022

AbstractEpigenetic mechanisms coordinate packaging, accessibility and read-out of the DNA sequence within the chromatin context. They significantly contribute to the regulation of gene expression. Thus, they play fundamental roles during differentiation on the one hand and maintenance and propagation of cell identity on the other. Epigenetic malfunctioning is associated with a large range of diseases, from neurodevelopmental disorders to cancer progression. In humans, hundreds of known epigenetic factors and complexes are involved in establishing covalent modifications on the DNA sequence itself and on associated histone proteins. Within the cellular context, the resulting combinatorial epigenomic patterns are neither established nor interpreted independently of each other and therefore exhibit high correlations in a region-specific manner. Post-translational modifications of histone proteins can be analysed using Chromatin Immunoprecipitation followed by sequencing (ChIP-Seq). Often, several assays for a number of different histone modifications are performed as part of the same experimental design. These measurements are, however, confounded by shared biases including chromatin accessibility and mappability. Existing computational methods analyse each histone modification separately. We introduce DecoDen, a new approach that leverages replicates and multi-histone ChIP-Seq experiments for a fixed cell type to learn and remove shared biases. DecoDen (Deconvolve and Denoise) consists of two major steps: We use non-negative matrix factorisation (NMF) to learn a joint cell-type specific background signal. Half-sibling regression (HSR) is then used to correct for these biases in the histone modification signals. We demonstrate that DecoDen is a robust and interpretable method that enables the unbiased discovery of subtle peaks, which are particularly important in an individual-specific context.
Mechanical management of weeds drops nymphal density ofXylella fastidiosavectors
Authors: López-Mercadal Júlia , Mercadal-Frontera Pau , Miranda Miguel Ángel 
Published: October 2022

AbstractXylella fastidiosaWells (1987) (Proteobacteria:Xanthomonadaceae) is a xylem pathogen bacterium transmitted by xylem feeder insects that causes several important plant diseases such as Pierce’s disease in grapes or leaf scorch in almond and olives trees. The bacterium was detected in the Balearic Islands in October 2016, including three subspecies:fastidiosa,multiplexandpauca. The major potential vectors described in the Balearics arePhilaenus spumariusL. andNeophilaenus campestrisFallen (1805). In order to interfere the life cycle of vectors, we tested the effect of mechanical control of the plant cover on the most vulnerable phases, such as nymphs and/or newly emerged adults. For this, we selected four organic orchards in Mallorca, three olive and one vineyard plots. Owners of each selected plot conducted mechanical control according to their common procedures and their own machinery, which in general included cut and tillage of the plant cover during March-April. Nymph abundance per surface (30 sampling points/treatment/orchard x 0,25 m2) was measured in each plot in a weekly basis before and after mechanical control. Our results indicated that either tillage and mowing decreased nymphal density ofX. fastidiosavectors in both types of crops. These results contribute to the integrated pest management of vectors by conducting feasible farm-based management of the regular plant cover.Abstract Figure
Osteosarcoma-enriched transcripts paradoxically generate osteosarcoma-suppressing extracellular proteins
Authors: Li Kexin , Huo Qingji , Dimmitt Nathan H. , Qu Guofan , Bao Junjie , Pandya Pankita H. , Saadatzadeh M. Reza , Bijangi-Vishehsaraei Khadijeh , Kacena Melissa A. , Pollok Karen E. , Lin Chien-Chi , Li Bai-Yan , Yokota Hiroki 
Published: October 2022

AbstractOsteosarcoma (OS) is the common primary bone cancer that affects mostly children and young adults. To augment the standard-of-care chemotherapy, we examined the possibility of protein-based therapy using mesenchymal stem cells (MSCs)-derived proteomes and osteosarcoma-elevated proteins. While a conditioned medium (CM), collected from MSCs, did not present tumor-suppressing ability, the activation of PKA converted MSCs into induced tumor-suppressing cells (iTSCs). In a mouse model, the direct and hydrogel-assisted administration of CM inhibited tumor-induced bone destruction, and its effect was additive with Cisplatin. CM was enriched with proteins such as Calreticulin, which acted as an extracellular tumor suppressor by interacting with CD47. Notably, the level of Calr transcripts was elevated in OS tissues, together with other tumor-suppressing proteins, including histone H4, and PCOLCE. PCOLCE acted as an extracellular tumor-suppressing protein by interacting with amyloid precursor protein (APP), a prognostic OS marker with poor survival. The results supported the possibility of employing a paradoxical strategy of utilizing OS transcriptomes for the treatment of OS.
Resistance exercise protects mice from protein-induced fat accretion
Authors: Trautman Michaela E. , Braucher Leah N. , Elliehausen Christian , Zhu Wenyuan G. , Zelenovskiy Esther , Green Madelyn , Sonsalla Michelle M. , Yeh Chung-Yang , Hornberger Troy A. , Konopka Adam R. , Lamming Dudley W. 
Published: October 2022

AbstractLow protein (LP) diets extend the lifespan of diverse species, and are associated with improved metabolic health in both rodents and humans. Paradoxically, many athletes and bodybuilders consume high protein (HP) diets and protein supplements, yet are both fit and metabolically healthy. Here, we examine this paradox using weight pulling, a validated progressive resistance exercise training regimen, in mice fed either an LP diet or an isocaloric HP diet. We find that despite having lower food consumption than the LP group, HP-fed mice gain significantly more fat mass than LP-fed mice when not exercising, while weight pulling protected HP-fed mice from this excess fat accretion. The HP diet augmented exercise-induced hypertrophy of the forearm flexor complex, and weight pulling ability increased more rapidly in the exercised HP-fed mice. Surprisingly, exercise did not protect from HP-induced changes in glycemic control. Our results confirm that HP diets can augment muscle hypertrophy and accelerate strength gain induced by resistance exercise without negative effects on fat mass, and also demonstrate that LP diets may be advantageous in the sedentary. Our results highlight the need to consider both dietary composition and activity, not simply calories, when taking a precision nutrition approach to health.
Multi-trait genome-wide association analyses leveraging alcohol use disorder findings identify novel loci for smoking behaviors in the Million Veteran Program
Authors: Cheng Youshu , Dao Cecilia , Zhou Hang , Li Boyang , Kember Rachel L. , Toikumo Sylvanus , Zhao Hongyu , Gelernter Joel , Kranzler Henry R. , Justice Amy , Xu Ke 
Published: October 2022

AbstractSmoking behaviors and alcohol use disorder (AUD), moderately heritable traits, commonly co-occur in the general population. Single-trait genome-wide association studies (GWAS) have identified multiple loci for smoking and AUD. However, GWASs that have aimed to identify loci contributing to comorbid smoking and AUD have used small samples and thus have not been highly informative. Applying multi-trait analysis of GWASs (MTAG), we conducted a joint GWAS of smoking and AUD with data from the Million Veteran Program (N=318,694). By leveraging GWAS summary statistics for AUD, MTAG identified 21 genome-wide significant (GWS) loci associated with smoking initiation and 18 loci associated with smoking cessation compared to 16 and 8 loci, respectively, identified by single-trait GWAS. The novel loci for smoking behaviors identified by MTAG included those previously associated with psychiatric or substance use traits. Colocalization analysis identified 10 loci shared by AUD and smoking status traits, all of which achieved GWS in MTAG, including variants onSIX3, NCAM1, and nearDRD2. Functional annotation of the MTAG variants highlighted biologically important regions onZBTB20, DRD2, PPP6C, andGCKRthat contribute to smoking behaviors. In contrast, MTAG of smoking behaviors and alcohol consumption (AC) did not enhance discovery compared with single-trait GWAS for smoking behaviors. We conclude that using MTAG to augment the power of GWAS enables the identification of novel genetic variants for commonly comorbid phenotypes, providing new insights into their pleiotropic effects on smoking behavior and AUD.
Deconstructing olfactory epithelium developmental pathways in esthesioneuroblastoma
Authors: Finlay John B. , Hachem Ralph Abi , Jang David , Osazuwa-Peters Nosayaba , Goldstein Bradley J. 
Published: October 2022

ABSTRACTImportanceEsthesioneuroblastoma (ENB) is a rare tumor arising from the olfactory cleft region of the nasal cavity. Due to the low incidence of this tumor, as well as an absence of established reagents such as cell lines or murine models, understanding the mechanisms driving ENB pathobiology has been challenging.ObjectiveHere, we sought to apply advances from research on the human olfactory epithelial neurogenic niche, along with new biocomputational approaches, to better understand the cellular and molecular factors in low and high grade ENB and how specific transcriptomic markers may predict prognosis.Design, Setting, and ParticipantsThis was a retrospective biocomputational analysis utilizing human ENB and normal olfactory mucosal tissue and clinical outcomes data. The setting was a large academic medical center. Participants were selected based on available datasets, and included ENB patients across all four tumor grades, and patients with normal olfactory mucosa.Main Outcomes and MeasuresOutcomes include deconvolution analysis, differential gene expression analysis, overall survival, and immunohistochemistry. A machine learning model was used to predict cell-type proportion signatures in ENB, and Kaplan-Meier curves with associated log-rank tests were used to estimate differences in overall survival.ResultsWe analyzed a total of 19 ENB samples (9 low grade I/II, 10 high grade III/IV) with available bulk RNA-Sequencing and survival data, along with 10 samples from normal olfactory mucosa (3 bulk RNA-Sequencing, 7 single cell RNA-Sequencing). The bulk RNA-Sequencing deconvolution model identified a significant increase in globose basal cell (GBC) and CD8 T cell identities in high grade tumors (GBC from approximately 0% to 8%, CD8 T cell from 0.7% to 2.2%), and significant decreases in mature neuronal, Bowman’s gland, and olfactory ensheathing programs, in high grade tumors (mature neuronal from 3.7% to approximately 0%, Bowman’s gland from 18.6% to 10.5%, olfactory ensheathing from 3.4% to 1.1%). Trajectory analysis identified potential regulatory pathways in proliferative ENB cells, including PRC2. Survival analysis guided by gene expression in bulk RNA-Sequencing data identified favorable prognostic markers such as SOX9, S100B, and PLP1 expression.Conclusions and RelevanceOur analyses provide a basis for additional translational research on ENB management, as well as identification of potential new prognostic markers.
Actigraphic Correlates of Neuropsychiatric Disability in Adult Patients with Focal Epilepsy
Authors: Abboud Mark A. , Kamen Jessica L , Bass John S , Lin Lu , Gavvala Jay R. , Rao Sindhu , Smagula Stephen F , Krishnan Vaishnav 
Published: October 2022

AbstractDisability in patients with epilepsy (PWE) is multifactorial: beyond seizure frequency/severity, PWE are prone to a range of neuropsychiatric, cognitive, and somatic comorbidities that significantly impact quality of life. In this study, we explored how variations in epilepsy severity and the burden of self-reported somatic/neuropsychiatric symptoms are associated with disruptions to 24h activity patterns (rest-activity rhythms, RARs), determined through wrist accelerometry/actigraphy. Continuous multiday recordings were obtained from 59 adult patients with focal epilepsy (44% male, ages 18-72), who contemporaneously provided responses to a range of validated psychometric instruments to measure the burden of anxiety, depression, sleepiness, and somatic symptoms. As a comparator, we conducted a similar psychometric-actigraphic correlation in 1761 subjects of Hispanic origin (35% male, ages 18-65) from the Study of Latinos (SOL) Sueño Ancillary Study. RARs were analyzed via a sigmoidally-transformed cosine model (quantifying RAR amplitude, steepness, acrophase and robustness) and non-parametric measures to estimate RAR stability, fragmentation, and sleep. Compared with age- and sex-matched SOL subjects, RARs from PWE subjects featured a significantly diminished amplitude, a wider rest phase and significantly more total daily sleep. Within PWE, similar RAR distortions were associated with seizure intractability and/or anticonvulsant polytherapy. In contrast, high anxiety, depression, and somatic symptom scores were associated with diminished RAR robustness and a delayed acrophase. We applied the complete SOL Sueño database to train logistic regression models to dichotomously classify anxiety, depression and sleepiness symptoms using age, sex, body mass index and a range of non-collinear RAR parameters. When tested on PWE, these models predicted prevalent anxiety and depression symptoms with modest success (accuracy ∼70%) but failed to predict subjective sleepiness. Together, these results demonstrate that RAR features may vary with depression and anxiety symptoms in ambulatory patients with focal epilepsy, potentially offering a set of objective wearable-derived endpoints to adjunct routine clinical care and drug/device treatment trials. With larger actigraphic-psychometric datasets in PWE, we may identify RAR signatures that can more precisely distinguish between variations in seizure risk, the burden of anticonvulsant therapy and prevalent mood/anxiety symptoms.
Residence time analysis on cerebral aneurysms treated with coils using planar-laser-induced fluorescence and computational fluid dynamics
Authors: Romero Bhathal Julia , Faisal Syed , Levitt Michael , Geindreau Christian , Aliseda Alberto 
Published: October 2022

AbstractBiofidelic numerical models have been developed such as the coil-resolved model to study hemodynamics in the treated aneurysm. In this model, the geometry of the coils is recreated from high-resolution tomography scans of a phantom aneurysm treated with coils. However, this model hasn’t been validated. The purpose of this work is to validate the coil-resolved model. To achieve this, we used the planar-laser induced fluorescence technique on phantom aneurysm treated with coils and measured the residence time and the evolution of rhodamine concentration during the washout. We run passive scalar simulations with the coil-resolved model and measured the evolution of concentration over time. The comparison of the numerical and the experimental results shows that the coil-resolved model reproduces the hemodynamics of the experimental setup. Therefore it can be used as a reference to study hemodynamics in the treated aneurysm or to validate porous media models developed for treatment outcomes prediction.
Genetically modified IL-2 bone marrow-derived myeloid cells reprogram the glioma immunosuppressive tumor microenvironment
Authors: Canella Alessandro , Nazzaro Matthew , Rajendran Sakthi , Schmitt Claire , Haffey Abigail , Nigita Giovanni , Thomas Diana , Wrightnour Haley , Fadda Paolo , Mardis Elaine R. , Cripe Timothy P. , Rajappa Prajwal 
Published: October 2022

ABSTRACTGliomas are the most prevalent type of brain tumors and one of the leading causes of cancer-related death in the adolescent and young adult population (AYA). Two-thirds of glioma AYA patients are affected by low-grade gliomas (LGGs), but there are no specific treatments. Therefore, a percentage of LGG patients experience tumor relapse and malignant progression to high-grade glioma which leads to fatal outcomes. In part, malignant progression is potentiated by the immunosuppressive stromal component of the tumor microenvironment (TME) underscored by M2-macrophages and a paucity of cytotoxic T cells. As a result, first-line immunotherapies have failed to improve outcomes for patients with progressive high-grade gliomas. Here, we report the efficacy of an in vivo approach that demonstrates the potential for a novel cell-mediated innate immunotherapy designed to abrogate immunosuppressive mechanisms within the glioma TME and enhance the recruitment of activated effector T cells. A single dose of engineered bone marrow-derived myeloid cells that release Interleukin-2 (GEMys-IL2) was used systemically to treat mice with LGG tumors systemically. Our results demonstrate that GEMys-IL2 efficiently crossed the blood brain barrier (BBB), infiltrated the glioma microenvironment, and reprogrammed the infiltrating immune cell composition and transcriptome. In addition, GEMys-IL2 impaired tumor progression and extended survival in a LGG immunocompetent mouse model. In conclusion, we demonstrated that GEMys-IL2 have a therapeutic effect in vivo, thus supporting its potential application as a novel immunotherapy that warrants further investigation.