bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extending non-targeted exposure discovery of environmental chemical exposures during pregnancy and their association with pregnancy complications—a cross-sectional study
Authors: Trowbridge Jessica , Abrahamsson Dimitri , Jiang Ting , Wang Miaomiao , Park June-Soo , Morello-Frosch Rachel , Sirota Marina , Goin Dana E. , Zlatnick Marya , Woodruff Tracey J. 
Published: March 2022

AbstractBackgroundNon-targeted Analysis (NTA) methods identify novel exposures; however, few chemicals have been quantified and interrogated with pregnancy complications.ObjectivesWe characterize levels of nine exogenous and endogenous chemicals in maternal and cord blood identified, selected, and confirmed in prior NTA steps including: linear and branched isomers perfluorooctane sulfonate (PFOS); perfluorohexane sulfonate (PFHxS); monoethylhexyl phthalate; 4-nitrophenol; tetraethylene glycol; tridecanedioic acid, octadecanedioic acid; and deoxycholic acid. We evaluate relationships between maternal and cord levels and the relationship gestational diabetes mellitus (GDM) and hypertensive disorders of pregnancy in a diverse pregnancy cohort in San Francisco.MethodsWe collected matched maternal and cord serum samples from 302 pregnant people at delivery from the Chemicals in Our Bodies cohort in San Francisco. Chemicals were identified via NTA and quantified using targeted approaches. We calculate distributions and Spearman correlation coefficients testing the relationship of chemicals within and between the maternal and cord blood matrices. We used logistic regression to calculate the odds of GDM and hypertensive disorders of pregnancy associated with an interquartile range increase in maternal chemical exposures.ResultsWe detected linear PFOS, PFHxS, octadecanedioic acid, and deoxycholic acid in at least 97% of maternal samples. Correlations ranged between -0.1 and 0.9. We observed strong correlations between cord and maternal levels of PFHxS (coefficient = 0.9), linear PFOS (0.8), and branched PFOS (0.8). An IQR increase in linear PFOS, branched PFOS, and octadecanedioic acid is associated with increased odds of GDM [OR (95%CI): 1.43 (0.96, 2.14), 1.56 (1.00, 2.44), and 1.26 (0.83, 1.92) respectively] and tridecanedioic acid positively associated with hypertensive disorders of pregnancy [1.28 (0.90, 1.86)].DiscussionWe identified both exogenous and endogenous chemicals, two of which (octadecanedioic acid and tridecanedioic acid) have both endogenous and exogenous sources, and which have seldom been quantified in pregnant people or related to pregnancy complications.
Factors Associated With Post-craniotomy Headache After Microvascular Decompression in Hemifacial Spasm
Authors: Huang Jiashang , Li Yi , Jiang Li , Li Xin , Zhan Yan 
Published: March 2022

AbstractObjectivePatients who undergo microvascular decompression (MVD) often experience post-craniotomy headache (PCH), while the PCH is always neglected. This study is aimed to describe the natural course and risk factors of PCH.MethodsThe severity and duration of PCH in 87 patients who undergo MVD were recorded. Factors related to the severity and duration of PCH were analyzed.ResultsMost patients (63.2%) had at least one assessment of moderate to severe PCH. Almost all patients (92%) would gradually decrease to disappear within 7 days. A small number of patients (25.5%) had PCH at the incision, and other patients had PCH inside the head. Younger age and gas in the prepontine cistern were the salient features of patients in the severe group. Younger, higher SAS, gas in the prepontine cistern area, and postoperative fever were independent risk factors that affect the duration of PCH.ConclusionsPCH is the most common and self-limiting complication after MVD among patients with HFS. Young age, temperature > 38°C after MVD within 24h, and gas around the TN are associated may predict the severity and duration of PCH.SignificanceThis is the first study to describe the severity, duration, location, and risk factors of PCH.
Emergence and Spread of the SARS-CoV-2 Omicron Variant in Alberta Communities Revealed by Wastewater Monitoring
Authors: Hubert Casey R.J. , Acosta Nicole , Waddell Barbara J. , Hasing Maria E. , Qiu Yuanyuan , Fuzzen Meghan , Harper Nathanael B.J. , Bautista María A. , Gao Tiejun , Papparis Chloe , Van Doorn Jenn , Du Kristine , Xiang Kevin , Chan Leslie , Vivas Laura , Pradhan Puja , McCalder Janine , Low Kashtin , England Whitney E. , Kuzma Darina , Conly John , Ryan M. Cathryn , Achari Gopal , Hu Jia , Cabaj Jason L. , Sikora Chris , Svenson Larry , Zelyas Nathan , Servos Mark , Meddings Jon , Hrudey Steve E. , Frankowski Kevin , Parkins Michael D. , Pang Xiaoli (Lilly) , Lee Bonita E. 
Published: March 2022

AbstractWastewater monitoring of SARS-CoV-2 allows for early detection and monitoring of COVID-19 burden in communities and can track specific variants of concern. Targeted assays enabled relative proportions of SARS-CoV-2 Omicron and Delta variants to be determined across 30 municipalities covering >75% of the province of Alberta (pop. 4.5M) in Canada, from November 2021 to January 2022. Larger cities like Calgary and Edmonton exhibited a more rapid emergence of Omicron relative to smaller and more remote municipalities. Notable exceptions were Banff, a small international resort town, and Fort McMurray, a more remote northern city with a large fly-in worker population. The integrated wastewater signal revealed that the Omicron variant represented close to 100% of SARS-CoV-2 burden prior to the observed increase in newly diagnosed clinical cases throughout Alberta, which peaked two weeks later. These findings demonstrate that wastewater monitoring offers early and reliable population-level results for establishing the extent and spread of emerging pathogens including SARS-CoV-2 variants.
KMCP: accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping
Authors: Shen Wei , Xiang Hongyan , Huang Tianquan , Tang Hui , Peng Mingli , Cai Dachuan , Hu Peng , Ren Hong 
Published: March 2022

AbstractMotivationThe growing number of microbial reference genomes enables the improvement of metagenomic profiling accuracy but also imposes greater requirements on the indexing efficiency, database size, and runtime of taxonomic profilers. Additionally, most profilers focus mainly on bacterial, archaeal, and fungal populations, while less attention is paid to viral communities.ResultsWe present KMCP, a novelk-mer-based metagenomic profiling tool that utilizes genome coverage information by splitting the reference genomes into chunks and then storesk-mers in a modified and optimized COBS index for fast alignment-free sequence searching. KMCP combinesk-mer similarity and genome coverage information to reduce the false positive rate ofk-mer-based taxonomic classification and profiling methods. Benchmarking results based on simulated and real data demonstrate that KMCP, despite a longer running time than all other methods, not only allows the accurate taxonomic profiling of prokaryotic and viral populations but also provides confident pathogen detection in clinical samples of low depth.Availability and ImplementationThe software is open-source under the MIT license and available athttps://github.com/shenwei356/kmcp.
Botrytis cinereastrains infecting grapevine and tomato display contrasted repertoires of accessory chromosomes, transposons and small RNAs
Authors: Simon Adeline , Mercier Alex , Gladieux Pierre , Poinssot Benoît , Walker Anne-Sophie , Viaud Muriel 
Published: March 2022

AbstractThe fungusBotrytis cinereais a polyphagous pathogen that encompasses multiple host-specialized lineages. While several secreted proteins, secondary metabolites and retrotransposons-derived small RNAs have been characterized as virulence factors, their roles in host specialization remain unknown. The aim of this study was to identify the genomic correlates of host-specialization in populations ofB. cinereaassociated with grapevine and tomato. Using PacBio sequencing, we produced complete assemblies of the genomes of strains Sl3 and Vv3 that represent the French populations T and G1 ofB. cinerea, specialized on tomato and grapevine, respectively. Both assemblies revealed 16 core chromosomes that were highly syntenic with chromosomes of the reference strain B05.10. The main sources of variation in gene content were the subtelomeric regions and the accessory chromosomes, especially the chromosome BCIN19 of Vv3 that was absent in Sl3 and B05.10. The repertoires and density of transposable elements were clearly different between the genomes of Sl3 and Vv3 with a larger number of subfamilies (26) and a greater genome coverage in Vv3 (7.7%) than in Sl3 (14 subfamilies, 4.5% coverage). An Helitron-like element was found in almost all subtelomeric regions of the Vv3 genome, in particular in the flanking regions of a highly duplicated gene encoding a Telomere-Linked Helicase, while both features were absent from the Sl3 and B05.10 genomes. Different retrotransposons in the Sl3 and the Vv3 strains resulted in the synthesis of distinct sets of small RNAs. Finally, extending the study to additional strains indicated that the accessory chromosome BCIN19 and the small RNAs producing retrotransposons Copia_4 and Gypsy_7 are common features of the G1 population that are scarcely if ever found in strains isolated from other populations. This research reveals that accessory chromosomes, repertoires of transposons and their derived small RNAs differ between populations ofB. cinereaspecialized on different hosts. The genomic data characterized in our study pave the way for further studies aiming at investigating the molecular mechanisms underpinning host specialization in a polyphagous pathogen.
Locus coeruleus integrity predicts ease of attaining and maintaining neural states of high attentiveness
Authors: Hussain Sana , Menchaca Isaac , Shalchy Mahsa Alizadeh , Yaghoubi Kimia , Langley Jason , Seitz Aaron R. , Hu Xiaoping P. , Peters Megan A. K. 
Published: March 2022

AbstractThe locus coeruleus (LC), a small subcortical structure in the brainstem, is the brain’s principal source of norepinephrine. It plays a primary role in regulating stress, the sleep-wake cycle, and attention, and its degradation is associated with aging and neurodegenerative diseases associated with cognitive deficits (e.g., Parkinson’s, Alzheimer’s). Yet precisely how norepinephrine drives brain networks to support healthy cognitive function remains poorly understood – partly because LC’s small size makes it difficult to study noninvasively in humans. Here, we characterized LC’s influence on brain dynamics using a hidden Markov model fitted to functional neuroimaging data from healthy young adults across four attention-related brain networks and LC. We modulated LC activity using a behavioral paradigm and measured individual differences in LC magnetization transfer contrast. The model revealed five hidden states, including a stable state dominated by salience-network activity that occurred when subjects actively engaged with the task. LC magnetization transfer contrast correlated with this state’s stability across experimental manipulations and with subjects’ propensity to enter into and remain in this state. These results provide new insight into LC’s role in driving spatiotemporal neural patterns associated with attention, and demonstrate that variation in LC integrity can explain individual differences in these patterns even in healthy young adults.
Modulation of brain activity by psycholinguistic information during naturalistic speech comprehension and production
Authors: Wu Wei , Morales Matías , Patel Tanvi , Pickering Martin J. , Hoffman Paul 
Published: March 2022

AbstractLanguage processing requires the integration of diverse sources of information across multiple levels of processing. A range of psycholinguistic properties have been documented in previous studies as having influence on brain activation during language processing. However, most of those studies have used factorial designs to probe the effect of one or two individual properties using highly controlled stimuli and experimental paradigms. Little is known about the neural correlates of psycholinguistic properties in more naturalistic discourse, especially during language production. The aim of our study is to explore the above issues in a rich fMRI dataset in which participants both listened to recorded passages of discourse and produced their own narrative discourse in response to prompts. Specifically, we measured 13 psycholinguistic properties of the discourse comprehended or produced by the participants, and we used principal components analysis (PCA) to address covariation in these properties and extract a smaller set of latent language characteristics. These latent components indexed vocabulary complexity, sensory-motor and emotional language content, discourse coherence and speech quantity. A parametric approach was adopted to study the effects of these psycholinguistic variables on brain activation during comprehension and production. We found that the pattern of effects across the cortex was somewhat convergent across comprehension and production. However, the degree of convergence varied across language properties, being strongest for the component indexing sensory-motor language content. We report the full, unthresholded effect maps for each psycholinguistic variable, as well as mapping how these effects change along a large-scale cortical gradient of brain function. We believe that our findings provide a valuable starting point for future, confirmatory studies of discourse processing.
Multi-scale model suggests the trade-off between protein and ATP demand as a driver of metabolic changes during yeast replicative ageing
Authors: Schnitzer Barbara , Österberg Linnea , Skopa Iro , Cvijovic Marija 
Published: March 2022

AbstractThe accumulation of protein damage is one of the major drivers of replicative ageing, describing a cell’s reduced ability to reproduce over time even under optimal conditions. Reactive oxygen and nitrogen species are precursors of protein damage and therefore tightly linked to ageing. At the same time, they are an inevitable by-product of the cell’s metabolism. Cells are able to sense high levels of reactive oxygen and nitrogen species and can subsequently adapt their metabolism through gene regulation to slow down damage accumulation. However, the older or damaged a cell is the less flexibility it has to allocate enzymes across the metabolic network, forcing further adaptions in the metabolism. To investigate changes in the metabolism during replicative ageing, we developed an multi-scale mathematical model using budding yeast as a model organism. The model consists of three interconnected modules: a Boolean model of the signalling network, an enzyme-constrained flux balance model of the central carbon metabolism and a dynamic model of growth and protein damage accumulation with discrete cell divisions. The model can explain known features of replicative ageing, like average lifespan and increase in generation time during successive division, in yeast wildtype cells by a decreasing pool of functional enzymes and an increasing energy demand for maintenance. We further used the model to identify three consecutive metabolic phases, that a cell can undergo during its life, and their influence on the replicative potential, and proposed an intervention span for lifespan control.
Composition and functionality of bacterioplankton communities in marine coastal zones adjacent to finfish aquaculture
Authors: Da Silva R.R.P. , White C.A. , Bowman J.P. , Ross D.J. 
Published: March 2022

AbstractFinfish aquaculture is one of the fastest-growing primary industries globally and is increasingly common in coastal ecosystems. Bacterioplankton is ubiquitous in marine environment and respond rapidly to environmental changes. However, little is known about the effect of the aquaculture in the bacterioplankton community. This study aims to examine aquaculture effects in the composition and functional profiles of the bacterioplankton community using amplicon sequencing along a distance gradient from two finfish leases in a marine embayment. Our results revealed natural stratification in bacterioplankton strongly associated to NOx, conductivity, salinity, temperature and PO4. Among the differentially abundant bacteria in leases, we found members associated with nutrient enrichment and aquaculture activities. Abundant predicted functions near leases were assigned to organic matter degradation, fermentation, and antibiotic resistance. This study provides a first effort to describe changes in the bacterioplankton community composition and function due to finfish aquaculture in a semi-enclosed and highly stratified embayment.
Circuit-Specific Targeting of Astrocytes for Genetic Control
Authors: Thompson Alyssa , Arano Rachel , Ramos Katarina , Kim Yerim , Li Ying , Xu Wei 
Published: March 2022

AbstractAstrocytes are integral functional components of brain circuits. They ensheath the connections between neurons to form tripartite synapses. They react to local neuronal activities and release signaling molecules to regulate synaptic transmission. Their dysfunctions impair synaptic functions and are implicated in neuropsychiatric disorders. Increasing evidence indicates that astrocytes are diverse and they have distinct features and functions in different circuits. However, selectively targeting and controlling astrocytes in a circuit-specific manner is technically challenging. Recently we constructed a series of anterograde transneuronal viral vectors based on the yellow fever vaccine YFV-17D. These YFV-17D derivatives express fluorescent proteins almost exclusively in neurons. However, we find that YFV-17D carrying DNA recombinase Cre infect astrocytes associated with the traced neuronal pathways and express Cre to turn on reporter genes. The targeting of astrocytes is at a whole-brain level but specific to the neuronal circuits traced. Therefore, YFV-17D vectors carrying DNA recombinases provide tools for selectively and genetically targeting pathway-specific astrocytes. This new technology will also allow us to reveal the roles of astrocytes in specific neuronal circuits in normal brain functions and diseases.
SARS-CoV-2 genomic surveillance enables the identification of Delta/Omicron co-infections in Argentina
Authors: Pisano María Belén , Sicilia Paola , Zeballos Maximiliano , Lucca Andrea , Fernandez Franco , Castro Gonzalo M. , Goya Stephanie , Viegas Mariana , López Laura , Barbás María Gabriela , Ré Viviana E. 
Published: March 2022

AbstractMolecular surveillance of SARS-CoV-2 is crucial to early detect new variants and lineages. In addition, detection of coinfections with more than one SARS-CoV-2 lineage have been sporadically reported. In this work, surveillance of SARS-CoV-2 variants was performed on 2067 RNA samples (Ct>30) obtained during December 2021 and January 2022 from Córdoba province, Argentina, by real time RT-PCR specific for VOC/VOI relevant mutations (TaqMan™ SARS-CoV-2 Mutation Panel, Applied Biosystems). The following distribution of variants was obtained: Omicron (54.9%), Delta (44.2%) and Lambda (0.8%). Three samples (0.1%), obtained the last week of December, presented a profile compatible with a Delta/Omicron co-infection. One of them was sequenced by NGS-Illumina, obtaining reads for both VOCs. One of the studied patients presented severe symptoms, although he was not vaccinated and presented risk factors (older than 60 years, arterial hypertension). We describe for the first time in Argentina, the identification of cases of co-infection with two SARS-CoV-2 lineages, VOCs Delta and Omicron, during the third COVID-19 wave in the country (a high viral circulation period), when Delta and Omicron co-circulated. Our findings highlight the importance of continuing with molecular surveillance and co-detection studies of VOC/VOIs, in order to elucidate possible recombination events and the emergence of new variants.
Analysis of the metabolic syndrome and its association with cART in HIV positive individuals receiving various cART regimens with review of literature
Authors: Joshi Kavita S. , Saraf Udit U. , Gujarathi Rushabh Y. 
Published: March 2022

ABSTRACTContextMany endocrine and metabolic disorders are seen in patients with HIV infection. Various comorbidities have been reported at a higher rate in HIV positive individuals, some at an earlier age. Since metabolic syndrome and its determinants are slowly developing, studies are needed in this regard.AimsThe study aimed to analyze various parameters associated with the metabolic syndrome in HIV positive individuals and stratify subjects based on their treatment regimens, and present a brief comparison based on the same.Settings and DesignA cross sectional study involving 155 participants was conducted at a tertiary care centre in Western India.Materials and MethodsDetailed history and clinical examination was carried out. Routine investigations were done and parameters of interest to the study were then analysed based on AHA/NHLBI definitions.Statistical Analysis usedUnivariate analysis of all parameters. Multiple logistic regression for statistically significant parameters.Results and ConclusionDeranged HDL cholesterol was the most common component of the metabolic syndrome seen amongst all participants (53.8%) which was significantly higher in the treatment naïve group (P = 0.001). The difference between the incidence of metabolic syndrome between the ART naïve group and patients receiving ART was not significant. Males had a significantly higher prevalence of metabolic syndrome than females (26.3%>12.4%, P = 0.026). There was a significant difference in the incidence between the Zidovudine and Tenofovir treatment groups(P=0.02). Patients on the TLE (Tenofovir, Lamivudine, and Efavirenz) regimen had the lowest prevalence (4.2%) of metabolic syndrome.
Hippocampal Interneuronal Dysfunction and Hyperexcitability in a Porcine Model of Concussion
Authors: Ulyanova Alexandra V. , Adam Christopher D. , Cottone Carlo , Maheshwari Nikhil , Grovola Michael R. , Fruchet Oceane E. , Alamar Jami , Koch Paul F. , Johnson Victoria E. , Cullen D. Kacy , Wolf John A. 
Published: March 2022

AbstractCognitive impairment is a common symptom following mild traumatic brain injury (mTBI or concussion) and can persist for years in some individuals. Hippocampal slice preparations following closed-head, rotational acceleration injury in swine have previously demonstrated reduced axonal function and hippocampal circuitry disruption. However, electrophysiological changes in hippocampal neurons and their subtypes in a large animal mTBI model have not been examined. Usingin vivoelectrophysiology techniques, we examined laminar oscillatory field potentials and single unit activity in the hippocampal network 7 days post-injury in anesthetized minipigs. Concussion altered the electrophysiological properties of pyramidal cells and interneurons differently in area CA1. While the firing rate, spike width and amplitude of CA1 interneurons were significantly decreased post-mTBI, these parameters were unchanged in CA1 pyramidal neurons. In addition, CA1 pyramidal neurons in TBI animals were less entrained to hippocampal gamma (40 - 80 Hz) oscillations. Stimulation of the Schaffer collaterals also revealed hyperexcitability across the CA1 lamina post-mTBI. Computational simulations suggest that reported changes in interneuronal physiology may be due to alterations in voltage-gated sodium channels. These data demonstrate that a single concussion can lead to significant neuronal and circuit level changes in the hippocampus, which may contribute to cognitive dysfunction following mTBI.