bluuebunny/crossref_metadata_2025_split huggingface dataset:
Environmental DNA is more effective than hand sorting in evaluating earthworm biodiversity recovery under regenerative agriculture
Authors: Llanos J. , Hipperson H. , Horsburgh G. , Lappage M.G. , Maher K.H. , Burke T. , Leake J.R. , Watt P. J. 
Published: November 2023

AbstractRegenerating soil biodiversity is vital to help reverse declines in the health of agricultural soils caused by intensification, and to support sustainable food production and agro-ecosystem services. Earthworms are key functional components of soil biodiversity, with different ecotypes and species delivering specific beneficial soil functions. However, conventional monitoring by hand-sorting from soil pits is highly labour intensive, can reliably identify only adults to species, and may under-record anecics (deep-burrowing ecotypes). Here, we compare soil environmental DNA (eDNA) metabarcoding using two different primer sets and next-generation sequencing, with hand-sorting from standard soil-pits. The experiment comprised four conventionally managed arable fields into which strips of grass-clover ley had been introduced three years earlier. Earthworm population responses had been recorded by hand-sorting for the first two years and our goal was to assess these in the third year and to compare them both by hand and with the use of eDNA. The eDNA method found the same 8 species as hand-sorting, but had greater power for detecting anecic earthworms and quantifying local species richness. Earthworm abundance increased by over 55% into the third year of the leys, surpassing abundances in adjacent permanent grasslands, helping to explain the observed soil health regeneration. Both overall relative abundances and site occupancy proportions of earthworm eDNA were found to have potential as proxies for abundance, and the performance of each of these measures and the implications for further work are discussed. We demonstrate that eDNA can overcome some of the significant barriers and limitations to monitoring earthworm diversity and recommend its wider use both to better understand the earthworm population benefits of different soil management practices, and to guide agricultural policy and practice decisions affecting soil health.
Protein thiol alterations drive aberrant phase separation in aging
Authors: Vignane Thibaut , Hugo Martín , Hoffmann Christian , Katsouda Antionia , Petric Jovan , Wang Han , Miler Marko , Comas Ferran , Petrovic Dunja , Chen Suyuan , Miljkovic Jan Lj. , Morris Jordan L , Chowdhury Suvagata Roy , Prudent Julien , Polovic Natalija , Murphy Michael P. , Papapetropoulos Andreas , Milovanovic Dragomir , Filipovic Milos R. 
Published: November 2023

AbstractCellular homeostasis relies on precise regulation through chemical processes, such as protein posttranslational modifications (PTM) and physical processes, such as biomolecular condensation. Aging disrupts this balance, increasing susceptibility to diseases and death. However, the mechanisms behind age-related pathogenesis remain elusive. In this study, we dissected various cysteine PTMs and their impact on protein-mediated biomolecular condensation in aging brain. Our findings reveal that aging is associated with significant remodeling of cysteine PTMs, which impacts protein ability to participate in liquid-liquid phase separation (LLPS). Specifically, aging leads to an increase in protein sulfenylation and sulfonylation, which promotes LLPS and through conformational change increases the propensity of proteins to aggregate. Protein persulfidation, a protective thiol modification, prevents this by causing condensate dissolution. We demonstrate that age-induced alterations in cysteine PTMs influence the LLPS properties of synapsin-1 and G3BP2, resulting in disruptions in neurotransmitter release and stress granule formation, respectively. Additionally, our study uncovers that GAPDH is susceptible to LLPS and cysteine sulfonylation exacerbates its transition from condensates to aggregates. Mice deficient in cystathionine gamma-lyase, a pro-longevity gene that regulates intracellular persulfide levels, exhibit a shorter lifespan and spontaneous development of neurofibrillary tangles.
Disuse-driven plasticity in the human thalamus and putamen
Authors: Chauvin Roselyne J. , Newbold Dillan J. , Nielsen Ashley N. , Miller Ryland L. , Krimmel Samuel R. , Metoki Athanasia , Wang Anxu , Van Andrew N. , Montez David F. , Marek Scott , Suljic Vahdeta , Baden Noah J. , Ramirez-Perez Nadeshka , Scheidter Kristen M. , Monk Julia S. , Whiting Forrest I. , Adeyemo Babatunde , Snyder Abraham Z. , Kay Benjamin P. , Raichle Marcus E. , Laumann Timothy O. , Gordon Evan M. , Dosenbach Nico U.F. 
Published: November 2023

AbstractMotor adaptation in cortico-striato-thalamo-cortical loops has been studied mainly in animals using invasive electrophysiology. Here, we leverage functional neuroimaging in humans to study motor circuit plasticity in the human subcortex. We employed an experimental paradigm that combined two weeks of upper-extremity immobilization with daily resting-state and motor task fMRI before, during, and after the casting period. We previously showed that limb disuse leads to decreased functional connectivity (FC) of the contralateral somatomotor cortex (SM1) with the ipsilateral somatomotor cortex, increased FC with the cingulo-opercular network (CON) as well as the emergence of high amplitude, fMRI signal pulses localized in the contralateral SM1, supplementary motor area and the cerebellum. From our prior observations, it remains unclear whether the disuse plasticity affects the thalamus and striatum. We extended our analysis to include these subcortical regions and found that both exhibit strengthened cortical FC and spontaneous fMRI signal pulses induced by limb disuse. The dorsal posterior putamen and the central thalamus, mainly CM, VLP and VIM nuclei, showed disuse pulses and FC changes that lined up with fmri task activations from the Human connectome project motor system localizer, acquired before casting for each participant. Our findings provide a novel understanding of the role of the cortico-striato-thalamo-cortical loops in human motor plasticity and a potential link with the physiology of sleep regulation. Additionally, similarities with FC observation from Parkinson Disease (PD) questions a pathophysiological link with limb disuse.
Dissection of figured wood trait in curly birch (Betula pendula var. carelica) using high-throughput genotyping
Authors: Gubaev Rim , Karzhaev Dmitry , Grigoreva Elizaveta , Lytkin Kirill , Safronycheva Elizaveta , Volkov Vladimir , Nesterchuk Veronika , Vetchinnikova Lidiya , Zhigunov Anatoly , Potokina Elena 
Published: November 2023

AbstractCurly (Karelian) birch is a special variety ofBetula penduladistributed in the northwestern part of Europe. Karelian birch is well-known for its valuable figured curly wood also known as “wooden marble”. The genetic basis underlying curly wood formation has been debated since last century, however, there was no data about loci responsible for the curly wood trait. In the present study, we analyzed two full-sibs populations derived from experimental crosses of curly birches and segregating for the trait. RADseq genotyping was applied to reveal how many loci are involved in ‘curliness’ formation and to search for genetic variants associated with this trait. One single interval on chromosome 10 was detected containing possible candidate genes. InDel marker BpCW1 was suggested for the first time for marker-assisted selection of trees with curly wood at their earliest stages of development.
Microdosing ketamine inDrosophiladoes not inhibit SERT like SSRIs, but causes behavioral changes mediated by glutamate and serotonin receptors
Authors: Dunham Kelly E. , Khaled Kani H. , Weizman Leah , Venton B. Jill 
Published: November 2023

AbstractRecently, the FDA approved microdosing ketamine for treatment resistant depression. Traditional antidepressants, like serotonin selective reuptake inhibitors (SSRIs), block serotonin reuptake, but it is not clear if ketamine blocks serotonin reuptake. Here, we tested the effects of feeding ketamine and SSRIs toDrosophila melanogasterlarvae, which has a similar serotonin system to mammals, and is a good model to track depression behaviors, such as locomotion and feeding. Fast-scan cyclic voltammetry (FSCV) was used to measure optogenetically-stimulated serotonin changes, and locomotion tracking software and blue dye feeding to monitor behavior. We fed larvae various doses (1-100 mM) of antidepressants for 24 hours and found that 1 mM ketamine did not affect serotonin, but increased locomotion and feeding. Low doses (≤ 10 mM) of escitalopram and fluoxetine inhibited dSERT and also increased feeding and locomotion behaviors. At 100 mM, ketamine inhibited dSERT and increased serotonin concentrations, but decreased locomotion and feeding due to its anesthetic properties. Since microdosing ketamine causes behavioral effects, we also investigated behavior changes with low doses of other NMDA receptor antagonists and 5-HT1Aand2agonists, which are other possible sites for ketamine action. NMDA receptor antagonism increased feeding, while serotonin receptor agonism increased locomotion, which could explain these effects with ketamine. Ultimately, this work shows thatDrosophilais a good model to discern antidepressant mechanisms, and that ketamine does not work on dSERT like SSRIs at microdoses, but affects behavior with other mechanisms.Graphical abstractMicrodosing ketamine is a novel depression treatment, but it is not clear how it changes serotonin in real-time.Drosophila melanogaster(fruit fly) is a good model to study depression behaviors. Here, we used fast-scan cyclic voltammetry, video tracking, and feeding assays to measure serotonin and behavior after feeding ketamine and SSRIs to larvae. At microdoses, ketamine did not affect serotonin, which was different from SSRIs. However, higher doses inhibited dSERT. Locomotion and feeding changes were also dose-dependent, and we saw separate effects with NMDA and serotonin receptor drugs. This work facilitates future behavioral and pharmacological testing with ketamine usingDrosophila.
Sleep disturbances as risk factors for neurodegeneration later in life
Authors: Simmonds Emily , Levine Kristin S , Han Jun , Iwaki Hirotaka , Koretsky Mathew J , Kuznetsov Nicole , Faghri Faraz , Solsberg Caroline Warly , Schuh Artur , Jones Lietsel , Bandres-Ciga Sara , Blauwendraat Cornelis , Singleton Andrew , Escott-Price Valentina , Leonard Hampton L , Nalls Mike A 
Published: November 2023

SUMMARYThe relationship between sleep disorders and neurodegeneration is complex and multi-faceted. Using over one million electronic health records (EHRs) from Wales, UK, and Finland, we mined biobank data to identify the relationships between sleep disorders and the subsequent manifestation of neurodegenerative diseases (NDDs) later in life. We then examined how these sleep disorders’ severity impacts neurodegeneration risk. Additionally, we investigated how sleep attributed risk may compensate for the lack of genetic risk factors (i.e. a lower polygenic risk score) in NDD manifestation.We found that sleep disorders such as sleep apnea were associated with the risk of Alzheimer’s disease (AD), amyotrophic lateral sclerosis, dementia, Parkinson’s disease (PD), and vascular dementia in three national scale biobanks, with hazard ratios (HRs) ranging from 1.31 for PD to 5.11 for dementia. These sleep disorders imparted significant risk up to 15 years before the onset of an NDD. Cumulative number of sleep disorders in the EHRs were associated with a higher risk of neurodegeneration for dementia and vascular dementia. Sleep related risk factors were independent of genetic risk for Alzheimer’s and Parkinson’s, potentially compensating for low genetic risk in overall disease etiology. There is a significant multiplicative interaction regarding the combined risk of sleep disorders and Parkinson’s disease.Poor sleep hygiene and sleep apnea are relatively modifiable risk factors with several treatment options, including CPAP and surgery, that could potentially reduce the risk of neurodegeneration. This is particularly interesting in how sleep related risk factors are significantly and independently enriched in manifesting NDD patients with low levels of genetic risk factors for these diseases.HIGHLIGHTSSleep disorders, particularly sleep apnea, are associated with the risk of Alzheimer’s disease, amyotrophic lateral sclerosis, dementia, Parkinson’s disease, and vascular dementia in national scale biobanks.These sleep disorders imparted significant risk up to 15 years before the onset of a neurodegenerative disease.The cumulative number of sleep disorders in the electronic health records were associated with a higher risk of neurodegeneration related to dementia and vascular dementia.Sleep related risk factors are independent of genetic risk for Alzheimer’s and Parkinson’s, potentially compensating for low genetic risk in overall disease etiology.Significant multiplicative interaction exists regarding the combined risk of sleep disorders and Parkinson’s disease.
Mapping the Middle East Respiratory Syndrome (MERS) related Research – A Scoping Review (2012-2023)
Authors: Hassan Maya , Yarow Halima , Mccabe Ruth , Dobschuetz Sophie Von , Khan Wasiq , Barakat Amal , Van Kerkhove Maria D. , Bakar Abdinasir Abu , Naja Hala Abou El 
Published: November 2023

AbstractBackgroundMiddle East respiratory syndrome (MERS), is a zoonotic disease caused by MERS coronavirus (MERS-CoV). The purpose of this scoping review was to take stock of the empirical research evidence for MERSDCoV, map the information to priority research areas as set out in existing MERS-CoV research roadmaps, identify technical areas that received less attention and set recommendations for the advancement of MERS-CoV research.MethodsWe undertook a scoping review for MERS-CoV, comprehensively searching the three databases PubMed, EMBASE, and CINAHL for studies published between 1 January 2012 and 24 January 2023. Two reviewers screened studies and extracted data using a pilot-tested screening form. We categorized studies into priority research areas outlined in existing roadmaps and summarized the evidence available for each category.ResultsA total of 1,264 records were included in the review, assigned into pre-defined categories. 33% of the included records were molecular genetics studies, followed by therapeutic studies (17.6%) and pathogenesis studies (15.6%). We found that, while there has been a substantial research effort on MERS-CoV, many technical themes pertaining to the areas of animal, human, animal-human interface, and environmental research identified by FAO, WHO, and WOAH in the past have not sufficiently been addressed to date. This includes asymptomatic human cases role in transmission, human exposure risk from dromedary products, reinfection, analyses of camel value chain and production systems, and anthropological studies characterizing interactions at the animal-human interface, in addition to studies highlighting the role of environmental factors in MERS-CoV transmission.ConclusionOur study highlights the continued need for coordinated action to better prepare for, prevent, detect, and respond to MERS-CoV. Examples include the need for enhancing collaborative surveillance, accelerating the development of MERS-CoV medical countermeasures, strengthening community protection, reducing MERS-CoV transmission at healthcare facility level and reinforcing multi-sectoral coordination using the One Health approach.
Serum proteomics revealsAPOEdependent and independent protein signatures in Alzheimer’s disease
Authors: Frick Elisabet A. , Emilsson Valur , Jonmundsson Thorarinn , Steindorsdottir Anna E. , Johnson Erik C. B. , Puerta Raquel , Dammer Eric B. , Shantaraman Anantharaman , Cano Amanda , Boada Mercè , Valero Sergi , García-González Pablo , Gudmundsson Elias F. , Gudjonsson Alexander , Loureiro Joseph J. , Orth Anthony P. , Seyfried Nicholas T. , Levey Allan I. , Ruiz Agustin , Aspelund Thor , Jennings Lori L. , Launer Lenore J. , Gudmundsdottir Valborg , Gudnason Vilmundur 
Published: November 2023

SummaryThe current demand for early intervention, prevention, and treatment of late onset Alzheimer’s disease (LOAD) warrants deeper understanding of the underlying molecular processes which could contribute to biomarker and drug target discovery. Utilizing high-throughput proteomic measurements in serum from a prospective population-based cohort of older adults (n=5,294), we identified 303 unique proteins associated with incident LOAD (median follow-up 12.8 years). Over 40% of these proteins were associated with LOADindependentlyofAPOE-ε4carrier status. These proteins were implicated in neuronal processes and overlapped with protein signatures of LOAD in brain and cerebrospinal fluid. We found 17 proteins which LOAD-association was stronglydependentonAPOE-ε4carrier status. Most of them showed consistent associations with LOAD in cerebrospinal fluid and a third had brain-specific gene expression. Remarkably, four proteins in this group (TBCA, ARL2, S100A13 and IRF6) were downregulated byAPOE-ε4yet upregulated as a consequence of LOAD as determined in a bi-directional Mendelian randomization analysis, reflecting a potential response to the disease onset. Accordingly, the direct association of these proteins to LOAD was reversed uponAPOE-ε4genotype adjustment, a finding which we replicate in an external cohort (n=719). Our findings provide an insight into the dysregulated pathways that may lead to the development and early detection of LOAD, including those both independent and dependent onAPOE-ε4. Importantly, many of the LOAD-associated proteins we find in the circulation have been found to be expressed - and have a direct link with AD - in brain tissue. Thus, the proteins identified here, and their upstream modulating pathways, provide a new source of circulating biomarker and therapeutic target candidates for LOAD.
The association of diet quality and physical activity with cardiovascular disease and mortality in 85,545 older Australians: A longitudinal study
Authors: Ding Ding , Van Buskirk Joe , Partridge Stephanie , Clare Philip , Giovannucci Edward , Bauman Adrian , Freene Nicole , Gallagher Robyn , Nguyen Binh 
Published: November 2023

AbstractBackgroundA quality diet and an active lifestyle are both important cornerstones of cardiovascular disease (CVD) prevention. However, despite their interlinked effects on metabolic health, the two behaviours are rarely jointly considered, particularly within the context of CVD prevention. We examined the independent, interactive and joint associations of diet and physical activity with CVD hospitalisation, CVD mortality and all-cause mortality.MethodsCVD-free Australian participants aged 45-74 years reported physical activity, diet and sociodemographic and lifestyle characteristics at baseline (2006-09) and follow-up (2012-15), and data were linked to hospitalisation and death registries (31/03/2019 for CVD hospitalisation and all-cause mortality and 08/12/2017 for CVD mortality). Diet quality was categorised as low, medium and high based on meeting dietary recommendations. Physical activity was operationalised as 1) total moderate-to-vigorous physical activity (MVPA) as per guidelines and 2) the composition of MVPA as the ratio of vigorous-intensity physical activity (VPA) to total MVPA. We used a left-truncated cause-specific Cox proportional hazards model using time-varying covariates.ResultsDuring a median of 10.7 years of follow-up, 6,581 participants were admitted to the hospital for CVD and 6,586 died from all causes (879 from CVD during 9.3 years). A high-quality diet was associated with a 17% lower risk of all-cause mortality than low-quality, and the highest MVPA category (compared with the lowest) was associated with 44% and 48% lower risks of CVD and all-cause mortality. Multiplicative interactions between diet and physical activity were non-significant. For all outcomes, the lowest risk combinations involved a high-quality diet and the highest MVPA categories. Accounting for total MVPA, some VPA was associated with further risk reduction of CVD hospitalisation and all-cause mortality.ConclusionFor CVD prevention and longevity, one should adhere to both a healthy diet and an active lifestyle and incorporate some VPA when possible.
Experience in the validation of a rapid test for NS1 and IgM for early diagnosis during a dengue epidemic in Colombia
Authors: Ramírez Rosa-Margarita Gélvez , Consuegra Mónika Patricia , Estupiñan María Isabel , Rangel Adriana Torres , Herrera Víctor Mauricio , de Lamballerie Xavier , Centeno Luis Ángel Villar 
Published: November 2023

AbstractDengue has a broad spectrum of syndromic presentations, making clinical diagnosis difficult in regions where acute febrile syndrome has multiple etiologies. Rapid tests for detecting NS1 and IgM are broadly proposed for the early diagnosis of dengue; however, their implementation in primary care settings is inconsistent, and the relevance of IgM detection in this context has not been firmly established. Our study aimed to describe the experience of validating an NS1-IgM rapid test in primary care settings in Bucaramanga, Colombia, during a dengue epidemic (2018 to 2020). We tested blood samples from 568 patients with a clinical diagnosis of dengue using the Bioline Dengue Duo rapid test and RT-PCR as a reference to estimate sensitivity, specificity, and positive and negative predictive values (SE, SP, PPV, and NPV, respectively). The prevalence of infection was 32.9% (95%CI: 29.1, 36.8), whereas SE and SP were 83.4% and 72.7% for NS1 without statistical heterogeneity across disease duration. NS1’s PPV and NPV were 60.0% and 89.9% at the observed prevalence. Our results show that NS1 and IgM rapid tests (POCT) are feasible in the primary care setting. The contribution of the NS1 test was indisputable, with high-performance levels far superior to those of the IgM test. The NS1+IgM combination did not offer a significant advantage over NS1 alone.
Highly amine-reactive graphene-oxide EM grids for biochemical surface modification in aqueous buffer
Authors: Brown Simon H.J. , Bouwer James C. , Cohen Scott B. 
Published: November 2023

AbstractGraphene oxide (GO), an oxidized derivative of graphene, has found application in cryo-electron microscopy (cryo-EM) as a hydrophilic and transparent solid support on which to adsorb biological macromolecules, providing an alternative to traditional aqueous films. Current applications generally adsorb the macromolecule directly onto unmodified GO or modify the GO surface with polyethylene glycol-amine reagents. This nucleophilic amine reaction must be performed in an aprotic organic solvent and therefore precludes the use of biological samples such as nucleic acids and peptides. The utility of GO could be expanded by the ability to covalently modify its surface with biochemical affinity reagents such as small- molecule metabolites, peptides, or nucleic acids, in aqueous buffer at neutral pH. Presented here is a chemical procedure that converts all oxygen functionalities of GO to highly amine- reactive glycidyl epoxide groups, achieved without the need of specialized laboratory equipment. We show that single sheets of glycidyl epoxide-modified GO react on the EM grid with primary amines at micromolar concentrations in minutes at room temperature in aqueous buffer. Given the ease of derivatizing biochemical reagents with amines, the chemistry described here will enable imaging of macromolecules immobilized on GO through specific biochemical and biologically relevant binding interactions.