bluuebunny/crossref_metadata_2025_split huggingface dataset:
The framework species method: harnessing natural regeneration to restore tropical forest ecosystems
Authors: Elliott Stephen , Tucker Nigel I. J. , Shannon Dia Panitnard , Tiansawat Pimonrat 
Published: November 2022

As interest in restoring tropical forests surges, so does the need for effective methods to ensure success. The framework species method (FSM) restores forest ecosystems by densely planting open sites, close to natural forest, with woody species, indigenous to the reference ecosystem and selected for their ability to accelerate ecological succession. Criteria for selecting framework species include: (i) representative of the reference forest ecosystem, (ii) tolerant of open conditions, (iii) ability to suppress weeds, (iv) attractiveness to seed-dispersing animals and (v) easily propagated. The method is effective where forest remnants and viable populations of seed dispersers remain. The origins and elements of the FSM are discussed. We review its adoption in 12 countries. Adherence to original principles was mostly high, but some misuse of the term was evident. The need for clearer definitions was identified. We place the FSM on a scale of restoration methods, matched with degradation levels and compare its establishment costs with those of other methods. Obstacles to its wider adoption, both technical and socio-economic, are discussed, along with how these might be overcome. Finally, the FSM is more clearly defined to facilitate its use in contributing towards the goals of the UN Decade on Restoration.This article is part of the theme issue ‘Understanding forest landscape restoration: reinforcing scientific foundations for the UN Decade on Ecosystem Restoration’.
Clinical Evaluation of the GeneXpert®Xpert®Xpress SARS-CoV-2/Flu/RSVPLUSCombination Test
Authors: Johnson Grant , Gregorchuk Branden S.J. , Zubrzycki Arek , Kolsun Kurt , Meyers Adrienne F.A. , Sandstrom Paul A. , Becker Michael G. 
Published: November 2022

AbstractThe GeneXpert®Xpert®Xpress SARS-CoV-2/Flu/RSVPLUScombination test (PLUSAssay) received Health Canada approval in January 2022. ThePLUSAssay is similar to the SARS-CoV-2/Flu/RSV combination test, with modifications to improve assay robustness against circulating and emerging variants. The performance characteristics of thePLUSAssay were assessed at the Lakeridge Health Oshawa Hospital Centre and the National Microbiology Laboratory of Canada. ThePLUSAssay was directly compared to the SARS-CoV-2/Flu/RSV combination test using SARS-CoV-2 culture from five variants and remnant clinical specimens collected across the COVID-19 pandemic. This included 50 clinical specimens negative for all pathogens, 110 clinical specimens positive for SARS-CoV-2, Influenza A, Influenza B, RSVA, and/or RSVB and an additional 11 mixed samples to screen for target interactions. ThePLUSAssay showed a high percent agreement with the widely used SARS-CoV-2/Flu/RSV combination test. Based on these findings, thePLUSAssay and the Xpert SARS-CoV-2/Flu/RSV combination test results are largely consistent with no observed difference in sensitivity, specificity, or time to result when challenged with various SARS-CoV-2 variants. The reported Ct values provided by the newPLUSAssay was also unchanged, with the exception of a possible 1-2 decrease reported Ct for RSVA across a limited sample size.
Dose-Response in Modulating Brain Function with Transcranial Direct Current Stimulation: From Local to Network Levels
Authors: Soleimani Ghazaleh , Kupliki Rayus , Paulus Martin , Ekhtiari Hamed 
Published: November 2022

AbstractBackgroundNon-invasive brain stimulation methods for modulating brain activity via transcranial technologies like transcranial direct current stimulation (tDCS) are increasingly prevalent to investigate the relationship between modulated brain regions and stimulation outcomes. However, the inter-individual variability of tDCS has made it challenging to detect intervention effects at the group level. Collecting multiple modalities of magnetic resonance imaging data (i.e., structural and functional MRI) helps to investigate how dose-response ultimately shapes brain function in response to tDCS.MethodWe collected data in a randomized, triple-blind, sham-controlled trial with two parallel arms. Sixty participants with MUD were randomly assigned to sham or active tDCS (n=30 per group, 2 mA, 20 minutes, anode/cathode over F4/Fp1). Structural and functional MRI (including high-resolution T1 and T2-weighted MRI, resting-state fMRI, and methamphetamine cue-reactivity task with meth versus neutral cues) were collected immediately before and after tDCS. T1 and T2-weighted MRI data were used to generate head models for each individual to simulate electric fields. Associations between electric fields (dose) and changes in brain function (response) were investigated at four different levels: (1) voxel level, (2) regional level (atlas-based parcellation), (3) cluster level (active clusters in the contrast of interest), and (4) network level (both task-based and resting-state networks).ResultAt the (1) voxel-level, (2) regional level, and (3) cluster level, our results showed no significant correlation between changes in the functional activity and electric fields. However, (4) at the network level, a significant negative correlation was found between the electric field and ReHo in the default mode network (r=-0.46 (medium effect size), p corrected=0.018). For the network-level analysis of task-based fMRI data, frontoparietal connectivity showed a positive significant correlation with the electric field in the frontal stimulation site (r=0.41 (medium effect size), p corrected=0.03).ConclusionThe proposed pipeline provides a methodological framework to analyze tDCS effects in terms of dose-response relationships at four different levels to directly link the electric field (dose) variability to the variability of the neural response to tDCS. The results suggest that network-based analysis might be a better approach to provide novel insights into the dependency of the neuromodulatory effects of tDCS on the brain’s regional current dose in each individual. Dose-response integration can be informative for dose optimization/customization or predictive/treatment-response biomarker extraction in future brain stimulation studies.
Incidence of perioperative anaphylaxis in 2021 in Japan: Survey of 34 hospitals of Social Welfare Organization Saiseikai Imperial Gift Foundation, Inc
Authors: Suzuki Yasuyuki , Liu Shuang , Yamashita Natsumi , Yamaguchi Naohito , Takasaki Yasushi , Yorozuya Toshihiro , Mogi Masaki 
Published: November 2022

AbstractPerioperative anaphylaxis (POA) is a severe complication with a low incidence and diverse risk factors. Its low incidence makes a detailed survey of POA challenging. Recent large-scale surveys in Japan have focused on identifying the causative agents using the basophil activation test. Only facilities, such as university hospitals, that can dispatch samples for this test participate, which may introduce bias. We surveyed the incidence of POA primarily in secondary hospitals, such as the Saiseikai hospitals, throughout Japan.We targeted data collection for the year 2021. Thirty-five facilities answered (Supplementary 1, 2); we excluded 1 reporting no surgeries. In total, 70,523 surgeries were performed, with POA diagnosed in 7 cases. For diagnosis, the skin test was used in 3 cases and quantification of histamine and tryptase in 1 case. In 3 cases, diagnosis was based on the time to onset of POA after drug use. Multiple tests are important to ensure patient safety. However, in this survey, no hospital performed in vitro tests to identify the cause. This is major limitation, however, as many hospitals do not have experimental laboratories, we believe that this study, which focuses on secondary care institutions, contributes to the literature significantly by presenting the current situation in clinical practice.
A Novel Use of a Tissue Oxygenation Monitor at Time of Uterus Transplantation and Hysterectomy – A Feasibility Study
Authors: Applebaum Jeremy , Zhao Dan , Barry Dan , Latif Nawar , O’Neill Kathleen 
Published: November 2022

AbstractWhile thrombosis is the most common indication for graft failure and immediate hysterectomy of a transplanted uterus, there is no optimal method to monitor graft perfusion. In this feasibility study, a near-infrared spectroscopy probe that monitors local tissue oxygenation (StO2) was attached to four uterine cervices and three donor cervices at the time of hysterectomy and transplantation respectively. Real-time StO2measurements were gathered at key surgical steps of the hysterectomies and uterus transplantations. The average StO2for the sequential steps of a hysterectomy of baseline, ovarian vessel ligation, contralateral ovarian vessel ligation, uterine vessel ligation, contralateral uterine vessel ligation, and colpotomy was 70.2%, 56.7%, 62.1%, 50.5%, 35.8%, and 8.5% respectively. The average StO2for the sequential steps of uterus transplantation of iliac vein anastomosis, iliac artery anastomosis, contralateral iliac vein anastomosis, contralateral iliac artery anastomosis, and vaginal anastomosis was 8.9%, 27.9%, 56.9%, 65.9%, and 65.2% respectively. As uterine blood supply decreases in a hysterectomy, the measured StO2also decreases, and vice versa for uterus transplantation. Tissue oximetry may be a reliable, non-invasive means of monitoring perfusion of a uterine graft. Additional studies are needed to determine if these devices complement current assessments of uterine graft viability and salvage thrombosed grafts.
White matter tract integrity is reduced in major depression and in individuals with genetic liability for depression
Authors: Nothdurfter David , Jawinski Philippe , Markett Sebastian 
Published: November 2022

0.AbstractMajor depression has been linked to alterations of the brain’s white matter architecture. Major depression has also a considerable genetic component. It is, however, unclear if genetic liability for depression relates directly to the suggested alterations at the brain level.We re-evaluated white matter fiber tract alterations in major depression and aimed to relate polygenic risk for depression in unaffected individuals to these alterations.We conducted a population-based retrospective cohort study with N=17183 participants (n=287 currently depressed, n=5536 formerly depressed, n= 13360 healthy) aged 44 to 82 from the UK Biobank imaging cohort, collected between 2015 and 2020.Depression status was assessed based on questionnaire data. We derived 27 major white matter tracts from diffusion MRI and indexed their integrity according to mean fractional anisotropy. Genetic liability for depression was quantified by polygenic scores based on three recent case-control GWAS.White matter integrity was globally reduced in depression. The reduction was most pronounced on thalamic and intracortical fiber tracts, where the reduction was observed irrespective of current symptom status. Non-depressed individuals showed already a reduction in relevant fiber tracts with increasing polygenic risk, particularly in thalamic radiations. Subsequent in-silico simulations and non-parametric tests confirmed that the polygenic association was stronger than expected given the low-level statistical dependencies between target and discovery samples. White matter integrity on thalamic and association tracts is reduced in depression irrespective of current disease status and relates to the underlying genetic risk factors in unaffected individuals. The observed statistical links between genes, brain, and disorder adhere to the definition of an intermediate phenotype at the brain level.
Artificial intelligence and MRI: the source of a new epilepsy taxonomy
Authors: Xiao Fenglai , Caciagli Lorenzo , Wandschneider Britta , Sone Daichi , Young Alexandra L. , Vos Sjoerd B. , Winston Gavin P. , Zhang Yingying , Liu Wenyu , An Dongmei , Kanber Baris , Zhou Dong , Sander Josemir W. , Duncan John S. , Alexander Daniel C. , Galovic Marian , Koepp Matthias J. 
Published: November 2022

AbstractArtificial intelligence (AI)-based tools are widely employed, but their use for diagnosis and prognosis of neurological disorders is still evolving. We capitalise on a large-scale, cross-sectional structural MRI dataset of 814 people with epilepsy. We use a recently developed machine-learning algorithm, Subtype and Stage Inference (SuStaIn), to develop a novel data-driven disease taxonomy based on distinct patterns of spatiotemporal progression of brain atrophy. We identify two subtypes common to focal and idiopathic generalised epilepsies, characterised by neocortical-driven or basal ganglia-driven progression, and a third subtype, only detected in focal epilepsies, characterised by hippocampus-driven progression. We corroborate external validity via an independent cohort of 254 people and decode associations between progression subtypes and clinical measures of epilepsy severity. Our findings suggest fundamental processes underlying the progression of epilepsy-related brain atrophy. We deliver a novel MRI- and AI-guided epilepsy taxonomy, which could be used for individualised prognostics and targeted therapeutics.
Decoding Motor Plans Using a Closed-Loop Ultrasonic Brain-Machine Interface
Authors: Griggs Whitney S. , Norman Sumner L. , Deffieux Thomas , Segura Florian , Osmanski Bruno-Félix , Chau Geeling , Christopoulos Vasileios , Liu Charles , Tanter Mickael , Shapiro Mikhail G. , Andersen Richard A. 
Published: November 2022

ABSTRACTBrain-machine interfaces (BMIs) can be transformative for people living with chronic paralysis. BMIs translate brain signals into computer commands, bypassing neurological impairments and enabling people with neurological injury or disease to control computers, robots, and more with nothing but thought. State-of-the-art BMIs have already made this future a reality in limited clinical trials. However, high performance BMIs currently require highly invasive electrodes in the brain. Device degradation limits longevity to about 5 years. Their field of view is small, restricting the number, and type, of applications possible. The next generation of BMI technology should include being longer lasting, less invasive, and scalable to sense activity from large regions of the brain. Functional ultrasound neuroimaging is a recently developed technique that meets these criteria. In this present study, we demonstrate the first online, closed-loop ultrasonic brain-machine interface. We used 2 Hz real-time functional ultrasound to measure the neurovascular activity of the posterior parietal cortex in two nonhuman primates (NHPs) as they performed memory-guided movements. We streamed neural signals into a classifier to predict the intended movement direction. These predictions controlled a behavioral task in real-time while the NHP did not produce overt movements. Both NHPs quickly succeeded in controlling up to eight independent directions using the BMI. Furthermore, we present a simple method to “pretrain” the BMI using data from previous sessions. This enables the BMI to work immediately from the start of a session without acquiring extensive additional training data. This work establishes, for the first time, the feasibility of an ultrasonic BMI and prepares for future work on a next generation of minimally invasive BMIs that can restore function to patients with neurological, physical, or even psychiatric impairments.
X-inactivation states of single cell transcriptomes reveal cellular phylogenies in human females
Authors: Predeus Alexander , Arutyunyan Anna , Jardine Laura , Suo Chenqu , Dann Emma , Hoo Regina , Prete Martin , Haniffa Muzlifah , Mitchell Thomas J. , Vento-Tormo Roser , Young Matthew D. 
Published: November 2022

AbstractHuman females undergo X-inactivation (Xi), whereby one copy of X is randomly inactivated early in development, then propagated through cell division. Because Xi state is inherited, its measurement in populations of cells encodes information about the phylogeny that created them and their relationships to other cells. We present a method, inactiveXX, to determine the Xi state of single cell transcriptomes, and demonstrate its accuracy using cancer and gold standard reference data. We apply inactiveXX to single cell transcriptomes from 190 human females, revealing that Xi in humans likely occurs around the 16 cell blastocyst stage and affects both embryonic and extra-embryonic tissues. We further find significant cell type specific variability in Xi skew, only detectable with cell type specific resolution, with certain cell types exhibiting strong population bottlenecks across tissues and disease state.
GlyLES: Grammar-based Parsing of Glycans from IUPAC-condensed to SMILES
Authors: Joeres Roman , Bojar Daniel , Kalinina Olga V. 
Published: November 2022

AbstractGlycans are important polysaccharides on cellular surfaces that are bound to glycoproteins and glycolipids. These are one of the most common post-translational modifications of proteins in eukaryotic cells. They play important roles in protein folding, cell-cell interactions, and other extracellular processes. Changes in glycan structures may influence the course of different diseases, such as infections or cancer.Glycans are commonly represented using the IUPAC-condensed notation. IUPAC-condensed is a textual representation of the Symbol Nomenclature for Glycans (SNFG) that assigns a colored, geometrical shape to the main monosaccharides. These symbols are then connected in tree-like structures, visualizing the glycan structure on a polymeric level. Yet for a representation on the atomic level, notations such as SMILES should be used. To our knowledge, there is no easy-to-use, general, open-source, and offline tool to convert the IUPAC-condensed notation to SMILES. Here, we present the open-access Python package GlyLES for the generalizable generation of SMILES representations out of IUPAC-condensed representations. GlyLES uses a grammar to read in the monomer tree from the IUPAC-condensed notation. From this tree, the tool can compute atomic structures of each monomer based on their IUPAC-condensed descriptions. In the last step, it merges all monomers into the atomic structure of a glycan in the SMILES notation.GlyLES is the first package that allows conversion between IUPAC-condensed notations of glycans and SMILES strings. This may have multiple applications, including straightforward visualization, substructure search, molecular modelling and docking, and a new featurization strategy for machine-learning algorithms. GlyLES is available athttps://github.com/kalininalab/GlyLES.
Slower, but deeper community change: anthropogenic impacts on species temporal turnover are regulated by intrinsic dynamics
Authors: Terry J. Christopher D. , Rossberg Axel G. 
Published: November 2022

AbstractUnderstanding the mechanisms behind biodiversity is central to assessing and forecasting anthropogenic impacts on ecological communities. However, quite how intrinsic ecological processes and external environmental drivers act together in natural systems to influence local temporal turnover is currently largely unexplored. Here, we determine how human impacts affect multiple metrics of bird community turnover to establish the ecological mechanisms behind compositional change. We used US Breeding Bird Survey data to calculate transect-level rates of three measures of temporal species turnover: a) short-term (initial rate of decline of Sørensen similarity), b) long-term (asymptotic Sørensen similarity), and c) overall species accumulation rate (species-time relationship exponents) over 2692 transects across 27 habitat types. We then hierarchically fit linear models to estimate the effect on these turnover metrics of anthropogenic impact via the Human Modification Index proxy, while accounting for observed species richness, the size of the species pool and annual environmental variability. We found broadly consistent impacts of increased anthropogenic pressures across diverse habitat types. The Human Modification Index was associated with greater turnover at long-timescales, but marginally slower short-term turnover. The species accumulation rate through time was not notably influenced. Examining anthropogenic impacts on different aspects of species turnover in combination allows greater ecological insight. Observed human impacts on short-term turnover were the opposite of existing expectations and suggest humans are disrupting the background turnover of these systems, rather than simply driving rapid directed turnover. The increased long-term turnover was driven by more frequent species changes between core and occasional status rather than greater arrival of ‘new’ species. These results highlight the role of intrinsic dynamics and caution against simple interpretations of increased species turnover as reflections of environmental change.Open Research StatementNo new empirical data are used in the manuscript as all primary data is publicly available, as cited in the manuscript. Our code repository (including fitted model objects and markdown documents detailing all steps) is available athttps://figshare.com/s/f5b9152ff7643efb347d.
Cholinergic-estrogen interaction underpins the effect of education on attenuating cognitive sex differences in a Thai healthy population
Authors: Chen Chen , Khanthiyong Bupachad , Charoenlappanit Sawanya , Roytrakul Sittiruk , Thanoi Samur , Nudmamud-Thanoi Sutisa 
Published: November 2022

AbstractThe development of human brain is shaped by both genetic and environmental factors. Sex differences in cognitive function have been found in humans as a result of sexual dimorphism in neural information transmission. Numerous studies have reported the positive effects of education on cognitive functions. However, little work has investigated the effect of education on attenuating cognitive sex differences and the neural mechanisms behind it based on healthy population. In this study, the Wisconsin Card Sorting Test (WCST) was employed to examine sex differences in cognitive function in 135 Thai healthy subjects, and label-free proteomic method and bioinformatic analysis were used to study sex-specific neurotransmission-related protein expression profiles. The results showed a sex difference in two WCST subscores: percentage of Total corrects and Total errors in the primary education group (Bayes factor>100) with males performed better, while such differences eliminated in secondary and tertiary education level. Moreover, 11 differentially expressed proteins (DEPs) between men and women (FDR<0.1) were presented in both education groups, with majority of them upregulated in females. Half of those DEPs interacted directly with nAChR3, whereas the other DEPs were indirectly connected to the cholinergic pathways through interaction with estrogen. These findings implied that Cholinergic-estrogen interaction underpins the effect of education on attenuating cognitive sex differences in a Thai healthy population.