bluuebunny/crossref_metadata_2025_split huggingface dataset:
Replacing non-emergency bleeps and long-range pagers with a hospital-wide, EHR-integrated secure messaging system: an implementer report
Authors: Ercole Ari , Tolliday Claire , Gelson William , Rudd James , Cameron Ewen , Chaudhry Afzal , Hamer Fiona , Davies Justin 
Published: November 2022

AbstractIntroductionObsolete bleep/long-range pager equipment remains firmly embedded in the NHS.ObjectiveTo introduce a secure, chart-integrated messaging system (Epic Secure Chat™) in a large NHS tertiary referral centre to replace non-emergency bleeps/long-range pagers.MethodsThe system was socialised in the months before go-live. Operational readiness was overseen by an implementation group with stakeholder engagement. Cutover was accompanied by a week of Secure Chat and bleeps running in parallel.ResultsEngagement due to socialisation was high with usage stabilising approximately 3 months after go-live. Contact centre internal call activity fell significantly after go-live. No significant patient safety concerns were reported.DiscussionStaff engagement and uptake was excellent. The majority of those who previously carried bleeps were content to use personal devices for messaging because of user convenience after reassurance about privacy.ConclusionAn integrated secure messaging system can replace non-emergency bleeps with beneficial impact on service.
Right amygdala lesions are associated with improved mood after epilepsy surgery
Authors: Albazron Fatimah M. , Tranel Daniel , Howard Matthew A. , Boes Aaron D. 
Published: November 2022

AbstractNeuroimaging studies in healthy and clinical populations strongly associate the amygdala with emotion, especially negative emotions. The consequences of surgical lesions of the amygdala on mood are not well characterized. We tested the hypothesis that amygdala lesions would result in mood improvement. In this study we evaluated a cohort of 52 individuals with medial temporal lobectomy for intractable epilepsy who had resections variably involving the amygdala. All individuals achieved good post-surgical seizure control and had pre- and post-surgery mood assessment with the Beck Depression Inventory (BDI) ratings. We manually segmented the surgical resection cavities and performed multivariate lesion-symptom mapping of change in BDI. Our results showed a significant improvement in average mood ratings from pre- to post-surgery across all patients. In partial support of our hypothesis, resection of the right amygdala was significantly associated with mood improvement (r = 0.5, p = 0.008). The lesion-symptom map also showed that resection of the right hippocampus and parahippocampal gyrus was associated with worsened post-surgical mood. Future studies could evaluate this finding prospectively in larger samples while including other neuropsychological outcome measures.
The burden of mortality due to injury in Cabo Verde, 2018
Authors: Fernandes Ngibo Mubeta , Mendonça Maria da Luz Lima , Gomez Lara Ferrero 
Published: November 2022

AbstractExternal causes continue to be one of the main causes of mortality in the world and Cabo Verde is no exception. Economic evaluations can be used to demonstrate the disease burden of public health problems such as injuries and external causes and support prioritization of interventions aimed at improving the health of the populations. The study objective was to estimate the indirect costs of premature mortality in 2018 due to injuries and other consequences of external causes in Cabo Verde. Years of potential life lost, years of potential productive life lost and human capital approach were used to estimate the burden and indirect costs of premature mortality in 2018. In 2018, 244 deaths were registered due to injury and other consequences of external causes. Males were responsible for 85.4% and 87.73% of years of potential life lost and years of potential productive life lost, respectively. The cost of productivity lost due to premature death caused by injury was 4,580,225.91 USD. The was social and economic burden due to trauma was significant. There is a need for more evidence on the burden of disease due to injuries and their consequences, to support the implementation of targeted multi-sectoral strategies and policies for the prevention, management, and reduction of costs due to injuries in Cabo Verde.
A human neural crest model reveals the developmental impact of neuroblastoma-associated chromosomal aberrations
Authors: Saldana-Guerrero Ingrid M. , Montano-Gutierrez Luis F. , Boswell Katy , Hafemeister Christoph , Poon Evon , Shaw Lisa E. , Stavish Dylan , Lea Rebecca A. , Wernig-Zorc Sara , Bozsaky Eva , Fetahu Irfete S. , Zoescher Peter , Pötschger Ulrike , Bernkopf Marie , Wenninger-Weinzierl Andrea , Sturtzel Caterina , Souilhol Celine , Tarelli Sophia , Shoeb Mohamed R. , Bozatzi Polyxeni , Rados Magdalena , Guarini Maria , Buri Michelle C. , Weninger Wolfgang , Putz Eva M. , Huang Miller , Ladenstein Ruth , Andrews Peter W. , Barbaric Ivana , Cresswell George D. , Bryant Helen E. , Distel Martin , Chesler Louis , Taschner-Mandl Sabine , Farlik Matthias , Tsakiridis Anestis , Halbritter Florian 
Published: November 2022

AbstractEarly childhood tumours arise from transformed embryonic cells, which often carry large copy number alterations (CNA). However, it remains unclear how CNAs contribute to embryonic tumourigenesis due to a lack of suitable models. Here we employ female human embryonic stem cell (hESC) differentiation and single-cell transcriptome and epigenome analysis to assess the effects of chromosome 17q/1q gains, which are prevalent in the embryonal tumour neuroblastoma (NB). We show that CNAs impair the specification of trunk neural crest (NC) cells and their sympathoadrenal derivatives, the putative cells-of-origin of NB. This effect is exacerbated upon overexpression ofMYCN, whose amplification co-occurs with CNAs in NB. Moreover, CNAs potentiate the pro-tumourigenic effects ofMYCNand mutant NC cells resemble NB cells in tumours. These changes correlate with a stepwise aberration of developmental transcription factor networks. Together, our results sketch a mechanistic framework for the CNA-driven initiation of embryonal tumours.
Magnetic resonance imaging datasets with anatomical fiducials for quality control and registration
Authors: Taha Alaa , Gilmore Greydon , Abbass Mohamad , Kai Jason , Kuehn Tristan , Demarco John , Gupta Geetika , Zajner Chris , Cao Daniel , Chevalier Ryan , Ahmed Abrar , Hadi Ali , Karat Bradley , Stanley Olivia W. , Park Patrick , Ferko Kayla M. , Hemachandra Dimuthu , Vassallo Reid , Jach Magdalena , Thurairajah Arun , Wong Sandy , Tenorio Mauricio C. , Ogunsanya Feyi , Khan Ali R. , Lau Jonathan C. 
Published: November 2022

AbstractTools available for reproducible, quantitative assessment of brain correspondence have been limited. We previously validated the anatomical fiducial (AFID) placement protocol for point-based assessment of image registration with millimetric (mm) accuracy. In this data descriptor, we release curated AFID placements for some of the most commonly used structural magnetic resonance imaging templates and datasets. The release of our accurate placements allows for rapid quality control of image registration, teaching neuroanatomy, and clinical applications such as disease diagnosis and surgical targeting. We release placements on individual subjects from four datasets (n = 132 subjects for a total of 15,232 fiducials) and more than 10 brain templates (4,288 fiducials), compiling over 300 human rater hours of annotation. We also validate human rater accuracy of released placements to be within 1-2 mm (using a total of 50,336 Euclidean distances), consistent with prior studies. Our data is compliant with the Brain Imaging Data Structure (BIDS) allowing for facile incorporation into modern neuroimaging analysis pipelines. Data is accessible on GitHub (https://github.com/afids/afids-data).
Adaptive biasing of action-selective cortical build-up activity by stimulus history
Authors: Braun A. , Donner T.H. 
Published: November 2022

AbstractDecisions under uncertainty are often biased by the history of preceding sensory input, behavioral choices, or received outcomes. Behavioral studies of perceptual decisions suggest that such history-dependent biases affect the accumulation of evidence and can be adapted to the correlation structure of the sensory environment. Here, we systematically varied this correlation structure while human participants performed a canonical perceptual choice task. We tracked the trial-by-trial variations of history biases via behavioral modeling and of a neural signature of decision formation via magnetoencephalography (MEG). The history bias was flexibly adapted to the environment and exerted a selective effect on the build-up (not baseline level) of action-selective motor cortical activity during decision formation. This effect added to the impact of the current stimulus. We conclude that the build-up of action plans in human motor cortical circuits is shaped by dynamic prior expectations that result from an adaptive interaction with the environment.
Effort Foraging Task reveals positive correlation between individual differences in the cost of cognitive and physical effort in humans
Authors: Bustamante Laura A. , Oshinowo Temitope , Lee Jeremy R. , Tong Elizabeth , Burton Allison R. , Shenhav Amitai , Cohen Jonathan D. , Daw Nathaniel D. 
Published: November 2022

AbstractEffort-based decisions, in which people weigh potential future rewards against effort costs required to achieve those rewards, have largely been studied separately for cognitive or physical effort, yet most real-world actions incur both effort costs. What is the relationship between cognitive and physical effort costs? Here we attempt to formalize the mechanisms underlying effort-based decisions and address methodological challenges to isolate and measure these mechanisms. Patch foraging is an ecologically valid reward rate maximization problem with well-developed theoretical tools to understand choices. We developed the Effort Foraging Task, which embedded cognitive or physical effort into a patch foraging sequential decision task, to isolate and quantify the cost of both cognitive and physical effort using a computational model. Participants chose between harvesting a depleting patch, or traveling to a new patch that was costly in time and effort. Participants’ exit thresholds (reflecting the reward they expected to receive by harvesting when they chose to travel to a new patch) were sensitive to cognitive and physical effort demands, allowing us to quantify the perceived effort cost in monetary terms. Individual differences in cognitive and physical effort costs were positively correlated, suggesting that these are perceived and processed in common terms across different domains. We found patterns of correlation of both cognitive and physical effort costs with self-reported anxiety, cognitive function, behavioral activation, and self-efficacy. This suggests the task captures decision mechanisms associated with real-world motivation and can be used to study individual variation in effort-based decisions across domains of cost.
A tRNA Modification-based strategy for Identifying amiNo acid Overproducers (AMINO)
Authors: Guo Hao , Ma Xiaoyan , Wang Ning , Ding Tingting , Zheng Bo , Guo Liwei , Huang Chaoyong , Zhang Wuyuan , Sun Lichao , Huo Yi-Xin 
Published: November 2022

AbstractAmino acids have a multi-billion-dollar market with rising demand, prompting the development of high-performance microbial factories. However, a general screening strategy applicable to all proteinogenic and non-proteinogenic amino acids is still lacking. Modification of the critical structure of tRNA could decrease the aminoacylation level of tRNA catalyzed by aminoacyl-tRNA synthetases. Involved in a two-substrate sequential reaction, amino acids with increased concentration could elevate the reduced aminoacylation rate caused by specific tRNA modification. Here, we developed a selection system for overproducers of specific amino acids using corresponding engineered tRNAs and reporter genes. As a proof-of-concept, overproducers of five amino acids such as L-tryptophan were screened out by growth-based and/or fluorescence-activated cell sorting (FACS)-based screening from random mutation libraries ofEscherichia coliandCorynebacterium glutamicum, respectively. This study provided a universal strategy that could be applied to screen overproducers of proteinogenic and non-proteinogenic amino acids in amber-stop-codon-recoded or non-recoded hosts.
Factors governing attachment ofRhizobium leguminosarumto legume roots
Authors: Parsons Jack D. , Cocker Clare R. , East Alison K. , Wheatley Rachel M. , Ramachandran Vinoy K. , Kaschani Farnusch , Kaiser Markus , Poole Philip S. 
Published: November 2022

AbstractPrimary attachment of rhizobia to host legume roots depends on pH and is the first physical interaction during nodulation. Genome-wide insertion sequencing, luminescence-based attachment assays and proteomic analysis demonstrate primary attachment ofRhizobium leguminosarumbiovarviciae3841 toPisum sativum(pea) roots is more complex than previously thought. In total, 115 proteins are needed for initial attachment under one or more test conditions (acid, neutral or alkaline pH), with 22 required under all conditions. These include cell-surface filamentous hemagglutinin adhesin (RL4382) and its transporter (RL4381), transmembrane protein RL2400, RL3752 (PssA, glycosyl transferase) affecting capsular polysaccharide and transcriptional regulator RL4145 (PckR). RNASeq was used to determine targets of RL4145 (PckR) and regulator RL3453. The 54 proteins required for attachment at pH 7.0 were investigated for nodulation phenotypes. Glucomannan biosynthesis protein A (GmsA) is needed at pH 6.5 and pH 7.0. Membrane proteins DgkA and ImpA are required specifically at pH 6.5, and RpoZ at pH 7.5. Sonicated cell surface fractions inhibited root attachment at alkaline pH but no overlap between proteins identified by proteomic and INseq analysis, suggests there is no single rhicadhesin needed for alkaline attachment. Our results demonstrate the complexity of primary root attachment and diversity of mechanisms involved.
Longitudinal associations between stroke and psychosis: a population-based study
Authors: Richards-Belle Alvin , Poole Norman , Osborn David P.J. , Bell Vaughan 
Published: November 2022

AbstractBackgroundThe co-occurrence of stroke and psychosis is a serious neuropsychiatric condition, but little is known about the course of this comorbidity.AimsTo estimate longitudinal associations between stroke and psychosis over 10 years.MethodsA 10-year population-based study using data from the English Longitudinal Study of Ageing. A structured health assessment recorded i) first-occurrence stroke and ii) psychosis, at each wave. Each were considered exposures and outcomes in separate analyses. Logistic and Cox proportional hazards regression and Kaplan-Meier methods were used. Models were adjusted for demographic and health behaviour covariates, with missing covariates imputed using random forest multiple imputation.ResultsOf 19,808 participants, 24 reported both stroke and psychosis (median Wave 1 age 63, 71% female, 50% lowest quintile of net financial wealth) at any point during follow-up. By 10 years, the probability of an incident first stroke in participants with psychosis was 21.4% (95% CI, 12.1 to 29.6) compared to 8.3% (95% CI, 7.8 to 8.8) in those without psychosis (absolute difference: 13.1%; 95% CI, 20.8 to 4.3, log rankp<0.001; fully-adjusted hazard ratio (HR): 3.63; 95% CI, 2.25 to 5.87). The probability of reporting incident psychosis in participants with stroke was 2.3% (95% CI, 1.4 to 3.2) compared to 0.9% (95% CI, 0.7 to 1.1) in those without (absolute difference: 1.4%; 95% CI, 0.7 to 2.1, log rankp<0.001; fully-adjusted HR: 5.81; 95% CI, 2.89 to 11.70).ConclusionsStroke is an independent predictor of psychosis (and vice versa), after adjustment for potential confounders.
Modeling COVID-19 in different countries as sequences of SI waves
Authors: Janssen Rainer , Mimkes Juergen 
Published: November 2022

AbstractThe COVID-19 pandemic has been a huge challenge worldwide for many institutions, researchers, national health organizations, and the pharmaceutical industry. As natural scientists and engineers, we attempted to contribute by calculating models and analyzing data to keep track of the pandemic.While a frequent goal is to predict the next pandemic wave by considering all influencing parameters, we examined methods to calculate a model course of the entire pandemic. This is done by reconstructing the course of infections into multiple model waves that sum up into a pandemic model that is close to the real course. The model wave parameters are varied by an algorithm, such as the Excel solver, to minimize the difference between the real and model courses.By reconstructing the course of infections using the commonly known SIR model, we found that the calculated model parameters were ambiguous and difficult to interpret. In contrast, we found that sequenced SI model waves provide an astonishing precise digital representation of the pandemic course. Until November 2022, we found between six and 16 waves (depending on the country) in each of the 14 countries investigated.The calculated parameters are easy to interpret and are comparable between different waves and countries. These wave parameters may be correlated with the virus types and measures in each country by other researchers. New waves are detectable early as they show a certain deviation from the actual model wave. After the maximum of the last real wave, the model indicates the further procedure for the pandemic course.
The role of short-chain fatty acids on insulin sensitivity: a systematic review and meta-analysis
Authors: Pham Nhan H.T. , Joglekar Mugdha V. , Wong Wilson K.M. , Nassif Najah T. , Simpson Ann M. , Hardikar Anandwardhan A. 
Published: November 2022

AbstractContextThere is substantial evidence that reduced gut short chain fatty acids (SCFAs) are associated with obesity and type 2 diabetes, although findings from clinical interventions that could increase SCFAs are inconsistent.ObjectiveThis work aimed to assess the effect of SCFA intervention on fasting glucose, fasting insulin, and HOMA-IR by performing a systematic review and meta-analysis.Data sourcesRelevant published articles up to 28thJuly 2022 were extracted from PubMed and EMBASE using the medical subject heading (MeSH) of the defined keywords [(short-chain fatty acids AND (obesity OR diabetes OR insulin sensitivity)] and their synonyms. Data analyses were performed using recommended Cochrane meta-analysis checklist and PRISMA guidelines and were registered in the PROSPERO system (ID: CRD42021257248).Data extractionClinical studies and trials that measured SCFAs along with reporting glucose homeostasis parameters were included in the analysis. Standardized mean differences (SMD) with 95% confidence intervals (CI) were calculated using a random-effects model in the data extraction tool Review Manager version 5.4 (RevMan 5.4). The risk of bias assessment was performed following the Cochrane checklist for randomised and crossover studies.Data analysisWe identified 6,040 non-duplicate studies; 23 met defined criteria and reported fasting insulin, fasting glucose, or HOMA-IR as well as a measured post-intervention change in SCFA concentrations. Our meta-analyses indicated that fasting insulin concentrations significantly reduced (overall effect: SMD = -0.15; 95% CI = -0.29, -0.01, p = 0.04) between placebo and treatment groups at the end of the intervention. Post-intervention increase in SCFAs had an even significant effect on lowering fasting insulin (p=0.008). Elevated levels of SCFAs were also associated with beneficial effects on HOMA-IR (p < 0.00001) compared to their baseline. Fasting glucose concentrations did not show any significant change.ConclusionsIncreased post-intervention SCFA is associated with lower fasting insulin, offering a beneficial effect on insulin sensitivity.
Acyl-CoA dehydrogenase substrate promiscuity limits the potential for development of substrate reduction therapy in disorders of valine and isoleucine metabolism
Authors: Houten Sander M. , Dodatko Tetyana , Dwyer William , Chen Hongjie , Stauffer Brandon , DeVita Robert J. , Vaz Frédéric M. , Yu Chunli , Leandro João 
Published: November 2022

AbstractToxicity of accumulating substrates is a significant problem in several disorders of valine and isoleucine degradation notably short-chain enoyl-CoA hydratase (ECHS1 or crotonase) deficiency, 3-hydroxyisobutyryl-CoA hydrolase (HIBCH) deficiency, propionic acidemia (PA) and methylmalonic aciduria (MMA). Isobutyryl-CoA dehydrogenase (ACAD8) and short/branched-chain acyl-CoA dehydrogenase (SBCAD,ACADSB) function in the valine and isoleucine degradation pathways, respectively. Deficiencies of these acyl-CoA dehydrogenase (ACAD) enzymes are considered biochemical abnormalities with limited or no clinical consequences. We investigated whether substrate reduction therapy through inhibition of ACAD8 and SBCAD can limit the accumulation of toxic metabolic intermediates in disorders of valine and isoleucine metabolism. Using analysis of acylcarnitine isomers, we show that 2-methylenecyclopropaneacetic acid (MCPA) inhibited SBCAD, isovaleryl-CoA dehydrogenase, short-chain acyl-CoA dehydrogenase and medium-chain acyl-CoA dehydrogenase, but not ACAD8. MCPA treatment of wild-type and PA HEK-293 cells caused a pronounced decrease in C3-carnitine. Furthermore, deletion ofACADSBin HEK-293 cells led to an equally strong decrease in C3-carnitine when compared to wild-type cells. Deletion ofECHS1in HEK-293 cells caused a defect in lipoylation of the E2 component of the pyruvate dehydrogenase complex, which was not rescued byACAD8deletion. MCPA was able to rescue lipoylation inECHS1KO cells, but only in cells with priorACAD8deletion. SBCAD was not the sole ACAD responsible for this compensation, which indicates substantial promiscuity of ACADs in HEK-293 cells for the isobutyryl-CoA substrate. Substrate promiscuity appeared less prominent for 2-methylbutyryl-CoA at least in HEK-293 cells. We suggest that pharmacological inhibition of SBCAD to treat PA should be investigated further.