bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbiological risk ranking of foodborne pathogens and food products in scarce-data settings
Authors: Crotta Matteo , Prakashbabu Bhagyalakshmi Chengat , Holt Hannah , Swift Ben , Kaur Paviter , Bedi Jasbir Singh , Pedada Venkata Chaitanya , Shaik Thahir Basha , Tumati Srinivasa Rao , Guitian Javier 
Published: April 2022

ABSTRACTIn the absence of epidemiological, microbiological or outbreak data, systematic identification of the hazards and food products posing the higher risk to the consumers is challenging. It is usually in Low- and Middle-Income Countries (LMICs), where the burden of foodborne disease is highest that data tend to be particularly scarce. In this study, we propose qualitative risk-ranking methods for pathogens and food products that can be used in settings where scarcity of data on the frequency/concentration of pathogens in foodstuff is a barrier towards the use of classical risk assessment frameworks. The approach integrates the existing knowledge on foodborne pathogens, manufacturing processes and intrinsic/extrinsic properties of food products with key context-specific information regarding the supply chain(s), characteristics of the Food Business Operators (FBOs) and cultural habits to identify: (i) the pathogens that should be considered as a “High” food safety priority and (ii) the food products posing the higher risk of consumer exposure to microbiological hazards via oral (ingestion) route. When applied to the dairy sector of Andhra Pradesh (India) as a case study, E. coli O157:H7, Salmonella spp., S. aureus and L. monocytogenes were identified as a “High” food safety priority across all FBOs, C. sakazakii a “High” priority for the FBOs producing infant formula/milk powder whilst Shigella spp. and Cryptosporidium spp. a “High” priority when considering the FBOs operating towards the informal end of the formal-informal spectrum. The risk ranking of dairy products was informed by a preliminary cluster analysis for early identification of products that are similar with regards to intrinsic/extrinsic features known to drive the microbiological risk. Products manufactured/retailed by FBOs in the informal market were considered as posing a “High” risk for the consumers due to a widespread lack of compliance to sanitary regulations. For dairy products produced by FBOs operating in the middle and formal end of the formal-informal spectrum, the risk of consumers exposure to microbiological hazards ranged from “Medium” to “Extremely low” depending on the FBO and the intrinsic/extrinsic properties of the products. While providing risk estimates of lower resolution if compared to data-driven risk assessments, the proposed method maximises the value of the information that can be easily gathered in LMICs and provide informative outputs to support food safety decision-making in contexts where resources to be allocated for prevention of foodborne diseases are limited and the food system is complex.
Heterologous Gam-COVID-Vac (Sputnik V) / mRNA-1273 (Moderna) vaccination induces a stronger humoral response than homologous Sputnik V in a real-world data analysis
Authors: Pereson Matías J. , Amaya Lucas , Neukam Karin , Bare Patricia , Echegoyen Natalia , Badano María Noel , Lucero Alicia , Martelli Antonella , Garcia Gabriel H. , Videla Cristina , Martínez Alfredo P. , Di Lello Federico A. 
Published: April 2022

ABSTRACTIntroductionGrowing data are demonstrating safety and immunogenicity of heterologous vaccination schemes against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. This strategy opens up the possibility of a shorter path towards the end of the pandemic.ObjectiveTo compare the homologous prime-boost vaccination scheme of Gam-COVID-Vac (Sputnik V, SpV) to its heterologous combination with mRNA-1273 (Moderna, Mod) vaccine.MethodsSARS-CoV-2 anti-spike (S)-receptor binding domain (RBD) IgG concentration was assessed three to seven weeks after complete vaccination. Reactogenicity was evaluated by declared side events and medical assistance required until day 7 post-boost.ResultsOf 190 participants enrolled, 105 received homologous SpV/SpV and the remaining heterologous SpV/Mod vaccination scheme, respectively. Median (interquartile range, IQR) age was 54 (37-63) years, 132 (69.5%) were female and 46 (24.2%) individuals had a prior confirmed COVID-19. Anti-S-RBD IgG median (IQR) titers were significantly higher for SpV/Mod [2511 (1476-3992) BAU/mL] than for SpV/SpV [582 (209-1609) BAU/mL, p<0.001] vaccination scheme. In a linear model adjusted for age, gender, time to the serological assay and time between doses, SpV/Mod [4.154 (6.585-615.554), p<0.001] and prior COVID [3.732 (8.641-202.010), p<0.001] were independently associated with higher anti-S-RBD IgG values. A higher frequency of mild-moderate adverse effects was associated with the heterologous scheme, although it was well tolerated by all individuals and no medical assistance was required.ConclusionThe heterologous SpV/Mod combination against SARS-CoV-2 is well tolerated and significantly increases humoral immune response as compared to the homologous SpV/SpV immunization.
Intellectual enrichment and genetic modifiers of cognitive function in Huntington’s disease
Authors: Papoutsi Marina , Flower Michael , Hensman Davina , Holmans Peter , Estevez-Fraga Carlos , Johnson Eileanor , Scahill Rachael I. , Rees Geraint , Langbehn Douglas , Tabrizi Sarah J. ,   the Track-HD Investigators
Published: April 2022

AbstractAn important step towards the development of treatments for cognitive impairment in ageing and neurodegenerative diseases is to identify genetic and environmental modifiers of cognitive function and understand the mechanism by which they exert an effect. In Huntington’s disease, the most common autosomal dominant dementia, a small number of studies have identified intellectual enrichment, i.e. a cognitively stimulating lifestyle, and genetic polymorphisms as potential modifiers of cognitive function. The aim of our study was to further investigate the relationship and interaction between genetic factors and intellectual enrichment on cognitive function and brain atrophy in Huntington’s disease. For this purpose, we analysed data from Track- HD, a multi-centre longitudinal study in Huntington’s disease gene-carriers, and focused on the role of intellectual enrichment (estimated at baseline) and the genes FAN1, MSH3, BDNF, COMT and MAPT in predicting cognitive decline and brain atrophy. We found that carrying the 3a allele in the MSH3 gene had a positive effect on global cognitive function and brain atrophy in multiple cortical regions, such that 3a allele carriers had a slower rate of cognitive decline and atrophy compared to non-carriers, in agreement with its role in somatic expansion instability. No other genetic predictor had a significant effect on cognitive function and the effect of MSH3 was independent of intellectual enrichment. Intellectual enrichment also had a positive effect on cognitive function; participants with higher intellectual enrichment, ie. those who were better educated, had higher verbal IQ and performed an occupation that was intellectually engaging, had better cognitive function overall, in agreement with previous studies in Huntington’s disease and other dementias. We also found that intellectual enrichment interacted with the BDNF gene, such that the positive effect of intellectual enrichment was greater in Met66 allele carriers than non- carriers. A similar relationship was also identified for changes in whole brain and caudate volume; the positive effect of intellectual enrichment was greater for Met66 allele carriers, rather than non- carriers. In summary, our study provides additional evidence for the beneficial role of intellectual enrichment and carrying the 3a allele in MSH3 in cognitive function in Huntington’s disease and their mechanism of action.
Multiple Cost Optimisation for Alzheimer’s Disease Diagnosis
Authors: McCombe Niamh , Ding Xuemei , Prasad Girijesh , Finn David P. , Todd Stephen , McClean Paula L. , Wong-Lin KongFatt ,   the Alzheimer’s Disease Neuroimaging Initiative
Published: April 2022

AbstractCurrent machine learning techniques for dementia diagnosis often do not take into account real-world practical constraints, which may include, for example, the cost of diagnostic assessment time and financial budgets. In this work, we built on previous cost-sensitive feature selection approaches by generalising to multiple cost types, while taking into consideration that stakeholders attempting to optimise the dementia care pathway might face multiple non-fungible budget constraints. Our new optimisation algorithm involved the searching of cost-weighting hyperparameters while constrained by total budgets. We then provided a proof of concept using both assessment time cost and financial budget cost. We showed that budget constraints could control the feature selection process in an intuitive and practical manner, while adjusting the hyperparameter increased the range of solutions selected by feature selection. We further showed that our budget-constrained cost optimisation framework could be implemented in a user-friendly graphical user interface sandbox tool to encourage non-technical users and stakeholders to adopt and to further explore and audit the model - a humans-in-the-loop approach. Overall, we suggest that setting budget constraints initially and then fine tuning the cost-weighting hyperparameters can be an effective way to perform feature selection where multiple cost constraints exist, which will in turn lead to more realistic optimising and redesigning of dementia diagnostic assessments.Clinical RelevanceBy optimising diagnostic accuracy against various costs (e.g. assessment administration time and financial budget), predictive yet practical dementia diagnostic assessments can be redesigned to suit clinical use.
Investigating direct and indirect genetic effects in attention deficit hyperactivity disorder (ADHD) using parent-offspring trios
Authors: Martin Joanna , Wray Matthew , Agha Sharifah Shameem , Lewis Katie J. S. , Anney Richard J. L. , O’Donovan Michael C. , Thapar Anita , Langley Kate 
Published: April 2022

AbstractBackgroundAttention deficit hyperactivity disorder (ADHD) is highly heritable, but little is known about the relative effects of transmitted (i.e. direct) and non-transmitted (i.e. indirect) common variant risks. Using parent-offspring trios, we tested whether polygenic liability for neurodevelopmental and psychiatric disorders and lower cognitive ability is over-transmitted to ADHD probands. We also tested for indirect or ‘genetic nurture’ effects, by examining whether non-transmitted ADHD polygenic liability is elevated. Finally, we examined whether complete trios are representative.MethodsPolygenic risk scores (PRS) for ADHD, anxiety, autism, bipolar disorder, depression, obsessive-compulsive disorder (OCD), schizophrenia, Tourette’s syndrome, and cognitive ability were calculated in UK controls (N=5,081), UK probands with ADHD (N=857), and, where available, their biological parents (N=328 trios), and also a replication sample of 844 ADHD trios.ResultsADHD PRS were over-transmitted and cognitive ability and OCD PRS were under-transmitted to probands. These results were independently replicated. Over-transmission of polygenic liability was not observed for other disorders. Non-transmitted alleles were not enriched for ADHD liability compared to controls. Probands from incomplete trios had more hyperactive-impulsive and conduct disorder symptoms, lower IQ, and lower socioeconomic status than complete trios. PRS did not vary by trio status.ConclusionsThe results support direct transmission of polygenic liability for ADHD and cognitive ability from parents to offspring, but not for other neurodevelopmental/psychiatric disorders. They also suggest that non-transmitted neurodevelopmental/psychiatric parental alleles do not contribute indirectly to ADHD via genetic nurture. Furthermore, ascertainment of complete ADHD trios may be non-random, in terms of demographic and clinical factors.
Domain expert evaluation of advanced visual computing solutions for the planning of left atrial appendage occluder interventions
Authors: Mill Jordi , Montoliu Helena , Moustafa Abdel H. , Olivares Andy L. , Albors Carlos , Aguado Ainhoa , Medina Elodie , Ceresa Mario , Freixa Xavier , Arzamendi Dabit , Cochet Hubert , Camara Oscar 
Published: April 2022

AbstractAdvanced visual computing solutions and 3D printing are starting to move from the engineering and development stage to being integrated into clinical pipelines for training, planning and guidance of complex interventions. Commonly, clinicians make decisions based on the exploration of patient-specific medical images in 2D flat monitors using specialised software with standard multi-planar reconstruction (MPR) visualisation. The new generation of visual computing technologies such as 3D imaging, 3D printing, 3D advanced rendering, Virtual Reality and in-silico simulations from Virtual Physiological Human models, provide complementary ways to better understand the structure and function of the organs under study and improve and personalise clinical decisions. Cardiology is a medical field where new visual computing solutions are already having an impact in decisions such as the selection of the optimal therapy for a given patient. A good example is the role of emerging visualisation technologies to choose the most appropriate settings of a left atrial appendage occluder (LAAO) device that needs to be implanted in some patients with atrial fibrillation having contraindications to drug therapies. Clinicians need to select the type and size of the LAAO device to implant, as well as the location to be deployed. Usually, interventional cardiologists make these decisions after the analysis of patient-specific medical images in 2D flat monitors with MPR visualisation, before and during the procedure, obtain manual measurements characterising the cardiac anatomy of the patient to avoid adverse events after the implantation. In this paper we evaluate several advanced visual computing solutions such as web-based 3D imaging visualisation (VIDAA platform), Virtual Reality (VRIDAA platform) and computational fluid simulations and 3D printing for the planning of LAAO device implantations. Six physicians including three interventional and three imaging cardiologists, with different level of experience in LAAO, tested the different technologies in preoperative data of 5 patients to identify the usability, friendliness, limitations and requirements for clinical translation of each technology through a qualitative questionnaire. The obtained results demonstrate the potential impact of advanced visual computing solutions to improve the planning of LAAO interventions but also a need of unification of them in order to be able to be uses in a clinical environment.
The incidence-based dynamic reproduction index: accurate determination, diagnostic sensitivity, and predictive power
Authors: Conradt Robert N. J. , Herminghaus Stephan 
Published: April 2022

Two methods of calculating the reproduction index from daily new infection data are considered, one by using the generation time tG as a shift (RG), and an incidence-based method directly derived from the differential equation system of an SIR epidemic dynamics model (RI). While the former is shown to have few in common with the true reproduction index, we find that the latter provides a sensitive detection device for intervention effects and other events affecting the epidemic, making it well-suited for diagnostic purposes in policy making. Furthermore, we introduce a similar quantity, , which can be calculated directly from RG. It shows largely the same behaviour as RI, with less fine structure. However, it is accurate in particular in the vicinity of R = 1, where accuracy is important for the corrrect prediction of epidemic dynamics. We introduce an entirely new, self-consistent method to derive, from both quantities, an improved which is both accurate and contains the details of the epidemic spreading dynamics. Hence we obtain R accurately from data on daily new infections (incidence) alone. Moreover, by using RI instead of RG in plots of R versus incidence, orbital trajectories of epidemic waves become visible in a particularly insightful way, demonstrating that the widespread use of only incidence as a diagniostic tool is clearly inappropriate.PACS numbers:
COVID-19 vaccine coverage among immigrants and refugees in Alberta: a population-based cross-sectional study
Authors: MacDonald Shannon E. , Paudel Yuba Raj , Du Crystal 
Published: April 2022

AbstractIntroductionStudies have shown that immigrants have lower vaccination rates than the Canadian-born population. We sought to assess COVID-19 vaccine coverage and factors associated with uptake among foreign-born immigrants relative to the non-immigrant population in Alberta, Canada.MethodsIn this cross-sectional study, we analyzed population-based linked administrative health data from Alberta to examine vaccine coverage for 3,931,698 Albertans, of which 731,217 were immigrants. We calculated COVID-19 vaccination coverage as the proportion of eligible Albertans with a record of receiving at least one dose of a COVID-19 vaccine as of November 29, 2021. We used multivariable logistic regression to examine the association of vaccine coverage with migration status (immigrants: four categories based on time since migration and non-immigrants) adjusting for socio-demographic variables.ResultsOverall, COVID-19 vaccination coverage was higher among immigrants (78.2%; 95% CI: 78.1%-78.3%) compared to non-immigrants (76.0%; 95% CI: 75.9%-76.0%). Coverage among immigrants differed by continent of origin, with North America, Oceania, and Europe having the lowest coverage. Although vaccine coverage was relatively uniform across neighborhood income quintiles for immigrants, immigrants living in rural areas had lower vaccine coverage compared to non-immigrants living in rural areas. Multivariable logistic regression analysis showed a significant interaction between age category and migration status. While immigrants below 50 years of age generally had significantly higher vaccine coverage compared to non-immigrants, there was some variation based on time since migration. Immigrants above 50 years of age showed significantly lower coverage compared to non-immigrants of the same age.ConclusionPublic health interventions should focus on older immigrants, immigrants living in rural areas, and immigrants from specific continental backgrounds in order to improve COVID-19 vaccination coverage.
Investigation of the association between high arachidonic acid synthesis and colorectal polyp incidence: a Mendelian randomisation approach
Authors: Moon Rachel , Moore J. Bernadette , Hull Mark A. , Zulyniak Michael A. 
Published: April 2022

ABSTRACTBackground & AimsArachidonic acid (ARA) is causally associated with colorectal cancer (CRC), a major public health concern. However, it is uncertain if ARA contributes to the development of colorectal polyps which are pre-malignant precursors of CRC. Therefore, this study aimed to investigate the association between lifelong exposure to elevated ARA and colorectal polyp incidence using Mendelian randomisation.MethodsSummary level GWAS data from European, Singaporean, and Chinese cohorts (n=10,171) identified 4 single nucleotide polymorphisms (SNPs) associated with blood ARA levels (p< 5 × 10−8). After pruning, 1 SNP was retained (rs174547; p=3.0×10−971) for 2-stage Mendelian randomisation to infer the causal effect of ARA on self-reported colorectal polyp outcomes within the UK Biobank (1,391 cases; 462,933 total).ResultsNo association between ARA and colorectal polyp incidence was observed [OR= 1.00 (95% CI: 0.99, 1.00); P-value = 0.50).ConclusionsBlood levels of ARA do not associate with colorectal polyp incidence. This work supports the contention that downstream lipid mediators, such as PGE2, are key for polyp formation during early-stage colorectal carcinogenesis
Discovery of Neurocognitive Phenotypes of Autism By Analyzing Functional Connectivity in the Default Mode Network and Dorsolateral Prefrontal Cortex
Authors: Vasantha Amith 
Published: April 2022

ABSTRACTAutism spectrum disorder (ASD) is a neurodevelopmental disorder usually presenting as reduced social interaction, lessened verbal communication, and repetitive behavior. Diagnosing ASD is extremely difficult because of its wide variety of symptoms, so it can only be diagnosed through behavioral tests and analysis of developmental history. Resting-state fMRI can help researchers discover a neural substrate for ASD to diagnose it earlier. One prominent fMRI database for ASD research is the Autism Brain Imaging Data Exchange, a large-scale collection of anonymized functional MRI scans subdivided by age, gender, handedness, and scores on behavioral assessments.This analysis focused on two brain networks: the default mode network (DMN), which is active when minds wander, and the executive network, which is active during the performance of tasks. The medial prefrontal cortex (mPFC), posterior cingulate cortex (PCC), and angular gyrus are nodes of the DMN, and the dorsolateral prefrontal cortex (DLPFC) is the main node in the executive network. Both networks are affected by ASD.This research used preprocessed resting-state fMRI data to establish neurocognitive phenotypes for ASD. Bivariate correlation was used to compare connectivity in the DMN and DLPFC between ASD and control fMRI scans, and these differences were analyzed for correlations with each patient’s assessment scores. After the Benjamini-Hochberg procedure was applied to reduce the false discovery rate, analysis of these metrics revealed that in ASD patients there was underconnectivity between the right PCC and the right mPFC, while in control patients there was overconnectivity between the right angular gyrus and left DLPFC. ASD is extremely heritable, so phenotypic research is absolutely necessary for discovering more about the genetic causes of ASD, which will speed up ASD diagnosis and help researchers develop more targeted treatments for ASD.