bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Deep Learning Model for Brain Age Prediction Using Minimally Pre-processed T1w-images as Input
Authors: Dartora Caroline , Marseglia Anna , Mårtensson Gustav , Rukh Gull , Dang Junhua , Muehlboeck J-Sebastian , Wahlund Lars-Olof , Moreno Rodrigo , Barroso José , Ferreira Daniel , Schiöth Helgi B. , Westman Eric ,   Alzheimer’s Disease Neuroimaging Initiative,   Australian Imaging Biomarkers and Lifestyle flagship study of ageing,   Japanese Alzheimer’s Disease Neuroimaging Initiative,   AddNeuroMed consortium
Published: September 2022

ABSTRACTIn the last few years, several models trying to calculate the biological brain age have been proposed based on structural magnetic resonance imaging scans (T1-weighted MRIs, T1w) using multivariate methods and artificial intelligence. We developed and validated a convolutional neural network (CNN)-based biological brain age prediction model that uses only one T1w MRI pre-processing step to simplify implementation and increase accessibility in research settings. Our model only requires rigid image registration to the MNI space, which is an advantage compared to previous methods that require more pre-processing steps, such as feature extraction. We used a multicohort dataset of cognitively healthy individuals (age range = 32.0 – 95.7 yrs.) comprising 17296 MRIs for training and evaluation. We compared our model using hold-out (CNN1) and cross-validation (CNN2-4) approaches. To verify generalizability, we used two external datasets with different population and MRI scan characteristics to evaluate the model. To demonstrate its usability, we included the external dataset’s images in the cross-validation training (CNN3). To ensure that our model used only the brain signal on the image, we also predicted brain age using skull-stripped images (CNN4). The trained models achieved a mean absolute error of 2.99, 2.67, 2.67, and 3.08 yrs. for the CNN1-4, respectively. The model’s performance in the external dataset was in the typical range of mean absolute error (MAE) found in the literature for testing sets. Adding the external dataset to the training set (CNN3), overall, MAE is unaffected, but individual cohort MAE improves (2.25 to 5.63 years). Salience maps of predictions reveal that periventricular, temporal, and insular regions are the most important for age prediction. We provide indicators for using biological (predicted) brain age as a metric for age correction in neuroimaging studies as an alternative to the traditional chronological age. In conclusion, using different approaches, our CNN-based model showed good performance using only one T1w brain MRI pre-processing step. The proposed CNN model is made publicly available for the research community to be easily implemented and used to study aging and age-related disorders.
Understanding the Experiences and Needs of LGBTIQA+ Individuals when Accessing Abortion Care and Pregnancy Options Counselling: A scoping review
Authors: Bowler Sally , Vallury Kari , Sofija Ernesta 
Published: September 2022

AbstractBackgroundSafe, accessible, and inclusive abortion care and pregnancy options counselling are essential components of sexual and reproductive health and rights. Recent research has documented LGBTIQA+ people are as or more likely than the general population of women to experience an abortion in their lifetime yet face significant barriers to accessing abortion and related care which undermine wellbeing.AimsThe present study undertakes a scoping review of research on the needs and experiences of the LGBTIQA+ population when accessing abortion care, pregnancy options, and post-abortion counselling, to support improved understanding of pregnant people’s preferences, needs, and experiences.Materials and MethodsOnline academic databases were searched using terms relating to gender identity and sexuality, abortion, pregnancy-options, and post-abortion counselling to identify peer reviewed papers published in English, from which we selected six publications from the United States, and one from Colombia that described experiences of LGBTIQA+ people accessing abortion-related care.ResultsFour of the seven studies reported in-depth or semi-structured interview studies while the remaining three examined cross-sectional surveys. Thematic analysis of all studies highlighted frequent discrimination and exclusion experienced by participants, healthcare avoidance, unsafe abortion, non-disclosure to providers, provision of poor quality of care, and poor health outcomes for LGBTIQA+ people.ConclusionsGender-inclusive services and training for health providers are key to the provision of safe and accessible abortion care, and imperative to overcome generations of mistrust held by the LGBTIQA+ community. Research into the needs of LGBTIQA+ people when accessing pregnancy options counselling is critically needed.Key messagesLGBTIQA+ people experience exclusion, isolation, misgendering, and denial of care when accessing abortion, and barriers faced are compounded by socioeconomic status and race.Poor provision of abortion care and negative experiences for this population result in deep mistrust of providers, non-disclosure of gender/sexuality, healthcare avoidance, and self-induced abortion.Appropriate, inclusive, and accessible care requires gender affirming and inclusive services, educational materials, and intake forms, community consultation, and improved healthcare provider training and knowledge.
“Just Saiyan: Tail-trimming Human Monkeypox Virus Assemblies Emphasizes Resolvable Regions in Inverted Terminal Repeats to Improve the Resolution of Reference and Production Genomes for Genomic Surveillance”
Authors: Gener Alejandro R. 
Published: September 2022

AbstractOur ability to track the spread of the human monkeypox virus (hMPXV) during the ongoing monkeypox (hMPX) outbreak of 2022 relies on the availability of high-quality reference genomes. However, the way the information content of these genomes is organized in genome databases leaves room for interpretation. A current limitation of hMPXV genomic analysis is that the variability occurring in the inverted terminal repeats (ITRs) cannot be effectively resolved. This is because of shortcomings of the leading short-read sequencing and reference-guided assembly and variant calling used in the ongoing global hMPXV outbreak surveillance effort. Here I propose ITR tail-trimming, a simple no-cost reframing of how we organize hMPXV reference genomes and future assemblies. This approach is based on long terminal repeat (LTR) tail-trimming, which is a common practice in HIV sequence analysis. The main point of repeat sequence trimming is to remove problematic sequences while paying attention to limitations of mapping and variant calling in remaining repeat-associated (but ideally no longer repetitive) sequence. ITR tail-trimming would neutralize ITRs as distracting features at the read- and assembly-levels, allowing the global community to focus our efforts to track variability across hMPXV genomes.
Hierarchical Two-Stage Cost-Sensitive Clinical Decision Support System for Screening Prodromal Alzheimer’s Disease and Related Dementias
Authors: Kleiman Michael J. , Ariko Taylor , Galvin James E. ,   the Alzheimer’s Disease Neuroimaging Initiative
Published: September 2022

ABSTRACTBackgroundThe detection of subtle cognitive impairment in a clinical setting is difficult, and because time is a key factor in small clinics and research sites, the brief cognitive assessments that are relied upon often misclassify patients with very mild impairment as normal. In this study, we seek to identify a parsimonious screening tool in one stage, followed by additional assessments in an optional second stage if additional specificity is desired, tested using a machine learning algorithm capable of being integrated into a clinical decision support system.MethodsThe best primary stage incorporated measures of short-term memory, executive and visuospatial functioning, and self-reported memory and daily living questions, with a total time of 5 minutes. The best secondary stage incorporated a measure of neurobiology as well as additional cognitive assessment and brief informant report questionnaires, totaling 30 minutes including delayed recall. Combined performance was evaluated using 25 sets of models, trained on 1181 ADNI participants and tested on 127 patients from a memory clinic.ResultsThe 5-minute primary stage was highly sensitive (96.5%) but lacked specificity (34.1%), with an AUC of 87.5% and DOR of 14.3. The optional secondary stage increased specificity to 58.6%, resulting in an overall AUC of 89.7% using the best model combination of logistic regression for stage 1 and gradient-boosted machine for stage 2.ConclusionsThe primary stage is brief and effective at screening, with the optional two-stage technique further increasing specificity. The hierarchical two-stage technique exhibited similar accuracy but with reduced costs compared to the more common single-stage paradigm.
Genomic epidemiology of SARS-CoV-2 infections in The Gambia, March 2020 to Jan 2022
Authors: Kanteh Abdoulie , Jallow Haruna S. , Manneh Jarra , Sanyang Bakary , Kujabi Mariama A. , Ndure Sainabou Laye , Jarju Sheikh , Sey Alhagie Papa , Damilare Dabiri K , Bah Yaya , Sambou Sana , Jarju Gibril , Manjang Buba , Jagne Abubacarr , Bittaye Sheikh Omar , Bittaye Mustapha , Forrest Karen , Tiruneh Desta Alamerew , Samateh Ahmadou Lamin , Jange Sheriffo , Hué Stéphane , Muhammed Nuredin , Amambua-Ngwa Alfred , Kampmann Beate , D’Alessandro Umberto , de Silva Thushan I. , Roca Anna , Sesay Abdul Karim 
Published: September 2022

AbstractBackgroundCOVID-19, caused by SARS-CoV-2, is one of the deadliest pandemics over the last 100 years. Sequencing is playing an important role in monitoring the evolution of the virus, including the detection of new viral variants. This study describes the genomic epidemiology of SARS-CoV-2 infections in The Gambia.MethodsNasopharyngeal and/or oropharyngeal swabs collected from suspected cases and travellers were tested for SARS-CoV-2 using standard RT-PCR methods. SARS-CoV-2 positive samples were sequenced following standard library preparation and sequencing protocols. Bioinformatic analysis was done using ARTIC pipelines and lineages assigned using Pangolin.FindingsBetween March 2020 to January 2022, there were almost 12,000 SARS-CoV-2 confirmed cases distributed into four waves, each of them lasting between 4 weeks and 4 months, with more cases during the rainy seasons (July-October). As shown by the 1643 sequenced samples, each wave occurred after new viral variants and/or lineages were introduced in The Gambia, generally those already established in Europe and/or in other African countries. Local transmission was higher during the first and third wave, with mostly B.1.416/Senegal/Gambian lineage and AY.34.1/Delta subtype, respectively. The second wave was driven by two variants, namely Alpha and Eta and B.1.1.420 lineage. The Omicron/fourth wave was the shortest.InterpretationEfficient surveillance, including strengthening entry points and screening asymptomatic individuals especially during the rainy seasons would be important to promptly detect and control future waves in The Gambia and the subregion.FundingMedical Research Unit The Gambia at LSHTM, UK Research and Innovation funding (grant reference MC_PC_19084), MRC/UKRI MC_PC_19084 and World Health Organisation.
Screening the use of DCA for the treatment of cancer in adult patients: a scoping review protocol
Authors: Bianchi Cecilia , Martinelli Romina P , Rozados Viviana R , Scharovsky O Graciela 
Published: September 2022

AbstractSodium dichloroacetate (DCA), a small-molecular-weight drug, is capable to shift the tumor metabolism by reactivating the oxidative phosphorylation in the mitochondria. As a consequence, apoptosis resistance in cancer cells decreased. Numerous studies have been performed in cell lines and animal models, to unveil its efficacy as an antitumor drug. It is also being studied in patients with different types of tumors, with a variety of doses and administration schedules. Even so, the lack of controlled studies makes the safety profile a concern. This scoping review aims to explore the existing scientific literature to provide an overview of the use of DCA (any dose, frequency, or route of administration) in adults with cancer. The search will be performed in MEDLINE/PubMed, and LILACS databases.Additional data sources will be consulted. Two reviewers will screen all identified records for relevance, and chart the data using a data charting form. Findings will be reported according to PRISMA for Scoping Reviews (PRISMA-ScR). No quality assessment will be performed.
The profile and distribution of skin disorders in ambulatory community-dwelling adult patients with Schizophrenia: a study from North India
Authors: Varadharajan Natarajan , Narang Tarun , Rani Seema , Mehta Hitaishi , Kathiravan Sanjana , Singh Shubh Mohan 
Published: September 2022

AbstractIntroductionSchizophrenia is a severe mental disorder. There is ample evidence to suggest that there are various multi-systemic co-morbidities in the patients with schizophrenia. However, data for dermatological comorbidities in these patients is scarce. This is relevant because of the common embryological basis of the central nervous system and skin, and also the disabling nature of schizophrenia itself.ObjectiveTo analyze the profile and distribution of cutaneous conditions in patients with schizophrenia.MethodsConsecutive adult patients with schizophrenia attending the follow-up service of the outpatient clinic of the department of psychiatry of a tertiary hospital in North India were evaluated for the presence of a skin disorder by a dermatologist.ResultsDermatological findings were seen in 71 patients (69.60%), 39 patients (38.23%) had multiple skin conditions. As a group, infections were the most prevalent diagnosis seen in 18 patients (17.64%) and fungal infections were commonly observed (n=14, 13.72%). Other common dermatoses were nevi, age related cutaneous changes, dyschromias and drug-induced acne. Among medical disorders, blood pressure was found to be elevated in 28 patients (27.45%) while sixty-four patients (69.74%) were either overweight or obese.ConclusionA high prevalence of dermatological diseases is seen in patients with schizophrenia. Both caregivers and psychiatrists managing these patients should familiarize themselves with these conditions and dermatology consultation should be sought for the prompt diagnosis and management.
The SumRank method efficiently detects valid pleiotropic variants using GWAS summary level data
Authors: Lamballais Sander , Roshchupkin Gennady V. , Poot Raymond A. , Kushner Steven A. , Ikram M. Arfan , Adams Hieab H. H. , Tiemeier Henning 
Published: September 2022

ABSTRACTGenome-wide association studies (GWASs) have illustrated that pleiotropy is the norm rather than the exception in the genetic architecture of complex traits. Previous methods have been proposed to investigate cross-trait associations; however, these typically suffer from substantially inflated false positive rates, are limited to associations between only two traits, or examine only a subset of genome-wide variants. Here, we introduce SumRank, a novel method for discovering cross-trait associations based on p-values from GWAS summary statistics. Using numerical and genotype simulations, we demonstrated that SumRank had a near-zero false positive rate, in contrast to contemporary meta-analytical approaches that yielded severely inflated rates. We applied SumRank to GWAS summary data of eight psychiatric disorders and identified 515 independent pleiotropic variants across 175 loci, of which 92 were novel and 71 had previously been associated with only one disorder. Overall, SumRank provides a valid and efficient method for genome-wide discovery of pleiotropic variants that underlie a scalable number of traits.
Brain-Based Gene Expression of Putative Risk Genes for Anorexia Nervosa in the Human Brain
Authors: Murray Stuart B. , Rokicki Jaroslav , Sartorius Alina , Winterton Adriano , Andreassen Ole A. , Westlye Lars T. , Nagata Jason M. , Quintana Daniel S. 
Published: September 2022

AbstractThe etiology of anorexia nervosa (AN) remains elusive. Here, we characterize spatially distributed expression patterns of risk genes for AN in the human brain, developing whole-brain maps of AN gene expression. We found that genes associated with AN are most expressed in the brain, relative to all other body tissue types, and demonstrate gene-specific expression patterns which extend to cerebellar, limbic and basal ganglia structures in particular. fMRI meta-analyses reveal that AN gene expression maps correspond with functional brain activity involved in processing and anticipating appetitive and aversive cues.
Safety and immunogenicity of a third dose of COVID-19 protein subunit vaccine (Covovax™) after homologous and heterologous two-dose regimens
Authors: Kanokudom Sitthichai , Chansaenroj Jira , Suntronwong Nungruthai , Assawakosri Suvichada , Yorsaeng Ritthideach , Nilyanimit Pornjarim , Aeemjinda Ratchadawan , Khanarat Nongkanok , Vichaiwattana Preeyaporn , Klinfueng Sirapa , Thongmee Thanunrat , Katanyutanon Apirat , Thanasopon Wichai , Arayapong Jirawan , Withaksabut Withak , Srimuan Donchida , Thatsanatorn Thaksaporn , Sudhinaraset Natthinee , Wanlapakorn Nasamon , Honsawek Sittisak , Poovorawan Yong 
Published: September 2022

AbstractObjectiveTo report the safety and immunogenicity profile of a protein subunit vaccine (Covovax™) given as a third (booster) dose to individuals primed with different primary vaccine regimens.MethodsIndividuals primed with two doses of COVID-19 vaccines for at least 3 months were enrolled and assigned to five groups according to their primary vaccine regimens: CoronaVac, BBIBP-CorV, AZD1222, BNT162b2, and CoronaVac/AZD1222. Immunogenicity analysis was performed to determine binding antibodies, neutralizing activity, and the T-cell response.ResultsOverall, 215 individuals were enrolled and boosted with the Covovax™ vaccine. The reactogenicity achieved was mild-to-moderate. Most participants elicited a high level of binding and neutralizing antibody responses against wild type and omicron variants following the booster dose. The 197 participants were classified by anti-N IgG. Of these, 141/197 (71.6%) were a seronegative population, and neutralizing activity and IFN-γ release were further monitored. A booster dose could elicit neutralizing activity to wild type and omicron variants by more than 95% and 70% inhibition at 28 days, respectively. The Covovax™ vaccine could elicit a cell-mediated immune response.ConclusionThe protein subunit vaccine (Covovax™) can be proposed as a booster dose after two different priming dose regimens. It has strong immunogenicity and good safety profiles.
A JOURNEY THROUGH RURAL COMMUNITY RADIOGRAPHY PRACTICE IN SOUTH-SOUTH NIGERIA: RADIOGRAPHERS’ PERCEPTION, WILLINGNESS AND BARRIERS
Authors: Ogolodom Michael Promise , Mbaba Awajimijan Nathaniel , Maduka Beatrice Ukamaka , Iloka Chima Jude , Erondu Ikechukwu Felix , Eja-Egwu Uche Nathaniel , Alazigha Nengi , Brownson Egop Egop , Nwodo Victor Kelechi , Akhigbe Robert O. 
Published: September 2022

ABSTRACTIntroductionThe lack of healthcare professionals and their retention in rural areas has become a serious concern to the health sector globally. Retaining health staff in rural areas has proven difficult as young professionals prefer urban postings. This study aimed to assess radiographers’ perception and willingness to work in rural areas of Rivers State.MethodThis cross-sectional questionnaire-based study was conducted among radiographers in Rivers State. The participants’ socio-demographic variables and their responses to willingness and perception to work in rural areas were obtained and analyzed.ResultsOnly few 30% (n=12) of the respondents were willing to work in the rural areas of Rivers state. However, the majority of 95 %(n=38) of the respondents perceived extra payment as an incentive for them to be willing to work in the rural areas of this study location. Most 88 %(n=35) of the respondents perceived unfavorable working conditions in rural areas as a barrier to their willingness. A large proportion of 55 %(n=22) of the respondents stated that their marital status was a barrier to working in rural areas. More than half (85%, n=34) of the respondents perceived poor accommodation as a barrier to working in rural areas. The majority 88% (n=35) of the respondents stated that militant activities was a barrier to their willingness to work in the rural areas of Rivers State. There were statistically significant relationships between the evaluated respondent’s socio-demographic variables gender (χ2 = 48.000, p = 0.000), years of working experience (χ2 = 47.500, p = 0.000), marital status (χ2 = 84.966, p = 0.000) and age (χ2 = 76.758, p = 0.021) and their willingness to work in the rural areas of Rivers State.ConclusionThe key findings suggest that the majority of the Radiographers were not willing to work in the rural areas of Rivers State. The reasons adduced for their strong disinclination were based on their perception of unfavorable working conditions in the rural areas. Nonetheless, they were of the opinion that financial inducement could influence their willingness to work in rural areas.
Higher-order epistasis creates idiosyncrasy, confounding predictions in protein evolution
Authors: Buda Karol , Miton Charlotte M. , Tokuriki Nobuhiko 
Published: September 2022

AbstractEpistasis shapes evolutionary outcomes during protein adaptation. In particular, when the effects of single mutations or mutational interactions are idiosyncratic, that is, unique to a genetic background, the predictability of protein evolution becomes greatly impaired. Here, we unveil a quantitative picture of the prevalence and role of idiosyncrasy in protein evolution by analysing 45 protein fitness landscapes, generated from seven enzymes. We found that mutational effects and epistasis are highly idiosyncratic across the landscapes. Idiosyncrasy obscured functional predictions of mutated proteins when using limited mutational data, and often continued to impair prediction upon incorporation of epistatic information. We show that idiosyncrasy stems from higher-order epistasis, and highlight examples where it permits, or restricts, evolutionary accessibility of certain genotypes. Our work suggests that idiosyncrasy deeply confounds predictions in protein evolution necessitating its incorporation into predictive models and in-depth exploration of its underlying molecular mechanisms.