bluuebunny/crossref_metadata_2025_split huggingface dataset:
Feasibility of 4D VMAT-CT
Authors: Zhao Xiaodong , Zhang Rui 
Published: October 2022

Abstract

Objective. Feasibility of three-dimensional (3D) tracking of volumetric modulated arc therapy (VMAT) based on VMAT–computed tomography (VMAT-CT) has been shown previously by our group. However, 3D VMAT-CT is not suitable for treatments that involve significant target movement due to patient breathing. The goal of this study was to reconstruct four-dimensional (4D) VMAT-CT and evaluate the feasibility of tracking based on 4D VMAT-CT. Approach. Synchronized portal images of phantoms and linac log were both sorted into four phases, and VMAT-CT+ was generated in each phase by fusing reconstructed VMAT-CT and planning CT using rigid or deformable registration. Dose was calculated in each phase and was registered to the mean position planning CT for 4D dose reconstruction. Trackings based on 4D VMAT-CT+ and 4D cone beam CT (CBCT) were compared. Potential uncertainties were also evaluated. Main results. Tracking based on 4D VMAT-CT+ was accurate, could detect phantom deformation and/or change of breathing pattern, and was superior to that based on 4D CBCT. The impact of uncertainties on tracking was minimal. Significance. Our study shows it is feasible to accurately track position and dose based on 4D VMAT-CT for patients whose VMAT treatments are subject to respiratory motion. It will significantly increase the confidence of VMAT and is a clinically viable solution to daily patient positioning, in vivo dosimetry and treatment monitoring.
Genome analysis of a plastisphere-associated Oceanimonas sp. NSJ1 sequenced on Nanopore MinION platform
Authors: Saini Nirupama , Bhadury Punyasloke 
Published: October 2022

Abstract

Oceanimonas sp. NSJ1 was isolated from macroplastic debris collected previously from Junput, an intertidal beach, facing the northeast coastal Bay of Bengal of the Northern Indian Ocean. The genome of this isolate is closely related to Oceanimonas doudoroffii with a genome size of 3.56 Mbp. The genome annotation confirmed the presence of 5919 total genes, out of which 5809 were CDSs (coding sequences) and all are protein-coding. The genome codes for 110 RNA with 25 rRNA, 84 tRNA (transfer RNA), and one tmRNA (transfer-messenger RNA). Analyses of the annotated genome of Oceanimonas sp. NSJ1 revealed the presence of enzymes involved in the degradation of polycyclic aromatic hydrocarbons. The presence of phthalate 4,5-dioxygenase oxygenase reductase subunit pht2 within the genome also highlights the novelty of this isolate and future functional potential for studying phthalate degradation in marine environment.
A systematic review and meta-analysis of reablement interventions for people in permanent residential aged care homes
Authors: Rahja Miia , Laver Kate , Whitehead Craig , Pietsch Ann , Oliver Eliza , Crotty Maria 
Published: October 2022

Abstract

Background
Most evidence for reablement comes from community-based interventions.

Objective
To determine the effect of reablement interventions provided in permanent residential aged care (PRAC) homes on residents’ level of function in activities of daily living (ADL) and quality of life (QoL).

Design
Systematic review and meta-analysis.

Setting
PRAC homes.

Subjects
Residents in PRAC.

Methods
Six databases and grey literature were searched until November 2021. Quantitative studies involving a control group or pre-post evaluation were included. Outcomes of interest were the effectiveness of the reablement intervention on overall ADL or QoL in the last available follow-up.

Results
Twelve studies involving 2,620 residents were included. The reablement interventions varied; the primary focus areas were organisational approaches (e.g. educating staff; n = 10) and improving physical function (e.g. increasing physical activity; n = 9). Not all studies could be pooled in the meta-analysis due to reported data and heterogeneity. There was no significant effect of reablement intervention versus usual care on ADL function (five studies, standardised mean difference (SMD): 0.17, 95% confidence interval (CI): −0.25 to 0.59, very low quality evidence). Reablement appeared more beneficial than usual care in improving QoL; however, the overall effect was not statistically significant (four studies, SMD: 0.73, 95% CI: −0.07 to 1.52; very low quality evidence).

Conclusions
Few studies focus on reablement in PRAC homes and their clinical heterogeneity is considerable. There is insufficient evidence for reablement in terms of improving ADL or QoL for residents in PRAC. Tools that are more sensitive to change may be beneficial.
Sarcopenia definition, diagnosis and treatment: consensus is growing
Authors: Sayer Avan Aihie , Cruz-Jentoft Alfonso 
Published: October 2022

Abstract
Sarcopenia is a skeletal muscle disorder that commonly occurs with advancing age as well as with a number of long-term conditions. Recognition in clinical practice is relatively recent but important because of the association between sarcopenia and a range of adverse effects on health including impaired mobility, increased morbidity and mortality. Originally characterised as loss of muscle mass, the definition has evolved to focus on loss of skeletal muscle function, particularly strength, through a number of international definitions such as that of the European Working Group on Sarcopenia in Older People most recently revised in 2019. Progress in the decades ahead is likely to be seen with regard to use of routine health data, prescription of resistance exercise, translation of biology and epidemiology into first in man studies for new treatments, and focus on sarcopenia in low and middle-income countries. Immediate next steps include the newly formed Global Leadership Initiative on Sarcopenia to develop international consensus on definition and diagnosis.
The Impact of COVID-19 on the All of Us Research Program
Authors: Hedden Sarra L , McClain James , Mandich Allison , Baskir Rubin , Caulder Mark S , Denny Joshua C , Hamlet Michelle R J , Prabhu Das Irene , McNeil Ford Nicole , Lopez-Class Maria , Elmi Ahmed , Wallace Roshedah , Linkie Amantha , Garriock Holly A 
Published: October 2022

Abstract
The All of Us Research Program, a health and genetics epidemiologic data collection program, has been substantially affected by the coronavirus disease 2019 (COVID-19) pandemic. Although the program is highly digital in nature, certain aspects of the data collection require in-person interaction between staff and participants. Before the pandemic, the program was enrolling approximately 12,500 participants per month at more than 400 clinical sites. In March 2020, because of the pandemic, all in-person activity at program sites and by engagement partners was paused to develop processes and procedures for in-person activities that incorporated strict safety protocols. In addition, the program adopted new data collection methodologies to reduce the need for in-person activities. Through February 2022, a total of 224 clinical sites had reactivated in-person activity, and all enrollment and engagement partners have adopted new data collection methods that can be used remotely. As the COVID-19 pandemic persists, the program continues to require safety procedures for in-person activity and continues to generate and pilot methodologies that reduce risk and make it easier for participants to provide information.
Provider beliefs about the ideal design of an opioid deprescribing and substitution intervention for older adults
Authors: Margraf Alissa M , Davoodi Natalie M , Chen Kevin , Shield Renee R , McAuliffe Laura M , Collins Christine M , Zullo Andrew R 
Published: October 2022

Abstract

Purpose
Opportunities exist to meaningfully reduce suboptimal prescription opioid use among older adults. Deprescribing is one possible approach to reducing suboptimal use. Appropriate interventions should outline how to carefully taper opioids, closely monitor adverse events, substitute viable alternative and affordable nonopioid pain treatments, and initiate medications for opioid use disorder to properly manage use disorders, as needed. We sought to document and understand provider perceptions to begin developing effective and safe opioid deprescribing interventions.

Methods
We conducted 3 semistructured focus groups that covered topics such as participant perspectives on opioid deprescribing in older adults, how to design an ideal intervention, and how to identify potential barriers or facilitators in implementing an intervention. Focus group transcripts were double coded and qualitatively analyzed to identify overarching themes.

Results
Healthcare providers (n = 17), including physicians, pharmacists, nurses, social workers, and administrative staff, participated in 3 focus groups. We identified 4 key themes: (1) involve pharmacists in deprescribing and empower them as leaders of an opioid deprescribing service; (2) ensure tight integration and close collaboration throughout the deprescribing process from the inpatient to outpatient settings; (3) more expansive inclusion criteria than age alone; and (4) provision of access to alternative pharmacological and nonpharmacological pain management modalities to patients.

Conclusion
Our findings, which highlight various healthcare provider beliefs about opioid deprescribing interventions, are expected to serve as a framework for other organizations to develop and implement interventions. Future studies should incorporate patients’ and family caregivers’ perspectives.
Black and orange coloration predict success during male–male competition in the guppy
Authors: Guerrera Alexa G , Daniel M J , Hughes K A 
Published: October 2022

AbstractInvestigating how intrasexual competition and intersexual mate choice act within a system is crucial to understanding the maintenance and diversity of sexually-dimorphic traits. These two processes can act in concert by selecting for the same trait, or in opposition by selecting for different extremes of the same trait; they can also act on different traits, potentially increasing trait complexity. We asked whether male–male competition and female mate choice act on the same male traits using Trinidadian guppies, which exhibit sexual size dimorphism and male-limited color patterns consisting of different colors arranged along the body and fins. We used behavioral assays to assess the relationship between color and competitive success and then compared our results to the plethora of data on female choice and color in our study population. Males initiated more contests if they were larger than their competitor. Males won contests more often if they had more black coloration than their competitor, and the effect of black was stronger when males had less orange than their competitor. Additionally, males won more often if they had either more structural color (iridescence) and more orange, or less structural color and less orange than their competitor, suggesting multiple combinations of color traits predict success. Females from our study population exhibit a strong preference for more orange coloration. Thus, traits favored in male contests differ from those favored by intersexual selection in this population. These results suggest that inter- and intrasexual selection, when acting concurrently, can promote increased complexity of sexually selected traits.
Leveraging a pharmacogenomics knowledgebase to formulate a drug response phenotype terminology for genomic medicine
Authors: Zhao Yiqing , Brush Matthew , Wang Chen , Wagner Alex H , Liu Hongfang , Freimuth Robert R 
Published: October 2022

Abstract

Motivation
Despite the increasing evidence of utility of genomic medicine in clinical practice, systematically integrating genomic medicine information and knowledge into clinical systems with a high-level of consistency, scalability and computability remains challenging. A comprehensive terminology is required for relevant concepts and the associated knowledge model for representing relationships. In this study, we leveraged PharmGKB, a comprehensive pharmacogenomics (PGx) knowledgebase, to formulate a terminology for drug response phenotypes that can represent relationships between genetic variants and treatments. We evaluated coverage of the terminology through manual review of a randomly selected subset of 200 sentences extracted from genetic reports that contained concepts for ‘Genes and Gene Products’ and ‘Treatments’.

Results
Results showed that our proposed drug response phenotype terminology could cover 96% of the drug response phenotypes in genetic reports. Among 18 653 sentences that contained both ‘Genes and Gene Products’ and ‘Treatments’, 3011 sentences were able to be mapped to a drug response phenotype in our proposed terminology, among which the most discussed drug response phenotypes were response (994), sensitivity (829) and survival (332). In addition, we were able to re-analyze genetic report context incorporating the proposed terminology and enrich our previously proposed PGx knowledge model to reveal relationships between genetic variants and treatments. In conclusion, we proposed a drug response phenotype terminology that enhanced structured knowledge representation of genomic medicine.

Supplementary information
Supplementary data are available at Bioinformatics online.
Improved pre-test likelihood estimation of coronary artery disease using phonocardiography
Authors: Larsen Bjarke Skogstad , Winther Simon , Nissen Louise , Diederichsen Axel , Bøttcher Morten , Renker Matthias , Struijk Johannes Jan , Christensen Mads Græsbøll , Schmidt Samuel Emil 
Published: October 2022

AbstractAimsCurrent early risk stratification of coronary artery disease (CAD) consists of pre-test probability scoring such as the 2019 ESC guidelines on chronic coronary syndromes (ESC2019), which has low specificity and thus rule-out capacity. A newer clinical risk factor model (risk factor-weighted clinical likelihood, RF-CL) showed significantly improved rule-out capacity over the ESC2019 model. The aim of the current study was to investigate if the addition of acoustic features to the RF-CL model could improve the rule-out potential of the best performing clinical risk factor models.Methods and resultsFour studies with heart sound recordings from 2222 patients were pooled and distributed into two data sets: training and test. From a feature bank of 40 acoustic features, a forward-selection technique was used to select three features that were added to the RF-CL model. Using a cutoff of 5% predicted risk of CAD, the developed acoustic-weighted clinical likelihood (A-CL) model showed significantly (P &lt; 0.05) higher specificity of 48.6% than the RF-CL model (specificity of 41.5%) and ESC 2019 model (specificity of 6.9%) while having the same sensitivity of 84.9% as the RF-CL model. Area under the curve of the receiver operating characteristic for the three models was 72.5% for ESC2019, 76.7% for RF-CL, and 79.5% for A-CL.ConclusionThe proposed A-CL model offers significantly improved rule-out capacity over the ESC2019 model and showed better overall performance than the RF-CL model. The addition of acoustic features to the RF-CL model was shown to significantly improve early risk stratification of symptomatic patients suspected of having stable CAD.
Effect of an enzyme-containing mouthwash on the dental biofilm and salivary microbiome in patients with fixed orthodontic appliances: a randomized placebo-controlled pilot trial
Authors: Hoffstedt Tove , Skov Hansen Lea Benedicte , Twetman Svante , Sonesson Mikael 
Published: October 2022

SummaryBackgroundMouthwashes containing oral antiseptics or enzymes are suggested suitable for controlling biofilm accumulation in patients with fixed appliances and thereby limiting unwanted side effects during the orthodontic treatment.ObjectivesTo evaluate the effect of an enzyme-based mouthwash on the amount of dental biofilm and the composition of the salivary microbiome in patients undergoing treatment with fixed orthodontic appliances.Trial designRandomized double-blind placebo-controlled trial.Material and methodsIn total, 35 young adolescents (14–18 years) under treatment with fixed appliances were consecutively enrolled and randomly allocated to an experimental or a placebo group by opening a computer-generated numbered envelope. The subjects were instructed to rinse twice daily during an intervention period of 8 days with experimental mouthwash or placebo without active enzymes. Unstimulated whole saliva samples were collected at baseline and after 8 days. The participants and examiner were blinded for the allocation. The primary outcome was the Orthodontic Plaque Index (OPI) and the secondary was the composition of the salivary microbiome.ResultsIn total, 28 adolescents (21 females and 7 males) completed the trial and there were no differences in age, clinical, or microbial findings between the test (n = 14) and the placebo group (n = 14) at baseline. We found a decreased OPI in the test group after 8 days and the difference was statistically significant compared with the placebo group (P &lt; 0.05). There were no significant treatment effects on the richness and global composition of the salivary microbiome.HarmsIn total, one participant in the test group claimed nausea and abandoned the project. In total, two participants did not like the taste of the mouthwash but used it as instructed. No other adverse events or side effects were reported.LimitationsShort-term pilot trials may by nature be sensitive for selection and performance biases and are not designed to unveil persisting effects.ConclusionDaily use of enzyme-containing mouthwash reduced the amount of dental biofilm in adolescents under treatment with the fixed orthodontic appliances, without affecting the composition of the salivary microbiota.Ethical approvalApproved by the Regional Ethical Board, Lund, Sweden (Dnr 2020-05221).Clinical Trial RegistrationNCT05033015.
Price minimizing behaviours by smokers in Europe (2006–20): evidence from the International Tobacco Control Project
Authors: Geboers Cloé , Nagelhout Gera E , de Vries Hein , Candel Math J J M , Driezen Pete , Mons Ute , Andler Raphaël , Fong Geoffrey T , Willemsen Marc C 
Published: October 2022

AbstractBackgroundEffectiveness of tobacco taxation can be undermined through smokers applying price-minimizing behaviours rather than quitting or reducing consumption. Common price-minimizing strategies are buying cheaper tobacco [discount brands or roll-your-own (RYO) tobacco], bulk buying and cross-border purchasing. This study analyses trends in and factors associated with such behaviours in four European countries from 2006 to 2020.MethodsData came from adult smokers participating in the International Tobacco Control (ITC) Surveys conducted between 2006 and 2020 in England (9 waves, n = 768–4149), France (4 waves, n = 1415–1735), Germany (5 waves, n = 513–1515) and the Netherlands (10 waves, n = 1191–2177). Country-specific generalized estimating equation regression models were fit to assess trends in smoking RYO tobacco, discount brands, bulk buying and cross-border purchasing within the European Union.ResultsBuying discount brands or RYO tobacco was the most common strategy in all countries, except France. Except for buying discount brands, estimates of price-minimizing behaviours were highest in France (2019: RYO = 27.2%, discount brands = 17.3%, bulk buying = 34.1%, cross-border purchasing = 34.2%), and lowest in Germany (2018: RYO = 18.6%, discount brands = 43.7%, bulk buying = 8.0%, cross-border purchasing = 9.8%). Direction and magnitude of trends differed by country, and behaviour. Young smokers were less likely to buy in bulk. Low-income and low-education smokers were more likely to purchase RYO tobacco or discount brands. The association with discount brands was not found for French low-income smokers.ConclusionsSmoking cheaper tobacco is the most prevalent price-minimizing strategy in three countries (England, Germany and Netherlands), and more prevalent among low-income individuals. Harmonizing prices across products and countries would reduce switching to cheaper tobacco.
Psychiatric and neurodevelopmental diagnoses in adolescence and adulthood over-indebtedness among Finns born in 1987
Authors: Hiilamo Aapo , Keski-Säntti Markus , Pirkola Sami , Lallukka Tea , Kääriälä Antti 
Published: October 2022

Abstract

Background
Adolescence psychiatric and neurodevelopmental diagnoses are common but their link to adulthood over-indebtedness is unknown. This study aims to determine this relationship and explores the possible mediating role of upper secondary education completion.

Methods
We analyzed the 1987 Finnish Birth Cohort, which consisted of a complete census of children born in Finland in 1987 and registered in the Medical Birth Register (n = 53 743). Records of debt payment defaults, at the age of 33, were used as a measure of over-indebtedness. Adolescent psychiatric and neurodevelopmental diagnoses at ages 13–17 were derived from the national hospital discharge register. Inverse probability treatment weighting was used to investigate the role of pre-exposure variables in this relationship, and the mediating role of upper secondary education completion.

Results
Compared to unexposed individuals, those affected by an adolescent psychiatric or neurodevelopmental diagnosis had a 15 percentage points higher prevalence of over-indebtedness in adulthood. This association was more common for males and was additionally notably strong for suicidality and conduct and oppositional disorders. Controlling for measured potential confounding factors, the diagnoses were linked to a 11-percentage point (95% confidence interval 9–12) higher risk of over-indebtedness. Completing at least upper secondary education reduced this effect by some 39%.

Conclusion
People with psychiatric and neurodevelopmental disorders diagnosed in adolescence are at elevated risk of over-indebtedness in adulthood. Recognizing this high risk may help in efforts to prevent further debt problems. Better education may serve as a protective factor against over-indebtedness and perhaps similar other behavioural consequences.
Adjuvants to increase immunogenicity of SARS-CoV-2 RBD and support maternal–fetal transference of antibodies in mice
Authors: Lima Gabrielle Gimenes , Portilho Amanda Izeli , De Gaspari Elizabeth 
Published: October 2022

Abstract
Adjuvants are important components of vaccines, increasing immunogenicity and modulating the immune response. SARS-CoV-2 vaccines are still being developed in order to improve worldwide access to immunization. Specific populations should be addressed in these investigations, such as pregnant women—to protect both mothers and neonates. In this study, female adult mice were immunized with Receptor-binding domain (RBD) from SARS-CoV-2 adjuvanted by a mixture of DDA and Saponin and put to mating to verify the maternal transference of IgG. For comparison, other group received RBD adjuvanted by OMVs from Neisseria meningitidis and Alum. The adjuvants enhanced IgG production and neutralization. DDA/Sap contributed to increase IgG1, IgG2a, IgG2b, and IgG3 isotypes. Total IgG avidity was considered high, as well as IgG1, IgG2a, and IgG2b avidity. IgG antibodies were effectively transferred to the offspring, predominantly IgG2a, IgG2b, and IgG3. The passive transferred immunoglobulin maintained the neutralizing ability, although it lost avidity. ELISA data was confirmed in Dot-ELISA and immunoblotting assays. DDA and Saponin seem a promising adjuvant mixture to enhance the humoral response of SARS-CoV-2 antigens. Further studies considering the effects of maternal immunization in the protection of offspring are needed, regardless the platform used in COVID-19 vaccines.