bluuebunny/crossref_metadata_2025_split huggingface dataset:
Infectious disease phylodynamics with occurrence data
Authors: Featherstone Leo A. , Di Giallonardo Francesca , Holmes Edward C. , Vaughan Timothy G. , Duchêne Sebastián 
Published: April 2021

Abstract

Phylodynamic models use pathogen genome sequence data to infer epidemiological dynamics. With the increasing genomic surveillance of pathogens, especially during the SARS‐CoV‐2 pandemic, new practical questions about their use are emerging.

One such question focuses on the inclusion of un‐sequenced case occurrence data alongside sequenced data to improve phylodynamic analyses. This approach can be particularly valuable if sequencing efforts vary over time.

Using simulations, we demonstrate that birth–death phylodynamic models can employ occurrence data to eliminate bias in estimates of the basic reproductive number due to misspecification of the sampling process. In contrast, the coalescent exponential model is robust to such sampling biases, but in the absence of a sampling model it cannot exploit occurrence data. Subsequent analysis of the SARS‐CoV‐2 epidemic in the northwest USA supports these results.

We conclude that occurrence data are a valuable source of information in combination with birth–death models. These data should be used to bolster phylodynamic analyses of infectious diseases and other rapidly spreading species in the future.
Severe mental illness is associated with increased mortality and severe course of COVID‐19
Authors: Barcella Carlo Alberto , Polcwiartek Christoffer , Mohr Grimur Høgnason , Hodges Gethin , Søndergaard Kathrine , Niels Bang Casper , Andersen Mikkel Porsborg , Fosbøl Emil , Køber Lars , Schou Morten , Torp‐Pedersen Christian , Kessing Lars Vedel , Gislason Gunnar , Kragholm Kristian 
Published: April 2021

AbstractObjectivePsychiatric disorders have been associated with unfavourable outcome following respiratory infections. Whether this also applies to coronavirus disease 2019 (COVID‐19) has been scarcely investigated.MethodsUsing the Danish administrative databases, we identified all patients with a positive real‐time reverse transcription‐polymerase chain reaction test for COVID‐19 in Denmark up to and including 2 January 2021. Multivariable cox regression was used to calculate 30‐day absolute risk and average risk ratio (ARR) for the composite end point of death from any cause and severe COVID‐19 associated with psychiatric disorders, defined using both hospital diagnoses and redemption of psychotropic drugs.ResultsWe included 144,321 patients with COVID‐19. Compared with patients without psychiatric disorders, the standardized ARR of the composite outcome was significantly increased for patients with severe mental illness including schizophrenia spectrum disorders 2.43 (95% confidence interval [CI], 1.79–3.07), bipolar disorder 2.11 (95% CI, 1.25–2.97), unipolar depression 1.70 (95% CI, 1.38–2.02), and for patients who redeemed psychotropic drugs 1.70 (95% CI, 1.48–1.92). No association was found for patients with other psychiatric disorders 1.13 (95% CI, 0.86–1.38). Similar results were seen with the outcomes of death or severe COVID‐19.Among the different psychiatric subgroups, patients with schizophrenia spectrum disorders had the highest 30‐day absolute risk for the composite outcome 3.1% (95% CI, 2.3–3.9%), death 1.2% (95% CI, 0.4–2.0%) and severe COVID‐19 2.7% (95% CI, 1.9–3.6%).ConclusionSchizophrenia spectrum disorders, bipolar disorder, unipolar depression and psychotropic drug redemption are associated with unfavourable outcomes in patients with COVID‐19.
Trends in Australian dental prescribing of antibiotics: 2005–2016
Authors: Walsh LJ , Ford PJ , McGuire T , van Driel M , Hollingworth SA 
Published: April 2021

AbstractBackgroundPrescribing of antibiotics by dentists for surgical prophylaxis or as an adjunct to managing dental infections is a substantial part of the overall landscape for prescribed antibiotics in health care settings.MethodsWe explored trends in the antibiotic prescribing patterns of Australian dentists over the 12‐year period, 2005–2016. We obtained data on dispensed prescriptions of antibiotics from registered dentists subsidized on the Pharmaceutical Benefits Scheme.ResultsAustralian dentists were responsible for almost 7 million dispensed prescriptions of antibiotics over 12 years; an average of 24 prescriptions per year per dentist. The most commonly prescribed antibiotic was amoxicillin, followed by amoxicillin + clavulanic acid and metronidazole. These top three antibiotics constituted more than 80% of all antibiotics prescribed and their use increased dramatically over time. There was a large increase in the prescribing of broad‐spectrum antibiotics over time, most of which occurred from 2011 to 2016.ConclusionsExcessive prescribing of broad‐spectrum antibiotics runs contrary to national antimicrobial stewardship (AMS) initiatives and guidelines. Multifaceted educational strategies are essential to align prescribing with current best practice. High‐level evidence to inform clear guidelines on antibiotic prescribing in dental infections, with audit and feedback, should reduce the inappropriate use of antibiotics in dentistry.
Dissemination of EAACI food allergy guidelines using a flexible, practical, whole school allergy awareness toolkit
Authors: Higgs Jennette , Styles Kathryn , Bowyer Sarah , Warner Amena , Dunn Galvin Audrey 
Published: April 2021

AbstractBackgroundEssential training for emergency adrenaline auto‐injector administration alone provides an inadequate safeguard in school environments. Recent UK deaths have reinforced the urgency for embedding whole school (WS) allergy awareness to minimise risk. We documented the development of a practical, flexible WS Food Allergy Awareness Toolkit for UK secondary schools.MethodsWe used a multidisciplinary participatory action research methodology, involving successive modification and retesting of a pragmatic toolkit in 3 case study schools. A School Allergy Action Group drives WS risk assessment, helping schools gradually implement best practice policy in line with their particular needs. Additional schools self‐piloted the resulting toolkit with only remote monitoring. School surveys, based on EAACI guidelines were developed to identify priorities and assess change.ResultsEffectiveness of the resulting process toolkit, now available online, was independently demonstrated via pre/post‐intervention questionnaires from 24/10 pupils with food allergy (FA) and 97/6 pupils without FA, respectively. Pearson correlational analysis showed strong negative relationships between Food Allergy Quality of Life Questionnaire (FAQLQ) at T0 and School Support (SS) at T0 (r = −0.8, P<0.01), and between SS and Self‐Efficacy (SE) (r = 0.73, P<0.05). Mean FAQLQ scores improved between T0 (3.3) and T1 (2.5). SE improved for those with FA (mean difference = 1.0). In those without FA, SE (mean difference = 0.9) and Attitudes and Knowledge (mean difference = 0.7) also improved.ConclusionsFull stakeholder involvement in toolkit development encourages usage and, therefore, improves WS community awareness; reduces risk of reactions; fosters a more accepting societal attitude and empowers pupils with/without allergies to self‐manage effectively.
Laparoscopic sigmoidectomy with splenic flexure mobilization for colon cancer in situs inversus totalis: Preoperative assessment and preparation
Authors: Kudo Takuya , Matsuda Takeru , Urakawa Naoki , Hasegawa Hiroshi , Kanaji Shingo , Yamashita Kimihiro , Oshikiri Taro , Kakeji Yoshihiro 
Published: April 2021

AbstractSitus inversus totalis (SIT) is a rare condition in which the internal organ's position is a mirror image of normal anatomy. Although several investigators reported laparoscopic surgery for colorectal cancer in patients with SIT, it is considered difficult even for an experienced surgeon because of the mirror position. We show a case report of laparoscopic sigmoidectomy with the splenic flexure mobilization (SFM) procedure in SIT. A 79‐year‐old woman with SIT was referred to our hospital for a locally advanced sigmoid cancer (cT3N1M0, cStageIIIB). We safely performed the laparoscopic sigmoidectomy with SFM, as shown in detail below. No postoperative complication occurred, and the patient is in good health with no recurrences 30 months after surgery, as of the writing this report. We propose three critical points; checking the CT angiography to understand the anatomy; using flip‐horizontal video of “normal” laparoscopic sigmoidectomy to confirm an unfamiliar situation; adding the epigastric trocar to make SFM procedures safe and comfortable.
Attitude change after a curriculum on the science and philosophy of well‐being and happiness for high school students: A classroom‐randomized trial
Authors: Desan Paul H. , Setton Mark K. , Holzer Allison A. , Young Kevin C. , Sun Yan , He Fei , Li Baosong , Weinstein Andrea J. , Yu Xiaoling 
Published: April 2021

AbstractBackgroundMultiple interventions have been tested to promote well‐being in high school students, often focusing on depression prevention.AimsTo test the impact of a one‐semester active learning curriculum covering the modern science and philosophy of well‐being and happiness on attitudinal measures related to the curriculum and standard measures of depression and well‐being.SampleSubjects were first‐year students in an urban high school in Beijing, China (equivalent to US tenth grade).MethodsNine classrooms were randomly assigned to the intervention curriculum (n = 252), and nine classrooms were randomly assigned to a traditional psychology curriculum (n = 263). Students completed questionnaires pre‐ and post‐semester including a Positive Attitude Scale (PAS, concerning Relatedness, Competence, Autonomy, Gratitude, Calmness, Mindfulness, and Hope), Positive and Negative Affect Scale (PANAS), Centers for Epidemiological Studies Depression Scale (CES‐D), Life Satisfaction Scale (LS), Subjective Happiness Scale (SHS), Meaning in Life Questionnaire (MLQ), and a test of knowledge about well‐being (Knowledge Test, KT).ResultsIn a hierarchical linear model, there were statistically significant intervention effects on six of the seven subscales of the PAS, on PANAS balance, and on the KT. CES‐D, LS, SHS, and MLQ were improved but not significantly so. Notable overall secular trends in measures of well‐being were observed, with a peak in September and nadir in April.ConclusionsA one‐semester course for high school students regarding well‐being and happiness demonstrated significant changes in positive attitudes, affective balance, and knowledge about happiness. Circannual trends in well‐being measures over the academic year have implications for those designing school intervention studies.
Computational design and modeling of nanobodies toward SARS‐CoV‐2 receptor binding domain
Authors: Yang Jingyi , Zhang Zhao , Yang Fengyuan , Zhang Haiwei , Wu Haibo , Zhu Feng , Xue Weiwei 
Published: April 2021

AbstractThe ongoing pandemic of coronavirus disease 2019 (COVID‐19) caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has become a global health concern and pose a serious threat to humanity. There is an urgent need for developing therapeutic drugs and (or) biologics to prevent the spread of the virus. The life cycle of SARS‐CoV‐2 shows that the virus enters host cells by first binding to angiotensin‐converting enzyme 2 (ACE2) through its spike protein receptor‐binding domain (RBD). Therefore, blocking the binding between of ACE2 and SARS‐CoV‐2 RBD can inhibit the virus infection in the host cells. In this study, by grafting the complementarity‐determining regions (CDRs) of developed SARS‐CoV, MERS‐CoVs specific neutralizing antibodies (nAbs) include monoclonal antibodies (mAbs) as well as SARS‐CoV‐2 mAbs onto a known stable nanobody (Nb) scaffold, and a total of 16 Nbs sequences were designed. Five Nbs, namely CS01, CS02, CS03, CS10, and CS16, were selected based on the free energy landscape of protein docking verified by the recently reported Nb‐RBD cocrystal structures. CS01, CS02, and CS03 occupied the ACE2 binding site of RBD, while CS10 and CS16 were proposed to inhibit the interaction between RBD and ACE2 through an allosteric mechanism. Based on the structures of the five Nbs in complex with RBD, seven brand‐new Nbs with enhanced binding affinities (CS02_RD01, CS03_RD01, CS03_RD02, CS03_RD03, CS03_RD04, CS16_RD01, and CS16_RD02) were generated by redesign of residues on the interface of the five Nbs contact with SARS‐CoV‐2 RBD. In addition, the identified “hot spots” on the interface of each complex provide useful information to understand the binding mechanism of designed Nbs to SARS‐CoV‐2 RBD. In sum, the predicted stabilities and high binding affinities of the 11 (re)designed Nbs indicating the potential of the developed computational framework in this work to design effective agents to block the infection of SARS‐CoV‐2.
A scoping review of pharmacy participation in dental and oral health care
Authors: Hu Jie , McMillan Sara S. , El‐Den Sarira , O'Reilly Claire L. , Collins Jack C. , Wheeler Amanda J. 
Published: April 2021

AbstractObjectivesTo explore the scope of dental and oral health care (DOHC) provided by the pharmacy profession and associated outcomes, and attitudes of pharmacy staff and other key stakeholders about pharmacy involvement in this context.MethodsA scoping review of full‐text articles describing outcomes related to pharmacy staff/student involvement in, knowledge of or attitudes towards DOHC in any setting, and stakeholder perspectives was conducted. Articles written in English were searched for using PubMed, EMBASE, EBSCO, International Pharmaceutical Abstracts, Education Resources Information Centre, Web of Science, Google Scholar, and ProQuest for Dissertations and Theses. No date restrictions were used. Key outcomes were mapped: role and practice, knowledge and attitudes, and training and education.ResultsSeventy studies met the inclusion criteria: 49 were conducted in developed countries; 60 were quantitative in design; and 38 involved community pharmacy settings only. Pharmacists and pharmacy support staff commonly managed DOHC inquiries (n = 13), including the provision of advice and products with or without a further referral. Integrated pharmacist‐led services in dental settings (n = 4) showed improved prescribing and quality use of medicines but low community pharmacy referrals were identified in studies involving mystery shoppers with potential oral cancer (n = 7). DOHC promotion programmes delivered by pharmacy staff and collaborations with dentists were limited. There was interest from the pharmacy profession for a role in DOHC; however, knowledge gaps were reported and needs for further training identified. Consumer participant DOHC outcomes were not reported.ConclusionsCommunity pharmacists and pharmacy staff were interested in an expanded role in DOHC; however, this scoping review identified lack of knowledge and sub‐optimal practice as potential barriers. Research on development, implementation and evaluation of DOHC‐related services and practice by pharmacy staff was scarce. Further evidence of consumer‐related oral health outcomes and their perceptions of the role of pharmacy is needed.
Thyroid nodules in childhood‐onset Hashimoto's thyroiditis: Frequency, risk factors, follow‐up course and genetic alterations of thyroid cancer
Authors: Lee Yun Jeong , Cho Yeon Jin , Heo You Joung , Chung Eun‐Jae , Choi Young Hun , Kim Jong‐Il , Park Young Joo , Shin Choong Ho , Lee Young Ah 
Published: April 2021

AbstractObjectiveWe evaluated the frequency, risk factors and the follow‐up outcomes of thyroid nodules, and genetic alterations in thyroid cancer, in youth with childhood‐onset Hashimoto thyroiditis (HT) residing in an iodine‐sufficient country.DesignA retrospective cohort study.Patients and measurementsA total of 213 patients (194 females, mean age 10.6 years at the time of HT diagnosis) were ultrasonographically evaluated. Thyroid nodules were categorized using the Korean Thyroid Imaging Reporting and Data System (K‐TIRADS) and the American College of Radiology Thyroid Imaging Reporting and Data System (ACR‐TI‐RADS).ResultsThyroid nodules were detected in 40 (18.8%) patients over a median follow‐up period of 3.4 years, usually after the onset of puberty. A family history of thyroid disease (hazard ratio 2.1, p = .031) was predictive of thyroid nodule detection. Papillary thyroid carcinoma (PTC) was diagnosed in 9 (4.2% of all and 22.5% of nodule‐positive patients). The malignant nodules had a higher K‐TIRADS or ACR‐TI‐RADS risk level compared with benign nodules (p < .01 for both). Genetic alterations were revealed in 7 (BRAFV600E in 6 and RET‐ERC1 fusion in 1) of the eight available tumour tissue samples. None showed evidence of disease over a median follow‐up period of 3.4 years.ConclusionsThe nodule detection rate was 18.8%, with a 22.5% risk of malignancy among the detected nodules in childhood‐onset HT patients, showing increased risk in those with a family history. Additional large‐scale studies are required to evaluate the usefulness of K‐TIRADS or ACR‐TI‐RADS risk level for the differentiation of paediatric thyroid nodules.
Anogenital syringocystadenocarcinoma papilliferum in situ or anaplastic extramammary Paget disease? A unifying concept and review of the literature
Authors: Sheldon Jesse D. , Buckley Kaila , Ulman Catherine , Chung Catherine G. 
Published: April 2021

AbstractExtramammary Paget disease (EMPD) is a rare cutaneous malignancy that typically involves the genital skin and can be primary or associated with an underlying internal malignancy. The typical histopathological appearance of EMPD consists of single or small aggregates of cells with abundant pale cytoplasm and large pleomorphic nuclei, known as Paget cells, scattered throughout the epidermis. We report a case of anogenital EMPD occurring in a 53‐year‐old man with unusual histopathologic findings of marked epidermal acanthosis, acantholysis, intraepidermal glandular differentiation, and prominent plasma cell‐rich fibrovascular cores. These features were entirely confined to the epidermis and adnexa with no evidence of dermal invasion or underlying systemic disease. We review and summarize the literature for atypical features noted in EMPD and summarize similar findings previously described under a variety of descriptions including anaplastic EMPD, anogenital syringocystadenocarcinoma papilliferum in situ (SCACPIS), SCACPIS‐like changes in EMPD, and EMPD mimicking acantholytic squamous cell carcinoma in situ. We propose that these features represent a single entity and be considered under a unifying diagnosis to facilitate recognition of this entity.
Altered precipitation dynamics lead to a shift in herbivore dynamical regime
Authors: Pepi Adam , Holyoak Marcel , Karban Richard 
Published: April 2021

AbstractThe interaction between endogenous dynamics and exogenous environmental variation is central to population dynamics. Although investigations into the effects of changing mean climate are widespread, changing patterns of variation in environmental forcing also affect dynamics in complex ways. Using wavelet and time series analyses, we identify a regime shift in the dynamics of a moth species in California from shorter to longer period oscillations over a 34‐year census, and contemporaneous changes in regional precipitation dynamics. Simulations support the hypothesis that shifting precipitation dynamics drove changes in moth dynamics, possibly due to stochastic resonance with delayed density‐dependence. The observed shift in climate dynamics and the interaction with endogenous dynamics mean that predicting future population dynamics will require information on both climatic shifts and their interaction with endogenous density‐dependence, a combination that is rarely available. Consequently, models based on historical data may be unable to predict future population dynamics.
Latitudinal patterns of terrestrial phosphorus limitation over the globe
Authors: Hou Enqing , Wen Dazhi , Jiang Lifen , Luo Xianzhen , Kuang Yuanwen , Lu Xiankai , Chen Chengrong , Allen Keanan T. , He Xianjin , Huang Xingzhao , Luo Yiqi 
Published: April 2021

AbstractPhosphorus limitation on terrestrial plant growth is being incorporated into Earth system models. The global pattern of terrestrial phosphorus limitation, however, remains unstudied. Here, we examined the global‐scale latitudinal pattern of terrestrial phosphorus limitation by analysing a total of 1068 observations of aboveground plant production response to phosphorus additions at 351 forest, grassland or tundra sites that are distributed globally. The observed phosphorus‐addition effect varied greatly (either positive or negative), depending significantly upon fertilisation regime and production measure, but did not change significantly with latitude. In contrast, phosphorus‐addition effect standardised by fertilisation regime and production measure was consistently positive and decreased significantly with latitude. Latitudinal gradient in the standardised phosphorus‐addition effect was explained by several mechanisms involving substrate age, climate, vegetation type, edaphic properties and biochemical machinery. This study suggests that latitudinal pattern of terrestrial phosphorus limitation is jointly shaped by macro‐scale driving forces and the fundamental structure of life.
Causal associations of serum matrix metalloproteinase‐8 level with ischaemic stroke and ischaemic stroke subtypes: a Mendelian randomization study
Authors: Jia Yiming , Guo Daoxia , Zhang Kaixin , Yang Pinni , Zang Yuhan , Sun Lulu , Wang Yu , Liu Fanghua , Shi Mengyao , Zhang Yonghong , Zhu Zhengbao 
Published: April 2021

AbstractBackground and purposeElevated serum matrix metalloproteinase‐8 (MMP‐8) concentrations are associated with high risk of vascular disease, but the causality remains unclear. A two‐sample Mendelian randomization (MR) study was performed to examine the causal effect of serum MMP‐8 concentrations on the risk of ischaemic stroke, ischaemic stroke subtypes and coronary artery disease.MethodsTen independent single‐nucleotide polymorphisms related to serum MMP‐8 concentrations were identified as instrumental variables from a genome‐wide association study of 6049 European subjects. Genetic association estimates for ischaemic stroke were obtained from the Multiancestry Genome‐wide Association Study of Stroke consortium with 446,696 European individuals. The inverse‐variance weighted method was applied to assess the causal associations of serum MMP‐8 with ischaemic stroke and its subtypes in the main analysis.ResultsNo significant causal association was observed for MMP‐8 levels with total ischaemic stroke, large artery stroke or cardioembolic stroke. Genetically determined 1 – unit higher log‐transformed serum MMP‐8 concentration was associated with an increased risk of small vessel stroke (odds ratio 1.25; 95% confidence interval 1.12–1.39; p < 0.001). In secondary analysis, a similar adverse impact was reported for MMP‐8 on coronary artery disease (odds ratio 1.05; 95% confidence interval 1.01–1.10; p = 0.017). Sensitivity analyses further confirmed the relationship between serum MMP‐8 level and small vessel stroke and coronary artery disease. Mendelian randomization Egger regression showed no evidence of pleiotropic bias.ConclusionsHigh serum MMP‐8 concentrations were causally associated with increased risks of small vessel stroke and coronary artery disease. The mechanism underlying the effect of serum MMP‐8 on the vascular system requires further investigation.