bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effectiveness of Quality Incentive Payments in General Practice (EQuIP-GP) cluster randomized trial: impact on patient-reported experience
Authors: Bonney Andrew , Russell Grant , Radford Jan , Zwar Nicholas , Mullan Judy , Batterham Marijka , Mazza Danielle , Peterson Gregory , Eckermann Simon , Metusela Christine 
Published: November 2021

Abstract

Background
Relational continuity, ‘a therapeutic relationship between a patient and provider/s that spans health care events’, has been associated with improved patient outcomes.

Objectives
To evaluate whether an intervention incorporating patient enrolment and a funding model for higher-risk patients influenced patient-reported experience measures, particularly relational continuity.

Methods
Cluster-randomized controlled trial over 12 months (1 August 2018–31 July 2019). Participating patients within intervention practices were offered enrolment with a preferred general practitioner, a minimum of 3 longer appointments, and review within 7 days of hospital admission or emergency department attendance. Intervention practices received incentives for longer consultations (dependent on reducing unnecessary prescriptions and tests), early post-hospital follow-up, and hospitalization reductions. The primary outcome was patient-reported relational continuity, measured by the Primary Care Assessment Tool Short Form.

Results
A total of 774 patients, aged 18–65 years with a chronic illness or aged over 65 years, from 34 general practices in metropolitan, regional, and rural Australia across 3 states participated. Response rates for questionnaires were &gt;90%. From a maximum of 4.0, mean baseline scores for relational continuity were 3.38 (SE 0.05) and 3.42 (SE 0.05) in control and intervention arms, respectively, with no significant between-group differences in changes pre-post trial. There were no significant changes in other patient-focussed measures.

Conclusion
Patient-reported relational continuity was high at baseline and not influenced by the intervention, signalling the need for caution with policies incorporating patient enrolment and financial incentives. Further research is required targeting at-risk patient groups with low baseline engagement with primary care.
Establishment of Host–Algal Endosymbioses: Genetic Response to Symbiont Versus Prey in a Sponge Host
Authors: Geraghty Sara , Koutsouveli Vasiliki , Hall Chelsea , Chang Lillian , Sacristan-Soriano Oriol , Hill Malcolm , Riesgo Ana , Hill April 
Published: November 2021

Abstract
The freshwater sponge Ephydatia muelleri and its Chlorella-like algal partner is an emerging model for studying animal: algal endosymbiosis. The sponge host is a tractable laboratory organism, and the symbiotic algae are easily cultured. We took advantage of these traits to interrogate questions about mechanisms that govern the establishment of durable intracellular partnerships between hosts and symbionts in facultative symbioses. We modified a classical experimental approach to discern the phagocytotic mechanisms that might be co-opted to permit persistent infections, and identified genes differentially expressed in sponges early in the establishment of endosymbiosis. We exposed algal-free E. muelleri to live native algal symbionts and potential food items (bacteria and native heat-killed algae), and performed RNA-Seq to compare patterns of gene expression among treatments. We found a relatively small but interesting suite of genes that are differentially expressed in the host exposed to live algal symbionts, and a larger number of genes triggered by host exposure to heat-killed algae. The upregulated genes in sponges exposed to live algal symbionts were mostly involved in endocytosis, ion transport, metabolic processes, vesicle-mediated transport, and oxidation–reduction. One of the host genes, an ATP-Binding Cassette transporter that is downregulated in response to live algal symbionts, was further evaluated for its possible role in the establishment of the symbiosis. We discuss the gene expression profiles associated with host responses to living algal cells in the context of conditions necessary for long-term residency within host cells by phototrophic symbionts as well as the genetic responses to sponge phagocytosis and immune-driven pathways.
Long-lived afterslip of the 2013Mw 6.1 Minab earthquake detected by Persistent Scatterer Interferometry along the Irer fault (western Makran-Zagros transition zone, Iran)
Authors: Plattner Christina , Parizzi Alessandro , Carena Sara , Rieger Stefanie M , Friedrich Anke M , Abolghasem Amir M , DeZan Francesco 
Published: November 2021

SUMMARYThe ratio of seismogenic to aseismic deformation along active faults is needed to estimate their seismogenic potential and hazards. Seismologic and geodetic methods routinely capture coseismic displacements, but data acquisition requirements to fully document post-seismic deformation are not well known. Our study documents afterslip between about 18 months and 4 years after a mid-size earthquake and, based on remote structural mapping, we document fault rupture segments not previously associated with that earthquake. Persistent scatterer interferometric analysis of Sentinel-1A aperture radar data acquired between October 2014 and December 2018 reveals prolonged post-seismic deformation following the 11 May 2013 Mw 6.1 Minab earthquake and its aftershocks. The surface deformation data yield a sharp contrast across both the main seismogenic fault (here named the Irer fault) and its northeastern splay, and it is compatible with left-lateral motion along both faults. The PSI data helped us to identify and map the splay fault in the satellite imagery. We could then measure the geological offset along both faults, finding maximum displacements of about 1 km (main fault) and 350 m (splay). Our modelling of the observed post-seismic surface deformation pattern shows that post-seismic deformation was accommodated by left-lateral afterslip, not viscoelastic relaxation. This result is consistent with previous propositions that Mw 6 earthquakes do not measurably excite deeply seated viscoelastic relaxation mechanisms. Our afterslip modelling yields a slip pattern from the surface to a depth of 6 km to maximum 16 km, in agreement with the depth of the coseismic slip-distribution, and a maximum displacement of ∼7 cm along the fault, but located ∼8 km to the east of the coseismic slip maximum. Moment release during the observed afterslip in our study is Mw 5.7, or 12% of the coseismic moment released by main shock and aftershocks together. Combined with previously published results for the early post-seismic period (first 2 months), we estimate the aseismic moment to be at least ∼37% of the total, implying a high ratio of aseismic to seismic moment release for the Irer fault. Our results show that observation time windows well beyond 5 years are needed to record afterslip following mid-sized earthquakes. Thus, progress in understanding the transition from post-seismic to interseismic fault behaviour critically depends on the availability of data provided by satellite missions such as Copernicus Sentinel-1A. Similarly, robust comparison of the post-seismic rates with long-term geological rates requires palaeoseismic study and dating of related morphotectonic features.
Heterogeneity analysis of the immune microenvironment in laryngeal carcinoma revealed potential prognostic biomarkers
Authors: Qian Zhipeng , Shang Desi , Fan Lin , Zhang Jiarui , Ji Linhao , Chen Kexin , Zhao Rui 
Published: November 2021

Abstract
Laryngeal squamous cell cancer (LSCC) is the second most prevalent malignancy occurring in the head and neck with a high incidence and mortality rate. Immunotherapy has recently become an emerging treatment for cancer. It is therefore essential to explore the role of tumour immunity in laryngeal cancer. Our study first delineated and evaluated the comprehensive immune infiltration landscapes of the tumour microenvironment in LSCC. A hierarchical clustering method was applied to classify the LSCC samples into two groups (high- and low-infiltration groups). We found that individuals with low immune infiltration characteristics had significantly better survival than those in the high-infiltration group, possibly because of the elevated infiltration of immune suppressive cells, such as regulatory T cells and myeloid-derived suppressor cells, in the high-infiltration group. Differentially expressed genes between two groups were involved in some immune-related terms, such as antigen processing and presentation. A univariate Cox analysis and least absolute shrinkage and selection operator analysis were performed to identify an immune gene-set-based prognostic signature (IBPS) to assess the risk of LSCC. The prognostic model comprising six IBPSs was successfully verified to be robust in different cohorts. The expression of the six IBPSs was detected by immunohistochemistry in 110 cases of LSCC. In addition, different inflammatory profiles and immune checkpoint landscape of LSCC were found between two groups. Hence, our model could serve as a candidate immunotherapeutic biomarker and potential therapeutic target for laryngeal cancer.
Quantifying the contribution of pathways of nosocomial acquisition of COVID-19 in English hospitals
Authors: Evans Stephanie , Stimson James , Pople Diane , Bhattacharya Alex , Hope Russell , White Peter J , Robotham Julie V 
Published: November 2021

Abstract

Background
Despite evidence of the nosocomial transmission of novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in hospitals worldwide, the contributions of the pathways of transmission are poorly quantified.

Methods
We analysed national records of hospital admissions and discharges, linked to data on SARS-CoV-2 testing, using an individual-based model that considers patient-to-patient, patient-to-healthcare worker (HCW), HCW-to-patient and HCW-to-HCW transmission.

Results
Between 1 March 2020 and 31 December 2020, SARS-CoV-2 infections that were classified as nosocomial were identified in 0.5% (0.34–0.74) of patients admitted to an acute National Health Service trust. We found that the most likely route of nosocomial transmission to patients was indirect transmission from other infected patients, e.g. through HCWs acting as vectors or contaminated fomites, followed by direct transmission between patients in the same bay. The risk of transmission to patients from HCWs over this time period is low, but can contribute significantly when the number of infected inpatients is low. Further, the risk of a HCW acquiring SARS-CoV-2 in hospital is approximately equal to that in the community, thereby doubling their overall risk of infection. The most likely route of transmission to HCWs is transmission from other infected HCWs.

Conclusions
Current control strategies have successfully reduced the transmission of SARS-CoV-2 between patients and HCWs. In order to reduce the burden of nosocomial COVID-19 infections on health services, stricter measures should be enforced that would inhibit the spread of the virus between bays or wards in the hospital. There should also be a focus on inhibiting the spread of SARS-CoV-2 between HCWs. The findings have important implications for infection-control procedures in hospitals.
Genomic Characterization of Group A Streptococci Causing Pharyngitis and Invasive Disease in Colorado, USA, June 2016– April 2017
Authors: Li Yuan , Dominguez Samuel , Nanduri Srinivas A , Rivers Joy , Mathis Saundra , Li Zhongya , McGee Lesley , Chochua Sopio , Metcalf Benjamin J , Van Beneden Chris A , Beall Bernard , Miller Lisa 
Published: November 2021

Abstract

Background
The genomic features and transmission link of circulating Group A Streptococcus (GAS) strains causing different disease types, such as pharyngitis and invasive disease, are not well understood.

Methods
We used whole-genome sequencing to characterize GAS isolates recovered from persons with pharyngitis and invasive disease in the Denver metropolitan area from June 2016 to April 2017.

Results
The GAS isolates were cultured from 236 invasive and 417 pharyngitis infections. Whole-genome sequencing identified 34 emm types. Compared with pharyngitis isolates, invasive isolates were more likely to carry the erm family genes (23% vs 7.4%, P&lt;.001), which confer resistance to erythromycin and clindamycin (including inducible resistance), and covS gene inactivation (7% vs 0.5%, P&lt;.001). Whole-genome sequencing identified 97 genomic clusters (433 isolates; 2–65 isolates per cluster) that consisted of genomically closely related isolates (median single-nucleotide polymorphism=3 [interquartile range, 1–4] within cluster). Thirty genomic clusters (200 isolates; 31% of all isolates) contained both pharyngitis and invasive isolates and were found in 11 emm types.

Conclusions
In the Denver metropolitan population, mixed disease types were commonly seen in clusters of closely related isolates, indicative of overlapping transmission networks. Antibiotic-resistance and covS inactivation was disproportionally associated with invasive disease.
BSAC Vanguard Report Series: The future of drug development
Authors: Piddock Laura J V 
Published: November 2021

Abstract
The discovery of antibiotics started a new era in medicine. However, antimicrobial resistance (AMR) is now outpacing the development of new antimicrobials. New political and economic models are required to tackle the developing crisis. In this article I look at the challenges and how we can work to overcome them.
Predicting Depression and Posttraumatic Stress Symptoms Following Burn Injury: A Risk Scoring System
Authors: Stockly Olivia R , Wolfe Audrey E , Goldstein Richard , Roaten Kimberly , Wiechman Shelley , Trinh Nhi-Ha , Goverman Jeremy , Stoddard Frederick J , Zafonte Ross , Ryan Colleen M , Schneider Jeffrey C 
Published: November 2021

Abstract
Depression and posttraumatic stress (DPTS) are common psychiatric comorbidities following burn injury. The purpose of this study was to develop an admission scoring system that assesses the risk of development of depression or posttraumatic symptoms in the burn population. This study is a retrospective review of the prospectively collected Burn Model System National Database. Adult burn survivors enrolled from 2014 to 2018 (n = 486) were included. The primary outcome was the presence of DPTS symptoms at 6, 12, or 24 months postinjury. Logistic regression analysis was used to identify demographic and clinical predictors of DPTS symptoms. A risk scoring system was then created based on assigning point values to relevant predictor factors. The study population had a mean age of 46.5 ± 15.8 years, mean burn size of 18.3 ± 19.7%, and was 68.3% male. Prior to injury, 71.3% of the population was working, 47.9% were married, and 50.8% had completed more than a high school education. An 8-point risk scoring system was developed using the following predictors of DPTS symptom development: gender, psychiatric treatment in the past year, graft size, head/neck graft, etiology of injury, and education level. This study is the first to develop a DPTS symptom risk scoring system for burn injury. This scoring system will aid in identifying burn survivors at high risk of long-term psychiatric symptoms that may be used to improve screening, monitoring, timely diagnosis, and interventions.
The Complex History of Genome Duplication and Hybridization in North American Gray Treefrogs
Authors: Booker William W , Gerhardt H Carl , Lemmon Alan R , Ptacek Margaret B , Hassinger Alyssa T B , Schul Johannes , Lemmon Emily Moriarty 
Published: November 2021

Abstract
Polyploid speciation has played an important role in evolutionary history across the tree of life, yet there remain large gaps in our understanding of how polyploid species form and persist. Although systematic studies have been conducted in numerous polyploid complexes, recent advances in sequencing technology have demonstrated that conclusions from data-limited studies may be spurious and misleading. The North American gray treefrog complex, consisting of the diploid Hyla chrysoscelis and the tetraploid H. versicolor, has long been used as a model system in a variety of biological fields, yet all taxonomic studies to date were conducted with only a few loci from nuclear and mitochondrial genomes. Here, we utilized anchored hybrid enrichment and high-throughput sequencing to capture hundreds of loci along with whole mitochondrial genomes to investigate the evolutionary history of this complex. We used several phylogenetic and population genetic methods, including coalescent simulations and testing of polyploid speciation models with approximate Bayesian computation, to determine that H. versicolor was most likely formed via autopolyploidization from a now extinct lineage of H. chrysoscelis. We also uncovered evidence of significant hybridization between diploids and tetraploids where they co-occur, and show that historical hybridization between these groups led to the re-formation of distinct polyploid lineages following the initial whole-genome duplication event. Our study indicates that a wide variety of methods and explicit model testing of polyploid histories can greatly facilitate efforts to uncover the evolutionary history of polyploid complexes.
Impact of concomitant chronic kidney disease on hospitalised infections and remission in patients with rheumatoid arthritis: results from the IORRA cohort
Authors: Higuchi Tomoaki , Tanaka Eiichi , Inoue Eisuke , Abe Mai , Saka Kumiko , Sugano Eri , Sugitani Naohiro , Higuchi Yoko , Ochiai Moeko , Yamaguchi Rei , Sugimoto Naoki , Ikari Katsunori , Yamanaka Hisashi , Harigai Masayoshi 
Published: November 2021

ABSTRACT

Objectives
To investigate the impact of concomitant chronic kidney disease (CKD) on unfavourable clinical events and remission in Japanese patients with rheumatoid arthritis (RA).

Methods
We included 5103 patients with RA and CKD from the Institute of Rheumatology Rheumatoid Arthritis (IORRA) cohort in 2012. CKD stages were classified into four groups: CKD with normal eGFR ≥60 ml/min/1.73 m2 and proteinuria; mild CKD, eGFR ≥45 to &lt; 60; moderate CKD, eGFR ≥30 to &lt; 45; and severe CKD, eGFR &lt;30. We assessed the association between concomitant CKD and the occurrence of unfavourable clinical events or achieving remission during a 5-year observational period.

Results
Of the 5103 patients with RA, 686 (86.6%) had CKD. Concomitant CKD was associated with hospitalised infections [adjusted hazard ratio (aHR) 1.52, 95% confidence interval (CI) 1.07–2.13, p = .02], especially in the moderate to severe CKD group (aHR 1.93, 95% CI 1.12–3.13, p = .02). Of all subjects, 2407 (47.2%) had active RA at baseline and 401 (16.7%) had CKD. Concomitant CKD was also associated with the failure of achieving remission (aHR 0.82, 95% CI 0.68–0.99, p = .04).

Conclusions
Concomitant CKD was a risk factor for hospitalised infections in Japanese patients with RA and failure of achieving remission in patients with active RA.
Decade-long disease, secondary malignancy, and brainstem injury outcomes in pediatric and young adult medulloblastoma patients treated with proton radiotherapy
Authors: Baliga Sujith , Gallotto Sara , Bajaj Benjamin , Lewy Jacqueline , Weyman Elizabeth , Lawell Miranda P , Yeap Beow Y , Ebb David E , Huang Mary , Caruso Paul , Perry Alisa , Jones Robin M , MacDonald Shannon M , Tarbell Nancy J , Yock Torunn I 
Published: November 2021

Abstract

Background
Survivors of pediatric medulloblastoma experience long-term morbidity associated with the toxic effects of postoperative radiotherapy (RT). Proton RT limits radiation dose to normal tissues thereby reducing side effects of treatment while maintaining high cure rates. However, long-term data on disease outcomes and long-term effects of proton RT remain limited.

Methods
One hundred seventy-eight pediatric medulloblastoma patients treated with proton RT between 2002 and 2016 at the Massachusetts General Hospital comprise the cohort of patients who were treated with surgery, radiation therapy, and chemotherapy. We evaluated event-free survival (EFS), overall survival (OS), and local control using the Kaplan-Meier method. The cumulative incidence of brainstem injury and secondary malignancies was assessed.

Results
Median follow-up was 9.3 years. One hundred fifty-nine patients (89.3%) underwent a gross total resection (GTR). The 10-year OS for the entire cohort, standard-risk (SR), and intermediate/high-risk (IR/HR) patients was 79.3%, 86.9%, and 68.9%, respectively. The 10-year EFS for the entire cohort, SR, and IR/HR cohorts was 73.8%, 79.5%, and 66.2%. The 10-year EFS and OS for patients with GTR/NTR were 75.3% and 81.0% vs 57.7% and 61.0% for subtotal resection (STR). On univariate analysis, IR/HR status was associated with inferior EFS, while both anaplastic histology and IR/HR status were associated with worse OS. The 10-year cumulative incidence of secondary tumors and brainstem injury was 5.6% and 2.1%, respectively.

Conclusions
In this cohort study of pediatric medulloblastoma, proton RT was effective, and disease outcomes were comparable to historically treated photon cohorts. The incidence of secondary malignancies and brainstem injury was low in this cohort with mature follow-up.