bluuebunny/crossref_metadata_2025_split huggingface dataset:
Strategies to improve deep learning-based salivary gland segmentation
Authors: van Rooij Ward , Dahele Max , Nijhuis Hanne , Slotman Berend J. , Verbakel Wilko F. 
Published: December 2020

Abstract
Background
Deep learning-based delineation of organs-at-risk for radiotherapy purposes has been investigated to reduce the time-intensiveness and inter-/intra-observer variability associated with manual delineation. We systematically evaluated ways to improve the performance and reliability of deep learning for organ-at-risk segmentation, with the salivary glands as the paradigm. Improving deep learning performance is clinically relevant with applications ranging from the initial contouring process, to on-line adaptive radiotherapy.

Methods
Various experiments were designed: increasing the amount of training data (1) with original images, (2) with traditional data augmentation and (3) with domain-specific data augmentation; (4) the influence of data quality was tested by comparing training/testing on clinical versus curated contours, (5) the effect of using several custom cost functions was explored, and (6) patient-specific Hounsfield unit windowing was applied during inference; lastly, (7) the effect of model ensembles was analyzed. Model performance was measured with geometric parameters and model reliability with those parameters’ variance.

Results
A positive effect was observed from increasing the (1) training set size, (2/3) data augmentation, (6) patient-specific Hounsfield unit windowing and (7) model ensembles. The effects of the strategies on performance diminished when the base model performance was already ‘high’. The effect of combining all beneficial strategies was an increase in average Sørensen–Dice coefficient of about 4% and 3% and a decrease in standard deviation of about 1% and 1% for the submandibular and parotid gland, respectively.

Conclusions
A subset of the strategies that were investigated provided a positive effect on model performance and reliability. The clinical impact of such strategies would be an expected reduction in post-segmentation editing, which facilitates the adoption of deep learning for autonomous automated salivary gland segmentation.
A randomised controlled trial of heavy shoulder strengthening exercise in patients with hypermobility spectrum disorder or hypermobile Ehlers-Danlos syndrome and long-lasting shoulder complaints: study protocol for the Shoulder-MOBILEX study
Authors: Liaghat Behnam , Skou Søren T. , Søndergaard Jens , Boyle Eleanor , Søgaard Karen , Juul-Kristensen Birgit 
Published: December 2020

AbstractBackgroundFour out of five patients with hypermobility spectrum disorder (HSD) or hypermobile Ehlers-Danlos syndrome (hEDS) experience shoulder complaints including persistent pain and instability. Evidence suggests that patients with HSD/hEDS who experience knee and back complaints improve with exercise-based therapy. However, no study has focused on exercise-based treatment for the shoulder in this patient group. The potential benefits of strengthening the shoulder muscles, such as increased muscle-tendon stiffness, may be effective for patients with HSD/hEDS who often display decreased strength and increased shoulder laxity/instability.The primary aim is to investigate the short-term effectiveness of a 16-week progressive heavy shoulder strengthening programme and general advice (HEAVY) compared with low-load training and general advice (LIGHT), on self-reported shoulder symptoms, function, and quality of life.MethodsA superiority, parallel group, randomised controlled trial will be conducted with 100 patients from primary care with HSD/hEDS and shoulder complaints (persistent pain and/or instability) for more than 3 months. Participants will be randomised to receive HEAVY (full range of motion, high load) or LIGHT (neutral to midrange of motion, low load) strengthening programme three times weekly with exercises targeting scapular and rotator cuff muscles. HEAVY will be supervised twice weekly, and LIGHT three times during the 16 weeks. The primary outcome will be between-group difference in change from baseline to 16-week follow-up in the Western Ontario Shoulder Instability Index (WOSI, 0-2100 better to worse). Secondary outcomes will include a range of self-reported outcomes covering symptoms, function, and quality of life, besides clinical tests for shoulder strength, laxity/instability, and proprioception. Outcome assessors will be blinded to group allocation. Participants will be kept blind to treatment allocation through minimal information about the intervention content and hypotheses. Primary analyses will be performed by a blinded epidemiologist.DiscussionIf effective, the current heavy shoulder strengthening programme will challenge the general understanding of prescribing low-load exercise interventions for patients with HSD/hEDS and provide a new treatment strategy. The study will address an important and severe condition using transparent, detailed, and high-quality methods to potentially support a future implementation.Trial registrationClinicalTrials.govNCT03869307. Registered on 11 March 2019.
Identification and characterization of a Babesia bigemina thrombospondin-related superfamily member, TRAP-1: a novel antigen containing neutralizing epitopes involved in merozoite invasion
Authors: Montenegro Valeria Noely , Paoletta Martina Soledad , Jaramillo Ortiz José M. , Suarez Carlos E. , Wilkowsky Silvina Elizabeth 
Published: December 2020

Abstract
Background
Thrombospondin-related anonymous protein (TRAP) has been described as a potential vaccine candidate for several diseases caused by apicomplexan parasites. However, this protein and members of this family have not yet been characterized in Babesia bigemina, one of the most prevalent species causing bovine babesiosis.

Methods
The 3186-bp Babesia bigemina TRAP-1 (BbiTRAP-1) gene was identified by a bioinformatics search using the B. bovis TRAP-1 sequence. Members of the TRAP and TRAP-related protein families (TRP) were identified in Babesia and Theileria through a search of the TSP-1 adhesive domain, which is the hallmark motif in both proteins. Structural modeling and phylogenetic analysis were performed with the identified TRAP proteins. A truncated recombinant BbiTRAP-1 that migrates at approximately 107 kDa and specific antisera were produced and used in Western blot analysis and indirect fluorescent antibody tests (IFAT). B-cell epitopes with neutralizing activity in BbiTRAP-1 were defined by enzyme-linked immunosorbent assays (ELISA) and invasion assays.

Results
Three members of the TRAP family of proteins were identified in B. bigemina (BbiTRAP-1 to -3). All are type 1 transmembrane proteins containing the von Willebrand factor A (vWFA), thrombospondin type 1 (TSP-1), and cytoplasmic C-terminus domains, as well as transmembrane regions. The BbiTRAP-1 predicted structure also contains a metal ion-dependent adhesion site for interaction with the host cell. The TRP family in Babesia and Theileria species contains the canonical TSP-1 domain but lacks the vWFA domain and together with TRAP define a novel gene superfamily. A variable number of tandem repeat units are present in BbiTRAP-1 and could be used for strain genotyping. Western blot and IFAT analysis confirmed the expression of BbiTRAP-1 by blood-stage parasites. Partial recognition by a panel of sera from B. bigemina-infected cattle in ELISAs using truncated BbiTRAP-1 suggests that this protein is not an immunodominant antigen. Additionally, bovine anti-recombinant BbiTRAP-1 antibodies were found to be capable of neutralizing merozoite invasion in vitro.

Conclusions
We have identified the TRAP and TRP gene families in several Babesia and Theileria species and characterized BbiTRAP-1 as a novel antigen of B. bigemina. The functional relevance and presence of neutralization-sensitive B-cell epitopes suggest that BbiTRAP-1 could be included in tests for future vaccine candidates against B. bigemina.

Graphical Abstract
Implications of increasing temperature stress for predatory biocontrol of vector mosquitoes
Authors: Buxton Mmabaledi , Nyamukondiwa Casper , Dalu Tatenda , Cuthbert Ross N. , Wasserman Ryan J. 
Published: December 2020

AbstractBackgroundPredators play a critical role in regulating larval mosquito prey populations in aquatic habitats. Understanding predator-prey responses to climate change-induced environmental perturbations may foster optimal efficacy in vector reduction. However, organisms may differentially respond to heterogeneous thermal environments, potentially destabilizing predator-prey trophic systems.MethodsHere, we explored the critical thermal limits of activity (CTLs; critical thermal-maxima [CTmax] and minima [CTmin]) of key predator-prey species. We concurrently examined CTL asynchrony of two notonectid predators (Anisops sardeaandEnithares chinai) and one copepod predator (Lovenula falcifera) as well as larvae of three vector mosquito species,Aedes aegypti,Anopheles quadriannulatusandCulex pipiens, across instar stages (early, 1st; intermediate, 2nd/3rd; late, 4th).ResultsOverall, predators and prey differed significantly in CTmaxand CTmin. Predators generally had lower CTLs than mosquito prey, dependent on prey instar stage and species, with first instars having the lowest CTmax(lowest warm tolerance), but also the lowest CTmin(highest cold tolerance). For predators,L. falciferaexhibited the narrowest CTLs overall, withE. chinaihaving the widest andA. sardeaintermediate CTLs, respectively. Among prey species, the global invaderAe. aegypticonsistently exhibited the highest CTmax, whilst differences among CTminwere inconsistent among prey species according to instar stage.ConclusionThese results point to significant predator-prey mismatches under environmental change, potentially adversely affecting natural mosquito biocontrol given projected shifts in temperature fluctuations in the study region. The overall narrower thermal breadth of native predators relative to larval mosquito prey may reduce natural biotic resistance to pests and harmful mosquito species, with implications for population success and potentially vector capacity under global change.Graphical Abstract
Transcriptome changes and polymyxin resistance of acid-adapted Escherichia coli O157:H7 ATCC 43889
Authors: Hwang Daekeun , Kim Seung Min , Kim Hyun Jung 
Published: December 2020

AbstractBackgroundAcid treatment is commonly used for controlling or killing pathogenic microorganisms on medical devices and environments; however, inadequate acid treatment may cause acid tolerance response (ATR) and offer cross-protection against environmental stresses, including antimicrobials. This study aimed to characterise anEscherichia colistrain that can survive in the acidic gastrointestinal environment.ResultsWe developed an acid-tolerantE. coliO157:H7 ATCC 43889 (ATCC 43889) strain that can survive at pH 2.75 via cell adaptation in low pH conditions. We also performed RNA sequencing and qRT-PCR to compare differentially expressed transcripts between acid-adapted and non-adapted cells. Genes related to stress resistance, includingkdpAandbshAwere upregulated in the acid-adapted ATCC 43889 strain. Furthermore, the polymyxin resistance genearnAwas upregulated in the acid-adapted cells, and resistance against polymyxin B and colistin (polymyxin E) was observed. As polymyxins are important antibiotics, effective against multidrug-resistant gram-negative bacterial infections, the emergence of polymyxin resistance in acid-adaptedE. coliis a serious public health concern.ConclusionThe transcriptomic and phenotypic changes analysed in this study during the adaptation ofE. colito acid environments can provide useful information for developing intervention technologies and mitigating the risk associated with the emergence and spread of antimicrobial resistance.
RETRACTED ARTICLE: Inter- and intraobserver agreement of the quantitative assessment of [99mTc]-labelled anti-programmed death-ligand 1 (PD-L1) SPECT/CT in non-small cell lung cancer
Authors: Hughes Daniel Johnathan , Chand Gitasha , Goh Vicky , Cook Gary J. R. 
Published: December 2020

Abstract
Purpose
Checkpoint inhibition therapy using monoclonal antibodies against programmed cell death protein 1 (PD-1) or its ligand (PD-L1) is now standard management of non-small cell lung cancer (NSCLC). PD-L1 expression is a validated and approved prognostic and predictive biomarker for anti-PD-1/PD-L1 therapy. Technetium-99 m [99mTc]-labelled anti-PD-L1 single-domain antibody (NM-01) SPECT/CT quantification correlates with PD-L1 expression in NSCLC, presenting an opportunity for non-invasive assessment. The aim of this study was to determine the inter- and intraobserver agreement of the quantitative assessment of [99mTc]NM-01 SPECT/CT in NSCLC.

Methods
[99mTc]NM-01 SPECT/CT studies of 21 consecutive NSCLC participants imaged for the evaluation of PD-L1 expression were analysed. Three independent observers measured maximum counts in a tumour region of interest (ROImax) of primary lung, metastatic lesions and normal tissue references of both 1 and 2 h post-injection (n = 42) anonymised studies using a manual technique. Intraclass correlation coefficients (ICC) were calculated, and Bland–Altman plot analysis was performed to determine inter- and intraobserver agreement.

Results
Intraclass correlation of primary lung tumour-to-blood pool (T:BP; ICC 0.83, 95% CI 0.73–0.90) and lymph node metastasis-to-blood pool (LN:BP; ICC 0.87, 0.81–0.92) measures of [99mTc]NM-01 uptake was good to excellent between observers. Freehand ROImax of T (ICC 0.94), LN (ICC 0.97), liver (ICC 0.97) and BP (ICC 0.90) reference tissues also demonstrated excellent interobserver agreement. ROImax scoring of healthy lung demonstrated moderate to excellent interobserver agreement (ICC 0.84) and improved when measured consistently at the level of the aortic arch (ICC 0.89). Manual ROImax re-scoring of T, LN, T:BP and LN:BP using [99mTc]NM-01 SPECT/CT following a 42-day interval was consistent with excellent intraobserver agreement (ICC range 0.95–0.97).

Conclusion
Good to excellent inter- and intraobserver agreement of the quantitative assessment of [99mTc]NM-01 SPECT/CT in NSCLC was demonstrated in this study, including T:BP which has been shown to correlate with PD-L1 status. [99mTc]NM-01 SPECT/CT has the potential to reliably and non-invasively assess PD-L1 expression.

Clinical trial registration
ClinicalTrials.gov identifier no. NCT02978196. Registered 30th November 2016.
Disparities in utilization of sexual and reproductive health services among high school adolescents from youth friendly service implemented and non-implemented areas of Southern Ethiopia
Authors: Haile Bayu , Shegaze Mulugeta , Feleke Tesfaye , Glagn Mustefa , Andarge Eshetu 
Published: December 2020

Abstract
Background
In recent years, much effort was made to improve access to sexual and reproductive health services (SRH) to adolescents and youths in Ethiopia particularly through establishment of youth friendly service (YFS) corners as part of the existing health care facilities. The existing evidences focused on investigating the utilization of SRH services at YFS established areas alone. There is a dearth of evidence which compares the SRH service use between the YFS implemented and non-implemented areas so that evidences can be drawn to suggest on the successes of the expansion of youth friendly corners.

Methods
A school-based comparative cross-sectional study was conducted by employing a multistage cluster sampling method. A pre-tested self-administered questionnaire was used to collect data and the collected data were entered in to Epidata version 4.4.1 software and then exported to SPSS version 20 for analysis. χ2 test was used to see a significant difference in SRH service utilization among adolescents from YFS implemented and non-implanted areas. The association between the SRH services utilization and the independent variables were examined using binary logistic regression. Finally, variables having p-value less than or equal to 0.05 in the multivariable logistic regression model were considered as statistically significant.

Results
There were a significant difference in the rate of SRH service utilization between YFS implemented (33.8%) and YFS non- implemented (9.9%) areas (χ2 = 37.49, p < 0.001). Higher educational status of mothers (AOR = 2.588, 95% CI: 1.220, 5.491), having open discussion with family (AOR = 3.175, 95%CI: 1.624, 6.206), having good knowledge (AOR = 4.511, 95% CI: 2.458, 8.278) and having positive attitude (AOR = 5.084, 95% CI: 2.764, 9.352) were factors positively associated with SRH services utilization.

Conclusion
Compared with high schools from YFS implemented areas, the SRH service utilization was significantly lower among students from high schools where health facilities did not implement YFS. There is a need for enhancing efforts to establish YFS corners by the stakeholders at different hierarchies at places where the centers were not established so that SRH service uptake would be improved. In addition, it is better to promote open discussion with adolescents at the family level, and emphasis should be given for women education in the broad sense. Furthermore, wide-range awareness creation strategies should be used to address poor knowledge and negative attitude.
Examining the determinants of global and local price passthrough in cereal markets: evidence from DCC-GJR-GARCH and panel analyses
Authors: Guo Jin , Tanaka Tetsuji 
Published: December 2020

AbstractExisting literature has not yet identified the common determinants of price volatility transmission in agricultural commodities from international to local markets and has rarely investigated the role of self-sufficiency measures in the context of national food security. We analyzed several factors to determine the degree of volatility transmission in wheat, rice and maize prices between world and domestic markets using GARCH models with dynamic conditional correlation specifications and panel feasible generalized least square models. Our findings indicate that a grain autarky system can reduce volatility passthroughs for three grain commodities. While the substitutive commodity consumption behaviour between maize and wheat buffers the volatility transmissions of both, rice does not function as a transmission-relieving element for the volatility implying that rice is not a substitute for wheat or maize consumption; grain consumption proves a more effective substitute than cereal self-sufficiency for insulating passthroughs from global markets. These findings may help the governments of developing nations to protect their domestic food markets from the uncertain movements of foreign markets and may thus improve food security.
Catquest-9SF functioning over a decade – a study from the Swedish National Cataract Register
Authors: Lundström Mats , Kugelberg Maria , Montan Per , Nilsson Ingela , Zetterberg Madeleine , Pesudovs Konrad , Behndig Anders 
Published: December 2020

AbstractBackgroundThe Swedish National Cataract Register (NCR) collects data on cataract surgery outcomes during March, including patient-reported outcomes using the Catquest-9SF questionnaire for over 11 years. Previous studies from NCR have shown that the preoperative visual acuity has improved over time. The main purpose of this study was to evaluate the Catquest-9SF Rasch scoring performance in this changing environment. A second purpose was to describe clinical data over the same period for those who completed the questionnaire.MethodsThe performance of the Catquest-9SF was analysed by a separate Rasch analysis for each year, resulting in a preoperative and postoperative score for each participating patient in the annual cohorts. The clinical data and questionnaire scoring were analysed for each year in the period 2008–2018 inclusive.ResultsData were available for 42,023 eyes for 11 annual cohorts (2008–2018). The psychometric properties of the questionnaire were stable during the study period. Person separation (precision) for the whole period was 2.58 and varied between 2.45 and 2.72. The person reliability was 0.87 and varied between 0.86 and 0.88. The targeting of question difficulty to person ability became less accurate over time meaning that the item activities became easier to carry out without difficulty. The average targeting for the whole period was −2.06 and changed from −1.92 in 2008 to −2.31 in 2018. The person score improved both before surgery and after surgery, indicating that patients are undergoing surgery at a more able level and getting better outcomes. The average improvement by surgery decreased from 3.41 logits in 2008 to 3.21 logits in 2018 (p = 0.003).Over time, patient age decreased from 75 to 74 years (p < 0.001) and the proportion of women decreased from 63.9 to 57.9% (p < 0.001). The mean preoperative visual acuity in both the operated eye and the better eye improved over time (0.47 to 0.40 logMAR,p < 0.001 and 0.22 to 0.19 logMAR,p < 0.001, respectively), as did the mean postoperative visual acuity in the operated eye (0.14 to 0.09 logMAR,p < 0.001).ConclusionsThe Catquest-9SF retained stable psychometric properties over this 11-year period although more recent cohorts included slightly younger patients with somewhat better vision.
Evaluation of surgical outcome of giant intracranial meningiomas
Authors: Teama Ramy , Adawy Mohamed , Emara Mohamed 
Published: December 2020

Abstract
Background
The surgery of giant intracranial meningiomas (GIM) is difficult due to its large size, prominent vascularity, including and limiting visualization of various neurovascular structures, and severe cerebral edema. In this study, we will evaluate the surgical outcome of giant meningiomas according to our experience at our hospital in management of giant intracranial meningioma.

Main body
A retrospective analysis of 48 patients with histologically proven meningioma (≥ 6-cm diameter) who underwent surgical treatment at Benha University hospitals over a period of 5 years (June 2014/June 2019) is presented. Details regarding clinical presentation, imaging findings, surgical results and complications, and follow-up status were collected. The study group was composed of 41 females and 7 males. The age of the study group ranged from 38 to 69 years with an average of 49 years. The mean follow-up period was 36 months. Different approaches were used according to tumor location with the aim of gross total removal. Gross total removal was achieved in 90% of cases (43 cases). There were 2 cases with intraoperative complications not related to surgery. Recurrence was present in 4 cases. Mortality in this series was 4% (2 cases) with no reported intraoperative mortality.

Conclusion
Management of giant intracranial meningioma is a relatively common practice in neurosurgical centers in developing countries with the aim of radical total surgical removal being the first and most optimum option. Large size makes surgery difficult, but young age, meticulous surgical techniques, proper localization, trying to minimize operative time, and Simpson grade are of special value. Interdisciplinary cooperation is essential to avoid the common complications like pulmonary embolism (PE), postoperative hematoma in tumor bed that leads to bad surgical outcome.