bluuebunny/crossref_metadata_2025_split huggingface dataset:
MetaCNV - a consensus approach to infer accurate copy numbers from low coverage data
Authors: Friedrich Stefanie , Barbulescu Remus , Helleday Thomas , Sonnhammer Erik L. L. 
Published: June 2020

Abstract
Background
The majority of copy number callers requires high read coverage data that is often achieved with elevated material input, which increases the heterogeneity of tissue samples. However, to gain insights into smaller areas within a tissue sample, e.g. a cancerous area in a heterogeneous tissue sample, less material is used for sequencing, which results in lower read coverage. Therefore, more focus needs to be put on copy number calling that is sensitive enough for low coverage data.

Results
We present MetaCNV, a copy number caller that infers reliable copy numbers for human genomes with a consensus approach. MetaCNV specializes in low coverage data, but also performs well on normal and high coverage data. MetaCNV integrates the results of multiple copy number callers and infers absolute and unbiased copy numbers for the entire genome. MetaCNV is based on a meta-model that bypasses the weaknesses of current calling models while combining the strengths of existing approaches. Here we apply MetaCNV based on ReadDepth, SVDetect, and CNVnator to real and simulated datasets in order to demonstrate how the approach improves copy number calling.

Conclusions
MetaCNV, available at https://bitbucket.org/sonnhammergroup/metacnv, provides accurate copy number prediction on low coverage data and performs well on high coverage data.
Capacity building for implementation research: a methodology for advancing health research and practice
Authors: Dako-Gyeke Phyllis , Asampong Emmanuel , Afari Edwin , Launois Pascal , Ackumey Mercy , Opoku-Mensah Kwabena , Dery Samuel , Akweongo Patricia , Nonvignon Justice , Aikins Moses 
Published: June 2020

Abstract
Background
Implementation research is increasingly being recognised as an important discipline seeking to maximise the benefits of evidence-based interventions. Although capacity-building efforts are ongoing, there has been limited attention on the contextual and health system peculiarities in low- and middle-income countries. Moreover, given the challenges encountered during the implementation of health interventions, the field of implementation research requires a creative attempt to build expertise for health researchers and practitioners simultaneously. With support from the Special Programme for Research and Training in Tropical Diseases, we have developed an implementation research short course that targets both researchers and practitioners. This paper seeks to explain the course development processes and report on training evaluations, highlighting its relevance for inter-institutional and inter-regional capacity strengthening.

Methods
The development of the implementation research course curriculum was categorised into four phases, namely the formation of a core curriculum development team, course content development, internal reviews and pilot, and external reviews and evaluations. Five modules were developed covering Introduction to implementation research, Methods in implementation research, Ethics and quality management in implementation research, Community and stakeholder engagement, and Dissemination in implementation research. Course evaluations were conducted using developed tools measuring participants’ reactions and learning.

Results
From 2016 to 2018, the IR curriculum has been used to train a total of 165 researchers and practitioners predominantly from African countries, the majority of whom are males (57%) and researchers/academics (79.4%). Participants generally gave positive ratings (e.g. integration of concepts) for their reactions to the training. Under ‘learnings’, participants indicated improvement in their knowledge in areas such as identification of implementation research problems and questions.

Conclusion
The approach for training both researchers and practitioners offers a dynamic opportunity for the acquisition and sharing of knowledge for both categories of learners. This approach was crucial in demonstrating a key characteristic of implementation research (e.g. multidisciplinary) practically evident during the training sessions. Using such a model to effectively train participants from various low- and middle-income countries shows the opportunities this training curriculum offers as a capacity-building tool.
Automatic kernel counting on maize ear using RGB images
Authors: Wu Di , Cai Zhen , Han Jiwan , Qin Huawei 
Published: June 2020

Abstract
Background
The number of kernels per ear is one of the major agronomic yield indicators for maize. Manual assessment of kernel traits can be time consuming and laborious. Moreover, manually acquired data can be influenced by subjective bias of the observer. Existing methods for counting of kernel number are often unstable and costly. Machine vision technology allows objective extraction of features from image sensor data, offering high-throughput and low-cost advantages.

Results
Here, we propose an automatic kernel recognition method which has been applied to count the kernel number based on digital colour photos of the maize ears. Images were acquired under both LED diffuse (indoors) and natural light (outdoor) conditions. Field trials were carried out at two sites in China using 8 maize varieties. This method comprises five steps: (1) a Gaussian Pyramid for image compression to improve the processing efficiency, (2) separating the maize fruit from the background by Mean Shift Filtering algorithm, (3) a Colour Deconvolution (CD) algorithm to enhance the kernel edges, (4) segmentation of kernel zones using a local adaptive threshold, (5) an improved Find-Local-Maxima to recognize the local grayscale peaks and determine the maize kernel number within the image. The results showed good agreement (> 93%) in terms of accuracy and precision between ground truth (manual counting) and the image-based counting.

Conclusions
The proposed algorithm has robust and superior performance in maize ear kernel counting under various illumination conditions. In addition, the approach is highly-efficient and low-cost. The performance of this method makes it applicable and satisfactory for real-world breeding programs.
Yield prediction by machine learning from UAS-based multi-sensor data fusion in soybean
Authors: Herrero-Huerta Monica , Rodriguez-Gonzalvez Pablo , Rainey Katy M. 
Published: June 2020

Abstract
Background
Nowadays, automated phenotyping of plants is essential for precise and cost-effective improvement in the efficiency of crop genetics. In recent years, machine learning (ML) techniques have shown great success in the classification and modelling of crop parameters. In this research, we consider the capability of ML to perform grain yield prediction in soybeans by combining data from different optical sensors via RF (Random Forest) and XGBoost (eXtreme Gradient Boosting). During the 2018 growing season, a panel of 382 soybean recombinant inbred lines were evaluated in a yield trial at the Agronomy Center for Research and Education (ACRE) in West Lafayette (Indiana, USA). Images were acquired by the Parrot Sequoia Multispectral Sensor and the S.O.D.A. compact digital camera on board a senseFly eBee UAS (Unnamed Aircraft System) solution at R4 and early R5 growth stages. Next, a standard photogrammetric pipeline was carried out by SfM (Structure from Motion). Multispectral imagery serves to analyse the spectral response of the soybean end-member in 2D. In addition, RGB images were used to reconstruct the study area in 3D, evaluating the physiological growth dynamics per plot via height variations and crop volume estimations. As ground truth, destructive grain yield measurements were taken at the end of the growing season.

Results
Algorithms and feature extraction techniques were combined to develop a regression model to predict final yield from imagery, achieving an accuracy of over 90.72% by RF and 91.36% by XGBoost.

Conclusions
Results provide practical information for the selection of phenotypes for breeding coming from UAS data as a decision support tool, affording constant operational improvement and proactive management for high spatial precision.
PET/CT of breast cancer regional nodal recurrences: an evaluation of contouring atlases
Authors: Beaton Laura , Nica Luminita , Tyldesley Scott , Sek Kenny , Ayre Gareth , Aparicio Maria , Gondara Lovedeep , Speers Caroline , Nichol Alan 
Published: June 2020

Abstract
Background
To validate the Radiation Therapy Oncology Group (RTOG) and European Society for Radiotherapy and Oncology (ESTRO) breast cancer nodal clinical target volumes (CTVs) and to investigate the Radiotherapy Comparative Effectiveness Consortium (RADCOMP) Posterior Neck volume in relation to regional nodal recurrences (RNR).

Methods
From a population-based database, 69 patients were identified who developed RNR after curative treatment for breast cancer. RNRs were detected with 18-fluorodeoxyglucose-positron emission tomography-computed tomography (PET/CT). All patients were treatment-naïve for RNR when imaged. The RTOG and ESTRO nodal CTVs and RADCOMP Posterior Neck volumes were contoured onto a template patient’s CT. RNRs were contoured on each PET/CT and deformed onto the template patient’s CT. Each RNR was represented by a 5 mm diameter epicentre, and categorized as ‘inside’, ‘marginal’ or ‘outside’ the CTV boundaries.

Results
Sixty-nine patients with 226 nodes (median 2, range 1–11) were eligible for inclusion. Thirty patients had received adjuvant tangent and regional nodal radiotherapy, 16 tangent-only radiotherapy and 23 no adjuvant radiotherapy. For the RTOG CTVs, the RNR epicentres were 70% (158/226) inside, 4% (8/226) marginal and 27% (60/226) outside. They included the full extent of the RNR epicentres in 38% (26/69) of patients. Addition of the RADCOMP Posterior Neck volume increased complete RNR coverage to 48% (33/69) of patients. For the ESTRO CTVs, the RNR epicentres were 73% (165/226) inside, 2% (4/226) marginal and 25% (57/226) outside. They included the full extent of the RNR epicentres in 57% (39/69) of patients. Addition of the RADCOMP Posterior Neck volume increased complete RNR coverage to 70% (48/69) of patients.

Conclusions
The RTOG and ESTRO breast cancer nodal CTVs do not fully cover all potential areas of RNR, but the ESTRO nodal CTVs provided full coverage of all RNR epicentres in 19% more patients than the RTOG nodal CTVs. With addition of the RADCOMP Posterior Neck volume to the ESTRO CTVs, 70% of patients had full coverage of all RNR epicentres.
Detection and dynamics of circulating tumor cells in patients with high-risk prostate cancer treated with radiotherapy and hormones: a prospective phase II study
Authors: Zapatero Almudena , Gómez-Caamaño Antonio , Cabeza Rodriguez María Ángeles , Muinelo-Romay Laura , Martin de Vidales Carmen , Abalo Alicia , Calvo Crespo Patricia , Leon Mateos Luis , Olivier Carlos , Vega Piris Lorena Vega 
Published: June 2020

Abstract
Background
Circulating tumor cells (CTCs) are an established prognostic marker in castration-resistant prostate cancer but have received little attention in localized high-risk disease. We studied the detection rate of CTCs in patients with high-risk prostate cancer before and after androgen deprivation therapy and radiotherapy to assess its value as a prognostic and monitoring marker.

Patients and methods
We performed a prospective analysis of CTCs in the peripheral blood of 65 treatment-naïve patients with high-risk prostate cancer. EpCAM-positive CTCs were enumerated using the CELLSEARCH system at 4 timepoints. A cut off of 0 vs ≥ 1 CTC/7.5 ml blood was defined as a threshold for negative versus positive CTCs status.

Results
CTCs were detected in 5/65 patients (7.5%) at diagnosis, 8/62 (12.9%) following neoadjuvant androgen deprivation and 11/59 (18.6%) at the end of radiotherapy, with a median CTC count/7.5 ml of 1 (range, 1–136). Only 1 patient presented a positive CTC result 9 months after radiotherapy. Positive CTC status (at any timepoint) was not significantly associated with any clinical or pathologic factors. However, when we analyzed variations in CTC patterns following treatment, we observed a significant association between conversion of CTCs and stages T3 (P = 0.044) and N1 (P = 0.002). Detection of CTCs was not significantly associated with overall survival (P > 0.40).

Conclusions
Our study showed a low detection rate for CTCs in patients with locally advanced high-risk prostate cancer. The finding of a de novo positive CTC count after androgen deprivation therapy is probably due to a passive mechanism associated with the destruction of the tumor. Further studies with larger samples and based on more accurate detection of CTCs are needed to determine the potential prognostic and therapeutic value of this approach in non-metastatic prostate cancer.

Trial registration
ClinicalTrials.gov ID: NCT01800058.
Effectiveness of salvage radiotherapy for superficial esophageal Cancer after non-curative endoscopic resection
Authors: Nishibuchi Ikuno , Murakami Yuji , Adachi Yoshinori , Imano Nobuki , Takeuchi Yuki , Tkahashi Ippei , Kimura Tomoki , Urabe Yuji , Oka Shiro , Tanaka Shinji , Nagata Yasushi 
Published: June 2020

Abstract
Background
Endoscopic resection is widely used as an effective treatment for superficial esophageal cancer. However, the risk of lymph node metastasis increases in cases of muscularis mucosae or deeper invasion, for which additional treatment such as radiotherapy or surgery is required. Accordingly, the current study investigated the efficacy and toxicity of salvage radiotherapy after non-curative endoscopic resection as an organ preservation strategy.

Methods
We retrospectively reviewed 37 esophageal cancer patients who received salvage radiotherapy after non-curative endoscopic resection. The pathological invasion depths were the muscularis mucosae, submucosal layer, and muscularis propria in 14, 22, and one patient, respectively. All patients received external beam radiotherapy. Among them, eight received intraluminal brachytherapy following external beam radiotherapy. Elective nodal irradiation was administered to all patients. Twenty-five patients received concurrent platinum and fluorouracil-based chemotherapy.

Results
The median follow-up time was 74 months (range: 3–212). The 5-year progression-free survival and overall survival rates were 64 and 78%, respectively. No local or regional lymph node recurrence was observed. The causes of death included esophageal cancer in one patient, metachronous esophageal cancer in one patient, other malignancies in eight patients, and other causes in six patients. Late cardiac toxicities ≥ grade 3 were observed in six patients, one of whom died of arrhythmia.

Conclusions
Salvage radiotherapy after non-curative esophageal endoscopic resection is an effective treatment as an organ preservation strategy. Although muscularis mucosae and submucosal cancer have a high risk of lymph node metastasis, our results suggest that elective nodal irradiation contributes to reduced regional node metastases.
Minimally invasive laparoscopic and robot-assisted emergency treatment of strangulated giant hiatal hernias: report of five cases and literature review
Authors: Ceccarelli Graziano , Pasculli Alessandro , Bugiantella Walter , De Rosa Michele , Catena Fausto , Rondelli Fabio , Costa Gianluca , Rocca Aldo , Longaroni Mattia , Testini Mario 
Published: June 2020

Abstract
Background
Giant hiatal hernia (GHH) is a condition where one-third of the stomach migrates into the thorax. Nowadays, laparoscopic treatment gives excellent postoperative outcomes. Strangulated GHH is rare, and its emergent repair is associated with significant morbidity and mortality rates. We report a series of five cases of strangulated GHH treated by a minimally invasive laparoscopic and robot-assisted approach, together with a systematic review of the literature.

Methods
During 10 years (December 2009–December 2019), 31 patients affected by GHH were treated by robot-assisted or conventional laparoscopic surgical approach. Among them, five cases were treated in an emergency setting. We performed a PubMed MEDLINE search about the minimally invasive emergent treatment of GHH, selecting 18 articles for review.

Results
The five cases were male patients with a mean age of 70 ± 18 years. All patients referred to the emergency service complaining of severe abdominal and thoracic pain, nausea and vomiting. CT scan and endoscopy were the main diagnostic tools. All patients showed stable hemodynamic conditions so that they could undergo a minimally invasive attempt. The surgical approach was robotic-assisted in three patients (60%) and laparoscopic in two (40%). Patients reported no complications or recurrences.

Conclusion
Reviewing current literature, no general recommendations are available about the emergent treatment of strangulated hiatal hernia. Acute mechanical outlet obstruction, ischemia of gastric wall or perforation and severe bleeding are the reasons for an emergent surgical indication. In stable conditions, a minimally invasive approach is often feasible. Moreover, the robot-assisted approach, allowing a stable 3D view and using articulated instruments, represents a reasonable option in challenging situations.
Single-stage treatment of chronic localized tibial osteomyelitis with local debridement and antibiotic-loaded calcium sulfate implantation: a retrospective study of 42 patients
Authors: Zhou Chun-Hao , Ren Ying , Ali Abdulnassir , Meng Xiang-Qing , Zhang Hong-An , Fang Jia , Qin Cheng-He 
Published: June 2020

Abstract
Background
Although various methods have been introduced, the management of chronic tibial osteomyelitis remains a challenge. This study aims to assess a combined treatment method, local debridement combined with antibiotic-loaded calcium sulfate implantation, for the management of the local (Cierny-Mader type III) tibial osteomyelitis.

Methods
Forty-two patients (43 limbs) with type III tibial osteomyelitis, from January 2012 to December 2018, who received the treatment method mentioned above were included in the study. The infection remission rate, recurrence rate, complications rate, and bone healing rate were respectively analyzed.

Results
With a mean follow-up of 42.8 months, 38 limbs (37 patients) (88.4%, 38/43) achieved infection remission without recurrence. Among those patients pain, limitation of movement, sinus tracts, topical redness, and swelling were generally eliminated. Only 4 patients felt slight pain after a long-distance walk, while another 6 patients showed minor but acceptable discomfort in affected limbs. Five patients (11.6%) suffered from osteomyelitis recurrence that required secondary surgical and medical treatment, but no amputation was necessary to eliminate the infection. Prolonged aseptic drainage was the most frequent complication that was observed in 13 patients (30.0%). They were successfully managed by appropriate wound caring in 10 patients and by surgical intervention, months later, in 3 patients. According to the final X-ray examination, bone losses caused by local debridement were generally repaired, though the shape of the tibia was not well-restored to its initial form in 17 limbs. No fracture was recorded during follow-up.

Conclusion
Local debridement combined with antibiotic-loaded calcium sulfate implantation is effective and safe in a single-stage treatment of chronic Cierny-Mader III tibial osteomyelitis.
Factors influencing Australian podiatrists' behavioural intentions to adopt a smart insole into clinical practice: a mixed methods study
Authors: Macdonald Emma M. , Perrin Byron M. , Kingsley Michael I. C. 
Published: June 2020

AbstractBackgroundDiabetes is the leading cause of lower limb amputation in Australia, costing the Australian health care system an estimated A$1.6 billion annually. Podiatrists are the primary foot health care provider in Australia. Research suggests that health professional attitudes can impact patient utilisation of e‐health technologies, such as wearable foot monitoring devices aimed at preventing foot ulceration. The aim of this study was to explore factors that impact the intentions of Australian podiatrists to adopt smart insole foot monitoring technology.MethodsA mixed methods explanatory sequential design was undertaken. One hundred and eleven Australian podiatrists completed an online version of the validated Unified Theory of Acceptance and Use of Technology (UTAUT) questionnaire. Multiple regression analysis was used to determine the strongest predictive model of podiatrists' behavioural intention to adopt technology. Additionally, two focus groups were conducted, and thematic analysis was performed to explore podiatrists' perceived barriers and enablers to smart insole adoption.ResultsOne hundred and eleven Australian podiatrists completed the online UTAUT questionnaire. The majority of respondents practiced in the private sector (58.6%) and were female (50.5%), with Victoria the most common practice location (39.6%). Significant positive correlations existed between behavioural intention and six psychosocial domains including performance expectancy (r = 0.64, p < 0.001), effort expectancy (r = 0.47, p < 0.001), attitude (r = 0.55, p < 0.001), social influence (r = 0.45, p < 0.001), facilitating conditions (r = 0.36, p < 0.001), and self‐efficacy (r = 0.30, p < 0.002). Multiple regression analysis determined that performance expectancy alone was most predictive of behavioural intention to adopt a smart insole into clinical practice (adjusted R2 = 42%, p < 0.001). Qualitative analyses revealed that podiatrists believed that the insole would increase patient knowledge, engagement and self‐efficacy. However, concerns were raised about cost, footwear issues and the device's utility with elderly and remote populations.ConclusionsPerformance expectancy was the most important psychosocial factor predicting the intentions of Australian podiatrists to adopt smart insole foot monitoring technologies. While Australian podiatrists are open to adopting smart insoles into clinical practice, evidence of the device's efficacy is a precursor to adoption. Other perceived barriers to adoption including device cost, compatibility with off‐loading, footwear issues and patient age also need to be addressed prior to implementation and clinical adoption.
Prevalence of hypertension in relation to anthropometric indices among secondary adolescents in Mbarara, Southwestern Uganda
Authors: Katamba Godfrey , Agaba David Collins , Migisha Richard , Namaganda Agnes , Namayanja Rosemary , Turyakira Eleanor 
Published: June 2020

Abstract
Background
Studies investigating the prevalence of hypertension and its correlation with anthropometric indices among adolescents are still scarce compared to those conducted in adults of greater than 40 years. So far, no other study estimating the prevalence and correlates of hypertension among adolescents in Uganda has been found.

Objective
The purpose of this study, therefore, was to asses the prevalence of hypertension and its correlation with anthropometric indices among adolescents in Mbarara Municipality, southwestern Uganda.

Methods
A cross-sectional study was carried out among 616 secondary school adolescents aged 12–19 years in Mbarara Municipality, Uganda. Blood pressure and anthropometric indices were determined by standard methods. In the statistical analysis, linear regression analysis was done to assess the relationship between blood pressure and anthropometric indices.

Results
Overall prevalence of hypertension among adolescents was at 3.1% (n = 19) while prehypertension was 7.1% (n = 44). There was a statistically significant correlation between blood pressure, neck circumference, waist to hip ratio and body mass index at bivariate analysis. In multivariate analysis for anthropometric indices and sex, only neck circumference remained significantly correlated with blood pressure (p < 0.05).

Conclusion
The prevalence of hypertension among adolescents in the study setting was low. An increase in neck circumference results in an increase in blood pressure among adolescents.