bluuebunny/crossref_metadata_2025_split huggingface dataset:
Obesity-associated changes in molecular biology of primary breast cancer
Authors: Desmedt Christine , Nguyen Ha-Linh , Geukens Tatjana , Maetens Marion , Aparicio Samuel , Bassez Ayse , Borg Åke , Brock Jane , Broeks Annegien , Caldas Carlos , Cardoso Fatima , De Schepper Maxim , Delorenzi Mauro , Drukker Caroline , Glas Annuska , Green Andrew , Isnaldi Edoardo , Eyfjörd Jórunn , Khout Hazem , Knappskog Stian , Krishnamurthy Savitri , Lakhani Sunil , Langerod Anita , Martens John , Reed Amy McCart , Murphy Leigh , Naulaerts Stefan , Nik-Zainal Serena , Nevelsteen Ines , Neven Patrick , Piccart Martine , Poncet Coralie , Punie Kevin , Purdie Colin , Rakha Emad , Richardson Andrea , Rutgers Emiel , Vincent-Salomon Anne , Simpson Peter , Schmidt Marjanka , Sotiriou Christos , Span Paul , Tan Kiat Tee Benita , Thompson Alastair , Tommasi Stefania , Baelen Karen Van , de Vijver Marc van , Laere Steven Van , Veer Laura Van 'T , Viale Giuseppe , Viari Alain , Vos Hanne , Witteveen Anke , Wildiers Hans , Floris Giuseppe , Garg Abhishek , Smeets Ann , Lambrechts Diether , Biganzoli Elia , Richard François 
Published: February 2023

Abstract
Worldwide, there is a growing proportion of women who are overweight or obese. While obesity has been associated with an increased risk of developing breast cancer (BC) and worse prognosis in BC patients, yet the impact of adiposity (abnormal or excess body fat) on BC biology remains understudied in humans. This retrospective study aimed to investigate how the biology of primary BC would differ according to patients’ body mass index (BMI). We examined clinicopathological data (including BMI at the time of diagnosis) and molecular data (including genomic, bulk and single-cell transcriptomic data) of treatment-naïve (early stage) BC patients from five cohorts (N = 2071). We identified several genomic alterations considered actionable or of potential clinical relevance which had a different prevalence in overweight or obese patients compared to lean patients, for instances, less PIK3CA gene mutations, and more CCND1, CCNE1 and IGFR1 amplifications. Moreover, we found evidence supporting an ageing accelerating effect of obesity at the genetic level, through its association with an age-associated mutational signature. We showed that BMI-associated differences in transcriptomic profile were subtle at the bulk resolution while single cell profiling allowed detection of more pronounced changes in different cell compartments. Investigation at the single cell resolution revealed an elevated and unresolved inflammation of the BC tumor microenvironment (TME) associated with obesity, which had distinct characteristics contingent on the estrogen receptor status. Collectively, analyses at both genomic and transcriptomic levels implied that obesity is associated with an inflammaging-like phenotype of the TME. Our results indicate that patient adiposity might play a significant role in the heterogeneity of BC and should be considered in the context of precision medicine.
A review of reviews exploring patient and public involvement in population health research
Authors: Vinnicombe Soo , Noyes Jane 
Published: February 2023

Abstract
Introduction

Patient and public involvement (PPI) is increasingly seen as something that is integral to research and of importance to research funders. There is general recognition that PPI is the right thing to do for both moral and practical reasons. The aim of this review of reviews is to examine how PPI can be done ‘properly’ by looking at the evidence that exists from published reviews and assessing it against the UK Standards for Public Involvement in Research, as well as examining the specific features of population health research that can make PPI more challenging.

Methods

A review of reviews was carried out following the 5-stage Framework Synthesis method.

Results

In total 31 reviews were included. There is a lack of current research or clarity around Governance and Impact when findings are mapped against UK Standards for Public Involvement in Research. It was also clear that there is little knowledge around PPI with under-represented groups. There are gaps in knowledge about how to ensure key specific attributes of population health research are addressed for PPI team members – particularly around how to deal with complexity and the data-driven nature of the research. Two tools were produced for researchers and PPI members to further improve their PPI activity within population health research and health research more generally: A framework of recommended actions to address PPI in population health research, and guidance on integrating PPI based on the UK Standards for Public Involvement in Research.

Conclusions

Facilitating PPI in population health research is challenging due to the nature of this type of research and there is far less evidence on how to do PPI well in this context. The tools can help researchers identify key aspects of PPI that can be integrated when designing PPI within projects. Findings also highlight specific areas where more research or discussion is needed.
Prognostic value of deep learning based mitotic count in hormonal receptor- and HER2-positive breast cancer
Authors: Balkenhol Maschenka , Mercan Caner , Tessier Leslie , Tellez David , Salgado Roberto , Joensuu Heikki , Loi Sherene , Michiels Stefan , Larsimont Denis , Wegscheider Anne-Sophie , Niendorf Axel , Sherman Mark , Bult Peter , Ciompi Francesco , Laak Jeroen van der 
Published: February 2023

Abstract
The discovery of molecular subtypes has corroborated the heterogeneity of breast cancers. But in clinical routine, treatment selection relies on measuring the aggressiveness of the tumor via histopathology, which is routinely based on grading, a prognostic yet laborious, poorly reproducible, and subjective procedure defined more than 30 years ago, before molecular subtypes existed.
In this paper, we present an interpretable deep learning-based computer-aided diagnosis method to automate mitotic count, one of the components of grading; the method complies with current guidelines and automates hot-spot finding on full digital whole-slide images of routinely prepared pathologic slides stained with hematoxylin and eosin. We use the computer model to query the current “one-size-fits-all” mitotic count procedure by investigating subtype-specific prognostic value of mitotic count using an external independent large-scale multicentric dataset of 1,709 breast cancers.
We show that for human epidermal growth factor-2 (HER2) positive tumors, mitotic count was not prognostic. In hormone-receptor positive/HER2 negative cancers, an average mitotic count density different from clinically used cut offs predicted worse recurrence free survival in multivariable analysis, adjusted for known clinical prognosticators. We provided some first experimental evidence that the prognostic role of mitotic count should be reviewed.
Three-dimensional nonlinear coupling vibration of drill string in deepwater riserless drilling and its influence on wellbore pressure field
Authors: Chen Yili , Liu Jun , Cai Mengqi 
Published: February 2023

Abstract
In deepwater riserless drilling operations, the vibration behavior of drill string may have a significant impact on wellbore pressure, which leads to serious risks of drilling accidents such as well leakage and well collapse in shallow risk areas. In order to solve this problem, based on Hamilton's principle, a three-dimensional nonlinear coupling dynamics model of drill string in deepwater riserless drilling is established to simulate the dynamic behavior of drill string under offshore drilling conditions, considering the influence of heave and offset motion of offshore platform, ocean current load, drillstring-borehole contact and bit-rock interaction. The Newmark-β method is used to solve the nonlinear discrete equations of the system, and the effectiveness of the model and calculation program is verified by the field test data. Meanwhile, a wellbore pressure field model under axial, lateral and torsional motion modes of drill string in deepwater riserless drilling is established. The three-dimensional nonlinear coupling vibration characteristic of drill string and its influence on wellbore pressure fluctuation are investigated. The results indicate that: excitation and natural frequency play a leading role in axial vibration response; the collision between the drill string and the borehole wall mostly occurs in the middle part of the formation section, and the lateral vibration at the bit is the most intense; and the closer to the upper platform, the more high-frequency components of torsional vibration response and the stronger the chaos. The larger the axial vibration amplitude of drill string is, the greater the influence on wellbore pressure field is; for the lateral vibration, the middle and bit position have great influence on the wellbore pressure field; for the torsional vibration, the bottom position has the greatest influence on wellbore pressure field. Compared with the axial and torsional vibration, the lateral vibration of drill string has the greatest influence on the wellbore pressure field.
Research on fault current control method of DC microgrid battery energy storage system
Authors: Wei Tianliu , Li Weiwei , Guo Fang , Wang Ruiyang , Wei Chengzhi , Zheng Bingyao , Jiang Jiaxi 
Published: February 2023

Abstract
Battery energy storage system has become an important link to maintain the stable operation of DC microgrid because of its flexible control and fast response speed. As the battery storage system generally does not have fault current control capability, when a fault occurs between the poles of the system, the battery storage system will provide a great short-circuit current to the fault point, which will cause a great danger to the system operation and equipment safety. At this stage, current-limiting reactors or fault current limiters are generally added to the ports of the energy storage system to reduce the fault current, which has the disadvantage of limited current-limiting effect or high cost and large area, so it is not suitable for wide application in DC microgrid. This paper proposes a fault current control method for DC microgrid battery storage system, which enables the battery storage system to be connected to DC microgrid through Buck DC/DC by increasing the rated voltage of the battery stack.The control mode of the battery storage system is power control mode when the DC microgrid is running on grid, and it will be changed to voltage control mode when the DC microgrid is running off-grid. In case of inter-pole fault, the Buck DC/DC of the battery storage system is controlled to operate with reduced voltage to achieve fault current limit. This scheme does not affect the normal operation of the system, and can quickly limit the peak short-circuit current without adding additional equipment, making the short-circuit current flexible and controllable. Therefore, this scheme has good fault current limiting capability and greatly reduces the technical requirements of DC microgrid for protection. Finally, this paper verifies the feasibility of the proposed scheme and its control strategy through PSCAD/EMTDC modeling simulation.
Does macauba cake alter nutrient digestibility and microorganism population in the rumen of sheep?
Authors: Geraseev Luciana Castro , Duarte Eduardo Robson , Vieira Edvaldo Alves , Ibarra Niurca González , Chaves Amália Saturnino , Santos Sarah Silva , Azevedo Alcinei Mistico , Passetti Rodrigo Augusto Cortêz 
Published: February 2023

Abstract

This study aimed to determine the effects of including macauba cake (MC) in the diets of Santa Ines sheep on nutrients digestibility, and the population of microorganism in the rumen (total bacteria, anaerobic fungi, methanogenic organisms,Ruminococcus flavefaciens, andFibrobacter succinogenes). Twenty male sheep were distributed in a randomized block design with four MC treatment diets (0, 10, 20, and 30% of total dry matter). MC inclusion did not affect the dry matter, organic matter, or crude protein intake, but increased the ether extract, neutral detergent fiber, and acid detergent fiber intake, mainly because of changes in the concentrations of these components in diets with a higher level of MC. With MC inclusion, a linear decreasing effect was observed for the dry matter and organic matter digestibility, and a quadratic effect with a maximum point of 21.5% was observed for the acid detergent fiber digestibility. MC inclusion reduced anaerobic fungal populations and increased methanogenic populations. The increase in methanogenic organisms can be associated with the higher fiber content in diets containing MC. The inclusion of macauba cake in the diet of lambs reduced the dry matter digestibility, promoted an antifungal effect and increased the methanogenic population.
The Impact of COVID-19 on Clerkship Preparedness in Third Year Medical Students
Authors: Lee Cynthia , Andersen Shaun , Patel Deepal , Leon Genesis , Simanton Edward 
Published: February 2023

Abstract
Background:
The COVID-19 pandemic presented a unique challenge to medical education, as students were abruptly required to adapt to a remote learning format. Previous studies show a decline in examination performance among medical students during their initial semester of the pandemic, relative to pre-COVID cohorts. The purpose of our study was to investigate whether such negative outcomes affected medical students’ preparedness for clerkship training.
Methods:
Medical students at the Kirk Kerkorian School of Medicine, consisting of both third-year students who completed pre-clinical training amid the COVID-19 pandemic, and fourth-year students from the pre-pandemic cohort, were administered a Qualtrics survey to assess their perceived preparedness for clerkship training. Students’ confidence in key clinical skills were measured, such as taking patient histories, conducting physical exams, and communicating with medical staff. Students rated the relative importance of didactic lectures versus experiential learning for clerkship preparation. Performance on National Board of Medical Examiners shelf examinations were compared.
Results:
There was a significant difference in perception of disadvantage prior to starting clerkships between the COVID-cohort and their pre-COVID counterparts (mean ratings of 4.3/5 vs. 3.4/5). A greater proportion of the COVID cohort deemed experiential learning as more important than didactic lectures (37.5% vs. 62.5%) as opposed to the pre-COVID cohort which considered didactic lectures as more important (53.2% vs. 46.8%). This difference in perception did not translate to a significant difference in academic performance in the six NBME subject exams taken: Family Medicine, Internal Medicine, Obstetrics and Gynecology, Pediatrics, Psychiatry, and Surgery.
Conclusion:
The implementation of online learning during the COVID-19 pandemic did not have a significant impact on the self-perceived preparedness for clerkship training among medical students. Despite the perception of disadvantage among students who matriculated during the pandemic, overall levels of preparedness do not appear to be affected by the shift to remote instruction. This may be due to a phenomenon the authors deem as the “Grass is Greener,” where individuals perceive that they have missed out on resources that were given to others.
Building an inpatient addiction medicine consult service in Sudbury, Canada: preliminary data and lessons learned in the era of COVID-19
Authors: Leary Tara , Aubin Natalie , Marsh David C , Roach Michael , Nikodem Paola , Caswell Joseph M , Irwin Bridget , Pillsworth Emma , McLelland Maureen , Long Brad , Bhagavatula Sastry , Eibl Joseph K , Morin Kristen A 
Published: February 2023

Abstract
Objective: The goal of this study was to 1) Describe the patient population of a newly implemented addiction medicine consult service (AMCS); 2) Evaluate referrals to community-based addiction support services and acute health service use, over time; 3) Provide lessons learned.
Methods: A retrospective observational analysis was conducted at Health Sciences North in Sudbury, Ontario, Canada, with a newly implemented AMCS from November 2018 and July 2021. Data were collected using the hospital's electronic medical records. The primary outcome was the number of referrals to community-based addiction support services over time. The secondary outcomes included the number of emergency department visits, inpatient admissions and re-visits over time. An interrupted time-series analysis was performed to measure the effect of AMCS implementation on acute health service use at Health Sciences North.
Results: From November 2019 to December 2020, 833 unique patients were assessed through the AMCS. A total of 1,294 referrals were made to community-based addiction support services, with the highest proportion of referrals between August and October 2020. The post-intervention trend for ED visits, ED re-visits, ED length of stay, inpatient visits, re-visits and inpatient length of stay did not significantly differ from the pre-intervention period.
Conclusion:Implementation of an AMCS provides a focused service for patients using substances of diagnosed with substance use disorders. The service resulted in a high referral rate to community-based addiction support services and limited changes in health service usage.
Clinical, Etiological and Management Aspects of Spondyloarthritis in Guinea
Authors: Condé Kaba , Othon Guelngar Carlos , Barry Abdoulaye , Touré Moriba , Kamissoko Alybadara , Cissé FodéAbass 
Published: February 2023

Abstract
Introduction- Spondyloarthritis is classically considered rare in sub-Saharan Africa where the majority of the population is considered HLA-B27 negative.The objective of this study was to describe the profile of spondyloarthritis in the rheumatology department of the Ignace Deen National Hospital in Conakry, Guinea.
Patients and method -This was a descriptive and analytical cross-sectional study, with both prospective and retrospective data collection over a 4-year period. The diagnosis of SpA was made in accordance with the ASAS (Assessment of Spondyloarthrisis) and modified New York criteria.
Results -During the study period, we evaluated 275 patients with spondyloarthritis. The mean age was 39.7 ±11 years with extremes (20 and 75 years), 150 patients (54.5%) were men. A history of familial SpA was present in 95 (34.5%) of the patients. The mean time to diagnosis was 8 ± 4 years. Axial involvement was dominated by involvement of the lumbar spine 225 (82%). Ankylosing spondylitis was the most common form in 198 (72%) of the cases. Extra-articular manifestations were dominated by uveitis in 55 (20%) of cases. HLA-B27 phenotyping was performed in 125 patients, 62 patients were HLA-B27 positive (49.6%). The treatment was based on nonsteroidal anti-inflammatory drugs 225 (81.8%).
Conclusion -SpA are growing in Guinean hospitals, the HLA-B27 antigen is increasingly found in African series. Treatment is mainly based on non-steroidal anti-inflammatory drugs.
CD40LG-associated X-linked Hyper-IgM Syndrome (XHIGM) with Pulmonary Alveolar Proteinosis: A Case Report
Authors: Xu Hongbo , Tian Maoqiang , Bai Yonghua , Ran Xiao , Li Lei , Chen Yan 
Published: February 2023

Abstract
Background: D40LG-associated X-linked hyper-IgM syndrome with pulmonary alveolar proteinosis has rarely been reported, and its genotype-phenotypic correlation remains elusive.
Case Presentation: We describe a five-month-old boy with CD40LG mutation (c.516T>A, p.Tyr172Ter) X-linked hyper-IgM syndrome with pulmonary alveolar proteinosis as the first manifestation. The patient completely recovered after immunotherapy and allogeneic hematopoietic stem cell transplantation. In addition, four previously reported patients with CD40LG mutation with pulmonary alveolar proteinosis were also analyzed. All of these patients presented with early onset of pulmonary infections and a good response to immunotherapy. The structural model of CD40LG indicated that all mutations caused the X-linked hyper-IgM syndrome with pulmonary alveolar proteinosisto be located within the tumor necrosis factor homology domain.
Conclusions: A case was presented, and the characteristics of four cases of CD40LG-associated X-linked hyper-IgM syndrome with pulmonary alveolar proteinosis were summarized. The variant locations may explain the phenotypic heterogeneity of patients with the CD40LG mutation.
New insights into method development and characterization of amorphous silica from wheat straw
Authors: Ramasamy Sangeetha Piriya , Veeraswamy Davamani , Ettiyagounder Parameswari , Arunachalam Lakshmanan , Devaraj Sivakumar Senjeriputhur , Krishna Kadirvelu , Oumabady Sadish , Sakrabani Ruben 
Published: February 2023

Abstract
Amorphous silica is extensively extracted from agricultural residues. Wheat straws are a rich source of silica that have earlier been overlooked however demand for value addition. The proposed study describes an innovative approach for extracting silica from wheat straw and evaluating its structural, textural, and physico-chemical characteristics. Optimum temperature, concentration and pH were identified for the cleaner production of silica. The crystallographic properties analysed by the X-Ray diffraction revealed amorphous nature of silica extracted from ash at 650°C for 4h. The structure of phytolith present in the wheat straw was observed in the form of articulated elongate undulate epidermal phytolith under scanning electron microscope. The energy dispersive X-ray spectrum exhibited higher amount of silica (Si %) of 70.10% with a minimal percentage of potassium (9.96%). The sharp bend at 1025 cm-1 attributed the siloxane (Si-O-Si) vibrations in Fourier transform infrared spectroscopic graph of amorphous silica. The specific surface area measurements of amorphous silica showed type II isotherm curve with a hysteresis of H3 type. The optimum conditions to obtain amorphous silica were 3M NaOH, 3M H2SO4 and pH 9.
Assessing PE teachers perceptions of the barriers to physical activity for inactive children and young people in secondary schools and identifying facilitators to support future public health intervention design using the COM-B model
Authors: Moore Richard , Edmondson Lee , Gregory Maxine , Griffiths Kerry , Freeman Elizabeth 
Published: February 2023

Abstract
Background: Research shows that schools’ efforts to improve children and young people’s (CYP) physical activity (PA) behaviours have been largely unsuccessful. The study investigates Physical Education (PE) teachers’ perceptions of barriers to physical activity (PA) for inactive CYP in secondary schools and to identify facilitators to support future public health intervention design, using the COM-B model of behaviour change and Theoretical Domains Framework.
Method: This study is a qualitative examination of the perceptions of PE teachers of inactive CYP in deprived secondary schools in England. The method involved structured telephone interviews with 156 Heads of PE in schools and analysed the data with thematic analysis.
Results: The study provides a comprehensive understanding of the barriers to PA in secondary schools from the unique perspective of PE teachers. The research identifies 21 barriers to PA and details the main sources of behaviour, intervention functions, policy functions and behaviour change tools that can be applied to support behaviour change for inactive adolescents. The authors suggest the use of digital approaches, particularly conversational AI, to provide a more personalised, natural language experience to engage CYP at scale and overcome barriers to PA.
Conclusion: The study is the first to apply the COM-B model, Behaviour Change Wheel, and TDF Framework to understand the habits and behaviours of inactive CYP. The findings of this study have important implications for policy and practice, providing a deeper understanding of the barriers to physical activity and potential solutions to overcome them.