bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural variant analysis of a cancer reference cell line sample using multiple sequencing technologies
Authors: Talsania Keyur , Shen Tsai-wei , Chen Xiongfong , Jaeger Erich , Li Zhipan , Chen Zhong , Chen Wanqiu , Tran Bao , Kusko Rebecca , Wang Limin , Pang Andy Wing Chun , Yang Zhaowei , Choudhari Sulbha , Colgan Michael , Fang Li Tai , Carroll Andrew , Shetty Jyoti , Kriga Yuliya , German Oksana , Smirnova Tatyana , Liu Tiantain , Li Jing , Kellman Ben , Hong Karl , Hastie Alex R. , Natarajan Aparna , Moshrefi Ali , Granat Anastasiya , Truong Tiffany , Bombardi Robin , Mankinen Veronnica , Meerzaman Daoud , Mason Christopher E. , Collins Jack , Stahlberg Eric , Xiao Chunlin , Wang Charles , Xiao Wenming , Zhao Yongmei 
Published: December 2022

AbstractBackgroundThe cancer genome is commonly altered with thousands of structural rearrangements including insertions, deletions, translocation, inversions, duplications, and copy number variations. Thus, structural variant (SV) characterization plays a paramount role in cancer target identification, oncology diagnostics, and personalized medicine. As part of the SEQC2 Consortium effort, the present study established and evaluated a consensus SV call set using a breast cancer reference cell line and matched normal control derived from the same donor, which were used in our companion benchmarking studies as reference samples.ResultsWe systematically investigated somatic SVs in the reference cancer cell line by comparing to a matched normal cell line using multiple NGS platforms including Illumina short-read, 10X Genomics linked reads, PacBio long reads, Oxford Nanopore long reads, and high-throughput chromosome conformation capture (Hi-C). We established a consensus SV call set of a total of 1788 SVs including 717 deletions, 230 duplications, 551 insertions, 133 inversions, 146 translocations, and 11 breakends for the reference cancer cell line. To independently evaluate and cross-validate the accuracy of our consensus SV call set, we used orthogonal methods including PCR-based validation, Affymetrix arrays, Bionano optical mapping, and identification of fusion genes detected from RNA-seq. We evaluated the strengths and weaknesses of each NGS technology for SV determination, and our findings provide an actionable guide to improve cancer genome SV detection sensitivity and accuracy.ConclusionsA high-confidence consensus SV call set was established for the reference cancer cell line. A large subset of the variants identified was validated by multiple orthogonal methods.
Assessing the efficacy and safety of mycophenolate mofetil versus azathioprine in patients with autoimmune hepatitis (CAMARO trial): study protocol for a randomised controlled trial
Authors: Snijders Romée J. A. L. M. , Stoelinga Anna E. C. , Gevers Tom J. G. , Pape Simon , Biewenga Maaike , Verdonk Robert C. , de Jonge Hendrik J. M. , Vrolijk Jan Maarten , Bakker Sjoerd F. , Vanwolleghem Thomas , de Boer Ynto S. , Pronk Martine A. M. C. Baven , Beuers Ulrich H. W. , van der Meer Adriaan J. , van Gerven Nicole M. F. , Sijtsma Marijn G. M. , Verwer Bart J. , Gisbertz Ingrid A. M. , Bartelink Maartje , van den Brand Floris F. , Sebib Korkmaz Kerem , van den Berg Aad P. , Guichelaar Maureen M. J. , Soufidi Khalida , Levens Amar D. , van Hoek Bart , Drenth Joost P. H. ,   on behalf of the Dutch Autoimmune Hepatitis Working Group
Published: December 2022

Abstract
Background
Currently, the standard therapy for autoimmune hepatitis (AIH) consists of a combination of prednisolone and azathioprine. However, 15% of patients are intolerant to azathioprine which necessitates cessation of azathioprine or changes in therapy. In addition, not all patients achieve complete biochemical response (CR). Uncontrolled data indicate that mycophenolate mofetil (MMF) can induce CR in a majority of patients. Better understanding of first-line treatment and robust evidence from randomised clinical trials are needed. The aim of this study was to explore the potential benefits of MMF as compared to azathioprine, both combined with prednisolone, as induction therapy in a randomised controlled trial in patients with treatment-naive AIH.

Methods
CAMARO is a randomised (1:1), open-label, parallel-group, multicentre superiority trial. All patients with AIH are screened for eligibility. Seventy adult patients with AIH from fourteen centres in the Netherlands and Belgium will be randomised to receive MMF or azathioprine. Both treatment arms will start with prednisolone as induction therapy. The primary outcome is biochemical remission, defined as serum levels of alanine aminotransferase and immunoglobulin G below the upper limit of normal. Secondary outcomes include safety and tolerability of MMF and azathioprine, time to remission, changes in Model For End-Stage Liver Disease (MELD)-score, adverse events, and aspects of quality of life. The study period will last for 24 weeks.

Discussion
The CAMARO trial investigates whether treatment with MMF and prednisolone increases the proportion of patients in remission compared with azathioprine and prednisolone as the current standard treatment strategy. In addition, we reflect on the challenges of conducting a randomized trial in rare diseases.

Trial registration
EudraCT 2016-001038-91. Prospectively registered on 18 April 2016.

Graphical Abstract
Effect of positive event recording based on positive psychology on healthy behaviors and readmission rate of patients after PCI: a study protocol for a prospective, randomized controlled trial
Authors: Hu Yao-Yao , Jiang Xin , Mao Fang-Ying , Zhang Jing , Liu Lin , Gu Jie , Wu Qing , Li Chun 
Published: December 2022

Abstract
Background
Unhealthy behaviors of coronary heart disease (CHD) patients are closely related to the occurrence of major heart events, which increases the readmission rate and brings a heavy economic burden to families and society. Therefore, it is necessary for health care workers to take active preventive and therapeutic measures to keep or establish healthy behaviors of patients. Positive psychological intervention has been proved to be effective, but it has not been reported in the field of CHD in China. The purpose of this study is to explore the effects of positive event recording based on positive psychology on the healthy behaviors, readmission rate, and anxiety of patients with CHD, in order to provide new ideas for the development of secondary prevention strategies for CHD.

Methods
This is a prospective, single-center, randomized controlled trial (RCT). The subjects will be enrolled from the Department of Cardiology, the First Affiliated Hospital of Soochow University. There are 80 cases in total; according to the random number table, the subjects are randomly divided into the intervention group (n = 40) and the control group (n = 40). The patients in the intervention group will receive the intervention of recording positive events once a week for 3 months, while the patients in the control group receive conventional nursing. The primary outcomes will include healthy behaviors, readmission rate, and anxiety, and the secondary outcomes will include psychological capital, subjective well-being, and corresponding clinical laboratory indicators. The protocol was approved by the Medical Ethics Committee of Soochow University (approval no. SUDA20200604H01) and is performed in strict accordance with the Declaration of Helsinki formulated by the World Medical Association. All participants provide written informed consent.

Discussion
This study will verify whether positive event recording based on positive psychology can make patients maintain healthy behaviors, reduce readmission rate, and improve anxiety after PCI. Then, this study will provide new ideas and references for the development of secondary prevention strategies for patients with CHD.

Trial registration
Chinese Clinical Trials Registry 2000034538. Registered on 10 July 2020.
Effect of B7-H4 downregulation induced by Toxoplasma gondii infection on dysfunction of decidual macrophages contributes to adverse pregnancy outcomes
Authors: Cui Lijun , Wang Yu , Ren Liqin , Li Zhidan , Jiang Yuzhu , Wang Chao , Liu Xianbing , Ren Yushan , Hu Xuemei 
Published: December 2022

Abstract
Background
Toxoplasma gondii infection during pregnancy can lead to fetal defect(s) or congenital complications. The inhibitory molecule B7-H4 expressed on decidual macrophages (dMφ) plays an important role in maternal–fetal tolerance. However, the effect of B7-H4 on the function of dMφ during T. gondii infection remains unclear.

Methods
Changes in B7-H4 expression on dMφ after T. gondii infection were explored both in vivo and in vitro. B7-H4-/- pregnant mice (pregnant mice with B7-H4 gene knockout) and purified primary human dMφ treated with B7-H4 neutralizing antibody were used to explore the role of B7-H4 signaling on regulating the membrane molecules, synthesis of arginine metabolic enzymes and cytokine production by dMφ with T. gondii infection. Also, adoptive transfer of dMφ from wild-type (WT) pregnant mice or B7-H4-/- pregnant mice to infected B7-H4-/- pregnant mice was used to examine the effect of B7-H4 on adverse pregnancy outcomes induced by T. gondii infection.

Results
The results illustrated that B7-H4-/- pregnant mice infected by T. gondii had poorer pregnancy outcomes than their wild-type counterparts. The expression of B7-H4 on dMφ significantly decreased after T. gondii infection, which resulted in the polarization of dMφ from the M2 toward the M1 phenotype by changing the expression of membrane molecules (CD80, CD86, CD163, CD206), synthesis of arginine metabolic enzymes (Arg-1, iNOS) and production of cytokines (IL-10, TNF-α) production. Also, we found that the B7-H4 downregulation after T. gondii infection increased iNOS and TNF-α expression mediated through the JAK2/STAT1 signaling pathway. In addition, adoptive transfer of dMφ from a WT pregnant mouse donor rather than from a B7-H4-/- pregnant mouse donor was able to improve adverse pregnancy outcomes induced by T. gondii infection.

Conclusions
The results demonstrated that the downregulation of B7-H4 induced by T. gondii infection led to the dysfunction of decidual macrophages and contributed to abnormal pregnancy outcomes. Moreover, adoptive transfer of B7-H4+ dMφ could improve adverse pregnancy outcomes induced by T. gondii infection.

Graphical Abstract
Molecular characterization and genetic authentication assay for Anopheles ‘hemocyte-like’ cell lines 4a-3A and 4a-3B
Authors: Eggleston Heather , Njoya Kimani , Anderson Cameron E. , Holm Inge , Eiglmeier Karin , Liang Jiangtao , Sharakhov Igor V. , Vernick Kenneth D. , Riehle Michelle M. 
Published: December 2022

Abstract
Background
Anopheles cell lines are used in a variety of ways to better understand the major vectors of malaria in sub-Saharan Africa. Despite this, commonly used cell lines are not well characterized, and no tools are available for cell line identification and authentication.

Methods
Utilizing whole genome sequencing, genomes of 4a-3A and 4a-3B ‘hemocyte-like’ cell lines were characterized for insertions and deletions (indels) and SNP variation. Genomic locations of distinguishing sequence variation and species origin of the cell lines were also examined. Unique indels were targeted to develop a PCR-based cell line authentication assay. Mitotic chromosomes were examined to survey the cytogenetic landscape for chromosome structure and copy number in the cell lines.

Results
The 4a-3A and 4a-3B cell lines are female in origin and primarily of Anopheles coluzzii ancestry. Cytogenetic analysis indicates that the two cell lines are essentially diploid, with some relatively minor chromosome structural rearrangements. Whole-genome sequence was generated, and analysis indicated that SNPs and indels which differentiate the cell lines are clustered on the 2R chromosome in the regions of the 2Rb, 2Rc and 2Ru chromosomal inversions. A PCR-based authentication assay was developed to fingerprint three indels unique to each cell line. The assay distinguishes between 4a-3A and 4a-3B cells and also uniquely identifies two additional An. coluzzii cell lines tested, Ag55 and Sua4.0. The assay has the specificity to distinguish four cell lines and also has the sensitivity to detect cellular contamination within a sample of cultured cells.

Conclusions
Genomic characterization of the 4a-3A and 4a-3B Anopheles cell lines was used to develop a simple diagnostic assay that can distinguish these cell lines within and across research laboratories. A cytogenetic survey indicated that the 4a-3A and Sua4.0 cell lines carry essentially normal diploid chromosomes, which makes them amenable to CRISPR/Cas9 genome editing. The presented simple authentication assay, coupled with screening for mycoplasma, will allow validation of the integrity of experimental resources and will promote greater experimental reproducibility of results.

Graphical abstract
A novel potential mechanism for the development of portal vein thrombosis in cirrhosis based on portal hemodynamics
Authors: Yan Yuling , Xiong Zhuxiang , Wang Xiaoze , Yang Li , Zheng Tinghui , Luo Xuefeng 
Published: December 2022

Abstract
Background
Marked changes in hemodynamics have been suggested to be a potential contributing factor to portal vein thrombosis (PVT) development. This study investigated the effect of portal hemodynamics based on the anatomical structure of the portal venous system on PVT development.

Methods
The morphological features of portal venous system in patients with PVT and those without PVT subgroups were compared. In addition, idealized PV models were established to numerically evaluate the effect of the variation in the angulation of superior mesenteric vein (SMV) and splenic vein (SV) on the hemodynamics of portal venous system.

Results
The angle α (angulation of SMV and SV) in patients with PVT was lower than that in patients without PVT (p < 0.0001), which was the only independent risk factor (odds ratio (OR), 0.90 (95% CI 0.84–0.95); p < 0.0001) for the presence of PVT. With the change in angle α, the flow pattern of blood flow changed greatly, especially the helical flow. When α = 80°, helical flow only appeared at the local PV near the intersection of SMV and SV. When α = 120°, most regions were occupied by the helical flow. In addition, the h2 gradually increased with increasing α, when α = 80°, h2 = 12.6 m/s2; when α = 120°, h2 = 29.3 m/s2.

Conclusions
The angulation of SV and SMV was closely associated with PVT development. Helical flow changed following the varying angulation of SV and SMV. Therefore, angulation of SV and SMV may help to identify high-risk cohorts for future PVT development earlier.
Dynamic edge computing empowered by reconfigurable intelligent surfaces
Authors: Di Lorenzo Paolo , Merluzzi Mattia , Calvanese Strinati Emilio , Barbarossa Sergio 
Published: December 2022

AbstractIn this paper, we propose a novel algorithm for energy-efficient low-latency dynamic mobile edge computing (MEC), in the context of beyond 5G networks endowed with reconfigurable intelligent surfaces (RISs). We consider a scenario where new computing requests are continuously generated by a set of devices and are handled through a dynamic queueing system. Building on stochastic optimization tools, we devise a dynamic learning algorithm that jointly optimizes the allocation of radio resources (i.e., power, transmission rates, sleep mode and duty cycle), computation resources (i.e., CPU cycles), and RIS reflectivity parameters (i.e., phase shifts), while guaranteeing a target performance in terms of average end-to-end delay. The proposed strategy enables dynamic control of the system, performing a low-complexity optimization on a per-slot basis while dealing with time-varying radio channels and task arrivals, whose statistics are unknown. The presence and optimization of RISs helps boosting the performance of dynamic MEC, thanks to the capability to shape and adapt the wireless propagation environment. Numerical results assess the performance in terms of service delay, learning, and adaptation capabilities of the proposed strategy for RIS-empowered MEC.
Use of digital technology to give and receive feedback in clinical training: a scoping review protocol
Authors: Singaram Veena S. , Bagwandeen Chauntelle I. , Abraham Reina M. , Baboolal Sandika , Sofika Dumisa N. A. 
Published: December 2022

Abstract

Background
Feedback is vital to improving trainee competencies in medical education. The challenges of the global COVID-19 pandemic related to social distancing to curb the spread of the virus ignited a rapid transition to online medical education. These changes highlight the need for digital feedback tools that enhance the efficacy and efficiency of feedback practices. This protocol is for a scoping review that aims to identify the different digital tools and applications in medical education as reported in the literature, as well as highlight gaps in the current literature and provide suggestions for future technological developments and research.

Methods and analysis
A review of the relevant literature will be guided using the Joanna Briggs Institute methodological framework for scoping studies. Using the search strategy developed by the authors, an electronic search of the following databases will be conducted: PubMed/MEDLINE, EBSCOhost (academic search complete, CINAHL with full text) Scopus, Google Scholar, Union Catalogue of Theses and Dissertations (UCTD) via SABINET Online and World Cat Dissertations and Theses via OCLC. Studies will be identified by searching literature from January 2010 to date of review. Using a validated data extraction form developed for the scoping review, the review team will screen eligible studies and import them onto an electronic library created specifically for this purpose. Data collection for the review will be documented through a PRISMA-P flowchart, and the scoping review will use a basic descriptive content analysis to analyse and categorise the extracted data. All review steps will involve two or more reviewers.

Dissemination
The review will provide a comprehensive list of digital tools and applications used to enhance feedback in clinical training and inform future technological developments. The findings will be disseminated through medical education conferences and publications.
Haptic feedback intervention decreases the spatial margin when older adults walk through a narrow space
Authors: Hakamata T. , Muroi D. , Kodama K. , Kondo Y. , Higuchi T. 
Published: December 2022

Abstract
Background
The ability to avoid obstacles efficiently and safely is important for older adults to prevent injuries from tripping and falling. It is important to find an optimal spatial margin between the body and an obstacle considering both safety and efficiency. One side of finding the optimal margin is to decrease the margin in terms of motor efficiency. In this study, we tested whether fingertip-contact intervention to obtain haptic feedback information to perceive the relationship between body and the environment could immediately improve spatial perception and collision avoidance behavior (an instantaneous effect).

Methods
Twenty-seven older adults (12 males and 15 females) participated in the experiment. In the intervention of the fingertip-contact group, they lightly touched the edge of a door with both fingertips while walking. The test task before and after the intervention involved grasping a horizontal bar and passing through a narrow opening. As dependent variables, we measured the spatial margin and the collision rate.

Results
The fingertip-contact group showed a significant decrease in the spatial margin after the intervention. On the other hand, there was no significant improvement in the collision rate after the intervention but rather a decrease only in the control group.

Conclusion
The results obtained in this study indicate that touching obstacles with the fingertips had an instantaneous effect, leading to efficient movement learning, although a possible side effect of an increased collision rated was also found. The proposed intervention might promote an efficiency-based strategy due to learning the spatial relationship between the body and the environment, and it may suppress the excessive avoidance of older adults.
High molar activity [18F]tetrafluoroborate synthesis for sodium iodide symporter imaging by PET
Authors: Soloviev Dmitry , Dzien Piotr , Mackintosh Agata , Malviya Gaurav , Brown Gavin , Lewis David 
Published: December 2022

Abstract
Background
Sodium iodide symporter (NIS) imaging by positron emission tomography (PET) is gaining traction in nuclear medicine, with an increasing number of human studies being published using fluorine-18 radiolabelled tetrafluoroborate ([18F]TFB). Clinical success of any radiotracer relies heavily on its accessibility, which in turn depends on the availability of robust radiolabelling procedures providing a radiotracer in large quantities and of high radiopharmaceutical quality.

Results
Here we publish an improved radiolabelling method and quality control procedures for high molar activity [18F]TFB. The use of ammonium hydroxide for [18F]fluoride elution, commercially available boron trifluoride-methanol complex dissolved in acetonitrile as precursor and removal of unreacted [18F]fluoride on Florisil solid-phase extraction cartridges resulted in the reliable production of [18F]TFB on SYNTHRA and TRACERLAB FXFN automated synthesizers with radiochemical yields in excess of 30%, radiochemical purities in excess of 98% and molar activities in the range of 34–217 GBq/µmol at the end of synthesis. PET scanning of a mouse lung tumour model carrying a NIS reporter gene rendered images of high quality and improved sensitivity.

Conclusions
A novel automated radiosynthesis procedure for [18F]tetrafluoroborate has been developed that provides the radiotracer with high molar activity, suitable for preclinical imaging of NIS reporter gene.
Reactive power optimization of a distribution network with high-penetration of wind and solar renewable energy and electric vehicles
Authors: Xu Biao , Zhang Guiyuan , Li Ke , Li Bing , Chi Hongyuan , Yao Yao , Fan Zhun 
Published: December 2022

AbstractAs high amounts of new energy and electric vehicle (EV) charging stations are connected to the distribution network, the voltage deviations are likely to occur, which will further affect the power quality. It is challenging to manage high quality voltage control of a distribution network only relying on the traditional reactive power control mode. If the reactive power regulation potentials of new energy and EVs can be tapped, it will greatly reduce the reactive power optimization pressure on the network. Keeping this in mind, our reasearch first adds EVs to the traditional distribution network model with new forms of energy, and then a multi-objective optimization model, with achieving the lowest line loss, voltage deviation, and the highest static voltage stability margin as its objectives, is constructed. Meanwihile, the corresponding model parameters are set under different climate and equipment conditions. Ultimately, the optimization model under specific scenarios is obtained. Furthermore, considering the supply and demand relationship of the network, an improved technique for order preference by similarity to an ideal solution decision method is proposed, which aims to judge the adaptability of different algorithms to the optimized model, so as to select a most suitable algorithm for the problem. Finally, a comparison is made between the constructed model and a model without new energy. The results reveal that the constructed model can provide a high quality reactive power regulation strategy.