bluuebunny/crossref_metadata_2025_split huggingface dataset:
An ontology-based documentation of data discovery and integration process in cancer outcomes research
Authors: Zhang Hansi , Guo Yi , Prosperi Mattia , Bian Jiang 
Published: December 2020

Abstract
Background
To reduce cancer mortality and improve cancer outcomes, it is critical to understand the various cancer risk factors (RFs) across different domains (e.g., genetic, environmental, and behavioral risk factors) and levels (e.g., individual, interpersonal, and community levels). However, prior research on RFs of cancer outcomes, has primarily focused on individual level RFs due to the lack of integrated datasets that contain multi-level, multi-domain RFs. Further, the lack of a consensus and proper guidance on systematically identify RFs also increase the difficulty of RF selection from heterogenous data sources in a multi-level integrative data analysis (mIDA) study. More importantly, as mIDA studies require integrating heterogenous data sources, the data integration processes in the limited number of existing mIDA studies are inconsistently performed and poorly documented, and thus threatening transparency and reproducibility.

Methods
Informed by the National Institute on Minority Health and Health Disparities (NIMHD) research framework, we (1) reviewed existing reporting guidelines from the Enhancing the QUAlity and Transparency Of health Research (EQUATOR) network and (2) developed a theory-driven reporting guideline to guide the RF variable selection, data source selection, and data integration process. Then, we developed an ontology to standardize the documentation of the RF selection and data integration process in mIDA studies.

Results
We summarized the review results and created a reporting guideline—ATTEST—for reporting the variable selection and data source selection and integration process. We provided an ATTEST check list to help researchers to annotate and clearly document each step of their mIDA studies to ensure the transparency and reproducibility. We used the ATTEST to report two mIDA case studies and further transformed annotation results into sematic triples, so that the relationships among variables, data sources and integration processes are explicitly standardized and modeled using the classes and properties from OD-ATTEST.

Conclusion
Our ontology-based reporting guideline solves some key challenges in current mIDA studies for cancer outcomes research, through providing (1) a theory-driven guidance for multi-level and multi-domain RF variable and data source selection; and (2) a standardized documentation of the data selection and integration processes powered by an ontology, thus a way to enable sharing of mIDA study reports among researchers.
A deep learning approach for identifying cancer survivors living with post-traumatic stress disorder on Twitter
Authors: Ismail Nur Hafieza , Liu Ninghao , Du Mengnan , He Zhe , Hu Xia 
Published: December 2020

AbstractBackgroundEmotions after surviving cancer can be complicated. The survivors may have gained new strength to continue life, but some of them may begin to deal with complicated feelings and emotional stress due to trauma and fear of cancer recurrence. The widespread use of Twitter for socializing has been the alternative medium for data collection compared to traditional studies of mental health, which primarily depend on information taken from medical staff with their consent. These social media data, to a certain extent, reflect the users’ psychological state. However, Twitter also contains a mix of noisy and genuine tweets. The process of manually identifying genuine tweets is expensive and time-consuming.MethodsWe stream the data using cancer as a keyword to filter the tweets with cancer-free and use post-traumatic stress disorder (PTSD) related keywords to reduce the time spent on the annotation task. Convolutional Neural Network (CNN) learns the representations of the input to identify cancer survivors with PTSD.ResultsThe results present that the proposed CNN can effectively identify cancer survivors with PTSD. The experiments on real-world datasets show that our model outperforms the baselines and correctly classifies the new tweets.ConclusionsPTSD is one of the severe anxiety disorders that could affect individuals who are exposed to traumatic events, including cancer. Cancer survivors are at risk of short-term or long-term effects on physical and psycho-social well-being. Therefore, the evaluation and treatment of PTSD are essential parts of cancer survivorship care. It will act as an alarming system by detecting the PTSD presence based on users’ postings on Twitter.
Shared decision making, physicians’ explanations, and treatment satisfaction: a cross-sectional survey of prostate cancer patients
Authors: Nakayama Kazuhiro , Osaka Wakako , Matsubara Nobuaki , Takeuchi Tsutomu , Toyoda Mayumi , Ohtake Noriyuki , Uemura Hiroji 
Published: December 2020

Abstract
Background
Hormone therapy is one option for some types of prostate cancer. Shared decision making (SDM) is important in the decision making process, but SDM between prostate cancer patients receiving hormone therapy and physicians is not fully understood. This study tested hypotheses: “Patients’ perception of SDM is associated with treatment satisfaction, mediated by satisfaction with physicians’ explanations and perceived effective decision making” and “The amount of information provided to patients by physicians on diseases and treatment is associated with treatment satisfaction mediated by patients’ perceived SDM and satisfaction with physicians’ explanations.”

Methods
This cross-sectional study was conducted using an online panel via a private research company in Japan. The participants in this study were patients registered with the panel who had received or were currently receiving hormone therapy for prostate cancer and physicians registered with the panel who were treating patients with prostate cancer. Measures used in this study included a nine-item Shared Decision Making Questionnaire, levels of satisfaction with physicians’ explanations and treatment satisfaction, and effective decision making for patients (feeling the choice is informed, value-based, likely to be implemented and expressing satisfaction with the choice), and a Shared Decision Making Questionnaire for Doctors. The hypotheses were examined using path analysis.

Results
In total, 124 patients and 150 physicians were included in the analyses. In keeping with our hypotheses, perceived SDM significantly correlated with the physicians’ explanations and perceived effective decision making for patients, and satisfaction with physicians’ explanations and perceived effective decision making for patients were both related to treatment satisfaction. Although the amount of information provided to patients was correlated with the perceived SDM, it was indirectly related to their satisfaction with physicians’ explanations.

Conclusions
When physicians encourage patients to be actively involved in making decisions about treatment through the SDM process while presenting a wide range of information at the start of hormone therapy, patients’ effective decision making and physicians’ explanations may be improved; consequently, the patients’ overall treatment satisfaction may be improved. Physicians who treat patients with prostate cancer may have underestimated the importance of SDM before starting hormone therapy, even greater extent than patients.
Patterns and patient factors associated with loss to follow-up in the Muhimbili sickle cell cohort, Tanzania
Authors: Masamu Upendo , Sangeda Raphael Z. , Kandonga Daniel , Ondengo Jesca , Ndobho Flora , Mmbando Bruno , Nkya Siana , Msami Khadija , Makani Julie 
Published: December 2020

Abstract
Background
Monitoring patient’s clinical attendance is a crucial means of improving retention in care and treatment programmes. Sickle cell patients’ outcomes are improved by participation in comprehensive care programmes, but these benefits cannot be achieved when patients are lost from clinical care. In this study, patients are defined as loss to follow-up when they did not attend clinic for more than 9 months. Precise information on the retention rate and characteristics of those who are not following their clinic appointments is needed to enable the implementation of interventions that will be effective in increasing the retention to care.

Method
This was a retrospective study involving sickle cell patients registered in the Muhimbili Sickle Cohort in Tanzania. Descriptive and survival analysis techniques both non-parametric methods (Kaplan-Meier estimator and Log-rank test) and semi-parametric method (Cox’s proportional hazard model), were used. A p-value of 0.05 was considered significant to make an inference from the analysis.

Results
A total of 5476 patients were registered in the cohort from 2004 to 2016. Of these, 3350 (58.13%) were actively participating in clinics, while 2126 (41.87%) were inactive, of which 1927 (35.19%) were loss to follow-up. We used data from 2004 to 2014 because between 2015 and 2016, patients were referred to other government hospitals. From the survival analysis results, pediatric (HR: 14.29,95% CI: 11.0071–18.5768, p <  0.001) and children between 5 and 17 years [HR:2.61,95% CI:2.2324–3.0705, p <  0.001] patients were more likely to be loss to follow-up than the adult (18 and above years) patients. It was found that patients with above averages for hematocrit (HR: 2.38, 95% CI: 1.0076–1.0404, p = 0.0039) or mean cell volume (HR: 4.28, (95% CI: 1.0260–1.0598, p < 0.001) were more likely to be loss to follow-up than their counterparts.

Conclusion
Loss to follow-up is evident in the cohort of patients in long term comprehensive care. It is, therefore, necessary to design interventions that improve patients’ retention. Suggested solutions include refresher training for health care workers and those responsible for patient follow-up on techniques for retaining patients and comprehensive transition programs to prepare patients who are moving from pediatric to adult clinics.
Expression of PAWR predicts prognosis of ovarian cancer
Authors: Tan Jiahong , Tao Kangjia , Zheng Xu , Liu Dan , Ma Ding , Gao Qinglei 
Published: December 2020

AbstractBackgroundOvarian cancer greatly threatens the general health of women worldwide. Implementation of predictive prognostic biomarkers aids in ovarian cancer management.MethodsUsing online databases, the general expression profile, target-disease associations, and interaction network of PAWR were explored. To identify the role of PAWR in ovarian cancer, gene correlation analysis, survival analysis, and combined analysis of drug responsiveness and PAWR expression were performed. The predictive prognostic value of PAWR was further validated in clinical samples.ResultsPAWR was widely expressed in normal and cancer tissues, with decreased expression in ovarian cancer tissues compared with normal tissues. PAWR was associated with various cancers including ovarian cancer. PAWR formed a regulatory network with a group of proteins and correlated with several genes, which were both implicated in ovarian cancer and drug responsiveness. High PAWR expression denoted better survival in ovarian cancer patients (OS: HR = 0.84, P = 0.0077; PFS, HR = 0.86, P = 0.049). Expression of PAWR could predict platinum responsiveness in ovarian cancer and there was a positive correlation between PAWR gene effect and paclitaxel sensitivity. In 12 paired clinical samples, the cancerous tissues exhibited significantly lower PAWR expression than matched normal fallopian tubes. The predictive prognostic value of PAWR was maintained in a cohort of 50 ovarian cancer patients.ConclusionsHigh PAWR expression indicated better survival and higher drug responsiveness in ovarian cancer patients. PAWR could be exploited as a predictive prognostic biomarker in ovarian cancer.
Seldom heard voices: a meta-narrative systematic review of Aboriginal and Torres Strait Islander peoples healthcare experiences
Authors: Jones Benjamin , Heslop David , Harrison Reema 
Published: December 2020

Abstract
Background
It is well established that Aboriginal and Torres Strait Islander populations face considerable health inequities, exacerbated by poorer healthcare quality. Patient experience is recognised as a major contributing factor to healthcare quality and outcomes, therefore, enriched knowledge of the patient experiences of Aboriginal and Torres Strait Islander populations is critical to redress health inequities. This review synthesises evidence of the healthcare experiences amongst Aboriginal and Torres Strait Islander patients through a metanarrative synthesis of qualitative literature.

Methods
A systematic search strategy was developed and applied to six electronic databases between January 2000 and July 2019. Titles and abstracts were screened before applying the inclusion criteria to full text articles. A meta-narrative synthesis was undertaken.

Results
Fifty-four publications were identified from four research traditions; each with a unique conceptualisation of patient experience. Three themes emerged that demonstrate Aboriginal and Torres Strait Islander patient experiences are informed by 1) beliefs about wellbeing and healthcare provision, 2) their level of trust in the healthcare system, and 3) individual and community health system interactions. The findings highlight a range of aspects of patient experience that were important to participating Aboriginal and Torres Strait Islanders in the included studies but not captured currently in health system surveys.

Conclusion
This review highlights the influence of beliefs about health and wellbeing on the patient experience amongst Aboriginal and Torres Strait Islander populations in the Australian health system. Patient experiences were informed by past experience and their trust in the health system. The different factors influencing patient experience and the gravity of their influence must be considered in current approaches to capturing patient experience data collection methods.

Trial registration
PROSPERO (ID: CRD42019134765).
Circular RNA: metabolism, functions and interactions with proteins
Authors: Zhou Wei-Yi , Cai Ze-Rong , Liu Jia , Wang De-Shen , Ju Huai-Qiang , Xu Rui-Hua 
Published: December 2020

AbstractCircular RNAs (CircRNAs) are single-stranded, covalently closed RNA molecules that are ubiquitous across species ranging from viruses to mammals. Important advances have been made in the biogenesis, regulation, localization, degradation and modification of circRNAs. CircRNAs exert biological functions by acting as transcriptional regulators, microRNA (miR) sponges and protein templates. Moreover, emerging evidence has revealed that a group of circRNAs can serve as protein decoys, scaffolds and recruiters. However, the existing research on circRNA-protein interactions is quite limited. Hence, in this review, we briefly summarize recent progress in the metabolism and functions of circRNAs and elaborately discuss the patterns of circRNA-protein interactions, including altering interactions between proteins, tethering or sequestering proteins, recruiting proteins to chromatin, forming circRNA-protein-mRNA ternary complexes and translocating or redistributing proteins. Many discoveries have revealed that circRNAs have unique expression signatures and play crucial roles in a variety of diseases, enabling them to potentially act as diagnostic biomarkers and therapeutic targets. This review systematically evaluates the roles and mechanisms of circRNAs, with the hope of advancing translational medicine involving circRNAs.
Recommendations for pre-symptomatic genetic testing for hereditary transthyretin amyloidosis in the era of effective therapy: a multicenter Italian consensus
Authors: Grandis M. , Obici L. , Luigetti M. , Briani C. , Benedicenti F. , Bisogni G. , Canepa M. , Cappelli F. , Danesino C. , Fabrizi G. M. , Fenu S. , Ferrandes G. , Gemelli C. , Manganelli F. , Mazzeo A. , Melchiorri L. , Perfetto F. , Pradotto L. G. , Rimessi P. , Tini G. , Tozza S. , Trevisan L. , Pareyson D. , Mandich P. 
Published: December 2020

AbstractHereditary transthyretin amyloidosis (ATTRv, v for variant) is a late-onset, autosomal dominant disease caused by progressive extracellular deposition of transthyretin amyloid fibrils, leading to organ damage and death. For other late-onset fatal diseases, as Huntington’s disease, protocols for pre-symptomatic genetic testing (PST) are available since decades. For ATTRv, limited experience has been reported to date, mostly gathered before the availability of approved therapies. We aimed at developing recommendations for a safe and feasible PST protocol in ATTRv in the era of emerging treatments, taking also into account Italian patients’ characteristics and healthcare system rules. After an initial survey on ongoing approaches to PST for ATTRv in Italy, two roundtable meetings were attended by 24 experts from 16 Italian centers involved in the diagnosis and care of this disease. Minimal requirements for PST offer and potential critical issues were highlighted. By November 2019, 457 families affected by ATTRv with 209 molecularly confirmed pre-symptomatic carriers were counted. The median age at PST was 41.3 years of age, regardless of the specific mutation. Half of the Italian centers had a multidisciplinary team, including a neurologist, an internist, a cardiologist, a medical geneticist and a psychologist, although in most cases not all the specialists were available in the same center. A variable number of visits was performed at each site. Experts agreed that PST should be offered only in the context of genetic counselling to at risk individuals aged 18 or older. Advertised commercial options for DNA testing should be avoided. The protocol should consist of several steps, including a preliminary clinical examination, a pre-test information session, an interval time, the genetic test and a post-test session with the disclosure of the test results, in the context of an experienced multidisciplinary team. Recommendations for best timing were also defined. Protocols for PST in the context of ATTRv can be refined to offer at risk individuals the best chance for early diagnosis and timely treatment start, while respecting autonomous decisions and promoting safe psychological adjustment to the genetic result.
Detailed molecular cytogenetic characterisation of the myeloid cell line U937 reveals the fate of homologous chromosomes and shows that centromere capture is a feature of genome instability
Authors: MacKinnon Ruth N. , Peverall Joanne , Campbell Lynda J. , Wall Meaghan 
Published: December 2020

Abstract
Background
The U937 cell line is widely employed as a research tool. It has a complex karyotype. A PICALM-MLLT10 fusion gene formed by the recurrent t(10;11) translocation is present, and the myeloid common deleted region at 20q12 has been lost from its near-triploid karyotype. We carried out a detailed investigation of U937 genome reorganisation including the chromosome 20 rearrangements and other complex rearrangements.

Results
SNP array, G-banding and Multicolour FISH identified chromosome segments resulting from unbalanced and balanced rearrangements. The organisation of the abnormal chromosomes containing these segments was then reconstructed with the strategic use of targeted metaphase FISH. This provided more accurate karyotype information for the evolving karyotype. Rearrangements involving the homologues of a chromosome pair could be differentiated in most instances. Centromere capture was demonstrated in an abnormal chromosome containing parts of chromosomes 16 and 20 which were stabilised by joining to a short section of chromosome containing an 11 centromere. This adds to the growing number of examples of centromere capture, which to date have a high incidence in complex karyotypes where the centromeres of the rearranged chromosomes are identified. There were two normal copies of one chromosome 20 homologue, and complex rearrangement of the other homologue including loss of the 20q12 common deleted region. This confirmed the previously reported loss of heterozygosity of this region in U937, and defined the rearrangements giving rise to this loss.

Conclusions
Centromere capture, stabilising chromosomes pieced together from multiple segments, may be a common feature of complex karyotypes. However, it has only recently been recognised, as this requires deliberate identification of the centromeres of abnormal chromosomes. The approach presented here is invaluable for studying complex reorganised genomes such as those produced by chromothripsis, and provides a more complete picture than can be obtained by microarray, karyotyping or FISH studies alone. One major advantage of SNP arrays for this process is that the two homologues can usually be distinguished when there is more than one rearrangement of a chromosome pair. Tracking the fate of each homologue and of highly repetitive DNA regions such as centromeres helps build a picture of genome evolution. Centromere- and telomere-containing elements are important to deducing chromosome structure. This study confirms and highlights ongoing evolution in cultured cell lines.
The biomarkers related to immune related adverse events caused by immune checkpoint inhibitors
Authors: Jia Xiao-Hui , Geng Lu-Ying , Jiang Pan-Pan , Xu Hong , Nan Ke-Jun , Yao Yu , Jiang Li-Li , Sun Hong , Qin Tian-Jie , Guo Hui 
Published: December 2020

AbstractThe enthusiasm for immune checkpoint inhibitors (ICIs), an efficient tumor treatment model different from traditional treatment, is based on their unprecedented antitumor effect, but the occurrence of immune-related adverse events (irAEs) is an obstacle to the prospect of ICI treatment. IrAEs are a discrete toxicity caused by the nonspecific activation of the immune system and can affect almost all tissues and organs. Currently, research on biomarkers mainly focuses on the gastrointestinal tract, endocrine system, skin and lung. Several potential hypotheses concentrate on the overactivation of the immune system, excessive release of inflammatory cytokines, elevated levels of pre-existing autoantibodies, and presence of common antigens between tumors and normal tissues. This review lists the current biomarkers that might predict irAEs and their possible mechanisms for both nonspecific and organ-specific biomarkers. However, the prediction of irAEs remains a major clinical challenge to screen and identify patients who are susceptible to irAEs and likely to benefit from ICIs.