bluuebunny/crossref_metadata_2025_split huggingface dataset:
Why does the NHS struggle to adopt eHealth innovations? A review of macro, meso and micro factors
Authors: Asthana Sheena , Jones Ray , Sheaff Rod 
Published: December 2019

Abstract
Background
Having a tax-funded and supposedly ‘National’ Health Service (NHS), one might assume that the UK is well-positioned to roll out eHealth innovations at scale. Yet, despite a strong policy push, the English NHS has been limited in the extent to which it has exploited the potential of eHealth.

Main body
This paper considers a range of macro, meso and micro factors influencing eHealth innovation in the English NHS.

Conclusions
While barriers to eHealth innovation exist at all scales, the fragmentation of the NHS is the most significant factor limiting adoption and diffusion. Rather than addressing problems of fragmentation, national policy seems to have intensified the digital divide. As the recently published NHS Long Term Plan places great emphasis on the role of digital transformation in helping health and care professionals communicate better and enabling people to access the care they need quickly and easily, the implications for the digital divide are likely to be significant for effectiveness, efficiency and equity.
Ultrasonic liver steatosis quantification by a learning-based acoustic model from a novel shear wave sequence
Authors: Shi Xiudong , Ye Wen , Liu Fengjun , Zhang Rengyin , Hou Qinguo , Shi Chunzi , Yu Jinhua , Shi Yuxin 
Published: December 2019

Abstract
Background
An efficient and accurate approach to quantify the steatosis extent of liver is important for clinical practice. For the purpose, we propose a specific designed ultrasound shear wave sequence to estimate ultrasonic and shear wave physical parameters. The utilization of the estimated quantitative parameters is then studied.

Results
Shear wave attenuation, shear wave absorption, elasticity, dispersion slope and echo attenuation were simultaneously estimated and quantified from the proposed novel shear wave sequence. Then, a regression tree model was utilized to learn the connection between the space represented by all the physical parameters and the liver fat proportion. MR mDIXON quantification was used as the ground truth for liver fat quantification. Our study included a total of 60 patients. Correlation coefficient (CC) with the ground truth were applied to mainly evaluate different methods for which the corresponding values were − 0.25, − 0.26, 0.028, 0.045, 0.46 and 0.83 for shear wave attenuation, shear wave absorption, elasticity, dispersion slope, echo attenuation and the learning-based model, respectively. The original parameters were extremely outperformed by the learning-based model for which the root mean square error for liver steatosis quantification is only 4.5% that is also state-of-the-art for ultrasound application in the related field.

Conclusions
Although individual ultrasonic and shear wave parameters were not perfectly adequate for liver steatosis quantification, a promising result can be achieved by the proposed learning-based acoustic model based on them.
Thoracic tumor resection combined with SVC replacement using autologous pericardium
Authors: Jiang Sicong , Hu Hao , Guo Changying , Jiang Feng , Liu Xi , Tang Lang , Tang Jianjun , Cheng Xiaoliang 
Published: December 2019

Abstract
Background
Invasion of the superior vena cava (SVC) by thoracic tumors and occurrence of SVC syndrome are often encountered in clinical practice; but the prognosis in these cases is poor. Replacement of the SVC with autologous pericardial tissue is rarely performed. In this study, we sought to investigate the postoperative outcomes of this rare procedure.

Methods
We performed a retrospective analysis of six patients who underwent SVC replacement using autologous pericardial tissue between October 2010 and November 2016. We collected data on the patients’ pathological features, operative characteristics, postoperative outcomes, and survival.

Results
All six patients were male with an average age of 52 years (range, 18–62 years). Three of the patients had lung cancer, one had stage III thymoma, and two had germinoma. Four of the six patients had mild or moderate superior vena cava compression and no corresponding clinical symptoms. The other two patients had severe compression and obvious symptoms of SVC syndrome, with the typical swelling of the face, eyelids, and upper extremities. All six patients underwent complete tumor resection, with two of the lung cancer patients undergoing right lobectomy and one undergoing right pneumonectomy. With respect to the postoperative outcomes, one patient died, whereas the others did not develop any major complications. At the end of the follow-up period, five of the patients were alive and none of the patients had developed thrombosis in the grafts.

Conclusions
Our findings indicated that SVC replacement with autologous pericardium is technically feasible and safe, with few postoperative complications and favorable long-term effects. Although it has some limitations, this method appears to be useful in achieving SVC reconstruction of moderate size. SVC replacement with autologous pericardium appears to have the potential for widespread clinical use.
Gender and active travel: a qualitative data synthesis informed by machine learning
Authors: Haynes Emily , Green Judith , Garside Ruth , Kelly Michael P. , Guell Cornelia 
Published: December 2019

Abstract
Background
Innovative approaches are required to move beyond individual approaches to behaviour change and develop more appropriate insights for the complex challenge of increasing population levels of activity. Recent research has drawn on social practice theory to describe the recursive and relational character of active living but to date most evidence is limited to small-scale qualitative research studies. To ‘upscale’ insights from individual contexts, we pooled data from five qualitative studies and used machine learning software to explore gendered patterns in the context of active travel.

Methods
We drew on 280 transcripts from five research projects conducted in the UK, including studies of a range of populations, travel modes and settings, to conduct unsupervised ‘topic modelling analysis’. Text analytics software, Leximancer, was used in the first phase of the analysis to produce inter-topic distance maps to illustrate inter-related ‘concepts’. The outputs from this first phase guided a second researcher-led interpretive analysis of text excerpts to infer meaning from the computer-generated outputs.

Results
Guided by social practice theory, we identified ‘interrelated’ and ‘relating’ practices across the pooled datasets. For this study we particularly focused on respondents’ commutes, travelling to and from work, and on differentiated experiences by gender. Women largely described their commute as multifunctional journeys that included the school run or shopping, whereas men described relatively linear journeys from A to B but highlighted ‘relating’ practices resulting from or due to their choice of commute mode or journey such as showering or relaxing. Secondly, we identify a difference in discourses about practices across the included datasets. Women spoke more about ‘subjective’, internal feelings of safety (‘I feel unsafe’), whereas men spoke more about external conditions (‘it is a dangerous road’).

Conclusion
This rare application of machine learning to qualitative social science research has helped to identify potentially important differences in co-occurrence of practices and discourses about practice between men’s and women’s accounts of travel across diverse contexts. These findings can inform future research and policy decisions for promoting travel-related social practices associated with increased physical activity that are appropriate across genders.
HTLV-1 CTCF-binding site is dispensable for in vitro immortalization and persistent infection in vivo
Authors: Martinez Michael P. , Cheng Xiaogang , Joseph Ancy , Al-Saleem Jacob , Panfil Amanda R. , Palettas Marilly , Dirksen Wessel P. , Ratner Lee , Green Patrick L. 
Published: December 2019

Abstract
Background
Human T-cell leukemia virus type 1 (HTLV-1) is the etiologic agent of adult T-cell leukemia/lymphoma (ATL) and the neurological disorder HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). The exact mechanism(s) through which latency and disease progression are regulated are not fully understood. CCCTC-binding factor (CTCF) is an 11-zinc finger, sequence-specific, DNA-binding protein with thousands of binding sites throughout mammalian genomes. CTCF has been shown to play a role in organization of higher-order chromatin structure, gene expression, genomic imprinting, and serve as a barrier to epigenetic modification. A viral CTCF-binding site (vCTCF-BS) was previously identified within the overlapping p12 (sense) and Hbz (antisense) genes of the HTLV-1 genome. Thus, upon integration, HTLV-1 randomly inserts a vCTCF-BS into the host genome. vCTCF-BS studies to date have focused primarily on HTLV-1 chronically infected or tumor-derived cell lines. In these studies, HTLV-1 was shown to alter the structure and transcription of the surrounding host chromatin through the newly inserted vCTCF-BS. However, the effects of CTCF binding in the early stages of HTLV-1 infection remains unexplored. This study examines the effects of the vCTCF-BS on HTLV-1-induced in vitro immortalization and in vivo viral persistence in infected rabbits.

Results
HTLV-1 and HTLV-1∆CTCF LTR-transactivation, viral particle production, and immortalization capacity were comparable in vitro. The total lymphocyte count, proviral load, and Hbz gene expression were not significantly different between HTLV-1 and HTLV-1∆CTCF-infected rabbits throughout a 12 week study. However, HTLV-1∆CTCF-infected rabbits displayed a significantly decreased HTLV-1-specific antibody response compared to HTLV-1-infected rabbits.

Conclusions
Mutation of the HTLV-1 vCTCF-BS does not significantly alter T-lymphocyte transformation capacity or early in vivo virus persistence, but results in a decreased HTLV-1-specific antibody response during early infection in rabbits. Ultimately, understanding epigenetic regulation of HTLV-1 gene expression and pathogenesis could provide meaningful insights into mechanisms of immune evasion and novel therapeutic targets.
Combination of the natural compound Periplocin and TRAIL induce esophageal squamous cell carcinoma apoptosis in vitro and in vivo: Implication in anticancer therapy
Authors: Han Lujuan , Dai Suli , Li Zhirong , Zhang Cong , Wei Sisi , Zhao Ruinian , Zhang Hongtao , Zhao Lianmei , Shan Baoen 
Published: December 2019

Abstract
Background
Esophageal cancer is one of the most common malignant tumors in the world. With currently available therapies, only 20% ~ 30% patients can survive this disease for more than 5 years. TRAIL, a natural ligand for death receptors that can induce the apoptosis of cancer cells, has been explored as a therapeutic agent for cancers, but it has been reported that many cancer cells are resistant to TRAIL, limiting the potential clinical use of TRAIL as a cancer therapy. Meanwhile, Periplocin (CPP), a natural compound from dry root of Periploca sepium Bge, has been studied for its anti-cancer activity in a variety of cancers. It is not clear whether CPP and TRAIL can have activity on esophageal squamous cell carcinoma (ESCC) cells, or whether the combination of these two agents can have synergistic activity.

Methods
We used MTS assay, flow cytometry and TUNEL assay to detect the effects of CPP alone or in combination with TRAIL on ESCC cells. The mechanism of CPP enhances the activity of TRAIL was analyzed by western blot, dual luciferase reporter gene assay and chromatin immunoprecipitation (ChIP) assay. The anti-tumor effects and the potential toxic side effects of CPP alone or in combination with TRAIL were also evaluated in vivo.

Results
In our studies, we found that CPP alone or in combination with TRAIL could inhibit the proliferation of ESCC cells and induce apoptosis, and we certificated that combination of two agents exert synergized functions. For the first time, we identified FoxP3 as a key transcriptional repressor for both DR4 and DR5. By down-regulating FoxP3, CPP increases the expression of DR4/DR5 and renders ESCC cells much more sensitive to TRAIL. We also showed that CPP reduced the expression of Survivin by inhibiting the activity of Wnt/β-catenin pathway. All these contributed to synergistic activity of CPP and TRAIL on ESCC cells in vitro and in vivo.

Conclusion
Our data suggest that CPP and TRAIL could be further explored as potential therapeutic approach for esophageal cancer.
The somatic mutation landscape of the human body
Authors: García-Nieto Pablo E. , Morrison Ashby J. , Fraser Hunter B. 
Published: December 2019

AbstractBackgroundSomatic mutations in healthy tissues contribute to aging, neurodegeneration, and cancer initiation, yet they remain largely uncharacterized.ResultsTo gain a better understanding of the genome-wide distribution and functional impact of somatic mutations, we leverage the genomic information contained in the transcriptome to uniformly call somatic mutations from over 7500 tissue samples, representing 36 distinct tissues. This catalog, containing over 280,000 mutations, reveals a wide diversity of tissue-specific mutation profiles associated with gene expression levels and chromatin states. For example, lung samples with low expression of the mismatch-repair geneMLH1show a mutation signature of deficient mismatch repair. In addition, we find pervasive negative selection acting on missense and nonsense mutations, except for mutations previously observed in cancer samples, which are under positive selection and are highly enriched in many healthy tissues.ConclusionsThese findings reveal fundamental patterns of tissue-specific somatic evolution and shed light on aging and the earliest stages of tumorigenesis.
The effect of an educational program for pregnant women to prevent allergic diseases in infants: study protocol for a randomized controlled trial
Authors: Nakamura Rie , Ishiguro Nao , Naru Eiji , Ishitsuka Yukiko , Nakade Masato , Nezu Yoko 
Published: December 2019

Abstract
Background
Allergic diseases in infants have dramatically increased in developed countries during the past few decades. To date, extensive research has been done on risk factors for allergies in infancy, and preventive measures against them. However, the effect of the primary approach to preventing infantile allergy is still limited.
The aim of this trial is to evaluate whether prenatal education interventions, including the latest public research results on allergic diseases, prevent the onset of infant allergies.

Methods/design
We designed a randomized controlled, two-arm (standard prenatal education vs our education), parallel-group, assessor-blind trial. A sample of 120 pregnant women will be recruited at Chiba Aiyu-kai Kinen Hospital and allocation is by computer-generated randomization.
Pregnant women in the intervention arm participate in the childbirth education program established by the specialist and a pediatric allergy educator. The program was developed based on evidences supporting interventions on primary prevention, which are suggested to be beneficial to infantile allergies in recent studies.
The primary objective of the study is to determine whether it is possible to establish effective behaviors for allergy prevention in early infancy in the children of pregnant women who participate in an educational program developed by pediatric allergy specialists. Four months after birth, their behaviors will be compared against those of pregnant women who did not participate in the program.

Discussion
Allergies are common in many individuals worldwide, and can be present from babyhood through the person’s lifetime. One of the strong points of this study is that it should provide pregnant women with accumulated information on preventive knowledge against allergy, that can be effective in some cases, and that women can apply a combination of these behaviors before and after pregnancy. The results of our program will be publicized to help change the behaviors of mothers, and, if the program is effective, for preventing allergies in infants, it will be disclosed worldwide as a new preventive strategy for allergy in infants.

Trial registration
UMIN-CTR, ID: UMIN000034730 Retrospectively registered on 1 December 2018.
A review on the eco-epidemiology and clinical management of human granulocytic anaplasmosis and its agent in Europe
Authors: Matei Ioana A. , Estrada-Peña Agustín , Cutler Sally J. , Vayssier-Taussat Muriel , Varela-Castro Lucía , Potkonjak Aleksandar , Zeller Herve , Mihalca Andrei D. 
Published: December 2019

AbstractAnaplasma phagocytophilum is the agent of tick-borne fever, equine, canine and human granulocytic anaplasmosis. The common route of A. phagocytophilum transmission is through a tick bite, the main vector in Europe being Ixodes ricinus. Despite the apparently ubiquitous presence of the pathogen A. phagocytophilum in ticks and various wild and domestic animals from Europe, up to date published clinical cases of human granulocytic anaplasmosis (HGA) remain rare compared to the worldwide status. It is unclear if this reflects the epidemiological dynamics of the human infection in Europe or if the disease is underdiagnosed or underreported. Epidemiologic studies in Europe have suggested an increased occupational risk of infection for forestry workers, hunters, veterinarians, and farmers with a tick-bite history and living in endemic areas. Although the overall genetic diversity of A. phagocytophilum in Europe is higher than in the USA, the strains responsible for the human infections are related on both continents. However, the study of the genetic variability and assessment of the difference of pathogenicity and infectivity between strains to various hosts has been insufficiently explored to date. Most of the European HGA cases presented as a mild infection, common clinical signs being pyrexia, headache, myalgia and arthralgia. The diagnosis of HGA in the USA was recommended to be based on clinical signs and the patient’s history and later confirmed using specialized laboratory tests. However, in Europe since the majority of cases are presenting as mild infection, laboratory tests may be performed before the treatment in order to avoid antibiotic overuse. The drug of choice for HGA is doxycycline and because of potential for serious complication the treatment should be instituted on clinical suspicion alone.
Factors affecting perception of the normal pediatric appendix on sonography
Authors: Castro Denise , Yang Joseph , Patel Prasan , Sauerbrei Eric , Hopman Wilma , Kolar Mila , Soboleski Don 
Published: December 2019

Abstract
Background
To determine if an inherent perception skill along with sonographer experience, knowledge base, scanning time play a role in the identification of the normal appendix in the pediatric population. This is a retrospective review of pediatric (< 18 years old) patients with a clinical suspicion of acute appendicitis presenting to the emergency department of two affiliated academic tertiary care hospitals over a 1-year time span. All patients had a sonogram performed by 1/15 sonographers or by 1/8 on-call radiology residents. Those with a normal or non-visualized appendix with subsequent discharge from ER were included in the study. Patient demographics, minutes spent scanning, and sonographer years of experience in general abdominal scanning and residents level of training were recorded.

Results
Of the 127 patients included in the study, 51 (40%) were male and 76 (60%) were female, with a mean age of 11.8 ± 4.2 years. Sonographers who failed to see a normal appendix had less experience (median 8 years) than those who did visualize the appendix (median 15 years), p ≤ 0.001. Longer time spent scanning was also associated with visualizing a normal appendix (20.4 versus 29.1 min, p = 0.001). In multivariable logistic regression, more time spent scanning (OR 1.04, 95% CI 1.01, 1.07, p = 0.012) and increased sonographer experience (OR 1.07, 95% CI 1.02, 1.13, p = 0.012) resulted in greater odds of perceiving the appendix. The top 4 were significantly more likely to visualize the appendix (88.0%) than all of the other combined (20.8%, p < 0.001), and they also had substantially more experience (median 15 years versus 8 years, p < 0.001). Overall, sonographers were more likely to see a normal appendix (61%) than the residents (14%), p < 0.001.

Conclusion
Sonography to rule out appendicitis in the pediatric patient is in general most successful when performed by experienced sonographers with adequate time to perform the scan. Triaging patients to those sonographers who have displayed optimal perceptual ability of the normal appendix may help optimize patient care and hospital resources. Having experienced sonographers available after hours would allow for optimal care in the setting of ‘query’ appendicitis.
Comparison of methylation patterns generated from genomic and cell-line derived DNA using the Illumina Infinium MethylationEPIC BeadChip array
Authors: Smyth L. J. , Kilner J. , Maxwell A. P. , McKnight A. J. 
Published: December 2019

Abstract
Objectives
Genomic DNA (gDNA) is the optimal source of DNA for methylation analysis. This study compared methylation patterns in gDNA derived from blood with cell-line derived DNA (clDNA) from the same individuals. The clDNA had been generated via an Epstein-Barr virus transformation of the participant’s lymphocytes. This analysis sought to determine whether clDNA has the potential to be utilised in lieu of finite/unavailable gDNA in methylation analyses using Illumina Infinium MethylationEPIC BeadChip arrays that assess 862,927 CpG sites.

Results
DNA samples were divided into two groups with eight gDNA and eight matched clDNA samples compared in each group (n = 16 individuals with 32 samples in total). Methylation patterns for gDNA samples generated for both groups were compared to the clDNA equivalent samples using Partek® Genomics Suite® to assess whether the significantly different CpG sites were consistent between both groups. In total, 28,632 CpG sites with significantly different levels of methylation (p < ×10−8) were common to both groups while 828,072 CpG sites assessed by the MethylationEPIC array were not significantly different in either group. This indicates that there is potential for clDNA to be used as a replacement for finite gDNA samples when absolutely necessary in DNA methylation studies.
Crowdsourced dataset to study the generation and impact of text highlighting in classification tasks
Authors: Ramírez Jorge , Baez Marcos , Casati Fabio , Benatallah Boualem 
Published: December 2019

AbstractObjectivesText classification is a recurrent goal in machine learning projects and a typical task in crowdsourcing platforms. Hybrid approaches, leveraging crowdsourcing and machine learning, work better than either in isolation and help to reduce crowdsourcing costs. One way to mix crowd and machine efforts is to have algorithms highlight passages from texts and feed these to the crowd for classification. In this paper, we present a dataset to study text highlighting generation and its impact on document classification.Data descriptionThe dataset was created through two series of experiments where we first asked workers to (i) classify documents according to a relevance question and to highlight parts of the text that supported their decision, and on a second phase, (ii) to assess document relevance but supported by text highlighting of varying quality (six human-generated and six machine-generated highlighting conditions). The dataset features documents from two application domains: systematic literature reviews and product reviews, three document sizes, and three relevance questions of different levels of difficulty. We expect this dataset of 27,711 individual judgments from 1851 workers to benefit not only this specific problem domain, but the larger class of classification problems where crowdsourced datasets with individual judgments are scarce.