bluuebunny/crossref_metadata_2025_split huggingface dataset:
Disseminating findings from the Data Analysis with Privacy Protection for Epidemiological Research (DAPPER) workshop
Authors: Wilson Rebecca , Burton Paul , Asher Innes , Carter Kim , Castelli Adriana , Cumin David , Evelo Chris , Stewart Lesley , Tsoi Kelvin , White Emma 
Published: April 2017

ABSTRACT
ObjectivesThe effective exploitation of what are often called big data is increasingly important. They provide the evidence in evidence-based health care and underpin scientific progress in many domains including social/economic policy. Typically, an optimal analysis involves working directly with microdata; i.e. the detailed data relating to each individual in the dataset. But there are many ethico-legal and other governance restrictions on physically sharing microdata. Furthermore, researchers or institutions may have an extensive intellectual property investment in complex microdata and although keen for other researchers to analyse their data they may not wish to give them a physical copy. These restrictions can discourage the use of optimum approaches to analysing pivotal data and slow scientific progress. Data science groups across the world are exploring privacy-protected approaches to analysing microdata without having to physically share the data.
ApproachA two day international workshop was arranged focussing on privacy protected approaches to data analysis – particularly federated analysis where raw data remain at their original site of collection. The workshop considered the range of approaches that exist, and those that are currently being developed. It explored the strengths, weaknesses, opportunities and challenges associated with these methods and identified situations where specific approaches have a particularly important role. The workshop included a number of practical sessions where potential users could watch demonstrations of the various approaches in action and run analyses themselves.
ResultsThe Data Analysis with Privacy Protection for Epidemiological Research (DAPPER) workshop was held 22-23rd August 2016, Bristol. We report back to the broader community on the outcomes of this workshop that focussed on exploring current approaches, tools and technical solutions that facilitate sensitive data to be shared and analysed.
ConclusionsThe workshop has helped map out key opportunities and challenges and assisted potential users, developers and other stakeholders (e.g. funders/journals) to recognise the strengths and weaknesses of different privacy protected analytic approaches. The workshop will encourage further methodological work in this field and better informed application of existing methods.
Comparing identification of children and young people with a life limiting condition from cause of death with use of an ICD-10 coding framework applied to routine clinical data
Authors: Jarvis Stuart , Fraser Lorna 
Published: April 2017

ABSTRACTObjectivesTo compare methods of estimating prevalence of life limiting conditions (LLC) among children and young people (CYP) using (i) cause of death recorded on death certificates and (ii) diagnostic codes in routinely collected inpatient and birth records.
ApproachCYP with a LLC were identified from NHS inpatient and birth records in Scotland from 1 April 2003 to 30 March 2014 using a LLC ICD-10 coding framework. The cohort was restricted to individuals who died in the study period. For each cohort member, the LLC coding framework was used to determine whether a diagnosis identified as a LLC was recorded as the underlying cause of death. For those without LLC as an underlying cause of death, the underlying cause was checked to determine whether it was related to LLC – either itself indicative of LLC when recorded on a death certificate or related to one or more of the LLCs identified in the individual’s inpatient and birth records. Finally, for those with underlying cause of death neither a LLC nor related to a LLC, the contributing causes of death were checked against the coding framework for LLC; where found, the individual was marked as having a LLC as a contributing cause of death. These analyses were undertaken for the whole cohort, per year, by age groups and by diagnostic categories.
Results20436 CYP with a LLC were identified between 1 April 2009 and 31 March 2014, of which 2249 had died and had a death register record. Of these, 1291 (57%) had a LLC as underlying cause of death; 319 (14%) had an LLC-related underlying cause of death and 268 (12%) had LLC only among contributing causes of death. 371 (16%) had no indication of LLC in their death records. Recording of a LLC as underlying cause of death was lower (41%) amongst under 1 year olds and also varied widely by diagnostic group.
ConclusionAround one in six of CYP identified using the coding framework as having a LLC (and almost one in five of under 1s) would not have been so identified using all causes of death in death records. More than a quarter (28%) would be missed if only underlying cause of death was used. This, combined with longer survival times, means use of death records has the potential to greatly underestimate prevalence of LLC in children and young people.
The seasonality and effects of temperature and rainfall on Campylobacter infections
Authors: Djennad Abdelmajid , Nichols Gordon , Loiacono Gianni , Fleming Lora , Kessel Anthony , Kovats Sari , Lake Iain , Sarran Christophe , Elson Richard , Lane Christopher , Hoeser Christophe , Bailey Trevor 
Published: April 2017

ABSTRACTBackground Campylobacteriosis is a major public health concern. Despite evidence that climate factors influence the spatio-temporal patterns of the infections; their impact is not fully described and understood.
ObjectivesTo examine methods for determining the impact of rainfall and temperature on Campylobacter cases in England and Wales.
MethodsReported cases for England and Wales were linked to local temperature and rainfall at laboratory postcode locations in the 30 days before the specimen date. Descriptive, statistical and spatial methods included a novel Comparative Conditional Incidence (CCI), wavelet analysis, hierarchical clustering, generalized additive model (GAM) and generalized structural time series model (GEST).ResultsThe Campylobacter increase in late spring was linked to temperature two weeks prior, with an increase in CCI of 0.175 cases per 100,000 per week for weeks 17 to 24; the relationship was non-linear and changed through the year. GEST with penalized varying temperature coefficient found 33% of the seasonal change was attributable to temperature, while with a fixed temperature coefficient found 8%. Wavelet analysis showed a strong annual cycle, with harmonics at six and four months and no simple association with temperature or rainfall. Geographic clustering showed three clusters with geographic similarities, representing metropolitan, rural, and other areas.
ConclusionsOur analyses provide more robust and convincing associations than simple regression analysis. The association with temperature is likely to be indirect and the primary driver remains to be determined. Local-temporal linkage of weather parameters and cases is important in improving the resolution of climate associations with infectious diseases and provides methods which can improve disease predictions. Further examination of data from a wider geographic area and longer time series should improve the understanding of the epidemiology and drivers of human Campylobacter infections.
Institute for Clinical Evaluative Sciences (ICES) Exploratory Data & Analytic Services Private Sector Pilot Project
Authors: Schull Michael , Paprica Alison P. , Victor Charles J. , Saskin Refik 
Published: April 2017

ABSTRACTObjectivesPrior to the launch of ICES Data & Analytic Services (DAS) in March 2014, only ICES scientists and analysts could access ICES data, and data could only be accessed at physical ICES locations. The DAS infrastructure, which allows public sector researchers to work with coded record level data remotely through a secure virtual environment, together with broader trends including high profile reports that call for increased access to data and the Ontario government’s Open Data initiative, prompted ICES to launch a pilot project to explore potential DAS work with the private sector.
ApproachThree mandatory principles were established for all work with the private sector: (i) alignment with ICES’ mission, vision and values; (ii) transparency; (iii) private sector work must not detract from ICES’ research institute work. The pilot included: a jurisdictional scan; informal conversations with private sector organizations to determine potential services/studies of interest; extensive discussions with data partners; the selection and conduct of two pilot studies; focus groups with members of the general public and scientists; external advice on business model options; and an external evaluation of the pilot. No changes to data sharing agreements or ICES processes were required as work with the private sector and public sector are equally allowed under Ontario law.
ResultsThe two pilot studies were successfully completed. The first study “The disease burden of gout in Ontario: A real world data retrospective study” was performed by researchers at IMS Brogan (a healthcare analytic services provider) who were provided with access to coded record-level data using the DAS iDAVE environment and performed their own analyses. In the second pilot study, “The impact of adherence to biologics on healthcare resource utilization in rheumatoid arthritis”, Janssen researchers established the research question and study design, and DAS staff and scientists provided advice about data holdings, performed the analyses, and provided Janssen and three government-funded decision making bodies with results tables. Research Ethics Board approval was required for both studies, and both private sector organizations are in the process of publishing findings.
ConclusionsICES was able to work with private sector organizations without compromising the three principles. Based on the evaluation of the private sector pilot, and the findings from the focus groups, ICES will begin offering limited analytic services to private sector researchers beginning June 2016 under ICES’ existing corporate structure, and bring recommendations regarding ongoing operations to the ICES Board in June 2017.
WBC Associates with Readmission Following Cystectomy
Authors: McIntosh Andrew G. , Li Tianyu , Ito Timothy , Mannion Jason , Dziemianowicz Mark , Waingankar Nikhil , Haseebuddin Mohammed , Chen David Y.T. , Greenberg Richard E. , Viterbo Rosalia , Kutikov Alexander , Uzzo Robert G. , Smaldone Marc C. , Abbosh Philip H. 
Published: April 2017

Background: Radical cystectomy is associated with perioperative complication rates exceeding 50% in some series. Readmission rates are increasingly used as a surgical quality metric. White blood cell count is a crude surrogate for physiologic processes which may reflect postoperative complications leading to readmission. Objective: We assessed the association between final white blood cell count at discharge and risk of readmission following radical cystectomy. Methods: Records on 477 patients undergoing radical cystectomy from 2006–2013 were reviewed. Final white blood cell count was defined as the last documented value during index admission. Univariate analysis was performed using Fisher’s exact, Wilcoxon rank sum test, and Spearman’s coefficient tests where appropriate. Multivariable logistic regression models were used to test the associations between final white blood cell count and readmission. Results: 34% of patients were readmitted within 90 days of surgery. Amongst this cohort, a cutoff final white blood cell count of 9000/mm3 was identified, with a significantly higher proportion of patients with values >9000/mm3 experiencing readmission than those with values≤9000/mm3 (42% vs 28%, p = 0.004). Other perioperative variables associated with an increased readmission rate included initial hospital length of stay≤10 days, and receipt of a continent diversion. Following adjustment, final white blood cell count >9000/mm3 was associated with increased risk of readmission (OR 2.09, 95% CI 1.23–3.53, p = 0.006). Conclusions: Final white blood cell count is associated with hospital readmission following radical cystectomy. This metric may provide important guidance in discharge algorithms.
Phase I Clinical Trial of Everolimus Combined with Trimodality Therapy in Patients with Muscle-Invasive Bladder Cancer
Authors: Bachir Bassel G. , Souhami Luis , Mansure Jose João , Cury Fabio , Vanhuyse Marie , Brimo Fadi , Aprikian Armen G. , Tanguay Simon , Sturgeon Jeremy , Kassouf Wassim 
Published: April 2017

Background: Local control following trimodality therapy (TMT) for muscle-invasive bladder cancer (MIBC) requires further optimization. Objective: Evaluating the biologic endpoint, feasibility, and toxicity of integrating everolimus to TMT in patients with MIBC. Methods: This was a phase I trial in patients with MIBC who were not surgical candidates or who refused cystectomy. Following maximal transurethral tumor resection, patients were treated by radiotherapy (50 Gy/20 fractions), gemcitabine (100 mg/m2/weekly) and escalating doses of everolimus (2.5–5.0 mg/day). Everolimus was given daily for one month prior to radiation, during treatment, and one month post-radiation. Toxicity assessment followed the Radiation Therapy Oncology Group Acute Radiation Morbidity Scoring Criteria. Biologic endpoint with downregulation of phospho-S6 (pS6) was assessed using immunohistochemistry. Local response was evaluated with imaging and bladder biopsy post-therapy. Results: 10 patients were recruited; 8 males, 2 females. Median age was 78 years (range: 63–85). Four patients entered everolimus 2.5 mg cohort. Six other patients entered everolimus 5.0 mg cohort. Toxicities were encountered in 2 patients (Grade I), 6 patients (Grade II), 9 patients (Grade III) and 1 patient (Grade IV), with some experiencing more than one toxicity. Most Grade III and IV toxicities were encountered from everolimus alone prior to combination testing. Trial was terminated early due to toxicity. Interestingly, 6/10 patients (60%) achieved a complete response with negative post-treatment biopsies. Significant decrease of pS6 was demonstrated post-therapy ( p = 0.03). Conclusions: Although combining everolimus with TMT achieved a biological endpoint and complete response in a significant number of patients with MIBC and negative prognostic factors, it was associated with unacceptable increased toxicity.
Lyme disease and Bell’s palsy: an epidemiological study of diagnosis and risk in England
Authors: Cooper Lilli , Branagan-Harris Michael , Tuson Richard , Nduka Charles 
Published: April 2017

BackgroundLyme disease is caused by a tick-borne spirochaete of the Borrelia species. It is associated with facial palsy, is increasingly common in England, and may be misdiagnosed as Bell’s palsy.AimTo produce an accurate map of Lyme disease diagnosis in England and to identify patients at risk of developing associated facial nerve palsy, to enable prevention, early diagnosis, and effective treatment.Design and settingHospital episode statistics (HES) data in England from the Health and Social Care Information Centre were interrogated from April 2011 to March 2015 for International Classification of Diseases 10th revision (ICD-10) codes A69.2 (Lyme disease) and G51.0 (Bell’s palsy) in isolation, and as a combination.MethodPatients’ age, sex, postcode, month of diagnosis, and socioeconomic groups as defined according to the English Indices of Deprivation (2004) were also collected.ResultsLyme disease hospital diagnosis increased by 42% per year from 2011 to 2015 in England. Higher incidence areas, largely rural, were mapped. A trend towards socioeconomic privilege and the months of July to September was observed. Facial palsy in combination with Lyme disease is also increasing, particularly in younger patients, with a mean age of 41.7 years, compared with 59.6 years for Bell’s palsy and 45.9 years for Lyme disease (P = 0.05, analysis of variance [ANOVA]).ConclusionHealthcare practitioners should have a high index of suspicion for Lyme disease following travel in the areas shown, particularly in the summer months. The authors suggest that patients presenting with facial palsy should be tested for Lyme disease.
Synchrotron Emission from Dark Matter Annihilation: Predictions for Constraints from Non-detections of Galaxy Clusters with New Radio Surveys
Authors: Storm Emma , Jeltema Tesla E. , Splettstoesser Megan , Profumo Stefano 
Published: April 2017

Abstract
The annihilation of dark matter particles is expected to yield a broad radiation spectrum via the production of Standard Model particles in astrophysical environments. In particular, electrons and positrons from dark matter annihilation produce synchrotron radiation in the presence of magnetic fields. Galaxy clusters are the most massive collapsed structures in the universe, and are known to host ∼μG-scale magnetic fields. They are therefore ideal targets to search for, or to constrain the synchrotron signal from dark matter annihilation. In this work, we use the expected sensitivities of several planned surveys from the next generation of radio telescopes to predict the constraints on dark matter annihilation models which will be achieved in the case of non-detections of diffuse radio emission from galaxy clusters. Specifically, we consider the Tier 1 survey planned for the Low Frequency Array (LOFAR) at 120 MHz, the Evolutionary Map of the Universe (EMU) survey planned for the Australian Square Kilometre Array Pathfinder (ASKAP) at 1.4 GHz, and planned surveys for Aperture Tile in Focus (APERTIF) at 1.4 GHz. We find that, for massive clusters and dark matter masses

, the predicted limits on the annihilation cross section would rule out vanilla thermal relic models for even the shallow LOFAR Tier 1, ASKAP, and APERTIF surveys.
Casting the Coronal Magnetic Field Reconstruction Tools in 3D Using the MHD Bifrost Model
Authors: D. Fleishman Gregory , Anfinogentov Sergey , Loukitcheva Maria , Mysh’yakov Ivan , Stupishin Alexey 
Published: April 2017

Abstract
Quantifying the coronal magnetic field remains a central problem in solar physics. Nowadays, the coronal magnetic field is often modeled using nonlinear force-free field (NLFFF) reconstructions, whose accuracy has not yet been comprehensively assessed. Here we perform a detailed casting of the NLFFF reconstruction tools, such as π-disambiguation, photospheric field preprocessing, and volume reconstruction methods, using a 3D snapshot of the publicly available full-fledged radiative MHD model. Specifically, from the MHD model, we know the magnetic field vector in the entire 3D domain, which enables us to perform a “voxel-by-voxel” comparison of the restored and the true magnetic fields in the 3D model volume. Our tests show that the available π-disambiguation methods often fail in the quiet-Sun areas dominated by small-scale magnetic elements, while they work well in the active region (AR) photosphere and (even better) chromosphere. The preprocessing of the photospheric magnetic field, although it does produce a more force-free boundary condition, also results in some effective “elevation” of the magnetic field components. This “elevation” height is different for the longitudinal and transverse components, which results in a systematic error in absolute heights in the reconstructed magnetic data cube. The extrapolations performed starting from the actual AR photospheric magnetogram are free from this systematic error, while other metrics are comparable with those for extrapolations from the preprocessed magnetograms. This finding favors the use of extrapolations from the original photospheric magnetogram without preprocessing. Our tests further suggest that extrapolations from a force-free chromospheric boundary produce measurably better results than those from a photospheric boundary.
Et demain, j’apprends quoi ? Le leurre démocratique du code informatique
Authors: Souchier Emmanuël 
Published: April 2017

Vouloir généraliser l’apprentissage du code informatique à l’école n’est-il pas un leurre démocratique nourri par le mythe d’une nouvelle écriture universelle ? Si l’idée est généreuse, sa réalisation n’est-elle pas une erreur stratégique pour l’Éducation nationale ? L’institution ne répond-elle pas à l’injonction des industriels, de la publicité ou du marketing plus qu’à l’intérêt des élèves et des citoyens que nous devons former ? Pour cerner les enjeux de ces questions, il faut interroger la nature de l’écriture numérique, de ses cadres instituants et de ce qu’ils induisent sur notre façon de penser et d’appréhender notre univers. Comment façonne-t-elle notre regard ? N’intègre-t-elle pas les outils intellectuels qui participent de notre intelligence au monde ? Le code informatique n’est pas ancré dans la culture, c’est une écriture fonctionnelle dont il faut comprendre la spécificité du fonctionnement dans une civilisation qui présente la particularité de textualiser ses pratiques sociales à travers les médias informatisés.
Commenter des textes littéraires en collaboration sur des forums et des blogs dans le secondaire
Authors: Moinard Pierre 
Published: April 2017

Quelques professeurs de collège et de lycée entretiennent le partage de lectures littéraires entre élèves sur des blogs ou en forum. Le caractère innovant de ces pratiques, souvent avancé à priori, peut être interrogé en examinant leur influence sur l’écriture métatextuelle. Quelles compétences de lecture littéraire les élèves développent-ils à travers la circulation en ligne des textes rendant compte de leurs lectures ? Quelles adaptations des professeurs favorisent-elles une diversification des écrits métatextuels ? Pour répondre à ces questions, l’étude rend compte d’une recherche en didactique du français menée auprès de classes de Troisième et de Seconde. L’analyse des séquences de « billets » a permis de suivre l’évolution des diverses verbalisations de réceptions à travers les fils de billets, en particulier l’émergence d’écrits interprétatifs. Complémentairement, des entretiens semi-directifs avec des élèves ont informé sur leur rapport à l’écriture asynchrone des lectures.
Urban form and impacts on urban heat for a corridor environment in Doha, Qatar
Authors: Skelhorn Cynthia , Ferwati Salim , Shawish Ayla , Shandas Vivek 
Published: April 2017

Doha, Qatar is a coastal city on the Arabian Gulf. Like all cities, temperatures can vary quite widely throughout the city due to various factors. In Doha, for instance, records of monitoring data from ten weather stations during 2015 show that, on average, the temperature varied by 7 degrees Celsius across the city.This paper will analyze temperature, traffic and built morphology data for 2016 along a major roadway in Doha. The research utilizes data from 3 main sources: seven days of vehicle traverses gathered in different seasons and for three times of day (morning, midday, and evening) in 2016 on the Al Salwa Rd corridor, reaching from the coast to approximately 10 km inland; daily traffic count data for intersections along the corridor; and data on building footprint and height within 500 m of the corridor.The paper will consider the influence of several factors on the temperature and air quality variation along this corridor, including: land cover, proximity to parks and vegetated areas, albedo, distance from the sea and built morphology.Temperature data will be analyzed in terms of Urban Heat Island Index (UHII), and time exceeding 37 degrees Celsius, the temperature above which conditions are considered as sweltering for human comfort. Temperature distribution maps will then be analyzed in relation to the factors noted previously.Finally, statistical analyses will be performed to test the correlation between the urban heat, built morphology, and traffic, using GIS to visualize the urban heat and built morphology.