bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Critical Role of the Clinical Research Coordinator for Clinical Trials: A Survey in Oncology
Authors: Cinefra Margherita , Cagnazzo Celeste , McMahon Laura , Arizio Francesca , Campora Sara , Camisa Roberta , Canzanella Giuliana , Contu Marianna , Frati Paola , Sottile Roberta , Gori Stefania , Procopio Giuseppe , Nanni Oriana ,   on behalf of the AIOM Working Group Coordinatori di Ricerca Clinica
Published: December 2017

Introduction Access to innovative medicine requires proper evidence from clinical trials with the growing demand of qualified and experienced personnel. The clinical research coordinator (CRC) plays an important role in the conduction of research activities and provides a strong support to the research team. In Italy, this role is not recognized at any institutional level and its professional outline is still indefinite. Several national associations (Associazione Italiana di Oncologia Medica, Collegio Italiano dei Primari Oncologi Medici Ospedalieri, Gruppo Italiano Data Manager) are committed to promoting the enhancement and recognition of the professional status of CRCs, underlining their role as fundamental. Methods A web survey, proposed by the AIOM CRC Working Group, was submitted to 319 Italian oncology sites with items focusing on the organization of sites, the research activities, the staff composition, and the presence of coordinators and the multidisciplinary team. Results A total of 115 sites (35.9%) responded to the web survey. Clinical studies were carried out at 88.7% of the investigated sites, and coordinators were on staff at 75.5% of the active investigational sites. Interestingly, there was a direct association between the number of clinical studies and the number of coordinators, whose contribution to the research activities is believed to be essential for trial conduct in 82.4% of cases. Most sites retain that the quality of clinical research has absolutely improved (83.3%) after the implementation of a coordinator as member of the team. Conclusions Given the constant growth of the number of clinical trials performed at Italian oncology sites, the CRC proves to be an essential component of the research team. However, there is an urgent need to institute the professional role alongside the need to standardize the training of coordinators to establish the minimum requirements enhanced by qualifying courses.
Renewed Estimates of Grassland Aboveground Biomass Showing Drought Impacts
Authors: Li F. , Chen J. Q. , Zeng Y. , Wu B. F. , Zhang X. Q. 
Published: December 2017

AbstractVariations in ecosystem composition and structure within a cover type of the same biome can be responsible for the large amounts of uncertainty in remote sensing modeling of aboveground biomass (AGB). Based on 820 ground measurements of AGB and the pure vegetation index models, we proposed a spatially variable remote sensing scalar (i.e.,Mscalar) in estimating AGB by addressing within‐type variations of vegetation. We tested this new modeling approach in Inner Mongolia grasslands and achieved a higherR2(>0.88) and lower RMSE value (<28.17 g/m2) than those in the conventional remote sensing models. The annual average (STD) of the grassland AGB for 2001–2016 was ~87 (±9) Tg, with an AGB density of 104 ± 74 g/m2. The interannual variation of AGB appeared insignificant over the study period, except in the western region where it increased significantly. The dynamics of AGB were highly correlated with drought severity during the growing season (R2 = 0.691,P < 0.001). AGB under normal climate (i.e., without drought) was ~90.88 Tg, but it increased by ~19% (17.11 Tg) in a wet year (2012) and decreased by 20% (18.16 Tg) in a dry year (2001). More importantly, the high grazing intensity played a less significant role in directing grassland AGB dynamics (R2 = 0.024,P = 0.599). Future efforts are needed to explore how within‐type variation of vegetation may change temporally and spatially in accurate estimate of AGB across heterogeneous landscapes, as well as the potential underlying mechanisms from biological, physical, and human perspectives.
Universal Basic Income in British Politics, 1918–2018: From a ‘Vagabond's Wage’ to a Global Debate
Authors: SLOMAN PETER 
Published: December 2017

AbstractThe idea of a Universal Basic Income (UBI) has moved rapidly up the British political agenda in recent years, with support from the Green Party, the Royal Society of Arts, and left-wing writers such as Paul Mason. Shadow Chancellor John McDonnell has set up a working group to examine its implications, and four Scottish councils are hoping to launch pilot schemes. Contemporary British interest in UBI forms part of a lively global debate about automation, inequality and precarious labour, but it also draws on a long history of proposals for tax-benefit reform within UK social policy. This article identifies five waves of enthusiasm for basic income in Britain over the past century and highlights patterns of continuity and change. It shows that interest in the proposal has been greatest at times of pessimism about the future of the labour market, though concerns about the ethics and affordability of unconditional payments have always been difficult to shake. Advocates of UBI have also struggled to reconcile the technocratic approach of its Conservative and Liberal supporters with the transformative ambitions of the radical left. It remains to be seen whether the recent growth of left-wing support for UBI will improve its prospects of implementation.
Assessing the impact of public education on a preventable zoonotic disease: rabies
Authors: HASANOV E. , ZEYNALOVA S. , GELEISHVILI M. , MAES E. , TONGREN E. , MARSHALL E. , BANYARD A. , MCELHINNEY L. M. , WHATMORE A. M. , FOOKS A. R. , HORTON D. L. 
Published: December 2017

SUMMARYEffective methods to increase awareness of preventable infectious diseases are key components of successful control programmes. Rabies is an example of a disease with significant impact, where public awareness is variable. A recent awareness campaign in a rabies endemic region of Azerbaijan provided a unique opportunity to assess the efficacy of such campaigns. A cluster cross-sectional survey concerning rabies was undertaken following the awareness campaign in 600 households in 38 randomly selected towns, in districts covered by the campaign and matched control regions. This survey demonstrated that the relatively simple awareness campaign was effective at improving knowledge of rabies symptoms and vaccination schedules. Crucially, those in the awareness campaign group were also 1·4 times more likely to report that they had vaccinated their pets, an essential component of human rabies prevention. In addition, low knowledge of appropriate post-exposure treatment and animal sources of rabies provide information useful for future public awareness campaigns in the region and other similar areas.
Du magst mich nicht, weil ich hässlich bin!
Authors: Schmidt Jennifer , Martin Alexandra 
Published: December 2017

Zusammenfassung. Theoretischer Hintergrund: Viele Personen befürchten Zurückweisungen aufgrund ihres Aussehens. Übermäßige „aussehensbezogene Zurückweisungssensitivität“ (ARS) kann jedoch zur Entstehung und Aufrechterhaltung von – insbesondere körperfokussierter – Psychopathologie beitragen. Fragestellung: ARS ist im deutschsprachigen Raum wenig untersucht, da Erhebungsinstrumente fehlen. Daher war die Validierung einer deutschen „Appearance-based-Rejection-Sensitivity-Scale“ (ARS-D; Park, 2007 ) Ziel der Studie. Methode: Nach Übersetzung des englischen Originals wurde die psychometrische Güte der ARS-D in einer Online-Befragung getestet (n = 391). Ermittelt wurden Itemcharakteristika, Faktorstruktur, Reliabilität und Konstruktvalidität. Ergebnisse: Die ARS-D zeigte bei einfaktorieller Struktur sehr gute Reliabilitätsindizes. Die psychometrischen Eigenschaften ließen sich bei einer auf 12 Items gekürzten Skalenvariante (Original: 15 Items) weiter verbessern. Signifikante Korrelationen mit körperdysmorpher Besorgnis, Essstörungssymptomatik und Depressivität (rs > .30) indizieren Konstruktvalidität. Schlussfolgerungen: Die ARS-D ist zur Erfassung und weiteren Erforschung der Rolle aussehensbezogener Zurückweisungssensitivität bei verschiedenen Störungsbildern geeignet.
Diffuse γ-ray emission
in the vicinity of young star cluster Westerlund 2
Authors: Yang Rui-zhi , de Oña Wilhelmi Emma , Aharonian Felix 
Published: December 2017

We report the results of our analysis of the publicly available data obtained by the Large Area Telescope (LAT) on board the Fermi satellite towards the direction of the young massive star cluster Westerlund 2. We found significant extended γ-ray emission in the vicinity of Westerlund 2 with a hard power-law energy spectrum extending from 1 to 250 GeV with a photon index of 2.0 ± 0.1. We argue that amongst several alternatives, the luminous stars in Westerlund 2 are likely sites of acceleration of particles responsible for the diffuse γ-ray emission of the surrounding interstellar medium. In particular, the young star cluster Westerlund 2 can provide sufficient non-thermal energy to account for the γ-ray emission. In this scenario, since the γ-ray production region is significantly larger than the area occupied by the star cluster, we conclude that the γ-ray production is caused by hadronic interactions of accelerated protons and nuclei with the ambient gas. In that case, the total energy budget in relativistic particles is estimated of the order of 1050 erg.
The Dibenzosuberenone Scaffold as a Privileged Substructure: From Synthesis to Application
Authors: Dastan Arif , Saracoglu Nurullah , Kilic Haydar 
Published: December 2017

Numerous studies on dibenzosuberenones, especially on 5-dibenzosuberenones, have emerged in recent years. This review focuses on the chemistry of dibenzosuberenones, including their synthesis and applications, which are currently used as tools by the synthetic and biological communities.1	Introduction2	5-Dibenzosuberenone (5H-Dibenzo[a,d]cyclohepten-5-one)2.1	Synthesis of 5-Dibenzosuberenone2.2	Reactions of 5-Dibenzosuberenone3	5H-Dibenzo[a,c]cyclohepten-5-one3.1	Synthesis of 5H-Dibenzo[a,c]cyclohepten-5-one3.2	Reactions of 5H-Dibenzo[a,c]cyclohepten-5-one4	6H-Dibenzo[a,c]cyclohepten-6-one and 10H-Dibenzo[a,d]cyclohepten-10-one4.1	Generation and Trapping of 6H-Dibenzo[a,c]cyclohepten-6-one and 10H-Dibenzo[a,d]cyclohepten-10-one5	Dibenzocycloheptenediones5.1	Synthesis of Dibenzocycloheptenediones5.2	Reactions of Dibenzocycloheptenediones6	Conclusion
Transition-Metal-Catalyzed Asymmetric Allylation of Carbonyl Compounds with Unsaturated Hydrocarbons
Authors: Gong Liu-Zhu , Wang Pu-Sheng , Shen Meng-Lan 
Published: December 2017

The asymmetric allylation of carbonyl compounds is an important process for the formation of carbon–carbon bonds, generating optically active homoallylic alcohols that are versatile building blocks with widespread applications in organic synthesis. The use of readily available unsaturated hydrocarbons as allylating reagents in the transition-metal-catalyzed asymmetric allylation has received increasing interest as either a step- or an atom-economy alternative. This review summarizes transition-metal-catalyzed enantioselective allylations on the basis of the ‘indirect’ and ‘direct’ use of simple unsaturated hydrocarbons (include dienes, allenes, alkynes, and alkenes) as allylating reagents, with emphasis on highlighting conceptually novel reactions.1	Introduction2	‘Indirect’ Use of Unsaturated Hydrocarbons in Asymmetric Allylation of Carbonyl Compounds2.1	Enantioselective Allylation with 1,3-Dienes2.2	Enantioselective Allylation with Allenes2.3	Enantioselective Allylation with Alkenes3	‘Direct’ Use of Unsaturated Hydrocarbons in Asymmetric Allylation of Carbonyl Compounds3.1	Enantioselective Allylation with 1,3-Dienes3.2	Enantioselective Allylation with Allenes3.3	Enantioselective Allylation with Alkynes3.4	Enantioselective Allylation with Alkenes4	Conclusions
Ethical Issues in the Neurology of Pregnancy
Authors: Cochrane Thomas 
Published: December 2017

AbstractDecision making for pregnant women and fetuses who suffer brain injuries is emotionally difficult and conceptually challenging. Occasionally, both the pregnant woman and the fetus have suffered an injury that confers a poor neurological prognosis, and decisions about one of them will have implications for the other—making the process of decision making even more problematic. In this article, decision-making standards and principles are reviewed for both pregnant women and fetuses, using a real case from the author's institution. Practical suggestions are made regarding deliberative processes and consultative models that can help with these difficult cases.
Reproductive Issues in MS
Authors: Kaplan Tamara , Houtchens Maria 
Published: December 2017

AbstractMultiple sclerosis (MS) is an autoimmune disease of the central nervous system, predominantly affecting women of childbearing age. Therefore, issues of conception, pregnancy, and delivery are of significant importance to patients and treating physicians. We discuss immunologic and clinical effects of pregnancy on the course of MS including both immunosuppression on a local level and a heightened state of immunocompetence on a global level. Clinical outcomes of the Pregnancy in Multiple Sclerosis trials are reported. We analyze and update the available data on safety and efficacy of immunomodulating MS treatments and symptomatic treatments for pregnant and lactating women, and address specific issues of MS management at the time of pregnancy. We review the data related to estrogen-based MS therapies currently or previously in trials. Pregnancy does not appear to be associated with adverse outcomes in MS patients. Some evidence suggests possible beneficial effects, although clear prospective data of sufficient length and quality are limited. Long-term relapse rates or disability progression do not seem to be affected by pregnancy in MS patients. The use of immunosuppressive or immunomodulatory agents in pregnancy is not routinely advisable but could be considered under special circumstances.
Pulmonale Immunität bei Tuberkulose
Authors: Herzmann C. , Dallenga T. , Kalinke U. 
Published: December 2017

ZusammenfassungTuberkulose wird durch Inhalation von bakterienhaltigen Aerosolen übertragen und 75 % der Erkrankungen betreffen die Lunge. Die Immunprozesse zwischen Exposition und Krankheitsentwicklung sind großenteils auf die Lunge beschränkt und nur teilweise entschlüsselt. Der Erreger wird in den meisten Fällen vermutlich durch Zellen des angeborenen Immunsystems kontrolliert oder eradiziert, ohne dass dies mit Standardmethoden in vivo nachgewiesen werden kann. Die anschließende adaptive Immunantwort wird wesentlich von CD4+- und CD8+-T-Lymphozyten vermittelt, während die humorale Immunität nur eine untergeordnete Bedeutung hat. Der Artikel gibt eine Übersicht über den aktuellen Wissensstand der intrapulmonalen Mechanismen, die im Verlauf von Exposition, latenter Infektion, aktiver Erkrankung und Therapie beobachtet werden.
Is Growing Oranges in Florida a Good Investment?
Authors: Trejo‐Pech Carlos J O , Spreen Thomas H , Zansler Marisa L 
Published: December 2017

AbstractWe provide a financial model to evaluate an orange grove investment in Florida, the producing region supplying around 90% of U.S. domestic production of orange juice. A representative orange grower planting early‐mid varieties for the processed market is featured in the case. The study assumes that an existing grove has become disease‐infested to a degree that there is little, if any economic value in maintaining it. The grower is left with the choice to replant the grove or to convert the land to other uses. The replanting baseline model yields a 9.7% Modified Internal Rate of Return (MIRR) and the Monte Carlo simulation shows that MIRR is equal or higher than the 7.5% hurdle rate around 81% times the model is simulated. The risk of managing an orange grove is higher than a decade ago mainly due to the presence of citrus greening, a disease that reduces yields and degrades fruit quality, causing variability in productivity and operating costs. Opportunities for growers include planting incentive programs implemented by both the government and major citrus processors and from policy changes such as the possibility of changes in depreciation of new investment for income tax purposes. Readers of this case study are expected to challenge the assumptions of the financial model and consider additional elements of risk and opportunities on their assessment of the potential orange grove investment.
Algorithmic identification of discrepancies between published ratios and their reported confidence intervals and P-values
Authors: Georgescu Constantin , Wren Jonathan D 
Published: December 2017

Abstract

Motivation
Studies, mostly from the operations/management literature, have shown that the rate of human error increases with task complexity. What is not known is how many errors make it into the published literature, given that they must slip by peer-review. By identifying paired, dependent values within text for reported calculations of varying complexity, we can identify discrepancies, quantify error rates and identify mitigating factors.

Results
We extracted statistical ratios from MEDLINE abstracts (hazard ratio, odds ratio, relative risk), their 95% CIs, and their P-values. We re-calculated the ratios and P-values using the reported CIs. For comparison, we also extracted percent–ratio pairs, one of the simplest calculation tasks. Over 486 000 published values were found and analyzed for discrepancies, allowing for rounding and significant figures. Per reported item, discrepancies were less frequent in percent–ratio calculations (2.7%) than in ratio–CI and P-value calculations (5.6–7.5%), and smaller discrepancies were more frequent than large ones. Systematic discrepancies (multiple incorrect calculations of the same type) were higher for more complex tasks (14.3%) than simple ones (6.7%). Discrepancy rates decreased with increasing journal impact factor (JIF) and increasing number of authors, but with diminishing returns and JIF accounting for most of the effect. Approximately 87% of the 81 937 extracted P-values were ≤ 0.05.

Conclusion
Using a simple, yet accurate, approach to identifying paired values within text, we offer the first quantitative evaluation of published error frequencies within these types of calculations.

Supplementary information
Supplementary data are available at Bioinformatics online.
Protein classification using modified n-grams and skip-grams
Authors: Islam S M Ashiqul , Heil Benjamin J , Kearney Christopher Michel , Baker Erich J 
Published: December 2017

Abstract

Motivation
Classification by supervised machine learning greatly facilitates the annotation of protein characteristics from their primary sequence. However, the feature generation step in this process requires detailed knowledge of attributes used to classify the proteins. Lack of this knowledge risks the selection of irrelevant features, resulting in a faulty model. In this study, we introduce a supervised protein classification method with a novel means of automating the work-intensive feature generation step via a Natural Language Processing (NLP)-dependent model, using a modified combination of n-grams and skip-grams (m-NGSG).

Results
A meta-comparison of cross-validation accuracy with twelve training datasets from nine different published studies demonstrates a consistent increase in accuracy of m-NGSG when compared to contemporary classification and feature generation models. We expect this model to accelerate the classification of proteins from primary sequence data and increase the accessibility of protein characteristic prediction to a broader range of scientists.

Availability and implementation
m-NGSG is freely available at Bitbucket: https://bitbucket.org/sm_islam/mngsg/src. A web server is available at watson.ecs.baylor.edu/ngsg.

Supplementary information
Supplementary data are available at Bioinformatics online.
polyPK: an R package for pharmacokinetic analysis of multi-component drugs using a metabolomics approach
Authors: Li Mengci , Wang Shouli , Xie Guoxiang , Ma Xiaohui , Chen Tianlu , Jia Wei 
Published: December 2017

Abstract

Summary
Pharmacokinetics (PK) is a long-standing bottleneck for botanical drug and traditional medicine research. By using an integrated phytochemical and metabolomics approach coupled with multivariate statistical analysis, we propose a new strategy, Poly-PK, to simultaneously monitor the performance of drug constituents and endogenous metabolites, taking into account both the diversity of the drug’s chemical composition and its complex effects on the mammalian metabolic pathways. Poly-PK is independent of specific measurement platforms and has been successfully applied in the PK studies of Puerh tea, a traditional Chinese medicine Huangqi decoction and many other multi-component drugs. Here, we introduce an R package, polyPK, the first and only automation of the data analysis pipeline of Poly-PK strategy. polyPK provides 10 functions for data pre-processing, differential compound identification and grouping, traditional PK parameters calculation, multivariate statistical analysis, correlations, cluster analyses and resulting visualization. It may serve a wide range of users, including pharmacologists, biologists and doctors, in understanding the metabolic fate of multi-component drugs.

Availability and implementation
polyPK package is freely available from the R archive CRAN (https://CRAN.R-project.org/package=polyPK).

Supplementary information
Supplementary data are available at Bioinformatics online.
A benchmark for comparing precision medicine methods in thyroid cancer diagnosis using tissue microarrays
Authors: Wang Ching-Wei , Lee Yu-Ching , Calista Evelyne , Zhou Fan , Zhu Hongtu , Suzuki Ryohei , Komura Daisuke , Ishikawa Shumpei , Cheng Shih-Ping 
Published: December 2017

Abstract

Motivation
The aim of precision medicine is to harness new knowledge and technology to optimize the timing and targeting of interventions for maximal therapeutic benefit. This study explores the possibility of building AI models without precise pixel-level annotation in prediction of the tumor size, extrathyroidal extension, lymph node metastasis, cancer stage and BRAF mutation in thyroid cancer diagnosis, providing the patients’ background information, histopathological and immunohistochemical tissue images.

Results
A novel framework for objective evaluation of automatic patient diagnosis algorithms has been established under the auspices of the IEEE International Symposium on Biomedical Imaging 2017— A Grand Challenge for Tissue Microarray Analysis in Thyroid Cancer Diagnosis. Here, we present the datasets, methods and results of the challenge and lay down the principles for future uses of this benchmark. The main contributions of the challenge include the creation of the data repository of tissue microarrays; the creation of the clinical diagnosis classification data repository of thyroid cancer; and the definition of objective quantitative evaluation for comparison and ranking of the algorithms. With this benchmark, three automatic methods for predictions of the five clinical outcomes have been compared, and detailed quantitative evaluation results are presented in this paper. Based on the quantitative evaluation results, we believe automatic patient diagnosis is still a challenging and unsolved problem.

Availability and implementation
The datasets and the evaluation software will be made available to the research community, further encouraging future developments in this field. (http://www-o.ntust.edu.tw/cvmi/ISBI2017/).

Supplementary information
Supplementary data are available at Bioinformatics online.