bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting enhancers in mammalian genomes using supervised hidden Markov models
Authors: Zehnder Tobias , Benner Philipp , Vingron Martin 
Published: March 2019

AbstractBackgroundEukaryotic gene regulation is a complex process comprising the dynamic interaction of enhancers and promoters in order to activate gene expression. In recent years, research in regulatory genomics has contributed to a better understanding of the characteristics of promoter elements and for most sequenced model organism genomes there exist comprehensive and reliable promoter annotations. For enhancers, however, a reliable description of their characteristics and location has so far proven to be elusive. With the development of high-throughput methods such as ChIP-seq, large amounts of data about epigenetic conditions have become available, and many existing methods use the information on chromatin accessibility or histone modifications to train classifiers in order to segment the genome into functional groups such as enhancers and promoters. However, these methods often do not consider prior biological knowledge about enhancers such as their diverse lengths or molecular structure.ResultsWe developedenhancer HMM(eHMM), a supervised hidden Markov model designed to learn the molecular structure of promoters and enhancers. Both consist of a central stretch of accessible DNA flanked by nucleosomes with distinct histone modification patterns. We evaluated the performance of eHMM within and across cell types and developmental stages and found that eHMM successfully predicts enhancers with high precision and recall comparable to state-of-the-art methods, and consistently outperforms those in terms of accuracy and resolution.ConclusionseHMM predicts active enhancers based on data from chromatin accessibility assays and a minimal set of histone modification ChIP-seq experiments. In comparison to other ’black box’ methods its parameters are easy to interpret. eHMM can be used as a stand-alone tool for enhancer prediction without the need for additional training or a tuning of parameters. The high spatial precision of enhancer predictions gives valuable targets for potential knockout experiments or downstream analyses such as motif search.
Recent trends from the results of clinical trials on gastric cancer surgery
Authors: Kiyokawa Takashi , Fukagawa Takeo 
Published: March 2019

AbstractThe Japan Clinical Oncology Group has recently conducted large scale clinical trials with findings that have revealed pivotal strategies for the treatment of resectable gastric cancer surgery. These findings include the fact that D3 lymphadenectomy does not improve survival rates when compared to D2 lymphadenectomy, and it is not recommended for resectable gastric cancer. Also, a transhiatal approach is recommended, instead of the left thoraco‐abdominal approach, for the treatment of adenocarcinoma of the esophago‐gastric junction or gastric cardia which has invaded ≤ 3 cm of the esophagus. Gastrectomy with splenectomy and bursectomy had been recommended as a part of the D2 lymphadenectomy. However, the results of the recent clinical trials revealed that splenectomy should be avoided in total gastrectomy with D2 lymphadenectomy for proximal gastric cancer and that bursectomy should be avoided in gastrectomy with D2 lymphadenectomy for resectable gastric cancer. Both splenectomy and bursectomy were found to be unable to improve survival, but instead increased operative morbidity. These trials revealed that the above‐mentioned invasive and aggressive procedures did not provide sufficient survival benefits and that gastric cancer surgery may be trending from an “invasive to less invasive” and “aggressive to more conservative” approach.
Predictors of Nephrolithiasis, Osteoporosis, and Mortality in Primary Hyperparathyroidism
Authors: Reid Laura J , Muthukrishnan Bala , Patel Dilip , Seckl Jonathan R , Gibb Fraser W 
Published: March 2019

AbstractContextPrimary hyperparathyroidism (PHPT) has a prevalence of 0.86% and is associated with increased risk of nephrolithiasis and osteoporosis. PHPT may also be associated with increased risk of cardiovascular disease and mortality.ObjectiveTo identify risk factors for nephrolithiasis, osteoporosis, and mortality in PHPT.DesignRetrospective cohort study.SettingUniversity teaching hospital.PatientsPresented with PHPT between 2006 and 2014 (n = 611).Main Outcome MeasureAssessment of nephrolithiasis, osteoporosis, and mortality.ResultsOf patients with PHPT, 13.9% had nephrolithiasis. Most had previously documented stone disease, and only 4.7% of asymptomatic patients who were screened for renal stones had calculi identified, not very dissimilar to the rate in the non-PHPT population. Younger age (P < 0.001) and male sex (P = 0.003) were the only independent predictors of nephrolithiasis. Of patients with dual-energy X-ray absorptiometry data, 48.4% had osteoporosis (223/461). Older age (P < 0.001), lower body mass index (P = 0.002), and lower creatinine (P = 0.006) were independently associated with a diagnosis of osteoporosis. Higher PTH was independently associated with lower z score at the hip (P = 0.009); otherwise, calcium and PTH were not associated with lower z scores. Mortality in PHPT was associated with older age (P < 0.008), social deprivation (P = 0.028), and adjusted calcium (P = 0.009) but not independently with PTH at diagnosis.ConclusionsScreening for nephrolithiasis has a low yield, particularly in lower risk patients. Osteoporosis is only minimally associated with biochemical indices of PHPT. Mortality is associated with higher calcium (and possibly vitamin D deficiency) but not PTH.
International Environmental Law for the 21st Century: The Constitutionalization of the Right to a Healthy Environment in the Inter-American Court of Human Rights Advisory Opinion No. 23
Authors: Feria-Tinta Mónica , Milnes Simon C. 
Published: March 2019

This article analyses the recent Advisory Opinion of the Inter-American Court of Human Rights on Environment and Human Rights and argues that it constitutes a milestone effectively reorientating international environmental law. The article is divided as follows. First, it analyses the most salient aspects of the Advisory Opinion inter alia (1) The right to a healthy environment as binding law and; (2) The Advisory Opinion as a landmark in the gradual development of international jurisprudence on cross-border (or “diagonal”) human rights obligations (i.e. the possibility for human rights claims to be brought by individuals not under the territorial jurisdiction of the State whose international responsibility for environmental harm is invoked). Second, it contextualizes the Advisory Opinion by discussing what we consider to be four key vectors currently affecting the trajectory of the ongoing development of international environmental law and how the advances made in the Advisory Opinion fit with those developments. Third, it places the Advisory Opinion in the wider context of developments moving towards a needed reorientation in international environmental law, in particular: integration (or de-fragmentation) of international law, the operationalization of environmental principles into working-level legal norms, and a focus on practical remedies. It is argued that as the world experiences the pressure for more effective environmental law and accountability, some of the most sophisticated and innovative thinking on international environmental law today, is emanating from countries in the Southern hemisphere, as attested to by the Advisory Opinion.
Who Benefits When Prescription Drug Manufacturers Offer Copay Coupons?
Authors: King Gregory J. , Chao Xiuli , Duenyas Izak 
Published: March 2019

The rising cost of prescription drugs is a concern in the United States. To manage drug costs, insurance companies induce patients to choose less-expensive medications by making them pay higher copayments for more-expensive drugs, especially when multiple drug options are available to treat a condition. However, drug manufacturers have responded by offering copay coupons—coupons intended to be used by those already with prescription drug coverage. Recent empirical work has shown that such coupons significantly increase insurer costs without much benefit to patients, who incur lower out-of-pocket expenses with coupons but may eventually see higher costs passed to them. As a result, there is pressure from the insurance industry and consumer advocacy groups to ban copay coupons. In this paper we analyze how copay coupons affect patients, insurance companies, and drug manufacturers, while addressing the question of whether insurance companies would in fact always benefit from a copay coupon ban. We find that copay coupons tend to benefit drug manufacturers with large profit margins relative to other manufacturers, while generally, but not always, benefiting patients; insurer costs tend to increase with coupons from high-price drug manufacturers and decrease with coupons from low-price manufacturers. Although often helping drug manufacturers and increasing insurer costs, we also identify situations in which copay coupons benefit both patients and insurers. Thus, a blanket ban on copay coupons would not necessarily benefit insurance companies. In addition to the policy implications of our work, we make concrete managerial recommendations to insurers. We discuss how they should set formulary selection policies taking into account the fact that drug manufacturers may offer coupons; and we suggest how they can benefit from subsidizing coupons from drug manufacturers with low-price drugs, or from having drug manufacturers compete on price, to receive a favorable formulary position (i.e., copay). This paper was accepted by Yossi Aviv, operations management.
Simultaneous Optimization of Speed and Buffer Times with an Application to Liner Shipping
Authors: Mulder Judith , van Jaarsveld Willem , Dekker Rommert 
Published: March 2019

Transport companies often have a published timetable. To maintain timetable reliability despite delays, companies include buffer times during timetable development and adjust the traveling speed during timetable execution. We develop an approach that integrates timetable development and execution. We model execution of the timetable as a stochastic dynamic program (SDP). An SDP is a natural framework to model random events causing (additional) delay, propagation of delays, and real-time optimal speed adjustments. However, SDPs alone cannot incorporate the buffer allocation during timetable development, as buffer allocation requires choosing the same action in different states of the SDP. Motivated by the practical need for timetables that operate well during timetable execution, our model seeks the buffer allocation that yields the SDP that has minimal long-run average costs. We derive several analytical insights into the model. We prove that costs are joint convex in the buffer times, and we develop theory to compute subgradients. Our fast and exact algorithm for buffer time allocation is based on these results. Our case study considers container vessels sailing a round tour consisting of 14 ports based on Maersk data. The algorithm finds the optimal timetable in roughly 70 seconds for realistic problem instances. The optimal timetable yields cost reductions of about four to 10 million U.S. dollars per route per year in comparison with the current timetable. Finally, we show the robustness of our solution approach for different parameter settings using a sensitivity analysis. The online appendices are available at https://doi.org/10.1287/trsc.2018.0842 .
FORMS OF REJUVENATION OF THE RUSSIAN FEDERATION POLITICAL AND STATE ELITE IN THE 2000S
Authors: Шарапов Алексей Владимирович 
Published: March 2019

We studied the effect of events for the recruitment of young people into the federal elite held by the state authorities and the United Russia party over the past 15 years. The article presents advantages and disadvantages of staff projects: "Political Plant", "Youth Primaries" and "Leaders of Russia". As a result of these projects implementation, the concept of “youth” has become essentially blurred. The degree of youth involvement in these projects has increased. But there was no significant influx of young personnel to leading managerial positions through these measures, which reveals an underestimation of the young people’s role in the social and political development of the country by the current elite. Each new project started before the beginning of the next federal election.
SOCIAL SECURITY OF A RUSSIAN INDUSTRIAL ENTERPRISE (ON THE MATERIALS OF SOCIOLOGICAL RESEARCH IN THE KRASNOYARSK REGION)
Authors: Немировский Валентин Геннадьевич , Кареева Анна Петровна 
Published: March 2019

The objectives of the research presented in the article are the study of the Institute of security and its institutional form «social security» at various levels of society and the analysis of the representations of employees of one of the Russian modern industrial enterprises of the existing social security. The qualitative analysis of documentary sources allowed to carry out the social and historical analysis of social risks and social reserves of work of Mining and chemical plant in a binding to historical periods of its development (in the period from 1950 to 2012 were used). Content analysis revealed the views of the leadership of the MCC on the existing social security of the plant. A mass questionnaire survey helped to analyze the views of employees regarding the existing social security of the Mining and chemical plant. The study was conducted twice-in 2013, in 2017. The study proved that during its existence, the MCC, faced with social risks, minimized them with the help of existing social security in the enterprise. The historical periods of its development were divided into stable and transitional types of society. A comparative analysis of the views of the management of the plant and employees regarding the existing social security at the MCC revealed significant differences between them.
Keywords: security, institutional approach, risky society, social security, stableand transitional type of society, social security effectiveness.
ETHNIC DIASPORAS: ADAPTIVE AND INTEGRATIVE POTENTIAL IN CROSS-BORDER REGIONS OF RUSSIA
Authors: Черепанова Мария Ивановна , Горбунова Анастасия Андреевна 
Published: March 2019

The social significance of scientific studies of ethnic communities is conditioned by the increase of diasporas becoming a common stationary phenomenon in most countries of the world. The scientific discourse of the problem is aimed at analyzing the integral and conflict-causing aspects of the activities of modern diasporas, which will be determined by the specificity of the historical, socio-economic situation, region of residence, features of interethnic policy, etc. The goal of the article was to analyze evaluations of representatives of diasporas in six regions of the Russian borderland about success of adaptation and integration of migrants in the host community. The set of indicators included attitudes towards migrant children in educational institutions, opinions about the restriction or stimulation of migration in the regions, attitudes towards illegal migrants, the problem of national enclaves. The presented results are based on a systems approach, the theory of interdependence in the world development, the essence of which is the formation of the transnational structure of the world community. Conclusions about the adaptive and integration potential of regional diasporas are made, differential assessments on a number of socially significant issues thatdetermine the scientific field of the phenomenon of transit migration in the border areas of the Russian Federation under study are presented. The scientific novelty of the proposed results consists in the study of the role of ethnic communities, in comparison with the local population of the recipient countries, which can be used in forecasting the effectiveness of integration processes and providing the scientific basis for regulating the risk of interethnic conflicts. The practical significance consists in the possibility of optimizing the activities of diasporas for effective social management in the field of migration policy.
The implementation of IFRS in Indonesian Islamic accounting
Authors: Arwani Agus 
Published: March 2019

This research examines the IFRS Â implementation in Indonesian Islamic accounting. It employs a literature review method to systematically explain the accounting theory, the Islamic Financial Accounting Standards, and International Financial Reporting Standards (IFRS).Â This study concludes that there is a conflict between the International Financial Reporting Standards (IFRS) and some Islamic principles which has not been yet resolved. The Islamic accounting is also facing some complex issues related to the convergence of International Financial Reporting Standards in Indonesia due to incorrect implementation of IFRS in some countries related to the translation problems from English to local languages. The biggest problem in implementing IFRS convergence for business is dealing with the expenses spent for the development of knowledge, supports and trainings for consultants
Introduction
Authors: Frieden Marie-Cécile , Graber Nils , M’zoughi Meriem 
Published: March 2019

« Maladies chroniques » et « Suds » sont des termes rarement associés mais qui constituent le cœur des réflexions menées au sein de ce numéro thématique. Si la catégorie de maladie chronique connaît un essor aux États-Unis puis en Europe occidentale au cours du XXe siècle, elle n’est que faiblement mobilisée dans le champ de la santé mondiale. Renvoyant à la « victoire » de la médecine occidentale sur les maladies infectieuses, l’expansion des maladies chroniques est perçue comme la conséquence de l’industrialisation et des progrès socioéconomiques. Une abondante littérature en sciences sociales, notamment en sociologie, s’est développée au « Nord » à partir des années 1970 pour aborder la trajectoire des patients atteints de maladies au long cours. Leur prise en charge requiert de multiples formes d’adaptations des comportements individuels et des dispositifs institutionnels, ce qui tranche avec le modèle thérapeutique des maladies aigües – diagnostic, traitement, guérison.
Possession et ensorcellement comme « maladies chroniques »
Authors: Cherak Fatima Zohra 
Published: March 2019

La rouqya, visible depuis les années 1990 en Algérie et en Égypte, se présente comme une pratique thérapeutique islamique. Ses acteurs, les malades et leurs familles, s’interrogent sur la maladie et le malheur qui perdurent. Leur itinéraire thérapeutique s’appuie sur la biomédecine et d’autres soins non conventionnels où la maladie « naturelle » côtoie les entités surnaturelles également tenues responsables de la souffrance. Les symptômes sont interprétés, évalués, pris en charge dans un processus de quête de guérison durant des mois, voire des années. La rouqya inscrit la souffrance dans la logique d’une agression extérieure par les djinns et les jeteurs de sort. Bien que Dieu soit reconnu comme acteur suprême, l’étiologie de la possession et de la sorcellerie est privilégiée pour expliquer une certaine chronicité de la maladie et la permanence ou le renouvellement du malheur, d’où l’intérêt de l’engagement thérapeutique dans un modèle exorcistique tel que la rouqya.
The strike has become social
Authors: Pirone Maurilio 
Published: March 2019

The article aims first of all to retrace the evolution of some paths of social mobilization around precariousness in Italy. The basic assumption is that such condition cannot be reduced to a sociological or economic category, but rather constitutes a ground for trade union organisation and political claims. I will articulate this analysis into two historically distinct moments on the basis of the ways in which precariousness has been described and opposed. Compared to a first moment in which the rise and narration of new working subjects took the centre of the stage, it seems possible to identify a second kind of mobilisations in which – while maintaining an alternation between specific disputes and general movements – the issue of precariousness spilled over and involved bio-political aspects as social reproduction and self-determination. Therefore, the forms of protest are also transformed: in the final part of the article I will try to clarify the main features of the social strike experiments that have occurred in Italy in recent years.
« Travail précaire », « précarité »
Authors: Cingolani Patrick 
Published: March 2019

Pour conclure ce dossier, Patrick Cingolani, essaie de penser ensemble les deux univers de sens que recouvre, dans son acception la plus large, la notion de précarité telle qu’elle a été enrichie par la circulation internationale : les luttes d’un travail privé de ses droits et les expérimentations communautaires. Il envisage les horizons qu’ouvrent la précarité et les précaires pour « repenser les solidarités » aujourd’hui. L’auteur fait ainsi de la polysémie du champ sémantique et intellectuel de la précarité un outil porteur de nouvelles ambitions ainsi que de désirs émancipés de ceux que le capitalisme impose, un outil à travers lequel on peut expérimenter des manières de faire, de penser et de se penser. C’est précisément dans l’épaisseur des marges, des situations, des conditions et des revendications liées à la précarité qu’auteur·e·s et acteurs·trices ont trouvé de la matière et de l’énergie heuristique à même de nous sortir de l’ensorcellement du capitalisme et de la sidération impuissante devant les effondrements à venir.
Laurent Di Filippo, Émilie Landais (dir.) – Penser les relations entre médias. Dispositifs transmédiatiques, convergences et constructions des publics
Authors: Campion Baptiste 
Published: March 2019

Dans un contexte d’évolution rapide et profonde du paysage médiatique sous l’emprise du développement des technologies numériques et, par conséquent, de transformation de la production et de la réception des médias, les notions de « convergence » médiatique, de « transmédia » et de « cross-média » apparaissent de plus en plus centrales dans l’étude des pratiques culturelles médiatisées.
Anne Gillet, Diane-Gabrielle Tremblay (dir.) – Les recherches partenariales et collaboratives
Authors: Demoulin Jeanne 
Published: March 2019

Recensé : Anne Gillet, Diane-Gabrielle Tremblay (dir.), Les recherches partenariales et collaboratives, Rennes/Québec, Presses universitaires de Rennes/Presses de l’Université du Québec, 2017.
Le rapport de la Communauté de l’Emmanuel avec ses paroisses parisiennes
Authors: Dolbeau Samuel 
Published: March 2019

Cet article propose d’étudier le rapport entretenu par la Communauté de l’Emmanuel avec le monde paroissial. En prenant comme échelle d’observation les quatre églises parisiennes qui lui ont été confiées, il s’agit de saisir dans la quotidienneté, l’intégration du plus important mouvement issu du Renouveau charismatique européen à de l’Église catholique. Cette intégration se traduit concrètement par des accommodements entre des conceptions issues de traditions religieuses distinctes (protestante et catholique). L’approche sociologique se focalise ici sur l’observation de l’adaptabilité de l’Emmanuel. L’intégration n’est pas seulement appréhendée comme un mouvement unilatéral de régulation par l’institution ecclésiale. Plus largement, cet article aborde la relation que des chrétiens convertis, les membres de la communauté, entretiennent avec des chrétiens nominaux, les paroissiens ordinaires. Comment en effet concilier en un seul lieu une certaine virtuosité religieuse, portée par l’Emmanuel, avec une vie paroissiale ordinaire ?