bluuebunny/crossref_metadata_2025_split huggingface dataset:
Risk of recurrence after endoscopic resection of early colorectal cancer with positive margins
Authors: Shin Je-Wook , Han Kyung , Hyun Jong , Lee Sang , Kim Bun , Hong Chang , Kim Byung , Sohn Dae , Chang Hee , Kim Min , Park Sung , Oh Jae 
Published: November 2017

Abstract
Background and study aim Additional surgery is recommended if an endoscopically resected T1 colorectal cancer (CRC) specimen shows a positive resection margin. We aimed to investigate the significance of a positive resection margin in endoscopically resected T1 CRC.
Patients and methods We enrolled 265 patients with T1 CRC who underwent endoscopic resection between January 2001 and December 2016. The inclusion criteria were: 1) complete resection by endoscopy, and 2) pathology of a positive margin. Among the 265 patients, 213 underwent additional surgery and 52 did not. In the additional surgery group, various clinicopathological factors were evaluated with respect to the presence or absence of residual tumor. The follow-up results were assessed in the group that did not undergo additional surgery.
Results In the 213 patients who underwent additional surgery, residual tumor was detected in 13 patients (6.1 %), and none of the clinicopathological factors was significantly associated with the presence of residual tumor. Among the 52 patients who did not undergo additional surgery, recurrence was detected in 4 (7.7 %), and all 4 underwent salvage surgery. Among these four patients, three had no risk factors for lymph node metastasis and recurrence was at the previous resection site; pathology was high grade dysplasia, rpT3N0M0, and rpT1N0M0, respectively.
Conclusions A positive resection margin in endoscopically resected T1 CRC is related to a relatively low incidence of residual tumor (6.1 %). Although current guidelines recommend additional surgery for such cases, surveillance and timely salvage surgery could be another option in selected cases.
Medikamentöse Therapie der Zöliakie – „from bench to bedside“
Authors: Stein Jürgen , Schulzke Jörg-Dieter , Schuppan Detlef 
Published: November 2017

ZusammenfassungDie Zöliakie ist eine der weltweit häufigsten Erkrankungen mit einer geschätzten Prävalenz von etwa 0,5 – 1 %. Die Erkrankung entsteht als Folge einer Kombination von Umweltfaktoren (Glutenproteine von Weizen, Roggen oder Gerste) und genetischen Faktoren (hauptsächlich humane Leukozytenantigene HLA-DQ2 oder -DQ8). Aktuell stellt eine strikte glutenfreie Diät (GFD) die einzige Therapiemöglichkeit dar. Allerdings ist die Einhaltung dieser Diät schwierig, nicht zuletzt deshalb, weil Gluten in vielen Fertignahrungsmitteln enthalten ist. Folglich kann die konsequente Vermeidung von Gluten tiefe Einschnitte sowohl in der Nahrungsauswahl als auch im Sozialleben zur Folge haben. Zudem führt die GFD auch bei völlig adhärenten Patienten nicht in jedem Fall zu einer klinischen und histologischen Normalisierung. Deshalb ist das Interesse an (adjunktiven) nicht-diätischen Therapieansätzen für die Zöliakie groß. Ziel dieser Arbeit ist es, basierend auf pathophysiologischen Konzepten zur Zöliakie neueste pharmakologische Therapieansätze vorzustellen und zu diskutieren.
Wireless Battery Management System of Electric Transport
Authors: Rahman Ataur , Rahman Mizanur , Rashid Mahbubur 
Published: November 2017

Abstract
Electric vehicles (EVs) are being developed and considered as the future transportation to reduce emission of toxic gas, cost and weight. The battery pack is one of the main crucial parts of the electric vehicle. The power optimization of the battery pack has been maintained by developing a two phase evaporative thermal management system which operation has been controlled by using a wireless battery management system. A large number of individual cells in a battery pack have many wire terminations that are liable for safety failure. To reduce the wiring problem, a wireless battery management system based on ZigBee communication protocol and point-to-point wireless topology has been presented. Microcontrollers and wireless modules are employed to process the information from several sensors (voltage, temperature and SOC) and transmit to the display devices respectively. The WBMS multistage charge balancing system offering more effective and efficient responses for several numbers of series connected battery cells. The concept of double tier switched capacitor converter and resonant switched capacitor converter is used for reducing the charge balancing time of the cells. The balancing result for 2 cells and 16 cells are improved by 15.12% and 25.3% respectively. The balancing results are poised to become better when the battery cells are increased.
10. Unfinished tasks
Authors: Bronner Stephen Eric 
Published: November 2017

The Frankfurt School never really thought about the world beyond Europe, the Soviet Union, and the United States. But there exists a global totality in which the most basic principles of solidarity are under attack. Resistance calls for linking liberal cosmopolitan principles with economic class interests. Reinvigorated regulative ideals are necessary. Linkages between liberalism and socialism still need to be drawn; class ideals still await realization; the emancipatory heritage of the past still requires reclaiming; and individual autonomy still remains threatened by religion and authoritarianism. New perspectives in critical theory are required to cultivate transformative prospects within an increasingly global society and, in turn, this calls for subjecting critical theory to ongoing critical interrogation.
Introduction
Authors: Davies Andrew 
Published: November 2017

Abstract
Projects have existed since the earliest agrarian societies. While they may differ in purpose, scale, and scope, each project is established to bring together people with diverse knowledge to complete a temporary assignment, solve a complex problem, or turn a novel idea into reality. The Introduction defines a project as a combination of people and other resources brought together in a temporary organization and process to achieve a specified goal. It considers the role of the project manager, the difference between projects and operations, and a brief history of projects. Traditionally, project performance has been measured by the three constraints of cost, time, and quality, but it is now recognized that project success is multidimensional and varies over time.
Perceptual theories—direct, indirect, and computational
Authors: Rogers Brian 
Published: November 2017

Abstract
‘Perceptual theories—direct, indirect, and computational’ considers three different conceptions of what it means to perceive and the processes involved in each theory. The origins of indirect or constructivist theory can be traced back to Hermann von Helmholtz in the 19th century, who emphasized the importance of experience in shaping our perceptual abilities. It was assumed that the primary purpose of perception was to create subjective experiences. The American psychologist James Gibson first suggested a direct theory—that the primary role of perceptual processes was to guide action. Since the 1960s, there have been many attempts to model the perceptual processes using computer algorithms, with David Marr at MIT being the most influential figure.
Truth functions—or not?
Authors: Priest Graham 
Published: November 2017

Abstract
We are strongly intuitive about the validity of various inferences. This may or may not be hard-wired into us. Intuition gets us into trouble sometimes. ‘Truth functions—or not?’ plays around with the idea of invalid and valid inferences and, using phrases such as ‘or’ or ‘it is not the case that’, shows that chaining valid inferences together doesn’t necessarily result in an invalid inference. People’s intuition can be misleading. Sentences can be true or false. Gottlob Frege called these truth values. If we assume that every sentence is either true or false, but not both, we can predict the conditions in what logicians call a truth table.
Necessity and possibility: what will be must be?
Authors: Priest Graham 
Published: November 2017

Abstract
We often say that something must be so (e.g. ‘It must be going to rain’). We also have ways of saying that, though something may not be the case, it could be (e.g. ‘It could rain tomorrow’). ‘Necessity and possibility: what will be must be?’ considers the notion of things that may happen, things that could happen, and modal operators (it is possible for something to be the case—so it is not necessarily the case that it is false). The argument for fatalism illustrates modal operators. Fatalism is the view that whatever happens must happen. We suppose that every situation comes furnished with a bunch of possibilities, or possible worlds.
Identity and change: is anything ever the same?
Authors: Priest Graham 
Published: November 2017

Abstract
We all think that objects can survive change, but the opposite can be argued. If a person changes their hairstyle, they are both the same person and a different person. ‘Identity and change: is anything ever the same?’ examines problems arising when things change and the identity of objects that change through time. Any change means that the old object no longer exists and is replaced by a different object. Logicians point to the difference between the object and its properties. Is this a language issue? In English, the verb ‘to be’ and its various grammatical forms can be used to express both the object and its properties.
Conceptual and computational framework for logical modelling of biological networks deregulated in diseases
Authors: Montagud Arnau , Traynard Pauline , Martignetti Loredana , Bonnet Eric , Barillot Emmanuel , Zinovyev Andrei , Calzone Laurence 
Published: November 2017

AbstractMathematical models can serve as a tool to formalize biological knowledge from diverse sources, to investigate biological questions in a formal way, to test experimental hypotheses, to predict the effect of perturbations and to identify underlying mechanisms. We present a pipeline of computational tools that performs a series of analyses to explore a logical model’s properties. A logical model of initiation of the metastatic process in cancer is used as a transversal example. We start by analysing the structure of the interaction network constructed from the literature or existing databases. Next, we show how to translate this network into a mathematical object, specifically a logical model, and how robustness analyses can be applied to it. We explore the visualization of the stable states, defined as specific attractors of the model, and match them to cellular fates or biological read-outs. With the different tools we present here, we explain how to assign to each solution of the model a probability and how to identify genetic interactions using mutant phenotype probabilities. Finally, we connect the model to relevant experimental data: we present how some data analyses can direct the construction of the network, and how the solutions of a mathematical model can also be compared with experimental data, with a particular focus on high-throughput data in cancer biology. A step-by-step tutorial is provided as a Supplementary Material and all models, tools and scripts are provided on an accompanying website: https://github.com/sysbio-curie/Logical_modelling_pipeline.
MOAT: efficient detection of highly mutated regions with the Mutations Overburdening Annotations Tool
Authors: Lochovsky Lucas , Zhang Jing , Gerstein Mark 
Published: November 2017

Abstract

Summary
Identifying genomic regions with higher than expected mutation count is useful for cancer driver detection. Previous parametric approaches require numerous cell-type-matched covariates for accurate background mutation rate (BMR) estimation, which is not practical for many situations. Non-parametric, permutation-based approaches avoid this issue but usually suffer from considerable compute-time cost. Hence, we introduce Mutations Overburdening Annotations Tool (MOAT), a non-parametric scheme that makes no assumptions about mutation process except requiring that the BMR changes smoothly with genomic features. MOAT randomly permutes single-nucleotide variants, or target regions, on a relatively large scale to provide robust burden analysis. Furthermore, we show how we can do permutations in an efficient manner using graphics processing unit acceleration, speeding up the calculation by a factor of ∼250.

Availability and implementation
MOAT is available at moat.gersteinlab.org.

Supplementary information
Supplementary data are available at Bioinformatics online.
PREFMD: a web server for protein structure refinement via molecular dynamics simulations
Authors: Heo Lim , Feig Michael 
Published: November 2017

Abstract

Summary
Refinement of protein structure models is a long-standing problem in structural bioinformatics. Molecular dynamics-based methods have emerged as an avenue to achieve consistent refinement. The PREFMD web server implements an optimized protocol based on the method successfully tested in CASP11. Validation with recent CASP refinement targets shows consistent and more significant improvement in global structure accuracy over other state-of-the-art servers.

Availability and implementation
PREFMD is freely available as a web server at http://feiglab.org/prefmd. Scripts for running PREFMD as a stand-alone package are available at https://github.com/feiglab/prefmd.git.

Supplementary information
Supplementary data are available at Bioinformatics online.
Cost-effective and accurate method of measuring fetal fraction using SNP imputation
Authors: Kim Minjeong , Kim Jai-Hoon , Kim Kangseok , Kim Sunshin 
Published: November 2017

Abstract

Motivation
With the discovery of cell-free fetal DNA in maternal blood, the demand for non-invasive prenatal testing (NIPT) has been increasing. To obtain reliable NIPT results, it is important to accurately estimate the fetal fraction. In this study, we propose an accurate and cost-effective method for measuring fetal fractions using single-nucleotide polymorphisms (SNPs).

Results
A total of 84 samples were sequenced via semiconductor sequencing using a 0.3× sequencing coverage. SNPs were genotyped to estimate the fetal fraction. Approximately 900 000 SNPs were genotyped, and 250 000 of these SNPs matched the semiconductor sequencing results. We performed SNP imputation (1000Genome phase3 and HRC v1.1 reference panel) to increase the number of SNPs. The correlation coefficients (R2) of the fetal fraction estimated using the ratio of non-maternal alleles when coverage was reduced to 0.01 following SNP imputation were 0.93 (HRC v1.1 reference panel) and 0.90 (1000GP3 reference panel). An R2 of 0.72 was found at 0.01× sequencing coverage with no imputation performed. We developed an accurate method to measure fetal fraction using SNP imputation, showing cost-effectiveness by using different commercially available SNP chips and lowering the coverage. We also showed that semiconductor sequencing, which is an inexpensive option, was useful for measuring fetal fraction.

Availability and implementation
python source code and guidelines can be found at https://github.com/KMJ403/fetalfraction-SNPimpute.

Supplementary information
Supplementary data are available at Bioinformatics online.
The Topology of Compact Lie Group Actions Through the Lens of Finite Models
Authors: Papadima Stefan , Suciu Alexander I 
Published: November 2017

AbstractGiven a compact, connected Lie group K, we use principal K-bundles to construct manifolds with prescribed finite-dimensional algebraic models. Conversely, let M be a compact, connected, smooth manifold, which supports an almost free K-action. Under a partial formality assumption on the orbit space and a regularity assumption on the characteristic classes of the action, we describe an algebraic model for M with commensurate finiteness and partial formality properties. The existence of such a model has various implications on the structure of the cohomology jump loci of M and of the representation varieties of π1(M). As an application, we show that compact Sasakian manifolds of dimension 2n + 1 are (n − 1)-formal, and that their fundamental groups are filtered-formal. Further applications to the study of weighted-homogeneous isolated surface singularities are also given.
Estimating the causal effects of chronic disease combinations on 30-day hospital readmissions based on observational Medicaid data
Authors: Casucci Sabrina , Lin Li , Hewner Sharon , Nikolaev Alexander 
Published: November 2017

AbstractObjectiveDemonstrate how observational causal inference methods can generate insights into the impact of chronic disease combinations on patients’ 30-day hospital readmissions.Materials and MethodsCausal effect estimation was used to quantify the impact of each risk factor scenario (ie, chronic disease combination) associated with chronic kidney disease and heart failure (HF) for adult Medicaid beneficiaries with initial hospitalizations in 2 New York State counties. The experimental protocol: (1) created matched risk factor and comparator groups, (2) assessed covariate balance in the matched groups, and (3) estimated causal effects and their statistical significance. Causality lattices summarized the impact of chronic disease comorbidities on readmissions.ResultsChronic disease combinations were ordered with respect to their causal impact on readmissions. Of disease combinations associated with HF, the combination of HF, coronary artery disease, and tobacco abuse (in that order) had the highest causal effect on readmission rate (+22.3%); of disease combinations associated with chronic kidney disease, the combination of chronic kidney disease, coronary artery disease, and diabetes had the highest effect (+9.5%).DiscussionMulti-hypothesis causal analysis reveals the effects of chronic disease comorbidities on health outcomes. Understanding these effects will guide the development of health care programs that address unique care needs of different patient subpopulations. Additionally, these insights bring new attention to individuals at high risk for readmission based on chronic disease comorbidities, allowing for more personalized attention and prioritization of care.ConclusionMulti-hypothesis causal analysis, a new methodological tool, generates meaningful insights from health care claims data, guiding the design of care and intervention programs.
Introduction
Authors: Oliver Peter , Macklem Patrick , Des Rosiers Nathalie 
Published: November 2017

Abstract
This Handbook is intended to be an authoritative first stop for Canadians and non-Canadians in search of a clear, concise, and critical account of Canadian constitutional law. This Introduction begins by setting out what makes the Canadian Constitution distinctive, before describing the extent to which that Constitution has become a focus for comparative constitutional law. The Introduction concludes by expressing the hope that Canadian readers of this Handbook will find themselves better equipped, and that foreign readers will better understand the types of questions for which Canadians are seeking answers in 2017 and beyond. These include at the very least: decolonization and reconciliation with Indigenous peoples; maintaining a federation and a democracy that works for all its communities and inhabitants; and protecting rights and freedoms in the face of global security, environmental, and other threats.
The British Legal Tradition in Canadian Constitutional Law
Authors: Walters Mark D. 
Published: November 2017

AbstractThis chapter examines the influence of the British legal tradition within Canadian constitutional law. The foundational text of Canada’s constitution, the British North America Act, 1867, was adopted when Canada was still a UK colony, and so it is hardly surprising that this influence would prove to be important—even after Canada emerged as an independent state. Still, the assertion in the preamble to the 1867 Act, that Canada’s constitution is ‘similar in Principle to that of the United Kingdom’, must be approached cautiously. The leading British constitutional scholar A.V. Dicey went so far as to describe this assertion as a piece of ‘official mendacity’. The analysis in Section 2 of this chapter focuses upon institutional structure and design. Here, it will be seen that Dicey was wrong. The analysis in Section 3 of the chapter is on the interpretive ethic or what Dicey called the ‘spirit’ of the constitution.
The Crown in Canada
Authors: Smith Jennifer , Firmini Marcella 
Published: November 2017

Abstract
In Canada, the monarch is habitually, albeit erroneously, considered a figurehead in the nation’s system of government. In fact, in a constitutional monarchy, Her Majesty Queen Elizabeth II’s capacity as head of state means that her position is substantive, not merely superficial. Certainly, the Constitution affirms that all executive authority is vested in her. Therefore, it is important to realize the scope and substance of the sovereign’s authority which is often underappreciated. We trace the development of the Crown in Canada, in particular the changes the institution experienced as the country progressed from remote colonial outpost to independent nation. Most importantly, we assess the Crown’s institutional function by explaining the statutory, prerogative, and reserve powers, and conclude with some reflections on the future of the institution in Canada.
Political Institutions in Canada in a New Era
Authors: Turnbull Lori 
Published: November 2017

Abstract
This chapter examines the meaning and significance of the parliamentary reform package introduced by Prime Minister Justin Trudeau’s government in 2015. The proposed measures address themes that have been part of democratic reform agendas for many years, and most of them can be fairly described as low-hanging fruit. The one that stands out from the rest is the Trudeau government’s approach to appointments. Historically, Prime Ministers have made appointments to the Senate, the Supreme Court, and other positions of profile and authority with little to no restrictions on their discretion. The Trudeau government’s creation of independent advisory boards to preside over appointments throughout federal government institutions, and the identification of specified criteria to guide these appointments, represents a major departure from historic practice and a potentially significant shift away from the concentration of power in the hands of the political Executive.
Courts, Administrative Agencies, and the Constitution
Authors: Sossin Lorne 
Published: November 2017

AbstractThis chapter sets out the constitutional foundation for courts and administrative agencies in Canada. It examines the constitutional foundations for Canadian courts, including Canada’s constitutional texts; unwritten constitutional principles such as judicial independence, access to justice, and the rule of law; quasi-constitutional statutes such as the Supreme Court Act; and the common law Constitution. The chapter next considers the constitutional foundations for administrative agencies, particularly around the extent to which agencies can implement and are subject to the Constitution. Finally, the chapter situates the discussion of administrative agencies against the backdrop of Canada’s separation of powers, including emerging dynamics flowing from Indigenous self-government.