bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Prospective, Randomized Phase II Study of Adjuvant Gemcitabine Versus S-1 After Major Hepatectomy for Biliary Tract Cancer (KHBO 1208)
Authors: Kobayashi Shogo , Nagano Hiroaki , Tomokuni Akira , Gotoh Kunihito , Sakai Daisuke , Hatano Etsuro , Seo Satoru , Terajima Hiroaki , Uchida Yoichiro , Ajiki Tetsuo , Satake Hironaga , Kamei Keiko , Tohyama Taiji , Hirose Tetsuro , Ikai Iwao , Morita Satoshi , Ioka Tatsuya 
Published: October 2018

Objective:
To evaluate each arm independently and compare adjuvant gemcitabine (GEM) and S-1 chemotherapy after major hepatectomy (hemihepatectomy or trisectionectomy) for biliary tract cancer (BTC).

Background:
Standardized adjuvant therapy is not performed after major hepatectomy for BTC, and we determined the recommended dose in the former study (KHBO1003).

Methods:
We performed a multicenter, randomized phase II study. The primary measure was 1-year recurrence-free survival (RFS); the secondary measures were other RFS, overall survival (OS), and others. The following 6-month adjuvant chemotherapy was administered within 12 weeks of R0/1: GEM (1000 mg/m2) every 2 weeks; or S-1 (80 mg/m2/d) for 28 days every 6 weeks. Thirty-five patients were assigned to each arm (alpha error, 10%; beta error, 20%).

Results:
No patients were excluded for the per-protocol analysis. There were no statistically significant differences in the patient characteristics of the 2 arms. The 1-year RFS and 1-year OS rates of the GEM arm were 51.4% and 80.0%, respectively, whereas those of the S-1 group were 62.9% and 97.1%. The comparison of the 2 arms revealed that 2-year RFS rate, 1 and 2-year OS rates, and OS curve of the S-1 arm were superior to GEM. With regard to OS, the hazard ratio of the S-1 group was 0.477 (90% confidence interval 0.245–0.927).

Conclusion:
The comparison of the survival of the 2 groups revealed that adjuvant S-1 therapy may be superior to adjuvant GEM therapy after major hepatectomy for BTC.
Genetic Analysis of Small Well-differentiated Pancreatic Neuroendocrine Tumors Identifies Subgroups With Differing Risks of Liver Metastases
Authors: Pea Antonio , Yu Jun , Marchionni Luigi , Noe Michael , Luchini Claudio , Pulvirenti Alessandra , de Wilde Roeland F. , Brosens Lodewijk A. , Rezaee Neda , Javed Ammar , Chianchiano Peter , Gobbo Stefano , Regi Paolo , Salvia Roberto , Bassi Claudio , He Jin , Weiss Matthew J. , Cameron John L. , Offerhaus G. Johan A. , Hruban Ralph H. , Lawlor Rita T. , Scarpa Aldo , Heaphy Christopher M. , Wood Laura D. , Wolfgang Christopher L. 
Published: October 2018

Objective:
The aim of this study was to investigate the key molecular alterations in small primary pancreatic neuroendocrine tumors (PanNETs) associated with the development of liver metastases.

Background:
Well-differentiated PanNETs with small size are typically indolent; however, a limited subset metastasize to the liver.

Methods:
A total of 87 small primary PanNETs (<3 cm), including 32 metastatic cases and 55 nonmetastatic cases after a 5-year follow-up, were immunolabeled for DAXX/ATRX and analyzed for alternative lengthening of telomeres (ALT) by Fluorescence In Situ Hybridization. A subset of these cases, 24 that metastasized and 24 that did not metastasize, were assessed by targeted next-generation sequencing and whole-genome copy number variation.

Results:
In the entire cohort, high Ki-67 (OR 1.369; 95% CI 1.121–1.673; P = 0.002), N-stage (OR 4.568; 95% CI 1.458–14.312; P = 0.009), and ALT-positivity (OR 3.486; 95% CI 1.093–11.115; P = 0.035) were independently associated with liver metastases. In the subset assessed by next-generation sequencing and copy number variation analysis, 3 molecular subtypes with differing risks of liver metastases were identified. Group 1 (n = 15; 73% metastasized) was characterized by recurrent chromosomal gains, CN-LOH, DAXX mutations, and ALT-positivity. Group 2 (n = 19; 42% metastasized, including 5 G1 tumors) was characterized by limited copy number alterations and mutations. Group 3 (n = 14; 35% metastasized) were defined by chromosome 11 loss.

Conclusions:
We identified genomic patterns of small PanNETs associated with a different risk for liver metastases. Molecular alterations, such as DAXX mutations, chromosomal gains, and ALT, are associated with an increased risk of metastasis in small PanNETs. Therefore, targeted sequencing and/or ALT analysis may help in the clinical decisions for these small PanNETs.
Reappraising the Concept of Conditional Survival After Pancreatectomy for Ductal Adenocarcinoma
Authors: Malleo Giuseppe , Maggino Laura , Ferrone Cristina R. , Marchegiani Giovanni , Warshaw Andrew L. , Lillemoe Keith D. , Bassi Claudio , Castillo Carlos Fernàndez-del , Salvia Roberto 
Published: October 2018

Objective:
To reappraise the concept of conditional survival (CS) following pancreatectomy for pancreatic ductal adenocarcinoma (PDAC), accounting for the patient's present disease status relative to recurrence.

Background:
CS, defined as the probability of surviving an additional time frame based on accrued lifespan, offers dynamic survival projections as compared with baseline overall survival.

Methods:
Patients undergoing pancreatectomy for PDAC at 2 institutions from 2000 to 2013 were retrospectively analyzed. The 12-month CS was estimated separately for patients who were disease-free or with recurrence at the given time points. Next, the conditional probability of reaching 60-months of survival was examined in each conditioning set across strata of prognostic covariates, including American Joint Committee on Cancer stage, tumor grade, R-status, and adjuvant treatment.

Results:
The study population consisted of 1005 patients. In disease-free patients, the 12-month CS increased as a function of time already survived, showing an opposite trend compared with overall survival. In patients who recurred, the 12-month CS was lower than the disease-free counterpart, especially within 24 months postoperatively. When stratifying by the levels of prognostic covariates, the 60-months CS estimates for disease-free patients tended to level off progressively, indicating that factors independently associated with survival at the time of pancreatectomy lost power over time. This concept did not apply to the conditioning set of patients with recurrence, where CS estimates across variables strata diverged with accrued lifespan.

Conclusion:
This paper provides new information on how prognosis following pancreatectomy for PDAC evolves over time, adjusting for the time the patient already survived, and for the patient's present disease status relative to recurrence.
The mitochondrial DNA content can not predict the embryo viability
Authors: Yong Qiu M.S. , Songchang Chen M.S. , Dayang Chen , Ping Liu M.S. , Jun Xia M.S. , Lin Yang B.S. , Zhe Song M.S. , Qianyu Shi M.S. , Lin Xie M.S. , Zhu Zhu M.S. , Ye Du , Jiang Hui , Wang Jian , Yang Huanming , Xu Chenming , Chen Fang 
Published: October 2018

ABSTRACTObjectiveTo investigate whether the mitochondrial DNA content could predict the embryo viabilityDesignRetrospective analysis.SettingReproductive genetics laboratoryPatient(s)A total of 421 biopsied samples obtained from 129 patientsIntervention(s)Embryo biopsies samples underwent whole genome amplification (WGA) and were tested by next generation sequencing (NGS) and array Comparative Genomic Hybridization (aCGH), 30 samples were selected randomly to undergo quantitative real-time polymerase chain reaction (qPCR).Main Outcome Measure(s)Those embryos which obtained the consistent chromosome status determined both aCGH and NGS platform were further classified. We investigated the relationship of mtDNA content with several factors including female patient age, embryo morphology, chromosome status, and live birth rate of both blastocysts and blastomeres.Result(s)A total of 386 (110 blastomeres and 276 blastocysts) out of 399 embryos showed consistent chromosome status outcome. We found no statistically difference was observed in aneuploid and euploid blastocysts (p=0.14), the same phenomenon was observed in aneuploid and euploid blastomeres (p=0.89). Similarly, the mtDNA content was independent of female patient age, embryo morphology and live birth rate.Conclusion(s)The mtDNA content did not provide a reliable prediction of the viability of blastocysts to initiate a pregnancy.
Identifying and classifying shared selective sweeps from multilocus data
Authors: Harris Alexandre M. , DeGiorgio Michael 
Published: October 2018

AbstractPositive selection causes beneficial alleles to rise to high frequency, resulting in a selective sweep of the diversity surrounding the selected sites. Accordingly, the signature of a selective sweep in an ancestral population may still remain in its descendants. Identifying signatures of selection in the ancestor that are shared among its descendants is important to contextualize the timing of a sweep, but few methods exist for this purpose. We introduce the statistic SS-H12, which can identify genomic regions under shared positive selection across populations and is based on the theory of the expected haplotype homozygosity statistic H12, which detects recent hard and soft sweeps from the presence of high-frequency haplotypes. SS-H12, is distinct from other statistics that detect shared sweeps because it requires a minimum of only two populations, and properly identifies and differentiates between independent convergent sweeps and true ancestral sweeps, with high power and robustness to a variety of demographic models. Furthermore, we can apply SS-H12 in conjunction with the ratio of a different set of expected haplotype homozygosity statistics to further classify identified shared sweeps as hard or soft. Finally, we identified both previously-reported and novel shared sweep candidates from whole-genome sequences of global human populations. Previously-reported candidates include the well-characterized ancestral sweeps atLCTandSLC24A5in Indo-European populations, as well asGPHNworldwide. Novel candidates include an ancestral sweep atRGS18in sub-Saharan African populations involved in regulating the platelet response and implicated in sudden cardiac death, and a convergent sweep atC2CD5between European and East Asian populations that may explain their different insulin responses.Introduction
A Mixed-Model Approach for Powerful Testing of Genetic Associations with Cancer Risk Incorporating Tumor Characteristics
Authors: Zhang Haoyu , Zhao Ni , Ahearn Thomas U. , Wheeler William , García-Closas Montserrat , Chatterjee Nilanjan 
Published: October 2018

AbstractCancers are routinely classified into subtypes according to various features, including histopathological characteristics and molecular markers. Previous genome-wide association studies have reported heterogeneous associations between loci and cancer subtypes. However, it is not evident what is the optimal modeling strategy for handling correlated tumor features, missing data, and increased degrees-of-freedom in the underlying tests of associations. We propose to test for genetic associations using a mixed-effect two-stage polytomous model score test (MTOP). In the first stage, a standard polytomous model is used to specify all possible sub-types defined by the cross-classification of the tumor characteristics. In the second stage, the subtype-specific case-control odds ratios are specified using a more parsimonious model based on the case-control odds ratio for a baseline subtype, and the case-case parameters associated with tumor markers. Further, to reduce the degrees-of-freedom, we specify case-case parameters for additional exploratory markers using a random-effect model. We use the Expectation-Maximization (EM) algorithm to account for missing data on tumor markers. Through simulations across a range of realistic scenarios and data from the Polish Breast Cancer Study (PBCS), we show MTOP outperforms alternative methods for identifying heterogeneous associations between risk loci and tumor subtypes. The proposed methods have been implemented in a user-friendly and high-speed R statistical package called TOP (https://github.com/andrewhaoyu/TOP).
Comparable genomic copy number aberrations differ across astrocytoma malignancy grades
Authors: Pećina-Šlaus Nives , Kafka Anja , Gotovac Kristina , Logara Monika , Bukovac Anja , Bakarić Robert , Borovečki Fran 
Published: October 2018

AbstractMalignancy grades of astrocytomas were analyzed for copy number aberrations by aCGH. Altogether 1438 CNA were found of which losses prevailed. We searched for regions that are more likely to drive cancer pathogenesis with Bioconductor package and Genomic Identification of Significant Targets in Cancer. On our total sample significant deletions affected 14 chromosomal regions, out of which deletions at 17p13.2, 9p21.3, 13q12.11, 22q12.3 remained significant even at 0.05 q-value. When divided to malignancy groups, the regions identified as significantly deleted in high grades were: 9p21.3; 17p13.2; 10q24.2; 14q21.3; 1p36.11 and 13q12.11, while amplified were: 3q28; 12q13.3 and 21q22.3. Low grades comprised significant deletions at 3p14.3; 11p15.4; 15q15.1; 16q22.1; 20q11.22 and 22q12.3 indicating their involvement in early stages of tumorigenesis. Significantly enriched pathways brought by DAVID software were PI3K-Akt, Cytokine-cytokine receptor, NODlike receptor, Jak-STAT, RIG-II-like receptor and Toll-like receptor pathways. HPV and herpex simplex infection and inflammation pathways were also represented. Present study brings new data to astrocytoma research amplifying the wide spectrum of changes which could help us identify the regions critical for tumorigenesis.
The mathematical model of UAV vertical take-off and landing
Authors: Chodnicki Marcin , Mazur Michal , Nowakowski Miroslaw , Kowaleczko Grzegorz 
Published: October 2018

Purpose
This paper aims to present a mathematical model of the dynamics of the unmanned aerial vehicle (UAV) vertical take-off and landing (VTOL). It will be used to develop control laws to a multirotor that is inherently unstable. Also, the model will be used to design algorithms to estimate the attitude of an object.

Design/methodology/approach
The physical model of UAV assumes that it is a rigid body with six degrees of freedom acted by forces generated by the propellers, motors, aerodynamic forces, gravity and disturbance forces. The mathematical model was described by differential equations. However, drive system (propeller, BLDC motor and BLDC motor controller) was described by six transfer functions. These transfer functions were demarcated with Matlab/Simulink identification toolbox from data received from a specially designed laboratory stand. Moments of inertia of the platform have been analytically determined and compared with empirical results from the pendulum. The mathematical model was implemented in Matlab/Simulink.

Findings
The paper confirms the need of designing mathematical models. Moreover, mathematical models show that some parts of the object are better to be replaced by experimental results than by equations, which is proved by the data. The paper also shows advantages of using Matlab/Simulink. What is more the simulation of the model proves that multirotor is an unstable object.

Research limitations/implications
The test results show that drive units are strongly dependent on ambient conditions. An additional problem is the different response of the drive set to increasing and decreasing the control signal amplitude. Next tests will be done at different temperatures and air densities of the environment, also it is need to explore drag forces.

Practical implications
The mathematical model is a simplification of the physical model expressed by means of equations. The results of simulation like accelerations and angular rate are noise-free. However, available sensors always have their errors and noise. To design control loops and attitude estimation algorithms, there is a need for identification of sensors’ errors and noise. These parameters have to be measured.

Originality/value
The paper describes a solution of correct identification of drive unit, which is a main component of the UAV.
Topology optimization in electromagnetism using SIMP method
Authors: Sanogo Satafa , Messine Frédéric 
Published: October 2018

Purpose
In this work, the authors deal with topology optimization in electromagnetism using solid isotropic material with penalization (SIMP) method associated with a gradient-based algorithm. The purpose of this study is to propose and investigate the impact of new generalized material interpolation scheme (MIS) used in SIMP approaches.

Design/methodology/approach
The variable domains of this kind of electromagnetism design problem are decomposed into small squares which represent a material point (iron here) or void. A least square function where the magnetic ﬁeld in a target zone has to be as close as possible to a ﬁxed one is minimized. Then the binary optimization problem is relaxed to a continuous one. By using the adjoint variable method, the gradient is provided. By penalizing the objective function using MIS, gradient-based algorithms can then be directly applied to provide eﬃcient solutions close to the binary ones.

Findings
In this work, new general MISs are proposed. It is shown on numerous numerical instances that the so-obtained design solutions are more precise to define the zones with or without materials.

Research limitations/implications
Only the linearity of the materials is addressed because the associated adjoint method needs this assumption. However, the new penalization approaches are not dependent directly on this assumption.

Originality/value
The new MISs are efficiently applied to design of a hall effect thruster (HET) magnetic circuits. Furthermore, these schemes are generic and can then be applied to other topology optimization applications in electromagnetism as well as and in mechanism.
Supply chain cooperation as a green supply chain management implementation strategy to achieve competitive advantages in natural disaster prone regions
Authors: Montshiwa Abednico Lopang 
Published: October 2018

Purpose
This study aims to present a competitive advantages framework suited for disaster prone regions in the era of climate change, present supply chain cooperation (SCC) as an integral part of GrSCM within the automobile industry and evaluate the competitive advantages framework merits based on SCC as a new implementation tool.

Design/methodology/approach
In an effort to address limited green supply chain management implementation strategies in disaster prone regions, the paper presents SCC as an economic, social and political implementation tool. To explore this; the study introduces SCC in a three-phase competitive advantages model adopted from the Barney 1995 model (with slight differences). Smart PLS 3.0 software package was adopted to carry out multi-variable data analysis. The study’s assumption is a capital economic system and bases its argument of analysis on stockholder theoretical lenses.

Findings
Big company size does not significantly affect SCC, suggesting that companies of all size can organize and enhance their network to be cooperative. Companies with cooperative supply chain network tend to have competitive advantages. SCC is also a viable way to manage business risks, be there internal or external.

Research limitations/implications
One of the study’s limitation is the stockholder theory it adopts, which shoulders its assumptions on a capital economic model of operation. Indeed, the study covered China, which is seen to be a communist-based economy. Another study’s limitation is that it narrows its data collection to disaster prone areas as documented by Guha-Sapir et al. (2012). Consequently, the findings of this study might be only applicable to areas that experience significant level of disruptions usually caused by disaster incidents.

Originality/value
The study is also the first of its kind to propose a model for automobile manufacturing in disaster prone regions. This is done by introducing SCC as an economic, social and political factor, while risk ranking is introduced as an environmental factor to constitute the external changes that Barney 1995 introduced.
"“La Vida de los Emigrantes”
Authors: McGinnis Theresa Ann 
Published: October 2018

Purpose
In September 2014, 1,200 unaccompanied immigrant youth, from a region of Central America known for high rates of violence and homicide, enrolled in a suburban school district of New York State. This paper aims to highlight the stories of the newly arrived Central American high school youth, as told through Bilingual (Spanish/English) digital testimonios completed in the English Language Arts classroom. The author examines how the telling of their stories of surviving migration offers a way for the youth to respond to political and emotional struggles. The author also explores how the youth become active participants in the telling of political narratives/testimonios.

Design/methodology/approach
Part of a larger ethnographic case study, the author adopts the ethnographic approaches of the new literacy studies. Testimonios as a research epistemology privilege the youth’s narratives as sources of knowledge, and allow the youth to reclaim their authority in telling their own stories.

Findings
The integration of critical digital texts into the English Language Arts classroom created a participatory classroom culture where the Central American youth’s digital testimonios can be seen as a shared history of struggles that make visible the physical toil of their journeys, the truth of their border crossings and their enactments of political identities. As a collective, the youth’s stories become part of national and global political dialogues.

Originality/value
At a time when immigrant youth struggle for rights, to further their education and to negotiate the daily experiences of living in a new country, this research offers a unique perspective on the politics of inclusion and exclusion for unaccompanied youth.