bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinicopathological analysis and risk factors of advanced colorectal neoplasms incidentally detected by 18F-FDG PET-CT
Authors: Chung Seung Min , Kim Kyeong Ok , Cho Ihn Ho , Kim Tae Nyeun 
Published: December 2016

Background
As the clinical use of fluorine-18-fluorodeoxyglucose PET-computed tomography (18F-FDG PET-CT) has increased, the incidental finding of 18F-FDG uptake with subsequent diagnosis of advanced neoplasm at colorectum has increased. The aim of this study is to analyze the characteristics and risk factors of advanced colorectal neoplasm incidentally detected by 18F-FDG PET-CT.

Patients and methods
Patients who underwent colonoscopy because of an incidental finding of 18F-FDG uptake at the colorectum from January 2006 to January 2015 at Yeungnam University Hospital were reviewed retrospectively. Advanced neoplasm was defined as adenoma of at least 10 mm, adenoma with serrated or villous component, high-grade dysplasia, and adenocarcinoma.

Results
Of the 19 798 candidates, 180 patients with incidental colorectal 18F-FDG uptake were included in this study. The indications of PET-CT were metastasis work-up, health screening, and others. The male to female ratio was 1.6 : 1 and the mean age was 62.7±11.4 years. A total of 156 lesions were detected in the colorectum and 86 (47.8%) were diagnosed as advanced neoplasms. Of the 86 patients with advanced neoplasms, 34 (39.5%) underwent an operation, 34 (39.5%) underwent endoscopic resection, and 18 (20.9%) underwent chemotherapy or conservative treatments. In univariate analysis, age of 62.5 years or older, carcinoembryonic antigen (CEA) of at least 3.4 ng/ml, maximum standardized uptake value (SUVmax) of at least 8.0, hypertension, 18F-FDG uptake on the rectosigmoid, and PET-CT for metastasis work-up showed a significant association with advanced neoplasm. In multivariate analysis, CEA (P=0.028), SUVmax (P<0.001) and an indication of PET-CT for metastasis work-up (P=0.008) were independent predictors of advanced neoplasm.

Conclusion
Colonoscopy should be recommended in case of 18F-FDG uptake at the colorectum, particularly in patients with CEA of at least 3.4 ng/ml, SUVmax of at least 8.0, or metastasis work-up of malignancy.
Should patients with acute myeloid leukemia and measurable residual disease be transplanted in first complete remission?
Authors: Buccisano Francesco , Walter Roland B. 
Published: December 2016

Purpose of review
Measurable (‘minimal’) residual disease in acute myeloid leukemia during first complete morphologic remission (MRDpos CR1) identifies patients with particularly high relapse risk and short survival. Here, we examine the evidence regarding optimal postremission treatment strategy for such patients.

Recent findings
With chemotherapy alone or chemotherapy/autologous hematopoietic cell transplantation (HCT), disease recurrence appears inevitable in patients with MRDpos CR1. Nonrandomized studies indicate that allogeneic HCT improves outcomes over chemotherapy and/or autologous HCT, although relapse risks remain substantial. Emerging data suggest that myeloablative cord blood HCT may overcome the negative impact of MRD to a greater degree than other transplants, but the relative contributions of intensified conditioning and stem cell source to this effect are unknown.

Summary
Available evidence supports the recommendation to consider allogeneic HCT for all acute myeloid leukemia patients in MRDpos CR1. Whether cord blood transplants should be prioritized deserves further investigation. To what degree outcomes of MRDpos CR1 patients could be improved by treatment intensification during induction, postremission therapy and/or before transplantation to revert the patient into an MRDneg state is currently unknown, as is the value of post-transplant preemptive therapies. These remain areas worthy of investigation, preferably in the setting of controlled clinical trials.
The Effect of Force Feedback in a Virtual Learning Environment on the Performance and Satisfaction of Dental Students
Authors: de Boer Ilse R. , Lagerweij Maxim D. , de Vries Merlijn W. , Wesselink Paul R. , Vervoorn Johanna M. 
Published: December 2016

Introduction
This study investigated the effect of force feedback (FFB) on student performance in a virtual learning environment (VLE) using the Simodont dental trainer (Moog, Nieuw-Vennep, the Netherlands) and evaluated the students' satisfaction with and without FFB.

Methods
The Simodont dental trainer, which was used as a VLE, was randomly assigned to 101 first-year dental students with no previous experience in cutting a tooth or working in a VLE with FFB. This study was designed as a crossover study. One half of the students practiced without FFB, whereas one half practiced with FFB. Both groups practiced four sessions lasting 45 minutes on a cross preparation. In the fifth session, test 1 was scheduled. After test 1, the same practicing and testing protocol was followed, although the environment was switched. After test 2, participants filled out a questionnaire. For the statistical analysis, only the questionnaires of the students who participated in both tests were processed.

Results
The results of test 1 and test 2 revealed that only students who used FFB were able to pass the tests. The questionnaire outcomes supported the results of both tests; 100% of the students preferred working with FFB.

Conclusions
The results suggest that FFB is important for performance in a VLE and essential for satisfaction.
Impact of Skeletal Muscle Mass Index, Intramuscular Adipose Tissue Content, and Visceral to Subcutaneous Adipose Tissue Area Ratio on Early Mortality of Living Donor Liver Transplantation
Authors: Hamaguchi Yuhei , Kaido Toshimi , Okumura Shinya , Kobayashi Atsushi , Shirai Hisaya , Yagi Shintaro , Kamo Naoko , Okajima Hideaki , Uemoto Shinji 
Published: December 2016

Background
Skeletal muscle depletion has been shown to be an independent risk factor for poor survival in various diseases. However, in surgery, the significance of other body components including visceral and subcutaneous adipose tissue remains unclear.

Methods
This retrospective study included 250 adult patients undergoing living donor liver transplantation (LDLT) between January 2008 and April 2015. Using preoperative plain computed tomography imaging at the third lumbar vertebra level, skeletal muscle mass, muscle quality, and visceral adiposity were evaluated by the skeletal muscle mass index (SMI), intramuscular adipose tissue content (IMAC), and visceral to subcutaneous adipose tissue area ratio (VSR), respectively. The cutoff values of these parameters were determined for men and women separately using the data of 657 healthy donors for LDLT between 2005 and 2016. Impact of these parameters on outcomes after LDLT was analyzed.

Results
VSR was significantly correlated with patient age (P = 0.041), neutrophil-lymphocyte ratio (P < 0.001), body mass index (P < 0.001), and SMI (P = 0.001). The overall survival probability was significantly lower in patients with low SMI (P < 0.001), high IMAC (P < 0.001), and high VSR (P < 0.001) than in each respective normal group. On multivariate analysis, low SMI (hazard ratio [HR], 2.367, P = 0.002), high IMAC (HR, 2.096, P = 0.004), and high VSR (HR, 2.213, P = 0.003) were identified as independent risk factors for death after LDLT.

Conclusions
Preoperative visceral adiposity, as well as low muscularity, was closely involved with posttransplant mortality.
Validating Regulatory Predictions from Diverse Bacteria with Mutant Fitness Data
Authors: Sagawa Shiori , Price Morgan N. , Deutschbauer Adam M. , Arkin Adam P. 
Published: December 2016

AbstractAlthough transcriptional regulation is fundamental to understanding bacterial physiology, the targets of most bacterial transcription factors are not known. Comparative genomics has been used to identify likely targets of some of these transcription factors, but these predictions typically lack experimental support. Here, we used mutant fitness data, which measures the importance of each gene for a bacterium’s growth across many conditions, to validate regulatory predictions from RegPrecise, a curated collection of comparative genomics predictions. Because characterized transcription factors often have correlated fitness with one of their targets (either positively or negatively), correlated fitness patterns provide support for the comparative genomics predictions. At a false discovery rate of 3%, we identified significant cofitness for at least one target of 158 TFs in 107 ortholog groups and from 24 bacteria. Thus, high-throughput genetics can be used to identify a high-confidence subset of the sequence-based regulatory predictions.
No evidence for genome editing in mouse zygotes and HEK293T human cell line using the DNA-guidedNatronobacterium gregoryiArgonaute (NgAgo)
Authors: Khin Nay Chi , Lowe Jenna L. , Jensen Lora M. , Burgio Gaetan 
Published: December 2016

AbstractA recently published research article reported that the extreme halophile archaebacteriumNatronobacterium gregoryiArgonaute enzyme (NgAgo) could cleave the cellular DNA under physiological temperature conditions in cell line and be implemented as an alternative to CRISPR/Cas9 genome editing technology. We assessed this claim in mouse zygotes for four loci (Sptb,Tet-1,Tet-2andTet-3) and in the human HEK293T cell line for the EMX1 locus. Over 100 zygotes were microinjected with nls-NgAgo-GK plasmid provided from Addgene and various concentrations of 5’- phosphorylated guide DNA (gDNA) from 2.5 ng/μl to 50 ng/μl and cultured to blastocyst stage of development. The presence of indels was verified using T7 endonuclease 1 assay (T7E1) and Sanger sequencing. We reported no evidence of successful editing of the mouse genome. We then assessed the lack of editing efficiency in HEK293T cell line for the EMX1 endogenous locus by monitoring the NgAgo protein expression level and the editing efficiency by T7E1 assay and Sanger sequencing. We reported that the NgAgo protein was expressed from 8 hours to a maximum expression at 48 hours post-transfection, confirming the efficient delivery of the plasmid and the gDNA but no evidence of successful editing of EMX1 target in all transfected samples. Together our findings indicate that we failed to edit using NgAgo.
Evolutionary variations in the biofilm-associated protein BslA from the genusBacillus
Authors: Morris Ryan J. , Schor Marieke , Gillespie Rachel M.C. , Ferreira Ana Sofia , Bromley Keith M. , Baldauf Lucia , Arnaouteli Sofia , Sukhodub Tetyana , Ostrowski Adam , Hobley Laura , Earl Chris , Stanley-Wall Nicola R. , MacPhee Cait E. 
Published: December 2016

AbstractBslA is a protein secreted byBacillus subtiliswhich forms a hydrophobic film that coats the biofilm surface and renders it water-repellent. We have characterised three orthologues of BslA fromBacillus amyloliquefaciens,Bacillus licheniformisandBacillus pumilusas well as a paralogue fromB. subtiliscalled YweA. We find that the three orthologous proteins can substitute for BslA inB. subtilisand confer a degree of protection, whereas YweA cannot. The degree to which the proteins functionally substitute for native BslA correlates with theirin vitrobiophysical properties. Our results demonstrate the use of naturally-evolved variants to provide a framework for teasing out the molecular basis of interfacial self-assembly.
Understanding genetic changes underlying the molybdate resistance and the glutathione production inSaccharomyces cerevisiaewine strains using an evolution-based strategy
Authors: Mezzetti Francesco , Fay Justin C. , Giudici Paolo , De Vero Luciana 
Published: December 2016

AbstractIn this work we have investigated the genetic changes underlying the high glutathione (GSH) production showed by the evolvedSaccharomyces cerevisiaestrain UMCC 2581, selected in a molybdate-enriched environment after sexual recombination of the parental wine strain UMCC 855. To reach our goal, we first generated strains with the desired phenotype, and then we mapped changes underlying adaptation to molybdate by using a whole-genome sequencing. Moreover, we carried out the RNA-seq that allowed an accurate measurement of gene expression and an effective comparison between the transcriptional profiles of parental and evolved strains, in order to investigate the relationship between genotype and high GSH production phenotype.Among all genes evaluated only two genes,MED2andRIM15both related to oxidative stress response, presented new mutations in the UMCC 2581 strain sequence and were potentially related to the evolved phenotype.Regarding the expression of high GSH production phenotype, it included over-expression of amino acids permeases and precursor biosynthetic enzymes rather than the two GSH metabolic enzymes, whereas GSH production and metabolism, transporter activity, vacuolar detoxification and oxidative stress response enzymes were probably added resulting in the molybdate resistance phenotype. This work provides an example of a combination of an evolution-based strategy to successful obtain yeast strain with desired phenotype and inverse engineering approach to genetic characterize the evolved strain. The obtained genetic information could be useful for further optimization of the evolved strains and for providing an even more rapid approach to identify new strains, with a high GSH production, through a marked-assisted selection strategy.
Homeostasis Back and Forth: An Eco-Evolutionary Perspective of Cancer
Authors: Basanta David , Anderson Alexander R. A. 
Published: December 2016

AbstractThe role of genetic mutations in cancer is indisputable: they are a key source of tumor heterogeneity and drive its evolution to malignancy. But the success of these new mutant cells relies on their ability to disrupt the homeostasis that characterizes healthy tissues. Mutated clones unable to break free from intrinsic and extrinsic homeostatic controls will fail to establish a tumor. Here we will discuss, through the lens of mathematical and computational modeling, why an evolutionary view of cancer needs to be complemented by an ecological perspective in order to understand why cancer cells invade and subsequently transform their environment during progression. Importantly, this ecological perspective needs to account for tissue homeostasis in the organs that tumors invade, since they perturb the normal regulatory dynamics of these tissues, often co-opting them for its own gain. Furthermore, given our current lack of success in treating advanced metastatic cancers through tumor centric therapeutic strategies, we propose that treatments that aim to restore homeostasis could become a promising venue of clinical research. This eco-evolutionary view of cancer requires mechanistic mathematical models in order to both integrate clinical with biological data from different scales but also to detangle the dynamic feedback between the tumor and its environment. Importantly, for these models to be useful, they need to embrace a higher degree of complexity than many mathematical modelers are traditionally comfortable with.
Non-random inversion landscapes in prokaryotic genomes are shaped by heterogeneous selection pressures
Authors: Repar Jelena , Warnecke Tobias 
Published: December 2016

AbstractInversions are a major contributor to structural genome evolution in prokaryotes. Here, using a novel alignment-based method, we systematically compare 1651 bacterial and 98 archaeal genomes to show that inversion landscapes are frequently biased towards (symmetric) inversions around the origin-terminus axis. However, symmetric inversion bias is not a universal feature of prokaryotic genome evolution but varies considerably across clades. At the extremes, inversion landscapes in Bacillus-Clostridium and Actinobacteria are dominated by symmetric inversions, while there is little or no systematic bias favouring symmetric rearrangements in archaea with a single origin of replication. Within clades, we find strong but clade-specific relationships between symmetric inversion bias and different features of adaptive genome architecture, including the distance of essential genes to the origin of replication and the preferential localization of genes on the leading strand. We suggest that heterogeneous selection pressures have converged to produce similar patterns of structural genome evolution across prokaryotes.
Customer orientation and firm’s business performance
Authors: Pekovic Sanja , Rolland Sylvie 
Published: December 2016

PurposeThe purpose of this study is to develop a better theoretical and empirical understanding of the causal and contextual mechanisms explaining the relationship between customer orientation and business performance.Design/methodology/approachA three-stage least squares model was used on a sample of 3,720 French firms with 20 or more employees.FindingsBy using a moderated mediation approach, it was found that the mediating effect of environmental customer innovation on the relationship between customer orientation and business performance under different contextual factors (market environment, firm size and sector of activity) can be significantly stronger or weaker.Research limitations/implicationsThis analysis is restricted by the choice of one particular country, and further research should use data from other countries to develop a general understanding of the issues examined. Additionally, examining relevant mechanisms other than firm performance measures will advance the understanding of the customer orientation–firm performance linkage. Because of the fact that the majority of variables used are binary and that each survey was conducted in a particular situation and in a particular context, the picture portrayed could be biased. Because environmental issues not only concern consumers but also all other market actors, it would be highly useful to verify the obtained results using broader concepts such as Hult’s (2011) “market orientation plus” concept or the “sustainable market orientation” developed by Mitchellet al.(2010).Practical implicationsAccording to the results, to achieve market success and sustain a competitive advantage, managers must simultaneously invest in customer orientation and innovation performance. Additionally, managers should consider market environment, firm size and sector of activity as important contingencies in their decision of whether to invest in customer orientation.Originality/valueThis study makes an important contribution by opening up a “black box” and offers a deeper perspective on how and why customer orientation affects firm performance. In particular, rather than providing separate analyses of mediating and moderating effects, this study proposes a simultaneous analysis that reveals how and under what conditions customer orientation improves business performance.
Comprehensive survey on effect of mobility over routing issues in wireless multimedia sensor networks
Authors: Borawake-Satao Rachana , Prasad Rajesh 
Published: December 2016

Purpose
Wireless Multimedia Sensor Network (WMSN) is expected to be a key technology for future network. The multimodal information along with very low-cost availability of the camera sensor nodes is promoting the extensive use of audio, image and video in various real-time implementations. The purpose of this paper is to study various routing issues and the effect of mobility on existing solutions for the applications in future internet.

Design/methodology/approach
This paper conducts a survey of the various methodologies for routing and the vital issues in the design of routing protocols for WMSN, and it also discusses about the effect of mobility on various routing methodologies of WMSN. WMSN ubiquitously performs data acquisition, processing and routing for scalar and multimedia data in a mobile environment. The routing protocols should be adaptive in nature and should have a dynamic approach to service effectively for future network. Many authors proposed the mobility of sink to improve lifetime of the network. This paper discusses some effective approaches for the network where not only the sink node but also some of the sensor nodes are mobile.

Findings
During the survey, the performance and lifetime of the network are discussed, other parameters like delay, packet loss, energy consumption and simulators used for implementation are also discussed.

Originality/value
The techniques in this paper represent a considerable solution for mobility issues in future internet applications.
Pharmaceutical innovation and market share: evidence from a generic market
Authors: Yousefi Nazila , Mehralian Gholamhossein , Rasekh Hamid Reza , Tayeba Hossein 
Published: December 2016

Purpose
Pharmaceutical market value in Iran exceeded to more than US$4bn in 2013, indicating annually over 20 per cent growth. In the past decades, Iranian pharmaceutical industry was supported by government policies, namely, generic substitution, import limitation and local production support; however, the local pharmaceutical manufacturer’s market share in value has been decreased gradually. This study aims to provide historical data on Iran pharmaceutical market to show the importance of new product development to attain greater market share and tries to motivate the pharmaceutical industry located in developing countries to develop more innovative medicines.

Design/methodology/approach
This is a descriptive cross-sectional study that investigates the Iranian pharmaceutical market by focusing on new products over a five-year period (2009-2014), and that was augmented by an expert panel to rank subjectively firms’ performance indicators to shed light on the importance of new product development to firms’ performance.

Findings
The expert panel results find out that new product development is one of the most important “result indicators” for Iranian pharmaceutical companies. Historically, in line with the experts’ opinion on the new product development, the Iranian pharmaceutical industry has shown its capability to develop new medicines by developing 3,095 new products (mostly new-to-firm) across about 100 firms. Despite this fact, the share of local manufacturers in new medicines’ market decreased from 52 per cent at the beginning of studied period to 24 per cent at the end, and the gap between the unit value of imported and domestically produced medicines has been significantly increased due to low-innovative medicines locally produced.

Research limitations/implications
This research was challenged with limitations such as lack of reliable published data on new medicines in the Iran pharmaceutical market.

Practical implications
This study highlights the fact that developing more innovative products in the generic pharmaceutical industry such as Iran can grant its market share.

Originality/value
This is an original study that shows the effect of innovative product development on market share through historical data.