bluuebunny/crossref_metadata_2025_split huggingface dataset:
Survival Outcomes for Patients With Indeterminate 18FDG-PET Scan for Extrahepatic Disease Before Liver Resection for Metastatic Colorectal Cancer
Authors: Wong Geoffrey Yuet Mun , Kumar Rajiv , Beeke Carol , Ullah Shahid , Chen John , Karapetis Christos , Price Timothy , Padbury Rob 
Published: February 2017

Objective:
The aim of this study was to evaluate overall survival (OS) and cancer recurrence for patients with indeterminate positron emission tomography (PET) scan for extrahepatic disease (EHD) before liver resection (LR) for colorectal liver metastases (CLMs).

Summary of Background Data:
Indeterminate EHD as determined by PET imaging indicates a probability of extrahepatic malignancy and potentially excludes patients from undergoing LR for CLM.

Methods:
In a retrospective analysis of prospectively collected data from February 2006 to December 2014, OS for patients with indeterminate EHD on 18FDG-PET scan before LR for CLM was performed using standard survival analysis methods, including Kaplan-Meier estimator and Cox proportional hazard models for multivariate analyses. Postoperative imaging was used as reference to evaluate the association between indeterminate EHD and recurrence.

Results:
Of 267 patients with PET scans before LR, 197 patients had no EHD and 70 patients had indeterminate EHD. Median follow-up was 33 months. The estimated 5-year OS was 60.8% versus 59.4% for indeterminate and absent EHD, respectively (P = 0.625). Disease-free survival was comparable between both groups (P = 0.975) and overall recurrence was 57.1% and 59.5% for indeterminate and absent EHD, respectively (P = 0.742). About 16.9% of recurrence was associated with the site of indeterminate EHD, with 80% of associated recurrence occurring in the thorax.

Conclusions:
The site of indeterminate EHD appears to have a predictive value for recurrence, with indeterminate EHD in the thorax having a higher probability of malignancy. The evidence in this report supports the critical evaluation of PET scan results and that patients are not denied potential curative LR unless the evidence for unresectable EHD is certain.
Apolipoprotein L1 and Chronic Kidney Disease Risk in Young Potential Living Kidney Donors
Authors: Locke Jayme E. , Sawinski Deirdre , Reed Rhiannon D. , Shelton Brittany , MacLennan Paul A. , Kumar Vineeta , Mehta Shikha , Mannon Roslyn B. , Gaston Robert , Julian Bruce A. , Carr John J. , Terry James G. , Kilgore Meredith , Massie Allan B. , Segev Dorry L. , Lewis Cora E. 
Published: February 2017

Objective:
The aim of this study was to develop a novel chronic kidney disease (CKD) risk prediction tool for young potential living kidney donors.

Summary of Background Data:
Living kidney donor selection practices have evolved from examining individual risk factors to a risk calculator incorporating multiple characteristics. Owing to limited long-term data and lack of genetic information, current risk tools lack precision among young potential living kidney donors, particularly African Americans (AAs).

Methods:
We identified a cohort of young adults (18–30 years) with no absolute contraindication to kidney donation from the longitudinal cohort study Coronary Artery Risk Development in Young Adults. Risk associations for CKD (estimated glomerular filtration rate <60 mL/min/1.73 m2) were identified and assigned weighted points to calculate risk scores.

Results:
A total of 3438 healthy adults were identified [mean age 24.8 years; 48.3% AA; median follow-up 24.9 years (interquartile range: 24.5–25.2)]. For 18-year olds, 25-year projected CKD risk varied by ethnicity and sex even without baseline clinical and genetic abnormalities; risk was 0.30% for European American (EA) women, 0.52% for EA men, 0.52% for AA women, 0.90% for AA men. Among 18-year-old AAs with apolipoprotein L1 gene (APOL1) renal-risk variants without baseline abnormalities, 25-year risk significantly increased: 1.46% for women and 2.53% for men; among those with 2 APOL1 renal-risk variants and baseline abnormalities, 25-year risk was higher: 2.53% to 6.23% for women and 4.35% to 10.58% for men.

Conclusions:
Young AAs were at highest risk for CKD, and APOL1 renal-risk variants drove some of this risk. Understanding the genetic profile of young AA potential living kidney donors in the context of baseline health characteristics may help to inform candidate selection and counseling.
En Bloc Cadaver Kidney Transplantation From a 9-Month-Old Donor to an Adult Recipient: Maturation of Glomerular Size and Podocyte in the Recipient
Authors: Hirukawa Takashi , Suzuki Hajime , Niimura Fumio , Fukagawa Masafumi , Kakuta Takatoshi 
Published: February 2017

Background
Favorable outcomes of en bloc pediatric donor kidney transplantation to adult recipients are attributed primarily to grafting of twice the nephron mass of a single kidney.

Methods
The kidneys of a 9-month-old male infant were transplanted en bloc in a 56-year-old man. Biopsies were performed 1 hour postreperfusion, 6 months and 3.5 years posttransplant.

Results
Warm and cold ischemia times were 21 and 426 minutes, respectively. The recipient was released from hemodialysis 10 days posttransplant and discharged 91 days posttransplant when serum creatinine was 0.9 mg/dL. At 4 years and 9 months posttransplant, serum creatinine was 1.0 mg/dL, and estimated glomerular filtration rate was 58.0 mL/min per 1.73 m2. The grafts increased in size until they reached adult size by 3 months posttransplant. The glomerular area and volume, respectively, increased from 5.9 × 103 μm2 and 0.34 × 106 μm3 at 1 hour postreperfusion to 14.9 × 103 μm2 and 1.27 × 106 μm3 at 3.5 years posttransplant, both of which were less than half of adult size. At 1 hour postreperfusion, podocytes were structurally immature. At 6 months posttransplant, podocyte immaturity was still evident. At 3.5 years posttransplant, podocytes were mature.

Conclusions
These findings suggest that podocytes and glomerular size of pediatric donor kidneys can continue to mature in adult recipients at rates appropriate for donor age when transplanted en bloc. The maturational levels of podocytes and glomeruli may also be a factor involved in favorable outcomes of en bloc pediatric donor kidney transplantation.
Acute Rejection Phenotypes in the Current Era of Immunosuppression: A Single-Center Analysis
Authors: Wehmeier Caroline , Amico Patrizia , Hirt-Minkowski Patricia , Georgalis Argyrios , Höenger Gideon , Menter Thomas , Mihatsch Michael , Burkhalter Felix , Steiger Juerg , Dickenmann Michael , Hopfer Helmut , Schaub Stefan 
Published: February 2017

Background
Besides ‘definitive rejection’, the Banff classification includes categories for ‘suspicious for rejection’ phenotypes. The aim of this study was to determine the frequency and phenotypes of rejection episodes in 316 consecutive renal transplants from 2009 to 2014 grouped into patients without/with pretransplant HLA-DSA (ptDSAneg, n = 251; ptDSApos, n = 65).

Methods
All adequate indication (n = 125) and surveillance biopsies (n = 538) performed within the first year posttransplant were classified according to the current Banff criteria.

Results
‘Suspicious for rejection’ phenotypes were 3 times more common than ‘definitive rejection’ phenotypes in biopsies from ptDSAneg patients (35% vs 11%) and equally common in biopsies from ptDSApos patients (25% vs 27%). In both groups, ‘suspicious for rejection’ phenotypes were more frequent in surveillance than in indication biopsies (28% vs 16% in ptDSAneg patients, and 37% vs 29% in ptDSApos patients). ‘Borderline changes: ‘Suspicious' for acute T-cell mediated rejection’ (91%) were the dominant ‘suspicious for rejection’ phenotype in ptDSAneg patients, whereas ‘borderline changes’ (58%) and ‘suspicious for acute/active antibody-mediated rejection’ (42%) were equally frequent in biopsies from ptDSApos patients. Inclusion of ‘suspicious for rejection’ phenotypes increased the 1-year incidence of clinical (ptDSAneg patients: 18% vs 8%, P = 0.0005; ptDSApos patients: 24% vs 18%, P = 0.31) and (sub)clinical rejection (ptDSAneg patients: 59% vs 22%, P < 0.0001; ptDSApos patients: 68% vs 40%, P = 0.004).

Conclusions
‘Suspicious for rejection’ phenotypes are very common in the current era and outnumber the frequency of ‘definitive rejection’ within the first year posttransplant.
Tumoral Presentation of Homonymous Hemianopia and Prosopagnosia in Cerebral Amyloid Angiopathy–Related Inflammation
Authors: Hainline Clotilde , Rucker Janet C. , Zagzag David , Golfinos John G. , Lui Yvonne W. , Liechty Benjamin , Warren Floyd A. , Balcer Laura J. , Galetta Steven L. 
Published: February 2017

Abstract:
While cerebral amyloid angiopathy is a common cause of lobar hemorrhage, rarely it may be associated with an inflammatory response, thought to be incited by amyloid deposits. We report a 73-year-old woman with an extensive cancer history who presented with tumor-like lesions and symptoms of homonymous hemianopia and prosopagnosia. Found to have cerebral amyloid angiopathy–related inflammation proven by brain biopsy, she was treated successfully with immunosuppression.
A target-specific assay for rapid and quantitative detection of Mycobacterium chimaera DNA in environmental and clinical specimens
Authors: Zozaya-Valdés Enrique , Porter Jessica L. , Coventry John , Fyfe Janet A. M. , Carter Glen P. , Gonçalves da Silva Anders , Seemann Torsten , Johnson Paul D. R. , Stewardson Andrew James , Bastian Ivan , Roberts Sally A. , Howden Benjamin P. , Williamson Deborah A. , Stinear Timothy P. 
Published: February 2017

AbstractMycobacterium chimaerais an opportunistic environmental mycobacterium, belonging to theMycobacterium intracellularecomplex. Although most commonly associated with pulmonary disease, there has been growing awareness of invasiveM. chimaerainfections following cardiac surgery. Investigations suggest world-wide spread of a specificM. chimaeraclone, associated with contaminated hospital heater-cooler units used during the surgery. Given the global dissemination of this clone, its potential to cause invasive disease, and the laboriousness of current culture-based diagnostic methods, there is a pressing need to develop rapid and accurate diagnostic assays, specific forM. chimaera. Here, we assessed 354 mycobacterial genome sequences and confirmed thatM. chimaerais a phylogenetically coherent group.In silicocomparisons indicated six DNA regions present only inM. chimaera. We targeted one of these regions and developed a TaqMan qPCR assay forM. chimaerawith a detection limit of 10 CFU in whole blood.In vitroscreening against DNA extracted from 40 other mycobacteria and 22 bacterial species from 21 diverse genera confirmedin silicopredicted specificity forM. chimaera. Screening 33 water samples from heater cooler units with this assay highlighted the increased sensitivity of PCR compared to culture, with 15 of 23 culture negative samples positive byM. chimaeraqPCR. We have thus developed a robust molecular assay that can be readily and rapidly deployed to screen clinical and environmental specimens forM. chimaera.
The Social Genome of Friends and Schoolmates in the National Longitudinal Study of Adolescent to Adult Health
Authors: Domingue Benjamin W. , Belsky Daniel W. , Fletcher Jason M. , Conley Dalton , Boardman Jason D. , Harris Kathleen Mullan 
Published: February 2017

AbstractHumans tend to form social relationships with others who resemble them. Whether this sorting of like with like arises from historical patterns of migration, meso-level social structures in modern society, or individual-level selection of similar peers remains unsettled. Recent research has evaluated the possibility that unobserved genotypes may play an important role in the creation of homophilous relationships. We extend this work by using data from 9,500 adolescents from the National Longitudinal Study of Adolescent to Adult Health (Add Health) to examine genetic similarities among pairs of friends. While there is some evidence that friends have correlated genotypes, both at the whole-genome level as well as at trait-associated loci (via polygenic scores), further analysis suggests that meso-level forces, such as school assignment, are a principal source of genetic similarity between friends. We also observe apparent social-genetic effects in which polygenic scores of an individual’s friends and schoolmates predict the individual’s own educational attainment. In contrast, an individual’s height is unassociated with the height genetics of peers.SignificanceOur study reported significant findings of a “social genome” that can be quantified and studied to understand human health and behavior. In a national sample of more than 9,000 American adolescents, we found evidence of social forces that act to make friends and schoolmates more genetically similar to one another as compared to random pairs of unrelated individuals. This subtle genetic similarity was observed across the entire genome and at sets of genomic locations linked with specific traits—educational attainment and body-mass index—a phenomenon we term “social-genetic correlation.” We also find evidence of a “social-genetic effect” such that the genetics of a person’s friends and schoolmates influenced their own education, even after accounting for the person’s own genetics.
Pairwise comparisons across species are problematic when analyzing functional genomic data
Authors: Dunn Casey W. , Zapata Felipe , Munro Catriona , Siebert Stefan , Hejnol Andreas 
Published: February 2017

AbstractThere is considerable interest in comparing functional genomic data across species. One goal of such work is to provide an integrated understanding of genome and phenotype evolution. Most comparative functional genomic studies have relied on multiple pairwise comparisons between species, an approach that does not incorporate information about the evolutionary relationships among species. The statistical problems that arise from not considering these relationships can lead pairwise approaches to the wrong conclusions, and are a missed opportunity to learn about biology that can only be understood in an explicit phylogenetic context. Here we examine two recently published studies that compare gene expression across species with pairwise methods, and find reason to question the original conclusions of both. One study interpreted pairwise comparisons of gene expression as support for the ortholog conjecture, the hypothesis that orthologs tend to be more similar than paralogs. The other study interpreted pairwise comparisons of embryonic gene expression across distantly related animals as evidence for a distinct evolutionary process that gave rise to phyla. In each study, distinct patterns of pairwise similarity among species were originally interpreted as evidence of particular evolutionary processes, but instead we find they reflect species relationships. These reanalyses concretely demonstrate the inadequacy of pairwise comparisons for analyzing functional genomic data across species. It will be critical to adopt phylogenetic comparative methods in future functional genomic work. Fortunately, phylogenetic comparative biology is also a rapidly advancing field with many methods that can be directly applied to functional genomic data.SignificanceComparisons of genome function between species are providing important insight into the evolutionary origins of diversity. Here we demonstrate that comparative functional genomics studies can come to the wrong conclusions if they do not take the relationships of species into account and instead rely on pairwise comparisons between species, as is common practice. We re-examined two previously published studies and found problems with pairwise comparisons that draw both their original conclusions into question. One study had found support for the ortholog conjecture and the other had concluded that the evolution of gene expression was different between animal phyla than within them. Our results demonstrate that to answer evolutionary questions about genome function, it is critical to consider evolutionary relationships.
A scalable method for parameter-free simulation and validation of mechanistic cellular signal transduction network models
Authors: Romers Jesper , Thieme Sebastian , Münzner Ulrike , Krantz Marcus 
Published: February 2017

AbstractThe metabolic modelling community has established the gold standard for bottom-up systems biology with reconstruction, validation and simulation of mechanistic genome-scale models. Similar methods have not been established for signal transduction networks, where the representation of internal states leads to scalability issues in both model formulation and execution. While rule- and agent-based methods allow efficient model definition and execution, respectively, model parametrisation introduces an additional layer of uncertainty due to the sparsity of reliably measured parameters. Here, we present a scalable method for parameter-free simulation of mechanistic signal transduction networks. It is based on rxncon and uses a bipartite Boolean logic with separate update rules for reactions and states. Using two generic update rules, we enable translation of any rxncon model into a unique Boolean model, which can be used for network validation and simulation - allowing the prediction of system level function directly from molecular mechanistic data. Through scalable model definition and simulation, and the independence of quantitative parameters, it opens up for simulation and validation of mechanistic genome-scale models of signal transduction networks.
PhyD3: a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization
Authors: Kreft Łukasz , Botzki Alexander , Coppens Frederik , Vandepoele Klaas , Van Bel Michiel 
Published: February 2017

AbstractMotivation:Comparative and evolutionary studies utilise phylogenetic trees to analyse and visualise biological data. Recently, several web-based tools for the display, manipulation, and annotation of phylogenetic trees, such as iTOL and Evolview, have released updates to be compatible with the latest web technologies. While those web tools operate an open server access model with a multitude of registered users, a feature-rich open source solution using current web technologies is not available.Results:Here, we present an extension of the widely used PhyloXML standard with several new options to accommodate functional genomics or annotation datasets for advanced visualization. Furthermore, PhyD3 has been developed as a lightweight tool using the JavaScript library D3.js to achieve a state-of-the-art phylogenetic tree visualisation in the web browser, with support for advanced annotations. The current implementation is open source, easily adaptable and easy to implement in third parties’ web sites.Availability:More information about PhyD3 itself, installation procedures, and implementation links are available athttp://phyd3.bits.vib.beand athttp://github.com/vibbits/phyd3/.Contact:bits@vib.be
Organisational change towards servitization: a theoretical framework
Authors: Ziaee Bigdeli Ali , Baines Tim , Bustinza Oscar F. , Guang Shi Victor 
Published: February 2017

Purpose
The need for a holistic framework for studying organisational transformation towards Servitization is implicit. This is particularly relevant as Servitization demands consideration of both business model and organisational change. The purpose of this paper is, therefore, to provide an integrative framework that systematically captures and evaluate existing literature on Servitization.

Design/methodology/approach
The aim of the paper has been achieved through three main objectives; comprehensively examine the literature in organisational change management that would assist with the selection of the most effective evaluation framework, classify previous studies against the proposed framework through a systematic literature review methodology and analyse the selected papers and propose research questions/propositions based on the identified gaps.

Findings
Results indicate that there are two somewhat macro opportunities for the Servitization community, namely, stronger infusion of generic theory into the Servitization debate and exploring Servitization in action through the lens of the theoretical framework.

Practical implications
The findings of the paper demonstrate the gaps in the Servitization literature, which indeed require further theoretical/empirical research.

Originality/value
It is discussed the usefulness and practicality of viewing research contributions that are setting out to be either “descriptive” or “prescriptive”. Consequently, the authors have proposed several avenues for future research based on these two viewpoints.
Numerical study of nanofluid flow and heat transfer over a rotating disk using Buongiorno’s model
Authors: Khan Junaid Ahmad , Mustafa M. , Hayat T. , Turkyilmazoglu Mustafa , Alsaedi A. 
Published: February 2017

Purpose
The purpose of the present study is to explore a three-dimensional rotating flow of water-based nanofluids caused by an infinite rotating disk.

Design/methodology/approach
Mathematical formulation is performed using the well-known Buongiorno model which accounts for the combined influence of Brownian motion and thermophoresis. The recently suggested condition of passively controlled wall nanoparticle volume fraction has been adopted.

Findings
The results reveal that temperature decreases with an increase in thermophoresis parameter, whereas it is negligibly affected with a variation in the Brownian motion parameter. Axial velocity is negative because of the downward flow in the vertical direction.

Originality/value
Two- and three-dimensional streamlines are also sketched and discussed. The computations are found to be in very good agreement with the those of existing studies in the literature for pure fluid.
Unsteady mixed convection stagnation-point flow over a plate moving along the direction of flow impingement
Authors: Muhad Saleh Siti Hidayah , Md. Arifin Norihan , Nazar Roslinda , Pop Ioan 
Published: February 2017

PurposeThe purpose of this paper is to present the results of an analysis performed to study unsteady mixed convection at the stagnation point flow over a plate moving along the direction of flow impingement. The similarity transformations are used to transform the governing nonlinear partial differential equation to a system of an ordinary differential equation.Design/methodology/approachThe transformed equations are then solved numerically by a shooting technique together with bvp4c function.FindingsThe numerical results are compared with the corresponding results from previous researchers. The effects of the unsteadiness Parameter A, Prandtl number Pr, mixed convection parameter λ for plane (m = 0) and axisymmetric (m = 1) flow on the shear stress or the skin friction and heat transfer coefficients, as well as the velocity and temperature profiles, are presented and discussed.Originality/valueDual solutions for the opposing flow and multiple solutions for the assisting flow are found.