bluuebunny/crossref_metadata_2025 huggingface dataset:
Experimental study on surface properties of the PMMA used in high power spark gaps
Authors: Han Ruoyu , Wu Jiawei , Ding Weidong , Liu Yunfei , Gou Yang
Published: October 2017

This paper studies the surface properties of the Polymethylmethacrylate (PMMA) insulator samples used in high power spark gaps. Experiments on surface morphology, surface profile, surface chemical composition and surface leakage current were performed. Metal particles ejected in tangent direction of discharge spots were researched on the sample surface. Three kinds of distinct bands were found on the surface after 1500 shots: colorless and transparent sinking band, black band, and grey powdered coating band. The thickness of the coating band was tens of microns and the maximum radial erosion rate was about 10 μm/C. Surface content analysis indicated that the powdered coating was a mixture of decomposed insulator material and electrode material oxides. In addition, leakage current significantly depended on water content in the chamber and presented an U-shape curve distribution along the insulator surface, in keeping with the amount of powdered coating due to shock waves. Possible reasons of the surface property changes were discussed. Electroconductive oxides of low valence states of Cu and W produced by the reactions between electrode materials and arc plasmas were considered to be the cause of dielectric performance degradation.
Effect of normalization methods on the performance of supervised learning algorithms applied to HTSeq-FPKM-UQ data sets: 7SK RNA expression as a predictor of survival in patients with colon adenocarcinoma
Authors: Shahriyari Leili
Published: October 2017

Motivation: One of the main challenges in machine learning (ML) is choosing an appropriate normalization method. Here, we examine the effect of various normalization methods on analyzing FPKM upper quartile (FPKM-UQ) RNA sequencing data sets. We collect the HTSeq-FPKM-UQ files of patients with colon adenocarcinoma from TCGA-COAD project. We compare three most common normalization methods: scaling, standardizing using z-score and vector normalization by visualizing the normalized data set and evaluating the performance of 12 supervised learning algorithms on the normalized data set. Additionally, for each of these normalization methods, we use two different normalization strategies: normalizing samples (files) or normalizing features (genes). Results: Regardless of normalization methods, a support vector machine (SVM) model with the radial basis function kernel had the maximum accuracy (78%) in predicting the vital status of the patients. However, the fitting time of SVM depended on the normalization methods, and it reached its minimum fitting time when files were normalized to the unit length. Furthermore, among all 12 learning algorithms and 6 different normalization techniques, the Bernoulli naive Bayes model after standardizing files had the best performance in terms of maximizing the accuracy as well as minimizing the fitting time. We also investigated the effect of dimensionality reduction methods on the performance of the supervised ML algorithms. Reducing the dimension of the data set did not increase the maximum accuracy of 78%. However, it leaded to discovery of the 7SK RNA gene expression as a predictor of survival in patients with colon adenocarcinoma with accuracy of 78%.
VecScreen_plus_taxonomy: imposing a tax(onomy) increase on vector contamination screening
Authors: Schäffer Alejandro A , Nawrocki Eric P , Choi Yoon , Kitts Paul A , Karsch-Mizrachi Ilene , McVeigh Richard
Published: October 2017

Motivation

Nucleic acid sequences in public databases should not contain vector contamination, but many sequences in GenBank do (or did) contain vectors. The National Center for Biotechnology Information uses the program VecScreen to screen submitted sequences for contamination. Additional tools are needed to distinguish true-positive (contamination) from false-positive (not contamination) VecScreen matches.

Results

A principal reason for false-positive VecScreen matches is that the sequence and the matching vector subsequence originate from closely related or identical organisms (for example, both originate in Escherichia coli). We collected information on the taxonomy of sources of vector segments in the UniVec database used by VecScreen. We used that information in two overlapping software pipelines for retrospective analysis of contamination in GenBank and for prospective analysis of contamination in new sequence submissions. Using the retrospective pipeline, we identified and corrected over 8000 contaminated sequences in the nonredundant nucleotide database. The prospective analysis pipeline has been in production use since April 2017 to evaluate some new GenBank submissions.

Availability and implementation

Data on the sources of UniVec entries were included in release 10.0 (ftp://ftp.ncbi.nih.gov/pub/UniVec/). The main software is freely available at https://github.com/aaschaffer/vecscreen_plus_taxonomy.

Supplementary information

Supplementary data are available at Bioinformatics online.
ROSC-Pred: web-service for rodent organ-specific carcinogenicity prediction
Authors: Lagunin Alexey , Rudik Anastasia , Druzhilovsky Dmitry , Filimonov Dmitry , Poroikov Vladimir
Published: October 2017

Motivation

Identification of rodent carcinogens is an important task in risk assessment of chemicals. SAR methods were proposed to reduce the number of animal experiments. Most of these methods ignore information about organ-specificity of tumorigenesis. Our study was aimed at the creation of classification models and a freely available online service for prediction of rodent carcinogens considering the species (rats, mice), sex and tissue-specificity from structural formula of compounds.

Results

The data from Carcinogenic Potency Database for 1011 organic compounds evaluated on the standard two-year rodent carcinogenicity bioassay was used for the creation of training sets. Structure-activity relationships models for prediction of rodent organ-specific carcinogenicity were created by PASS software, which was based on Bayesian-like approach and Multilevel Neighborhoods of Atoms descriptors. The average prediction accuracy for training sets calculated by leave-one-out and 10-fold cross-validation was 79 and 78.2%, respectively.

Availability and implementation

Freely available on the web at http://www.way2drug.com/ROSC.

Supplementary information

Supplementary data are available at Bioinformatics online.
Estimating autoantibody signatures to detect autoimmune disease patient subsets
Authors: Wu Zhenke , Casciola-Rosen Livia , Shah Ami A , Rosen Antony , Zeger Scott L
Published: October 2017

Autoimmune diseases are characterized by highly specific immune responses against molecules in self-tissues. Different autoimmune diseases are characterized by distinct immune responses, making autoantibodies useful for diagnosis and prediction. In many diseases, the targets of autoantibodies are incompletely defined. Although the technologies for autoantibody discovery have advanced dramatically over the past decade, each of these techniques generates hundreds of possibilities, which are onerous and expensive to validate. We set out to establish a method to greatly simplify autoantibody discovery, using a pre-filtering step to define subgroups with similar specificities based on migration of radiolabeled, immunoprecipitated proteins on sodium dodecyl sulfate (SDS) gels and autoradiography [Gel Electrophoresis and band detection on Autoradiograms (GEA)]. Human recognition of patterns is not optimal when the patterns are complex or scattered across many samples. Multiple sources of errors—including irrelevant intensity differences and warping of gels—have challenged automation of pattern discovery from autoradiograms.

In this article, we address these limitations using a Bayesian hierarchical model with shrinkage priors for pattern alignment and spatial dewarping. The Bayesian model combines information from multiple gel sets and corrects spatial warping for coherent estimation of autoantibody signatures defined by presence or absence of a grid of landmark proteins. We show the pre-processing creates more clearly separated clusters and improves the accuracy of autoantibody subset detection via hierarchical clustering. Finally, we demonstrate the utility of the proposed methods with GEA data from scleroderma patients.
An iterative frequency-sweeping approach for stability analysis of linear systems with multiple delays
Authors: Li Xu-Guang , Niculescu Silviu-Iulian , Çela Arben
Published: October 2017

In this article, we study the stability of linear systems with multiple (incommensurate) delays, by extending a recently proposed frequency-sweeping approach. First, we consider the case where only one delay parameter is free while the others are fixed. The complete stability w.r.t. the free delay parameter can be systematically investigated by proving an appropriate invariance property. Next, we propose an iterative frequency-sweeping approach to study the stability under any given multiple delays. Moreover, we may effectively analyse the asymptotic behaviour of the critical imaginary roots (if any) w.r.t. each delay parameter, which provides a possibility for stabilizing the system through adjusting the delay parameters. The approach is simple (graphical test) and can be applied systematically to the stability analysis of linear systems including multiple delays. A deeper discussion on its implementation is also proposed. Finally, various numerical examples complete the presentation.
Relative Szegő Asymptotics for Toeplitz Determinants
Authors: Duits Maurice , Kozhan Rostyslav
Published: October 2017

We study the asymptotic behaviour, as $n \to \infty$, of ratios of Toeplitz determinants $D_n({\rm e}^h {\rm d}\mu)/D_n({\rm d}\mu)$ defined by a measure $\mu$ on the unit circle and a sufficiently smooth function $h$. The approach we follow is based on the theory of orthogonal polynomials. We prove that the second order asymptotics depends on $h$ and only a few Verblunsky coefficients associated to $\mu$. As a result, we establish a relative version of the Strong Szegő Limit Theorem for a wide class of measures $\mu$ with essential support on a single arc. In particular, this allows the measure to have a singular component within or outside of the arc.
Are all certified EHRs created equal? Assessing the relationship between EHR vendor and hospital meaningful use performance
Authors: Holmgren A Jay , Adler-Milstein Julia , McCullough Jeffrey
Published: October 2017

Objective

The federal electronic health record (EHR) certification process was intended to ensure a baseline level of system quality and the ability to support meaningful use criteria. We sought to assess whether there was variation across EHR vendors in the degree to which hospitals using products from those vendors were able to achieve high levels of performance on meaningful use criteria.

Materials and Methods

We created a cross-sectional national hospital sample from the Office of the National Coordinator for Health Information Technology EHR Products Used for Meaningful Use Attestation public use file and the Centers for Medicare & Medicaid Services Medicare EHR Incentive Program Eligible Hospitals public use file. We used regression models to assess the relationship between vendor and hospital performance on 6 Stage 2 Meaningful Use criteria, controlling for hospital characteristics. We also calculated how much variation in performance is explained by vendor choice.

Results

We found significant associations between specific vendor and level of hospital performance for all 6 meaningful use criteria. Epic was associated with significantly higher performance on 5 of the 6 criteria; relationships for other vendors were mixed, with some associated with significantly worse performance on multiple criteria. EHR vendor choice accounted for between 7% and 34% of performance variation across the 6 criteria.

Discussion

A nontrivial proportion of variation in hospital meaningful use performance is explained by vendor choice, and certain vendors are more often associated with better meaningful use performance than others. Our results suggest that policy-makers should improve the certification process by including more “real-world” scenario testing and provider feedback or ratings to reduce this variation. Hospitals can use these results to guide interactions with vendors.

Conclusion

Vendor choice accounts for a meaningful proportion of variation in hospital meaningful use performance, and specific vendors are consistently associated with higher or lower performance across criteria.
Permanent budget surpluses as a fiscal regime
Authors: Haffert Lukas
Published: October 2017

This article challenges the focus on budget deficits that permeates the literature on the comparative political economy of fiscal policy. It analyzes countries running budget surpluses and asks why some preserved these surpluses while others did not. Whereas several OECD members recorded surpluses for just a few years, balanced budgets became the norm in Australia, Canada, Denmark, Finland, New Zealand and Sweden in the late 1990s. The article compares both types of countries. Focusing on Canada and Sweden, it argues that a path-dependent shift in the balance of power among competing fiscal policy coalitions explains why surpluses persisted in one group of countries but not in the other. This reconfiguration of fiscal conflict was triggered by a deep fiscal crisis and an ensuing expenditure-led consolidation. It can be interpreted as creating a ‘surplus regime,’ in which fiscal policy became structured around the goals of balancing the budget and cutting taxes.
Vision and Vestibular System Dysfunction Predicts Prolonged Concussion Recovery in Children
Authors: Master Christina L. , Master Stephen R. , Wiebe Douglas J. , Storey Eileen P. , Lockyer Julia E. , Podolak Olivia E. , Grady Matthew F.
Published: October 2017

Objective:

Up to one-third of children with concussion have prolonged symptoms lasting beyond 4 weeks. Vision and vestibular dysfunction is common after concussion. It is unknown whether such dysfunction predicts prolonged recovery. We sought to determine which vision or vestibular problems predict prolonged recovery in children.

Design:

A retrospective cohort of pediatric patients with concussion.

Setting:

A subspecialty pediatric concussion program.

Patients (or Participants):

Four hundred thirty-two patient records were abstracted.

Assessment of Risk Factors:

Presence of vision or vestibular dysfunction upon presentation to the subspecialty concussion program.

Main Outcome Measures:

The main outcome of interest was time to clinical recovery, defined by discharge from clinical follow-up, including resolution of acute symptoms, resumption of normal physical and cognitive activity, and normalization of physical examination findings to functional levels.

Results:

Study subjects were 5 to 18 years (median = 14). A total of 378 of 432 subjects (88%) presented with vision or vestibular problems. A history of motion sickness was associated with vestibular dysfunction. Younger age, public insurance, and presence of headache were associated with later presentation for subspecialty concussion care. Vision and vestibular problems were associated within distinct clusters. Provocable symptoms with vestibulo-ocular reflex (VOR) and smooth pursuits and abnormal balance and accommodative amplitude (AA) predicted prolonged recovery time.

Conclusions:

Vision and vestibular problems predict prolonged concussion recovery in children. A history of motion sickness may be an important premorbid factor. Public insurance status may represent problems with disparities in access to concussion care. Vision assessments in concussion must include smooth pursuits, saccades, near point of convergence (NPC), and accommodative amplitude (AA). A comprehensive, multidomain assessment is essential to predict prolonged recovery time and enable active intervention with specific school accommodations and targeted rehabilitation.
Transcatheter Arterial Embolization Compared With Surgery for Uncontrolled Peptic Ulcer Bleeding
Authors: Sverdén Emma , Mattsson Fredrik , Lindström David , Sondén Anders , Lu Yunxia , Lagergren Jesper
Published: October 2017

Objective:

To compare key outcomes after transcatheter arterial embolization (TAE) with conventional surgery for peptic ulcer bleeding when endoscopic intervention fails to achieve hemostasis.

Background:

Mortality in peptic ulcer bleeding remains high, especially in patients who require surgical treatment.

Methods:

A population-based cohort study in Stockholm, Sweden, in 2000 to 2014, assessing the main outcome all-cause mortality and the secondary outcomes re-bleeding, re-intervention, length of hospitalization, and complications, was conducted. Data were taken from well-maintained registries and medical records. Multivariable Cox-regression provided hazard ratios (HRs) with 95% confidence intervals (CIs) adjusted for age, sex, ulcer history, comorbidity, and calendar period were considered.

Results:

Included were 282 patients, 97 in the TAE group and 185 in the surgery group. Compared with the surgery group, the overall hazard of death was 34% decreased in the TAE group (adjusted HR 0.66, 95% CI 0.46–0.96). The corresponding HRs for mortality within 30 days, 90 days, 1 year, and 5 years were 0.70 (95% CI 0.37–1.35), 0.69 (95% CI 0.38–1.26), 0.88 (95% CI 0.53–1.47), and 0.67 (95% CI 0.45–1.00), respectively. The risk of re-bleeding was higher after TAE compared with surgery (HR 2.48, 95% CI 1.33–4.62). The median length of hospital stay was shorter in the TAE group—8 versus 16 days—acceleration factor 0.59 (95% CI 0.45–0.77) and the risk of complications was lower (8.3% vs 32.2%; P < 0.0001).

Conclusions:

This study indicates that TAE compares favorably with surgery regarding prognosis after refractory peptic ulcer bleeding, and the shorter length of hospital stay and fewer complications outweigh a higher risk of re-bleeding. TAE could be recommended as first-line treatment for these patients.
The niche construction of cultural complexity: interactions between innovations, population size and the environment
Authors: Fogarty Laurel , Creanza Nicole
Published: October 2017

Niche construction is a process through which organisms alter their environments and, in doing so, influence or change the selective pressures to which they are subject. ‘Cultural niche construction’ refers specifically to the effect of cultural traits on the selective environments of other biological or cultural traits and may be especially important in human evolution. In addition, the relationship between population size and cultural accumulation has been the subject of extensive debate, in part because anthropological studies have demonstrated a significant association between population size and toolkit complexity in only a subset of studied cultures. Here, we review the role of cultural innovation in constructing human evolutionary niches and introduce a new model to describe the accumulation of human cultural traits that incorporates the effects of cultural niche construction. We consider the results of this model in light of available data on human toolkit sizes across populations to help elucidate the important differences between food-gathering societies and food-producing societies, in which niche construction may be a more potent force. These results support the idea that a population's relationship with its environment, represented here by cultural niche construction, should be considered alongside population size in studies of cultural complexity.

This article is part of the themed issue ‘Process and pattern in innovations from cells to societies’.
A new polymorph of 2,6-diaminopyridine
Authors: Hall Victoria M. , Bertke Jeffery A. , Swift Jennifer A.
Published: October 2017

2,6-Diaminopyridine (26-DAP, C5H7N3) is a common intermediate in the synthesis of aromatic azo chromophores, which are widespread in the dyes and pigments industry. Sublimation of commercial 26-DAP powder yielded a new polymorph, denoted Form II, which grew as colorless orthorhombic needles. Recrystallization from acetone or toluene also yielded Form II as the major phase. Thermal analysis shows that Form II is a less stable polymorph and it converts upon heating at 335 K to the previously reported Form I.
Unusual thermolysis of azacyclic allene under microwave conditions: crystal structure of (3RS,3aSR,8RS,8aRS)-methyl 5,6-dimethoxy-3a,10-dimethyl-1-phenyl-3,3a,8,8a-tetrahydro-3,8-(epiminomethano)cyclopenta[a]indene-2-carboxylate from synchrotron X-ray diffraction
Authors: Anh Le Tuan , Titov Alexander A. , Kobzev Maxim S. , Voskressensky Leonid G. , Varlamov Alexey V. , Dorovatovskii Pavel V. , Khrustalev Victor N.
Published: October 2017

The title compound, C25H27NO4(I), the product of the unusual thermolysis of azacyclic allene methyl 10,11-dimethoxy-3,8-dimethyl-6-phenyl-3-azabenzo[d]cyclodeca-4,6,7-triene-5-carboxylate, represents a bicyclic heterosystem and crystallizes in the monoclinic space groupP21/cwith three crystallographically independent molecules in the unit cell. These independent molecules adopt very similar geometries and differ only in the conformations of the two methoxy substituents on the benzene ring. In two of the three independent molecules, both methoxy groups are almost coplanar with the benzene ring [the C—C—O—Me torsion angles are 10.8 (2), 12.3 (2), 9.1 (2) and 13.6 (3)°], whereas in the third molecule, one of the methoxy groups is practically coplanar to and the other methoxy group is roughly perpendicular to the benzene ring, the C—C—O—Me torsion angles being 14.1 (2) and 76.5 (2)°. The molecule of (I) comprises a fused tetracyclic system containing two five-membered rings (cyclopentenes) and two six-membered rings (piperidine and benzene). The five-membered rings have the usual envelope conformation, with the methyl-subsituted C atom as the flap in each molecule, and the six-membered piperidine ring has a chair conformation. The methyl substituent at the N atom occupies the sterically favourable equatorial position. The carboxylate group lies almost within the basal plane of the parent cyclopentene ring [making dihedral angle of 11.68 (8), 18.94 (9) and 15.16 (9)° in the three independent molecules], while the phenyl substituent is twisted by 48.26 (6), 42.04 (6) and 41.28 (6)° (for the three independent molecules) relative to this plane. In the crystal, molecules of (I) form stacks along theb-axis direction. The molecules are arranged at van der Waals distances.
Crystal structure of tetraisobutylthiuram disulfide
Authors: Fontenot Patricia R. , Wang Bo , Chen Yueli , Donahue James P.
Published: October 2017

Tetrakis(2-methylpropyl)thioperoxydicarbonic diamide, or tetraisobutylthiuram disulfide, C18H36N2S4, crystallizes in a general position in the triclinic space groupP-1 but shows pseudo-C2symmetry about the disulfide bond. The C—S—S—C torsion angle [−85.81 (2)°] and the dihedral angle between the two NCS2mean planes [85.91 (5)°] are within the range observed for this compound type. Multiple intra- and intermolecular S...H—C close contacts appear to play a role in assisting the specific conformation of the pendant isobutyl groups and the packing arrangement of molecules within the cell. Tetraisobutylthiuram disulfide molecules of one optical configuration form sheets in the plane of theaandbaxes. Inversion centers exist between adjoining sheets, which stack along thecaxis and alternate in the handedness of their constituent molecules.
Divergent migration within lake sturgeon (Acipenser fulvescens) populations: Multiple distinct patterns exist across an unrestricted migration corridor
Authors: Kessel Steven T. , Hondorp Darryl W. , Holbrook Christopher M. , Boase James C. , Chiotti Justin A. , Thomas Michael V. , Wills Todd C. , Roseman Edward F. , Drouin Richard , Krueger Charles C.
Published: October 2017

Population structure, distribution, abundance and dispersal arguably underpin the entire field of animal ecology, with consequences for regional species persistence, and provision of ecosystem services. Divergent migration behaviours among individuals or among populations are an important aspect of the ecology of highly mobile animals, allowing populations to exploit spatially or temporally distributed food and space resources.

This study investigated the spatial ecology of lake sturgeon (Acipenser fulvescens) within the barrier free Huron‐Erie Corridor (HEC), which connects Lake Huron and Lake Erie of the North American Laurentian Great Lakes.

Over 6 years (2011–2016), movements of 268 lake sturgeon in the HEC were continuously monitored across the Great Lakes using acoustic telemetry (10 years battery life acoustic transmitters). Five distinct migration behaviours were identified with hierarchical cluster analysis, based on the phenology and duration of river and lake use.

Lake sturgeon in the HEC were found to contain a high level of intraspecific divergent migration, including partial migration with the existence of residents. Specific behaviours included year‐round river residency and multiple lake‐migrant behaviours that involved movements between lakes and rivers. Over 85% of individuals were assigned to migration behaviours as movements were consistently repeated over the study, which suggested migration behaviours were consistent and persistent in lake sturgeon. Differential use of specific rivers or lakes by acoustic‐tagged lake sturgeon further subdivided individuals into 14 “contingents” (spatiotemporally segregated subgroups).

Contingents associated with one river (Detroit or St. Clair) were rarely detected in the other river, which confirmed that lake sturgeon in the Detroit and St. Clair represent two semi‐independent populations that could require separate management consideration for their conservation. The distribution of migration behaviours did not vary between populations, sexes, body size or among release locations, which indicated that intrapopulation variability in migratory behaviour is a general feature of the spatial ecology of lake sturgeon in unfragmented landscapes.
An evolutionary framework outlining the integration of individual social and spatial ecology
Authors: Webber Quinn M. R. , Vander Wal Eric
Published: October 2017

Behaviour is the interface between an organism and its environment, and behavioural plasticity is important for organisms to cope with environmental change. Social behaviour is particularly important because sociality is a dynamic process, where environmental variation influences group dynamics and social plasticity can mediate resource acquisition. Heterogeneity in the ecological environment can therefore influence the social environment. The combination of the ecological and social environments may be interpreted collectively as the “socioecological environment,” which could explain variation in fitness.

Our objective was to outline a framework through which individual social and spatial phenotypes can be integrated and interpreted as phenotypes that covary as a function of changes in the socioecological environment. We propose the socioecological environment is composed of individual behavioural traits, including sociality and habitat selection, both of which are repeatable, potentially heritable and may reflect animal personality traits. We also highlight how ecological and social niche theory can be applied to the socioecological environment framework, where individuals occupy different socioecological niches. Individual sociality and habitat selection are also density‐dependent, and theory predicts that density‐dependent traits should affect reproduction, survival, and therefore fitness and population dynamics.

We then illustrate the proximate links between sociality, habitat selection and fitness as well as the ultimate, and possibly adaptive, consequences associated with changes in population density. The ecological, evolutionary and applied implications of our proposed socioecological environment framework are broad and changes in density could influence individual fitness and population dynamics. For instance, human‐induced environmental changes can influence population density, which can affect the distribution of social and spatial phenotypes within a population. In summary, we outline a conceptual framework that incorporates individual social and spatial behavioural traits with fitness and we highlight a range of ecological and evolutionary processes that are likely associated with the socioecological environment.
Neoadjuvant chemoradiation for non‐metastatic pancreatic cancer increases margin‐negative and node‐negative rates at resection
Authors: Berriochoa Camille A. , Abdel‐Wahab May , Leyrer Charles M. , Khorana Alok , Matthew Walsh R. , Kumar Aryavarta M. S.
Published: October 2017

OBJECTIVE

To compare neoadjuvant to adjuvant chemoradiation in non‐metastatic pancreatic cancer patients.

METHODS

Single‐institution data were obtained for patients with non‐metastatic pancreatic cancer treated with concurrent chemoradiation from 2011 to 2014. Univariate analyses were performed to evaluate clinical and pathological outcomes.

RESULTS

Fifty‐two well‐matched patients were enrolled (21 underwent neoadjuvant chemoradiation, 11 with adjuvant chemoradiation and 20 in the definitive group). Median tumor size was 2.6 cm pretreatment and 2.5 cm after neoadjuvant chemoradiation but 3.2 cm on pathology, with a treatment effect in 95.2% of specimens. Clinical node positivity at diagnosis for neoadjuvant and adjuvant chemoradiation groups was similar (28.6% vs 27.3%, P = 0.12). Of the 36 neoadjuvant patients, 21 (58.3%) underwent complete resection. In the neoadjuvant vs adjuvant chemoradiation groups, positive margins were decreased (4.8% vs 63.6%, P < 0.001), as was pathological nodal positivity (23.8% vs 90.9%, P < 0.001). After a median follow‐up of 13.3 months, locoregional control for neoadjuvant and adjuvant chemoradiation was 7.7 and 7.2 months, respectively (P = 0.12) and the definitive group was 1.2 months (P = 0.014 compared with the surgical cohort). One‐year overall survival was better with neoadjuvant than with adjuvant chemoradiation but this was not significant (94% vs 82%, P = 0.20); 1‐year survival for the definitive group was 59% (P = 0.03 compared with the surgical cohort).

CONCLUSIONS

Neoadjuvant chemoradiation remains a promising approach for non‐metastatic pancreatic cancer for improving resectability and pathological and clinical findings. Computed tomography may not fully demonstrate the effectiveness of neoadjuvant treatment.
Genetic association and phenotypic correlation of TLR4 but not NOD2 variants with Tunisian inflammatory bowel disease
Authors: Feki Sawsan , Bouzid Dorra , Abida Olfa , Chtourou Lassaad , Elloumi Nesrine , Toumi Amina , Hachicha Hend , Amouri Ali , Tahri Nabil , Masmoudi Hatem
Published: October 2017

OBJECTIVE

The common association between NOD2/CARD15 and TLR4 gene variants with inflammatory bowel disease (IBD) has not been replicated in all studies. We studied the polymorphism of these two genes in Tunisian patients with IBD.

METHODS

Polymorphisms of NOD2 (R702W, G908R and L1007fs) and TLR4 (Asp299Gly and Thr399Ile) genes were analyzed in 106 patients with IBD (68 with ulcerative colitis [UC], 38 with Crohn's disease [CD]) and 160 healthy controls using polymerase chain reaction‐restriction fragment length polymorphism. Genotypes and phenotypes were correlated.

RESULTS

The mutated allele of TLR4‐Thr399Ile was strongly associated with IBD (9.4% in IBD, 7.4% in UC and 13.2% in CD vs 2.5% in controls; P = 0.0004, 0.014 and 0.00006, respectively). Heterozygous genotypes were significantly more frequent in patients with IBD (17.0%), UC (14.7%) and CD (21.1%) than in controls (5.0%) (P = 0.0012, 0.012 and 0.001, respectively). Interestingly, the wild genotype was found to be protective (odds ratio 0.24). The mutated allele of TLR4‐Asp299Gly was more frequent in controls (6.8%) than in patients with IBD (2.9%). A phenotypic correlation of Asp299Gly‐AG genotype with arthritis in UC patients was detected (P = 0.003). Regarding the NOD2 gene, the common variations studied were not polymorphic and there was no genetic association with IBD.

CONCLUSION

The TLR4‐Thr399Ile variant was strongly associated with susceptibility to IBD, whereas TLR4‐Asp299Gly seems to play a role in the clinical expression of UC. The rarity and non‐association of NOD2 mutations with IBD may reveal a genetic characteristic of the population in our region.
Performance of non‐traditional hyperglycemia biomarkers by chronic kidney disease status in older adults with diabetes: Results from the Atherosclerosis Risk in Communities Study
Authors: Jung Molly , Warren Bethany , Grams Morgan , Kwong Yuenting D. , Shafi Tariq , Coresh Josef , Rebholz Casey M. , Selvin Elizabeth
Published: October 2017

Background

In people with chronic kidney disease (CKD), HbA1c may be a problematic measure of glycemic control. Glycated albumin and fructosamine have been proposed as better markers of hyperglycemia in CKD. In the present study we investigated associations of HbA1c, glycated albumin, and fructosamine with fasting glucose by CKD categories.

Methods

A cross‐sectional analysis was performed of 1665 Atherosclerosis Risk in Communities Study participants with diagnosed diabetes aged ≥65 years. Spearman's rank correlations (r) were compared and Deming regression was used to obtain root mean square errors (RMSEs) for the associations across CKD categories defined using estimated glomerular filtration rate and urine albumin:creatinine ratio.

Results

Correlations of HbA1c, glycated albumin, and fructosamine with fasting glucose were lowest in people with severe CKD (HbA1c r = 0.52, RMSE = 0.91; glycated albumin r = 0.39, RMSE = 1.89; fructosamine r = 0.41, RMSE = 1.87) and very severe CKD (r = 0.48 and RMSE = 1.01 for HbA1c; r = 0.36 and RMSE = 2.14 for glycated albumin; r = 0.36 and RMSE = 2.22 for fructosamine). Associations of glycated albumin and fructosamine with HbA1c were relatively similar across CKD categories.

Conclusions

In older adults with severe or very severe CKD, HbA1c, glycated albumin, and fructosamine were not highly correlated with fasting glucose. The results suggest there may be no particular advantage of glycated albumin or fructosamine over HbA1c for monitoring glycemic control in CKD.
Unmanned aerial systems measure structural habitat features for wildlife across multiple scales
Authors: Olsoy Peter J. , Shipley Lisa A. , Rachlow Janet L. , Forbey Jennifer S. , Glenn Nancy F. , Burgess Matthew A. , Thornton Daniel H.
Published: October 2017

Assessing habitat quality is a primary goal of ecologists. However, evaluating habitat features that relate strongly to habitat quality at fine‐scale resolutions across broad‐scale extents is challenging. Unmanned aerial systems (UAS) provide an avenue for bridging the gap between relatively high spatial resolution, low spatial extent field‐based habitat quality measurements and lower spatial resolution, higher spatial extent satellite‐based remote sensing. Our goal in this study was to evaluate the potential forUASstructure from motion (SfM) to estimate several dimensions of habitat quality that provide potential security from predators, and forage for pygmy rabbits (Brachylagus idahoensis) in a sagebrush steppe environment.

At the plant and patch scales, we comparedUAS‐derived estimates of vegetation height, volume (estimate of food availability) and canopy cover to estimates from ground‐based terrestrial laser scanning (TLS) and field‐based measurements. Then, we mapped habitat features across two sagebrush landscapes in Idaho,USA, using point clouds derived fromUASSfM.

At the individual plant scale, theUAS‐derived estimates matched those fromTLSfor height (R2 = 0.85), volume (R2 = 0.94) and canopy cover (R2 = 0.68). However, there was less agreement with field‐based measurements of height (R2 = 0.67), volume (R2 = 0.31) and canopy cover (R2 = 0.29). At the patch scale,UAS‐derived estimates provided a better fit to field‐based measurements (R2 = 0.51–0.75) than at the plant scale. Landscape‐scale maps created fromUASwere able to distinguish structural heterogeneity between key patch types.

Our work demonstrates thatUASwas able to accurately estimate habitat heterogeneity for a key terrestrial vertebrate at multiple spatial scales. Given that many of the vegetation metrics we focus on are important for a wide variety of species, our work illustrates a general remote sensing approach for mapping and monitoring fine‐resolution habitat quality across broad landscapes for use in studies of animal ecology, conservation and land management.
Are germination cues for soil‐stored seed banks different in structurally different fire‐prone communities?
Authors: Maikano Gloria Neo , Cohn Janet , Di Stefano Julian
Published: October 2017

Many plant species are dependent on soil‐stored seeds for their persistence in fire‐prone systems. Seed germination is often stimulated by fire‐related cues including heat and smoke, but the way these cues promote germination may differ between structurally distinct plant communities with historically different fire regimes. In this study, we examined the effects of heat, smoke and their interactions on the germination of soil‐stored seeds from shrubby woodlands and herbaceous forests in south‐east Australia. The effect of these treatments on species richness, diversity and composition, and species richness and density of germinants within life‐forms (grass, forb and shrub) were assessed. Soils from each community were subjected to low heat (40°C), low heat with smoke, smoke, high heat (80°C), high heat with smoke and untreated (control) before being placed in a glasshouse, where the germinants were identified and counted. Greater species richness was stimulated by high heat treatments and smoke in both communities, a trend driven by shrubs and forbs, rather than grasses. Greater species diversity was stimulated by high heat with smoke in both communities. Greater densities of grass germinants were stimulated by all treatments, except low heat, in both communities. For forbs and shrubs, the effect of treatment depended on community. Compared to the control, low heat with smoke (forbs) and both low heat and low heat with smoke (shrubs) increased densities in the woodland but not in the forest. There were unique species compositions, different from the control, in all treatments in the forest but not in the woodland, where composition in low heat was not different from the control. These results indicate the importance of high soil temperatures and smoke in both communities. In the absence of wildfires, recurring prescribed burns that heat the soil to low temperatures are likely to reduce plant richness, diversity, and density resulting in a change in understorey species composition and structure.
Peak hour in the bush: linear anthropogenic clearings funnel predator and prey species
Authors: Dawson Stuart J. , Adams Peter J. , Moseby Katherine E. , Waddington Kris I. , Kobryn Halina T. , Bateman Philip W. , Fleming Patricia A.
Published: October 2017

Linear clearings, such as roads and tracks, are an obvious anthropogenic feature in many remote environments, even where infrastructure is sparse. Predator species have been shown to prefer moving down linear clearings, and therefore, clearings could increase predation risk for other species. We investigated whether tracks cleared for seismic surveys are preferentially used by predators and herbivores in a landscape inhabited by bilbies (Macrotis lagotis), a vulnerable species of conservation concern. We used a paired camera trap array to investigate the use of cleared seismic lines at four time points after clearing (1 month, 3 months, 7 months, 48 months) by six mammal species. Bilbies, cattle (Bos indicus/B. taurus), dingoes (Canis familiaris), feral cats (Felis catus) and agile wallabies (Macropus agilis) preferred to use seismic lines compared with adjacent undisturbed vegetation for almost all surveys, while spectacled hare wallabies (Lagorchestes conspicillatus) avoided them. Bilbies and agile wallabies showed similar temporal activity patterns on and off seismic lines but feral cats, dingoes and cattle used seismic lines at different times of day to control areas. We also investigated microhabitat selection by spool tracking individual bilbies. Bilbies selected a route through vegetation that was more open than surrounding vegetation. While spatial and temporal funnelling of bilbies and their predators (especially cats) may increase the frequency of encounter between the two, it is important to note that bilbies were active at significantly different times to predators both on and off seismic lines. The identified selection for seismic lines, and changes in spatial and temporal overlap between species, can be used to develop effective management strategies, to minimize potential impacts on native species.
Diagnostic relevance of IgE sensitization profiles to eight recombinant Phleum pratense molecules
Authors: Cipriani F. , Mastrorilli C. , Tripodi S. , Ricci G. , Perna S. , Panetta V. , Asero R. , Dondi A. , Bianchi A. , Maiello N. , Miraglia del Giudice M. , Frediani T. , Macrì F. , Lucarelli S. , Dello Iacono I. , Patria M. F. , Varin E. , Peroni D. , Chini L. , Moschese V. , Bernardini R. , Pingitore G. , Pelosi U. , Tosca M. , Paravati F. , Sfika I. , Businco A. Di Rienzo , Povesi Dascola C. , Comberiati P. , Frediani S. , Lambiase C. , Verga M. C. , Faggian D. , Plebani M. , Calvani M. , Caffarelli C. , Matricardi P. M. ,   the Italian Pediatric Allergy Network (I‐PAN)
Published: October 2017

Background

Grass pollen‐related seasonal allergic rhinoconjunctivitis (SARg) is clinically heterogeneous in severity, comorbidities, and response to treatment. The component‐resolved diagnostics disclosed also a high heterogeneity at molecular level. Our study aimed at analyzing the characteristics of the IgE sensitization to Phleum pratense molecules and investigating the diagnostic relevance of such molecules in childhood.

Methods

We examined 1120 children (age 4‐18 years) with SARg. Standardized questionnaires on atopy were acquired through informatics platform (AllergyCARD™). Skin prick tests were performed with pollen extracts. Serum IgE to airborne allergens and eight P. pratense molecules (rPhl p 1, rPhl p 2, rPhl p 4, rPhl p 5b, rPhl p 6, rPhl p 7, rPhl p 11, rPhl p 12) were tested by ImmunoCAP FEIA.

Results

The analysis of IgE responses against eight P. pratense molecules showed 87 profiles. According to the number of molecules recognized by IgE, the more complex profiles were characterized by higher serum total IgE, higher grass‐specific serum IgE, and higher number and degree of sensitization to pollens. The most frequent IgE sensitization profile was the monomolecular Phl p 1. Sensitization to Phl p 7 was a reliable biomarker of asthma, whereas Phl p 12 of oral allergy syndrome. Sensitization to Phl p 7 was associated with a higher severity of SARg, and complex profiles were associated with longer disease duration.

Conclusions

In a large pediatric population, the complexity of IgE sensitization profiles against P. pratense molecules is related to high atopic features although useless for predicting the clinical severity. The detection of serum IgE to Phl p 1, Phl p 7, and Phl p 12 can be used as clinical biomarkers of SARg and comorbidities. Further studies in different areas are required to test the impact of different IgE molecular profiles on AIT response.
Pregnancy before recurrent pregnancy loss more often complicated by post‐term birth and perinatal death
Authors: Wagner Marise M. , Visser Jantien , Verburg Harjo , Hukkelhoven Chantal W.P.M. , Van Lith Jan M.M. , Bloemenkamp Kitty W.M.
Published: October 2017

Introduction

The cause of recurrent pregnancy loss often remains unknown. Possibly, pathophysiological pathways are shared with other pregnancy complications.

Material and methods

All women with secondary recurrent pregnancy loss (SRPL) visiting Leiden University Medical Center (January 2000–2015) were included in this retrospective cohort to assess whether women with SRPL have a more complicated first pregnancy compared with control women. SRPL was defined as three or more consecutive pregnancy losses before 22 weeks of gestation, with a previous birth. The control group consisted of all Dutch nullipara delivering a singleton (January 2000–2015). Information was obtained from the Dutch Perinatal Registry. Outcomes were preeclampsia, preterm birth, post‐term birth, intrauterine growth restriction, breach position, induction of labor, cesarean section, congenital abnormalities, perinatal death and severe hemorrhage in the first ongoing pregnancy. Subgroup analyses were performed for women with idiopathic SRPL and for women ≤35 years.

Results

In all, 172 women with SRPL and 1 196 178 control women were included. Women with SRPL were older and had a higher body mass index; 29.7 years vs. 28.8 years and 25.1 kg/m2 vs. 24.1 kg/m2, respectively. Women with SRPL more often had a post‐term birth (OR 1.86, 95% CI 1.10–3.17) and more perinatal deaths occurred in women with SRPL compared with the control group (OR 5.03, 95% CI 2.48–10.2). Similar results were found in both subgroup analyses.

Conclusions

The first ongoing pregnancy of women with (idiopathic) SRPL is more often complicated by post‐term birth and perinatal death. Revealing possible links between SRPL and these pregnancy complications might lead to a better understanding of underlying pathophysiology.
Longitudinal study showed that the quality of life of Finnish adolescents with cerebral palsy continued to be relatively good
Authors: Böling Sanna , Varho Tarja , Haataja Leena
Published: October 2017

Aim

This longitudinal study examined what perceptions paediatric patients with cerebral palsy (CP) and their caregivers had of the patient's quality of life (QoL). It examined changing trends as children with CP became adolescents and examined the feasibility of the Finnish version of the CP QOL‐Teen questionnaire.

Methods

Carried out in autumn 2015, this study formed part of the multi‐centre Finnish national CP project and aimed to validate the CP QOL‐Teen questionnaire, which was posted to 54 adolescents and their caregivers. They included 24 who had responded to CP QOL‐Child questionnaire in 2013.

Results

The questionnaires were returned by 27 pairs of adolescents and caregivers and one extra caregiver also responded. Of these, 24 pairs had taken part in the 2013 survey. The internal consistencies of the sum variables were found to be acceptable in all cases. Overall QoL showed an average score of 81.8 on a scale from 0 to 100. Adolescents reported significantly higher QoL than their caregivers. There were no significant differences between the responses of the children and adolescents.

Conclusion

We showed that QoL was relatively good in childhood and adolescence. The Finnish version of the CP QOL‐Teen questionnaire was an appropriate clinical tool for assessing QoL.
Systematic review found that there was moderate evidence that vaccinating healthcare workers prevented pertussis in infants
Authors: van den Hoogen A. , Duijn J.M. , Bode L.G.M. , Vijlbrief D.C. , de Hooge L. , Ockhuijsen H.D.L.
Published: October 2017

This systematic review investigated the effectiveness of vaccinating healthcare workers against pertussis on the occurrence of nosocomial pertussis outbreaks or infections among unprotected infants. We focused on eight studies, with five different study designs, that involved 39,129 healthy adolescents and adults, 115 healthcare workers, 2000 simulated healthcare workers and a simulated population of 200,000 people.

Conclusion

There was moderate evidence that tetanus–diphtheria acellular pertussis vaccinations for healthcare workers were effective in preventing pertussis in all age groups and specifically in infants. The results must be interpreted with caution due to the low quality and heterogeneity of the studies.