bluuebunny/crossref_metadata_2025_split huggingface dataset:
IRF4 rs12203592 functional variant and melanoma survival
Authors: Potrony Miriam , Rebollo‐Morell Aida , Giménez‐Xavier Pol , Zimmer Lisa , Puig‐Butille Joan Anton , Tell‐Marti Gemma , Sucker Antje , Badenas Celia , Carrera Cristina , Malvehy Josep , Schadendorf Dirk , Puig Susana 
Published: January 2017

Inherited genetic factors may modulate clinical outcome in melanoma. Some low‐to‐medium risk genes in melanoma susceptibility play a role in melanoma outcome. Our aim was to assess the role of the functional IRF4 SNP rs12203592 in melanoma prognosis in two independent sets (Barcelona, N = 493 and Essen, N = 438). Genotype association analyses showed that the IRF4 rs12203592 T allele increased the risk of dying from melanoma in both sets (Barcelona: odds ratio [OR] = 6.53, 95% CI 1.38–30.87, Adj p = 0.032; Essen: OR = 1.68, 95% CI 1.04–2.72, Adj p = 0.035). Survival analyses only showed significance for the Barcelona set (hazard ratio = 4.58, 95% CI 1.11–18.92, Adj p = 0.036). This SNP was also associated with tumour localization, increasing the risk of developing melanoma in head or neck (OR = 1.79, 95% CI 1.07–2.98, Adj p = 0.032) and protecting from developing melanoma in the trunk (OR = 0.59, 95% CI 0.41–0.85, Adj p = 0.004). These findings suggest for the first time that IRF4 rs12203592 plays a role in the modulation of melanoma outcome and confirms its contribution to the localization of the primary tumour.
Observational study comparing the performance of first‐trimester screening protocols for detecting trisomy 21 in a North Indian population
Authors: Kaul Anita , Singh Chanchal , Gupta Rachna , Arora Nidhi , Gupta Abha 
Published: January 2017

AbstractObjectiveTo evaluate first‐trimester screening protocols for detecting trisomy 21 in an Indian population.MethodsThe present prospective study collected data from women with singleton pregnancies and a crown‐to‐rump length of 45–84 mm who presented at the fetal medicine unit of a tertiary care center in North India between June 1, 2006, and December 31, 2015, for combined first‐trimester screening. Maternal age, nuchal translucency, nasal bone, and maternal serum levels of free beta human chorionic gonadotropin and pregnancy‐associated plasma protein A were assessed for calculating the risk of trisomy 21. Tricuspid regurgitation and qualitative analysis of ductus venosus data were available from June 2010, and were included where available. Trisomy‐21 detection rates were calculated for various screening protocols and were compared.ResultsThere were 4523 women screened and 24 records of trisomy 21. Combined screening with maternal age, nuchal translucency, nasal bone, tricuspid regurgitation, and ductus venosus demonstrated optimal detection and false‐positive rates of 93.8% and 1.9%, respectively. Screening using only maternal age yielded a detection rate of 37.5%; using fixed nuchal translucency cut‐off values of 2.5 and 3 mm resulted in detection rates of 66.7% and 37.5%, respectively.ConclusionCombined first‐trimester screening performed well in an Indian population; combining maternal age, nuchal translucency, nasal bone, ductus venosus, and tricuspid regurgitation yielded the most accurate screening.
Preferential recognition of auto‐antibodies against 4‐hydroxynonenal modified DNA in the cancer patients
Authors: Faisal Mohammad , Shahab Uzma , Alatar Abdulrahman A. , Ahmad Saheem 
Published: January 2017

BackgroundThe structural perturbations in DNA molecule may be caused by a break in a strand, a missing base from the backbone, or a chemically changed base. These alterations in DNA that occurs naturally can result from metabolic or hydrolytic processes. DNA damage plays a major role in the mutagenesis, carcinogenesis, aging and various other patho‐physiological conditions. DNA damage can be induced through hydrolysis, exposure to reactive oxygen species (ROS) and other reactive carbonyl metabolites including 4‐hydroxynonenal (HNE). 4‐HNE is an important lipid peroxidation product which has been implicated in the mutagenesis and carcinogenesis processes.MethodsThe present study examines to probe the presence of auto‐antibodies against 4‐hydroxynonenal damaged DNA (HNE–DNA) in various cancer subjects. In this study, the purified calf thymus DNA was damaged by the action of 4‐HNE. The DNA was incubated with 4‐HNE for 24 h at 37°C temperature. The binding characteristics of cancer auto‐antibodies were assessed by direct binding and competitive inhibition ELISA.ResultsDNA modifications produced hyperchromicity in UV spectrum and decreased fluorescence intensity. Cancer sera exhibited enhanced binding with the 4‐HNE modified calf thymus DNA as compared to its native conformer. The 4‐HNE modified DNA presents unique epitopes which may be one of the factors for the auto‐antibody induction in cancer patients.ConclusionThe HNE modified DNA presents unique epitopes which may be one of the factors for the autoantibody induction in cancer patients.
A nomogram to predict distant metastasis after neoadjuvant chemoradiotherapy and radical surgery in patients with locally advanced rectal cancer
Authors: Sun Yanwu , Lin Huiming , Lu Xingrong , Huang Ying , Xu Zongbin , Huang Shenghui , Wang Xiaojie , Chi Pan 
Published: January 2017

PURPOSETo compare distant metastasis (DM) in locally advanced rectal cancer (LARC) patients treated with neoadjuvant chemoradiotherapy (nCRT) and surgery alone, and to develop a predictive nomogram for DM following nCRT.METHODSPropensity‐scoring match analysis was performed to compare DM in LARC treated with nCRT (n = 375) and surgery alone (n = 375). Cox regression was performed to identify predictors of DM following nCRT. A nomogram was developed and validated by internal (n = 425) and external validation (n = 97).RESULTSThe 5‐year local recurrence rate was significantly lower in the nCRT group (5.6% vs. 10.4%; P = 0.020). The 5‐year DM rates (nCRT vs. surgery alone: 25.3% vs. 24.4%; P = 0.235) were similar between groups. Cox regression showed that the post‐nCRT pathologic stage (ypTNM stage, OR = 2.022, P = 0.002), IMA nodal metastasis (OR = 2.171, P = 0.023), and CRM involvement (OR = 2.535, P = 0.016) were independently associated with DM following nCRT. A predictive nomogram was developed with a C‐index of 0.70 on internal validation, and 0.71 on the external validation.CONCLUSIONNCRT improved local control, but not distant metastasis. A nomogram to predict 3‐ and 5‐year DM rates, using clinicopathological parameters, was successfully developed. This prognostic tool could support decision‐making in clinical practice and follow‐up strategies.
Nanostructured Surfaces through Immobilization of Self‐Assembled Polymer Architectures Using Thiol–Ene Chemistry
Authors: Gunkel‐Grabole Gesine , Palivan Cornelia , Meier Wolfgang 
Published: January 2017

An efficient strategy for engineering nanostructured surfaces by coupling soft polymeric nanoarchitectures to functionalized surfaces is presented. Self‐assembly of polymeric nanoarchitectures from amphiphilic triblock copolymers can yield both filled and hollow spherical nanoarchitectures, depending on the properties of the polymer chosen. These nanoarchitectures are immobilized on solid substrates via a biocompatible thiol–ene reaction, and conditions are optimized to maintain structural integrity of polymeric assemblies. Two routes of surface modification are also implemented to allow inclusion of a polymeric spacer that can mediate between soft polymeric assemblies and solid substrates. Nanostructured surfaces with both filled and hollow nanoarchitectures attached to the surface directly or with a spacer are successfully generated with this protocol. This concept of generating nanostructured surfaces using preassembled polymeric architectures is an important step toward active surfaces, because entrapment of active molecules in the nanoarchitectures prior to their immobilization opens the door to easy generation of surfaces with predetermined activities.
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Effect of copper ion and soil humic acid on biodegradation of decabromodiphenyl ether (BDE‐209) by Pseudomonas aeruginosa
Authors: Liu Yu , Gong Aijun , Qiu Lina , Li Jingrui , Li Fukai 
Published: January 2017

AbstractPseudomonas aeruginosa is a good environmental microorganism capable of degrading decabromodiphenyl ether (BDE‐209). This paper studied the effect of Cu2+ and humic acid (HA) extracted from e‐waste contaminated soils on biodegradation of BDE‐209 by P. aeruginosa. The adsorption isotherms of Cu2+ on HA, the crude enzyme activity, cell surface morphology, and biodegradation pathway were also investigated. The results showed that BDE‐209 biodegradation by P. aeruginosa was inhibited at Cu2+ concentrations above 5 mg L−1, but exhibited the best effect at the condition of 40 mg L−1 Cu2+ + 3 g L−1 HA. At the condition of 40 mg L−1 Cu2+ + 3 g L−1 HA, 97.35 ± 2.33% of the initial BDE‐209 was degraded after 5 days, debromination efficiency was 72.14 ± 1.89%, crude enzyme activity reached the maximum of 0.519 ± 0.022U g−1 protein, cell surface of P. aeruginosa was smooth with normal short‐rod shapes, and biodegradation pathway mainly include debromination, hydroxylation, and cleavage of the diphenyl ether bond. It was suggested that soil HA could eliminate the toxic effect of high Cu2+ concentrations and biodegradation of BDE‐209 was improved by synergistic effect of HA and Cu2+.
A portal dosimetry dose prediction method based on collapsed cone algorithm using the clinical beam model
Authors: Martínez Ortega J. , Gómez González N. , Castro Tejero P. , Pinto Monedero M. , Tolani N. B. , Núñez Martín L. , Sánchez Montero R. 
Published: January 2017

PurposeAmorphous silicon electronical portal imaging devices (EPIDs) are widely used for dosimetric measurements in Radiation Therapy. The purpose of this work was to determine if a portal dose prediction method can be utilized for dose map calculations based on the linear accelerator model within a commercial treatment planning system (Pinnacle3 v8.0 m).MethodsThe method was developed for a 6 MV photon beam on the Varian Clinac 21‐EX, at a nominal dose rate of 400 MU/min. The Varian aS1000 EPID was unmounted from the linear accelerator and scanned to acquire CT images of the EPID. The CT images were imported into Pinnacle3 and were used as a quality assurance phantom to calculate dose on the EPID setup at a source to detector distance of 105 cm. The best match of the dose distributions was obtained considering the image plane located at 106 cm from the source to detector plane. The EPID was calibrated according to the manufacturer procedure and corrections were made for output factors. Arm‐backscattering effect, based on profile correction curves, has been introduced. Five low‐modulated and three high‐modulated clinical planned treatments were predicted and measured with the method presented here and with MatriXX (IBA Dosimetry, Schwarzenbruck, Germany).ResultsA portal dose prediction method based on Pinnacle3 was developed without modifying the commissioned parameters of the model in use in the clinic. CT images of the EPID were acquired and used as a quality assurance phantom. The CT images indicated a mean density of 1.16 g/cm3 for the sensitive area of the EPID. Output factor measured with the EPID were lower for small fields and larger for larger fields (beyond 10 × 10 cm2). Arm‐backscatter correction showed a better agreement at the target side of the EPID. Analysis of Gamma index comparison (3%, 3 mm) indicated a minimum of 97.4% pass rate for low modulated and 98.3% for high modulated treatments. Pass rates were similar for MatriXX measurements.ConclusionsThe method developed here can be easily implemented into clinic, as neither additional modeling of the clinical energy nor an independent image prediction algorithm are necessary. The main advantage of this method is that portal dose prediction is calculated with the same algorithm and beam model used for patient dose distribution calculation. This method was independently validated with an ionization chamber matrix.
Comparison of five cluster validity indices performance in brain [18F]FET‐PET image segmentation using k‐means
Authors: Abualhaj Bedor , Weng Guoyang , Ong Melissa , Attarwala Ali Asgar , Molina Flavia , Büsing Karen , Glatting Gerhard 
Published: January 2017

PurposeDynamic [18F]fluoro‐ethyl‐L‐tyrosine positron emission tomography ([18F]FET‐PET) is used to identify tumor lesions for radiotherapy treatment planning, to differentiate glioma recurrence from radiation necrosis and to classify gliomas grading. To segment different regions in the brain k‐means cluster analysis can be used. The main disadvantage of k‐means is that the number of clusters must be pre‐defined. In this study, we therefore compared different cluster validity indices for automated and reproducible determination of the optimal number of clusters based on the dynamic PET data.MethodsThe k‐means algorithm was applied to dynamic [18F]FET‐PET images of 8 patients. Akaike information criterion (AIC), WB, I, modified Dunn's and Silhouette indices were compared on their ability to determine the optimal number of clusters based on requirements for an adequate cluster validity index. To check the reproducibility of k‐means, the coefficients of variation CVs of the objective function values OFVs (sum of squared Euclidean distances within each cluster) were calculated using 100 random centroid initialization replications RCI100 for 2 to 50 clusters. k‐means was performed independently on three neighboring slices containing tumor for each patient to investigate the stability of the optimal number of clusters within them. To check the independence of the validity indices on the number of voxels, cluster analysis was applied after duplication of a slice selected from each patient. CVs of index values were calculated at the optimal number of clusters using RCI100 to investigate the reproducibility of the validity indices. To check if the indices have a single extremum, visual inspection was performed on the replication with minimum OFV from RCI100.ResultsThe maximum CV of OFVs was 2.7 × 10−2 from all patients. The optimal number of clusters given by modified Dunn's and Silhouette indices was 2 or 3 leading to a very poor segmentation. WB and I indices suggested in median 5, [range 4–6] and 4, [range 3–6] clusters, respectively. For WB, I, modified Dunn's and Silhouette validity indices the suggested optimal number of clusters was not affected by the number of the voxels. The maximum coefficient of variation of WB, I, modified Dunn's, and Silhouette validity indices were 3 × 10−2, 1, 2 × 10−1 and 3 × 10−3, respectively. WB‐index showed a single global maximum, whereas the other indices showed also local extrema.ConclusionFrom the investigated cluster validity indices, the WB‐index is best suited for automated determination of the optimal number of clusters for [18F]FET‐PET brain images for the investigated image reconstruction algorithm and the used scanner: it yields meaningful results allowing better differentiation of tissues with higher number of clusters, it is simple, reproducible and has an unique global minimum.
Sex and dark times’ strategy: The Dark Triad and time perspective
Authors: Moraga Fernando R. G. , Nima Ali A. , Garcia Danilo 
Published: January 2017

AbstractWe investigated the effect of sex on associations between dark traits and time perspective dimensions. Responses by participants (N = 338) to the Short Dark Triad Inventory and the Zimbardo Time Perspective Inventory showed that while sex was involved in different time perspective associations of Machiavellianism, psychopathy, and narcissism, it did not moderate the dark times’ strategy.
CDAI: a novel collaborative detection approach for impersonation attacks in vehicular ad‐hoc networks
Authors: Pougajendy Jayashree , Parthiban Arun Raj Kumar 
Published: January 2017

AbstractEnsuring security in vehicular ad‐hoc networks remains a challenging task because of the high mobility of vehicles and the wireless communication environment. The wireless environment, which is un‐trusted, paves a way for the attackers to perform various attacks at the cost of time, money, safety and human lives. One such attack that needs attention is the impersonation attack because of its ability to disrupt the proper functioning of the network. Existing defense mechanisms viz., public key infrastructure (PKI) methods incur infrastructural overheads, position based verification methods face limitations such as inadaptability to certain environments (one way roads, heavy traffic conditions), high storage, and communication overheads. In this paper, collaborative detection approach for impersonation attacks (CDAI), a position‐based verification scheme based on received signal strength, is proposed to overcome all the existing limitations. Further, a comparative study of CDAI and the existing non‐public key infrastructure defence methods are reported in the paper. Simulation experiments have been conducted on CDAI. From the simulation experiments, it is evident that CDAI achieves a detection rate of 97.85% and a false positive rate of 0.015%. Copyright © 2017 John Wiley & Sons, Ltd.
A collusion‐resistant dynamic key management scheme for WSNs
Authors: Zhan Furui , Yao Nianmin 
Published: January 2017

AbstractKey management is an important security service for protecting wireless sensor networks (WSNs). Among various existing schemes, exclusion basis system (EBS) is a practical solution that can be easily implemented to provide long‐term and flexible protection for WSNs. The involved rekeying strategy in EBS can efficiently evict the compromised node and update the key system. However, the relatively small key pool leads to high correlation among the generated key rings. Consequently, it is almost impossible for EBS‐based schemes to efficiently defend collusion attack with their rekeying mechanisms. In this paper, we first analyze the impact of collusion attack on WSNs, especially that in the case where the keys of the compromised nodes can form a connected graph. Then, we propose a novel key management scheme based on EBS. The proposed scheme is termed as t‐EEBS because it can effectively resist the referred collusion attack formed by t(t > 1) nodes. Furthermore, we assume that the proposed scheme is implemented in hierarchical WSNs. In this case, two layers of t‐EEBS administrative keys are used. The upper layer is implemented among the base station and all cluster leaders, while the lower layer involves a t‐EEBS for each cluster. The results of performance evaluation show that the proposed scheme has better resistance to collusion attack than other schemes. Therefore, the proposed scheme can provide better security service for WSNs. Copyright © 2017 John Wiley & Sons, Ltd.
Mining unit test cases to synthesize API usage examples
Authors: Ghafari Mohammad , Rubinov Konstantin , Pourhashem K. Mohammad Mehdi 
Published: January 2017

AbstractSoftware developers study and reuse existing source code to understand how to properly use application programming interfaces (APIs). However, manually finding sufficient and adequate code examples for a given API is a difficult and a time‐consuming activity. Existing approaches to find or generate examples assume availability of a reasonable set of client code that uses the API. This assumption does not hold for newly released API libraries, non‐widely used APIs, nor private ones.In this work we reuse the important information that is naturally present in test code to circumvent the lack of usage examples for an API when other sources of client code are not available. We propose an approach for automatically identifying the most representative API uses within each unit test case. We then develop an approach to synthesize API usage examples by extracting relevant statements representing the usage of such APIs. We compare the output of a prototype implementation of our approach to both human‐written examples and to a state‐of‐the‐art approach. The obtained results are encouraging; the examples automatically generated with our approach are superior to the state‐of‐the‐art approach and highly similar to the manually constructed examples.
How to detect an elusive aquatic mammal in complex environments? A study of the Endangered Antillean manateeTrichechus manatus manatusin French Guiana
Authors: Castelblanco-Martínez Delma Nataly , dos Reis Virginie , de Thoisy Benoit 
Published: January 2017

AbstractThe Antillean manateeTrichechus manatus manatusis a cryptic mammal that inhabits, among other areas, murky rivers and estuaries of Central and South America. The difficulty in detecting and counting manatees is an obstacle to monitoring their population status, as traditional count sampling is unsuitable. We conducted a quantitative analysis of the distribution and abundance of the manatee across its known range in the rivers and estuaries of French Guiana, based on data from a range-wide line transect visual survey combined with a side-scan sonar survey, identification of feeding sites, and silent observations at fixed points. A total effective effort of 248 hours and 1,129 km of boat survey was completed. We used two relative abundance indices: the combined encounter rate, which combines encounters per km from either visual or side-scan sonar surveys, and the global detection index, which is defined as the sum of all evidence per unit time. Manatees were detected in all nine study units. Niche modelling was used to analyse the space selection by manatees, and helped to detect differential use of habitats according to the season. The model predicted that coastal areas are used more extensively during the dry season. In the absence of better techniques to detect wild manatees in complex habitats this monitoring protocol may be relevant and replicable in hydrological systems where manatee detectability is constrained by biogeographical characteristics.
Local awareness and perceptions: consequences for conservation of marsh habitat at Lake Alaotra for one of the world's rarest lemurs
Authors: Waeber Patrick O. , Reibelt Lena M. , Randriamalala Ihoby H. , Moser Gabrielle , Raveloarimalala Lucile M. , Ralainasolo Fidy B. , Ratsimbazafy Jonah , Woolaver Lance 
Published: January 2017

AbstractManagement and monitoring of community-based protected areas in Madagascar remain challenging because of a lack of financial, human and technical resources, and capacity. At Lake Alaotra, conversion of marshland for rice cultivation and a lack of effective habitat protection have pushed the locally endemic Alaotra gentle lemur Hapalemur alaotrensis to the brink of extinction. The highest density of the species is found in the locally managed Park Bandro, a high-priority conservation zone within the Lake Alaotra New Protected Area. We evaluated local awareness and perceptions of Park Bandro, and discussed preferred management options with local communities. Two questionnaire surveys were carried out, one with 180 participants at six sites around the lake and marsh, and another with 50 participants in the village adjacent to Park Bandro. The majority of participants knew of the existence of Park Bandro but most did not know its purpose or size. Values and perceptions of local communities were influenced by occupation and distance to the Park, with fishers being most aware of the Park. We found that local people had a high level of environmental awareness and were willing to discuss zonation and alternative resource management strategies as long as these activities could provide a tangible livelihood benefit. Lack of awareness among local resource users regarding the purpose and status of protected areas such as Park Bandro is a challenge that needs to be addressed, and one that is relevant for environmental education and management of protected areas throughout Madagascar.