bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical next‐generation sequencing successfully applied to fine‐needle aspirations of pulmonary and pancreatic neoplasms
Authors: Young Geneva , Wang Kai , He Jie , Otto Geoff , Hawryluk Matthew , Zwirco Zac , Brennan Tina , Nahas Michelle , Donahue Amy , Yelensky Roman , Lipson Doron , Sheehan Christine E. , Boguniewicz Ann B. , Stephens Philip J. , Miller Vincent A. , Ross Jeffrey S. 
Published: July 2013

BACKGROUNDNext‐generation sequencing was performed on pulmonary and pancreatic fine‐needle aspirations (FNAs) and on paired FNAs and resected primary tumors from the same patient.METHODSDNA was isolated in formalin‐fixed, paraffin‐embedded cell blocks from 16 pulmonary FNAs, 23 pancreatic FNAs, and 5 resected pancreatic primary tumors. Next‐generation sequencing was performed for 4561 exons of 287 cancer‐related genes and for 47 introns of 19 genes on indexed, adaptor‐ligated, hybridization‐captured libraries using a proprietary sequencing system (the Illumina HiSeq 2000).RESULTSGenomic profiles were generated successfully from 16 of 16 (100%) pulmonary FNAs, which included 14 nonsmall cell lung cancers (NSCLCs) and 2 small cell lung cancers (SCLCs). The NSCLC group included 6 adenocarcinomas, 5 squamous cell carcinomas, and 3 NSCLCs not otherwise specified. Genomic profiles were successfully obtained from 23 of 23 (100%) pancreatic FNAs and from 5 of 5 (100%) matched pancreatic primary tumors, which included 17 ductal adenocarcinomas, 3 mucinous adenocarcinomas, 2 adenocarcinomas NOS, and 1 neuroendocrine tumor. Eighty‐one genomic alterations were identified in the 16 pulmonary FNAs (average, 5.1 genomic alterations per patient); and the most common genomic alterations were TP53, RB1, SOX2, PIK3CA, and KRAS. Eighty‐seven genomic alterations were identified in the 23 pancreatic tumor FNAs (average, 3.8 genomic alterations per patient); and the most common genomic alterations were KRAS, TP53, CDKN2A/B, SMAD4, and PTEN. Among the pancreatic tumors, there was 100% concordance of 20 genomic alterations that were identified in 5 patient‐matched FNA and surgical primary tumor pairs.CONCLUSIONSThe authors were able to perform next‐generation sequencing reliably on FNAs of pulmonary and pancreatic tumors, and the genomic alterations discovered correlated well with those identified in matched resected pancreatic tumors. Cancer (Cancer Cytopathol) 2013;121:688–694. © 2013 American Cancer Society.
A camera calibration method based on two orthogonal vanishing points
Authors: Lugang Zhao , Chengke Wu , Jifeng Ning 
Published: July 2013

SUMMARYA camera calibration method based on the two vanishing points, which are orthogonal to each other, is presented in this paper. On the basis of the facts that the modulus constraint can provide an equation and that two equations can be obtained from two pairs of vanishing points, which are orthogonal to each other, the self‐calibration is quasilinearly realized. The experiment results with simulate data and real image sequences show that the presented method is efficient. Copyright © 2013 John Wiley & Sons, Ltd.
Extending the scope of the Checkpoint‐on‐Failure protocol for forward recovery in standard MPI
Authors: Bland Wesley , Du Peng , Bouteiller Aurelien , Herault Thomas , Bosilca George , Dongarra Jack J. 
Published: July 2013

SUMMARYMost predictions of exascale machines picture billion ways parallelism, encompassing not only millions of cores but also tens of thousands of nodes. Even considering extremely optimistic advances in hardware reliability, probabilistic amplification entails that failures will be unavoidable. Consequently, software fault tolerance is paramount to maintain future scientific productivity. Two major problems hinder ubiquitous adoption of fault tolerance techniques: (i) traditional checkpoint‐based approaches incur a steep overhead on failure free operations and (ii) the dominant programming paradigm for parallel applications (the message passing interface (MPI) Standard) offers extremely limited support of software‐level fault tolerance approaches. In this paper, we present an approach that relies exclusively on the features of a high quality implementation, as defined by the current MPI Standard, to enable advanced forward recovery techniques, without incurring the overhead of customary periodic checkpointing. With our approach, when failure strikes, applications regain control to make a checkpoint before quitting execution. This checkpoint is in reaction to the failure occurrence rather than periodic. This checkpoint is reloaded in a new MPI application, which restores a sane environment for the forward, application‐based recovery technique to repair the failure‐damaged dataset. The validity and performance of this approach are evaluated on large‐scale systems, using the QR factorization as an example. Published 2013. This article is a US Government work and is in the public domain in the USA.
Contribution of Water Molecules in the Spontaneous Release of Protein by Graphene Sheets
Authors: Liang Li‐Jun , Wang Qi , Wu Tao , Sun Tian‐Yang , Kang Yu 
Published: July 2013

AbstractApplications of graphene sheets in the fields of biosensors and biomedical devices are limited by the aqueous solubility of graphene. Consequently, understanding the role of water molecules in the aggregation or dispersion of graphene in aqueous solution with a biomolecule is of vital importance to its application. Herein, protein is spontaneously released by the layer‐to‐layer aggregation of two single‐layer graphene sheets due to van der Waals force between the sheets. The properties of water molecules, including density and dynamics, are discussed in detail. The dynamic behavior of aggregation of graphene sheets is triggered by the dynamics of water molecules. To stabilize dispersed graphene sheets in aqueous solution, the density of water molecules between the graphene sheets should be larger than 0.83 g cm−3, and graphene modified by hydroxyl groups could be a good choice. The stability of a model protein on the graphene sheet is studied to investigate the biological compatibility of graphene sheets. To be a material with good biocompatibility, graphene should be functionalized by hydrophilic groups. The results presented herein could be helpful in the research and application of graphene sheets in the fields of biomaterials, biosensors, and biomedical devices.
Enhancing the Deperoxidation Activity of Cobalt(II)Acetylacetonate by the Addition of Octanoic Acid
Authors: Spier Eyal , Hermans Ive 
Published: July 2013

AbstractThe homolytic scission of peroxides with catalytic amounts of cobalt(II) complexes is used in several industrial oxidation processes. In this contribution, we report that addition of small amounts of octanoic acid significantly enhances the catalytic deperoxidation activity of the cobalt(II)acetylacetonate complex. We attribute this to the stabilization of the CoOOR bond upon coordination of octanoic acid, preventing the unimolecular scission. As such, the cobalt peroxo intermediate is forced to enter an alternative catalytic cycle which causes its rapid conversion to the highly reactive cobalt hydroxy. This shift in catalytic cycle results in a higher pre‐exponential rate factor, over‐compensating the higher barrier of the new rate‐determining step.
Determinants of Health and Disability in Ageing Population: The COURAGE in Europe Project (Collaborative Research on Ageing in Europe)
Authors: Leonardi Matilde , Chatterji Somnath , Koskinen Seppo , Ayuso‐Mateos Jose Luis , Haro Josep Maria , Frisoni Giovanni , Frattura Lucilla , Martinuzzi Andrea , Tobiasz‐Adamczyk Beata , Gmurek Michal , Serrano Ramon , Finocchiaro Carla ,   on behalf of COURAGE in Europe Project's Consortium
Published: July 2013

COURAGE in Europe was a 3‐year project involving 12 partners from four European countries and the World Health Organization. It was inspired by the pressing need to integrate international studies on disability and ageing in light of an innovative perspective based on a validated data‐collection protocol. COURAGE in Europe Project collected data on the determinants of health and disability in an ageing population, with specific tools for the evaluation of the role of the built environment and social networks on health, disability, quality of life and well‐being. The main survey was conducted by partners in Finland, Poland and Spain where the survey has been administered to a sample of 10 800 persons, which was completed in March 2012. The newly developed and validated COURAGE Protocol for Ageing Studies has proven to be a valid tool for collecting comparable data in ageing population, and the COURAGE in Europe Project has created valid and reliable scientific evidence, demonstrating cross‐country comparability, for disability and ageing research and policy development. It is therefore recommended that future studies exploring determinants of health and disability in ageing use the COURAGE‐derived methodology. Copyright © 2013 John Wiley & Sons, Ltd.Key Practitioner Message

COURAGE in Europe Project collected data on the determinants of health and disability in an ageing population, with specific tools for the evaluation of the role of built environment and social networks on health, disability quality of life and well‐being.
The COURAGE Protocol for Ageing Studies has proven to be a valid tool for collecting comparable data in the ageing population.
The COURAGE in Europe Consortium recommends that future studies exploring determinants of health and disability in ageing use COURAGE‐derived methodology.
Formation of the Matrix‐Isolated Difluoromethylselanes XCF2SeH (X = H, Cl) Through Photolysis of Selenoacetic Acids, XCF2C(O)SeH
Authors: Gómez Castaño Jovanny A. , Romano Rosana M. , Beckers Helmut , Willner Helge , Della Védova Carlos O. 
Published: July 2013

AbstractTwo hitherto unknown difluoromethylselanes, HCF2SeH and ClCF2SeH, were formed by photolysis of difluoroselenoacetic and chlorodifluoroselenoacetic acids isolated in solid argon. The progress of the photolysis was monitored by FTIR spectroscopy. The photoproducts were identified by comparison of experimental with theoretically predicted spectra and reported spectra for known species. The photochemical decomposition mechanisms of HCF2C(O)SeH and ClCF2C(O)SeH is presented.
Switchable Biosensor Controlled by Biocatalytic Process
Authors: Basso Caroline R. , Santos Bruna L. , Pedrosa Valber A. 
Published: July 2013

AbstractThe poly(dimethylamino methacrylate) (PDMAEMA) brush‐modified indium tin oxide (ITO) electrode was used to test the switch properties of interfacial activity caused by bioelectrochemical signals. The swelling of the polymer brushes increased when the medium’s pH changed from alkaline to acid after glucose was added to the system. A pH change generated in situ by means of biocatalytic reactions enabled bioelectrocatalytic interface’s reversible activation.
Electrochemical Detection of Duplex DNA Using Intercalation‐Triggered Decomplexation of Ferrocene with β‐Cyclodextrin
Authors: Takenaka Hirotomo , Sato Shinobu , Takenaka Shigeori 
Published: July 2013

AbstractThe redox peak of ferrocenylnaphthalene diimide used as a threading intercalator shifted positively due to the formation of its complex with β‐cyclodextrin. This complex collapsed upon the addition of double‐stranded DNA, and its redox potential shifted negatively. This behavior was applied for the homogenous detection of a polymerase chain reaction (PCR) product from Porphyromonas gingivalis, which is important for the diagnosis of periodontal disease, and its quantitative detection was achieved with a detection limit of 2.7 nM.
The genetic and neuroanatomical basis of social dysfunction: Lessons from neurofibromatosis type 1
Authors: Pride Natalie A. , Korgaonkar Mayuresh S. , Barton Belinda , Payne Jonathan M. , Vucic Steve , North Kathryn N. 
Published: July 2013

AbstractNeurofibromatosis type 1 (NF1) is a common genetic condition associated with cognitive and social dysfunction as well as abnormal brain structure. The pathophysiology underlying social dysfunction in NF1 is poorly understood. Here, we investigate for the first time whether there is a broad deficit of social cognition in NF1 and explore the neural correlates for these deficits. Twenty‐nine adults with NF1 and 30 controls were administered an ecologically based test of social cognition, The Awareness of Social Inference Test (TASIT), to identify deficits in emotion recognition and sarcasm detection. We employed voxel‐based morphometry in a subset of NF1 patients (n = 16) and 16 additional controls to examine the neural correlates of these deficits. Results indicated that adults with NF1 were impaired in their ability to understand paradoxical sarcasm and their capacity to recognize emotion, particularly anger. TASIT performance was not associated with measures of attention, visuospatial skills or executive function. Relative to controls, gray matter (GM) volume within the right superior temporal gyrus (STG) was decreased, after controlling for total brain volume. Decreased volume in this region was significantly associated with social cognitive deficits in adults with NF1. We conclude that patients with NF1 are at high risk for a social cognitive deficit and provide evidence for a neuroanatomical basis for this deficit; GM volumetric reductions in the right STG. These findings improve our understanding of the nature of social interaction impairments in NF1 and add to the growing body of literature indicating the STG as a critical brain region for social cognition. Hum Brain Mapp 35:2372–2382, 2014. © 2013 Wiley Periodicals, Inc.
Outcomes after primary chemoradiotherapy for N3 (>6 cm) head and neck squamous cell carcinoma after an FDG‐PET‐‐guided neck management policy
Authors: Adams Gerard , Porceddu Sandro V. , Pryor David I. , Panizza Benedict , Foote Matthew , Rowan Ann , Burmeister Bryan 
Published: July 2013

ABSTRACTBackgroundThe purpose of this study was to assess whether a positron emission tomography (PET)‐directed policy remains appropriate for managing neck nodes (N3; >6 cm) in head and neck squamous cell carcinoma (HNSCC).MethodsAll patients with N3 (>6 cm) HNSCC treated with definitive chemoradiotherapy (CRT) at our institution between 2005 and 2012 were included in the analysis. Patients underwent PET assessment before and 12 weeks after CRT. Neck dissections were performed for PET‐avid residual nodal abnormalities after complete response at the primary site. Rate of isolated nodal failure (INF) was the primary outcome.ResultsMedian follow‐up from diagnosis for 33 patients was 30 months (range, 6−76 months). INF occurred in 2 patients (6%) with neck dissections performed in 4 cases (12%). First failure was predominantly distant metastatic (10; 30%).ConclusionThe rate of INF remains low when following a PET‐directed neck management policy after definitive CRT for N3 (>6 cm) HNSCC. © 2013 Wiley Periodicals, Inc. Head Neck 36: 1200–1206, 2014
Presence and composition of cathinone derivatives in drug samples taken from a Drug Test Service in Spain (2010–2012)
Authors: Caudevilla‐Gálligo Fernando , Ventura Mireia , Indave Ruiz Blanca Iciar , Fornís Iván 
Published: July 2013

ObjectiveThe aim of this study was to describe the presence and composition of cathinone derivatives (CDs) in drug samples analyzed at a Drug Testing Service.Material and methodsData provided by the Drug Testing Service at Energy Control (a Spanish organization working in risk reduction among recreational drug users) were obtained from samples delivered as, or containing CDs, between January 2010 and June 2012. Specimens were identified by combining thin layer chromatography and gas chromatography associated with mass spectrometry.ResultsTwo hundred and thirty‐seven (3.8%) of the 6199 samples were delivered as, or contained CDs. 22 different CDs were detected, alone or in different combinations. Methylone (24.9%), mephedrone (24.5%), 4‐methylethcathinone (9.28%), and methylenedioxypyrovalerone (6.8%) were the most common CDs. These substances were also found in 80 (1.3%) of 6042 samples delivered allegedly containing drugs different from CDs (such as 3,4‐methylenedioxy‐N‐methylamphetamine (MDMA), amphetamines, ketamine…).ConclusionsCathinone derivatives were markedly present in the Spanish drug market during the studied period. There is no evidence to conclude that use of CDs will become widespread or relevant for public health, but the phenomenon must be followed, as the potential risks of these new drugs of abuse are substantial. Copyright © 2013 John Wiley & Sons, Ltd.
Recreational use of 1‐(2‐naphthyl)‐2‐(1‐pyrrolidinyl)‐1‐pentanone hydrochloride (NRG‐1), 6‐(2‐aminopropyl) benzofuran (Benzofury/ 6‐APB) and NRG‐2 with review of available evidence‐based literature
Authors: Jebadurai Jeshoor , Schifano Fabrizio , Deluca Paolo 
Published: July 2013

ObjectiveThis study aimed to review the available evidence‐based literature on novel psychoactive substances and to inform health care professionals.MethodsInternet searches were carried out using Google and Yahoo by using specific key words. For each set of key words, the first 100 websites identified by Google and Yahoo were fully assessed, together with a further 5% of random samples selected by research randomizer of the remaining websites. Thus, a list of unique web forums was identified, and qualitative information was extracted. Available evidence‐based literature were reviewed along with a user's experimentation with mephedrone, NRG‐1, NRG‐2 and Benzofury.ResultsIt showed that when a substance (mephedrone) became controlled, the vendors aggressively promote the sale of other new compounds (NRG‐1, NRG‐2, Benzofury) to attract vulnerable adults. The characteristics, toxicity and suggested management of these new compounds (NRG‐1, NRG‐2, Benzofury) are discussed.ConclusionsThe arrival of hundreds of novel psychoactive substances for sale online has raised a number of public health and legal issues. Although evidence‐based literature remains limited, few studies identified that most products do not contain the ingredients as advertised. Better levels of international cooperation and rapid share of available information may be needed to tackle this emerging problem. Copyright © 2013 John Wiley & Sons, Ltd.
Computer‐aided (in silico) approaches in the mode‐of‐action analysis and safety assessment of Ostarine and 4‐methylamphetamine
Authors: Mohd Fauzi Fazlin , Koutsoukas Alexios , Cunningham Andrew , Gallegos Ana , Sedefov Roumen , Bender Andreas 
Published: July 2013

ObjectiveThis study exemplifies computer‐aided (in silico) approaches in assessing the risks of new psychoactive substances emerging in the European Union. In this work, we (i) consider the potential of Ostarine exhibiting psychoactivity and (ii) anticipate potential activities and toxicities of 4‐methylamphetamine.MethodThe approach, termed in silico target prediction, suggests potential protein targets modulated by compounds given their chemical structure. This is achieved by first establishing the associations between chemical structure and protein targets using data from the bioactivity database, ChEMBL, via the use of two different computational algorithms. On the basis of the associations, protein targets and consequently the mode of action of novel compounds were predicted.ResultsFor Ostarine, none of the targets anticipated are currently known to elicit psychoactivity. Furthermore, Ostarine is unlikely to cross the blood–brain barrier to reach relevant target sites on the basis of its physicochemical properties. For 4‐methylamphetamine, toxicities were anticipated, that is, serotonin syndrome (based on the prediction of SERT) and other effects similar to related substances, that is, methamphetamine.ConclusionFrom the two case studies, we showed that in silico target prediction appears to have potential in assessing new psychoactive compounds where experimental data are scarce. The applicability domain of target predictions when applied to psychoactive compounds needs to be established in future work. Copyright © 2013 John Wiley & Sons, Ltd.
Agricultural management impacts on groundwater: simulations of existing and alternative management options in Peninsular India
Authors: Dourte Daniel R. , Shukla Sanjay , Haman Dorota Z. , Reddy M. Devender , Devi M. Uma , Mani Adusumilli 
Published: July 2013

AbstractUnderstanding the principal causes and possible solutions for groundwater depletion in India is important for its water security, especially as it relates to agriculture. A study was conducted in an agricultural watershed in Andhra Pradesh, India to assess the impacts on groundwater of current and alternative agricultural management. Hydrological simulations were used as follows: (1) to evaluate the recharge benefits of water‐harvesting tillage through a modified Soil and Water Assessment Tool (SWAT) model and (2) to predict the groundwater response to changing extent and irrigation management of rice growing areas. The Green–Ampt infiltration routine was modified in SWAT was modified to represent water‐harvesting tillage using maximum depression storage parameter. Water‐harvesting tillage in rainfed croplands was shown to increase basin‐scale groundwater recharge by 3% and decrease run‐off by 43% compared with existing conventional tillage. The groundwater balance (recharge minus irrigation withdrawals), negative 11 mm/year under existing management changed to positive (18–45 mm/year) when rice growing areas or irrigation depths were reduced. Groundwater balance was sensitive to changes in rice cropland management, meaning even small changes in rice cropland management had large impacts on groundwater availability. The modified SWAT was capable of representing tillage management of varying maximum depression storage, and tillage for water‐harvesting was shown to be a potentially important strategy for producers to enhance infiltration and groundwater recharge, especially in semi‐arid regions where rainfall may be becoming increasingly variable. This enhanced SWAT could be used to evaluate the landscape‐scale impacts of alternative tillage management in other regions that are working to develop strategies for reducing groundwater depletion. Copyright © 2013 John Wiley & Sons, Ltd.
Variation in the susceptibility of humic acids from the sediments of water reservoirs to oxidation
Authors: Cieślewicz Joanna 
Published: July 2013

AbstractThe aim of this study was to determine whether, and to what extent, structures of pigment‐origin affect the susceptibility of humic acids (HAs) to oxidation, with the primary focus on derivatives of chlorophyll. The sediment samples were collected from lakes with different catchment management, and the Szczecin Lagoon, which is the estuary of the Odra River. HAs were extracted from sediments using 0.5 M NaOH solution. Sediments differed in their contents of total organic carbon (3.8–456.0 g kg−1) and total nitrogen (0.8–33.7 g kg−1). HAs extracted from sediments were characterized by the highly diverse composition of chemical elements and spectrometric properties regarding the visible‐light spectrum and ultraviolet radiation. HAs extracted from the sediments of lakes situated in the Chodzież and Wałcz Lake Districts (ChWLD) with forest catchment areas, were most susceptible to oxidation, indicating that the processes that occur during oxidation are affected by the content of pigment‐originated structures (the derivatives of chlorophyll) in the molecules of HAs. These structures are relatively resistant to oxidation, because they are present in the spectra of alkaline solutions of HAs after oxidation. The conducted studies also proved that the susceptibility of HAs of sediment origin to oxidation cannot be interpreted in the standard way applied to values obtained for soil HAs.