bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhancing studies of the connectome in autism using the autism brain imaging data exchange II
Authors: Di Martino Adriana , O’Connor David , Chen Bosi , Alaerts Kaat , Anderson Jeffrey S. , Assaf Michal , Balsters Joshua H. , Baxter Leslie , Beggiato Anita , Bernaerts Sylvie , Blanken Laura M. E. , Bookheimer Susan Y. , Braden B. Blair , Byrge Lisa , Castellanos F. Xavier , Dapretto Mirella , Delorme Richard , Fair Damien A. , Fishman Inna , Fitzgerald Jacqueline , Gallagher Louise , Keehn R. Joanne Jao , Kennedy Daniel P. , Lainhart Janet E. , Luna Beatriz , Mostofsky Stewart H. , Müller Ralph-Axel , Nebel Mary Beth , Nigg Joel T. , O’Hearn Kirsten , Solomon Marjorie , Toro Roberto , Vaidya Chandan J. , Wenderoth Nicole , White Tonya , Craddock R. Cameron , Lord Catherine , Leventhal Bennett , Milham Michael P. 
Published: March 2017

AbstractThe second iteration of the Autism Brain Imaging Data Exchange (ABIDE II) aims to enhance the scope of brain connectomics research in Autism Spectrum Disorder (ASD). Consistent with the initial ABIDE effort (ABIDE I), that released 1112 datasets in 2012, this new multisite open-data resource is an aggregate of resting state functional magnetic resonance imaging (MRI) and corresponding structural MRI and phenotypic datasets. ABIDE II includes datasets from an additional 487 individuals with ASD and 557 controls previously collected across 16 international institutions. The combination of ABIDE I and ABIDE II provides investigators with 2156 unique cross-sectional datasets allowing selection of samples for discovery and/or replication. This sample size can also facilitate the identification of neurobiological subgroups, as well as preliminary examinations of sex differences in ASD. Additionally, ABIDE II includes a range of psychiatric variables to inform our understanding of the neural correlates of co-occurring psychopathology; 284 diffusion imaging datasets are also included. It is anticipated that these enhancements will contribute to unraveling key sources of ASD heterogeneity.
Comprehensive RNA-seq transcriptomic profiling in the malignant progression of gliomas
Authors: Zhao Zheng , Meng Fanlin , Wang Wen , Wang Zheng , Zhang Chuanbao , Jiang Tao 
Published: March 2017

AbstractGliomas are the most common and lethal intracranial tumours. RNA sequencing technologies and advanced data analyses recently enabled the characterization of transcriptomic information, including protein-coding gene expression, non-coding gene expression, alternative splicing, and fusion gene detection, to facilitate detection of diseases and altered phenotypes. As a part of the Chinese Glioma Genome Atlas (CGGA) project, our aim was to delineate comprehensive transcriptome profiling in the malignant progression of human gliomas. Three hundred twenty five gliomas with different grades were collected over the past twelve years. Using the Illumina HiSeq 2,000 system, over 92 million high quality 101-bp paired-end reads were generated per sample, yielding a total of 30 billion reads. This comprehensive dataset will be useful to deepen the comprehensive understanding of gliomas, providing an opportunity to generate new therapies, diagnoses, and preventive strategies.
High-resolution data on the impact of warming on soil CO2 efflux from an Asian monsoon forest
Authors: Liang Naishen , Teramoto Munemasa , Takagi Masahiro , Zeng Jiye 
Published: March 2017

AbstractThis paper describes a project for evaluation of global warming’s impacts on soil carbon dynamics in Japanese forest ecosystems. We started a soil warming experiment in late 2008 in a 55-year-old evergreen broad-leaved forest at the boundary between the subtropical and warm-temperate biomes in southern Japan. We used infrared carbon-filament heat lamps to increase soil temperature by about 2.5 °C at a depth of 5 cm and continuously recorded CO2 emission from the soil surface using a multichannel automated chamber system. Here, we present details of the experimental processes and datasets for the CO2 emission rate, soil temperature, and soil moisture from control, trenched, and warmed trenched plots. The long term of the study and its high resolution make the datasets meaningful for use in or development of coupled climate-ecosystem models to tune their dynamic behaviour as well as to provide mean parameters for decomposition of soil organic carbon to support future predictions of soil carbon sequestration.
Replication data collection highlights value in diversity of replication attempts
Authors: DeSoto K. Andrew , Schweinsberg Martin 
Published: March 2017

AbstractResearchers agree that replicability and reproducibility are key aspects of science. A collection of Data Descriptors published in Scientific Data presents data obtained in the process of attempting to replicate previously published research. These new replication data describe published and unpublished projects. The different papers in this collection highlight the many ways that scientific replications can be conducted, and they reveal the benefits and challenges of crucial replication research. The organizers of this collection encourage scientists to reuse the data contained in the collection for their own work, and also believe that these replication examples can serve as educational resources for students, early-career researchers, and experienced scientists alike who are interested in learning more about the process of replication.
A standard database for drug repositioning
Authors: Brown Adam S. , Patel Chirag J. 
Published: March 2017

AbstractDrug repositioning, the process of discovering, validating, and marketing previously approved drugs for new indications, is of growing interest to academia and industry due to reduced time and costs associated with repositioned drugs. Computational methods for repositioning are appealing because they putatively nominate the most promising candidate drugs for a given indication. Comparing the wide array of computational repositioning methods, however, is a challenge due to inconsistencies in method validation in the field. Furthermore, a common simplifying assumption, that all novel predictions are false, is intellectually unsatisfying and hinders reproducibility. We address this assumption by providing a gold standard database, repoDB, that consists of both true positives (approved drugs), and true negatives (failed drugs). We have made the full database and all code used to prepare it publicly available, and have developed a web application that allows users to browse subsets of the data (http://apps.chiragjpgroup.org/repoDB/).
Collocated observations of cloud condensation nuclei, particle size distributions, and chemical composition
Authors: Schmale Julia , Henning Silvia , Henzing Bas , Keskinen Helmi , Sellegri Karine , Ovadnevaite Jurgita , Bougiatioti Aikaterini , Kalivitis Nikos , Stavroulas Iasonas , Jefferson Anne , Park Minsu , Schlag Patrick , Kristensson Adam , Iwamoto Yoko , Pringle Kirsty , Reddington Carly , Aalto Pasi , Äijälä Mikko , Baltensperger Urs , Bialek Jakub , Birmili Wolfram , Bukowiecki Nicolas , Ehn Mikael , Fjæraa Ann Mari , Fiebig Markus , Frank Göran , Fröhlich Roman , Frumau Arnoud , Furuya Masaki , Hammer Emanuel , Heikkinen Liine , Herrmann Erik , Holzinger Rupert , Hyono Hiroyuki , Kanakidou Maria , Kiendler-Scharr Astrid , Kinouchi Kento , Kos Gerard , Kulmala Markku , Mihalopoulos Nikolaos , Motos Ghislain , Nenes Athanasios , O’Dowd Colin , Paramonov Mikhail , Petäjä Tuukka , Picard David , Poulain Laurent , Prévôt André Stephan Henry , Slowik Jay , Sonntag Andre , Swietlicki Erik , Svenningsson Birgitta , Tsurumaru Hiroshi , Wiedensohler Alfred , Wittbom Cerina , Ogren John A. , Matsuki Atsushi , Yum Seong Soo , Myhre Cathrine Lund , Carslaw Ken , Stratmann Frank , Gysel Martin 
Published: March 2017

AbstractCloud condensation nuclei (CCN) number concentrations alongside with submicrometer particle number size distributions and particle chemical composition have been measured at atmospheric observatories of the Aerosols, Clouds, and Trace gases Research InfraStructure (ACTRIS) as well as other international sites over multiple years. Here, harmonized data records from 11 observatories are summarized, spanning 98,677 instrument hours for CCN data, 157,880 for particle number size distributions, and 70,817 for chemical composition data. The observatories represent nine different environments, e.g., Arctic, Atlantic, Pacific and Mediterranean maritime, boreal forest, or high alpine atmospheric conditions. This is a unique collection of aerosol particle properties most relevant for studying aerosol-cloud interactions which constitute the largest uncertainty in anthropogenic radiative forcing of the climate. The dataset is appropriate for comprehensive aerosol characterization (e.g., closure studies of CCN), model-measurement intercomparison and satellite retrieval method evaluation, among others. Data have been acquired and processed following international recommendations for quality assurance and have undergone multiple stages of quality assessment.
Aboriginal Australian mitochondrial genome variation – an increased understanding of population antiquity and diversity
Authors: Nagle Nano , van Oven Mannis , Wilcox Stephen , van Holst Pellekaan Sheila , Tyler-Smith Chris , Xue Yali , Ballantyne Kaye N. , Wilcox Leah , Papac Luka , Cooke Karen , van Oorschot Roland A. H. , McAllister Peter , Williams Lesley , Kayser Manfred , Mitchell R. John ,   The Genographic Consortium, Adhikarla Syama , Adler Christina J. , Balanovska Elena , Balanovsky Oleg , Bertranpetit Jaume , Clarke Andrew C. , Comas David , Cooper Alan , Der Sarkissian Clio S. I. , Dulik Matthew C. , Gaieski Jill B. , GaneshPrasad ArunKumar , Haak Wolfgang , Haber Marc , Hobbs Angela , Javed Asif , Jin Li , Kaplan Matthew E. , Li Shilin , Martínez-Cruz Begoña , Matisoo-Smith Elizabeth A. , Melé Marta , Merchant Nirav C. , Owings Amanda C. , Parida Laxmi , Pitchappan Ramasamy , Platt Daniel E. , Quintana-Murci Lluis , Renfrew Colin , Royyuru Ajay K. , Santhakumari Arun Varatharajan , Santos Fabrício R. , Schurr Theodore G. , Soodyall Himla , Soria Hernanz David F. , Swamikrishnan Pandikumar , Vilar Miguel G. , Wells R. Spencer , Zalloua Pierre A. , Ziegle Janet S. 
Published: March 2017

AbstractAboriginal Australians represent one of the oldest continuous cultures outside Africa, with evidence indicating that their ancestors arrived in the ancient landmass of Sahul (present-day New Guinea and Australia) ~55 thousand years ago. Genetic studies, though limited, have demonstrated both the uniqueness and antiquity of Aboriginal Australian genomes. We have further resolved known Aboriginal Australian mitochondrial haplogroups and discovered novel indigenous lineages by sequencing the mitogenomes of 127 contemporary Aboriginal Australians. In particular, the more common haplogroups observed in our dataset included M42a, M42c, S, P5 and P12, followed by rarer haplogroups M15, M16, N13, O, P3, P6 and P8. We propose some major phylogenetic rearrangements, such as in haplogroup P where we delinked P4a and P4b and redefined them as P4 (New Guinean) and P11 (Australian), respectively. Haplogroup P2b was identified as a novel clade potentially restricted to Torres Strait Islanders. Nearly all Aboriginal Australian mitochondrial haplogroups detected appear to be ancient, with no evidence of later introgression during the Holocene. Our findings greatly increase knowledge about the geographic distribution and phylogenetic structure of mitochondrial lineages that have survived in contemporary descendants of Australia’s first settlers.
Using Delaunay triangulation and Voronoi tessellation to predict the toxicities of binary mixtures containing hormetic compound
Authors: Qu Rui , Liu Shu-Shen , Zheng Qiao-Feng , Li Tong 
Published: March 2017

AbstractConcentration addition (CA) was proposed as a reasonable default approach for the ecological risk assessment of chemical mixtures. However, CA cannot predict the toxicity of mixture at some effect zones if not all components have definite effective concentrations at the given effect, such as some compounds induce hormesis. In this paper, we developed a new method for the toxicity prediction of various types of binary mixtures, an interpolation method based on the Delaunay triangulation (DT) and Voronoi tessellation (VT) as well as the training set of direct equipartition ray design (EquRay) mixtures, simply IDVequ. At first, the EquRay was employed to design the basic concentration compositions of five binary mixture rays. The toxic effects of single components and mixture rays at different times and various concentrations were determined by the time-dependent microplate toxicity analysis. Secondly, the concentration-toxicity data of the pure components and various mixture rays were acted as a training set. The DT triangles and VT polygons were constructed by various vertices of concentrations in the training set. The toxicities of unknown mixtures were predicted by the linear interpolation and natural neighbor interpolation of vertices. The IDVequ successfully predicted the toxicities of various types of binary mixtures.
Influence of substrate modulus on gecko adhesion
Authors: Klittich Mena R. , Wilson Michael C. , Bernard Craig , Rodrigo Rochelle M. , Keith Austin J. , Niewiarowski Peter H. , Dhinojwala Ali 
Published: March 2017

AbstractThe gecko adhesion system fascinates biologists and materials scientists alike for its strong, reversible, glue-free, dry adhesion. Understanding the adhesion system’s performance on various surfaces can give clues as to gecko behaviour, as well as towards designing synthetic adhesive mimics. Geckos encounter a variety of surfaces in their natural habitats; tropical geckos, such as Gekko gecko, encounter hard, rough tree trunks as well as soft, flexible leaves. While gecko adhesion on hard surfaces has been extensively studied, little work has been done on soft surfaces. Here, we investigate for the first time the influence of macroscale and nanoscale substrate modulus on whole animal adhesion on two different substrates (cellulose acetate and polydimethylsiloxane) in air and find that across 5 orders of magnitude in macroscale modulus, there is no change in adhesion. On the nanoscale, however, gecko adhesion is shown to depend on substrate modulus. This suggests that low surface-layer modulus may inhibit the gecko adhesion system, independent of other influencing factors such as macroscale composite modulus and surface energy. Understanding the limits of gecko adhesion is vital for clarifying adhesive mechanisms and in the design of synthetic adhesives for soft substrates (including for biomedical applications and wearable electronics).
Plumbagin sensitizes breast cancer cells to tamoxifen-induced cell death through GRP78 inhibition and Bik upregulation
Authors: Kawiak Anna , Domachowska Anna , Jaworska Anna , Lojkowska Ewa 
Published: March 2017

AbstractThe glucose regulated protein 78 (GRP78) is a major chaperone of the endoplasmic reticulum, and a prosurvival component of the unfolded protein response. GRP78 is upregulated in many types of cancers, including breast cancer. Research has suggested that GRP78 overexpression confers chemoresistance to anti-estrogen agents through a mechanism involving the inhibition of a pro-apoptotic BH3-only protein, Bik. In the present research the role of plumbagin, a naturally occurring naphthoquinone, in GRP78-associated cell death inhibition was examined. The results demonstrated that plumbagin inhibits GRP78 activity and GRP78 inhibition contributes to plumbagin-mediated cell death induction. Furthermore, Bik upregulation was associated with plumbagin-induced cell death and an increase in plumbagin-mediated Bik induction was observed upon GRP78 downregulation. Plumbagin sensitized estrogen-positive breast cancer cells to tamoxifen and the association of GRP78 inhibition and Bik upregulation in plumbagin-mediated cell sensitization was shown. Collectively, the results of this research suggest that plumbagin inhibits the antiapoptotic activity of GRP78 leading to Bik upregulation and apoptosis induction, which contributes to the sensitization of breast cancer cells to tamoxifen.
Optimizing non-invasive radiofrequency hyperthermia treatment for improving drug delivery in 4T1 mouse breast cancer model
Authors: Ware Matthew J. , Krzykawska-Serda Martyna , Chak-Shing Ho Jason , Newton Jared , Suki Sarah , Law Justin , Nguyen Lam , Keshishian Vazrik , Serda Maciej , Taylor Kimberly , Curley Steven A. , Corr Stuart J. 
Published: March 2017

AbstractInteractions of high-frequency radio waves (RF) with biological tissues are currently being investigated as a therapeutic platform for non-invasive cancer hyperthermia therapy. RF delivers thermal energy into tissues, which increases intra-tumoral drug perfusion and blood-flow. Herein, we describe an optical-based method to optimize the short-term treatment schedules of drug and hyperthermia administration in a 4T1 breast cancer model via RF, with the aim of maximizing drug localization and homogenous distribution within the tumor microenvironment. This method, based on the analysis of fluorescent dyes localized into the tumor, is more time, cost and resource efficient, when compared to current analytical methods for tumor-targeting drug analysis such as HPLC and LC-MS. Alexa-Albumin 647 nm fluorphore was chosen as a surrogate for nab-paclitaxel based on its similar molecular weight and albumin driven pharmacokinetics. We found that RF hyperthermia induced a 30–40% increase in Alexa-Albumin into the tumor micro-environment 24 h after treatment when compared to non-heat treated mice. Additionally, we showed that the RF method of delivering hyperthermia to tumors was more localized and uniform across the tumor mass when compared to other methods of heating. Lastly, we provided insight into some of the factors that influence the delivery of RF hyperthermia to tumors.
Enhanced osteogenesis and angiogenesis by mesoporous hydroxyapatite microspheres-derived simvastatin sustained release system for superior bone regeneration
Authors: Yu Wei-Lin , Sun Tuan-Wei , Qi Chao , Zhao Hua-Kun , Ding Zhen-Yu , Zhang Zhi-Wang , Sun Ben-Ben , Shen Ji , Chen Feng , Zhu Ying-Jie , Chen Dao-Yun , He Yao-Hua 
Published: March 2017

AbstractBiomaterials with both excellent osteogenic and angiogenic activities are desirable to repair massive bone defects. In this study, simvastatin with both osteogenic and angiogenic activities was incorporated into the mesoporous hydroxyapatite microspheres (MHMs) synthesized through a microwave-assisted hydrothermal method using fructose 1,6-bisphosphate trisodium salt (FBP) as an organic phosphorous source. The effects of the simvastatin-loaded MHMs (S-MHMs) on the osteogenic differentiation of rat bone marrow mesenchymal stem cells (rBMSCs) and angiogenesis in EA.hy926 cells were investigated. The results showed that the S-MHMs not only enhanced the expression of osteogenic markers in rBMSCs but also promoted the migration and tube formation of EA.hy926 cells. Furthermore, the S-MHMs were incorporated into collagen matrix to construct a novel S-MHMs/collagen composite scaffold. With the aid of MHMs, the water-insoluble simvastatin was homogenously incorporated into the hydrophilic collagen matrix and presented a sustained release profile. In vivo experiments showed that the S-MHMs/collagen scaffolds enhanced the bone regeneration and neovascularization simultaneously. These results demonstrated that the water-insoluble simvastatin could be incorporated into the MHMs and maintained its biological activities, more importantly, the S-MHMs/collagen scaffolds fabricated in this study are of immense potential in bone defect repair by enhancing osteogenesis and angiogenesis simultaneously.
Radiation-associated circulatory disease mortality in a pooled analysis of 77,275 patients from the Massachusetts and Canadian tuberculosis fluoroscopy cohorts
Authors: Tran Van , Zablotska Lydia B. , Brenner Alina V. , Little Mark P. 
Published: March 2017

AbstractHigh-dose ionising radiation is associated with circulatory disease. Risks associated with lower-dose (<0.5 Gy) exposures remain unclear, with little information on risk modification by age at exposure, years since exposure or dose-rate. Tuberculosis patients in Canada and Massachusetts received multiple diagnostic x-ray fluoroscopic exposures, over a wide range of ages, many at doses <0.5 Gy. We evaluated risks of circulatory-disease mortality associated with <0.5 Gy radiation exposure in a pooled cohort of 63,707 patients in Canada and 13,568 patients in Massachusetts. Under 0.5 Gy there are increasing trends for all circulatory disease (n = 10,209; excess relative risk/Gy = 0.246; 95% CI 0.036, 0.469; p = 0.021) and for ischaemic heart disease (n = 6410; excess relative risk/Gy = 0.267; 95% CI 0.003, 0.552; p = 0.048). All circulatory-disease and ischaemic-heart-disease risk reduces with increasing time since exposure (p < 0.005). Over the entire dose range, there are negative mortality dose trends for all circulatory disease (p = 0.014) and ischaemic heart disease (p = 0.003), possibly due to competing causes of death over this dose interval.These results confirm and extend earlier findings and strengthen the evidence for circulatory-disease mortality radiation risk at doses <0.5 Gy. The limited information on well-known lifestyle/medical risk factors for circulatory disease implies that confounding of the dose trend cannot be entirely excluded.
Endogenous TNFα orchestrates the trafficking of neutrophils into and within lymphatic vessels during acute inflammation
Authors: Arokiasamy Samantha , Zakian Christian , Dilliway Jessica , Wang Wen , Nourshargh Sussan , Voisin Mathieu-Benoit 
Published: March 2017

AbstractNeutrophils are recognised to play a pivotal role at the interface between innate and acquired immunities following their recruitment to inflamed tissues and lymphoid organs. While neutrophil trafficking through blood vessels has been extensively studied, the molecular mechanisms regulating their migration into the lymphatic system are still poorly understood. Here, we have analysed neutrophil-lymphatic vessel interactions in real time and in vivo using intravital confocal microscopy applied to inflamed cremaster muscles. We show that antigen sensitisation of the tissues induces a rapid but transient entry of tissue-infiltrated neutrophils into lymphatic vessels and subsequent crawling along the luminal side of the lymphatic endothelium. Interestingly, using mice deficient in both TNF receptors p55 and p75, chimeric animals and anti-TNFα antibody blockade we demonstrate that tissue-release of TNFα governs both neutrophil migration through the lymphatic endothelium and luminal crawling. Mechanistically, we show that TNFα primes directly the neutrophils to enter the lymphatic vessels in a strictly CCR7-dependent manner; and induces ICAM-1 up-regulation on lymphatic vessels, allowing neutrophils to crawl along the lumen of the lymphatic endothelium in an ICAM-1/MAC-1-dependent manner. Collectively, our findings demonstrate a new role for TNFα as a key regulator of neutrophil trafficking into and within lymphatic system in vivo.