bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dense, shape‐optimized posterior 32‐channel coil for submillimeter functional imaging of visual cortex at 3T
Authors: Farivar Reza , Grigorov Filip , van der Kouwe Andre J. , Wald Lawrence L. , Keil Boris 
Published: July 2015

PurposeFunctional neuroimaging of small cortical patches such as columns is essential for testing computational models of vision, but imaging from cortical columns at conventional 3T fields is exceedingly difficult. By targeting the visual cortex exclusively, we tested whether combined optimization of shape, coil placement, and electronics would yield the necessary gains in signal‐to‐noise ratio (SNR) for submillimeter visual cortex functional MRI (fMRI).MethodWe optimized the shape of the housing to a population‐averaged atlas. The shape was comfortable without cushions and resulted in the maximally proximal placement of the coil elements. By using small wire loops with the least number of solder joints, we were able to maximize the Q factor of the individual elements. Finally, by planning the placement of the coils using the brain atlas, we were able to target the arrangement of the coil elements to the extent of the visual cortex.ResultsThe combined optimizations led to as much as two‐fold SNR gain compared with a whole‐head 32‐channel coil. This gain was reflected in temporal SNR as well and enabled fMRI mapping at 0.75 mm resolutions using a conventional GRAPPA‐accelerated gradient echo echo planar imaging.ConclusionIntegrated optimization of shape, electronics, and element placement can lead to large gains in SNR and empower submillimeter fMRI at 3T. Magn Reson Med 76:321–328, 2016. © 2015 Wiley Periodicals, Inc.
Embedded beam element with interaction surface for lateral loading of piles
Authors: Turello Diego F. , Pinto Federico , Sánchez Pablo J. 
Published: July 2015

SummaryThis paper presents a numerical formulation of a three dimensional embedded beam element for the modeling of piles, which incorporates an explicit interaction surface between soil and pile. The formulation is herein implemented for lateral loading of piles but is able to represent soil–pile interaction phenomena in a general manner for different types of loading conditions or ground movements. The model assumes perfect adherence between beam and soil along the interaction surface. The paper presents a comparison of the results obtained by means of the present formulation and by means of a previously formulated embedded pile element without interaction surface, as well as reference semi‐analytical solutions and a fully 3D finite element (FE) model. It is seen that the proposed embedded element provides a better convergence behavior than a previously formulated embedded element and is able to reproduce key features of a full 3D FE model. Copyright © 2015 John Wiley & Sons, Ltd.
Integrated scheduling of loading and transportation with tractors and semitrailers separated
Authors: Tang Lixin , Li Feng , Liu Jiyin 
Published: July 2015

AbstractMotivated by some practical applications, we study a new integrated loading and transportation scheduling problem. Given a set of jobs, a single crane is available to load jobs, one by one, onto semitrailers with a given capacity. Loaded semitrailers are assigned to tractors for transportation tasks. Subject to limited resources (crane, semitrailers, and tractors), the problem is to determine (1) an assignment of jobs to semitrailers for loading tasks, (2) a sequence for the crane to load jobs onto semitrailers, (3) an assignment of loaded semitrailers to tractors for transportation tasks, and (4) a transportation schedule of assigned tractors such that the completion time of the last transportation task is minimized. We first formulate the problem as a mixed integer linear programming model (MILPM) and prove that the problem is strongly NP‐hard. Then, optimality properties are provided which are useful in establishing an improved MILPM and designing solution algorithms. We develop a constructive heuristic, two LP‐based heuristics, and a recovering beam search heuristic to solve this problem. An improved procedure for solutions by heuristics is also presented. Furthermore, two branch‐and‐bound (B&B) algorithms with two different lower bounds are developed to solve the problem to optimality. Finally, computational experiments using both real data and randomly generated data demonstrate that our heuristics are highly efficient and effective. In terms of computational time and the number of instances solved to optimality in a time limit, the B&B algorithms are better than solving the MILPM. © 2015 Wiley Periodicals, Inc. Naval Research Logistics 62: 416–433, 2015
The Cancer Stories Project: narratives of encounters with cancer in Aotearoa, New Zealand
Authors: Egan Richard , Llewellyn Rebecca , Wood Sarah , Doherty Joanne , Albert Tira , Walsh Chris , Atkinson Kelly , Kerslake Phil 
Published: July 2015

AbstractObjectiveThe Cancer Stories Study aimed to identify the factors that empower people who have experienced cancer. More specifically the project sought to explore the coping and support mechanisms people adopted to help understand and manage their cancer experience.MethodsA participatory research approach involved researchers and consumers working in partnership on the project. This research team agreed on a qualitative method that focused on cancer survivors' personal stories. Semi‐structured interviews were conducted with 38 cancer survivors in the lower half of the North Island, New Zealand (NZ). Generic qualitative analysis methods were employed including the recording, transcribing and thematic coding of interview narratives.ResultsSeven distinct themes were classified under the overarching theme of empowerment: attitude, change, family/whānau and friends, healthcare professionals and services, sources of support, employment and tangata whenua (NZ's indigenous peoples). The unique needs of each individual were strongly emphasised throughout all the themes indicating a ‘one‐size‐fits‐all’ approach has its limitations. The need for improvements in communication, cultural and spiritual care was highlighted by many participants.ConclusionsIt is anticipated that this project will contribute to a greater understanding of the factors that might empower people in their cancer journey. An empowerment lens, that asks how those affected by cancer may be further enabled at an individual, family/whānau, employer and healthcare professional level may be useful in assisting people navigate and manage their cancer. Copyright © 2015 John Wiley & Sons, Ltd.
Statistical metrics for assessing the quality of wind power scenarios for stochastic unit commitment
Authors: Sari Didem , Lee Youngrok , Ryan Sarah , Woodruff David 
Published: July 2015

AbstractIn power systems with high penetration of wind generation, probabilistic scenarios are generated for use in stochastic formulations of day‐ahead unit commitment problems. To minimize the expected cost, the wind power scenarios should accurately represent the stochastic process for available wind power. We employ some statistical evaluation metrics to assess whether the scenario set possesses desirable properties that are expected to lead to a lower cost in stochastic unit commitment. A new mass transportation distance rank histogram is developed for assessing the reliability of unequally likely scenarios. Energy scores, rank histograms and Brier scores are applied to alternative sets of scenarios that are generated by two very different methods. The mass transportation distance rank histogram is best able to distinguish between sets of scenarios that are more or less calibrated according to their bias, variability and autocorrelation. Copyright © 2015 John Wiley & Sons, Ltd.
Investigation of a leptospirosis outbreak in triathlon participants, Réunion Island, 2013
Authors: PAGÈS F. , LARRIEU S. , SIMOES J. , LENABAT P. , KURTKOWIAK B. , GUERNIER V. , LE MINTER G. , LAGADEC E. , GOMARD Y. , MICHAULT A. , JAFFAR-BANDJEE M. C. , DELLAGI K. , PICARDEAU M. , TORTOSA P. , FILLEUL L. 
Published: July 2015

SUMMARYWe report herein the investigation of a leptospirosis outbreak occurring in triathlon competitors on Réunion Island, Indian Ocean. All participants were contacted by phone or email and answered a questionnaire. Detection and molecular characterization of pathogenicLeptospirawas conducted in inpatients and in rodents trapped at the vicinity of the event. Of the 160 athletes competing, 101 (63·1%) agreed to participate in the study. Leptospirosis was biologically confirmed for 9/10 suspected cases either by real-time PCR or serological tests (MAT or ELISA). The total attack rate, children's attack rate, swimmers’ attack rate, and the attack rate in adult swimmers were respectively estimated at 8·1% [95% confidence interval (CI) 4·3–14·7], 0%, 12·7% (95% CI 6·8–22·4) and 23·1% (95% CI 12·6–33·8). Leptospirosis cases reported significantly more wounds [risk ratio (RR) 4·5, 95% CI 1·6–13], wore complete neoprene suits less often (RR 4·3, 95% CI 1·3–14·5) and were most frequently unlicensed (RR 6·6, 95% CI 2·9–14·8). The epidemiological investigation supported that some measures such as the use of neoprene suits proved efficient in protecting swimmers against infection. PCR detection in rats revealed highLeptospirainfection rates. Partial sequencing of the 16S gene and serology on both human and animal samples strongly suggests that rats were the main contaminators and were likely at the origin of the infection in humans.
How and when plume zonation appeared during the 132 Myr evolution of the Tristan Hotspot
Authors: Hoernle Kaj , Rohde Joana , Hauff Folkmar , Garbe-Schönberg Dieter , Homrighausen Stephan , Werner Reinhard , Morgan Jason P. 
Published: July 2015

AbstractIncreasingly, spatial geochemical zonation, present as geographically distinct, subparallel trends, is observed along hotspot tracks, such as Hawaii and the Galapagos. The origin of this zonation is currently unclear. Recently zonation was found along the last ∼70 Myr of the Tristan-Gough hotspot track. Here we present new Sr–Nd–Pb–Hf isotope data from the older parts of this hotspot track (Walvis Ridge and Rio Grande Rise) and re-evaluate published data from the Etendeka and Parana flood basalts erupted at the initiation of the hotspot track. We show that only the enriched Gough, but not the less-enriched Tristan, component is present in the earlier (70–132 Ma) history of the hotspot. Here we present a model that can explain the temporal evolution and origin of plume zonation for both the Tristan-Gough and Hawaiian hotspots, two end member types of zoned plumes, through processes taking place in the plume sources at the base of the lower mantle.
Prediction of drug-induced nephrotoxicity and injury mechanisms with human induced pluripotent stem cell-derived cells and machine learning methods
Authors: Kandasamy Karthikeyan , Chuah Jacqueline Kai Chin , Su Ran , Huang Peng , Eng Kim Guan , Xiong Sijing , Li Yao , Chia Chun Siang , Loo Lit-Hsin , Zink Daniele 
Published: July 2015

AbstractThe renal proximal tubule is a main target for drug-induced toxicity. The prediction of proximal tubular toxicity during drug development remains difficult. Any in vitro methods based on induced pluripotent stem cell-derived renal cells had not been developed, so far. Here, we developed a rapid 1-step protocol for the differentiation of human induced pluripotent stem cells (hiPSC) into proximal tubular-like cells. These proximal tubular-like cells had a purity of >90% after 8 days of differentiation and could be directly applied for compound screening. The nephrotoxicity prediction performance of the cells was determined by evaluating their responses to 30 compounds. The results were automatically determined using a machine learning algorithm called random forest. In this way, proximal tubular toxicity in humans could be predicted with 99.8% training accuracy and 87.0% test accuracy. Further, we studied the underlying mechanisms of injury and drug-induced cellular pathways in these hiPSC-derived renal cells and the results were in agreement with human and animal data. Our methods will enable the development of personalized or disease-specific hiPSC-based renal in vitro models for compound screening and nephrotoxicity prediction.
Spontaneous Regeneration of Human Photoreceptor Outer Segments
Authors: Horton Jonathan C. , Parker Alicia B. , Botelho James V. , Duncan Jacque L. 
Published: July 2015

AbstractPhotoreceptors are damaged in many common eye diseases, such as macular degeneration, retinal detachment and retinitis pigmentosa. The development of methods to promote the repair or replacement of affected photoreceptors is a major goal of vision research. In this context, it would be useful to know whether photoreceptors are capable of undergoing some degree of spontaneous regeneration after injury. We report a subject who lost retinal function in a wide zone around the optic disc, giving rise to massive enlargement of the physiological blind spot. Imaging with an adaptive optics scanning laser ophthalmoscope (AOSLO) showed depletion of cone outer segments in the affected retina. A year later visual function had improved, with shrinkage of the enlarged blind spot. AOSLO imaging showed repopulation of cone outer segments, although their density remained below normal. There was a one-to-one match between sites of formerly missing outer segments and new outer segments that had appeared over the course of the year’s recovery. This correspondence provided direct morphological evidence that damaged cones are capable, under some circumstances, of generating new outer segments.
VaccineDA: Prediction, design and genome-wide screening of oligodeoxynucleotide-based vaccine adjuvants
Authors: Nagpal Gandharva , Gupta Sudheer , Chaudhary Kumardeep , Kumar Dhanda Sandeep , Prakash Satya , Raghava Gajendra P. S. 
Published: July 2015

AbstractImmunomodulatory oligodeoxynucleotides (IMODNs) are the short DNA sequences that activate the innate immune system via toll-like receptor 9. These sequences predominantly contain unmethylated CpG motifs. In this work, we describe VaccineDA (Vaccine DNA adjuvants), a web-based resource developed to design IMODN-based vaccine adjuvants. We collected and analyzed 2193 experimentally validated IMODNs obtained from the literature. Certain types of nucleotides (e.g., T, GT, TC, TT, CGT, TCG, TTT) are dominant in IMODNs. Based on these observations, we developed support vector machine-based models to predict IMODNs using various compositions. The developed models achieved the maximum Matthews Correlation Coefficient (MCC) of 0.75 with an accuracy of 87.57% using the pentanucleotide composition. The integration of motif information further improved the performance of our model from the MCC of 0.75 to 0.77. Similarly, models were developed to predict palindromic IMODNs and attained a maximum MCC of 0.84 with the accuracy of 91.94%. These models were evaluated using a five-fold cross-validation technique as well as validated on an independent dataset. The models developed in this study were integrated into VaccineDA to provide a wide range of services that facilitate the design of DNA-based vaccine adjuvants (http://crdd.osdd.net/raghava/vaccineda/).
Laser-scanning cytometry can quantify human adipocyte browning and proves effectiveness of irisin
Authors: Kristóf Endre , Doan-Xuan Quang-Minh , Bai Péter , Bacso Zsolt , Fésüs László 
Published: July 2015

AbstractLaser-scanning cytometry is presented as a tool allowing population scale analysis ofex vivohuman brown adipogenic differentiation. It combines texture analysis and detection of Ucp1 protein content in single brown adipocytes of mixed cell populations with gene expression pattern and functional characteristics of browning. Using this method we could validate mouse data in human samples demonstrating the effectiveness of irisin to induce “beige” differentiation of subcutaneous white adipocytes.
Proteomic analysis reveals that COP9 signalosome complex subunit 7A (CSN7A) is essential for the phase transition of migratory locust
Authors: Tong Xi-Wen , Chen Bing , Huang Li-Hua , Feng Qi-Li , Kang Le 
Published: July 2015

AbstractThe migratory locust displays a reversible, density-dependent transition between the two phases of gregaria and solitaria. This phenomenon is a typical kind of behavior plasticity. Here, we report that COP9 signalosome complex subunit 7A (CSN7A) is involved in the regulation of locust phase transition. Firstly, 90 proteins were identified to express differentially between the two phases by quantitative proteomic analysis. Gregaria revealed higher levels in proteins related to structure formation, melanism and energy metabolism, whereas solitaria had more abundant proteins related to digestion, absorption and chemical sensing. Subsequently, ten proteins including CSN7A were found to reveal differential mRNA expression profiles between the two phases. The CSN7A had higher mRNA level in the gregaria as compared with the solitaria and the mRNA amount in the gregaria decreased remarkably during the 32 h-isolation. However, the mRNA level in the solitaria kept constant during the crowding rearing. Finally and importantly, RNA interference of CSN7A in gregaria resulted in obvious phase transition towards solitaria within 24 h. It suggests that CSN7A plays an essential role in the transition of gregaria towards solitaria in the migratory locust. To our knowledge, it’s the first time to report the role of CSN in behavior plasticity of animals.
Anti-CD antibody microarray for human leukocyte morphology examination allows analyzing rare cell populations and suggesting preliminary diagnosis in leukemia
Authors: Khvastunova Alina N. , Kuznetsova Sofya A. , Al-Radi Liubov S. , Vylegzhanina Alexandra V. , Zakirova Anna O. , Fedyanina Olga S. , Filatov Alexander V. , Vorobjev Ivan A. , Ataullakhanov Fazly 
Published: July 2015

AbstractWe describe a method for leukocyte sorting by a microarray of anti-cluster-of-differentiation (anti-CD) antibodies and for preparation of the bound cells for morphological or cytochemical examination. The procedure results in a “sorted” smear with cells positive for certain surface antigens localised in predefined areas. The morphology and cytochemistry of the microarray-captured normal and neoplastic peripheral blood mononuclear cells are identical to the same characteristics in a smear. The microarray permits to determine the proportions of cells positive for the CD antigens on the microarray panel with high correlation with flow cytometry. Using the anti-CD microarray we show that normal granular lymphocytes and lymphocytes with radial segmentation of the nuclei are positive for CD3, CD8, CD16 or CD56 but not for CD4 or CD19. We also show that the described technique permits to obtain a pure leukemic cell population or to separate two leukemic cell populations on different antibody spots and to study their morphology or cytochemistry directly on the microarray. In cases of leukemias/lymphomas when circulating neoplastic cells are morphologically distinct, preliminary diagnosis can be suggested from full analysis of cell morphology, cytochemistry and their binding pattern on the microarray.
Passively mode-locked fiber laser by a cell-type WS2 nanosheets saturable absorber
Authors: Yan Peiguang , Liu Aijiang , Chen Yushan , Wang JinZhang , Ruan Shuangchen , Chen Hao , Ding Jinfei 
Published: July 2015

AbstractA cell-type saturable absorber has been demonstrated by filling the single mode photonic crystal fiber (SMPCF) with tungsten disulfide (WS2) nanosheets. The modulation depth, saturable intensity and non-saturable loss of this SA are measured to be 3.53%, 159 MW/cm2 and 23.2%, respectively. Based on this SA, a passively mode-locked EDF laser has been achieved with pulse duration of 808 fs and repetition rate of 19.57 MHz and signal-noise-ratio (SNR) of 60.5 dB. Our results demonstrate that the cell-type WS2 nanosheets SA can serve as a good candidate for short-pulse mode locker.
Calcium ion-induced formation of β-sheet/-turn structure leading to alteration of osteogenic activity of bone morphogenetic protein-2
Authors: Zhang Wenjing , He Hongyan , Tian Yu , Gan Qi , Zhang Jing , Yuan Yuan , Liu Changsheng 
Published: July 2015

AbstractPreserving bioactivity of bone morphogenetic protein 2 (BMP-2) still remains a challenge in protein-based therapy. It is not known how Ca2+ released from extracellular matrix or existing in physiological environment influences bioactivity in situ till now. Here, effects of extracellular Ca2+ on conformation and osteogenic bioactivity of recombinant human BMP-2 (rhBMP-2) were investigated systematically. In vitro results indicated that Ca2+ could bind rhBMP-2 rapidly and had no obvious effect on cell behaviors. Low concentration of Ca2+ (0.18 mM) enhanced rhBMP-2-induced osteogenic differentiation, while high Ca2+ concentration (>1.80 mM) exerted negative effect. In vivo ectopic bone formation exhibited similar trend. Further studies by circular dichroism spectroscopy, fluorescence spectroscopy, together with cell culture experiments revealed at low concentration, weak interaction of Ca2+ and rhBMP-2 slightly increased β-sheet/-turn content and facilitated recognition of BMP-2 and BMPRIA. But, high Ca2+ concentration (>1.8 mM) induced formation of Ca-rhBMP-2 complex and markedly increased content of β-sheet/-turn, which led to inhibition binding of rhBMP-2 and BMPRIA and thus suppression of downstream Smad1/5/8, ERK1/2 and p38 mitogen-associated protein kinase signaling pathways. Our work suggests osteogenic bioactivity of BMP-2 can be adjusted via extracellular Ca2+, which should provide guide and assist for development of BMP-2-based materials for bone regeneration.
Crystallographic analysis of the N-terminal domain ofMiddle East respiratory syndrome coronavirusnucleocapsid protein
Authors: Wang Yong-Sheng , Chang Chung-ke , Hou Ming-Hon 
Published: July 2015

The N-terminal domain of the nucleocapsid protein fromMiddle East respiratory syndrome coronavirus(MERS-CoV NP-NTD) contains many positively charged residues and has been identified to be responsible for RNA binding during ribonucleocapsid formation by the virus. In this study, the crystallization and crystallographic analysis of MERS-CoV NP-NTD (amino acids 39–165), with a molecular weight of 14.7 kDa, are reported. MERS-CoV NP-NTD was crystallized at 293 K using PEG 3350 as a precipitant and a 94.5% complete native data set was collected from a cooled crystal at 77 K to 2.63 Å resolution with an overallRmergeof 9.6%. The crystals were monoclinic and belonged to space groupP21, with unit-cell parametersa= 35.60,b= 109.64,c = 91.99 Å, β = 101.22°. The asymmetric unit contained four MERS-CoV NP-NTD molecules.