bluuebunny/crossref_metadata_2025 huggingface dataset:
Genomic and metabolic characterization of a chromophobe renal cell carcinoma cell line model (UOK276)
Authors: Yang Youfeng , Vocke Cathy D. , Ricketts Christopher J. , Wei Darmood , Padilla‐Nash Hesed M. , Lang Martin , Sourbier Carole , Killian J. Keith , Boyle Shawna L. , Worrell Robert , Meltzer Paul S. , Ried Thomas , Merino Maria J. , Metwalli Adam R. , Linehan W. Marston
Published: July 2017

Chromophobe renal cell carcinoma (ChRCC) represents 5% of all RCC cases and frequently demonstrates multiple chromosomal losses and an indolent pattern of local growth, but can demonstrate aggressive features and resistance to treatment in a metastatic setting. Cell line models are an important tool for the investigation of tumor biology and therapeutic drug efficacy. Currently, there are few ChRCC‐derived cell lines and none is well characterized. This study characterizes a novel ChRCC‐derived cell line model, UOK276. A large ChRCC tumor with regions of sarcomatoid differentiation was used to establish a spontaneously immortal cell line, UOK276. UOK276 was evaluated for chromosomal, mutational, and metabolic aberrations. The UOK276 cell line is hyperdiploid with a modal number of 49 chromosomes per cell, and evidence of copy‐neutral loss of heterozygosity, as opposed to the classic pattern of ChRCC chromosomal losses. UOK276 demonstrated a TP53 missense mutation, expressed mutant TP53 protein, and responded to treatment with a small‐molecule therapeutic agent, NSC319726, designed to reactivate mutated TP53. Xenograft tumors grew in nude mice and provide an in vivo animal model for the investigation of potential therapeutic regimes. The xenograft pathology and genetic analysis suggested that UOK276 was derived from the sarcomatoid region of the original tumor. In summary, UOK276 represents a novel in vitro and in vivo cell line model for aggressive, sarcomatoid‐differentiated, TP53 mutant ChRCC. This preclinical model system could be used to investigate the novel biology of aggressive, sarcomatoid ChRCC and evaluate the new therapeutic regimes.
Selective dissolution of alkali feldspars and its effect on Lower Triassic sandy conglomerate reservoirs in the Junggar Basin, northwestern China
Authors: Kang Xun , Hu Wenxuan , Cao Jian , Jin Jun , Wu Haiguang , Zhao Yang , Wang Jian
Published: July 2017

Feldspar dissolution resulting from fluid–rock reactions in clastic rocks is common in petroliferous sedimentary basins and significantly affects the quality of reservoirs. The objective of this study is a case study of this phenomenon in the sandy conglomerate reservoirs, based on the Lower Triassic Baikouquan Formation in the Mahu Sag at the northwestern margin of the Junggar Basin in northwestern China, which has obtained exploration breakthroughs recently. In these rocks, orthoclase has undergone dissolution and the dissolution intensity decreases gradually from the basal member (T1b1) to the upper member (T1b3) of the formation, whereas albite remained stable or has even overgrown crystals, displaying a selective dissolution of alkali feldspars. This is interpreted to be mainly controlled by two factors. First, illitization of mixed‐layer illite/smectite in the sandy conglomerates consumed K, thereby increasing Na/K ratios in the formation waters and leading to orthoclase dissolution and albite overgrowths on perthite and microcline. Second, the charge of acidic, hydrocarbon‐related fluids further promoted orthoclase dissolution. These relationships are confirmed by the fact that hydrocarbon charging intensity shows a gradual upward reduction from member T1b1 to T1b3, as does the scale of orthoclase dissolution. This selective dissolution resulted from the influence of different mineral components on diagenesis, the acidic nature of reservoir fluids, and the extent of water–rock interaction. The dissolution significantly improved porosity and permeability of the reservoirs by generating substantial secondary porosity. The results indicate a favorable exploration prospect located in the up‐dip area of the Ma 18 and Aihu 2 wells on the western slope of the Mahu Sag.
Petrography and geochemistry of sandstone–mudstone from Barakar Formation (early Permian), Raniganj Basin, India: Implications for provenance, weathering and marine depositional conditions during Lower Gondwana sedimentation
Authors: Bhattacharjee Joyeeta , Ghosh Kaushik Kiran , Bhattacharya Biplab
Published: July 2017

Post‐glacial Permian coal‐bearing sedimentary successions are traditionally interpreted as fluvially deposited within the Gondwanaland continental set‐up throughout the globe. Recent attempts to reinterpret such successions in terms of marine flooding events, mainly based on sedimentological and ichnological attributes, raised doubt on the existing palaeogeographic model of the Late Palaeozoic Gondwanaland. Reassessing these sedimentary successions using other proxies, like petrographic and geochemical properties, may provide more reliable clues to improve the present understanding.

In this paper, petrographic and geochemical analysis of sandstones, sandstone–mudstone heteroliths, and mudstones of the early Permian Barakar Formation of Lower Gondwana Supergroup, Raniganj coal Basin, India, is presented to understand the provenance, palaeoweathering pattern and palaeodepositional conditions. Petrographically, the sandstones are arkosic to sub‐arkosic in nature, with abundant unstable components and heavy minerals. Clay minerals in the matrix and the mudstones are dominated by kaolinite, illite‐smectite with authigenic glauconite, indicating a marine diagenetic realm. Mineralogical assemblage attests to sedimentation in craton interior passive margin conditions. Geochemically, the lithounits show large variations in major element and trace element (including rare earth element) concentrations. Chemical index of alteration and A–CN–K ternary plot indicate moderate to strong chemical weathering, leading to deposition of compositionally immature sediments close to their source without much recycling. Ratios of major elements (e.g., MgO, K2O, Fe2O3, Al2O3, and SiO2) signify a continental–marine transitional depositional environment developed in a stable passive margin setting under gradually warming up climatic conditions. Trace element ratios manifest an estuarine depositional setting during Barakar sedimentation, comparable with modern major river mouth estuaries.

Thus, this paper provides unequivocal evidence of significant marine influence during sedimentation in the Lower Gondwana basins in India, particularly during the Permian time, and signifies the importance of re‐examining the so called “continental fluvial” coal‐bearing deposits as considerably marine‐influenced. The interpretations provide important clues in understanding and reconstructing the Permian Lower Gondwana palaeogeography in eastern peninsular India.
Trajectories of depressive and anxiety symptoms in older adults: a 6‐year prospective cohort study
Authors: Holmes Sophie E. , Esterlis Irina , Mazure Carolyn M. , Lim Yen Ying , Ames David , Rainey‐Smith Stephanie , Fowler Chris , Ellis Kathryn , Martins Ralph N. , Salvado Olivier , Doré Vincent , Villemagne Victor L. , Rowe Christopher C. , Laws Simon M. , Masters Colin L. , Pietrzak Robert H. , Maruff Paul ,   for the Australian Imaging, Biomarkers and Lifestyle Research Group
Published: July 2017

Objective

Depressive and anxiety symptoms are common in older adults, significantly affect quality of life, and are risk factors for Alzheimer's disease. We sought to identify the determinants of predominant trajectories of depressive and anxiety symptoms in cognitively normal older adults.

Method

Four hundred twenty‐three older adults recruited from the general community underwent Aβ positron emission tomography imaging, apolipoprotein and brain‐derived neurotrophic factor genotyping, and cognitive testing at baseline and had follow‐up assessments. All participants were cognitively normal and free of clinical depression at baseline. Latent growth mixture modeling was used to identify predominant trajectories of subthreshold depressive and anxiety symptoms over 6 years. Binary logistic regression analysis was used to identify baseline predictors of symptomatic depressive and anxiety trajectories.

Results

Latent growth mixture modeling revealed two predominant trajectories of depressive and anxiety symptoms: a chronically elevated trajectory and a low, stable symptom trajectory, with almost one in five participants falling into the elevated trajectory groups. Male sex (relative risk ratio (RRR) = 3.23), lower attentional function (RRR = 1.90), and carriage of the brain‐derived neurotrophic factor Val66Met allele in women (RRR = 2.70) were associated with increased risk for chronically elevated depressive symptom trajectory. Carriage of the apolipoprotein epsilon 4 allele (RRR = 1.92) and lower executive function in women (RRR = 1.74) were associated with chronically elevated anxiety symptom trajectory.

Conclusion

Our results indicate distinct and sex‐specific risk factors linked to depressive and anxiety trajectories, which may help inform risk stratification and management of these symptoms in older adults at risk for Alzheimer's disease. Copyright © 2017 John Wiley & Sons, Ltd.
Dynamic coupling between fMRI local connectivity and interictal EEG in focal epilepsy: A wavelet analysis approach
Authors: Omidvarnia Amir , Pedersen Mangor , Vaughan David N. , Walz Jennifer M. , Abbott David F. , Zalesky Andrew , Jackson Graeme D.
Published: July 2017

Simultaneous scalp EEG‐fMRI recording is a noninvasive neuroimaging technique for combining electrophysiological and hemodynamic aspects of brain function. Despite the time‐varying nature of both measurements, their relationship is usually considered as time‐invariant. The aim of this study was to detect direct associations between scalp‐recorded EEG and regional changes of hemodynamic brain connectivity in focal epilepsy through a time‐frequency paradigm. To do so, we developed a voxel‐wise framework that analyses wavelet coherence between dynamic regional phase synchrony (DRePS, calculated from fMRI) and band amplitude fluctuation (BAF) of a target EEG electrode with dominant interictal epileptiform discharges (IEDs). As a proof of concept, we applied this framework to seven patients with focal epilepsy. The analysis produced patient‐specific spatial maps of DRePS‐BAF coupling, which highlight regions with a strong link between EEG power and local fMRI connectivity. Although we observed DRePS‐BAF coupling proximate to the suspected seizure onset zone in some patients, our results suggest that DRePS‐BAF is more likely to identify wider ‘epileptic networks’. We also compared DRePS‐BAF with standard EEG‐fMRI analysis based on general linear modelling (GLM). There was, in general, little overlap between the DRePS‐BAF maps and GLM maps. However, in some subjects the spatial clusters revealed by these two analyses appeared to be adjacent, particularly in medial posterior cortices. Our findings suggest that (1) there is a strong time‐varying relationship between local fMRI connectivity and interictal EEG power in focal epilepsy, and (2) that DRePS‐BAF reflect different aspects of epileptic network activity than standard EEG‐fMRI analysis. These two techniques, therefore, appear to be complementary. Hum Brain Mapp 38:5356–5374, 2017. © 2017 Wiley Periodicals, Inc.
Towards a unified analysis of brain maturation and aging across the entire lifespan: A MRI analysis
Authors: Coupé Pierrick , Catheline Gwenaelle , Lanuza Enrique , Manjón José Vicente ,   for the Alzheimer's Disease Neuroimaging Initiative
Published: July 2017

There is no consensus in literature about lifespan brain maturation and senescence, mainly because previous lifespan studies have been performed on restricted age periods and/or with a limited number of scans, making results instable and their comparison very difficult. Moreover, the use of nonharmonized tools and different volumetric measurements lead to a great discrepancy in reported results. Thanks to the new paradigm of BigData sharing in neuroimaging and the last advances in image processing enabling to process baby as well as elderly scans with the same tool, new insights on brain maturation and aging can be obtained. This study presents brain volume trajectory over the entire lifespan using the largest age range to date (from few months of life to elderly) and one of the largest number of subjects (N = 2,944). First, we found that white matter trajectory based on absolute and normalized volumes follows an inverted U‐shape with a maturation peak around middle life. Second, we found that from 1 to 8–10 y there is an absolute gray matter (GM) increase related to body growth followed by a GM decrease. However, when normalized volumes were considered, GM continuously decreases all along the life. Finally, we found that this observation holds for almost all the considered subcortical structures except for amygdala which is rather stable and hippocampus which exhibits an inverted U‐shape with a longer maturation period. By revealing the entire brain trajectory picture, a consensus can be drawn since most of the previously discussed discrepancies can be explained. Hum Brain Mapp 38:5501–5518, 2017. © 2017 Wiley Periodicals, Inc.
Clinical outcomes for patients presenting with N3 head and neck squamous cell carcinoma: Analysis of the National Cancer Database
Authors: Ko Huaising C. , Chen Shuai , Wieland Aaron M. , Yu Menggang , Baschnagel Andrew M. , Hartig Gregory K. , Harari Paul M. , Witek Matthew E.
Published: July 2017

Background

There is a paucity of data regarding head and neck squamous cell carcinomas (HNSCCs) and N3 nodal disease.

Methods

Retrospective analysis of patients with N3 HNSCC identified in the National Cancer Database (NCDB) was performed.

Results

We identified 4867 patients with N3 HNSCC treated with primary surgery or chemoradiotherapy (CRT). Propensity‐adjusted median survival was 54.2 and 44.8 months for surgery and CRT, respectively (P = .06). Oropharyngeal primary subsite demonstrated a survival advantage with surgery versus CRT with propensity‐adjusted median survivals of 86.0 and 61.9 months, respectively (P < .05).

Conclusion

Management of N3 HNSCC relies largely on CRT. Patients with N3 nodal disease with nonoropharyngeal primary tumors exhibit 5‐year overall survival approaching 30% independent of initial treatment modality. Patients with oropharyngeal primaries exhibit improved outcomes with surgery largely influenced by the human papillomavirus (HPV)‐negative subset. These data represent the most comprehensive analysis of N3 HNSCC outcomes and serves as a foundation for future research and clinical management.
In vivo Raman spectroscopy–assisted early identification of potential second primary/recurrences in oral cancers: An exploratory study
Authors: Malik Akshat , Sahu Aditi , Singh S. P. , Deshmukh Atul , Chaturvedi Pankaj , Nair Deepa , Nair Sudhir , Murali Krishna C.
Published: July 2017

Background

Higher rates of local recurrences and second primaries, ascribable to field cancerization, are known problem in oral cancers. The present study explored utility of identification of potential recurrences by Raman spectroscopy, which has been shown to identify oral precancers, cancers, and field cancerization in humans and micro‐sized mechanical irritation‐induced tumors in animals.

Methods

Raman spectra were acquired from tumor and contralateral normal mucosa in 99 patients with oral cancer who were then followed up for appearance of clinically apparent cancerous lesions. Misclassifications observed in subsequent multivariate statistical analysis between contralateral normal and tumor spectra were correlated with appearance of new malignant lesions.

Results

The patients with mismatched spectra had 1.5 times higher chances of developing local recurrence. The sensitivity of Raman spectroscopy in predicting the recurrences was 80% and the specificity was 29.7%.

Conclusion

Findings provide proof‐of‐concept for Raman spectroscopy‐based identification of sites that have higher propensity to progress to carcinomas before becoming clinically apparent. Prospective validation of Raman spectroscopy by including additional oral cavity subsites and use of multifiber bundles may improve rate of identification of recurrence‐prone subjects.
Increased myocardial native T1 relaxation time in patients with nonischemic dilated cardiomyopathy with complex ventricular arrhythmia
Authors: Nakamori Shiro , Bui An H. , Jang Jihye , El‐Rewaidy Hossam A. , Kato Shingo , Ngo Long H. , Josephson Mark E. , Manning Warren J. , Nezafat Reza
Published: July 2017

Purpose

To study the relationship between diffuse myocardial fibrosis and complex ventricular arrhythmias (ComVA) in patients with nonischemic dilated cardiomyopathy (NICM). We hypothesized that NICM patients with ComVA would have a higher native myocardial T1 time, suggesting more extensive myocardial diffuse fibrosis.

Materials and Methods

We prospectively enrolled NICM patients with a history of ComVA (n = 50) and age‐matched NICM patients without ComVA (n = 57). Imaging was performed at 1.5T with a protocol that included cine magnetic resonance imaging (MRI) for left ventricular (LV) function, late gadolinium enhancement (LGE) for focal scar, and native T1 mapping for diffuse fibrosis assessment.

Results

Global native T1 time was significantly higher in patients with NICM with ComVA when compared to patients with NICM without ComVA (1131 ± 42 vs. 1107 ± 45 msec, P = 0.006), and this finding remained after excluding segments with scar on LGE (1124 ± 36 vs. 1102 ± 44 msec, P = 0.006). Native T1 was similar in NICM patients with and without the presence of LGE (1121 ± 39 vs. 1117 ± 48 msec, P = 0.68) and mildly correlated with LV end‐diastolic volume index (r = 0.27, P = 0.005), LV end‐systolic volume index (r = 0.24, P = 0.01), and LV ejection fraction (r = –0.28, P = 0.003). Native T1 value for each 10‐msec increment was an independent predictor of ComVA (odds ratio 1.14, 95% confidence interval 1.03–1.25; P = 0.008) beyond LV function and LGE.

Conclusion

NICM patients with ComVA have higher native T1 compared to NICM without any documented ComVA. Native myocardial T1 is independently associated with ComVA, after adjusting for LV function and LGE.

Level of Evidence: 2

Technical Efficacy: Stage 2

J. Magn. Reson. Imaging 2018;47:779–786.

In memoriam: The authors are grateful for Dr. Josephson's inspiring guidance and contributions to this study.
Network meta‐analysis of disconnected networks: How dangerous are random baseline treatment effects?
Authors: Béliveau Audrey , Goring Sarah , Platt Robert W. , Gustafson Paul
Published: July 2017

In network meta‐analysis, the use of fixed baseline treatment effects (a priori independent) in a contrast‐based approach is regularly preferred to the use of random baseline treatment effects (a priori dependent). That is because, often, there is not a need to model baseline treatment effects, which carry the risk of model misspecification. However, in disconnected networks, fixed baseline treatment effects do not work (unless extra assumptions are made), as there is not enough information in the data to update the prior distribution on the contrasts between disconnected treatments. In this paper, we investigate to what extent the use of random baseline treatment effects is dangerous in disconnected networks. We take 2 publicly available datasets of connected networks and disconnect them in multiple ways. We then compare the results of treatment comparisons obtained from a Bayesian contrast‐based analysis of each disconnected network using random normally distributed and exchangeable baseline treatment effects to those obtained from a Bayesian contrast‐based analysis of their initial connected network using fixed baseline treatment effects. For the 2 datasets considered, we found that the use of random baseline treatment effects in disconnected networks was appropriate. Because those datasets were not cherry‐picked, there should be other disconnected networks that would benefit from being analyzed using random baseline treatment effects. However, there is also a risk for the normality and exchangeability assumption to be inappropriate in other datasets even though we have not observed this situation in our case study. We provide code, so other datasets can be investigated.
Rural and remote SMEs’ innovative behavior: Is it in the genes or location? An examination of entrepreneurial traits and characteristics
Authors: Blanchard Kevin
Published: July 2017

Remote rural businesses have a higher developed form of innovative ability that gives them an innate sense of survival over rural businesses. Innovation and its use within a remote rural environment, is more highly developed with these geographically located businesses. Entrepreneurial characteristics/traits establish a value in relation to the level of innovative capability/ability. Remote rural SMEs have a better understanding of strategic awareness in relation to their customers.
Which board members when you innovate? Board selection as a strategic change for innovation
Authors: Allemand Isabelle , Brullebaut Bénédicte , Galia Fabrice , Zenou Emmanuel
Published: July 2017

Firms with high innovation intensity hire directors with specific skills, and different forms of innovation require different profiles of directors. Board members may bring human and social capital that support the innovative strategies of firms. In a sample of 735 French companies, firms with high innovation intensity hire directors with specific skills, while the profiles of directors required on boards are different according to the forms of innovation implemented. Board human capital is important for innovative firms and gives them benchmarks concerning board appointment criteria.
Optimal timing for a technology shift in mature markets of mobile communication
Authors: Adamauskas Saulius , Krušinskas Rytis
Published: July 2017

The new‐generation 5G mobile technology will likely have a business cycle of approximately 24–25 years. Investment timing in the adoption of new technologies is becoming crucial for science and technology‐based companies to remain competitive. Further investment timing depends on the companies’ current financial state. Mobile technology‐based companies have their own resource lifecycle in which technological changes are inevitable and depend on the uncertainty of the market.
Entrepreneurial growth aspirations in challenging environment: The role of institutional quality, human and social capital
Authors: Lajqi Saranda , Krasniqi Besnik A.
Published: July 2017

The role of formal and informal institutions is crucial in forming growth aspirations. Firms use their resources and personal network, trusting to overcome or compensate for inadequate informal institutions. Transition countries can unlock their growth potential by targeting entrepreneurs with high growth aspiration through policy measures (increasing their level of human capital through a higher quality of educational system, aligning formal and informal institutions, promoting well‐functioning and impartial courts). Entrepreneurs use the informal institutions to complement deficient or inadequate formal institutions. Firm size as an indicator of better access to resources moderates positively the effects of informal institution barriers by having a positive influence on growth aspiration. Training, networking, and trust have a positive effect on growth aspiration and entrepreneurs use these practices in response to institutional deficiencies (inadequate educational systems, inefficient courts and other formal institutions). Policy initiatives should consider small firms as being affected by formal institutions.
Linking strategic orientation with performance: Implication for Indian banks
Authors: Bapat Dhananjay
Published: July 2017

While cost orientation is found to be the major antecedent to perceived performance, innovation orientation moderates the relationship between both the competitive orientation and performance, and the customer orientation and performance. This article explores the relationship between strategy and performance in the context of the Indian banking sector. Cost orientation is identified as the major determinant for perceived performance. Innovation orientation moderates the relationship between both the competitive orientation and performance, and the customer orientation and performance. Banks need to reorient the marketing strategy to derive long‐term performance benefits, since too much focus on cost orientation may prevent existing banks adapting to the market.
In‐gel and OFFGEL‐based proteomic approach for authentication of meat species from minced meat and meat products
Authors: Naveena Basappa M , Jagadeesh Deepak S , Kamuni Veeranna , Muthukumar Muthupalani , Kulkarni Vinayak V , Kiran Mohan , Rapole Srikanth
Published: July 2017

BACKGROUND

Fraudulent mislabelling of processed meat products on a global scale that cannot be detected using conventional techniques necessitates sensitive, robust and accurate methods of meat authentication to ensure food safety and public health. In the present study, we developed an in‐gel (two‐dimensional gel electrophoresis, 2DE) and OFFGEL‐based proteomic method for authenticating raw and cooked water buffalo (Bubalus bubalis), sheep (Ovis aries) and goat (Caprus hircus) meat and their mixes.

RESULTS

The matrix‐assisted liquid desorption/ionization time‐of‐flight mass spectrometric analysis of proteins separated using 2DE or OFFGEL electrophoresis delineated species‐specific peptide biomarkers derived from myosin light chain 1 and 2 (MLC1 and MLC2) of buffalo–sheep–goat meat mix in definite proportions at 98:1:1, 99:0.5:0.5 and 99.8:0.1:0.1 that were found stable to resist thermal processing. In‐gel and OFFGEL‐based proteomic approaches are efficient in authenticating meat mixes spiked at minimum 1.0% and 0.1% levels, respectively, in triple meat mix for both raw and cooked samples.

CONCLUSIONS

The study demonstrated that authentication of meat from a complex mix of three closely related species requires identification of more than one species‐specific peptide due to close similarity between their amino acid sequences. © 2017 Society of Chemical Industry
Organic carbon patterns and budgets in the Long Island Sound estuary
Authors: Vlahos Penny , Whitney Michael M.
Published: July 2017

A multi‐year observational time series was evaluated across the 150 km central axis of the U.S. east coast's Long Island Sound (LIS) estuary, in three distinct regions. Fluxes were calculated at the boundaries of the regions using observations coupled to a hydrodynamic model and applied to a mass balance to assess organic carbon (OC) export from LIS. For all years, during stratified summer periods, LIS was a net exporter of OC to the continental shelf. LIS annual net carbon export however, varied with river flow. The heterotrophic or autotrophic nature of LIS also shifted inter‐annually. During the mass balance analysis period (2009–2012), LIS ranged between net OC import from the continental shelf and heterotrophy in the lowest river flow year (2012) and net export of OC and autotrophy in the highest flow year (2011). Analysis suggests that LIS switches from net OC import to export when the annual river inputs exceed 19 km3 yr−1. Applying these thresholds to the annual river flow record suggests that net import occurred in 15% of the last 20 years and that LIS usually is a net exporter of OC (85%). Annually averaged LIS carbon export values based on river flow conditions over the last 20 yr are estimated at 56 ± 64 × 106 kg yr−1. Analysis also suggests that LIS shifts from net heterotrophic to net autotrophic when annual river flow exceeds 26 km3 yr−1 (35% of the last 20 yr). Net heterotrophic conditions are most common, representing 65% of the last 20 yr.
Advancing Graduate Limnology Education Through Active Learning and Community Partnerships: A Pilot Program at the Large Lakes Observatory
Authors: Schreiner Kathryn M. , Katsev Sergei , Steinman Byron , Sterner Robert W. , Williams Julia , Zak Kevin
Published: July 2017

At the Large Lakes Observatory at the University of Minnesota Duluth (UMD), we are addressing issues with an outdated limnology graduate curriclum by designing a flipped‐classroom, interdisciplinary limnology course sequence that incorporates partnerships with industry, meaningful field and analytical work, and integrated skills learning for our graduate students. This new curriculum is co‐taught by four instructors with different research backgrounds and is meant to teach students with a wide range of undergraduate preparation without significant time spent on in‐class review, or leaving anyone behind. The courses, which include lecture and practice classes each semester in the graduate students' first year, are built around a course website, www.studywater.org, which will go public in fall of 2018. Funded by the National Science Foundation Division of Graduate Education, this pilot program will provide a new interdisciplinary curriculum applicable to graduate limnology programs and a public website with limnology modules designed to be searchable and open to the public. Here, we describe in detail our new course sequence, including curriculum, industry partnerships, and field work with the students; provide information on the challenges we faced in developing and teaching this course; and our advice for overcoming those challenges.
Enhanced Photoelectric and Photothermal Responses on Silicon Platform by Plasmonic Absorber and Omni‐Schottky Junction
Authors: Wen Long , Chen Yifu , Liu Wanwan , Su Qiang , Grant James , Qi Zhiyang , Wang Qilong , Chen Qin
Published: July 2017

Recent progresses in plasmon‐induced hot electrons open up the possibility to achieve photon harvesting beyond the fundamental limit imposed by band‐to‐band transitions in semiconductors. To obtain high efficiency, both the optical absorption and electron emission/collection are crucial factors that need to be addressed in the design of hot electron devices. Here, we demonstrate a photoresponse as high as 3.3mA/W at 1500nm on a silicon platform by plasmonic absorber (PA) and omni‐Schottky junction integrated photodetector, reverse biased at 5V and illuminated with 10mW. The PA fabricated on silicon consists of a monolayer of random Au nanoparticles (NPs), a wide‐band gap semiconductor (TiO2) and an optically thick Au electrode, resulting in broadband near‐infrared (NIR) absorption and efficient hot‐electron transfer via an all‐around Schottky emission path. Meanwhile, time and spectral‐resolved photoresponse measurements reveal that embedded NPs with superior absorption resembling plasmonic local heating sources can transfer their energy to electricity via the photothermal mechanism, which until now has not been adequately assessed or rigorously differentiated from the photoelectric process in plasmon‐mediated photon harvesting nano‐systems.
Brain tumor segmentation using holistically nested neural networks in MRI images
Authors: Zhuge Ying , Krauze Andra V. , Ning Holly , Cheng Jason Y. , Arora Barbara C. , Camphausen Kevin , Miller Robert W.
Published: July 2017

Purpose

Gliomas are rapidly progressive, neurologically devastating, largely fatal brain tumors. Magnetic resonance imaging (MRI) is a widely used technique employed in the diagnosis and management of gliomas in clinical practice. MRI is also the standard imaging modality used to delineate the brain tumor target as part of treatment planning for the administration of radiation therapy. Despite more than 20 yr of research and development, computational brain tumor segmentation in MRI images remains a challenging task. We are presenting a novel method of automatic image segmentation based on holistically nested neural networks that could be employed for brain tumor segmentation of MRI images.

Methods

Two preprocessing techniques were applied to MRI images. The N4ITK method was employed for correction of bias field distortion. A novel landmark‐based intensity normalization method was developed so that tissue types have a similar intensity scale in images of different subjects for the same MRI protocol. The holistically nested neural networks (HNN), which extend from the convolutional neural networks (CNN) with a deep supervision through an additional weighted‐fusion output layer, was trained to learn the multiscale and multilevel hierarchical appearance representation of the brain tumor in MRI images and was subsequently applied to produce a prediction map of the brain tumor on test images. Finally, the brain tumor was obtained through an optimum thresholding on the prediction map.

Results

The proposed method was evaluated on both the Multimodal Brain Tumor Image Segmentation (BRATS) Benchmark 2013 training datasets, and clinical data from our institute. A dice similarity coefficient (DSC) and sensitivity of 0.78 and 0.81 were achieved on 20 BRATS 2013 training datasets with high‐grade gliomas (HGG), based on a two‐fold cross‐validation. The HNN model built on the BRATS 2013 training data was applied to ten clinical datasets with HGG from a locally developed database. DSC and sensitivity of 0.83 and 0.85 were achieved. A quantitative comparison indicated that the proposed method outperforms the popular fully convolutional network (FCN) method. In terms of efficiency, the proposed method took around 10 h for training with 50,000 iterations, and approximately 30 s for testing of a typical MRI image in the BRATS 2013 dataset with a size of 160 × 216 × 176, using a DELL PRECISION workstation T7400, with an NVIDIA Tesla K20c GPU.

Conclusions

An effective brain tumor segmentation method for MRI images based on a HNN has been developed. The high level of accuracy and efficiency make this method practical in brain tumor segmentation. It may play a crucial role in both brain tumor diagnostic analysis and in the treatment planning of radiation therapy.
Impact of respiratory motion and acquisition settings on SPECT liver dosimetry for radioembolization
Authors: Bastiaannet Remco , Viergever Max A. , de Jong Hugo W. A. M.
Published: July 2017

Purpose

Respiratory motion may impose significant inaccuracies on emission activity estimation in quantitative SPECT. This effect may be a major issue in dosimetry as used in the management of liver radioembolization. The purpose of this study was to investigate the impact of respiratory motion on radioembolization liver dosimetry for different SPECT acquisition settings.

Methods

In a series of SPECT/CT Monte Carlo simulations using several digital XCAT phantoms, the following parameters were varied: breathing/nonbreathing, liver tumor size (0.3–35 ml) and location, patient properties (body mass index ranging from underweight to obese; male and female), acquisition time (10–30 s/view), collimator setup (High Sensitivity, High Resolution, Ultra High Resolution) and tumor VOI. The effect of applying a respiratory gating scheme was examined as well.

Results

Breathing decreased activity recovery and tumor/non‐tumor (T/N) ratios on average from 90% to 66%. VOIs based on SPECT images instead of breath‐hold CT improved T/N values significantly. The most accurate results were obtained using a gating scheme combined with SPECT‐based VOIs. Scan duration, body mass index, sex, and location all had a minor effect. Lung shunt fraction estimations were relatively unaffected by any of the varied parameters.

Conclusions

Respiratory motion has a large effect on SPECT activity quantitation of liver tumors as used in radioembolization treatment planning and assessment. As compared with the other parameters that were varied in this study, respiration is the predominant degrading effect on image quantitation. Gating alleviates much of this detrimental effect.
True constructive interference in the steady state (trueCISS)
Authors: Hilbert Tom , Nguyen Damien , Thiran Jean‐Philippe , Krueger Gunnar , Kober Tobias , Bieri Oliver
Published: July 2017

Purpose

To introduce a novel time‐efficient method, termed true constructive interference in the steady state (trueCISS), that not only solves the problem of banding artifacts for balanced steady‐state free precession (bSSFP) but also provides its genuine, that is, true, on‐resonant signal.

Methods

After a compressed sensing reconstruction from a set of highly undersampled phase‐cycled bSSFP scans, the local off‐resonance, relaxation time ratio, and equilibrium magnetization are voxel‐wise estimated using a dictionary‐based fitting routine. Subsequently, on‐resonant bSSFP images are generated using the previously estimated parameters. Due to the high undersampling factors used, the acquisition time is not prolonged with respect to a standard CISS acquisition.

Results

From a set of 16 phase‐cycled SSFP scans in combination with an eightfold undersampling, both phantom and in vivo whole‐brain experiments demonstrate that banding successfully can be removed. Additionally, trueCISS allows the derivation of synthetic bSSFP images with arbitrary flip angles, which enables image contrasts that may not be possible to acquire in practice due to safety constraints.

Conclusion

TrueCISS offers banding‐free bSSFP images with on‐resonant signal intensity and without requiring additional acquisition time compared to conventional methods. Magn Reson Med 79:1901–1910, 2018. © 2017 International Society for Magnetic Resonance in Medicine.
An algorithmically consistent macroscopic tangent operator for FFT‐based computational homogenization
Authors: Göküzüm Felix Selim , Keip Marc‐André
Published: July 2017

The present work addresses a multiscale framework for fast‐Fourier‐transform–based computational homogenization. The framework considers the scale bridging between microscopic and macroscopic scales. While the macroscopic problem is discretized with finite elements, the microscopic problems are solved by means of fast‐Fourier‐transforms (FFTs) on periodic representative volume elements (RVEs). In such multiscale scenario, the computation of theeffective propertiesof the microstructure is crucial. While effective quantities in terms of stresses and deformations can be computed from surface integrals along the boundary of the RVE, the computation of the associated moduli is not straightforward. The key contribution of the present paper is the derivation and implementation of analgorithmically consistent macroscopic tangent operatorwhich directly resembles the effective moduli of the microstructure. The macroscopic tangent is derived by means of the classical Lippmann‐Schwinger equation and can be computed from a simple system of linear equations. This is performed through an efficient FFT‐based approach along with a conjugate gradient solver. The viability and efficiency of the method is demonstrated for a number of two‐ and three‐dimensional boundary value problems incorporating linear and nonlinear elasticity as well as viscoelastic material response.
Exercise capacity is not decreased in children who have undergone lung resection early in life for congenital thoracic malformations compared to healthy age‐matched children
Authors: Dunn Ashlee , Pearce Kasey , Callister Robin , Collison Adam , Morten Matthew , Mandaliya Payal , Platt Lauren , Dascombe Ben , Kumar Rajendra , Selvadurai Hiran , Robinson Paul D. , Mattes Joerg
Published: July 2017

Purpose

The purpose of this study was to compare (i) the exercise capacity and (ii) lung function prior to and immediately post cardiopulmonary exercise tests (CPET) of children who underwent early life lung resection for Congenital Pulmonary Airway Malformations (CPAM) to healthy control children.

Method

Eight children with CPAM (four males, age 9.6 ± 1.8 years) and eight control children without respiratory disease (three males, age 9.4 ± 1.4 years) performed a CPET on a cycle ergometer, during which maximal oxygen consumption (V̇O2max) and heart rate were measured. Prior to and immediately post CPET, lung function measures including Nitrogen Multiple Breath Washout (MBW) and spirometry were performed.

Results

There were no significant between group differences in pre CPET lung function (P > 0.05) or maximal exercise capacity (V̇O2max CPAM: 39.4 mL.kg−1.min−1, Control: 40.5 mL.kg−1.min−1). Post CPET, FEV1 was significantly lower in the CPAM group, with two participants diagnosed subsequently with exercise induced bronchospasm based on post‐CPET spirometry and follow‐up clinical investigations.

Conclusion

Early life lung resection for CPAM does not appear to have negative implications for exercise capacity later in childhood. Clinicians should be aware that dyspnoea following exercise may be due to asthma rather than residual effects of CPAM in these children.
Non‐additive stabilization by halogenated amino acids reveals protein plasticity on a sub‐angstrom scale
Authors: Hosseini Azade S. , Pace Christopher J. , Esposito Adam A. , Gao Jianmin
Published: July 2017

It has been a long‐standing goal to understand the structure‐stability relationship of proteins, as optimal stability is essential for protein function and highly desirable for protein therapeutics. Halogenation has emerged as a minimally invasive strategy to probe the physical characteristics of proteins in solution, as well as enhance the structural stabilities of proteins for therapeutic applications. Although advances in synthetic chemistry and genetic code expansion have allowed for the rapid synthesis of proteins with diverse chemical sequences, much remains to be learned regarding the impact of these mutations on their structural integrity. In this contribution, we present a systematic study of three well‐folded model protein systems, in which their structural stabilities are assessed in response to various hydrogen‐to‐halogen atom mutations. Halogenation allows for the perturbation of proteins on a sub‐angstrom scale, offering unprecedented precision of protein engineering. The thermodynamic results from these model systems reveal that in certain cases, proteins can display modest steric tolerance to halogenation, yielding non‐additive consequences to protein stability. The observed sub‐angstrom sensitivity of protein stability highlights the delicate arrangement of a folded protein core structure. The stability data of various halogenated proteins presented herein should also provide guidelines for using halogenation as a strategy to improve the stability of protein therapeutics.
Evaluation of lumazine synthase from Bacillus anthracis as a presentation platform for polyvalent antigen display
Authors: Wei Yangjie , Wahome Newton , VanSlyke Greta , Whitaker Neal , Kumar Prashant , Barta Michael L. , Picking Wendy L. , Volkin David B. , Mantis Nicholas J. , Middaugh C. Russell
Published: July 2017

Polyvalent antigen display is an effective strategy to enhance the immunogenicity of subunit vaccines by clustering them in an array‐like manner on a scaffold system. This strategy results in a higher local density of antigens, increased high avidity interactions with B cells and other antigen presenting cells, and therefore a more effective presentation of vaccine antigens. In this study, we used lumazine synthase (LS), an icosahedral symmetry capsid derived from Bacillus anthracis, as a scaffold to present 60 copies of a linear B cell epitope (PB10) from the ricin toxin fused to the C terminus of LS via four different linkers. We then investigated the effects of linker length, linker rigidity and formaldehyde crosslinking on the protein assembly, conformational integrity, thermal stability, in vitro antibody binding, and immunogenicity in mice. Fusion of the PB10 peptide onto LS, with varying linker lengths, did not affect protein assembly, thermal stability or exposure of the epitope, but had a minor impact on protein conformation. Formaldehyde crosslinking considerably improved protein thermal stability with only minor impact on protein conformation. All LS_PB10 constructs, when administered to mice by injection without adjuvant, elicited measurable anti‐ricin serum IgG titers, although the titers were not sufficient to confer protection against a 10× lethal dose ricin challenge. This work sheds light on the biophysical properties, immunogenicity and potential feasibility of LS from B. anthracis as a scaffold system for polyvalent antigen display.
Quantized sliding mode control in delta operator framework
Authors: Zheng Bo‐Chao , Yu Xinghuo , Xue Yanmei
Published: July 2017

This paper is concerned with quantized sliding mode control in the unified delta operator system framework. To solve the quantization measurement saturating problem, a dynamic quantization strategy including discrete on‐line open‐loop zooming‐out and closed‐loop zooming‐in policies is presented. By analyzing the sign relation between the traditional linear switching function and the quantized linear switching function, a novel quantized sliding mode control method is proposed, and both the amplitude of the control gain and the value of the quantization measurement saturating parameter are reduced compared with previous results. Some simulation results are presented to verify the effectiveness of the proposed method.
The fabrication of layer‐by‐layer mode LaCoO3 film by pulsed laser deposition
Authors: Liu Yue , Ma Kai , Yu Yanlong
Published: July 2017

The relationship between strain and growth conditions in LaCoO3 thin film was obtained to control the magnetic‐electric characteristics. The LaCoO3 thin films on the SrTiO3 substrates have been achieved by the pulsed laser deposition method, and the reflection high‐energy electron diffraction method (RHEED) was applied to monitor the growth process in situ; the layer‐by‐layer growth mode was discovered. The X‐ray diffraction and atomic force microscopy were applied to the phase analysis, and the layer thickness and the layer‐by‐layer growth mode were uncovered. Compared with the 100‐nm LaCoO3 thin films, the strain in the layer‐by‐layer ultra thin film was more controllable. The enhanced magnetic properties of the layer‐by‐layer mode ultra‐thin films could be tested in future work.
Chiral Copper(0) Nanoparticles: Direct Synthesis and Interfacial Chiral Induction via Phase Transfer of Copper Nanoparticles
Authors: Imanaka Yu , Nakahodo Tsukasa , Fujihara Hisashi
Published: July 2017

No clear‐cut example has been hitherto known for the phase transfer involving the ligand exchange of copper nanoparticles (NPs) from an aqueous phase into an organic phase, and chiral copper NPs. We present the first isolation of chiral copper(0) NPs prepared by either the reduction of copper ions with hydrazine in the presence of a new chiral binaphthyl carboxylic acid 1 as a protective ligand in an organic solvent or the two‐phase transfer involving the chiral ligand exchange of the polyvinyl pyrrolidone‐protected copper NPs from the water phase to organic phase in the presence of the chiral protective ligand 1. This is the first example for the asymmetric (chiral) induction on the surface of the copper NPs by two‐phase transfer of the achiral copper NPs.