bluuebunny/crossref_metadata_2025_split huggingface dataset:
The transcriptome of the veiled chameleon (Chamaeleo calyptratus): A resource for studying the evolution and development of vertebrates
Authors: Pinto Brendan J. , Card Daren C. , Castoe Todd A. , Diaz Raul E. , Nielsen Stuart V. , Trainor Paul A. , Gamble Tony 
Published: March 2019

AbstractPurposeThe veiled chameleon (Chamaeleo calyptratus) is an emerging model system for studying functional morphology and evolutionary developmental biology (evo‐devo). Chameleons possess body plans that are highly adapted to an arboreal life style, featuring laterally compressed bodies, split hands/ft for grasping, a projectile tongue, turreted independently moving eyes, and a prehensile tail. Despite being one of the most phenotypically divergent clades of tetrapods, genomic resources for chameleons are severely lacking.MethodsTo address this lack of resources, we used RNAseq to generate 288 million raw Illumina sequence reads from four adult tissues (male and female eyes and gonads) and whole embryos at three distinct developmental stages. We used these data to assemble a largely complete de novo transcriptome consisting of only 82 952 transcripts. In addition, a majority of assembled transcripts (67%) were successfully annotated.ResultsWe then demonstrated the utility of these data in the context of studying visual system evolution by examining the content of veiled chameleon opsin genes to show that chameleons possess all five ancestral tetrapod opsins.ConclusionWe present this de novo, annotated, multi‐tissue transcriptome assembly for the Veiled Chameleon, Chamaeleo calyptratus, as a resource to address a range of evolutionary and developmental questions. The associated raw reads and final annotated transcriptome assembly are freely available for use on NCBI and Figshare, respectively.
The past and future roles of competition and habitat in the range‐wide occupancy dynamics of Northern Spotted Owls
Authors: Yackulic Charles B. , Bailey Larissa L. , Dugger Katie M. , Davis Raymond J. , Franklin Alan B. , Forsman Eric D. , Ackers Steven H. , Andrews Lawrence S. , Diller Lowell V. , Gremel Scott A. , Hamm Keith A. , Herter Dale R. , Higley J. Mark , Horn Rob B. , McCafferty Christopher , Reid Janice A. , Rockweit Jeremy T. , Sovern Stan G. 
Published: March 2019

AbstractSlow ecological processes challenge conservation. Short‐term variability can obscure the importance of slower processes that may ultimately determine the state of a system. Furthermore, management actions with slow responses can be hard to justify. One response to slow processes is to explicitly concentrate analysis on state dynamics. Here, we focus on identifying drivers of Northern Spotted Owl (Strix occidentalis caurina) territorial occupancy dynamics across 11 study areas spanning their geographic range and forecasting response to potential management actions. Competition with Barred Owls (Strix varia) has increased Spotted Owl territory extinction probabilities across all study areas and driven recent declines in Spotted Owl populations. Without management intervention, the Northern Spotted Owl subspecies will be extirpated from parts of its current range within decades. In the short term, Barred Owl removal can be effective. Over longer time spans, however, maintaining or improving habitat conditions can help promote the persistence of northern spotted owl populations. In most study areas, habitat effects on expected Northern Spotted Owl territorial occupancy are actually greater than the effects of competition from Barred Owls. This study suggests how intensive management actions (removal of a competitor) with rapid results can complement a slower management action (i.e., promoting forest succession).
Occupancy dynamics of semi‐aquatic herbivores in riparian systems in Illinois, USA
Authors: Holland Angela M. , Schauber Eric M. , Nielsen Clayton K. , Hellgren Eric C. 
Published: March 2019

AbstractStreams and local riparian habitats are a product of the landscapes they drain. Consequently, aspects of the landscape, as well as local stream morphology, are likely to affect riparian and stream communities, including occupancy of semi‐aquatic mammals. To gain a better understanding of how changing landscapes may affect the occupancy of semi‐aquatic mammals, we sought to identify aspects of the riparian system and stream structure at multiple scales that relate to the presence of beaver (Castor canadensis) and muskrat (Ondatra zibethicus), including their interactions with mink (Neovison vison) and river otter (Lontra canadensis). We estimated multi‐season occupancy using 103 sites sampled over six seasons (2012–2014) in southern Illinois, USA. We hypothesized beaver and muskrat occupancy was related to multiple aspects of landscape and local habitat including land‐cover, water availability, human disturbance, stream characteristics, and the presence of other semi‐aquatic mammals. Beaver occupancy varied over time and was predicted by stream size, stream density, and land‐cover at the landscape scale. Muskrat occupancy also varied over time and was related to local aspects of habitat including percentage of forest in the riparian area, channel incision, land‐cover, and aspects of sediment chemistry. Our results indicate the importance of spatial and temporal variation, scale, and food and water availability for these semi‐aquatic species. Beaver and muskrat are most likely to be affected by changes to water regimes including availability of permanent water sources due to changing landscapes.
Spatial simulation of redistribution of fishing effort in Nigerian coastal waters using Ecospace
Authors: Adebola Tunde , de Mutsert Kim 
Published: March 2019

AbstractIn the late 1990s, depletion of the target species Penaeus notialis (Pink Shrimp) in deeper waters (50 m) of the Nigerian coast resulted in a change of target species from P. notialis (Pink Shrimp) to shallower water species such as Penaeus monodon (Brown Shrimp). This study investigates the hypothesis that ecosystem impacts increased as industrial fleets increased fishing in shallower areas of the Nigerian coast by comparing the state of the ecosystem before and 20 yr after commercial shrimping commenced in Nigerian coastal waters (NCW). Two fishing scenarios were developed in Ecospace, the spatial modeling module of Ecopath with Ecosim software (Ecopath with Ecosim is a mass balanced trophic model that accounts for fishing impacts on food webs), with one having trawlers fishing everywhere beginning at the turn of the century (year 2000) and the other with no trawling in the first 5 nautical miles off the Nigerian coast through the entire period of model simulation (1985–2004). Modeling results showed increases in catch for some fisheries during the study period. In addition, estimated biomass for some functional groups increased especially for Small Pelagic fishes along with Rays, Reef fishes, Large Pelagics, and shallow water shrimps. All other exploited species in our modeling scenarios were estimated to have declining biomasses. Our expectation that redistribution of fishing effort in NCW will increase negative impacts of fishing the nearshore ecosystem was not supported by model results. This counterintuitive result may be because fishing effort on average was mostly distributed in the deeper areas of the inshore waters. Although specie such as Reef fishes appear to benefit from closure of the first 5 NM to fishing, the benefits appear to be negligible. We present the first ecosystem model developed for NCW, and our research contributes to fisheries ecology by furthering understanding of tropical coastal food webs and ecological response to fishing, especially in highly perturbed ecosystems like NCW.
Comparison of GC–MS and MEKC methods for caffeine determination in preworkout supplements
Authors: Waraksa Emilia , Pokrywka Andrzej , Konop Marek , Namieśnik Jacek , Kłodzińska Ewa 
Published: March 2019

AbstractIn this study, GC–MS‐ and MEKC‐based methods for determination of caffeine (CAF) in preworkout supplements were developed and validated. The proposed protocols utilized minimal sample preparation (simple dilution and syringe filtration). The developed methods achieved satisfactory validation parameters, i.e. good linearity (R2 > 0.9988 and R2 > 0.9985 for GC–MS‐ and MEKC‐based method, respectively), satisfactory intra‐ and interaccuracy (within 92.6–100.7% for method utilizing GC–MS and 92.1–110.3% for protocol based on MEKC) and precision (CV < 15.9% and CV < 6.3% for GC–MS‐ and MEKC‐based method, respectively) and recovery (within 100.1–100.8% for method utilizing GC–MS and 101.5–106.2% for protocol based on MEKC). The LOD was 0.03 and 3 μg/mL for method utilizing GC–MS and MEKC, respectively. The CAF concentrations determined by GC–MS‐ and MEKC‐based methods were found to be in the range of 8.53–11.23 and 8.20–11.61 μg/mL, respectively. Taking into consideration information on the labels, the investigated supplements were found to contain from 110.0 to 167.3% of the declared CAF content, which confirmed the literature reports on incompatibility of the declared product compositions with real ones. Nevertheless, the consumption of examined supplements as recommended by producers did not lead to exceeding the CAF safe limit of 400 mg per day. Additionally, the MEKC‐based method allowed for detection and identification of vitamin B3 and B6 in all of the investigated supplement samples, which demonstrated that MEKC‐based protocols may be an appropriate assays for simultaneous determination of CAF and vitamins.
An improved packing equivalent circuit modeling method with the cell‐to‐cell consistency state evaluation of the internal connected lithium‐ion batteries
Authors: Wang Shun‐Li , Shi Jian‐You , Fernandez Carlos , Zou Chuan‐Yun , Bai De‐Kui , Li Jian‐Chao 
Published: March 2019

AbstractThe existing equivalent modeling methods reported in literature focuses mainly on the battery cells and do not take the packing consistency state into consideration, which exists on the internal connected cells of the lithium‐ion battery pack. An improved equivalent circuit model is constructed and reported in this manuscript for the first time, which can be used to characterize the working characteristics of the packing lithium‐ion batteries. A new equilibrium concept named as state of balance is proposed as well as the calculation process, which is realized by considering the real‐time detected internal battery cell voltages. In addition, this new equilibrium concept aims to obtain more information on the real‐time consistency characterization of the battery pack. The improved adaptive equivalent circuit model is investigated by using the improved splice modeling method, in which the statistical noise properties are corrected and the additional parallel resistance‐capacitance circuit is introduced. The parameter correction treatment is carried out by comparing the estimated and experimental detected closed circuit voltages. Furthermore, the tracking error is found to be 0.005 V and accounts for 0.119% of the nominal battery voltage. By taking the packing consistency state and temperature correction into consideration, the accurate working characteristic expression is realized in the improved equivalent circuit modeling process. Finally, the model proposed in this manuscript presents a great number of advantages compared to other methods reported so far, like has the high accuracy, and the ability to protect the security of the lithium‐ion battery pack in the power supply application.
Evaluation and research needs for seismically isolating nuclear power plants
Authors: Zhou Zhiguang , Hu Xiaorong , Wong Jenna , Xue Songtao 
Published: March 2019

AbstractThe main focus of this paper was to examine some of the principal advantages and disadvantages cited for the application of seismic isolation to nuclear power facilities. This discussion is followed by an examination of the potential relative impacts on cost and schedule of a conventional fixed‐base design approach vs one based on seismic isolation. This examination considers issues associated with planning, design, operation, and decommission. Some of the challenges related to design and maintenance (during normal operations and following a significant earthquake) are then discussed, and specific research and development topics are identified that are necessary to allow seismic isolation to be pursued with confidence. Finally, overall conclusions and recommendations are offered.
The development of low‐calorie sugar and functional jujube food using biological transformation and fermentation coupling technology
Authors: Men Yan , Zhu Ping , Zhu Yueming , Zeng Yan , Yang Jiangang , Sun Yuanxia 
Published: March 2019

AbstractJujube juice has been used as ingredient in a range of foods and dietary supplements. In this study, an enzyme transformation and fermentation coupling technology was applied to increase the nutritional value of concentrated/extracted Jinsi jujube juice. Two enzymes, D‐glucose isomerase (GI) and D‐allulose 3‐epimerase (DAE), were employed to convert the glucose and fructose to a low‐calorie sweeter D‐allulose with a concentration of 110 g/L in jujube juice. Furthermore, the mixed cultures of Pediococcus pentosaceus PC‐5 and Lactobacillus plantarum M were employed to increase the content of nutrition components related to bioactivities and flavor volatiles in jujube juice. Accordingly, this fermentation accumulated 100 mg/L gamma‐aminobutyric acid (GABA), which has neurotransmission, hypotension, diuretic, and tranquilizer effects, and increased the content of branched‐chain amino acids (BCAAs) and many free amino acids (Asp, Glu, Gly, and Ala) at different level. The fermentation not only maintained the concentration of native functional components such as cyclic adenosine monophosphate (cAMP) and minerals, but also increased the content of iron (Fe2+) and zinc (Zn2+), which have blood and eyesight tonic function. The value‐added jujube juice might serve as a low‐calorie and probiotic functional beverage and show high application potential in food industry.
Preoperative serum VEGF‐C but not VEGF‐A level is correlated with lateral neck metastasis in papillary thyroid carcinoma
Authors: Jang Jeon Yeob , Kim Deok‐Soo , Park Hee‐Young , Shin Sung‐Chan , Cha Wonjae , Lee Jin‐Choon , Wang Soo‐Geun , Lee Byung‐Joo 
Published: March 2019

AbstractBackgroundThis study aimed to investigate the relationships between serum vascular endothelial growth factor (VEGF)‐A or VEGF‐C levels and lymph node metastasis (LNM) status in patients with papillary thyroid carcinoma (PTC).MethodsThe study enrolled 150 patients with pathologically proven PTC who underwent surgery: PTC without LNM, PTC with central neck metastasis, and PTC with lateral neck metastasis.ResultsPreoperative serum VEGF‐A levels were 300.12 ± 80.80 pg/mL overall and were not correlated with the presence of LNM. Preoperative serum VEGF‐C levels were 132.41 ± 48.48 pg/mL overall and were significantly correlated with the presence of LNM. Serum VEGF‐C levels were further increased in patients with lateral neck metastasis and positively correlated with the number of metastatic LNs (rho = 0.252, P = 0.002). Serum VEGF‐C, but not VEGF‐A, was identified as a significant predictor of lateral neck metastasis.ConclusionSerum VEGF‐C might be a clinically relevant biomarker of lateral neck metastasis in patients with PTC.
A gene signature associated with prognosis and immune processes in head and neck squamous cell carcinoma
Authors: Bai Shuang , Zhang Ping , Zhang Jian‐Cheng , Shen Jun , Xiang Xu , Yan Ying‐Bin , Xu Zhen‐Qi , Zhang Jun , Long Li , Wang Chao , Shi Ping , Yang Li , Chen Wei , Liu Hao 
Published: March 2019

AbstractBackgroundHead and neck squamous cell carcinoma (HNSCC) has a poor prognosis that has not significantly improved in the past several decades. A prognostic‐related signature was needed.MethodsThe Cancer Genome Atlas and GSE41613 databases were downloaded as a training and validation set, respectively. We identified 12 genes that demonstrated progression and prognostic value, and then, a gene signature was constructed.ResultsThis classification could reflect distinct characteristics, phenotypically and molecularly, among HNSCC tumors. It could stratify patients with significantly different survival rates (median survival: 2083 days vs 927 days; P = 3.85E‐08) in the training cohort and validation cohort (P = 0.007) and was significantly involved in immune/inflammatory response and tumor progression processes.ConclusionsThis bioinformatics‐based signature suggested the presence of two distinct populations of patients with HNSCC with distinguishable phenotypic characteristics and clinical outcomes and might provide insight for new types of immune therapy.
The Milan System for Reporting Salivary Gland Cytopathology—Proposed modifications to improve clinical utility
Authors: Mazzola Francesco , Gupta Ruta , Luk Peter P. , Palme Carsten , Clark Jonathan R. , Low Tsu‐Hui (Hubert) 
Published: March 2019

AbstractBackgroundFine‐needle aspiration of a salivary gland lesion is a well‐established diagnostic procedure that aids management decisions. Recently, the Milan System for Reporting Salivary Gland Cytopathology (MSRSGC) classification has been proposed in order to improve the reproducibility and communication in the management of salivary gland lesions.MethodsA total of 375 patient's cytological reports collected between January 2010 and December 2017 were reviewed and reclassified according to MSRSGC and a risk of malignancy was calculated for each of the category.ResultsThe rate of malignancy in MSRSGC classification was 19.0%, 11.8%, 25.0%, 5.5%, 50.0%, 71.4%, and 94.6% for each of the category (I, II, III, IVa, IVb, V, and VI), respectively.ConclusionThe MSRSGC classification is a valuable tool in everyday practice. The modified version of MSRSGC aims to improve the surgical relevance and facilitate uniform management.
Incidence trends for upper aerodigestive tract cancers in rural United States counties
Authors: Pagedar Nitin A. , Kahl Amanda R. , Tasche Kendall K. , Seaman Aaron T. , Christensen Alan J. , Howren M. Bryant , Charlton Mary E. 
Published: March 2019

AbstractBackgroundRecent declines in cancer incidence and mortality have not been distributed equally across the United States. Factors such as tobacco cessation and human papillomavirus presence might differentially affect urban and rural portions of the country.MethodsWe used the Surveillance, Epidemiology, and End Results database to assess cancer incidence rates and trends from 1973 to 2015. We compared incidence rates for oral cavity, oropharynx, and larynx cancer in urban and rural counties and identified trends using Joinpoint software.ResultsIncidence of larynx and oral cavity cancer are decreasing faster in urban areas than in rural areas, while incidence of oropharynx cancer is increasing faster in rural areas than urban areas.ConclusionsRelative trends in incidence of larynx, oral cavity, and oropharynx cancer over the past 40 years are unfavorable for rural United States counties compared with urban areas. Cancer control programs should take this into account.
Aberrant expression of serum circANRIL and hsa_circ_0123996 in children with Kawasaki disease
Authors: Wu Junhua , Zhou Qianqin , Niu Yadan , Chen Jiayi , Zhu Yingchao , Ye Shazhou , Xi Yang , Wang Fuyan , Qiu Haiyan , Bu Shizhong 
Published: March 2019

BackgroundKawasaki disease is a childhood systemic vasculitis that causes coronary artery abnormalities. The etiology remains unknown and there are no specific diagnostic tests. Circular non‐coding RNAs are a special class of endogenous RNAs that display some characteristics of an ideal biomarker. However, few studies have examined the expression of circRNAs in the serum of Kawasaki disease (KD) patients. The aim of this study was to identify circRNAs in the serum that can serve as potential biomarkers for KD diagnosis.MethodsThe cases were children diagnosed with KD (n = 56). The controls comprised healthy children (n = 56). Blood was collected from the patients before and after intravenous immunoglobulin therapy, and from the healthy controls. Levels of circANRIL and hsa_circ_0123996 in the serum were measured by quantitative reverse transcription PCR. Then, the potential relationship between serum circRNA levels and patients’ biochemical parameter levels was investigated. Receiver operating characteristic curves were constructed for evaluating the diagnostic value of these circRNAs.ResultsThe serum levels of circANRIL were lower in patients with KD before therapy than in the controls, but became higher in the patients after therapy than before therapy. The serum levels of hsa_circ_0123996 were higher in patients with KD before therapy than in healthy controls.ConclusionOur study indicated that the circANRIL and hsa_circ_0123996 levels in the serum of patients with KD were significantly different from those in healthy individuals. circANRIL and hsa_circ_0123996 may become potential biomarkers for early KD diagnosis.
Neural network sliding mode controller of atomic force microscope‐based manipulation with different cantilever probes
Authors: Korayem Moharram H. , Esmaeilzadehha Soliman 
Published: March 2019

AbstractDevelopment of nanotechnology has given rise to various applications, including the nano‐manipulation process within small‐size environments. The implementation of such processes requires the use of tools and proper equipment and understanding of various factors influencing it. One such tool is the atomic force microscope (AFM) and its probe, used for imaging surfaces and manipulation tools. The AFM probe is the most important element of the AFM with a key role in system function. The dynamic analysis and control of AFM are necessary to increase efficiency. In this paper, a model of AFM is reviewed and rewritten by considering various cantilever probes, including rectangular, V‐shaped, and dagger. The AFM actuator was modeled and analyzed on uncertain conditions. The position of the stage was controlled to the desired position through the desired motion profiles. To overcome the problem of model nonlinearity, a neural network (NN) sliding mode controller was used to optimize the controller parameter and provide the desired output. The simulation of system was performed by the effective parameters, its control was implemented, and the results were analyzed. The simulation revealed that the modified sliding mode controller with learnable NN improved controller performance by decreasing the rise time and eliminating the overshot.