bluuebunny/crossref_metadata_2025_split huggingface dataset:
miPrimer: an empirical-based qPCR primer design method for small noncoding microRNA
Authors: Kang Shih-Ting , Hsieh Yi-Shan , Feng Chi-Ting , Chen Yu-Ting , Yang Pok Eric , Chen Wei-Ming 
Published: December 2017

MicroRNAs (miRNAs) are 18–25 nucleotides (nt) of highly conserved, noncoding RNAs involved in gene regulation. Because of miRNAs’ short length, the design of miRNA primers for PCR amplification remains a significant challenge. Adding to the challenge are miRNAs similar in sequence and miRNA family members that often only differ in sequences by 1 nt. Here, we describe a novel empirical-based method, miPrimer, which greatly reduces primer dimerization and increases primer specificity by factoring various intrinsic primer properties and employing four primer design strategies. The resulting primer pairs displayed an acceptable qPCR efficiency of between 90% and 110%. When tested on miRNA families, miPrimer-designed primers are capable of discriminating among members of miRNA families, as validated by qPCR assays using Quark Biosciences’ platform. Of the 120 miRNA primer pairs tested, 95.6% and 93.3% were successful in amplifying specifically non-family and family miRNA members, respectively, after only one design trial. In summary, miPrimer provides a cost-effective and valuable tool for designing miRNA primers.
Developing data interoperability using standards: A wheat community use case
Authors: Dzale Yeumo Esther , Alaux Michael , Arnaud Elizabeth , Aubin Sophie , Baumann Ute , Buche Patrice , Cooper Laurel , Ćwiek-Kupczyńska Hanna , Davey Robert P. , Fulss Richard Allan , Jonquet Clement , Laporte Marie-Angélique , Larmande Pierre , Pommier Cyril , Protonotarios Vassilis , Reverte Carmen , Shrestha Rosemary , Subirats Imma , Venkatesan Aravind , Whan Alex , Quesneville Hadi 
Published: December 2017

In this article, we present a joint effort of the wheat research community, along with data and ontology experts, to develop wheat data interoperability guidelines. Interoperability is the ability of two or more systems and devices to cooperate and exchange data, and interpret that shared information. Interoperability is a growing concern to the wheat scientific community, and agriculture in general, as the need to interpret the deluge of data obtained through high-throughput technologies grows. Agreeing on common data formats, metadata, and vocabulary standards is an important step to obtain the required data interoperability level in order to add value by encouraging data sharing, and subsequently facilitate the extraction of new information from existing and new datasets. During a period of more than 18 months, the RDA Wheat Data Interoperability Working Group (WDI-WG) surveyed the wheat research community about the use of data standards, then discussed and selected a set of recommendations based on consensual criteria. The recommendations promote standards for data types identified by the wheat research community as the most important for the coming years: nucleotide sequence variants, genome annotations, phenotypes, germplasm data, gene expression experiments, and physical maps. For each of these data types, the guidelines recommend best practices in terms of use of data formats, metadata standards and ontologies. In addition to the best practices, the guidelines provide examples of tools and implementations that are likely to facilitate the adoption of the recommendations. To maximize the adoption of the recommendations, the WDI-WG used a community-driven approach that involved the wheat research community from the start, took into account their needs and practices, and provided them with a framework to keep the recommendations up to date. We also report this approach’s potential to be generalizable to other (agricultural) domains.
Scaling Limit of a Limit Order Book Model via the Regenerative Characterization of Lévy Trees
Authors: Lakner Peter , Reed Josh , Simatos Florian 
Published: December 2017

We consider the following Markovian dynamic on point processes: at constant rate and with equal probability, either the rightmost atom of the current configuration is removed, or a new atom is added at a random distance from the rightmost atom. Interpreting atoms as limit buy orders, this process was introduced by Lakner et al. [Lakner et al. (2016) High frequency asymptotics for the limit order book. Mark. Microstructure Liq. 2:1650004 [83 pages]] to model a one-sided limit order book. We consider this model in the regime where the total number of orders converges to a reflected Brownian motion, and complement the results of Lakner et al. [Lakner P, Reed J, Stoikov S (2016) High frequency asymptotics for the limit order book. Mark. Microstructure Liq. 2:1650004 [83 pages]] by showing that, in the case where the mean displacement at which a new order is added is positive, the measure-valued process describing the whole limit order book converges to a simple functional of this reflected Brownian motion. Our results make it possible to derive useful and explicit approximations on various quantities of interest such as the depth or the total value of the book. Our approach leverages an unexpected connection with Lévy trees. More precisely, the cornerstone of our approach is the regenerative characterization of Lévy trees due to Weill [Weill M (2007) Regenerative real trees. Ann. Probab. 35:2091–2121. MR2353384 (2008j:60205)], which provides an elegant proof strategy which we unfold.
Prognostic factors for the outcome of extracorporeal shockwave therapy for calcific tendinitis of the shoulder
Authors: Chou W-Y. , Wang C-J. , Wu K-T. , Yang Y-J. , Ko J-Y. , Siu K-K. 
Published: December 2017

AimsWe conducted a study to identify factors that are prognostic of the outcome of extracorporeal shockwave therapy (ESWT) for calcific tendinitis of the shoulder.Patients and MethodsSince 1998, patients with symptomatic calcific tendinitis of the rotator cuff have been treated with ESWT using an electrohydraulic mode shockwave device. One year after ESWT, patients were grouped according to the level of resorption of calcification.ResultsOf 241 symptomatic shoulders, complete resorption (CR) of calcification occurred in 134 (CR group). The remaining 107 shoulders had incomplete resorption (ICR) (ICR group). Gartner type I calcification was most common (64.5%) in the ICR group. The mean duration of symptoms before ESWT was significantly longer in the ICR group. Overall, 81% of the CR group and 23.4% of the ICR group were symptom free. There was a strong relationship between subsidence of symptoms and remission of calcification. Poor prognosis was significantly related to Gartner type I calcification, calcification extent > 15 mm and duration of symptoms > 11 months.ConclusionPatients with calcific tendinitis of the shoulder who have the factors identified for a poor outcome after ESWT should undergo a different procedure. Cite this article: Bone Joint J 2017;99-B:1643–50.
[RETRACTED] Comparative study on the effectiveness of a corticosteroid injection for carpal tunnel syndrome in patients with and without Raynaud’s phenomenon
Authors: Roh Y. H. , Noh J. H. , Gong H. S. , Baek G. H. 
Published: December 2017

Aims The aim of this study was to compare the efficacy of a corticosteroid injection for the treatment of carpal tunnel syndrome (CTS) in patients with and without Raynaud’s phenomenon. Patients and Methods In a prospective study, 139 patients with CTS were treated with a corticosteroid injection (10 mg triamcinolone acetonide); 34 had Raynaud’s phenomenon and 105 did not (control group). Grip strength, perception of touch with a Semmes-Weinstein monofilament and the Boston Carpal Tunnel Questionnaires (BCTQ) were assessed at baseline and at six, 12 and 24 weeks after the injection. The Cold Intolerance Severity Score (CISS) questionnaire was also assessed at baseline and 24 weeks after the injection. Results The two groups had similar baseline BCTQ scores, but the scores in the Raynaud’s phenomenon group were significantly higher than those in the control group at 12 and 24 weeks after the injection. Throughout the 24-week follow-up, there were no significant differences in the mean grip strength between the groups, whereas the mean Semmes-Weinstein monofilament sensory index for the control group was significantly higher than that of the Raynaud’s phenomenon group. The mean CISSs were not significantly different between the groups at baseline and at 24 weeks. After 24 weeks, 11 patients (32%) in the Raynaud’s phenomenon group and 16 (15%) in the control group required carpal tunnel decompression (p = 0.028). Multivariable analysis indicated that concurrent Raynaud’s phenomenon (odds ratio (OR) 2.6) and severe electrophysiological grade (OR 2.1) were independently associated with a failure of treatment after a corticosteroid injection. Conclusion Although considerable improvements in symptoms will probably occur in patients with Raynaud’s phenomenon who have CTS, they have higher risk of poor functional outcomes and failure of treatment than those without Raynaud’s phenomenon. Cite this article: Bone Joint J 2017;99-B:1637-1642.
Exploring Security Issues and Solutions in Cloud Computing Services – A Survey
Authors: Kumar P. Ravi , Raj P. Herbert , Jelciana P. 
Published: December 2017

Abstract
Cloud computing is emerging as one of the powerful computing technologies in the field of Information Technology due to its flexibility and cost reduction. This paper provides a detailed survey on security issues of the services provided by cloud computing and solutions to mitigate them. The main objective of this paper is to empower a new researcher to figure out the concepts of cloud computing, the services provided by them, and the security issues in the services. It also provides solutions to avoid or mitigate the different security issues which occur in the services provided by cloud computing. Additionally, it provides insight into the cloud computing model proposed by the National Institute of Standards and Technology (NIST), data stages and data security basics in a multi-tenant environment. This paper explores the different security methods proposed by different researchers and analyzes them.
Application of Genetic Algorithm Based Intuitionistic Fuzzy k-Mode for Clustering Categorical Data
Authors: Goyal Akarsh , Sourav Patra Anupam , Kalyanaraman P. 
Published: December 2017

Abstract
In present times a great number of clustering algorithms are available which group objects having similar features. But most of the datasets have data values that are categorical, which makes it difficult to implement these algorithms. The concept of genetic algorithm on intuitionistic fuzzy k-Mode method is proposed in the paper to cluster categorical data. This model is an extension of intuitionistic fuzzy k-Mode in which the notion of fitness related objective functions, crossovers, mutations and probability has been added to provide better clusters for the data objects. Also the intuitionistic parameter has been retained for the calculation of membership values of element x in a given cluster. UCI repository datasets were used for assessing efficacy of algorithms. The qualified analysis and results depict much consistent performance, where a significant improvement is achieved as compared to intuitionistic fuzzy k-Mode and simulated annealing based intuitionistic fuzzy k-mode. Genetic Algorithm based intuitionistic fuzzy k-Mode is very efficient when clustering is applied on large datasets that are categorical in nature, which proves to be very critical for data mining processes.
Real-Time Thermal Mapping for Heat & Cool Archipelagos of Bengaluru, India
Authors: Gopinath Rajesh , Banerjee Aditya , Sachin S. , Tiwari Prakhar , Wilson Sunny 
Published: December 2017

AbstractBlessed with a salubrious climate, the city of Bengaluru over the past few decades has constantly witnessed thermal discomfort owing to several Urban Heat islands that have mushroomed within the city. The subsequent increase in builtup area, consequent loss of productive agricultural lands/green zones, encroachment of surface water bodies coupled with the ill-preparedness of decision makers to handle the demand for land have invariably crumbled the natural micro-climate of the city. In this present research, an attempt has been made to detect the distribution of Urban Heat Islands in Bengaluru City by conducting real-time survey at 100 observatories marked across the entire urban & rural locations; with thermohygrometers as per the W.M.O. guidelines. The study confirmed the violation of the Human Thermal Comfort Range in 9, 83, 98, 99, 98 and 80 observatories for the monitoring at 6 AM, 9 AM, 12 PM, 3 PM, 6 PM and 9 PM respectively.
Ramp - Metering Algorithms Evaluated within Simplified Conditions
Authors: Janota Aleš , Holečko Peter , Gregor Michal , Hruboš Marián 
Published: December 2017

Abstract
Freeway networks reach their limits, since it is usually impossible to increase traffic volumes by indefinitely extending transport infrastructure through adding new traffic lanes. One of the possible solutions is to use advanced intelligent transport systems, particularly ramp metering systems. The paper shows how two particular algorithms of local and traffic-responsive control (Zone, ALINEA) can be adapted to simplified conditions corresponding to Slovak freeways. Both control strategies are modelled and simulated using PTV Vissim software, including the module VisVAP. Presented results demonstrate the properties of both control strategies, which are compared mutually as well as with the initial situation in which no control strategy is applied
An Accuracy Problem of the Fwd Time History with Regard to the Application of the Sasw Method
Authors: Komačka Jozef 
Published: December 2017

Abstract
A Falling Weight Deflectometer (FWD) represents one group of the devices used for diagnostics of pavement bearing capacity. Usually, the FWD dynamic load is substituted by a static load in the evaluation process to determine the equivalent modulus of a pavement structure or modulus of pavement layers. However, the data recorded during a bearing capacity test by FWD can be used to reveal the propagation of a dynamic impulse generated by FWD. It gives a possibility to use them in an evaluation method based on the propagation of waves generated by dynamic impulse. Therefore, the FWD time history data was assessed with regard to possible using in the method of the Spectral Analysis of Surface Waves. Basically, the possibility to determine the velocity of a generated surface wave was evaluated. It was found out the same deflection values exist at consecutive time intervals in the relevant part of the time history data (the arrival of the front of the wave or the area of maximum deflection value). Two methods were used to determine the exact time of the wave occurrence at receivers. It was concluded the differences between the used methods exist. It means the calculated velocities of a wave and shear modulus are also different. Importance of the shear modulus differences were estimated using the Slovak bearing capacity classification based on elastic modulus values. Taking into account the range of modulus in one classification class it can be stated the differences in the shear modulus determined according to used two methods could be very significant if the values calculated for short distance of the receiver are used. In the case of longer distance of the receivers the differences are not so high and significant.
Pressure Coefficients Acting Upon the Cylinder Obtained by Numerical and Experimental Analysis
Authors: Medvecká Soňa , Ivánková Oľga , Macák Marek 
Published: December 2017

Abstract
Analysis of wind flow acting upon high-rise buildings is a very common topic. This paper deals with experiment in the Boundary Layer Wind Tunnel (BWLT) in Bratislava and comparison with the computational fluid dynamics (CFD) simulation and values given in the Eurocode. The analyzed object was the model of building with circular cross section (cylinder). External wind pressure coefficients were compared in three height levels of model.
Dynamics of the adoption of improved aquaculture technologies among fish farmers in Lagos State, Nigeria
Authors: Olaoye Olalekan Jacob , Ezeri Godfrey Nnamdi Onyenoro , Akegbejo-Samsons Yemi , Awotunde Joseph Mubo , Ojebiyi Wahab Gbenga 
Published: December 2017

Abstract
The study assessed the adoption of improved aquaculture technologies among fish farmers in Lagos State, Nigeria. A total of 90 fish farmers were sampled through the multistage sampling technique. A validated and pretested interview schedule was used to obtain primary information from the fish farmers. Obtained data were analyzed using descriptive and inferential statistics. Results obtained revealed that more than half and about one-third of the fish farmers sourced credit facilities from cooperative societies and Esusu, respectively, while almost all sold their fishes as smoked fish. Higher proportions of the fish farmers were aware, tried and adopted most of the improved aquaculture technologies with some of the fish farmers also discontinuing most of the previously adopted technologies. The findings of the study also reported that the fish farmers had positive attitude towards the adoption of improved aquaculture technologies. Results of regression analysis revealed that secondary occupation of the fish farmers (β=−0.324, p<0.01), annual income level (β=−0.471, p<0.05), cost of pond construction (β=0.477, p<0.05) and total profit realized (β=−0.466, p<0.05) were significant predictors of the adoption of improved technologies by the fish farmers with an R2 implying that 46.0% of the variability in the fish farmers’ adoption of improved aquaculture technologies is explained by the socio-economic and production characteristics of the fish farmers. The study concluded that the adoption of improved aquaculture technologies is dynamic and highly influenced by the socio-economic characteristics of the fish farmers which also change with time. It is therefore recommended that technologies that received low level of adoption or which discontinued after earlier adoption should be worked on so that the adoption of those technologies would translate to increased income level of fish farmers, reduced cost of pond construction and increased profit of the fish farmers.
Length-weight relationships of five Cultrinae fish species and two of their hybrids from China
Authors: Xiong Xue-Mei , Zhao Bo-Wen , Nie Chun-Hong , Wang Wei-Min , Gao Ze-Xia 
Published: December 2017

Abstract
TThe length-weight relationships (LWRs) were determined for five freshwater fish species collected from Liangzi Lake, the Xi River and Longxi River in China, including Megalobrama amblycephala, Megalobrama skolkovii, Megalobrama pellegrini and Megalobrama terminalis belonging to the genus Megalobrama, as well as white Amur bream (Parabramis pekinensis) of the genus Parabramis. Three of these five species had no previous LWR estimates in the FishBase. The LWRs of hybrids from Megalobrama amblycephala ♀ × Parabramis pekinensis ♂ and Megalobrama amblycephala ♀ × Megalobrama terminalis ♂ were also reported for the first time.
The Protective Role of Vitamin C and Chitosan Against Paraquat-induced Oxidative Stress in Muscles of Common Carp (Cyprinus carpio)
Authors: Sharifinasab Zeinab , Banaee Mahdi , Mohiseni Mohammad , Noori Ahmad 
Published: December 2017

AbstractThe purpose of this study was to examine the effects of antioxidants, including vitamin C, chitosan or a combination of both, on oxidative stress markers in muscles, as edible tissues of fish, exposed to paraquat. Fish exposed to 0.02 mg/L paraquat for 21 days were fed different diets: a normal diet, a diet containing chitosan (1000 mg/kg diet), a diet with vitamin C (1000 mg/kg diet) or both vitamin C and chitosan. Oxidative stress markers, including the activity of catalase, total antioxidant and malondialdehyde (MDA), as well as biochemical parameters including the activity of aspartate aminotransferase (AST), alanine aminotransferase (ALT), creatine phosphokinase (CPK), lactate dehydrogenase (LDH) and acetylcholinesterase (AChE), were measured in muscles. Fish exposure to paraquat increased LDH, CPK, catalase and MDA activity significantly, while it significantly decreased AST, ALT and AChE activity and total antioxidant capacity in muscles. Administration of vitamin C, combined with chitosan, to fish exposed to paraquat was effective in regulating AChE, AST, ALT, LDH, CPK and catalase activity. A significant increase in the total antioxidant status and a significant decrease in MDA levels were observed in fish fed chitosan-vitamin C complex. In conclusion, it is suggested that combined supplementation with vitamin C and chitosan may improve the detoxification system in the muscles of fish and protect common carp from paraquat toxicity.
Threatened Fishes of the World: Telestes Croaticus (Steindachner, 1866) (Cypriniformes: Cyprinidae)
Authors: Jelić Dušan , Krivek Gabriella 
Published: December 2017

Abstract
Telestes croaticus is a freshwater fish endemic in Croatia. It is a stygophile species, living above ground but occasionally retreating into subterranean waters. This species is found in the southwest region of Croatia, in the Lika-Jadova and Ričica drainages, in cold and clear waters in lowland habitats with little current, and in springs and associated wetlands. It is protected under Croatian law and was listed by the IUCN Red List as Endangered (EN). It has an extremely limited distribution which makes it vulnerable to different kind of traits such as habitat destruction, water extraction, dam construction, agricultural water pollution and especially the introduction of non-indigenous fish species. Suggested conservation actions for this species are: bans on watercourse regulation, reduction of pollution and eradication of alien fish species. Due to its fast decline in the last 10 years, it is our proposition that T. croaticus should be upgraded to a Critically Endangered species under criterion A2ace A4ace.
Wild-Caught Versus Farmed Fish – Consumer Perception
Authors: Tomić Marina , Lucević Zoran , Tomljanović Tea , Matulić Daniel 
Published: December 2017

Abstract
We have limited knowledge of determinants of consumer preferences for wild-caught versus farmed-raised fish, so this work aims to investigate the impact of sociodemographics, habits and frequency of fresh fish consumption, such as involvement in cooking, on the preferences for wild versus farmed fish. A survey was done on a sample of 1151 fish consumers in Croatia. Results showed that female, older consumers, consumers with higher income and those living in coastal parts of Croatia give higher preferences for wild fish and they detect differences between the taste of wild and farmed fish. Consumers with higher levels of habits of fresh fish consumption, who eat fresh fish often and are more involved in cooking, prefer wild-caught fish. These findings provide valuable information for the aquaculture sector, especially for planning marketing strategies for the promotion of farmed fish.