bluuebunny/crossref_metadata_2025_split huggingface dataset:
ShinyKGode: an interactive application for ODE parameter inference using gradient matching
Authors: Wandy Joe , Niu Mu , Giurghita Diana , Daly Rónán , Rogers Simon , Husmeier Dirk 
Published: February 2018

Abstract

Motivation
Mathematical modelling based on ordinary differential equations (ODEs) is widely used to describe the dynamics of biological systems, particularly in systems and pathway biology. Often the kinetic parameters of these ODE systems are unknown and have to be inferred from the data. Approximate parameter inference methods based on gradient matching (which do not require performing computationally expensive numerical integration of the ODEs) have been getting popular in recent years, but many implementations are difficult to run without expert knowledge. Here, we introduce ShinyKGode, an interactive web application to perform fast parameter inference on ODEs using gradient matching.

Results
ShinyKGode can be used to infer ODE parameters on simulated and observed data using gradient matching. Users can easily load their own models in Systems Biology Markup Language format, and a set of pre-defined ODE benchmark models are provided in the application. Inferred parameters are visualized alongside diagnostic plots to assess convergence.

Availability and implementation
The R package for ShinyKGode can be installed through the Comprehensive R Archive Network (CRAN). Installation instructions, as well as tutorial videos and source code are available at https://joewandy.github.io/shinyKGode.

Supplementary information
Supplementary data are available at Bioinformatics online.
Draft genome of the protandrous Chinese black porgy, Acanthopagrus schlegelii
Authors: Zhang Zhiyong , Zhang Kai , Chen Shuyin , Zhang Zhiwei , Zhang Jinyong , You Xinxin , Bian Chao , Xu Jin , Jia Chaofeng , Qiang Jun , Zhu Fei , Li Hongxia , Liu Hailin , Shen Dehua , Ren Zhonghong , Chen Jieming , Li Jia , Gao Tianheng , Gu Ruobo , Xu Junmin , Shi Qiong , Xu Pao 
Published: February 2018

Abstract

Background
As one of the most popular and valuable commercial marine fishes in China and East Asian countries, the Chinese black porgy (Acanthopagrus schlegelii), also known as the blackhead seabream, has some attractive characteristics such as fast growth rate, good meat quality, resistance to diseases, and excellent adaptability to various environments. Furthermore, the black porgy is a good model for investigating sex changes in fish due to its protandrous hermaphroditism. Here, we obtained a high-quality genome assembly of this interesting teleost species and performed a genomic survey on potential genes associated with the sex-change phenomenon.

Findings
We generated 175.4 gigabases (Gb) of clean sequence reads using a whole-genome shotgun sequencing strategy. The final genome assembly is approximately 688.1 megabases (Mb), accounting for 93% of the estimated genome size (739.6 Mb). The achieved scaffold N50 is 7.6 Mb, reaching a relatively high level among sequenced fish species. We identified 19 465 protein-coding genes, which had an average transcript length of 17.3 kb. By performing a comparative genomic analysis, we found 3 types of genes potentially associated with sex change, which are useful for studying the genetic basis of the protandrous hermaphroditism.

Conclusions
We provide a draft genome assembly of the Chinese black porgy and discuss the potential genetic mechanisms of sex change. These data are also an important resource for studying the biology and for facilitating breeding of this economically important fish.
Rapid M1 Hemoclips Arteriotomy Repair After Emergency Coil Embolectomy
Authors: Saad Hassan , Krisht Khaled M , Yang Wei-hsun , Aboud Emad , Krisht Ali F 
Published: February 2018

Abstract

BACKGROUND
The vascular closure staple clips have been studied in animal models and shown to have comparable results with sutured repair when it comes to the healing process, degree of vessel narrowing, and risk of thrombosis. However, they are clearly superior when the speed of application is taken into account, and they were clinically used in many vascular repair processes. Nevertheless, their usefulness in intracranial vascular surgery has not been described.

OBJECTIVE
To describe the usefulness of hemoclips in fast and efficient repair of medium-sized and large intracranial vessels.

METHODS
Two female patients diagnosed with giant symptomatic cavernous sinus aneurysms were undergoing elective endovascular procedures that were complicated by the dislodgement of coils into the M1 segment of the middle cerebral artery. Both patients were treated performing M1 arteriotomies and coil embolectomy. To avoid prolonged temporary occlusion in the M1 perforator's territory, the arteriotomies were repaired using microhemoclips in less than 10 min with re-establishment of flow.

RESULTS
In both patients, flow was re-established in the M1 segments. In 1 patient, the coils extended to the temporal M2 causing intimal injury and leading to diminished flow. M1 segments in both patients were patent on later angiographic studies.

CONCLUSION
We describe the advantage of emergent cerebrovascular arteriotomy and embolectomy in a rapid repair process that helped avoid massive ischemic injury. We believe this technique should be added to the armamentarium of neurosurgical cerebrovascular options.
Cas-CLIP: a method for customizing pooled CRISPR libraries
Authors: Kweon Jiyeon , Kim Da-eun , Jang An-Hee , Kim Yongsub 
Published: February 2018

ABSCTRACTAlthough pooled CRISPR libraries are widely used in high-throughput screening to study various biological processes, library construction for researcher’s own study is a time-consuming, labor-intensive, and expensive process. In this study, we develop a simple, scalable method, called Cas-CLIP, to customize conventional pooled CRISPR libraries using the CRISPR/Cas9 system. We show that conventional pooled CRISPR libraries can be modified by eliminating gRNAs that target positive genes, enabling the identification of unknown target genes in CRISPR screening. Cas-CLIP is a precise method for customizing conventional pooled CRISPR libraries and will broaden the scope of high-throughput screening technology.
A linear mixed model approach to study multivariate gene-environment interactions
Authors: Moore Rachel , Casale Francesco Paolo , Bonder Marc Jan , Horta Danilo ,   BIOS Consortium, Franke Lude , Barroso Inês , Stegle Oliver 
Published: February 2018

AbstractDifferent environmental factors, including diet, physical activity, or external conditions can contribute to genotype-environment interactions (GxE). Although high-dimensional environmental data are increasingly available, and multiple environments have been implicated with GxE at the same loci, multi-environment tests for GxE are not established. Such joint analyses can increase power to detect GxE and improve the interpretation of these effects. Here, we propose the structured linear mixed model (StructLMM), a computationally efficient method to test for and characterize loci that interact with multiple environments. After validating our model using simulations, we apply StructLMM to body mass index in UK Biobank, where our method detects previously known and novel GxE signals. Finally, in an application to a large blood eQTL dataset, we demonstrate that StructLMM can be used to study interactions with hundreds of environmental variables.
Directed Conservative Causal Core Gene Networks
Authors: Altay Gokmen 
Published: February 2018

AbstractMotivation:Inferring large scale directional networks with higher accuracy has important applications such as gene regulatory network or finance.Results:We modified a well-established conservative causal core network inference algorithm, C3NET, to be able to infer very large scale networks with direction information. This advanced version is called Ac3net. We demonstrate that Ac3net outperforms C3NET and many other popular algorithms when considering the directional interaction information of gene/protein networks. We provide and R package and present performance results that are reproducible via the Supplementary file.Availability:Ac3net is available on CRAN and at github.com/altayg/Ac3netContact:altay@lji.orgSupplementary information:Supplementary file is available online.
Membrane proteins with high N-glycosylation, high expression, and multiple interaction partners were preferred by mammalian viruses as receptors
Authors: Zhang Zheng , Zhu Zhaozhong , Chen Wenjun , Cai Zena , Xu Beibei , Tan Zhiying , Wu Aiping , Ge Xingyi , Guo Xinhong , Tan Zhongyang , Xia Zanxian , Zhu Haizhen , Jiang Taijiao , Peng Yousong 
Published: February 2018

AbstractReceptor mediated entry is the first step for viral infection. However, the relationship between viruses and receptors is still obscure. Here, by manually curating a high-quality database of 268 pairs of mammalian virus-host receptor interaction, which included 128 unique viral species or sub-species and 119 virus receptors, we found the viral receptors were structurally and functionally diverse, yet they had several common features when compared to other cell membrane proteins: more protein domains, higher level of N-glycosylation, higher ratio of self-interaction and more interaction partners, and higher expression in most tissues of the host. Additionally, the receptors used by the same virus tended to co-evolve. Further correlation analysis between viral receptors and the tissue and host specificity of the virus shows that the virus receptor similarity was a significant predictor for mammalian virus cross-species. This work could deepen our understanding towards the viral receptor selection and help evaluate the risk of viral zoonotic diseases.
Generating retinal flow maps from structural optical coherence tomography with artificial intelligence
Authors: Lee Cecilia S. , Tyring Ariel J. , Wu Yue , Xiao Sa , Rokem Ariel S. , Deruyter Nicolaas P. , Zhang Qinqin , Tufail Adnan , Wang Ruikang K. , Lee Aaron Y. 
Published: February 2018

ABSTRACTDespite advances in artificial intelligence (AI), its application in medical imaging has been burdened and limited by expert-generated labels. We used images from optical coherence tomography angiography (OCTA), a relatively new imaging modality that measures retinal blood flow, to train an AI algorithm to generate flow maps from standard optical coherence tomography (OCT) images, exceeding the ability and bypassing the need for expert labeling. Deep learning was able to infer flow from single structural OCT images with similar fidelity to OCTA and significantly better than expert clinicians (P < 0.00001). Our model allows generating flow maps from large volumes of previously collected OCT data in existing clinical trials and clinical practice. This finding demonstrates a novel application of AI to medical imaging, whereby subtle regularities between different modalities are used to image the same body part and AI is used to generate detailed inferences of tissue function from structure imaging.
Animal learning in a multidimensional discrimination task as explained by dimension-specific allocation of attention
Authors: Aluisi Flavia , Rubinchik Anna , Morris Genela 
Published: February 2018

AbstractReinforcement learning describes the process by which during a series of trial-and-error attempts, actions that culminate in reward are strengthened. When the actions are based on sensory stimuli, an association is formed between the stimulus, the action and the reward. Computational, behavioral and neurobiological accounts of this process successfully explain simple stimulus-response learning. However, if the cue is multi-dimensional, identifying which of its features are relevant for the reward is not trivial, and the underlying cognitive process is poorly understood. To study this we adapted an intra-dimensional/ extra-dimensional set-shifting paradigm to train rodents on a multidimensional sensory discrimination task. In our setup, stimuli of different modalities (spatial, olfactory and visual) are combined into complex cues and manipulated independently. In each set, only a single stimulus dimension is relevant for reward. To distinguish between learning and decision-making we suggest a weighted attention model (WAM). It combines a learning model where each feature-dimension is reinforced separately with a decision rule that chooses an alternative according to a weighted average of learnt values, in which weight is associated with each dimension. We estimated the parameters of the WAM (decision weights, learning rate and noise) and demonstrated that is outperforms an alternative model in which a value learnt is assigned to each combination of features, or every state. Estimated decision weights of WAM reveal an experience-based bias in learning. The intra-dimensional set shift separated the decision weights. While in the first phase of the experiment the weights were roughly the same, in the second phase the weight on the dimension that was key to finding the reward became higher than others. After the extra-dimensional shift this dimension became irrelevant, however its decision weight remained high for the early learning stage in this last phase, providing an explanation for the poor performance of the animals. By the end of the phase when the rats performance improved, the weights for the two dimensions converged. Thus, estimated weights can be viewed as a possible way to quantify the experience-based bias.
What drives organic food purchasing? – evidence from Croatia
Authors: Ham Marija , Pap Ana , Stanic Marina 
Published: February 2018

Purpose
The purpose of this paper is to examine the direction and strength of the influence of inherent factors of the theory of planned behaviour (TPB) and to extend a model with the variable “uniqueness-seeking lifestyle” to better explain the variance in the intention to purchase organic food and the referent actual behaviour.

Design/methodology/approach
The authors empirically investigated what drives consumers to purchase organic food using structural equation modelling in AMOS. The research was based on an in-person survey carried out on a convenient sample of 411 primary household shoppers in Croatia.

Findings
The study was able to capture not only the influence of inherent factors in TPB and the extension variable (all proposed constructs were shown to have a significant positive influence on intention, and intention had a significant positive influence on actual behaviour), but also the indirect and mediation effects of the variables within the model, which explain 87 per cent of the variance in intention and 21 per cent of the variance in actual behaviour.

Originality/value
This study provides empirical evidence of the role that desired uniqueness plays in a situation involving the purchase of organic food and responds to the requests of many researchers to investigate beyond intention and to try to identify what influences actual behaviour. This study proposes a new way of measuring actual purchases by asking a respondent to consider their actual purchase in different product categories. Furthermore, this research proposes measuring intention as a latent variable that consists of the variable “willingness to pay more” as well as the “commitment” to the decision regardless of any perceived obstacles.
Passive body touch and perceived intensity of spice: softer means spicier
Authors: Tu Yangjun , Ma Chaoqun , Wu Yueyan , Yang Zhi 
Published: February 2018

Purpose
Active touch experienced by the hand and mouth can influence the evaluation of the taste of food. The purpose of this paper is to examine the effect of a passive body touch experience on the perceived intensity of spiciness.

Design/methodology/approach
This study includes three experiments. In Experiment 1, 32 college students tasted half of one piece of spicy bean curd while sitting on either a hard wooden chair or a soft padded chair. Experiment 2 was conducted using the blindfold method to avoid the influence of visual cues on taste, keeping the other details the same as in Experiment 1. Experiment 3 was performed with two changes from Experiment 2: the participants were blindfolded immediately before entering the lab from the waiting room to completely block all visual cues for the experimental materials, and armless stools were used to eliminate the passive touch on the participants’ backs.

Findings
All three experiments consistently found that the participants sitting on the soft padded chair or the soft armless stool perceived the spicy bean curd as significantly spicier than those sitting on the hard wooden chair or the hard armless stool.

Originality/value
These results preliminarily support the hypothesis that a crossmodal correspondence exists between passive body touch and sense of taste (especially spiciness, as in this study), demonstrating the importance of passive body touch and, more generally, of the touchable features in places where food is consumed, such as hotels, restaurants and bars.
Real fruit substitution: the case of at-risk American families
Authors: Maher Jill K. , Crawley Daria , Potter Jodi 
Published: February 2018

Purpose
Children’s fruit intake is a part of healthy nutrition. Several children’s food products “look like” fruit; hence potentially fruit substitutes. Packaging includes brand names, indicators, and health claims related to fruit. These packaging cues may potentially lead to misperceptions of the products. The purpose of this paper is to examine at-risk parents’ substitutions of children’s fruit-branded products for real fruit. At-risk parents are of particular interest as they are a vulnerable segment when it comes to nutrition.

Design/methodology/approach
At-risk families (n=149) completed a survey of their perceptions of children’s nutritional needs, fruit product substitutions, and brand purchase behavior.

Findings
At-risk parents report erroneous perceptions of children’s nutritional fruit intake needs. The results suggest that parents believe fruit-branded products are equivalent to real fruit. Parents’ knowledge and beliefs of fruit equivalency impact purchase decisions.

Research limitations/implications
Limitations include potential self-reporting and convenience sampling bias. The study did not attend to the complete product nutritional profile; only on fruit content. Future research should investigate other factors affecting food purchase decisions.

Practical implications
Industry and policy implications include the balance between governmental regulation of food marketing, voluntary corporate responsibility, and the need for education.

Originality/value
This study provides insights into children’s food product packaging on at-risk family perceptions of real fruit substitutes and purchase behaviors. With the market for these products increasing, there is limited research investigating the impact of these products on children’s nutritional intake.
Older adults’ involvement in developing satisfactory pasta sauces with healthy ingredients
Authors: Predieri Stefano , Sotis Gianluca , Rodinò Paola , Gatti Edoardo , Magli Massimiliano , Rossi Federica , Daniele Giulia Maria , Cianciabella Marta , Volpe Roberto 
Published: February 2018

Purpose
The third age can be a period of major food consumption changes. Either voluntary or imposed by health issues, they may be accompanied by alterations in sensory acuity. The purpose of this paper is to investigate how lifelong food habits and health-age issues affect food choice at a later age, with the aim of developing strategies to direct aged people toward healthier food habits.

Design/methodology/approach
A survey, aimed to investigate differences between current and past food habits, was carried out in a group of 170 Italian older adults. Questions focused on the composition of the main meal, asking participants to describe its actual structure and to highlight differences in previous years’ food habits. A discrete choice experiment (DCE) was planned, during which participants were asked to help formulating innovative pasta sauces with healthy ingredients.

Findings
This survey clearly illustrated gender-related differences: women were characterized by a higher consumption of vegetables, while men revealed a more frequent use of wine, pasta and meat. The DCE technique suited older adults’ abilities and enabled the development of innovative sauces, indicating a clear preference for extra virgin olive oil, as compared to cream or butter. Gender-related differences were confirmed: women mainly chose a vegetarian sauce, while men expressed an inclination for red meat.

Originality/value
This is the first report of a successful application of the DCE technique to investigate older adults’ dietary choices. The outspoken preference for olive oil as fat in sauce composition is a positive finding for future actions aimed at directing older adults toward healthier food habits.
Food fraud detection by Czech Agricultural and Food Inspection Authority in retail market
Authors: Koubová Jana , Samková Eva , Hasonová Lucie 
Published: February 2018

Purpose
The purpose of this paper is to evaluate food fraud detection in the Czech food retail market based on the findings of the Czech Agricultural and Food Inspection Authority (CAFIA).

Design/methodology/approach
The outcomes of administrative proceedings from 2009 and 2013 were used. Data were collected from e-databases of the CAFIA and sorted by the current valid qualification for food fraud following Article 16, Regulation (EC) No. 178/2002 of the European Parliament and of the Council.

Findings
Food fraud was detected, almost to the same extent, in both selected years by laboratory testing as well as on the basis of “on the spot” controls in retail establishments. The meat products were a food group with the most fraudulent tendency in both selected years.

Originality/value
This paper contributes to the overview of food fraud and could help to detect ways of food deception for the competent authorities and consumers.
Measuring the performance efficiency of banks in a developing economy
Authors: Chaluvadi Sashank , Raut Rakesh , Gardas Bhaskar B. 
Published: February 2018

Purpose
The purpose of this paper is to measure and evaluate the performance efficiency of 44 Indian commercial banks, out of which 26 banks belong to the public sector, and 18 banks are from the private sector for the period of 2008-2013.

Design/methodology/approach
The two-stage network data envelopment analysis (DEA) approach (i.e. variable return to scale and constant return to scale) is used for the measurement of performance in the Indian banking sector. To verify the robustness of the proposed study, sensitivity analysis is also performed.

Findings
A comparative study between public sector banks (PSBs) and private sector banks (PVBs) showed that latter being more productive compared to the former. The investigation highlighted that two banks are most efficient among the PSBs, and eight banks from PVBs are found to be most effective. On the other side, the performance of State Bank of Bikaner & Jaipur and Lakshmi Vilas Bank is discovered to be less significant from PSB and PVB category, respectively.

Research limitations/implications
This study will guide the Indian banks to improve upon the factors in which they are lagging, for the improvement of their overall performance. The quality category parameters, i.e. quality of service, quality of equipment, are not considered due to unavailability of information in the output measures, and the methodology used for the study does not identify the causes or remedies for the inefficiency of the banks.

Originality/value
The developed DEA model would help the decision maker to take decisions on the issues related to the performance of the banks. This paper discusses very practical issues in an analytic manner.