bluuebunny/crossref_metadata_2025_split huggingface dataset:
Caliban: Accurate cell tracking and lineage construction in live-cell imaging experiments with deep learning
Authors: Schwartz Morgan Sarah , Moen Erick , Miller Geneva , Dougherty Tom , Borba Enrico , Ding Rachel , Graf William , Pao Edward , Van Valen David 
Published: October 2019

AbstractWhile live-cell imaging is a powerful approach to studying the dynamics of cellular systems, converting these imaging data into quantitative, single-cell records of cellular behavior has been a longstanding challenge. Deep learning methods have proven capable of performing cell segmentation—a critical task for analyzing live-cell imaging data—but their performance in cell tracking has been limited by a lack of dynamic datasets with temporally consistent single-cell labels. We bridge this gap through the integrated development of labeling and deep learning methodology. We present a new framework for scalable, human-in-the-loop labeling of live-cell imaging movies, which we use to label a large collection of movies of fluorescently labeled cell nuclei. We use these data to create a new deep-learning-based cell-tracking method that achieves state-of-the-art performance in cell tracking. We have made all of the data, code, and software publicly available with permissive open-source licensing through the DeepCell project’s web portalhttps://deepcell.org.
Imputing missing RNA-seq data from DNA methylation by using transfer learning based neural network
Authors: Zhou Xiang , Chai Hua , Zhao Huiying , Luo Ching-Hsing , Yang Yuedong 
Published: October 2019

AbstractBackgroundGene expression plays a key intermediate role in linking molecular features at DNA level and phenotype. However, due to various limitations in experiments, the RNA-seq data is missing in many samples while there exists high-quality of DNA methylation data. As DNA methylation is an important epigenetic modification to regulate gene expression, it can be used to predict RNA-seq data. For this purpose, many methods have been developed. A common limitation of these methods is that they mainly focus on single cancer dataset, and do not fully utilize information from large pan-cancer dataset.ResultsHere, we have developed a novel method to impute missing gene expression data from DNA methylation data through transfer learning-based neural network, namely TDimpute. In the method, the pan-cancer dataset from The Cancer Genome Atlas (TCGA) was utilized for training a general model, which was then fine-tuned on the specific cancer dataset. By testing on 16 cancer datasets, we found that our method significantly outperforms other state-of-the-art methods in imputation accuracy with 7%-11% increase under different missing rates. The imputed gene expression was further proved to be useful for downstream analyses, including the identification of both methylation-driving and prognosis-related genes, clustering analysis, and survival analysis on the TCGA dataset. More importantly, our method was indicated to be useful for general purpose by the independent test on the Wilms tumor dataset from the Therapeutically Applicable Research To Generate Effective Treatments (TARGET) project.ConclusionsTDimpute is an effective method for RNA-seq imputation with limited training samples.
ROOT PATTERNING AND REGENERATION ARE MEDIATED BY THE QUIESCENT CENTER AND INVOLVE BLUEJAY, JACKDAW AND SCARECROW REGULATION OF VASCULATURE FACTORS
Authors: Sanchez-Corrionero Alvaro , Perez-Garcia Pablo , Cabrera Javier , Silva-Navas Javier , Perianez-Rodriguez Juan , Gude Inmaculada , del Pozo Juan Carlos , Moreno-Risueno Miguel A. 
Published: October 2019

ABSTRACTStem cells are central to plant development. During root postembryonic development stem cells generating tissues are patterned in layers around a stem cell organizer or quiescent center (QC). How stem cell lineages are initially patterned is unclear. Here, we describe a role for BLUEJAY (BLJ), JACKDAW (JKD) and SCARECROW (SCR) transcription factors in patterning of cell lineages during growth and in patterning reestablishment during regeneration through regulation of number of QC cells and their regenerative capacities. In blj jkd scr mutants, QC cells are progressively lost which results in loss of tissue layers. Upon laser ablation blj jkd scr is impaired in QC division and specification resulting in severe impairment in pattern regeneration. Beyond direct regulation of QC activity by these transcription factors, reduced levels of SHORT-ROOT (SHR) and of PIN auxin transporters were observed in the vasculature of blj jkd scr, leading to strong reduction in the auxin response in the QC. We narrowed down non-cell-autonomous regulation of vascularly expressed genes in blj jkd scr to C-REPEAT BINDING FACTOR 3 (CBF3). cbf3 mutant shows reduced levels of SHR in the vasculature, and in addition QC disorganization and downregulation of the QC regulator WUSCHEL-RELATED HOMEODOMAIN 5 (WOX5). CBF3 gene is primarily expressed in the ground tissue downstream of BLJ, JKD and SCR, while CBF3 protein may move. Targeted-expression of CBF3 to the ground tissue of blj jkd scr recovers radial patterning and regeneration. We propose that BLJ, JKD and SCR regulate QC-mediated patterning, and that part of this regulation involves CBF3.
Territory establishment, song learning strategies and survival in song sparrows
Authors: Akçay Çağlar , Campbell S. Elizabeth. , Darling Saethra , Beecher Michael D. 
Published: October 2019

AbstractIn most songbirds the processes of song learning and territory establishment overlap in the early life of young birds who usually winds up with songs matching those of their territorial neighbors in their first breeding season. In the present study, we examined the relationships among the timing of territory establishment, the pattern of song learning and territorial success in a sedentary population of song sparrows (Melospiza melodia). Males in this population show high song sharing within neighborhoods derving from their learning most of their songs from neighboring males. These shared songs are preferentially used in interactions with neighbors. Males also show significant variation in the timing of territory establishment, ranging from their first summer until the next spring. Using a three-year dataset, we found that the timing of territory establishment did not systematically affect the composition of the song repertoire of the tutee: early establishers and late establishers learned equally as much from their primary tutors, and had a similar number of tutors and repertoire size. Timing of territory establishment also did not have an effect on subsequent survival on territory. Therefore, the song learning program of song sparrows seems versatile enough to lead to high song sharing even for birds that establish territories relatively late.
Searching for relief: Drosophila melanogaster navigation in a virtual bitter maze
Authors: Meda Nicola , Frighetto Giovanni , Megighian Aram , Zordan Mauro Agostino 
Published: October 2019

AbstractAnimals use pain-relief learning to discern which actions can diminish or abolish noxious stimuli. If relief from pain is provided in a specific location, place learning is the mechanism used to pinpoint that location in space. Little is known about how physiological and non-directly damaging stimuli can alter visual-based searching behaviour in animals. Here we show how the optogenetically-induced activation of bitter-sensing neurons urges Drosophila melanogaster to seek relief from bitter taste stimulation and that this distressful, but ecologically relevant stimulus, innately wired to the threat of intoxication, is sufficient to elicit pain-relief-like behavioural responses. Specifically, freely walking flies inside an open circular arena are trained to seek relief from the unpleasant stimulation by searching for a safe area alternatively positioned in the proximity of a pair of identical, diametrically opposed, visual markers. Moreover, and perhaps more importantly, under this paradigm flies develop visual place learning manifested by their seeking relief in the zone associated with bitter relief during the last trial of training, even when exposed to constant bitter stimulation with no relief provided. An important implication is that this form of learning does not lead to operant conditioning generalization. We further propose that kinematic indexes, such as the spatially-specific reduction of locomotor velocity, may provide immediate evidence of relief-based place learning and spatial memory.
Indirect versus Direct Effects of Freshwater Browning on Larval Fish Foraging
Authors: Leech Dina M. , Clift Troy L. , Littlefield Jessica L. , Ravagli Nicholas R. , Spain Jacob E. 
Published: October 2019

ABSTRACTFish foraging and energy flow are both predicted to decline with freshwater ‘browning’ due to reductions in light availability. Studies investigating these predictions have focused on juveniles and adults; however, the larval stage represents a ‘critical period’ in fish development. We investigated the indirect versus direct effects of browning on zooplankton-larval fish interactions by altering water color with SuperHume (absorbance at 440 nm = 1.6 – 10.8 m−1). Phytoplankton and zooplankton densities were monitored across experimental tanks in the laboratory for one month leading up to fish spawning. Larval largemouth bass were then introduced to assess indirect effects on fish feeding rates and growth. Direct effects on foraging of largemouth bass and bluegill were determined with separate short-term feeding experiments. Browning did not directly alter the ability of larval fish to capture prey. However, significant indirect effects on larval fish foraging, growth, and survival were observed as phytoplankton and zooplankton decreased with increased browning. Our data suggest lake browning will reduce energy transfer to larval fish due to a reduction in prey availability but not visual foraging.
The Effects of Motor Modularity on Performance, Learning, and Generalizability in Upper-Extremity Reaching: a Computational Analysis
Authors: Borno Mazen Al , Hicks Jennifer L. , Delp Scott L. 
Published: October 2019

AbstractIt has been hypothesized that the central nervous system simplifies the production of movement by limiting motor commands to a small set of modules known as muscle synergies. Recently, investigators have questioned whether a low-dimensional controller can produce the rich and flexible behaviors seen in everyday movements. To study this issue, we implemented muscle synergies in a biomechanically realistic model of the human upper extremity and performed computational experiments to determine whether synergies introduced task performance deficits, facilitated the learning of movements, and generalized to different movements. We derived sets of synergies from the muscle excitations our dynamic optimizations computed for a nominal task (reaching in a plane). Then we compared the performance and learning rates of a controller that activated all muscles independently to controllers that activated the synergies derived from the nominal reaching task. We found that a controller based on synergies had errors within 1 cm of a full-dimensional controller and achieved faster learning rates (as estimated from computational time to converge). The synergy-based controllers could also accomplish new tasks–such as reaching to targets on a higher or lower plane, and starting from alternate initial poses–with average errors similar to a full-dimensional controller.
Combined use of design of experiments and metabolic engineering for optimization of nogalamycin production
Authors: Maki Kayla , Coe Marlon , Brown Katelyn , Tran Jennifer , Sohn Minji , Nybo S. Eric 
Published: October 2019

ABSTRACTNogalamycin is an anthracycline antibiotic produced fromStreptomyces nogalaterthat exerts its mechanism of action via inhibition of topoisomerase I. Nogalamycin has a unique tetracyclic structure composed of a 7-O-glycosidically linked L-nogalose sugar and a C2-C5”-linked L-nogalamine residue that forms an epoxyoxacin ring. Nogalamycin was originally developed as an anticancer agent in the 1970s, however, it exhibited dose-limiting cardiotoxicity. Shortly after the discovery of nogalamycin, the semi-synthetic analogue 7-O-methylnogarol, or menogaril, was synthesized and exhibited a mild improvement in cardiotoxicity and anticancer efficacy. Menogaril lacks the 7-O-L-nogalose moiety and functions as a topoisomerase II inhibitor, like most anthracyclines, however this agent still proved too toxic for clinical use. Our laboratory is developing a production platform for microbial synthesis of novel nogalamycin analogs useful for treatment of human cancers or as antibiotics. Our initial hypothesis is that overexpression of structural genes responsible for synthesis of TDP-deoxysugar and polyketide precursor substrates, respectively, will increase carbon flux towards nogalamycin production. In this study, we have employed metabolic engineering to enhance nogalamycin production inStreptomyces nogalater. In this work, we used an optimized soytone glucose production medium to produce nogalamycin. We also overexpressed copies of structural biosynthetic genes to bolster substrate precursor building blocks for nogalamycin production. First, overexpression of the TDP-glucose synthase and TDP-D-glucose-4,6-dehydratase enzymes (mtmDE) resulted in a 50% increase in nogalamycin production (160 mg/L) as compared to wildtypeS. nogalater(100 mg/L). Secondly, overexpression of the minimal polyketide synthase genes (snoa123) resulted in a fourfold production increase in nogalamycin (400 mg/L). This production platform will serve as the fundament for production of nogalamycin analogues for future drug development efforts.
Locating complex eigenvalues for analytical eddy-current models used to detect flaws
Authors: Tytko Grzegorz , Dawidowski Łukasz 
Published: October 2019

Purpose
Discrete eigenvalues occur in eddy current problems in which the solution domain was truncated on its edge. In case of conductive material with a hole, the eigenvalues are complex numbers. Their computation consists of finding complex roots of a complex function that satisfies the electromagnetic interface conditions. The purpose of this paper is to present a method of computing complex eigenvalues that are roots of such a function.

Design/methodology/approach
The proposed approach involves precise determination of regions in which the roots are found and applying sets of initial points, as well as the Cauchy argument principle to calculate them.

Findings
The elaborated algorithm was implemented in Matlab and the obtained results were verified using Newton’s method and the fsolve procedure. Both in the case of magnetic and nonmagnetic materials, such a solution was the only one that did not skip any of the eigenvalues, obtaining the results in the shortest time.

Originality/value
The paper presents a new effective method of locating complex eigenvalues for analytical solutions of eddy current problems containing a conductive material with a hole.
Bridging the divide
Authors: Holden Matt , Shipway Richard , Lamont Matthew 
Published: October 2019

Purpose
In sport tourism, an undeniable recent participation trend is the gravitation of amateur athletes to participatory sport events, particularly cycling sport tourism events. This trend presents numerous policy, applied, and scholarly opportunities and challenges. Contemporary trends are identified to guide future research addressing cycling sport tourism events. The paper aims to discuss these issues.

Design/methodology/approach
This is a collaborative initiative between a major global sport event management organisation and established sport tourism scholars. Industry data are drawn upon to identify contemporary sport event participation trends and thus inform a future research agenda.

Findings
This paper draws upon industry data and insights to tease out five emerging trends in the participatory sport event sector which scholars should engage with.

Research limitations/implications
Due to the confidential nature of the company data, there were restrictions in the detail which could be reported.

Practical implications
Increasing growth in premium quality, physically challenging cycling sport tourism events is analysed. A five-pronged future research agenda is proposed to address contemporary sport event management issues around measuring event impacts; strategic management of events; and leveraging globalisation and emerging markets.

Originality/value
Based on trends identified in this paper, theoretical concepts are drawn upon to propose a timely, industry-relevant future research agenda into cycling sport tourism events.
Experimental analysis of Medicare data using hierarchical grouping mechanism
Authors: P. Naga Jyothi , D. Rajya Lakshmi , K.V.S.N. Rama Rao 
Published: October 2019

Purpose
Analyzing medicare data is a role undertaken by the government and commercial companies for accepting the appeals and sanctioning the claims of those insured under Medicare. As the data of medicare is robust and made up of heterogeneous typed columns, traditional approaches consist of a laborious and time-consuming process. The understanding and processing of such data sets and finding the role of each attribute for data analysis are tricky tasks which this research will attempt to ease. The paper aims to discuss these issues.

Design/methodology/approach
This paper proposes a Hierarchical Grouping (HG) with an experimental model to handle the complex data and analysis of the categorical data which consist of heterogeneous typed columns. The HG methodology starts with feature subset selection. HG forms a structure by quantitatively estimating the similarities and forms groups of the features for data. This is carried by applying metrics like decomposition; it splits the dataset and helps to analyze thoroughly under different labels with different selected attributes of Medicare data. The method of fixed regression includes metrics of re-indexing and grouping which works well for multiple keys (multi-index) of categorical data. The final stage of structure is applying multiple aggregation function on each attribute for quantitative computation.

Findings
The data are analyzed quantitatively with the HG mechanism. The results shown in this paper took less computation cost and speed, which are usually incurred on the publicly available data sets.

Practical implications
The motive of this paper is to provide a supportive work for the tasks like outlier detection, prediction, decision making and prescriptive tasks for multi-dimensional data.

Originality/value
It provides a new efficient approach to analyze medicare data sets.
Islamic marketing and consumer behaviour: a systematic literature review
Authors: Floren Jessen , Rasul Tareq , Gani Azmat 
Published: October 2019

Purpose
The purpose of this study is to systematically review the existing literature on Islamic marketing and its major impacts on consumer behaviours. In addition, this study seeks to shed light on global trends and dynamics beyond Islamic marketing and how Islam, as one of the most prominent religions worldwide, affects the consumption and purchasing choices of Muslim consumers.

Design/methodology/approach
A systematic literature review of published peer-reviewed articles on Islamic marketing was conducted. A comprehensive search strategy was applied on different databases, including Google Scholar, JSTOR, ScienceDirect, MUSE and Directory of Open Access Journals, and the retrieved articles were then selected from 14 leading journals published between 2010 and 2018.

Findings
Islam as a religion has been found to impact the ethical beliefs and behaviours of Muslim consumers from different countries, as well as consumers’ choice of services and some taboo products on the basis of Islamic Shariah law. The results show that Islamic marketing has a significant impact on the characteristics of Muslim consumers and therefore affects their key choices about certain products and services.

Research limitations/implications
The studies included in this review are extensively based on peer-reviewed articles published in high-ranked marketing journals (A* and A in the Australian Business Deans Council list), which may be perceived as a limitation in the present study. Another limitation is that this study only took into account peer-reviewed articles written in English.

Practical implications
The important relationship between Islam and the heterogeneous Muslim consumer will have a considerable practical implication for companies that explore the marketing supply capacity in the Islamic world. The authors hereby expect the current review to significantly impact the identification of methodologies for the main trends in the academic analysis of Islamic marketing and Islamic consumer behaviour.

Originality/value
This review provides a strong contribution to Islamic marketing literature by recommending the need to integrate the Islamic practices related to consumer consumption of goods and services in studies focused on consumer behaviour analysis.
Effectiveness of Mental Health First Aid: a meta-analysis
Authors: Maslowski Amy K. , LaCaille Rick A. , LaCaille Lara J. , Reich Catherine M. , Klingner Jill 
Published: October 2019

Purpose
The purpose of this paper, a meta-analysis and systematic review of Mental Health First Aid (MHFA), is to focus on studies that reported trainees’ mental health literacy, attitudes and helping-related behaviors, as well as the impact of the program for the people who came into contact with trainees (i.e. recipients).

Design/methodology/approach
A systematic search included several online databases of published studies, dissertations or theses, and journals commonly publishing research in this area. Studies were randomized or non-randomized control trials using an intervention based upon the adult or youth MHFA curriculum.

Findings
Of the 8,257 initial articles, 16 met inclusion criteria. Small-to-moderate effect sizes (Hedges’ g=0.18–0.53) were found for the primary outcomes for the trainees with effects appearing to be maintained at follow-up. Study quality was inversely associated with effect size. No evidence of investigator allegiance was detected. Few studies examined the effects for those who received aid from a MHFA trainee. Preliminary quantitative evidence appeared lacking (Hedges’ g=−0.04 to 0.12); furthermore, a qualitative review found limited positive effects.

Research limitations/implications
MHFA trainees appear to benefit from MHFA; however, objective behavioral changes are in need of greater emphasis. Additionally, considerably greater attention and effort in testing effects on distressed recipients is needed with future empirical investigations.

Originality/value
This is the first known review that includes preliminary findings on the effects of MHFA on the distressed recipients of the aid. It is anticipated that this will prompt further investigation into the impact of MHFA.