bluuebunny/crossref_metadata_2025 huggingface dataset:
DIffusion-Prepared Phase Imaging (DIPPI): quantifying myelin in crossing fibres
Authors: Cottaar Michiel , Wu Wenchuan , Tendler Benjamin , Nagy Zoltan , Miller Karla , Jbabdi Saad
Published: November 2020

Purpose

Myelin has long been the target of neuroimaging research due to its importance in brain development, plasticity, and disease. However, most available techniques can only provide a voxel-averaged estimate of myelin content. In the human brain, white matter fibre pathways connecting different brain areas and carrying different functions often cross each other in the same voxel. A measure that can differentiate the degree of myelination of crossing fibres would provide a more specific marker of myelination.

Theory & Methods

One MRI signal property sensitive to myelin is the phase accumulation, which to date has also been limited to voxel-averaged myelin estimates. We use this sensitivity by measuring the phase accumulation of the signal remaining after diffusion weighting, which we call DIffusion-Prepared Phase Imaging (DIPPI). Including diffusion weighting before estimating the phase accumulation has two distinct advantages for estimating the degree of myelination: (1) it increases the relative contribution of intra-axonal water, whose phase is related linearly to the amount of myelin surrounding the axon (in particular the logg-ratio) and (2) it gives directional information, which can be used to distinguish between crossing fibres.

Results

Using simulations and phantom data we argue that other sources of phase accumulation (i.e., movement-induced phase shift during the diffusion gradients, eddy currents, and other sources of susceptibility) can be either corrected for or are sufficiently small to still allow theg-ratio to be reliably estimated.

Conclusions

This new sequence is capable of providing ag-ratio estimate per fibre population crossing within a voxel.
Neural network fast-classifies biological images using features selected after their random-forests-importance to power smart microscopy
Authors: Balluet Maël , Sizaire Florian , Habouz Youssef El , Walter Thomas , Pont Jérémy , Giroux Baptiste , Bouchareb Otmane , Tramier Marc , Pecreaux Jacques
Published: November 2020

Artificial intelligence is nowadays used for cell detection and classification in optical microscopy, during post-acquisition analysis. The microscopes are now fully automated and next expected to be smart, to make acquisition decisions based on the images. It calls for analysing them on the fly. Biology further imposes training on a reduced dataset due to cost and time to prepare the samples and have the datasets annotated by experts. We propose here a real-time image processing, compliant with these specifications by balancing accurate detection and execution performance. We characterised the images using a generic, high-dimensional feature extractor. We then classified the images using machine learning for the sake of understanding the contribution of each feature in decision and execution time. We found that the non-linear-classifier random forests outperformed Fisher’s linear discriminant. More importantly, the most discriminant and time-consuming features could be excluded without any significant loss in accuracy, offering a substantial gain in execution time. It suggests a feature-group redundancy likely related to the biology of the observed cells. We offer a method to select fast and discriminant features. In our assay, a 79.6 ± 2.4 % accurate classification of a cell took 68.7 ± 3.5 ms (mean ± SD, 5-fold cross-validation nested in 10 bootstrap repeats), corresponding to 14 cells per second, dispatched into 8 phases of the cell cycle using 12 feature-groups and operating a consumer market ARM-based embedded system. Interestingly, a simple neural network offered similar performances paving the way to faster training and classification, using parallel execution on a general-purpose graphic processing unit. Finally, this strategy is also usable for deep neural networks paving the way to optimising these algorithms for smart microscopy.
The impact of exercise intensity on neurophysiological indices of food-related inhibitory control and cognitive control: A randomized crossover event-related potential (ERP) study
Authors: Bailey Bruce W. , Muir Alexandra M. , Bartholomew Ciera L. , Christensen William F. , Carbine Kaylie A. , Marsh Harrison , LaCouture Hunter , McCutcheon Chance , Larson Michael J.
Published: November 2020

Food-related inhibitory control, the ability to withhold a dominant response towards highly palatable foods, influences dietary decisions. Food-related inhibitory control abilities may increase following a bout of aerobic exercise; however, the impact of exercise intensity on both food-related inhibitory control and broader cognitive control processes is currently unclear. We used a high-powered, within-subjects, crossover design to test how relative intensity of aerobic exercise influenced behavioral (response time, accuracy) and neural (N2 and P3 components of the scalp-recorded event-related potential [ERP]) measures of food-related inhibitory and cognitive control. Two hundred and thirteen participants completed three separate conditions separated by approximately one week in randomized order: two exercise conditions (35% [moderate] or 70% [vigorous] of VO2max) and seated rest. Directly following exercise or rest, participants completed a food-based go/no-go task and a flanker task while electroencephalogram data were recorded. Linear mixed models showed generally faster response times (RT) and improved accuracy following vigorous exercise compared to rest, but not moderate-intensity exercise; RTs and accuracy did not differ between moderate intensity exercise and rest conditions. N2 and P3 amplitudes were larger following vigorous exercise for the food-based go/no-go task compared to rest and moderate intensity exercise. There were no differences between exercise conditions for N2 amplitude during the flanker task; however, P3 amplitude was more positive following vigorous compared to rest, but not moderate exercise. Gender did not moderate exercise outcomes. Results suggest improved and more efficient food- related recruitment of later inhibitory control and cognitive control processes following vigorous exercise.
There is more than chitin synthase in insect resistance to benzoylureas: Molecular markers associated with teflubenzuron resistance inSpodoptera frugiperda
Authors: Bezerra do Nascimento Antonio Rogério , Corrêa Pavinato Vitor Antonio , Rodrigues Juliana Gonzales , Silva-Brandão Karina Lucas , Consoli Fernando Luis , Michel Andrew , Omoto Celso
Published: November 2020

Chitin synthesis inhibitors are successfully used in pest control and are an excellent option for use in integrated pest management programs due to their low non-target effects. Reports on field-evolved resistance of lepidopteran pests to chitin synthesis inhibitors and the selection of laboratory resistant strains to these products require a detailed investigation on the resistance mechanisms and on the identification of molecular markers to support the implementation of efficient monitoring and resistance management programs. Teflubenzuron is a chitin synthesis inhibitor highly effective in controlling lepidopteran pests, including nowadays the world widely distributed fall armyworm (FAW),Spodoptera frugiperda(J.E. Smith, 1797) (Lepidoptera: Noctuidae). We report the selection of a laboratory strain ofS. frugiperdaresistant to teflubenzuron, and its use for the characterization of the inheritance of resistance, evaluation of cross-resistance to other chitin-synthesis inhibitors and the identification of a set of single nucleotide polymorphisms (SNPs) for use as candidate molecular markers for monitoring the evolution of resistance ofS. frugiperdato teflubenzuron. The resistance of the selected strain ofS. frugiperdato teflubenzuron was characterized as polygenic, autosomal, and incompletely recessive. The resistance ratio observed was nearly 1,365-fold. Teflubenzuron-resistant strain showed some cross-resistance to lufenuron and novaluron but not to chlorfluazuron. We also detected a set of 72 SNPs that could support monitoring of the resistance frequency to teflubenzuron in field populations. Our data contribute to the understanding of the resistance mechanisms and the inheritance of polygenic resistance ofS. frugiperdato benzoylureas. We also contribute with candidate markers as tools for monitoring the emergence and spread of teflubenzuron resistance inS. frugiperda.
FASTAFS: file system virtualisation of random access compressed FASTA files
Authors: Hoogstrate Youri , Jenster Guido , van de Werken Harmen J. G.
Published: November 2020

Background

The FASTA file format used to store polymeric sequence data has become a bioinformatics file standard used for decades. The relatively large files require additional files beyond the scope of the original format, to identify sequences and provide random access. Currently, multiple compressors have been developed to archive FASTA files back and forth, but these lack direct access to targeted content or metadata of the archive. Moreover, these solutions are not directly backwards compatible to FASTA files, resulting in limited software integration.

Results

We designed linux based a toolkit using Filesystem in Userspace (FUSE) that virtualises the content of DNA, RNA and protein FASTA archives into the filesystem. This guarantees in-sync virtualised metadata files and offers fast random-access decompression using Zstandard (zstd). The toolkit, FASTAFS, can track all system wide running instances, allows file integrity verification and can provide, instantly, scriptable access to sequence files and is easy to use and deploy.

Conclusions

FASTAFS is a user-friendly and easy to deploy backwards compatible generic purpose solution to store and access compressed FASTA files, since it offers file system access to FASTA files as well as in-sync metadata files through file virtualisation. Using virtual filesystems as in-between layer offers the possibility to design format conversion without the need to rewrite code into different languages while preserving compatibility.

Code Availability

https://github.com/yhoogstrate/fastafs
snpXplorer: a web application to explore SNP-associations and annotate SNP-sets
Authors: Tesi Niccolo , van der Lee Sven J , Hulsman Marc , Holstege Henne , Reinders Marcel
Published: November 2020

Genetic association studies are frequently used to study the genetic basis of numerous human phenotypes. However, the rapid interrogation of how well a certain genomic region associates across traits as well as the interpretation of genetic associations is often complex and requires the integration of multiple sources of annotation, which involves advanced bioinformatic skills. We developed snpXplorer, an easy-to-use web-server application for exploring Single Nucleotide Polymorphisms (SNP) association statistics and to functionally annotate sets of SNPs. snpXplorer can superimpose association statistics from multiple studies, and displays regional information including SNP associations, structural variations, recombination rates, eQTL, linkage disequilibrium patterns, genes and gene-expressions per tissue. By overlaying multiple GWAS studies, snpXplorer can be used to compare levels of association across different traits, which may help the interpretation of variant consequences. Given a list of SNPs, snpXplorer can also be used to perform variant-to-gene mapping and gene-set enrichment analysis to identify molecular pathways that are overrepresented in the list of input SNPs. snpXplorer is freely available at https://snpxplorer.net. Source code, documentation, example files and tutorial videos are available within the Help section of snpXplorer and at https://github.com/TesiNicco/snpXplorer.
A conserved superlocus regulates above- and belowground root initiation
Authors: Omary Moutasem , Gil-Yarom Naama , Yahav Chen , Steiner Evyatar , Efroni Idan
Published: November 2020

During plant post-embryonic growth new meristems and associated stem cells form in different development contexts in order to respond to environmental cues. While underground lateral roots initiate from designated cells in the main root, an unknown mechanism allows cells to bypass the root/shoot identity trajectory and generate shoot-borne-roots. Using single-cell profiling of tomato (Solanum lycoperiscum)stems we isolated a rare transient cell population that serve as progenitors for shoot-borne-root meristems. Analysis of this population identified a transcription factor required for the formation of shoot-borne-roots which we namedSHOOT BORNE ROOTLESS (SBRL). Evolutionary analysis revealed thatSBRLfunction is deeply conserved in angiosperms and that it arose as part of an ancient duplicated superlocus, only lost in root-less plants, containing both shoot-borne and lateral root initiation regulators. We propose that the ability to activate a common transition state with context-specific regulators allows the remarkable developmental plasticity found in plants.

One Sentence Summary

Highly conserved superlocus of LBD genes, acting within an early transition identity, regulates shoot-borne and lateral root formation.
The Palmitoyl Acyltransferase ZDHHC14 Controls Kv1-Family Potassium Channel Clustering at the Axon Initial Segment
Authors: Sanders Shaun S. , Hernandez Luiselys M. , Soh Heun , Karnam Santi , Walikonis Randall S. , Tzingounis Anastasios V. , Thomas Gareth M.
Published: November 2020

The palmitoyl acyltransferase (PAT) ZDHHC14 is highly expressed in the hippocampus and is the only PAT predicted to bind Type I PDZ domain-containing proteins. However, ZDHHC14’s neuronal roles are unknown. Here, we identify the PDZ domain-containing Membrane-associated Guanylate Kinase (MaGUK) PSD93 as a direct ZDHHC14 interactor and substrate. PSD93, but not other MaGUKs, localizes to the Axon Initial Segment (AIS). Using lentiviral-mediated shRNA knockdown in rat hippocampal neurons, we find that ZDHHC14 controls palmitoylation and AIS clustering of PSD93 and also of Kv1 potassium channels, which directly bind PSD93. Neurodevelopmental expression of ZDHHC14 mirrors that of PSD93 and Kv1 channels and, consistent with ZDHHC14’s importance for Kv1 channel clustering, loss of ZDHHC14 decreases outward currents and increases action potential firing in hippocampal neurons. To our knowledge, these findings identify the first neuronal roles and substrates for ZDHHC14 and reveal a previously unappreciated role for palmitoylation in control of neuronal excitability.

Impact Statement

ZDHHC14 controls palmitoylation and axon initial segment targeting of PSD93 and Kv1-family potassium channels, events that are essential for normal neuronal excitability.
Longitudinal effects of antibiotics and fecal transplant on lemur gut microbiota structure, associations, and resistomes
Authors: Bornbusch Sally L. , Harris Rachel L. , Grebe Nicholas M. , Roche Kimberly , Dimac-Stohl Kristin , Drea Christine M.
Published: November 2020

Antibiotics alter the diversity, structure, and dynamics of host-associated microbial consortia, including via development of antibiotic resistance; however, patterns of recovery from dysbiosis and methods to mitigate negative effects, remain poorly understood. We applied an ecological framework via long-term, integrated study of community structure, across scales, to improve understanding of host-microbe symbiosis during dysbiosis and recovery. We experimentally administered a broad-spectrum antibiotic alone or with subsequent fecal transfaunation to healthy, male ring-tailed lemurs (Lemur catta) and longitudinally tracked the diversity, composition, associations, and resistomes of their gut microbiota. Whereas microbial diversity recovered rapidly in lemurs, antibiotics caused long-term instability in community composition – effects that were attenuated by fecal transfaunation. Antibiotic resistance genes, which were universally present, including in treatment-naïve subjects, increased during and persisted after antibiotic treatment. Long-term, integrated study post antibiotic-induced dysbiosis revealed differential, metric-dependent evidence of recovery, beneficial effects of fecal transfaunation, and negative consequences to lemur resistomes.
HumanPRE-PIK3C2Bexhibits long-range intra- and inter-chromosomal interactions with genomic regions enriched in repressive marks
Authors: Maini Jayant , Pathak Ankit Kumar , Bhattacharyya Kausik , Kumar Narendra , Narang Ankita , Jain Neha , Singh Inderpreet , Dhingra Vanika , Brahmachari Vani
Published: November 2020

Human PRE-PIK3C2B is a dual nature polycomb response element that interacts with both polycomb as well as trithorax members. In the current study, using 4C-Seq (CapturingCircularChromosomalConformation-Sequencing), we identified long-range chromatin interactions associated withPRE-PIK3C2Band validated them with 3C-PCR. We identified both intra-as well as inter-chromosomal interactions, a large proportion of which were found to be closely distributed around transcriptional start sites (TSS). A significant number of interactions were also found to be associated with heterochromatic regions. Meta-analysis of ENCODE ChIP-Seq data identified an overall enrichment of YY1, CTCF as well as histone modification such as H3K4me3 and H3K27me marks in different cell lines. Almost 90% interactions were derived from either intronic or intergenic regions. among which large proportions of intronic interactors were either unique sequences or LINE/SINE derived. In case of intergenic interactions, majority of the interaction were associated with LINE/SINE repeats. We further found that genes proximal to the interactor sequences were co-expressed, they showed reduced expression. To the best of our knowledge this is one of the early demonstrations of long-range interaction of PRE sequences in human genome.
Quantitative metaproteomics of patient fecal microbiota identifies host and microbial proteins associated with ulcerative colitis
Authors: Thuy-Boun Peter S. , Wang Ana Y. , Crissien-Martinez Ana , Xu Janice H. , Chatterjee Sandip , Stupp Gregory S. , Su Andrew I. , Coyle Walter J. , Wolan Dennis W.
Published: November 2020

Mass spectrometry-based metaproteomics technologies enable the direct observation of proteins within complex multi-organism environments. A major hurdle in mapping metaproteomic fragmentation spectra to their corresponding peptides is the need for large peptide databases encompassing all anticipated species contained within a biological sample. As we cannot predict the taxonomic composition of microbiomesa priori, we developed the ComPIL database which contains a comprehensive collection of 4.8 billion unique peptides from public sequencing repositories to enable our proteomics analyses. We analyzed fecal samples from ulcerative colitis (UC) patients using a tandem mass spectrometry (LC-MS/MS) workflow coupled to ComPIL in search of aberrant UC-associated proteins. We found 176 host and microbial protein groups differentially enriched between the healthy (control) or UC volunteer groups. Notably, gene ontology (GO) enrichment analysis revealed that serine-type endopeptidases are overrepresented in UC compared to healthy volunteers. Additionally, we demonstrate the feasibility of serine hydrolase chemical enrichment from fecal samples using a biotinylated fluorophosphate (FP) probe. Our findings illustrate that probe-susceptible hydrolases from hosts and microbes are likely active in the distal gut. Finally, we appliedde novopeptide sequencing methods to our metaproteomics data to estimate the size of the “dark peptidome,” the complement of peptides unidentified using ComPIL. We posit that our metaproteomics methods are generally applicable to future microbiota analyses and that our list of FP probe-enriched hydrolases may represent an important functionality to understanding the etiology of UC.
The demographic contributions of connectivity versus local dynamics to population growth of an endangered bird
Authors: Reichert Brian E. , Fletcher Robert J. , Kitchens Wiley M.
Published: November 2020

Conservation and management increasingly focus on connectivity, because connectivity driven by variation in immigration rates across landscapes is thought to be crucial for maintaining local population and metapopulation persistence. Yet, efforts to quantify the relative role of immigration on population growth across the entire range of species and over time have been lacking.

We assessed whether immigration limited local and range‐wide population growth of the endangered snail kite Rostrhamus sociabilis in Florida, USA, over 18 years using multi‐state, reverse‐time modelling that accounts for imperfect detection of individuals and unobservable states. Demographic contributions of immigration varied depending on the dynamics and geographic position of the local populations, were scale‐dependent and changed over time.

By comparing the relative contributions of immigration versus local demography for periods of significant change in local abundance, we found empirical evidence for a disproportionately large role of immigration in facilitating population growth of a centrally located population—a connectivity ‘hub’. The importance of connectivity changed depending of the spatial scale considered, such that immigration was a more important driver of population growth at small versus large spatial scales. Furthermore, the contribution of immigration was much greater during time periods when local population size was small, emphasizing abundance‐dependent rescue effects.

Our findings suggest that efforts aimed at improving local breeding habitat will likely be most effective at increasing snail kite population growth. More broadly, our results provide much needed information on the role of connectivity for population growth, suggesting that connectivity conservation may have the greatest benefits when efforts focus on centrally located habitat patches and small populations. Furthermore, our results highlight that connectivity is highly dynamic over time and that interpreting the effects of connectivity at local scales may not transfer to region‐wide dynamics.
Bees provide pollination service to Campsis radicans (Bignoniaceae), a primarily ornithophilous trumpet flowering vine
Authors: Van Nest Byron N. , Edge Andrea A. , Feathers Michael V. , Worley Anne C. , Moore Darrell
Published: November 2020

Pollination syndromes refer to stereotyped floral characteristics (flower colour, shape, etc.) that are associated with a functional group of pollinators (bee, bird, etc.).

The trumpet creeper Campsis radicans, endemic to the southeast and mid‐west United States, has been assigned to the hummingbird‐pollination syndrome, due mainly to its red, trumpet‐shaped flowers.

Previous studies demonstrated that the ruby‐throated hummingbird Archilochus colubris is C. radicans' primary pollinator, but anecdotal data suggest various bee species may provide pollination service when hummingbirds are absent.

This study characterised C. radicans nectar volume and concentration by time of day. Nectar volume was suitable for hummingbirds, but concentration was higher than typical hummingbird‐pollinated plants (∼20% w/w); at ∼30% w/w, it approached the concentration expected in bee‐pollinated plants (∼50% w/w). We also found substantial amounts of nectar at night.

Two C. radicans populations received virtually no hummingbird visits, but the number of bees were markedly higher than in the populations previously described. Interestingly, there were no night‐time visitors despite the large quantity of nocturnal nectar.

Based on previously published pollen delivery per visit by various species, this study estimated that cumulative deposition by bees routinely reached pollen deposition thresholds for setting fruit in C. radicans. They are, unequivocally, the predominant pollinators in these populations, thus providing pollination service in the absence of hummingbirds.

These results highlight C. radicans as a food source for native bees and add to the understanding of how floral phenotypes can facilitate pollination by disparate functional groups.
Hydroxyurea: a reappraisal of its cutaneous side effects and their management
Authors: Bulte Camille A. , Hoegler Karl M. , Kutlu Ömer , Khachemoune Amor
Published: November 2020

Hydroxyurea (HU) is known to cause a broad spectrum of cutaneous side effects, ranging from relatively benign to severe. Although dermatologists are often consulted for the treatment of these side effects, a comprehensive resource discussing the different types and their management is lacking. In this study, we conducted a literature search in order to critically evaluate the reported types and management of hydroxyurea's cutaneous side effects, as well as review its mechanism of action, dermatologic uses, and common systemic side effects. Relatively common and benign side effects include hyperpigmentation, xerosis, and skin atrophy. While serious cutaneous side effects such as leg ulcers or nonmelanoma skin cancers occur in a substantial proportion of patients, these may resolve with HU discontinuation and proper dermatologic management. Therefore, it is crucial for dermatologists to be aware of these various cutaneous side effects and their management as prompt diagnosis and proper treatment will improve patient outcomes.
Tidal-charge effects on the superradiance of rotating black holes
Authors: de Oliveira Ednilton S.
Published: November 2020

The changes a (negative) tidal charge causes at the phenomenon of superradiance which occurs around rotating black holes are investigated. This is made by computing the amplification factors of massless scalar waves being scattered by the black hole. It is shown that the increase of the tidal-charge intensity leads to a considerable enhancement of energy extraction from near-extreme black holes. Such improvement results from the fact that extreme black holes with more negative tidal charges spin faster. Maximum amplification decreases with the increase of the tidal charge intensity if the angular momentum of the black hole per unit mass is fixed. The tidal charge may also change crucially the superradiance phenomenon of massless scalar waves causing maximum amplification to occur for $$m > 1$$

m
>
1

differently from the case of Kerr black holes.
The Science and Practice of Item Response Theory in Organizations
Authors: Lang Jonas W.B. , Tay Louis
Published: November 2020

Item response theory (IRT) is a modeling approach that links responses to test items with underlying latent constructs through formalized statistical models. This article focuses on how IRT can be used to advance science and practice in organizations. We describe established applications of IRT as a scale development tool and new applications of IRT as a research and theory testing tool that enables organizational researchers to improve their understanding of workers and organizations. We focus on IRT models and their application in four key research and practice areas: testing, questionnaire responding, construct validation, and measurement equivalence of scores. In so doing, we highlight how novel developments in IRT such as explanatory IRT, multidimensional IRT, random item models, and more complex models of response processes such as ideal point models and tree models can potentially advance existing science and practice in these areas. As a starting point for readers interested in learning IRT and applying recent developments in IRT in their research, we provide concrete examples with data and R code.
Vaping disrupts ventilation-perfusion matching in asymptomatic users
Authors: Kizhakke Puliyakote Abhilash S. , Elliott Ann R. , Sá Rui C. , Anderson Kevin M. , Crotty Alexander Laura E. , Hopkins Susan R.
Published: November 2020

This research provides evidence of vaping-induced disruptions in ventilation-perfusion matching in young, healthy, asymptomatic adults with normal spirometry who habitually vape. The changes in ventilation and perfusion distributions, both at baseline and acutely after vaping, and the potential implications on hypoxic vasoconstriction are particularly relevant in understanding the pathogenesis of vaping-induced dysfunction. Our imaging-based approach provides evidence of potential subclinical alterations in lung function below thresholds of detection using spirometry.
Research on Quality Anomaly Recognition Method Based on Optimized Probabilistic Neural Network
Authors: Li Li-li , Chen Kun , Gao Jian-min , Li Hui
Published: November 2020

Aiming at the problems of the lack of abnormal instances and the lag of quality anomaly discovery in quality database, this paper proposed the method of recognizing quality anomaly from the quality control chart data by probabilistic neural network (PNN) optimized by improved genetic algorithm, which made up deficiencies of SPC control charts in practical application. Principal component analysis (PCA) reduced the dimension and extracted the feature of the original data of a control chart, which reduced the training time of PNN. PNN recognized successfully both single pattern and mixed pattern of control charts because of its simple network structure and excellent recognition effect. In order to eliminate the defect of experience value, the key parameter of PNN was optimized by the improved (SGA) single-target optimization genetic algorithm, which made PNN achieve a higher rate of recognition accuracy than PNN optimized by standard genetic algorithm. Finally, the above method was validated by a simulation experiment and proved to be the most effective method compared with traditional BP neural network, single PNN, PCA-PNN without parameters optimized, and SVM optimized by particle swarm optimization algorithm.
Investigation of the miRNA and mRNA Coexpression Network and Their Prognostic Value in Hepatocellular Carcinoma
Authors: Zhang Hao , Chen Xi , Yuan Yufeng
Published: November 2020

Purpose. To identify pivotal differentially expressed miRNAs and genes and construct their regulatory network in hepatocellular carcinoma. Methods. mRNA (GSE101728) and microRNA (GSE108724) microarray datasets were obtained from the NCBI Gene Expression Omnibus (GEO) database. Then, we identified the differentially expressed miRNAs and mRNAs. Sequentially, transcription factor enrichment and gene ontology (GO) enrichment analysis for miRNA were performed. Target genes of these differential miRNAs were obtained using packages in R language (R package multiMiR). After that, downregulated miRNAs were matched with target mRNAs which were upregulated, while upregulated miRNAs were paired with downregulated target mRNA using scripts written in Perl. An miRNA‐mRNA network was constructed and visualized in Cytoscape software. For miRNAs in the network, survival analysis was performed. And for genes in the network, we did gene ontology (GO) and KEGG pathway enrichment analysis. Results. A total of 35 miRNAs and 295 mRNAs were involved in the network. These differential genes were enriched in positive regulation of cell‐cell adhesion, positive regulation of leukocyte cell‐cell adhesion, and so on. Eight differentially expressed miRNAs were found to be associated with the OS of patients with HCC. Among which, miR‐425 and miR‐324 were upregulated while the other six, including miR‐99a, miR‐100, miR‐125b, miR‐145, miR‐150, and miR‐338, were downregulated. Conclusion. In conclusion, these results can provide a potential research direction for further studies about the mechanisms of how miRNA affects malignant behavior in hepatocellular carcinoma.
Image Restoration Based on Stochastic Resonance in a Parallel Array of Fitzhugh–Nagumo Neuron
Authors: Zhang Huage , Yu Jinfei , Ma Yumei , Pan Zhenkuan , Zhao Jingjing
Published: November 2020

The poor denoising effect for noisy grayscale images with traditional processing methods would be obtained under strong noise condition, and some image details would be lost. In this paper, a parallel array model of Fitzhugh–Nagumo (FHN) neurons was proposed, which can restore noisy grayscale images well with low peak signal-to-noise ratio (PSNR) conditions and the image details are better preserved. Firstly, the row-column scanning method was used to convert the 2D grayscale image into a 1D signal, and then the 1D signal was converted into a binary pulse amplitude modulation (BPAM) signal by signal modulation. The modulated signal was input to an FHN parallel array for stochastic resonance (SR). Finally, the array output signal was restored to a 2D gray image, and the image restoration effect was analyzed based on the PSNR and Structural SIMilarity (SSIM) index. It is shown that the SR effect can be exhibited in an array of FHN neuron nonlinearities by increasing the array size, and the image restoration effect is significantly better than the traditional image restoration method, and larger PSNR and SSIM can be obtained. It provides a new idea for grayscale image restoration in a low PSNR environment.
Deep Learning for Retail Product Recognition: Challenges and Techniques
Authors: Wei Yuchen , Tran Son , Xu Shuxiang , Kang Byeong , Springer Matthew
Published: November 2020

Taking time to identify expected products and waiting for the checkout in a retail store are common scenes we all encounter in our daily lives. The realization of automatic product recognition has great significance for both economic and social progress because it is more reliable than manual operation and time-saving. Product recognition via images is a challenging task in the field of computer vision. It receives increasing consideration due to the great application prospect, such as automatic checkout, stock tracking, planogram compliance, and visually impaired assistance. In recent years, deep learning enjoys a flourishing evolution with tremendous achievements in image classification and object detection. This article aims to present a comprehensive literature review of recent research on deep learning-based retail product recognition. More specifically, this paper reviews the key challenges of deep learning for retail product recognition and discusses potential techniques that can be helpful for the research of the topic. Next, we provide the details of public datasets which could be used for deep learning. Finally, we conclude the current progress and point new perspectives to the research of related fields.
Refugee status is associated with double the odds of psychological distress in mid-to-late life: Findings from the Canadian Longitudinal Study on Aging
Authors: Tong Hongmei , Lung Yu , Lin Shen (Lamson) , Kobayashi Karen M , Davison Karen M , Agbeyaka Senyo , Fuller-Thomson Esme
Published: November 2020

Psychological distress is associated with a range of negative outcomes including lower quality of life and an increased risk of premature all-cause mortality. The prevalence of, and factors associated with, psychological distress among middle-aged and older Canadians are understudied. Using the Canadian Longitudinal Study on Aging (CLSA) baseline data, this study examined factors associated with psychological distress among adults between 45 and 85 years, including refugee status and a wide range of sociodemographic, health-related and social support characteristics. Psychological distress was measured by Kessler’s Psychological Distress Scale-K10 scores. Bivariate and multivariable binary logistic regression analyses were conducted. The prevalence of psychological distress was significantly higher among the 244 refugees (23.8%), compared to 23,149 Canadian-born Canadians (12.8%) and 4,765 non-refugee immigrants (12.6%), despite the fact that the average time the refugees had lived in Canada was more than four decades. The results of the binary logistic regression analysis indicated refugees had twice the age-sex adjusted odds of psychological distress (OR = 2.31, 95% CI: 1.74, 3.07). Even after further adjustment for 16 potential risk factors, a significant relationship remained between refugee status and psychological distress (OR = 1.56; 95% CI = 1.12, 2.17). Other significant factors associated with psychological distress included younger age, female gender, visible minority status, lower household income, not having an undergraduate degree, multimorbidities, chronic pain, and lack of social support. Policies and interventions addressing psychological distress among Canadians in mid- to later life should target refugees and other vulnerable groups.
A latent variable approach to measuring wartime sexual violence
Authors: Krüger Jule , Nordås Ragnhild
Published: November 2020

Conflict-related sexual violence is an international security problem and is sometimes used as a weapon of war. It is also a complex and hard-to-observe phenomenon, constituting perhaps one of the most hidden forms of wartime violence. Latent variable models (LVM) offer a promising avenue to account for differences in observed measures. Three annual human rights sources report on the sexual violence practices of armed conflict actors around the world since 1989 and were coded into ordinal indicators of conflict-year prevalence. Because information diverges significantly across these measures, we currently have a poor scientific understanding with regard to trends and patterns of the problem. In this article, we use an LVM approach to leverage information across multiple indicators of wartime sexual violence to estimate its true extent, to express uncertainty in the form of a credible interval, and to account for temporal trends in the underlying data. We argue that a dynamic LVM parametrization constitutes the best fit in this context. It outperforms a static latent variable model, as well as analysis of observed indicators. Based on our findings, we argue that an LVM approach currently constitutes the best practice for this line of inquiry and conclude with suggestions for future research.
Bereavement Outcomes for Atheist Individuals: The Role of Spirituality, Discrimination, and Meaning
Authors: Sawyer Jacob S.
Published: November 2020

The present study applied several concepts typically included in thanatology research to an atheist sample. Atheists are a growing segment of the population in the United States, though little is known about this group. A sample of 355 adults who self-identify as atheist completed an online survey assessing forms of spirituality, anti-atheist discrimination, and meaning reconstruction in order to examine associations between these variables and bereavement outcomes of complicated grief and psychological distress. Results of a multiple regression analysis suggested that spirituality was not related to bereavement outcomes, anti-atheist discrimination was related to poorer bereavement outcomes, while the relationship between meaning reconstruction and bereavement outcomes was mixed. These results provide a foundation for additional exploration of bereavement processes in atheist individuals, and implications for future research and practice are discussed.
Reversing the flow of short-term missions within a partnership model: Perceptual outcomes
Authors: Twibell Simone Mulieri
Published: November 2020

Short-term missions provide opportunities for the formation of cross-cultural relationships and joint evangelistic endeavors. Scholars have challenged the typical unidirectional nature of short-term mission and partnership efforts, advocating for a more bidirectional flow of resources. This article analyzes the dynamics of reverse short-term missions with the goal of understanding their contributions from the perspective of the American hosts. The author suggests that reverse short-term missions bridge social capital across social networks and function as “networks of invigoration” by bringing information benefits to their hosts. These types of exchanges have the potential to help the American church reinterpret familiar experiences and see the mission of the church in a new way. Five perceptual outcomes are identified: alteration of perspectives; service opportunities for the hosts; renewal of spiritual commitments; first-hand exposure to a different culture; and contact with faith-mission models.
Intraluminal thrombus effect on the progression of abdominal aortic aneurysms by using a multistate continuous-time Markov chain model
Authors: Zhang Liangliang , Zambrano Byron A. , Choi Jongeun , Lee Whal , Baek Seungik , Lim Chae Young
Published: November 2020

Objective

To investigate the relationship between the characteristics of intraluminal thrombus (ILT) with abdominal aortic aneurysm (AAA) expansion.

Methods

This retrospective clinical study applied homogeneous multistate continuous-time Markov chain models to longitudinal computed tomography (CT) data from Korean patients with AAA. Four AAA states were considered (early, mild, severe, fatal) and the maximal thickness of the ILT (maxILT), the fraction of the wall area covered by the ILT (areafrac) and the fraction of ILT volume (volfrac) were used as covariates.

Results

The analysis reviewed longitudinal CT images from 26 patients. Based on likelihood-ratio statistics, the areafrac was the most significant biomarker and maxILT was the second most significant. In addition, within AAAs that developed an ILT layer, the analysis found that the AAA expands relatively quickly during the early stage but the rate of expansion reduces once the AAA has reached a larger size.

Conclusion

The results recommend surgical intervention when a patient has an areafrac more than 60%. Although this recommendation should be considered with caution given the limited sample size, physicians can use the proposed model as a tool to find such recommendations with their own data.
Proctor-guided virtual reality–enhanced three-dimensional video-assisted thoracic surgery: an excellent tutoring model for lung segmentectomy
Authors: Guerrera Francesco , Nicosia Samanta , Costardi Lorena , Lyberis Paraskevas , Femia Federico , Filosso Pier Luigi , Arezzo Alberto , Ruffini Enrico
Published: November 2020

Objective:

Lung segmentectomy using video-assisted thoracoscopic surgery (VATS) is an effective strategy to treat early-stage lung cancer. The objective of this case report is to show the efficacy of Hyper Accuracy 3D™ (HA3D) reconstruction as a tool for trainee surgeons and expert surgeons to perform complex procedures.

Methods:

An 84-year-old man was treated for colon-rectal cancer. During follow-up, a pulmonary nodule on the right anterior upper lobe suspected for intestinal metastasis was revealed by a computed tomography scan. According to functional tests and radiology, a right anterior upper lobe segmentectomy was planned. HA3D lung reconstruction was used during surgery.

Results:

Using the HA3D virtual model, the procedure was performed with healthy tissue sparing, ensuring safe resection margins. No postoperative morbidities were noted. The patient referred good pain control. The hospital stay was 6 days.

Conclusions:

VATS segmentectomy is a technically demanding procedure. HA3D lung reconstruction can help surgeons effectively perform the resection, aiding at individuating intersegmental planes, bronchi, and vessels, guaranteeing oncologic radicality and safe surgical margins, and preserving respiratory function.
Securing Fixed Orthodontic Components With Vinyl Polysiloxane for Ease During Orthognathic Surgery
Authors: Ram RSVM Raghu , Ranganayakulu I , Viswanadh K Anand
Published: November 2020

Unease from brackets, archwires, and ligature ties during orthognathic surgery makes oral and maxillofacial surgeons to distract from their work field, which in turn makes precise maneuvering and fixation of the jaws challenging. The present article describes a simple, useful clinical tip which eliminates the above problem by covering the fixed orthodontic components using vinyl polysiloxane impression material (putty).
Writing With Data: A Study of Coding on a Data-Journalism Team
Authors: Lindgren Chris Aaron
Published: November 2020

Coding has typically been understood as an engineering practice, where the meaning of code has discrete boundaries as a technology that does precisely what it says. Multidisciplinary code studies reframed this technological perspective by positing code as the latest form of writing, where code’s meaning is always partial and dependent on situational factors. Building out from this premise, this article theorizes coding as a form of writing with data through a qualitative case study of a web developer’s coding on a data-journalism team. I specifically theorize code as a form of intermediary writing to examine how his coding to process and analyze data sets involved the construction and negotiation of emergent problems throughout his coding tasks. Findings suggest how he integrated previous coding experience with an emerging sense of how code helped him write and revise the data. I conclude by considering the implications of these findings and discuss how writing and code studies could develop mutually informative approaches to coding as a situated and relational writing activity.
The Influence of Training in Cross-Culturalism on Future Nurses: Can Education Change Prejudiced Attitudes Toward Migrants?
Authors: Sánchez-Ojeda María Angustias , Fernández-Gomez Elisabet , Ortiz-Gómez María del Mar , Alemany-Arrebola Inmaculada
Published: November 2020

Introduction

Increased migration may lead to an increase in prejudiced attitudes in the host population, which may affect the nursing care provided to this group.

Objectives

To identify the attitudes of nursing students toward Moroccan patients and to analyze whether changes in attitude toward this population have taken place after completing a course on cross-culturalism.

Method

A quasi-experimental design with a single group and pretest/posttest measurements. The sample consisted of 116 nursing students.

Results

There were significant differences after receiving the course on cross-culturalism, with a more positive influence on students who exhibited the most negative attitudes in the pretest phase.

Discussion

Nursing students have negative attitudes toward the Moroccan population as do the rest of the host population, but these attitudes improve after their training in the course on cross-culturalism.
Adaptive consensus building in emergency group decision-making with hesitant fuzzy linguistic information: a perspective based on disappointment theory
Authors: Zhang Shitao , Ma Zhenzhen , Liu Xiaodi , Xu Hao
Published: November 2020

In this article, an adaptive consensus model that considers individual disappointment emotion is proposed for emergency multi-attribute group decision-making (MAGDM) problems with hesitant fuzzy linguistic information. Subsequently, it is applied to choose the optimal emergency alternative(s) for the prevention and control of COVID-19 on a college campus. The main innovations and contributions of this article are as follows: (a) Individual modified perceived utility (MPU) based on disappointment theory is integrated into the determination of attribute weights and construction of consensus reaching process (CRP). (b) The MPU-based individual contribution degree and the MPU-based soft group consensus degree are developed. (c) The new emergency CRP mechanism not only considers the rewards and penalties of expert weights but also regards the adaptive updating of attribute weights. Compared with the existing emergency MAGDM models in a hesitant fuzzy linguistic environment, the proposed consensus model has some advantages in improving consensus efficiency and simulating uncertain psychological behavior.