bluuebunny/crossref_metadata_2025 huggingface dataset:
Septic arthritis of the hip joint due to Bacteroides fragilis in a paraplegic patient
Authors: Shalman Anna , Acker Asaf , Shalman Alexander , Frank Dmitry , Borer Abraham , Koyfman Leonid , Kotlovker Vladimir , Saidel-Odes Lisa , Gabay Ohad , Klein Moti , Brotfain Evgeni
Published: October 2019

Septic arthritis of native joints is a potentially life-threatening disease. The most frequently isolated pathogens are Gram-positive cocci.

Bacteroides fragilis

is a rare pathogen in joint infections and is usually associated with immunocompromised and debilitated patients. Most cases of

B. fragilis

joint infection are related to skin or local perineal infections or are secondary to

B. fragilis

bacteraemia from another source, for example from the gastrointestinal tract. We present a clinical case of

B. fragilis

septic arthritis involving a native hip joint in a previously healthy paraplegic patient.
Wikidata as a FAIR knowledge graph for the life sciences
Authors: Waagmeester Andra , Stupp Gregory , Burgstaller-Muehlbacher Sebastian , Good Benjamin M. , Griffith Malachi , Griffith Obi , Hanspers Kristina , Hermjakob Henning , Hudson Toby S. , Hybiske Kevin , Keating Sarah M. , Manske Magnus , Mayers Michael , Mietchen Daniel , Mitraka Elvira , Pico Alexander R. , Putman Timothy , Riutta Anders , Queralt-Rosinach Núria , Schriml Lynn M. , Shafee Thomas , Slenter Denise , Stephan Ralf , Thornton Katherine , Tsueng Ginger , Tu Roger , Ul-Hasan Sabah , Willighagen Egon , Wu Chunlei , Su Andrew I.
Published: October 2019

Wikidata is a community-maintained knowledge base that epitomizes the FAIR principles of Findability, Accessibility, Interoperability, and Reusability. Here, we describe the breadth and depth of biomedical knowledge contained within Wikidata, assembled from primary knowledge repositories on genomics, proteomics, genetic variants, pathways, chemical compounds, and diseases. We built a collection of open-source tools that simplify the addition and synchronization of Wikidata with source databases. We furthermore demonstrate several use cases of how the continuously updated, crowd-contributed knowledge in Wikidata can be mined. These use cases cover a diverse cross section of biomedical analyses, from crowdsourced curation of biomedical ontologies, to phenotype-based diagnosis of disease, to drug repurposing.
Connectivity characterization of the mouse basolateral amygdalar complex
Authors: Hintiryan Houri , Bowman Ian , Johnson David L. , Korobkova Laura , Zhu Muye , Khanjani Neda , Gou Lin , Gao Lei , Yamashita Seita , Bienkowski Michael S. , Garcia Luis , Foster Nicholas N. , Benavidez Nora L. , Song Monica Y. , Lo Darrick , Cotter Kaelan , Becerra Marlene , Aquino Sarvia , Cao Chunru , Cabeen Ryan , Stanis Jim , Fayzullina Marina , Ustrell Sarah , Boesen Tyler , Zhang Zheng-Gang , Fanselow Michael S. , Golshani Peyman , Hahn Joel D. , Wickersham Ian R. , Ascoli Giorgio A. , Zhang Li I. , Dong Hong-Wei
Published: October 2019

The basolateral amygdalar complex (BLA) is implicated in behavioral processing ranging from fear acquisition to addiction. Newer methods like optogenetics have enabled the association of circuit-specific functionality to uniquely connected BLA cell types. Thus, a systematic and detailed connectivity profile of BLA projection neurons to inform granular, cell type-specific interrogations is warranted. In this work, we applied computational analysis techniques to the results of our circuit-tracing experiments to create a foundational, comprehensive, multiscale connectivity atlas of the mouse BLA. The analyses identified three domains within the classically defined anterior BLA (BLAa) that house target-specific projection neurons with distinguishable cell body and dendritic morphologies. Further, we identify brain-wide targets of projection neurons located in the three BLAa domains as well as in the posterior BLA (BLAp), ventral BLA (BLAv), lateral (LA), and posterior basomedial (BMAp) nuclei. Projection neurons that provide input to each nucleus are also identifed. Functional characterization of some projection-defined BLA neurons were demonstrated via optogenetic and recording experiments. Hypotheses relating function to connection-defined BLA cell types are proposed.
Unifying single-cell annotations based on the Cell Ontology
Authors: Wang Sheng , Pisco Angela Oliveira , McGeever Aaron , Brbic Maria , Zitnik Marinka , Darmanis Spyros , Leskovec Jure , Karkanias Jim , Altman Russ B.
Published: October 2019

Single cell technologies have rapidly generated an unprecedented amount of data that enables us to understand biological systems at single-cell resolution. However, joint analysis of datasets generated by independent labs remains challenging due to a lack of consistent terminology to describe cell types. Here, we present OnClass, an algorithm and accompanying software for automatically classifying cells into cell types part of the controlled vocabulary that forms the Cell Ontology. A key advantage of OnClass is its capability to classify cells into cell types not present in the training data because it uses the Cell Ontology graph to infer cell type relationships. Furthermore, OnClass can be used to identify marker genes for all the cell ontology categories, independently of whether the cells types are present or absent in the training data, suggesting that OnClass can be used not only as an annotation tool for single cell datasets but also as an algorithm to identify marker genes specific to each term of the Cell Ontology, offering the possibility of refining the Cell Ontology using a data-centric approach.
Mapping the brain-wide network effects by optogenetic activation of the corpus callosum
Authors: Chen Yi , Sobczak Filip , Pais-Roldán Patricia , Schwarz Cornelius , Koretsky Alan P. , Yu Xin
Published: October 2019

The optogenetically driven manipulation of circuit-specific activity enabled functional causality studies in animals, but its global effect on the brain is rarely reported. Here, we applied simultaneous fMRI with calcium recording to map brain-wide activity by optogenetic activation of fibers running in one orientation along the corpus callosum(CC) connecting the barrel cortex(BC). Robust positive BOLD signals were detected in the ipsilateral BC due to antidromic activity, which spread to ipsilateral motor cortex(MC) and posterior thalamus(PO). In the orthodromic target (contralateral barrel cortex), positive BOLD signals were reliably evoked by 2Hz light pulses, whereas 40Hz light pulses led to a reversed sign of BOLD - indicative of CC-mediated inhibition. This presumed optogenetic CC-mediated inhibition was further elucidated by pairing light with peripheral whisker stimulation at varied inter-stimulus intervals. Whisker induced positive BOLD, and calcium signals were reduced at inter-stimulus intervals of 50/100ms. The calcium-amplitude modulation (AM)-based correlation with whole-brain fMRI signal revealed that the inhibitory effects spread to contralateral BC as well as ipsilateral MC and PO. This work raises the need of fMRI to elucidate the brain-wide network activation in response to projection-specific optogenetic stimulation.
EGFR Oncogenes Expressed In Glioblastoma Are Activated As Covalent Dimers And Paradoxically Stimulated By Erlotinib
Authors: O’Connor Matthew , Zhang Jie , Markovic Sandra , Romashko Darlene , Salomatov Andrei , Ishiyama Noboru , Iacone Roberto , Flohr Alexander , Nicolaides Theodore , Mayweg Alexander , Epstein David , Buck Elizabeth
Published: October 2019

Mutation of both the intracellular catalytic domain and the extracellular domain of the receptor for epidermal growth factor (EGFR) can drive oncogenicity. Despite clinical success with targeting EGFR catalytic site mutations, no drugs have proven effective in patients expressing allosteric extracellular domain EGFR mutations, including glioblastomas (GBM) where these mutations are highly expressed. We define the molecular mechanism for oncogenic activation of families of extracellular EGFR mutations and reveal how this mechanism renders current generation small molecule ATP-site inhibitors ineffective. We demonstrate that a group of commonly expressed extracellular domain EGFR mutants expressed in GBM is activated by disulfide-bond mediated covalent dimerization, collectively referred to as locked dimerization (LoDi) EGFR oncogenes. Strikingly, small molecules binding to the active kinase conformation (Type I), but not those binding to the inactive kinase conformation (Type II), potently inhibit catalytic site mutants, but induce covalent dimerization and activate LoDi-EGFR oncogenes, manifesting in paradoxical acceleration of proliferation.

Significance

Our data demonstrate how the locked-dimer mechanism of EGFR oncogenesis has a profound impact on the activity of small molecule inhibitors. This provides a mechanistic understanding for the failure of current generation EGFR inhibitors to effectively treat LoDi-EGFR mutants in GBM, and sets guidelines for discovery of selective LoDi-EGFR inhibitors.
Same father, same face: deep-learning reveals paternally-derived signalling of kinship in a wild primate
Authors: Charpentier Marie JE , Harté Mélanie , Poirotte Clémence , Bellefon Jade Meric de , Laubi Benjamin , Kappeler Peter M , Renoult Julien P
Published: October 2019

Animal faces convey important information such as individual health status1 or identity2,3. Human and nonhuman primates rely on highly heritable facial traits4,5 to recognize their kin6–8. However, whether these facial traits have evolved for this specific function of kin recognition remains unknown. We present the first unambiguous evidence that inter-individual facial similarity has been selected to signal kinship using a state-of-the-art artificial intelligence approach based on deep neural networks and long-term data on a natural population of nonhuman primates. The typical matrilineal society of mandrills, is characterized by an extreme male’s reproductive skew with one male generally siring the large majority of offspring born into the different matrilines each year9. Philopatric females are raised and live throughout their lives with familiar maternal half-sisters (MHS) but because of male’s reproductive monopolization, they also live with unfamiliar paternal half-sisters (PHS). Because kin selection predicts differentiated interactions with kin rather than nonkin10 and that PHS largely outnumber MHS in a mandrills’ social group, natural selection should favour mechanisms to recognize PHS. Here, we first show that PHS socially interact with each other as much as MHS do, both more than nonkin. Second, using artificial intelligence trained to recognize individual mandrills from a database of 16k portrait pictures, we demonstrate that facial similarity increases with genetic relatedness. However, PHS resemble more to each other than MHS do, despite both kin categories sharing similar degrees of genetic relatedness. We propose genomic imprinting as a plausible genetic mechanism to explain paternally-derived facial similarity among PHS selected to improve kin recognition. This study further highlights the potential of artificial intelligence to study evolutionary mechanisms driving variation between phenotypes.
A virus-encoded protein suppresses methylation of the viral genome in the Cajal body through its interaction with AGO4
Authors: Wang Liping , Ding Yi , He Li , Zhang Guiping , Zhu Jian-Kang , Lozano-Duran Rosa
Published: October 2019

In plants, establishment ofde novoDNA methylation is regulated by the RNA-directed DNA methylation (RdDM) pathway. RdDM machinery is known to concentrate in the Cajal body, but the biological significance of this localization has remained elusive. Here, we show that the anti-viral methylation of theTomato yellow leaf curl virus(TYLCV) genome occurs specifically in the Cajal body ofNicotiana benthamianacells. Methylation of the viral genome is countered by a virus-encoded protein, V2, which interacts with the central RdDM component AGO4, interfering with its binding to the viral DNA; Cajal body localization of the V2-AGO4 interaction is required for the viral protein to exert this function. Taken together, our results draw a long sought-after functional connection between RdDM, the Cajal body, and anti-viral DNA methylation, paving the way for a deeper understanding of DNA methylation and anti-viral defences in plants.
Poor concordance of floxed sequence recombination in single neural stem cells: Implications for cell autonomous studies
Authors: Dause Tyler Joseph , Kirby Elizabeth Diana
Published: October 2019

To manipulate target gene function in specific adult cell populations, tamoxifen-dependent CreERT2 is widely used to drive inducible, site-specific recombination of LoxP flanked sequences. In studies of cell autonomous target gene function, it is common practice to combine these CreERT2-lox systems with a ubiquitously-expressed stop-floxed fluorescent reporter gene to identify single cells supposedly undergoing target gene recombination. Here, we studied the reliability of using Cre-induced recombination of one gene to predict recombination in another gene at the single cell level in adult hippocampal neural stem and progenitor cells. Using two separate stop-floxed reporters plus a Nestin promoter-driven CreERT2, we found that, in individual cells, expression of one reporter was a poor predictor of expression of the other. These findings imply that use of stop-floxed reporters to investigate cell autonomous gene function is likely to lead to false conclusions because recombination in separate genes shows poor concordance in individual cells.
FuzzyVariantsExplorer: Graded exploration of genomic data and fuzzy queries
Authors: Falda Marco
Published: October 2019

FuzzyVariantExplorer is a web interface and a fuzzy search system for exploring richly annotated genomes in a flexible way. The application allows combining vague constraints in expressive logical queries to retrieve graded sets of genes and their associated variants. Results can be further refined in a visual way by selecting keywords and categories that are extracted from the underlying annotations and weighted with a statistical significance score; keywords can then be clustered using Latent Dirichlet Allocation and explored visually. The system has been applied to a set of Saccharomyces cerevisiae genome annotations and a few variants.

Availability

FuzzyVariantExplorer source code is available at the URL https://bitbucket.org/mfalda/fuzzyvariantsexplorer/src/ and has been developed in Scala, TypeScript and R.

Contact

marco.falda@unipd.it
Pattern similarity and connectivity of hippocampal-neocortical regions support empathy for pain
Authors: Wagner Isabella C. , Rütgen Markus , Lamm Claus
Published: October 2019

Empathy is thought to engage mental simulation, which in turn is known to rely on hippocampal-neocortical processing. Here, we tested how hippocampal-neocortical pattern similarity and connectivity contributed to pain empathy. Using this approach, we analyzed a data set of 102 human participants who underwent functional MRI while painful and non-painful electrical stimulation was delivered to themselves or to a confederate. As hypothesized, results revealed increased pattern similarity between fist-hand pain and pain empathy (compared to non-painful control conditions) within the hippocampus, retrosplenial cortex, the temporo-parietal junction and anterior insula. While representations in these regions were unaffected by confederate similarity, pattern similarity in the dorsal MPFC was increased the more dissimilar the other individual was perceived. Moreover, hippocampal connectivity with regions engaged in first-hand pain was also increased during pain empathy, during which hippocampal coupling with the fusiform gyrus positively scaled with self-report measures of individual perspective taking skills. These findings highlight that shared representations and interactions within a hippocampal-neocortical network support pain empathy. This potentially reflects memory-based mental simulation processes, which seem partially modulated by personality traits and the perceived similarity of the other individual in pain.
Phenylpropionc acid produced by gut microbiota alleviates acetaminophen-induced hepatotoxicity
Authors: Cho Sungjoon , Yang Xiaotong , Won Kyoung-Jae , Leone Vanessa , Hubert Nathaniel , Chang Eugene , Chung Eunah , Park Joo-Seop , Guzman Grace , Lee Hyunwoo , Jeong Hyunyoung
Published: October 2019

Acetaminophen (APAP) overdose causes hepatic injury and is major contributor to acute liver injury cases. To investigate potential roles of gut microbiota in APAP-induced liver injury, C57BL/6 mice from Jackson (JAX) or Taconic (TAC) were challenged with APAP. TAC mice were more susceptible to APAP toxicity, and this disappeared upon co-housing of JAX and TAC mice. When the cecum contents from JAX and TAC mice were transplanted to germ-free mice, the mice that received TAC gut microbiota exhibited more significant hepatotoxicity after APAP administration. Non-targeted metabolomic analysis using portal vein serum and liver tissue of the mice led to identification of 19 metabolites the levels of which are associated with JAX or TAC gut microbiota. A gut bacteria-derived metabolite phenylpropionic acid (PPA) levels in cecum contents and blood were higher in mice harboring JAX gut microbiota. PPA supplementation in drinking water alleviated APAP-induced hepatotoxicity in TAC mice. This was accompanied by reduced hepatic protein levels of cytochrome P450 (CYP) 2E1, the enzyme responsible for APAP bioactivation to a toxic metabolite. This illustrates a gut microbe-liver interaction mediated by a gut bacteria-derived metabolite in modulating drug-induced liver injury.
A presynaptic spectrin network controls active zone assembly and neurotransmitter release
Authors: Wang Qi , Friend Lindsey , Vicidomini Rosario , Han Tae Hee , Nguyen Peter , Ting Chun-Yuan , Serpe Mihaela
Published: October 2019

We have previously reported thatDrosophilaTenectin (Tnc) recruits αPS2/βPS integrin to ensure structural and functional integrity at larval NMJs (Wang et al., 2018). In muscles, Tnc/integrin engages the spectrin network to regulate the size and architecture of synaptic boutons. In neurons, Tnc/integrin controls neurotransmitter release. Here we show that presynaptic Tnc/integrin modulates the synaptic accumulation of key active zone components, including the Ca2+channel Cac and the active zone scaffold Brp. Presynaptic α-Spectrin appears to be both required and sufficient for the recruitment of Cac and Brp. We visualized the endogenous α-Spectrin and found that Tnc controls spectrin recruitment at synaptic terminals. Thus, Tnc/integrin anchors the presynaptic spectrin network and ensures the proper assembly and function of the active zones. Since pre- and postsynaptic Tnc/integrin limit each other, we hypothesize that this pathway links dynamic changes within the synaptic cleft to changes in synaptic structure and function.
Toxic PR poly-dipeptides encoded by the C9orf72 repeat expansion target Kapβ2 and dysregulate phase separation of low-complexity domains
Authors: Nanaura Hitoki , Kawamukai Honoka , Fujiwara Ayano , Uehara Takeru , Nakanishi Mari , Shiota Tomo , Hibino Masaki , Aiba Yuichiro , Wiriyasermkul Pattama , Kikuchi Sotaro , Nagata Riko , Matsubayashi Masaya , Nagamori Shushi , Shoji Osami , Ishimori Koichiro , Matsumura Hiroyoshi , Sugie Kazuma , Saio Tomohide , Yoshizawa Takuya , Mori Eiichiro
Published: October 2019

Low-complexity (LC) domains of proteins are found in about one fifth of human proteome, and a group of LC-domains form labile cross-β polymers and liquid-like droplets. Polymers and droplets formed from LC-domains are dynamically regulated by posttranslational modifications and molecular chaperones including nuclear transport receptors. Repeat expansion in the first intron of a gene designated C9orf72, which is the most prevalent form of familial amyotrophic lateral sclerosis (ALS), causes nucleocytoplasmic transport deficit, however, the detailed mechanism remains unsolved. Here we show that the proline:arginine (PR) poly-dipeptides encoded by the C9orf72 repeat expansion bound nuclear transport receptor Kapβ2 through its nuclear localization signal (NLS) recognition motif, and inhibited the ability of Kapβ2 to melt fused in sarcoma (FUS) droplets by competing interaction with FUS. The findings in this study offer mechanistic insights as to how the C9orf72 repeat expansion disables nucleocytoplasmic transport and causes neurodegenerative diseases.
multiSLIDE: a web server for exploring connected elements of biological pathways in multi-omics data
Authors: Ghosh Soumita , Datta Abhik , Choi Hyungwon
Published: October 2019

Emerging multi-omics experiments pose new challenges for exploration of quantitative data sets. We present multiSLIDE, a web-based interactive tool for simultaneous heatmap visualization of interconnected molecular features in multi-omics data sets. multiSLIDE operates by keyword search for visualizing biologically connected molecular features, such as genes in pathways and Gene Ontologies, offering convenient functionalities to rearrange, filter, and cluster data sets on a web browser in a real time basis. Various built-in querying mechanisms make it adaptable to diverse omics types, and visualizations are fully customizable. We demonstrate the versatility of the tool through three example studies, each of which showcases its applicability to a wide range of multi-omics data sets, ability to visualize the links between molecules at different granularities of measurement units, and the interface to incorporate inter-molecular relationship from external data sources into the visualization. Online and standalone versions of multiSLIDE are available athttps://github.com/soumitag/multiSLIDE.
PWAS: Proteome-Wide Association Study
Authors: Brandes Nadav , Linial Nathan , Linial Michal
Published: October 2019

Over the last two decades, GWAS (Genome-Wide Association Study) has become a canonical tool for exploratory genetic research, generating countless gene-phenotype associations. Despite its accomplishments, several limitations and drawbacks still hinder its success, including low statistical power and obscurity about the causality of implicated variants. We introduce PWAS (Proteome-Wide Association Study), a new method for detecting protein-coding genes associated with phenotypes through protein function alterations. PWAS aggregates the signal of all variants jointly affecting a protein-coding gene and assesses their overall impact on the protein’s function using machine-learning and probabilistic models. Subsequently, it tests whether the gene exhibits functional variability between individuals that correlates with the phenotype of interest. By collecting the genetic signal across many variants in light of their rich proteomic context, PWAS can detect subtle patterns that standard GWAS and other methods overlook. It can also capture more complex modes of heritability, including recessive inheritance. Furthermore, the discovered associations are supported by a concrete molecular model, thus reducing the gap to inferring causality. To demonstrate its applicability for a wide range of human traits, we applied PWAS on a cohort derived from the UK Biobank (~330K individuals) and evaluated it on 49 prominent phenotypes. We compared PWAS to existing methods, proving its capacity to recover causal protein-coding genes and highlighting new associations with plausible biological mechanism.
Optimal spatial prioritization of control resources for elimination of invasive species under demographic uncertainty
Authors: Pepin Kim M. , Smyser Timothy J. , Davis Amy J. , Miller Ryan S. , McKee Sophie , VerCauteren Kurt C. , Slootmaker Chris
Published: October 2019

Populations of invasive species often spread heterogeneously across a landscape, consisting of local populations that cluster in space but are connected by dispersal. A fundamental dilemma for invasive species control is how to optimally allocate limited fiscal resources across local populations. Theoretical work based on perfect knowledge of demographic connectivity suggests that targeting local populations from which migrants originate (sources) can be optimal. However, demographic processes such as abundance and dispersal can be highly uncertain, and the relationship between local population density and damage costs (damage function) is rarely known. We used a metapopulation model to understand how observational uncertainty in abundance and connectivity, and imperfect knowledge of the damage function, affect return on investment (ROI) for optimal control strategies. Budget, observational uncertainty, and the damage function had strong effects on the optimal resource allocation strategy. Uncertainty in dispersal probability was the least important determinant of ROI. The damage function determined which resource prioritization strategy was optimal when connectivity was symmetric but not when it was asymmetric. When connectivity was asymmetric, prioritizing source populations had a higher ROI than allocating effort equally across local populations, regardless of the damage function, but uncertainty in connectivity structure and abundance reduced ROI of the optimal prioritization strategy by 57% on average depending on the control budget. With low budgets (monthly removal rate of 6.7% of population), there was little advantage to prioritizing resources, especially when connectivity was high or symmetric, and observational uncertainty had only minor effects on ROI. Allotting funding for improved monitoring appeared to be most important when budgets were moderate (monthly removal of 13-20% of the population). Our result showed that multiple sources of observational uncertainty should be considered concurrently for optimizing ROI. Accurate estimates of connectivity direction and abundance were more important than accurate estimates of dispersal rates. Developing cost-effective surveillance methods to reduce observational uncertainties, and quantitative frameworks for determining how resources should be spatially apportioned to multiple monitoring and control activities are important and challenging future directions for optimizing ROI for invasive species control programs.
Cross-species machine learning improves diagnostic classification of human psychiatric disorders
Authors: Zhan Yafeng , Wei Jianze , Liang Jian , Xu Xiu , He Ran , Robbins Trevor W. , Wang Zheng
Published: October 2019

Psychiatric disorders often exhibit shared (co-morbid) symptoms, raising controversies over accurate diagnosis and the overlap of their neural underpinnings. Because the complexity of data generated by clinical studies poses a formidable challenge, we have pursued a reductionist framework using brain imaging data of a transgenic primate model of autism spectrum disorder (ASD). Here we report an interpretable cross-species machine learning approach which extracts transgene-related core regions in the monkey brain to construct the classifier for diagnostic classification in humans. The cross-species classifier based on core regions, mainly distributed in frontal and temporal cortex, identified from the transgenic primate model, achieved an accuracy of 82.14% in one clinical ASD cohort obtained from Autism Brain Imaging Data Exchange (ABIDE-I), significantly higher than the human-based classifier (61.31%,p< 0.001), which was validated in another independent ASD cohort obtained from ABIDE-II. Such monkey-based classifier generalized to achieve a better classification in obsessive-compulsive disorder (OCD) cohorts, and enabled parsing of differential connections to right ventrolateral prefrontal cortex being attributable to distinct traits in patients with ASD and OCD. These findings underscore the importance of investigating biologically homogeneous samples, particularly in the absence of real-world data adequate for deconstructing heterogeneity inherited in the clinical cohorts.

One Sentence Summary

Features learned from transgenic monkeys enable improved diagnosis of autism-related disorders and dissection of their underlying circuits.
The Establishment of CDK9/ RNA PolII/H3K4me3/DNA Methylation Feedback Promotes HOTAIR Expression by RNA Elongation Enhancement in Cancer
Authors: Wong Chi Hin , Li Chi Han , He Qifang , Tong Joanna Hung Man , To Ka-Fai , Chen Yangchao
Published: October 2019

Long non-coding RNA HOX Transcript Antisense RNA (HOTAIR) is overexpressed in multiple cancers with diverse genetic profiles, which heavily contributed to cancer progression. However, the underlying mechanism leading to HOTAIR deregulation is largely unexplored. Here, we revealed that gene body methylation promoted HOTAIR expression through enhancing the transcription elongation process in cancer. We linked up the aberrant gene body histone and DNA methylation in promoting transcription elongation via phosphorylation of Polymerase II Ser 2 by CDK7-CDK9, and elucidated the mechanism of a positive feedback loop involving CDK7, MLL1 and DNMT3A in promoting gene body methylation and overexpressing HOTAIR. To our knowledge, this is the first time to demonstrate that a positive feedback loop that involved CDK9-mediated phosphorylation of PolII and histone and gene body methylation induced robust transcriptional elongation, which heavily contributed to the upregulation of oncogenic lncRNA in cancer.
Gender and credibility in branded storytelling
Authors: Kang Jin-Ae , Hubbard Glenn T. , Hong Sookyeong
Published: October 2019

Purpose

This paper aims to explore gender differences regarding how men and women perceive the story of a CEO and a customer of different genders in audio advertising.

Design/methodology/approach

A Web-based three-way factorial experiment was designed with three storyteller types (founder’s story, customer’s story vs informational ad), story teller’s gender (male voice vs female voice) and research participants’ gender (men vs women). In total, 549 participants were recruited through Amazon’s Mechanical Turk.

Findings

Researchers found gender-based differences in how audiences evaluated messages from the founder versus the customer of a company. There was a relationship between a male speaker’s perceived authoritativeness and audiences’ favorability to the ad, but no such relationship when the speaker was a woman.

Practical implications

A female voice elicited more favorable attitudes toward the non-story informational ad. In the customer’s story ad, relatability between the speaker and the audience mattered. Participants perceived the ad as more credible and convincing when the gender of the customer in the ad was the same as their gender.

Social implications

Women showed more favorable attitudes toward the male founder’s story compared to the female founder’s story. In evaluating the credibility of the female founder, audiences cared about her character (likability) rather than authoritativeness (expertise).

Originality/value

This study enriches the gender-related advertising-effect literature based on role congruity theory. The research contributes to the understanding of how gender bias still shapes the audiences’ evaluation of storyteller credibility.
Environmental management accounting practices, management system, and performance
Authors: Fuzi Nursyazwani Mohd , Habidin Nurul Fadly , Janudin Sharul Effendy , Ong Sharon Yong Yee
Published: October 2019

Purpose

The purpose of this paper is to examine the relationship between environmental management accounting practices (EMAP), environmental management system (EMS) and organizational performance (OPM) for Malaysian manufacturing industry by using structural equation modeling (SEM) approach.

Design/methodology/approach

The population of the Malaysian manufacturing industry comprised 2,600 manufacturing companies. The unit of analysis is the organization that participated in the survey comprised of automotive/machinery, plastics/rubber/metal, food/tobacco, electrical/electronics and chemical/woods. Out of the 2,600 questionnaires sent to the respondents, 395 were received from manufacturing companies. The collected data are analyzed with the IBM SPSS Statistics and SEM technique.

Findings

Findings found that EMS implementation as a partial mediator to improve EMAP and OPM for Malaysian manufacturing industry. Further, the implementation of EMS was found to mediate the relationship between EMAP and OPM.

Research limitations/implications

The understanding of the importance of studying the relationship between EMAP, EMS and OPM has been emphasized in the present study. In fact, the findings of this study along with its limitations have paved the way for future research in EMAP, EMS and OPM areas.

Practical implications

This research provides important guidelines for manufacturers and related companies to implement EMAP and EMS in order to improve OPM. Hence, the Malaysian manufacturing industry may need to consider the measurement of EMAP, EMS and OPM as beneficial to their manufacturing companies.

Originality/value

The research contributes to the environmental management accounting by empirically linking the relationship between EMAP, EMS and OPM for Malaysian manufacturing industry.
Optimal trajectory planning of industrial robot for improving positional accuracy
Authors: Rout Amruta , BBVL Deepak , Biswal Bibhuti B. , Mahanta Golak Bihari
Published: October 2019

Purpose

The purpose of this paper is to improve the positional accuracy, smoothness on motion and productivity of industrial robot through the proposed optimal joint trajectory planning method. Also a new improved algorithm, i.e. non-dominated sorting genetic algorithm-II (NSGA-II) with achievement scalarizing function (ASF) has been proposed to obtain better optimal results compared to previously used optimization methods.

Design/methodology/approach

The end effector positional errors can be reduced by limiting the uncertainties of dynamic parameter variations like torque rate of joints. The jerk induced in robot joints due to acceleration variations are need to be minimized which otherwise induces vibrations in the manipulator that causes deviation in the encoders. But these lead to a vast increase in total travel time which affects the cost function of trajectory planning. Therefore, these three objectives need to be minimized individually so that an optimal trajectory path can be achieved with minimum positional error.

Findings

The simulation results have been obtained by running the proposed hybrid NSGA-II with ASF in MATLAB R2017a software. The optimal time intervals have been used to calculate jerk, acceleration and torque values for consecutive points on the trajectory path. From the simulation and experimental results, it can be concluded that the optimization technique could be used effectively for the trajectory planning of six-axis industrial manipulator in the joint space on the basis of minimum time-jerk-torque rate criteria.

Originality/value

In this paper, a new approach based on hybrid multi-objective optimization technique by combining NSGA-II with ASF has been applied to find the minimal time-jerk- torque rate joint trajectory of a six-axis industrial robot for obtaining higher positional accuracy. The results obtained from the execution of algorithm have been validated through experimentation using Kawasaki RS06L industrial robot for a particular defined path.
The interest rate sensitivity of output and prices with different levels of financial inclusion
Authors: Nguyen Huong Thi Truc
Published: October 2019

Purpose

The purpose of this paper is to evaluate the interest rate (IR) sensitivity of output and prices in developing economies with different levels of financial inclusion (FI) for the period 2007Q1–2017Q4.

Design/methodology/approach

By using the PCA method to construct an FI index for each country, the author divides the sample into two groups (high and low FI levels). Then, with panel vector autoregressions on per group estimated to assess the strength of the impulse response of output and prices to IR shock.

Findings

The findings show that the impact of an IR shock on output and inflation is greater in economies with a higher degree of FI.

Practical implications

The finding indicates the link between FI and the effectiveness of IRs as a monetary policy tool, thereby helping Central banks to have a clearer goal of FI to implement their monetary policy.

Originality/value

This study emphasizes the important role of FI in the economy. From there, an FI solution is integrated into the construction and calculation of its impact on monetary policy, improving the efficiency of monetary policy transmission, contributing to price stability and sustainable growth.
Supporting integrated care in practice
Authors: Billings Jenny , Mikelyte Rasa , Coleman Anna , MacInnes Julie , Allen Pauline , Croke Sarah , Checkland Kath
Published: October 2019

Purpose

The purpose of this paper is to investigate the perceptions of key informants on a national support programme for the development of new care models (NCM) in England (2015/2016–2017/2018). It focuses on the perceived facilitators and barriers affecting the development and implementation of the NCM programme and offers some insight into the role of national level support in enabling local integration initiatives.

Design/methodology/approach

A set of 29 interviews were carried out with a variety of respondents at the national level (including current and past programme leads, strategic account managers, advisors to the programme and external regulators) between October 2017 and March 2018, and analysed thematically.

Findings

A set of facilitative elements of the programme were identified: the development of relationships and alliances, strong local and national leadership, the availability of expert knowledge and skills, and additional funding. Challenges to success included perceived expectations from the national Vanguard programme, oversight and performance monitoring, engagement with regulators, data availability and quality, as well as timetables and timescales. Crucially, the facilitators and challenges were found to interact in dynamic and complex ways, which resulted in significant tensions and ambiguities within the support programme.

Research limitations/implications

While the sample was drawn from a range of different senior players and the authors ensured a diverse sample associated with the NCM support programme, it inevitably cannot be complete and there may have been valuable perspectives absent.

Originality/value

The paper demonstrates that the analysis of facilitators and challenges with respect to the national support of implementation of integrated care initiatives should move beyond the focus on separate influencing factors and address the tensions that the complex interplay among these factors create.
Pretreatment of silk for digital printing: identifying influential factors using fractional factorial experiments
Authors: Faisal Saira , Tronci Aurelio , Ali Muhammad , Lin Long , Mao Ningtao
Published: October 2019

Purpose

The purpose of this study is to identify the most influential factors affecting the printing properties and print quality of digitally printed silk fabrics in terms of colour strength and fixation percentage.

Design/methodology/approach

In this study, five factors (concentration of thickener, concentration of urea, concentration of alkali, pH of pretreatment liquor and steaming duration) were investigated using a blocked 25−1fractional factorial experiment. The type of thickeners [polyacrylic acid and polyacrylamide (PAM)] were considered as a block.

Findings

Linear models were obtained and statistically tested using both analysis of variance and coefficient of determination (R2), and they were found to be accurate at 90 per cent confidence level. It was revealed that concentration of alkali, concentrations of urea and pH of the pretreatment liquor had an increasing effect on colour strength, whereas concentration of thickener and steaming duration showed decreasing effect on colour strength of digitally printed silk fabrics. Furthermore, concentration of alkali, concentrations of urea had increasing effect on dye fixation percentage, whereas steaming duration showed decreasing effect on dye fixation percentage of digitally printed silk fabrics. In addition, PAM thickener based pretreatment recipe exhibited better printing properties for the digitally printing of silk fabrics.

Originality/value

The main influences and significant two-factor interactions were discussed in detail to gain a better understanding of the printing properties of digitally printed silk fabrics. The findings of this study are useful for further optimisation of pre- and post-treatment processes for digital printing of silk fabrics.
Engineering of surface properties of polypropylene nonwovens through oxygen plasma for enhanced color yield of pigment prints
Authors: Javid Amjed , Irshad Awais , Ashraf Munir , Rehman Abdur , Riaz Shagufta , Iqbal Kashif
Published: October 2019

Purpose

This paper aims to evaluate the effect of plasma treatment on the performance and color strength of pigment printed polypropylene nonwovens fabrics.

Design/methodology/approach

Melt spun nonwoven fabrics have been treated with plasma discharge using oxygen as a reactive gas to activate their surfaces for better interfacial interactions. The untreated and plasma treated fabrics are printed using pigment print pastes to investigate the print properties of nonwoven fabrics that are correlated to surface characteristics. The printed fabrics are characterized through FTIR, color fastness to washing and rubbing, flexural rigidity and moisture management observations.

Findings

The fabrics treated with oxygen plasma exhibited higher wettability, higher overall moisture management capability, enhanced color strength and superior color fastness to washing. However, bending length and flexural rigidity have been increased.

Originality/value

This study offers promising findings regarding the surface activation of polypropylene nonwovens for enhanced performance, comfort and color fastness characteristics.
Food fraud: economic insights into the dark side of incentives
Authors: Ehmke Mariah Dolsen , Bonanno Alessandro , Boys Kathryn , Smith Trenton G.
Published: October 2019

In this review, we contextualise the articles in this special issue, relating them to existing food fraud research, and identify food fraud research trends, challenges and priorities for the near term. We accomplish these aims through a comprehensive review of research by food scientists, economists, other social scientists, legal experts, government research groups and international trade organisations. Existing food fraud research is heavily weighted towards food science, packaging and labelling, and legal areas of knowledge discovery. Moving forward, research is needed pertaining to general economic welfare outcomes from food fraud incidences, economic incentives to deter frauds, economic spillovers from fraud incidences to other food products and markets (domestic and international) and further delineation of the effect of different types of food fraud on consumer and producer welfare. The articles in this special issue make significant contributions to understanding of the role of food fraud in consumer decisions, measuring consumer welfare losses from fraud, food fraud spillover effects to other markets and new frameworks for fraud analysis.
Physicochemical, microbiological, rheological, and sensory properties of yoghurts with new polysaccharide extracts from Lactarius volemus Fr. using three probiotics
Authors: Huang Yanyan , Zhao Shan , Yao Kun , Liu Dongmei , Peng Xin , Huang Juan , Huang Yongyao , Li Li
Published: October 2019

Polysaccharide extracts (0.05 ~ 0.15% w/w) from Lactarius volemus Fr. were used as growth factors and were incorporated into three different probiotic yoghurts. Yoghurts with polysaccharide extracts had a significantly improved water‐retention capacity and reduced pH (P < 0.05). Polysaccharide extracts also significantly increased the viable count and essential amino acid content in the probiotic yoghurts (P < 0.05). The best sensory properties were achieved with the addition of 0.10% polysaccharide extracts. Our study suggests that polysaccharide extracts from L. volemus Fr. are a highly efficient growth factor for shortening the fermentation period and improving the quality of probiotic yoghurts.
Long‐term predictors of residual or recurrent cervical intraepithelial neoplasia 2–3 after treatment with a large loop excision of the transformation zone: a retrospective study
Authors: Fernández‐Montolí M‐E , Tous S , Medina G , Castellarnau M , García‐Tejedor A , de Sanjosé S
Published: October 2019

Objective

To assess the long‐term risk factors predicting residual/recurrent cervical intraepithelial neoplasia (CIN 2–3) and time to recurrence after large loop excision of the transformation zone (LLETZ).

Design

Retrospective study.

Setting

Colposcopy clinic.

Population

242 women with CIN 2–3 treated between 1996 and 2006 and followed up until June 2016.

Methods

Age, margins, and high‐risk human papillomavirus (HR‐HPV) were estimated using Cox proportional hazard and unconditional logistic regression models. The cumulative probability of treatment failure was estimated by Kaplan–Meier analysis.

Main outcome measure

Histologically confirmed CIN 2–3, HR‐HPV, margins, age.

Results

CIN 2–3 was associated with HR‐HPV (HR = 30.5, 95% confidence interval [CI] = 3.80–246.20), age >35 years (HR = 5.53, 95% CI = 1.22–25.13), and margins (HR = 7.31, 95% CI = 1.60–33.44). HR‐HPV showed a sensitivity of 88.8% and a specificity of 80%. Ecto+/endocervical+ (16.7%), uncertain (19.4%) and ecto−/endocervical+ margins (9.1%) showed a higher risk of recurrence (odds ratio [OR] = 13.20, 95% CI = 1.02–170.96; OR = 15.84, 95% CI = 3.02–83.01; and OR = 6.60, 95% CI = 0.88–49.53, respectively). Women with involved margins and/or who were HR‐HPV positive had more treatment failure than those who were HR‐HPV negative or had clear margins (P‐log‐rank <0.001).

Conclusions

HR‐HPV and margins seem essential for stratifying post‐LLETZ risk, and enable personalised management. Given that clear margins present a lower risk, a large excision may be indicated in older women to reduce the risk.

Tweetable abstract

After LLETZ for CIN 2–3, recurrences appear more often in women with positive HR‐HPV and involved margins and aged over 35.
Sperm Ultrastructure of corydalid Corydalus diasi Navás (Megaloptera, Neuropterida, Insecta) with phylogenetic considerations
Authors: Cuquetto‐Leite Lívia , Barbosa Aline , Salles Frederico Falcão , Mancini Karina Carvalho
Published: October 2019

Spermatozoa of the Megaloptera Corydalus diasi (Corydalidae) showed a two‐layered acrosome, similar to Raphidioptera, but different from the acrosomal arrangement in Ascalaphidae, Coniopterygidae and Myrmeleontidae (Neuroptera families) and Sialidae (Megaloptera). Also, the acrosomal shape differs from both Raphidioptera and Neuroptera examined so far. The nucleus is cylindrical with condensed chromatin, resembling the sperm of Sialidae, Raphidioptera and Neuroptera. The transition region of C. diasi does not have the nucleus surrounded by centriolar microtubules, and thus, it differs from Sialidae, whose character has been previously considered a synapomorphy between Megaloptera and Raphidioptera. The flagella analysed here possess a 9 + 9 + 2 axoneme arrangement, two elongated circular mitochondrial derivatives and triangular accessory bodies, which are also reported in Raphidioptera. In summary, there are numerous sperm differences between Corydalidae and Sialidae, besides several characters shared between Corydalidae and Raphidioptera. However, several of these similarities appear to be plesiomorphisms rather than synapomorphies. Additionally, this is the first spermatic description for Corydalidae and the second for Megaloptera order. Therefore, considering the number of genres that comprise this family and the lack of spermiocladistics studies for Corydalidae, we recommended that new studies on the field should be performed to better understand the sperm pattern within the Corydalidae genus.