bluuebunny/crossref_metadata_2025_split huggingface dataset:
NOJAH: Not Just Another Heatmap for Genome-Wide Cluster Analysis
Authors: Rupji Manali , Dwivedi Bhakti , Kowalski Jeanne 
Published: September 2018

AbstractSince their inception, several tools have been developed for cluster analysis and heatmap construction. The application of such tools to the number and types of genome-wide data available from next generation sequencing (NGS) technologies requires the adaptation of statistical concepts, such as in defining a most variable gene set, and more intricate cluster analyses method to address multiple omic data types. Additionally, the growing number of publicly available datasets has created the desire to estimate the statistical significance of a gene signature derived from one dataset to similarly group samples based on another dataset. The currently available number of tools and their combined use for generating heatmaps, along with the several adaptations of statistical concepts for addressing the higher dimensionality of genome-wide NGS-derived data, has created a further challenge in the ability to replicate heatmap results. We introduce NOJAH (NOt Just Another Heatmap), an interactive tool that defines and implements a workflow for genome-wide cluster analysis and heatmap construction by creating and combining several tools into a single user interface. NOJAH includes several newly developed scripts for techniques that though frequently applied are not sufficiently documented to allow for replicability of results. These techniques include: defining a most variable gene set (a.k.a., ‘core genes’), estimating the statistical significance of a gene signature to separate samples into clusters, and performing a result merging integrated cluster analysis. With only a user uploaded dataset, NOJAH provides as output, among other things, the minimum documentation required for replicating heatmap results. Additionally, NOJAH contains five different existing R packages that are connected in the interface by their functionality as part of a defined workflow for genome-wide cluster analysis. The NOJAH application tool is available at http://bbisr.shinyapps.winship.emory.edu/NOJAH/ with corresponding source code available at https://github.com/bbisr-shinyapps/NOJAH/.
Multi-Omic Profiling Reveals Dynamics of the Phased Progression of Pluripotency
Authors: Yang Pengyi , Humphrey Sean J. , Cinghu Senthilkumar , Pathania Rajneesh , Oldfield Andrew J. , Kumar Dhirendra , Perera Dinuka , Yang Jean Y.H. , James David E. , Mann Matthias , Jothi Raja 
Published: September 2018

SUMMARYPluripotency is highly dynamic and progresses through a continuum of pluripotent stem-cell states. The two states that bookend the pluripotency continuum, naïve and primed, are well characterized, but our understanding of the intermediate states and transitions between them remain incomplete. Here, we dissect the dynamics of pluripotent state transitions underlying pre-to post-implantation epiblast differentiation. Through comprehensive mapping of the proteome, phosphoproteome, transcriptome, and epigenome of mouse embryonic stem cells transitioning from naïve to primed pluripotency, we find that rapid, acute, and widespread changes to the phosphoproteome precede ordered changes to the epigenome, transcriptome, and proteome. Reconstruction of kinase-substrate networks reveals signaling cascades, dynamics, and crosstalk. Distinct waves of global proteomic changes demarcate discrete phases of pluripotency, characterized by cell-state-specific surface marker expression. Our data provide new insights into the multi-layered control of the phased progression of pluripotency and a foundation for modeling mechanisms underlying pre-to post-implantation epiblast differentiation.HIGHLIGHTSMulti-ome maps of cells transitioning from naïve to primed pluripotencyPhosphoproteome dynamics precede changes to epigenome, transcriptome, and proteomeKinase-substrate network reconstruction uncovers signaling dynamics and crosstalkProteins and cell surface markers that track pluripotent state transitionsComparative analysis of mouse and human pluripotent states
Complete Genome Sequence of the Wolbachia wAlbB Endosymbiont of Aedes albopictus
Authors: Sinha Amit , Li Zhiru , Sun Luo , Carlow Clotilde K. S. 
Published: September 2018

AbstractWolbachia, an alpha-proteobacterium closely related to Rickettsia is a maternally transmitted, intracellular symbiont of arthropods and nematodes. Aedes albopictus mosquitoes are naturally infected with Wolbachia strains wAlbA and wAlbB. Cell line Aa23 established from Ae. albopictus embryos retains only wAlbB and is a key model to study host-endosymbiont interactions. We have assembled the complete circular genome of wAlbB from the Aa23 cell line using long-read PacBio sequencing at 500X median coverage. The assembled circular chromosome is 1.48 megabases in size, an increase of more than 300 kb over the published draft wAlbB genome. The annotation of the genome identified 1,205 protein coding genes, 34 tRNA, 3 rRNA, 1 tmRNA and 3 other ncRNA loci. The long reads enabled sequencing over complex repeat regions which are difficult to resolve with short-read sequencing. Thirteen percent of the genome is comprised of IS elements distributed throughout the genome, some of which cause pseudogenization. Prophage WO genes encoding some essential components of phage particle assembly are missing, while the remainder are scattered around the genome. Orthology analysis identified a core proteome of 536 orthogroups across all completed Wolbachia genomes. The majority of proteins could be annotated using Pfam and eggNOG analyses, including ankyrins and components of the T4SS. KEGG analysis revealed the absence of 5 genes in wAlbB which are present in other Wolbachia. The availability of a complete circular chromosome from wAlbB will enable further biochemical, molecular and genetic analyses on this strain and related Wolbachia.Data depositionRaw data from PacBio sequencing have been deposited in the NCBI SRA database under BioProject accession number PRJNA454708, as runs SRR7784284, SRR7784285, SRR7784286, SRR7784287. The paired-end reads from Illumina library used for indel correction are available from NCBI SRA database as accession SRR7623731. The assembled genome and annotations have been submitted to the NCBI GenBank database with accession number CP031221.
Methane-linked mechanisms of electron uptake from cathodes byMethanosarcina barkeri
Authors: Rowe Annette R. , Xu Shuai , Gardel Emily , Bose Arpita , Girguis Peter , Amend Jan P. , El-Naggar Mohamed Y. 
Published: September 2018

AbstractTheMethanosarcinales, a lineage of cytochrome-containing methanogens, have recently been proposed to participate in direct extracellular electron transfer interactions within syntrophic communities. To shed light on this phenomenon, we applied electrochemical techniques to measure electron uptake from cathodes byMethanosarcina barkeri, which is an important model organism that is genetically tractable and utilizes a wide range of substrates for methanogenesis. Here we confirm the ability ofM. barkerito perform electron uptake from cathodes and show that this cathodic current is linked to quantitative increases in methane production. The underlying mechanisms we identified include, but are not limited to, a recently proposed association between cathodes and methanogen-derived extracellular enzymes (e.g. hydrogenases) that can facilitate current generation through the formation of reduced and diffusible methanogenic substrates (e.g. hydrogen). However, after minimizing the contributions of such extracellular enzymes and using a mutant lacking hydrogenases, we observe a lower potential hydrogen-independent pathway that facilitates cathodic activity coupled to methane production inM. barkeri. Our electrochemical measurements of wild-type and mutant strains point to a novel and extracellular-enzyme-free mode of electron uptake able to take up electrons at potentials lower than - 498 mV vs. SHE (over 100 mV more reduced than the observed hydrogenase midpoint potential under these conditions). These results suggest thatM. barkerican perform multiple modes (hydrogenase-mediated and free extracellular enzyme-independent) of electrode interactions on cathodes including a mechanism pointing to a direct interaction, which has significant applied and ecological implications.ImportanceMethanogenic Archaea are of fundamental applied and environmental relevance. This is largely due to their activities in a wide range of anaerobic environments, generating gaseous reduced carbon that can be utilized as a fuel source. While the bioenergetics of a wide variety of methanogens has been well studied with respect to soluble substrates, mechanistic understanding of their interaction with solid phase redox active compounds is limited. This work provides insight into solid phase redox interactions inMethanosarcinausing electrochemical methods. We highlight a previously undescribed mode of electron uptake from cathodes, that is potentially informative of direct interspecies electron transfer interactions in theMethanosarcinales.
A new approach to journal ranking: social structure in hospitality and tourism journals
Authors: Koseoglu Mehmet Ali 
Published: September 2018

PurposeThis study introduces a new approach, called the social structure approach, for ranking academic journals by focusing on hospitality and tourism journals; and a hybrid metric, including the combination of the journal impact factor via citations and a social network metric, called the journal knowledge domain index (JKDI).Design/methodology/approachTwenty-five hospitality and tourism journals were selected to test this approach. Collaboration-based metrics, productivity-based metrics, and network-based metrics are considered components of the social structure approach. Additionally, a hybrid metric, including the combination of the journal impact factor via citations and a social network metric, JKDI, is developed.FindingsThe study’s findings show that top or leading journals have a weaker position in some social structure approach metrics compared to other (or follower) journals. However, according to the JKDI, leading journals have remained constant with the other ranking studies.Practical implicationsThe ranking of academic journals is vital for the stakeholders of academia. Consequently, the findings of this study may help stakeholders to design an optimal ranking system and formulate and implement effective research strategies for knowledge creation and dissemination.Originality/valueAs one of the first in the journal-ranking literature, this study has significant implications, as it introduces a new ranking approach.
Extending the job embeddedness-life satisfaction relationship
Authors: Ampofo Emmanuel Twumasi , Coetzer Alan , Poisat Paul 
Published: September 2018

PurposeThis exploratory study adopts a stakeholder perspective on organisational effectiveness. The purpose of this paper is to examine the job embeddedness (JE)–life satisfaction relationship, moderating roles of gender and community embeddedness and mediating role of innovative behaviour.Design/methodology/approachUsing a snowballing approach, data were collected from 549 participants employed in organisations located in four major metropolitan centres in South Africa.FindingsAnalyses revealed a positive relationship between JE and life satisfaction. Gender moderated the JE–life satisfaction relationship, such that the relationship was stronger among females than males. Community embeddedness moderated the organisation embeddedness–life satisfaction relationship, such that the relationship was stronger when participants were highly embedded in their community. Finally, innovative behaviour mediated the relationship between organisation embeddedness and life satisfaction.Practical implicationsManagers could enhance employees’ life satisfaction through practices that increase on-the-job and off-the-job embeddedness. Furthermore, organisations could encourage employees’ innovative behaviours through workplace supervisors’ supportive responses to innovative employees.Originality/valueJE researchers have yet to focus on the personal benefits of embeddedness for employees. Results of the study provide several contributions to this research direction. The study uses JE as a composite construct to confirm its relationship with life satisfaction. It also expands the JE–life satisfaction relationship by examining moderators of the relationship and a mediating variable in the relationship.
Alcohol Intake Interacts with CDKAL1, HHEX, and OAS3 Genetic Variants, Associated with the Risk of Type 2 Diabetes by Lowering Insulin Secretion in Korean Adults
Authors: Park Sunmin , Liu Meiling , Kang Suna 
Published: September 2018

BackgroundSince alcohol intake increases the prevalence of type 2 diabetes (T2DM) in Koreans, we tested the hypothesis that the interactions of genetic variants involved in β‐cell function and mass with alcohol intake increase the T2DM risk.MethodsThe single nucleotide polymorphisms (SNPs) were selected by genome‐wide association study for insulin secretion after adjusting for age, gender, area of residence, body mass index, and alcohol intake (p < 1 × 10−4) in 8,842 middle‐aged adults in the Ansan/Ansung cohort. Genetic risk scores (GRSs) were calculated by summing the risk alleles of 4 selected SNPs, CDKAL1 rs7754840 and rs9460546, HHEX rs5015480, and OAS3 rs2072134. The GRSs were categorized into 3 groups by tertiles, and the association between GRS and insulin secretion was measured using logistic regression after adjusting for confounding factors in the Ansan/Ansung cohort. The results were confirmed by the Rural cohort.ResultsHOMA‐IR was higher and HOMA‐B was much lower in the High‐GRS than the Low‐GRS in both cohorts. T2DM risk was higher by approximately 1.5‐fold in the High‐GRS than in the Low‐GRS in both cohorts. In the High‐GRS group, HOMA‐B decreased by 0.89‐ and 0.62‐fold in comparison with the Low‐GRS in the Ansan/Ansung cohort and Rural cohort. The GRS interacted with alcohol intake to increase the risk of developing T2DM in the Ansan/Ansung cohort (p = 0.036) and Rural cohort (p = 0.071). The risk of T2DM increased in the High‐GRS group with high alcohol intake and it was associated with decreased HOMA‐B. High alcohol intake decreased HOMA‐B regardless of GRS, and HOMA‐B was lower in the descending order of Medium‐GRS, Low‐GRS, and High‐GRS. However, HOMA‐IR was not altered by alcohol intake, but was elevated in the High‐GRS more than in the other groups.ConclusionsSubjects with a High‐GRS had an elevated risk of T2DM even with moderate alcohol intakes due to lower HOMA‐B. High alcohol intake appears to be a risk factor for all Asians regardless of alcohol intake.
Oesophagectomy at a New Zealand regional centre: where to now?
Authors: Yuan Lance , Hider Phillip , Walsh Michael , Srinivasa Sanket , Rodgers Michael , Booth Michael , Grant Mark , Brown Anna , Koea Jonathan 
Published: September 2018

BackgroundThis study aims to define contemporary trends in characteristics, costs and management of patients diagnosed with oesophageal adenocarcinoma in New Zealand.MethodsClinical, pathological and management data of the 135 patients presenting with histologically proven adenocarcinoma to our institution over a 5‐year period (January 2010 to December 2014) was collected. Primary analysis reviewed patient demographics, co‐morbidities, treatment strategy and survival. Secondary analysis defined operative outcomes including complications, mortality rates and overall survival to December 2016.ResultsThirty‐eight patients underwent oesophago‐gastrectomy (resection rate 28%) with curative intent following neoadjuvant chemotherapy with Clavien‐Dindo ≥3 complications in 17 patients (46%). Actuarial survivals from surgery at 1, 3 and 5 years were (79, 55 and 50%), with 19 patients (54%) alive and disease free at a median follow‐up of 26.5 months (range 1–82 months). Overall, this represented one sixth of the national volume of oesophagectomy. Ninety‐seven patients were managed non‐surgically due to metastatic or advanced local disease (n = 64), co‐morbid status (n = 27), patients choice (n = 2) and unknown (n = 4). Median survival from diagnosis in non‐resected patients was 9 months (range 1–40 months).ConclusionOesophagectomy remains a challenging procedure for any institution, although good results can be achieved. Foci for referral are emerging in New Zealand for the surgical management of oesophageal cancer.
Review of epiglottitis in the post Haemophilus influenzae type‐b vaccine era
Authors: Baird Samantha M. , Marsh Philip A. , Padiglione Alex , Trubiano Jason , Lyons Bernard , Hays Andrew , Campbell Matthew C. , Phillips Damien 
Published: September 2018

BackgroundThis study reviewed the demographics, presentation, management, complications and outcomes of acute epiglottitis post Haemophilus influenzae type‐b vaccine introduction in Australia.MethodsRetrospective review of acute epiglottitis at four Victorian tertiary centres from 2011 to 2016 was conducted. Patient characteristics, presentation, investigations, management, complications and outcomes were recorded. Subgroup analysis aiming to identify risk factors for patients requiring acute airway management was performed.ResultsEighty‐seven adult and six paediatric cases were identified. The most frequent clinical findings in adults were sore throat (88.5%), dysphagia (71.3%), odynophagia (57.5%), dysphonia (56.3%) and fever (55.2%); 75.9% required intensive care unit admission. Airway compromise requiring intubation occurred in 27.6%, with 12.5% of these patients undergoing emergency surgical airways. Stridor, hypoxia, shortness of breath, odynophagia and lymphadenopathy were statistically more frequent amongst cases requiring airway intervention (P < 0.05). Cultures revealed mixed results with no aetiological pattern. H. influenzae type‐b was never cultured. Amongst paediatric cases, fever, tachycardia and stridor were frequently observed and all were admitted to intensive care unit. Two of six required intubation and one underwent surgical intervention. There were no deaths, but one patient suffered a hypoxic brain injury.ConclusionModern epiglottitis is not the disease previously encountered by clinicians. With changing demographics and varying organisms, management is adapting to reflect this. Complications are rare, and symptomatology at presentation aids earlier recognition of patients who may require airway protection.
Computational design of transformables
Authors: Yuan Ye , Zheng Changxi , Coros Stelian 
Published: September 2018

AbstractWe present a computational approach to designing transformables, physical characters that can shape‐shift to take on vastly different forms. The design process begins with a morphological description of an input character and a target object that it should transform into. Guided by a set of objectives that model the core attributes of desirable transformable designs, optimized embeddings are interactively generated. Intuitively, embeddings represent tightly folded character configurations that fit within the target object. From any feasible embedding, skin meshes are then generated for each body part of the character. The process for generating these 3D models is based on a segmentation of the target object, which is achieved through a growth‐based model applied to a multiple level set representation of the transformable. A set of transformation‐aware post‐processing algorithms ensure the feasibility of the final designs. Building on this technical core, our computational design system provides many opportunities for users to inject their intuition and personal preferences into the process of creating transformables, while shielding them from tasks that are challenging and tedious. As a result, they can intuitively explore the vast space of design possibilities. We demonstrated the effectiveness of our computational approach by creating a variety of transformable designs, three of which we fabricate.
FTP‐SC: Fuzzy Topology Preserving Stroke Correspondence
Authors: Yang Wenwu , Seah Hock‐Soon , Chen Quan , Liew Hong‐Ze , Sýkora Daniel 
Published: September 2018

AbstractStroke correspondence construction is a precondition for vectorized 2D animation inbetweening and remains a challenging problem. This paper introduces the FTP‐SC, a fuzzy topology preserving stroke correspondence technique, which is accurate and provides the user more effective control on the correspondence result than previous matching approaches. The method employs a two‐stage scheme to progressively establish the stroke correspondence construction between the keyframes. In the first stage, the stroke correspondences with high confidence are constructed by enforcing the preservation of the so‐called “fuzzy topology” which encodes intrinsic connectivity among the neighboring strokes. Starting with the high‐confidence correspondences, the second stage performs a greedy matching algorithm to generate a full correspondence between the strokes. Experimental results show that the FTP‐SC outperforms the existing approaches and can establish the stroke correspondence with a reasonable amount of user interaction even for keyframes with large geometric and spatial variations between strokes.
877. ANDIRA ANTHELMIA
Authors: Pennington R. Toby , de Lima Haroldo C. , Watherston Neil , Inches Fiona 
Published: September 2018

SummaryThe history, taxonomy, distribution, habitat and cultivation requirements of the unusual legume tree Andira anthelmia (Vellozo) J.F. MacBride, are discussed; a full botanical description, pollination, colour illustration and dissection drawings are also provided.
879. PASSIFLORA EMARGINATA
Authors: Hilgenhof Rebecca , Aguirre Morales Adriana Carolina , Caetano Creucí Maria 
Published: September 2018

SummaryPassiflora emarginataBonpl. (synonymsAstrophea emarginata(Bonpl.) M.Roem. andPassiflora caucaensisHolm‐Niels.), a medium‐sized tree from Colombia, is described and illustrated. Its history, taxonomy, conservation status, observations from the wild and cultivation including its propagation are discussed.
Political change and informality
Authors: Elsayed Ahmed , Wahba Jackline 
Published: September 2018

AbstractThis paper examines informality during the political and economic turmoil that accompanied the Arab Spring revolution in Egypt. The paper focuses on unprotected employment and the extent to which it changed by educational level immediately after the January Uprising of 2011. We find that over time and particularly after the revolution, informal employment has increased for both high‐ and low‐educated workers, albeit through different paths: high‐educated workers were more likely to be stuck in informality, while low‐educated formal workers were more likely to lose their contracts. The increase in informal employment in the wake of the Arab Spring is more pronounced for the high‐educated. The results suggest a high level of rigidity in the Egyptian labour market, even in the wake of the Arab Spring.