bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conservation and Divergence of YODA MAPKKK Function in Regulation of Grass Epidermal Patterning
Authors: Abrash Emily , Gil M Ximena Anleu , Matos Juliana L , Bergmann Dominique C 
Published: March 2018

AbstractAll multicellular organisms must properly pattern cell types to generate functional tissues and organs. The organized and predictable cell lineages of the Brachypodium leaf enabled us to characterize the role of the MAPK kinase kinase gene BdYODA1 in regulating asymmetric cell divisions. We find that YODA genes promote normal stomatal spacing patterns in both Arabidopsis and Brachypodium, despite species-specific differences in those patterns. Using lineage tracing and cell fate markers, we show that, unexpectedly, patterning defects in bdyoda1 mutants do not arise from faulty physical asymmetry in cell divisions but rather from improper enforcement of alternative cellular fates after division. These cross-species comparisons allow us to refine our interpretations of MAPK activities during plant asymmetric cell divisions.Summary StatementAnalysis of Brachypodium leaf epidermis development reveals that the MAPKKK, BdYODA1, regulates asymmetric divisions by enforcing resultant cell fates rather than driving initial physical asymmetries.
Roles of G1 cyclins in the temporal organization of yeast cell cycle - a transcriptome-wide analysis
Authors: Teufel Lotte , Tummler Katja , Flöttmann Max , Herrmann Andreas , Barkai Naama , Klipp Edda 
Published: March 2018

AbstractOscillating gene expression is crucial for correct timing and progression through cell cycle. In Saccharomyces cerevisiae, G1 cyclins Cln1-3 are essential drivers of the cell cycle and have an important role for temporal fine-tuning. We measured time-resolved transcriptome-wide gene expression for wild type and cyclin single and double knockouts over cell cycle with and without osmotic stress. Clustering of expression profiles, peak-time detection of oscillating genes, integration with transcription factor network dynamics, and assignment to cell cycle phases allowed us to quantify the effect of genetic or stress perturbations on the duration of cell cycle phases. Cln1 and Cln2 showed functional differences, especially affecting later phases. Deletion of Cln3 led to a delay of START followed by normal progression through later phases. Our data and network analysis suggest mutual effects of cyclins with the transcriptional regulators SBF and MBF.
Nach is a novel ancestral subfamily ofthe CNC-bZIP transcription factors selected during evolution from the marine bacteria to human
Authors: Zhu Yuping , Wang Meng , Xiang Yuancai , Qiu Lu , Hu Shaofan , Zhang Zhengwen , Mattjus Peter , Zhang Yiguo 
Published: March 2018

ABSTRACTAll living organisms have undergone the evolutionary selection under the changing natural environments to survive as diverse life forms. All life processes including normal homeostatic development and growth into organismic bodies with distinct cellular identifications, as well as their adaptive responses to various intracellular and environmental stresses, are tightly controlled by signaling of transcriptional networks towards regulation of cognate genes by many different transcription factors. Amongst them, one of the most conserved is the basic-region leucine zipper (bZIP) family. They play vital roles essential for cell proliferation, differentiation and maintenance in complex multicellular organisms. Notably, an unresolved divergence on the evolution of bZIP proteins is addressed here. By a combination of bioinformatics with genomics and molecular biology, we have demonstrated that two of the most ancestral family members classified into BATF and Jun subgroups are originated from viruses, albeit expansion and diversification of the bZIP superfamily occur in different vertebrates. Interestingly, a specific ancestral subfamily of bZIP proteins is identified and also designated Nach (Nrf and CNC homology) on account of their highly conservativity with NF-E2 p45 subunit-related factors Nrf1/2. Further experimental evidence reveals that Nach1/2 from the marine bacteria exerts distinctive functions from Nrf1/2 in the transcriptional ability to regulate antioxidant response element (ARE)-driven cytoprotective genes. Collectively, an insight into Nach/CNC-bZIP proteins provides a better understanding of distinct biological functions between these factors selected during evolution from the marine bacteria to human.SignificanceWe identified the novel ancestral subfamily (i.e. Nach) of CNC-bZIP transcription factors with highly conservativity from marine bacteria to human. Combination of bioinformatics with genomics and molecular biology demonstrated that two of the most ancestral family members classified into BATF and Jun subgroups are originated from viruses. The Jun and CNC subfamilies also share a common origin of these bZIP proteins. Further experimental evidence reveals that Nach1/2 from the marine bacteria exerts nuance functions from human Nrf1/2 in the transcriptional ability to regulate antioxidant response element (ARE)-driven genes, responsible for the host cytoprotection against inflammation and cancer. Overall, this study is of multidisciplinary interests to provide a better understanding of distinct biological functions between Nach/CNC-bZIPs selected during evolution.
The Origins and Consequences of Localized and Global Somatic Hypermutation
Authors: Yousif Fouad , Prokopec Stephenie D. , Sun Ren X. , Fan Fan , Lalansingh Christopher M. , Park David H. , Szyca Lesia ,   PCAWG Network, Boutros Paul C. 
Published: March 2018

AbstractCancer is a disease of the genome, but the dramatic inter-patient variability in mutation number is poorly understood. Tumours of the same type can differ by orders of magnitude in their mutation rate. To understand potential drivers and consequences of the underlying heterogeneity in mutation rate across tumours, we evaluated both local and global measures of mutation density: both single-stranded and double-stranded DNA breaks in 2,460 tumours of 38 cancer types. We find that SCNAs in thousands of genes are associated with elevated rates of point-mutations, while similarly point-mutation patterns in dozens of genes are associated with specific patterns of DNA double-stranded breaks. These candidate drivers of mutation density are enriched for known cancer drivers, and preferentially occur early in tumour evolution, appearing clonally in all cells of a tumour. To supplement this understanding of global mutation density, we developed and validated a tool called SeqKat to identify localized “rainstorms” of point-mutations (kataegis). We show that rates of kataegis differ by four orders of magnitude across tumour types, with malignant lymphomas showing the highest. Tumours withTP53mutations were 2.6-times more likely to harbour a kataegic event than those without, and 239 SCNAs were associated with elevated rates of kataegis, including loss of the tumour-suppressorCDKN2A. We identify novel subtypes of kataegic events not associated with aberrant APOBEC activity, and find that these are localized to specific cellular regions, enriched for MYC-target genes. Kataegic events were associated with patient survival in some, but not all tumour types, highlighting a combination of global and tumour-type specific effects. Taken together, we reveal a landscape of genes driving localized and tumour-specific hyper-mutation, and reveal novel mutational processes at play in specific tumour types.
Transcriptional read-through of the long non-coding RNA SVALKA governs plant cold acclimation
Authors: Kindgren Peter , Ard Ryan , Ivanov Maxim , Marquardt Sebastian 
Published: March 2018

SummaryMost DNA in the genomes of higher organisms does not encode proteins, but is transcribed by RNA polymerase II (RNAPII) into long non-coding RNA (lncRNA). The biological significance of most lncRNA is largely unclear. Here, we identify a lncRNA (SVALKA) in a cold-sensitive region of the Arabidopsis genome. Mutations in SVALKA affect the timing of maximal CBF1 expression and freezing tolerance. RNAPII read-through transcription of SVALKA results in a cryptic lncRNA overlapping CBF1 on the antisense strand, termed asCBF1. asCBF1 transcription is anti-correlated with CBF1 expression. Our molecular dissection reveals that CBF1 is suppressed by RNAPII collision stemming from the SVALKA-asCBF1 lncRNA cascade. The SVK-asCBF1 cascade provides a mechanism to tightly control CBF1 expression and timing that could be exploited to maximize freezing tolerance with mitigated fitness costs. Inversion of the transcriptional direction of a lncRNA cascade relative to the genes in a co-regulated cluster provides an elegant inbuilt negative feedback for cluster expression. Our results provide a compelling example of local gene regulation by lncRNA transcription having a profound impact on the ability of plants to appropriately acclimate to suboptimal environmental conditions.
TETyper: a bioinformatic pipeline for classifying variation and genetic contexts of transposable elements from short-read whole-genome sequencing data
Authors: Sheppard Anna E , Stoesser Nicole , German-Mesner Ian , Vegesana Kasi , Walker A Sarah , Crook Derrick W , Mathers Amy J 
Published: March 2018

ABSTRACTMuch of the worldwide dissemination of antibiotic resistance has been driven by resistance gene associations with mobile genetic elements (MGEs), such as plasmids and transposons. Although increasing, our understanding of resistance spread remains relatively limited, as methods for tracking mobile resistance genes through multiple species, strains and plasmids are lacking. We have developed a bioinformatic pipeline for tracking variation within, and mobility of, specific transposable elements (TEs), such as transposons carrying antibiotic resistance genes. TETyper takes short-read whole-genome sequencing data as input and identifies single-nucleotide mutations and deletions within the TE of interest, to enable tracking of specific sequence variants, as well as the surrounding genetic context(s), to enable identification of transposition events. To investigate global dissemination ofKlebsiella pneumoniaecarbapenemase (KPC) and its associated transposon Tn4401, we applied TETyper to a collection of >3000 publicly available Illumina datasets containingblaKPC. This revealed surprising diversity, with >200 distinct flanking genetic contexts for Tn4401, indicating high levels of transposition. Integration of sample metadata revealed insights into associations between geographic locations, host species, Tn4401sequence variants and flanking genetic contexts. To demonstrate the ability of TETyper to cope with high copy number TEs and to track specific short-term evolutionary changes, we also applied it to the insertion sequence IS26within a definedK. pneumoniaeoutbreak. TETyper is implemented in python and is freely available athttps://github.com/aesheppard/TETyper.
Genome sequencing and assessment of plant growth-promoting properties of a Serratia marcescens strain isolated from vermicompost
Authors: Matteoli Filipe P. , Passarelli-Araujo Hemanoel , A. Reis Régis Josué , da Rocha Letícia O. , de Souza Emanuel M. , Aravind L. , Olivares Fabio L. , Venancio Thiago M. 
Published: March 2018

ABSTRACTPlant-bacteria associations have been extensively studied for their potential in increasing crop productivity in a sustainable manner. Serratia marcescens is a Gram-negative species found in a wide range of environments, including soil. Here we describe the genome sequencing and assessment of plant-growth promoting abilities of S. marcescens UENF-22GI (SMU), a strain isolated from mature cattle manure vermicompost. In vitro, SMU is able to solubilize P and Zn, to produce indole compounds (likely IAA), to colonize hyphae and counter the growth of two phytopathogenic fungi. Inoculation of maize with SMU remarkably increased seedling growth and biomass under greenhouse conditions. The SMU genome has 5 Mb, assembled in 17 scaffolds comprising 4,662 genes (4,528 are protein-coding). No plasmids were identified. SMU is phylogenetically placed within a clade comprised almost exclusively of environmental strains. We were able to find the genes and operons that are likely responsible for all the interesting plant-growth promoting features that were experimentally described. Genes involved other interesting properties that were not experimentally tested (e.g. tolerance against metal contamination) were also identified. The SMU genome harbors a horizontally-transferred genomic island involved in antibiotic production, antibiotic resistance, and anti-phage defense via a novel ADP-ribosyltransferase-like protein and possible modification of DNA by a deazapurine base, which likely contributes to the SMU competitiveness against other bacteria. Collectively, our results suggest that S. marcescens UENF-22GI is a strong candidate to be used in the enrichment of substrates for plant growth promotion or as part of bioinoculants for Agriculture.
AmpUMI: Design and analysis of unique molecular identifiers for deep amplicon sequencing
Authors: Clement Kendell , Farouni Rick , Bauer Daniel E. , Pinello Luca 
Published: March 2018

AbstractMotivationUnique molecular identifiers (UMIs) are added to DNA fragments before PCR amplification to discriminate between alleles arising from the same genomic locus and sequencing reads produced by PCR amplification. While computational methods have been developed to take into account UMI information in genome-wide and single-cell sequencing studies, they are not designed for modern amplicon based sequencing experiments, especially in cases of high allelic diversity. Importantly, no guidelines are provided for the design of optimal UMI length for amplicon-based sequencing experiments.ResultsBased on the total number of DNA fragments and the distribution of allele frequencies, we present a model for the determination of the minimum UMI length required to prevent UMI collisions and reduce allelic distortion. We also introduce a user-friendly software tool called AmpUMI to assist in the design and the analysis of UMI-based amplicon sequencing studies. AmpUMI provides quality control metrics on frequency and quality of UMIs, and trims and deduplicates amplicon sequences with user specified parameters for use in downstream analysis. AmpUMI is open-source and freely available at http://github.com/pinellolab/AmpUMI.ContactIpinello@mgh.harvard.edu
The ethic of care: an HR strategy to address obesity in the workplace
Authors: Prieto Leon C. , Mathur-Helm Babita , Dawson Kasey N. 
Published: March 2018

Purpose
This paper aims to highlight an ethic of care approach human resource (HR) departments can use to address obesity in the workplace.

Design/methodology/approach
This paper is prepared by experts who add their unbiased views to a very pertinent topic.

Findings
This paper focused on an ethic of care approach to addressing obesity in the workplace and provides advice that HR departments can adopt to address this issue.

Originality/value
This paper addresses a pertinent topic in a succinct manner that saves time for practitioners and scholars alike. This paper addresses the topic of obesity in the workplace which is of a growing concern worldwide.
Machine criticality based maintenance prioritization
Authors: Gopalakrishnan Maheshwaran , Skoogh Anders 
Published: March 2018

Purpose
The purpose of this paper is to identify the productivity improvement potentials from maintenance planning practices in manufacturing companies. In particular, the paper aims at understanding the connection between machine criticality assessment and maintenance prioritization in industrial practice, as well as providing the improvement potentials.

Design/methodology/approach
An explanatory mixed method research design was used in this study. Data from literature analysis, a web-based questionnaire survey, and semi-structured interviews were gathered and triangulated. Additionally, simulation experimentation was used to evaluate the productivity potential.

Findings
The connection between machine criticality and maintenance prioritization is assessed in an industrial set-up. The empirical findings show that maintenance prioritization is not based on machine criticality, as criticality assessment is non-factual, static, and lacks system view. It is with respect to these finding that the ways to increase system productivity and future directions are charted.

Originality/value
In addition to the empirical results showing productivity improvement potentials, the paper emphasizes on the need for a systems view for solving maintenance problems, i.e. solving maintenance problems for the whole factory. This contribution is equally important for both industry and academics, as the maintenance organization needs to solve this problem with the help of the right decision support.
Cold chains, interrupted
Authors: Comes Tina , Bergtora Sandvik Kristin , Van de Walle Bartel 
Published: March 2018

Purpose
The purpose of this paper is to analyze how far technology and information enable, facilitate or support the planning and implementation decisions in humanitarian vaccine cold chains for vaccination campaigns. The authors specifically focus on three emerging technologies that have the potential to create more flexible conditions in the field, and identify the need to further explore the link between uncertainty, information and irreversibility.

Design/methodology/approach
The authors present a basic structure for the analysis of cold chain disruptions in terms of three distinct yet connected layers of deficient infrastructure and capacity, information gaps and failures in decision making. The authors then review three humanitarian technologies and their impact on vaccine campaigns along these layers. From there, a research agenda is developed to address research gaps this review brought forward.

Findings
Three critical research gaps in the areas of technology innovation for humanitarian vaccine cold chain management are presented. The authors argue that technology to improve capacity, information and decisions need to be aligned, and that the areas of uncertainty, information and irreversibility require further investigation to achieve this alignment. In this way, the paper contributes to setting the research agenda on vaccine cold chains and connects humanitarian logistics to technology, information management and decision making.

Originality/value
This paper presents the humanitarian vaccine cold chain problem from an original angle by illuminating the implications of technology and information on the decisions made during the planning and implementation phases of a vaccine campaign. The authors develop an agenda to provide researchers and humanitarians with a perspective to improve cold chain planning and implementation at the intersection of technology, information and decisions.
Publication trends in a high impact journal: the case of World Psychiatry
Authors: Elango Bakthavachalam , Hartley James 
Published: March 2018

Purpose
The purpose of this paper is to examine the bibliometric characteristics of papers published in a high impact journal World Psychiatry during the period 2006-2015.

Design/methodology/approach
The data for this study were obtained from Thompson Reuters’ “Web of Science”. Publication details were extracted for the journal title “World Psychiatry”. This study covers authorship patterns, annual growth, impact factors, document types, top contributors, international collaborations, highly cited papers and keyword analyses. Software programs such as “Histcite”, “intcoll.exe”, “Pajek” and “Leximancer” were used to analyze the publications.

Findings
More than half of the publications were by editorial materials and number of publications from low and middle income countries is very low when compared to proportion of editorial board members. Almost 40 per cent of papers came from the USA and editorial board members had considerable number of papers. Kings College London led the institutions.

Originality/value
Analysis of high impact journals in the field of psychiatry has been carried out in a very few. Hence, the results of this study will be useful to compare with other journals.
Trichoscopy of alopecia areata: An update
Authors: Waśkiel Anna , Rakowska Adriana , Sikora Mariusz , Olszewska Małgorzata , Rudnicka Lidia 
Published: March 2018

AbstractThe diagnosis of alopecia areata is usually based on clinical manifestations. However, there are several hair and scalp disorders that share similar clinical features with alopecia areata, such as tinea capitis, trichotillomania or traction alopecia. Trichoscopy as a fast, non‐invasive and easy‐to‐perform technique may help to identify subtle details and establish the correct diagnosis. The aim of this review is to present the spectrum of trichoscopic findings in alopecia areata. A systematic review of the published work was performed by searching the PubMed, Scopus and EBSCO databases, complemented by a thorough hand search of reference lists. Of 427 articles retrieved, 30 studies were eligible for quantitative analysis. The reported features of alopecia areata were: yellow dots (6–100% patients), short vellus hairs (34–100%), black dots (0–84%), broken hairs (0–71%) and exclamation mark hairs (12–71%). Tapered hairs (5–81%) were reported in few studies, but a relatively high frequency of this finding in alopecia areata may indicate their important role in the differential diagnosis of hair loss. Rarely reported features, which include upright regrowing hairs (11–96%), pigtail (circle) hairs (4–61%) and Pohl‐Pinkus constrictions (2–10%), may also be helpful in the diagnosis of alopecia areata. There is no pathognomonic trichoscopic marker for alopecia areata and the most common trichoscopic features are not the most specific. Therefore, the diagnosis should be based on the coexistence of several trichoscopic findings, not on the presence of a single feature.
Guselkumab, a human interleukin‐23 monoclonal antibody in Japanese patients with generalized pustular psoriasis and erythrodermic psoriasis: Efficacy and safety analyses of a 52‐week, phase 3, multicenter, open‐label study
Authors: Sano Shigetoshi , Kubo Hiroshi , Morishima Hitomi , Goto Ryosuke , Zheng Richuan , Nakagawa Hidemi 
Published: March 2018

AbstractGeneralized pustular psoriasis (GPP) and erythrodermic psoriasis (EP) are the rare and severe subtypes of psoriasis, which are often difficult to treat. The aim of this phase 3, open‐label study was to evaluate efficacy and safety of guselkumab, a human interleukin‐23 monoclonal antibody, in Japanese patients with GPP and EP. Guselkumab 50 mg was administrated to GPP (n = 10) and EP (n = 11) patients at weeks 0, 4 and thereafter every 8 weeks (q8w). Beginning at week 20, patients were escalated to 100 mg q8w if they met the dose escalation criteria. The primary end‐point was the proportion of patients achieving treatment success (Clinical Global Impression score of “very much improved”, “much improved” or “minimally improved”) at week 16. Safety evaluations included assessment of treatment‐emergent adverse events (TEAE) through week 52. At week 16, the proportions of GPP and EP patients achieving treatment success were 77.8% (7/9) and 90.9% (10/11), respectively. Furthermore, guselkumab treatment consistently showed improvement in responses of secondary end‐points such as Psoriasis Area and Severity Index, Investigator's Global Assessment, Japanese Dermatological Association severity index and improvement in body surface area involvement. Improvements in quality of life, as assessed by the Dermatology Life Quality Index, were also observed through week 52. The most commonly reported TEAE was nasopharyngitis (28.6%, 6/21). Safety findings were consistent with those observed previously in other studies. In conclusion, guselkumab treatment demonstrated efficacy and showed no safety concerns in Japanese patients with GPP and EP through week 52.