bluuebunny/crossref_metadata_2025 huggingface dataset:
Sensitivity and Efficacy of Boscalid, Fluazinam, and Thiophanate-Methyl for White Mold Control in Snap Bean in New York
Authors: Lehner M. S. , Del Ponte E. M. , Gugino B. K. , Kikkert J. R. , Pethybridge S. J.
Published: March 2017

White mold (Sclerotinia sclerotiorum) of leguminous crops in New York is generally managed with preventive applications of fungicides. However, no research has been conducted during the last decade to assess the sensitivity of the S. sclerotiorum population to fungicides or compare their performance under field conditions. The sensitivity of S. sclerotiorum to boscalid, fluazinam, and thiophanate-methyl was assessed in 151 isolates from 15 fields across New York using an agar dilution method with discriminatory concentrations. In addition, the effective concentration at which mycelial growth is reduced by 50% (EC50) was estimated for one representative isolate from each field. The efficacy of commercial formulations of each fungicide on white mold incidence in plants and pods was also tested in two field trials (2015 and 2016). The EC50 values ranged from 0.068 to 0.219, 0.001 to 0.002, and 1.23 to 2.15 µg/ml for boscalid, fluazinam, and thiophanate-methyl, respectively. Evidence of resistance was not found using the discriminatory concentration tests. The mycelial growth inhibition relative to the control ranged from 56 to 83%, 66 to 84%, and 53 to 83% at discriminatory concentrations of boscalid (5 µg a.i./ml), fluazinam (0.05 µg a.i./ml), and thiophanate-methyl (5 µg a.i./ml), respectively. Fourteen isolates with mycelial growth inhibition lower than 60% at 5 µg/ml of thiophanate-methyl, did not exhibit point mutations within a partial sequence of the β-tubulin gene. In the field trials, fungicides effectively reduced white mold incidence on plants by 75% (2015) and 93% (2016) and on pods by 81% (2015) and 87% (2016), both relative to the nontreated plots. However, fungicide applications led to significant increases in pod yield, relative to the nontreated plots, only in 2015 when the incidence of white mold on plants and pods were higher (85 and 49.2%) than in 2016 (31.3 and 10.3%). Although fungicide resistance was not detected, and thus control failures reported by New York snap bean growers may be due to other factors, further monitoring of sensitivity within the S. sclerotiorum population is encouraged as well as the use of rational systems to base their judicious and economic use.
Comparison of the lateral and posterior approaches in the treatment of pediatric supracondylar humeral fractures
Authors: Uzer Gökçer , Yildiz Fatih , Elmadağ Mehmet , Bilsel Kerem , Erden Tunay , Pulatkan Anil , Çelik Derya , Gürkan Volkan
Published: March 2017

This study explored the radiological, functional, and cosmetic results of treatment of supracondylar humeral fractures with open reduction and percutaneous pinning, comparing posterior triceps V-splitting (group I, n=22) and lateral (group II, n=25) approaches. The time to union, the functional and cosmetic results, and the flexor and extensor muscle strengths were measured and compared with the contralateral extremities. There were no statistical differences between the groups. The V-splitting posterior approach is as safe and effective as the lateral approach in the surgical treatment of pediatric supracondylar humeral fractures.
Registered Nurses in Primary Care
Authors: Flinter Margaret , Hsu Clarissa , Cromp DeAnn , Ladden MaryJoan D. , Wagner Edward H.
Published: March 2017

The years since the passage of the Affordable Care Act have seen substantial changes in the organization and delivery of primary care. These changes have emphasized greater team involvement in care and expansion of the roles of each team member including registered nurses (RNs). This study examined the roles of RNs in 30 exemplary primary care practices. We identified the emergence of new roles and activities for RNs characterized by greater involvement in face-to-face patient care and care management, their own daily schedule of patient visits and contacts, and considerable autonomy in the care of their patients.
Short article: Evaluation of O6-methylguanine-DNA methyltransferase as a predicting factor of response to temozolomide-based chemotherapy in well-differentiated metastatic pancreatic neuroendocrine tumors
Authors: Girot Paul , Dumars Clotilde , Mosnier Jean-François , Muzellec Léa , Senellart Hélène , Foubert Fanny , Caroli-Bosc François-Xavier , Cauchin Estelle , Regenet Nicolas , Matysiak-Budnik Tamara , Touchefeu Yann
Published: March 2017

Objective

Temozolomide (TMZ) is an alkylating agent frequently used in well-differentiated metastatic pancreatic neuroendocrine tumors (PNETs) with very variable responses. O6-methylguanine-DNA methyltransferase (MGMT) is a DNA repair enzyme whose loss of expression has been suggested to be predictive of response to TMZ in various human tumors. We evaluated the predictive value of MGMT status, assessed by immunohistochemistry (IHC) and methylation-specific PCR (MS-PCR), in well-differentiated metastatic PNETs treated by a TMZ-based chemotherapy.

Patients and methods

All patients with metastatic PNETs treated with TMZ-based chemotherapy between 2010 and 2016 in two academic centers, for whom the tumor samples were available, were included. Clinical data were collected and the MGMT status of the tumors was analyzed using MS-PCR and IHC.

Results

Twenty-two patients (nine men, median age 61 years) were included. The loss of MGMT protein expression detected by IHC was observed in 13 (59%) patients and MGMT promoter hypermethylation was detected by MS-PCR in three (15%) out of 20 interpretable cases. MGMT status did not correlate significantly with the best radiological response according to the Response Evaluation Criteria In Solid Tumors criteria or with progression-free survival. There was no correlation between MGMT protein expression and MGMT gene promoter methylation.

Conclusion

These results indicate that a deficient MGMT status in PNETs, determined by loss of protein expression in IHC or by the presence of MGMT gene promoter methylation measured by MS-PCR, is not associated with a better response to TMZ-based chemotherapy and cannot be used as a predictive marker to lead treatment decisions.
Crew Resource Management in the trauma room: a prospective 3-year cohort study
Authors: Haerkens Marck H.T.M. , Kox Matthijs , Noe Pieter M. , Van Der Hoeven Johannes G. , Pickkers Peter
Published: March 2017

Objective

Human factors account for the majority of adverse events. Human factors awareness training entitled Crew Resource Management (CRM) is associated with improved safety and reduced complications and mortality in critically ill patients. We determined the effects of CRM implementation in the trauma room of an Emergency Department (ED).

Patients and methods

A prospective 3-year cohort study was carried out in a level 1 ED, admitting more than 12 000 patients annually (>1500 trauma related). At the end of the baseline year, CRM training was performed, followed by an implementation year. The third year was defined as the clinical effect year. The primary outcomes were safety climate, measured using the Safety Attitudes Questionnaire, and ED length of stay. The secondary outcome measures were hospital length of stay and 48-h crude mortality of trauma patients.

Results

All 5070 trauma patients admitted to the ED during the study period were included. Following CRM implementation, safety climate improved significantly in three out of six Safety Attitudes Questionnaire domains, both at the end of the implementation and clinical effect years: teamwork climate, safety climate, and stress recognition. ED length of stay of these patients increased from 141 (102–192) in the baseline year to 161 (116–211) and 170 (128–223) min in the implementation and clinical effect years, respectively (P<0.05 vs. baseline). Hospital length of stay was prolonged by 1 day in the implementation and clinical effect years (P<0.05 vs. baseline), whereas mortality was unaltered.

Conclusion

Although CRM implementation in the ED was associated with an improved safety climate, the time spent by trauma patients in the ED increased.
A global optimization perspective on molecular clusters
Authors: Marques J. M. C. , Pereira F. B. , Llanio-Trujillo J. L. , Abreu P. E. , Albertí M. , Aguilar A. , Pirani F. , Bartolomei M.
Published: March 2017

Although there is a long history behind the idea of chemical structure, this is a key concept that continues to challenge chemists. Chemical structure is fundamental to understanding most of the properties of matter and its knowledge for complex systems requires the use of state-of-the-art techniques, either experimental or theoretical. From the theoretical view point, one needs to establish the interaction potential among the atoms or molecules of the system, which contains all the information regarding the energy landscape, and employ optimization algorithms to discover the relevant stationary points. In particular, global optimization methods are of major importance to search for the low-energy structures of molecular aggregates. We review the application of global optimization techniques to several molecular clusters; some new results are also reported. Emphasis is given to evolutionary algorithms and their application in the study of the microsolvation of alkali-metal and Ca
2+
ions with various types of solvents.

This article is part of the themed issue ‘Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces’.
Phase-space methods for the spin dynamics in condensed matter systems
Authors: Hurst Jérôme , Hervieux Paul-Antoine , Manfredi Giovanni
Published: March 2017

Using the phase-space formulation of quantum mechanics, we derive a four-component Wigner equation for a system composed of spin-

fermions (typically, electrons) including the Zeeman effect and the spin–orbit coupling. This Wigner equation is coupled to the appropriate Maxwell equations to form a self-consistent mean-field model. A set of semiclassical Vlasov equations with spin effects is obtained by expanding the full quantum model to first order in the Planck constant. The corresponding hydrodynamic equations are derived by taking velocity moments of the phase-space distribution function. A simple closure relation is proposed to obtain a closed set of hydrodynamic equations.

This article is part of the themed issue ‘Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces’.
Perspective: chemical dynamics simulations of non-statistical reaction dynamics
Authors: Ma Xinyou , Hase William L.
Published: March 2017

Non-statistical chemical dynamics are exemplified by disagreements with the transition state (TS), RRKM and phase space theories of chemical kinetics and dynamics. The intrinsic reaction coordinate (IRC) is often used for the former two theories, and non-statistical dynamics arising from non-IRC dynamics are often important. In this perspective, non-statistical dynamics are discussed for chemical reactions, with results primarily obtained from chemical dynamics simulations and to a lesser extent from experiment. The non-statistical dynamical properties discussed are: post-TS dynamics, including potential energy surface bifurcations, product energy partitioning in unimolecular dissociation and avoiding exit-channel potential energy minima; non-RRKM unimolecular decomposition; non-IRC dynamics; direct mechanisms for bimolecular reactions with pre- and/or post-reaction potential energy minima; non-TS theory barrier recrossings; and roaming dynamics.

This article is part of the themed issue ‘Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces’.
Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces
Authors: Spezia Riccardo , Martínez-Nuñez Emilio , Vazquez Saulo , Hase William L.
Published: March 2017

In this Introduction, we show the basic problems of non-statistical and non-equilibrium phenomena related to the papers collected in this themed issue. Over the past few years, significant advances in both computing power and development of theories have allowed the study of larger systems, increasing the time length of simulations and improving the quality of potential energy surfaces. In particular, the possibility of using quantum chemistry to calculate energies and forces ‘on the fly’ has paved the way to directly study chemical reactions. This has provided a valuable tool to explore molecular mechanisms at given temperatures and energies and to see whether these reactive trajectories follow statistical laws and/or minimum energy pathways. This themed issue collects different aspects of the problem and gives an overview of recent works and developments in different contexts, from the gas phase to the condensed phase to excited states.

This article is part of the themed issue ‘Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces’.
Skin infection caused by a novel strain of Staphylococcus pseudintermedius in a Siberian husky dog owner
Authors: Robb Andrew R , Wright Elizabeth D , Foster Adele M. E , Walker Robert , Malone Colin
Published: March 2017

Introduction.
Staphylococcus pseudintermedius, an opportunistic pathogen of dogs and cats, is rarely reported to cause infection in humans. Here, we describe a case of severe skin infection caused by S. pseudintermedius, in a 47-year-old male, a dog owner; to the best of our knowledge, this is the first such case reported from Scotland.

Case presentation. The patient presented with a short history of a severe ecthyma-like lesion on his forehead, with smaller lesions on his abdomen and legs. Bacterial culture revealed Clostridium perfringens, thought to be colonizing the wound, and a Staphylococcus species, identified as S. pseudintermedius by matrix-assisted laser desorption/ionization-time of flight MS and confirmed by molecular methods using a PCR-RFLP approach. The patient was treated with flucloxacillin, penicillin V and Fucibet cream, and recovered fully. Zoonotic infection was considered likely; however, screening swabs from his dogs grew S. pseudintermedius of a different clonal type. Both patient and dog strains carried Staphylococcus intermedius exfoliative toxin and leucocidin I, closely related to Panton–Valentine leucocidin, possibly contributing to the severity of the infection. S pseudintermedius, although coagulase positive, is normally negative by rapid slide clumping and latex agglutination tests routinely used to identify Staphylococcus aureus. Hence, S. pseudintermedius may easily be misidentified as a coagulase-negative staphylococcus and considered insignificant.

Conclusion. This is, to the best of our knowledge, the first reported case of a human S. pseudintermedius infection in Scotland. Zoonotic transmission of S. pseudintermedius between pets and owners has been shown. However, in this case zoonosis could not be confirmed.
Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data
Authors: McMurry Julie A , Juty Nick , Blomberg Niklas , Burdett Tony , Conlin Tom , Conte Nathalie , Courtot Mélanie , Deck John , Dumontier Michel , Fellows Donal K , Gonzalez-Beltran Alejandra , Gormanns Philipp , Grethe Jeffrey , Hastings Janna , Hermjakob Henning , Hériché Jean-Karim , Ison Jon C , Jimenez Rafael C , Jupp Simon , Kunze John , Laibe Camille , Le Novère Nicolas , Malone James , Martin Maria Jesus , McEntyre Johanna R , Morris Chris , Muilu Juha , Müller Wolfgang , Rocca-Serra Philippe , Sansone Susanna-Assunta , Sariyar Murat , Snoep Jacky L , Stanford Natalie J , Soiland-Reyes Stian , Swainston Neil , Washington Nicole , Williams Alan R , Wimalaratne Sarala , Winfree Lilly , Wolstencroft Katherine , Goble Carole , Mungall Christopher J , Haendel Melissa A , Parkinson Helen
Published: March 2017

In many disciplines, data is highly decentralized across thousands of online databases (repositories, registries, and knowledgebases). Wringing value from such databases depends on the discipline of data science and on the humble bricks and mortar that make integration possible; identifiers are a core component of this integration infrastructure. Drawing on our experience and on work by other groups, we outline ten lessons we have learned about the identifier qualities and best practices that facilitate large-scale data integration. Specifically, we propose actions that identifier practitioners (database providers) should take in the design, provision and reuse of identifiers; we also outline important considerations for those referencing identifiers in various circumstances, including by authors and data generators. While the importance and relevance of each lesson will vary by context, there is a need for increased awareness about how to avoid and manage common identifier problems, especially those related to persistence and web-accessibility/resolvability. We focus strongly on web-based identifiers in the life sciences; however, the principles are broadly relevant to other disciplines.
A transformation from temporal to ensemble coding in a model of piriform cortex
Authors: Stern Merav , Bolding Kevin A. , Abbott L.F. , Franks Kevin M.
Published: March 2017

Different coding strategies are used to represent odor information at various stages of the mammalian olfactory system. A temporal latency code represents odor identity in olfactory bulb (OB), but this temporal information is discarded in piriform cortex (PCx) where odor identity is instead encoded through ensemble membership. We developed a spiking PCx network model to understand how this transformation is implemented. In the model, the impact of OB inputs activated earliest after inhalation is amplified within PCx by diffuse recurrent collateral excitation, which then recruits strong, sustained feedback inhibition that suppresses the impact of later-responding glomeruli. Simultaneous OB-PCx recordings indicate that indeed, over a single sniff, the earliest-active OB inputs are most effective at driving PCx activity. We model increasing odor concentrations by decreasing glomerulus onset latencies while preserving their activation sequences. This produces a multiplexed cortical odor code in which activated ensembles are robust to concentration changes while concentration information is encoded through population synchrony. Our model demonstrates how PCx circuitry can implement multiplexed ensemble-identity/temporal-concentration odor coding.
Genomic inferences of domestication events are corroborated by written records inBrassica rapa
Authors: Qi Xinshuai , An Hong , Ragsdale Aaron , Hall Tara E. , Gutenkunst Ryan N. , Chris Pires J. , Barker Michael S.
Published: March 2017

Demographic modeling is often used with population genomic data to infer the relationships and ages among populations. However, relatively few analyses are able to validate these inferences with independent data. Here, we leverage written records that describe distinctBrassica rapacrops to corroborate demographic models of domestication.Brassica rapacrops are renowned for their outstanding morphological diversity, but the relationships and order of domestication remains unclear. We generated genome-wide SNPs from 126 accessions collected globally using high-throughput transcriptome data. Analyses of more than 31,000 SNPs across theB. rapagenome revealed evidence for five distinct genetic groups and supported a European-Central Asian origin ofB. rapacrops. Our results supported the traditionally recognized South Asian and East AsianB. rapagroups with evidence that pak choi, Chinese cabbage, and yellow sarson are likely monophyletic groups. In contrast, the oil-typeB. rapasubsp.oleiferaand brown sarson were polyphyletic. We also found no evidence to support the contention that rapini is the wild type or the earliest domesticated subspecies ofB. rapa.Demographic analyses suggested thatB. rapawas introduced to Asia 2400-4100 years ago, and that Chinese cabbage originated 1200-2100 years ago via admixture of pak choi and European-Central AsianB. rapa.We also inferred significantly different levels of founder effect among theB. rapasubspecies. Written records from antiquity that document these crops are consistent with these inferences. The concordance between our age estimates of domestication events with historical records provides unique support for our demographic inferences.
Adaptive evolution of transcription factor binding affinities
Authors: Hong Jungeui , Brandt Nathan , Yang Ally , Hughes Tim , Gresham David
Published: March 2017

Understanding the molecular basis of gene expression evolution is a central problem in evolutionary biology. However, connecting changes in gene expression to increased fitness, and identifying the functional basis of those changes, remains challenging. To study adaptive evolution of gene expression in real time, we performed long term experimental evolution (LTEE) ofSaccharomyces cerevisiae(budding yeast) in ammonium-limited chemostats. Following several hundred generations of continuous selection we found significant divergence of nitrogen-responsive gene expression in lineages with increased fitness. In multiple independent lineages we found repeated selection for non-synonymous mutations in the zinc finger DNA binding domain of the activating transcription factor (TF), GAT1, that operates within incoherent feedforward loops to control expression of the nitrogen catabolite repression (NCR) regulon. Missense mutations in the DNA binding domain of GAT1 reduce its binding affinity for the GATAA consensus sequence in a promoter-specific manner, resulting in increased expression of ammonium permease genes via both direct and indirect effects, thereby conferring increased fitness. We find that altered transcriptional output of the NCR regulon results in antagonistic pleiotropy in alternate environments and that the DNA binding domain of GAT1 is subject to purifying selection in natural populations. Our study shows that adaptive evolution of gene expression can entail tuning expression output by quantitative changes in TF binding affinities while maintaining the overall topology of a gene regulatory network.
MELODI - Mining Enriched Literature Objects to Derive Intermediates
Authors: Elsworth Benjamin , Dawe Karen , Vincent Emma E , Langdon Ryan , Lynch Brigid M , Martin Richard M , Relton Caroline , Higgins Julian PT , Gaunt Tom R
Published: March 2017

Motivation

The scientific literature contains a wealth of information from different fields on potential disease mechanisms. However, prioritising mechanisms for further analytical evaluation presents enormous challenges in terms of the quantity and diversity of published research. The application of data mining approaches to the literature offers the potential to identify and prioritise mechanisms for more focused and detailed analysis.

Results

Here we present MELODI, a literature mining platform that can identify mechanistic pathways between any two biomedical concepts. Two case studies demonstrate the potential uses of MELODI and how it can generate hypotheses for further investigation. Firstly, an analysis of ERG and prostate cancer derives the intermediate transcription factor SP1, recently confirmed to be physically interacting with ERG. Secondly, examining the relationship between a new potential risk factor for pancreatic cancer identifies possible mechanistic insights which can be studiedin vitro.

Availability

MELODI has been implemented as a Python/Django web application, and is freely available to use atwww.melodi.biocompute.org.uk

Contact

melodi@biocompute.org.uk
Bootstrapping and Empirical Bayes Methods Improve Rhythm Detection in Sparsely Sampled Data
Authors: Hutchison Alan L. , Allada Ravi , Dinner Aaron R.
Published: March 2017

Motivation

There is much interest in using genome-wide expression time series to identify circadian genes. However, the cost and effort of such measurements often limits data collection. Consequently, it is difficult to assess the experimental uncertainty in the measurements and, in turn, to detect periodic patterns with statistical confidence.

Results

We show that parametric bootstrapping and empirical Bayes methods for variance shrinkage can improve rhythm detection in genome-wide expression time series. We demonstrate these approaches by building on the empirical JTK_CYCLE method (eJTK) to formulate a method that we term BooteJTK. Our procedure rapidly and accurately detects cycling time series by combining information about measurement uncertainty with information about the rank order of the time series values. We exploit a publicly available genome-wide dataset with high time resolution to show that BooteJTK provides more consistent rhythm detection thanexisting methods at typical sampling frequencies. Then, we apply BooteJTK to genome-wide expression time series from multiple tissues and show that it reveals biologically sensible tissue relationships that eJTK misses.

Availability

Bootstrap eJTK (BooteJTK) is implemented in Python and is freely available on GitHub athttps://github.com/alanlhutchison/BooteJTK.
Correcting for Dependent P-values in Rhythm Detection
Authors: Hutchison Alan L. , Dinner Aaron R.
Published: March 2017

There is much interest in using genome-wide expression time series to identify circadian genes. Several methods have been developed to test for rhythmicity in sparsely sampled time series typical of such measurements. Because these methods are statistical in nature, they rely on estimating the probabilities that patterns arise by chance (i.e., p-values). Here we show that leading methods implicitly make inappropriate assumptions of independence when estimating p-values. We show how to correct for the dependence to obtain accurate estimates for statistical significance during rhythm detection.
Conserved microRNA targeting reveals preexisting gene dosage sensitivities that shaped amniote sex chromosome evolution
Authors: Naqvi Sahin , Bellott Daniel W. , Lin Kathy S. , Page David C.
Published: March 2017

Mammalian X and Y chromosomes evolved from an ordinary autosomal pair. Genetic decay of the Y led to X chromosome inactivation (XCI) in females, but some Y-linked genes were retained during the course of sex chromosome evolution, and many X-linked genes did not become subject to XCI. We reconstructed gene-by-gene dosage sensitivities on the ancestral autosomes through phylogenetic analysis of microRNA (miRNA) target sites and compared these preexisting characteristics to the current status of Y-linked and X-linked genes in mammals. Preexisting heterogeneities in dosage sensitivity, manifesting as differences in the extent of miRNA-mediated repression, predicted either the retention of a Y homolog or the acquisition of XCI following Y gene decay. Analogous heterogeneities among avian Z-linked genes predicted either the retention of a W homolog or gene-specific dosage compensation following W gene decay. Genome-wide analyses of human copy number variation indicate that these heterogeneities consisted of sensitivity to both increases and decreases in dosage. We propose a model of XY/ZW evolution incorporating such preexisting dosage sensitivities in determining the evolutionary fates of individual genes. Our findings thus provide a more complete view of the role of dosage sensitivity in shaping the mammalian and avian sex chromosomes, and reveal an important role for post-transcriptional regulatory sequences (miRNA target sites) in sex chromosome evolution.
Preservation of Chromatin Organization after Acute Loss of CTCF in Mouse Embryonic Stem Cells
Authors: Kubo Naoki , Ishii Haruhiko , Gorkin David , Meitinger Franz , Xiong Xiong , Fang Rongxin , Liu Tristin , Ye Zhen , Li Bin , Dixon Jesse R. , Desai Arshad , Zhao Huimin , Ren Bing
Published: March 2017

The CCCTC-binding factor (CTCF) is widely regarded as a key player in chromosome organization in mammalian cells, yet direct assessment of the impact of loss of CTCF on genome architecture has been difficult due to its essential role in cell proliferation and early embryogenesis. Here, using auxin-inducible degron techniques to acutely deplete CTCF in mouse embryonic stem cells, we show that cell growth is severely slowed yet chromatin organization remains largely intact after loss of CTCF. Depletion of CTCF reduces interactions between chromatin loop anchors, diminishes occupancy of cohesin complex genome-wide, and slightly weakens topologically associating domain (TAD) structure, but the active and inactive chromatin compartments are maintained and the vast majority of TAD boundaries persist. Furthermore, transcriptional regulation and histone marks associated with enhancers are broadly unchanged upon CTCF depletion. Our results suggest CTCF-independent mechanisms in maintenance of chromatin organization.
Accurate and Reproducible Functional Maps in 127 Human Cell Types via 2D Genome Segmentation
Authors: Zhang Yu , Hardison Ross C.
Published: March 2017

The Roadmap Epigenomics consortium has published whole-genome functional annotation maps in 127 human cell types and cancer cell lines by integrating data from multiple epigenetic marks. These maps have thereby been widely used by the community for studying gene regulation in cell type specific contexts and predicting functional impacts of DNA mutations on disease. Here, we present a new map of functional elements produced by a recently published method called IDEAS on the same data set. The IDEAS method has several unique advantages and was shown to outperform existing methods, including the one used by the Roadmap Epigenomics consortium. We further introduce a simple but highly effective pipeline to greatly improve the reproducibility of functional annotation. Using five categories of independent experimental results, we extensively compared the annotation produced by IDEAS and the Roadmap Epigenomics consortium. While the overall concordance between the two maps was high, we observed many differences in the details and in the position-wise consistency of annotation across cell types. We show that the IDEAS annotation was uniformly and often substantially more accurate than the Roadmap Epigenomics result. This study therefore reports on the quality of an existing functional map in 127 human genomes and provides an alternative and better map to be used by the community. The annotation result can be visualized in the UCSC genome browser via the hub athttp://bx.psu.edu/~yuzhang/Roadmap_ideas/ideas_hub.txt
Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts
Authors: Bell Jason C. , Jukam David , Teran Nicole A. , Risca Viviana I. , Smith Owen K. , Johnson Whitney L. , Skotheim Jan , Greenleaf William J. , Straight Aaron F.
Published: March 2017

RNA is a critical component of chromatin in eukaryotes, both as a product of transcription, and as an essential constituent of ribonucleoprotein complexes that regulate both local and global chromatin states. Here we present a proximity ligation and sequencing method calledChromatin-AssociatedRNAsequencing (ChAR-seq) that maps all RNA-to-DNA contacts across the genome. ChAR-seq provides unbiased,de novoidentification of targets of chromatin-bound RNAs including nascent transcripts, chromosome-specific dosage compensation ncRNAs, and genome-wide trans-associated RNAs involved in co-transcriptional RNA processing.
Respiratory-gated KES imaging of a rat model of acute lung injury at the Canadian Light Source
Authors: Deman P. , Tan S. , Belev G. , Samadi N. , Martinson M. , Chapman D. , Ford N. L.
Published: March 2017

In this study, contrast-enhanced X-ray tomographic imaging for monitoring and quantifying respiratory disease in preclinical rodent models is proposed. A K-edge imaging method has been developed at the Canadian Light Source to very accurately obtain measurements of the concentration of iodinated contrast agent in the pulmonary vasculature and inhaled xenon in the airspaces of rats. To compare the iodine and xenon concentration maps, a scout projection image was acquired to define the region of interest within the thorax for imaging and to ensure the same locations were imaged in each K-edge subtraction (KES) acquisition. A method for triggering image acquisition based on the real-time measurements of respiration was also developed to obtain images during end expiration when the lungs are stationary, in contrast to other previously published studies that alter the respiration to accommodate the image acquisition. In this study, images were obtained in mechanically ventilated animals using physiological parameters at the iodine K-edge in vivo and at the xenon K-edge post mortem (but still under mechanical ventilation). The imaging techniques were performed in healthy Brown Norway rats and in age-matched littermates that had an induced lung injury to demonstrate feasibility of the imaging procedures and the ability to correlate the lung injury and the quantitative measurements of contrast agent concentrations between the two KES images. The respiratory-gated KES imaging protocol can be easily adapted to image during any respiratory phase and is feasible for imaging disease models with compromised lung function.
The influence of P/As substitution in the melilite-like Na2Co(P2–xAsx)O7(x= 0.40 and 0.93) solid solutions
Authors: Issaoui Chokri , Chebbi Hammouda , Guesmi Abderrahmen
Published: March 2017

To investigate the influence of P/As substitution on structures and electrical properties,e.g.the effect on material densities, two new solid P/As-doped solutions, Na2CoP1.60As0.40O7(disodium cobalt diphosphorus arsenic heptaoxide) and Na2CoP1.07As0.93O7(disodium cobalt phosphorus arsenic heptaoxide), with melilite-like structures have been synthesized by solid-state reactions. Their unit-cell parameters are in agreement with Vegard's law. The obtained structural models were investigated by the bond valence sum (BVS) and charge distribution (CHARDI) validation tools and, for the latter, the structures are described as being built on anion-centred polyhedra. The frameworks can be described as layered and formed by {[Co(P,As)2O7]2−}∞slabs, with alkali cations sandwiched between the layers and with the interlayer spaces increased due to P/As substitution. The BVS model was extended to a preliminary simulation of the sodium conduction properties in the studied structural type and suggests that the most probable sodium conduction pathways are bidimensional, at the (002) planes.
Weak hydrogen bonding and fluorous interactions in the chloride and bromide salts of 4-[(2,2,3,3-tetrafluoropropoxy)methyl]pyridinium
Authors: Lu Norman , Wei Rong-Jyun , Lin Kwan-Yu , Alagesan Mani , Wen Yuh-Sheng , Liu Ling-Kang
Published: March 2017

Neutralization of 4-[(2,2,3,3-tetrafluoropropoxy)methyl]pyridine with hydrohalo acids HX(X= Cl and Br) yielded the pyridinium salts 4-[(2,2,3,3-tetrafluoropropoxy)methyl]pyridinium chloride, C9H10F4NO+·Cl−, (1), and 4-[(2,2,3,3-tetrafluoropropoxy)methyl]pyridinium bromide, C9H10F4NO+·Br−, (2), both carrying a fluorous side chain at theparaposition of the pyridinium ring. Single-crystal X-ray diffraction techniques revealed that (1) and (2) are isomorphous. The halide anions accept four hydrogen bonds from N—H,ortho-C—H and CF2—H groups. Two cations and two anions form a centrosymmetric dimeric building block, utilizing complimentary N—H...X...H—Csp3connections. These dimers are further crosslinked, utilizing another complimentary Csp2—H...X...H—Csp2connection. The pyridinium rings are π-stacked, forming columns running parallel to theaaxis that make angles ofca44–45° with the normal to the pyridinium plane. There are also supramolecular C—H...F—C interactions, namely bifurcated C—H...F and bifurcated C—F...H interactions; additionally, one type II C—F...F—C halogen bond has been observed.
Crystal structure of 4,5-dibromophenanthrene
Authors: Kim Nicholas S. , Thamattoor Dasan M.
Published: March 2017

The synthesis and crystal structure of the title compound, C14H8Br2, is described. The molecule is positioned on a twofold rotation axis and the asymmetric unit consists of half a molecule with the other half being generated by symmetry. The presence of two large bromine atoms in the bay region significantly distorts the molecule from planarity and the mean planes of the two terminal rings of the phenanthrene system are twisted away from each other by 28.51 (14)°. The torsion angle between the two C—Br bonds is 74.70 (14)° and the distance between the two Br atoms is 3.2777 (13) Å. The molecules pack in layers in the crystal, with the centroids of the central rings of the phenanthrene units in adjacent layers separated by a distance of 4.0287 (10) Å. These centroids are shifted by 2.266 (6) Å relative to each other, indicating slippage in the stacking arrangement. Furthermore, the distance between the centroids of the terminal and central rings of the phenanthrene units in adjacent layers is slightly shorter at 3.7533 (19) Å. While all of the molecules within each layer are oriented in the same direction, those in adjacent layers are oriented in the opposite direction, leading to anti-parallel stacks.
Ruthenium(II) carbonyl compounds with the 4′-chloro-2,2′:6′,2′′-terpyridine ligand
Authors: Tatikonda Rajendhraprasad , Haukka Matti
Published: March 2017

Two ruthenium carbonyl complexes with the 4′-chloro-2,2′:6′,2′′-terpyridine ligand (tpy-Cl, C15H10ClN3),i.e.[RuCl(tpy-Cl)(CO)2][RuCl3(CO)3] (I) [systematic name:cis-dicarbonylchlorido(4′-chloro-2,2′:6′,2′′-terpyridine-κ3N)ruthenium(II)fac-tricarbonyltrichloridoruthenate(II)], and [RuCl2(tpy-Cl)(CO)2] (II) [cis-dicarbonyl-trans-dichlorido(4′-chloro-2,2′:6′,2′′-terpyridine-κ2N1,N1′)ruthenium(II)], were synthesized and characterized by single-crystal X-ray diffraction. The RuIIatoms in both centrosymmetric structures (I) and (II) display similar, slightly distorted octahedral coordination spheres. The coordination sphere in the complex cation in compound (I) is defined by three N atoms of the tridentate tpy-Cl ligand, two carbonyl carbon atoms and one chlorido ligand; the charge is balanced by an octahedral [Ru(CO)3Cl3]−counter-anion. In the neutral compound (II), the tpy-Cl ligand coordinates to the metal only through two of its N atoms. The coordination sphere of the RuIIatom is completed by two carbonyl and two chlorido ligands. In the crystal structures of both (I) and (II), weak C—H...Cl interactions are observed.
A cinnamaldehyde Schiff base ofS-(4-methylbenzyl) dithiocarbazate: crystal structure, Hirshfeld surface analysis and computational study
Authors: Yusof Enis Nadia Md , Tahir Mohamed I. M. , Ravoof Thahira B. S. A. , Tan Sang Loon , Tiekink Edward R. T.
Published: March 2017

The title dithiocarbazate ester (I), C18H18N2S2[systematic name: (E)-4-methylbenzyl 2-[(E)-3-phenylallylidene]hydrazinecarbodithioate, comprises an almost planar central CN2S2residue [r.m.s. deviation = 0.0131 Å]. The methylene(tolyl-4) group forms a dihedral angle of 72.25 (4)° with the best plane through the remaining non-hydrogen atoms [r.m.s. deviation = 0.0586 Å] so the molecule approximates mirror symmetry with the 4-tolyl group bisected by the plane. The configuration about both double bonds in the N—N=C—C=C chain isE; the chain has an alltransconformation. In the crystal, eight-membered centrosymmetric thioamide synthons, {...HNCS}2, are formedviaN—H...S(thione) hydrogen bonds. Connections between the dimersviaC—H...π interactions lead to a three-dimensional architecture. A Hirshfeld surface analysis shows that (I) possesses an interaction profile similar to that of a closely related analogue with anS-bound benzyl substituent, (II). Computational chemistry indicates the dimeric species of (II) connectedviaN—H...S hydrogen bonds is about 0.94 kcal mol−1more stable than that in (I).
Crystal structure ofO-benzyl-L-tyrosineN-carboxy anhydride
Authors: Inada Aya , Kanazawa Hitoshi
Published: March 2017

In the title compound, C17H15NO4(alternative name;O-benzyl-L-tyrosineN-carboxy anhydride), the oxazolidine ring is planer, with an r.m.s. deviation of 0.039 Å. The benzyloxy and benzyl rings are almost coplanar, making a dihedral angle of 0.078 (10)°, and are inclined to the oxazolidine ring by 59.16 (11) and 58.42 (11)°, respectively. In the crystal, molecules are linked by N—H...O and C—H...O hydrogen bonds, forming ribbons propagating along [010]. The ribbons are linked by C—H...π interactions, forming a three-dimensional supramolecular structure. The oxazolidine rings of adjacent ribbons are arranged into a layer parallel to theabplane. This arrangement is favourable for the polymerization of the compound in the solid state.
7-Acetyl-8-(4-chlorophenyl)-3-ethylsulfanyl-6-hydroxy-1,6-dimethyl-5,6,7,8-tetrahydroisoquinoline-4-carbonitrile
Authors: Mague Joel T. , Mohamed Shaaban K. , Akkurt Mehmet , Bakhite Etify A. , Albayati Mustafa R.
Published: March 2017

In the title compound, C22H23ClN2O2S, the chlorophenyl ring is inclined to the pyridine ring of the isoquinoline ring system by 79.78 (4)°. The cyclohexane ring adopts a flattened boat conformation. In the crystal, dimers form through complementary sets of inversion-related O—H...O and C—H...O hydrogen bonds. These are connected into zigzag chains along the c-axis direction by pairwise C—H...N interactions that also form inversion dimers.
A new approach to steady state analysis of nonlinear electrical circuits
Authors: Sobczyk Tadeusz , Radzik Michał
Published: March 2017

Purpose

The purpose of this study is to identify a novel methodology for direct calculation of steady-state periodic solutions for electrical circuits described by nonlinear differential equations, in the time domain.

Design/methodology/approach

An iterative algorithm was created to determine periodic steady-state solutions for circuits with nonlinear elements in a chosen set of time instants.

Findings

This study found a novel differential operator for periodic functions and its application in the steady-state analysis.

Research limitations/implications

This approach can be extended to the determination of two- or multi-periodic solutions of nonlinear dynamic systems.

Practical implications

The complexity of the steady-state analysis can be reduced in comparison with the frequency-domain approach.

Originality/value

This study identified novel difference equations for direct steady-state analysis of nonlinear electrical circuits.
Modelling anisotropy in non-oriented electrical steel sheet using vector Jiles–Atherton model
Authors: Upadhaya Brijesh , Martin Floran , Rasilo Paavo , Handgruber Paul , Belahcen Anouar , Arkkio Antero
Published: March 2017

Purpose

Non-oriented electrical steel presents anisotropic behaviour. Modelling such anisotropic behaviour has become a necessity for accurate design of electrical machines. The main aim of this study is to model the magnetic anisotropy in the non-oriented electrical steel sheet of grade M400-50A using a phenomenological hysteresis model.

Design/methodology/approach

The well-known phenomenological vector Jiles–Atherton hysteresis model is modified to correctly model the typical anisotropic behaviour of the non-oriented electrical steel sheet, which is not described correctly by the original vector Jiles–Atherton model. The modification to the vector model is implemented through the anhysteretic magnetization. Instead of the commonly used classical Langevin function, the authors introduced 2D bi-cubic spline to represent the anhysteretic magnetization for modelling the magnetic anisotropy.

Findings

The proposed model is found to yield good agreement with the measurement data. Comparisons are done between the original vector model and the proposed model. Another comparison is also made between the results obtained considering two different modifications to the anhysteretic magnetization.

Originality/value

The paper presents an original method to model the anhysteretic magnetization based on projections of the anhysteretic magnetization in the principal axis, and apply such modification to the vector Jiles–Atherton model to account for the magnetic anisotropy. The replacement of the classical Langevin function with the spline resulted in better fitting. The proposed model could be used in the numerical analysis of magnetic field in an electrical application.
Effect of mechanical stress on different iron loss components up to high frequencies and magnetic flux densities
Authors: Karthaus Jan , Steentjes Simon , Leuning Nora , Hameyer Kay
Published: March 2017

Purpose

The purpose of this paper is to study the variation of the specific iron loss components of electrical steel sheets when applying a tensile mechanical load below the yield strength of the material. The results provide an insight into the iron loss behaviour of the laminated core of electrical machines which are exposed to mechanical stresses of diverse origins.

Design/methodology/approach

The specific iron losses of electrical steel sheets are measured using a standardised single-sheet tester equipped with a hydraulic pressure cylinder which enables application of a force to the specimen under test. Based on the measured data and a semi-physical description of specific iron losses, the stress-dependency of the iron loss components can be studied.

Findings

The results show a dependency of iron loss components on the applied mechanical stress. Especially for the non-linear loss component and high frequencies, a large variation is observed, while the excess loss component is not as sensitive to high mechanical stresses. Besides, it is shown that the stress-dependent iron loss prediction approximates the measured specific iron losses in an adequate way.

Originality/value

New applications such as high-speed traction drives in electric vehicles require a suitable design of the electrical machine. These applications require particular attention to the interaction between mechanical influences and magnetic behaviour of the machine. In this regard, knowledge about the relation between mechanical stress and magnetic properties of soft magnetic material is essential for an exact estimation of the machine’s behaviour.
Impact of supply voltage variations on external magnetic field emitted by induction machines
Authors: Younsi Mohamed Omar , Ninet Olivier , Morganti Fabrice , Lecointe Jean-Philippe , Zidat Farid , Buire Matthieu
Published: March 2017

Purpose

This paper aims to study the influence of supply voltage variations on the external magnetic field emitted by grid-powered induction machines (IMs).

Design/methodology/approach

Two models are developed in the paper to analyse, for different supply voltage values, the influence of the variations of the magnetizing voltage for which there is a link with the tangential component of the external flux. The first is an analytical model based on the IM single-phase-equivalent circuit with variable magnetizing reactance to take into account the saturation of the magnetic circuit. The second is a numerical finite element simulation to model the same phenomenon. Results of both models are analysed with experimental measures of the external flux.

Findings

The study shows that the amplitude of the external field strongly depends on supply voltage values.

Research limitations/implications

The investigation is mainly focused on the tangential component of the external magnetic field which is of high importance concerning the applicability of non-invasive methods of diagnosis, as electromagnetic torque estimation developed by the authors or internal fault determination.

Originality/value

The originality of the paper concerns the characterization of the external flux with the supply voltage for IMs. It is shown that the magnetic circuit radiates external flux differently with the load and with the supply voltage.