bluuebunny/crossref_metadata_2025_split huggingface dataset:
Smooth Equivalence of Deformations of Domains in Complex Euclidean Spaces
Authors: Gaussier Hervé , Gong Xianghong 
Published: July 2018

Abstract
We prove that two smooth families of 2-connected domains in $\mathbf{C}$ are smoothly equivalent if they are equivalent under a possibly discontinuous family of biholomorphisms. We construct, for $\infty &gt; m \geq 3$, two smooth families of smoothly bounded $m$-connected domains in $\mathbf{C}$, and for $n\geq 2$, two families of strictly pseudoconvex domains in $\mathbf{C}^n$, which are equivalent under discontinuous families of biholomorphisms but not under any continuous family of biholomorphisms. Finally, we give sufficient conditions for the smooth equivalence of two smooth families of domains.
Anticoagulant medication errors in hospitals and primary care: a cross-sectional study
Authors: Dreijer Albert R , Diepstraten Jeroen , Bukkems Vera E , Mol Peter G M , Leebeek Frank W G , Kruip Marieke J H A , van den Bemt Patricia M L A 
Published: July 2018

Abstract

Objective
To assess the proportion of all medication error reports in hospitals and primary care that involved an anticoagulant. Secondary objectives were the anticoagulant involved, phase of the medication process in which the error occurred, causes and consequences of 1000 anticoagulant medication errors. Additional secondary objectives were the total number of anticoagulant medication error reports per month, divided by the total number of medication error reports per month and the proportion of causes of 1000 anticoagulant medication errors (comparing the pre- and post-guideline phase).

Design
A cross-sectional study.

Setting
Medication errors reported to the Central Medication incidents Registration reporting system.

Participants
Between December 2012 and May 2015, 42 962 medication errors were reported to the CMR.

Intervention
N/A.

Main outcome measure
Proportion of all medication error reports that involved an anticoagulant. Phase of the medication process in which the error occurred, causes and consequences of 1000 anticoagulant medication errors. The total number of anticoagulant medication error reports per month, divided by the total number of medication error reports per month (comparing the pre- and post-guideline phase) and the total number of causes of 1000 anticoagulant medication errors before and after introduction of the LSKA 2.0 guideline.

Results
Anticoagulants were involved in 8.3% of the medication error reports. A random selection of 1000 anticoagulant medication error reports revealed that low-molecular weight heparins were most often involved in the error reports (56.2%). Most reports concerned the prescribing phase of the medication process (37.1%) and human factors were the leading cause of medication errors mentioned in the reports (53.4%). Publication of the national guideline on integrated antithrombotic care had no effect on the proportion of anticoagulant medication error reports. Human factors were the leading cause of medication errors before and after publication of the guideline.

Conclusions
Anticoagulant medication errors occurred in 8.3% of all medication errors. Most error reports concerned the prescribing phase of the medication process. Leading cause was human factors. The publication of the guideline had no effect on the proportion of anticoagulant medication errors.
Management of Insecticide-Resistant Soybean Aphids in the Upper Midwest of the United States
Authors: Koch Robert L , Hodgson Erin W , Knodel Janet J , Varenhorst Adam J , Potter Bruce D 
Published: July 2018

Abstract
Since the first observation of soybean aphid, Aphis glycines Matsumura (Hemiptera: Aphididae), in North America in 2000, it has become the most economically damaging insect of soybean in the Upper Midwest of the United States. For the last 17 yr, soybean aphid management has relied almost entirely on the use of foliar-applied broad-spectrum insecticides. However, in 2015 in Minnesota, failures of foliar-applied pyrethroid insecticides were reported and pyrethroid resistance was confirmed with laboratory bioassays using lambda-cyhalothrin and bifenthrin. In 2016 and 2017, further reports of failures of pyrethroid insecticides and/or laboratory confirmation of resistance occurred in Iowa, North Dakota, South Dakota, and Manitoba. In response to the challenge posed by insecticide-resistant soybean aphids, we recommend several management strategies for minimizing further development of resistance and subsequent pest-induced crop losses: 1) scout and use the economic threshold to determine when to apply insecticides, 2) apply the insecticides properly, 3) assess efficacy 3–5 d after application, and 4) alternate to a different insecticide group if another application is required. In the long term, soybean aphid management must move beyond insecticide-based management to true integrated pest management by incorporating multiple tactics.
Gender Matters in Economic Empowerment Interventions: A Research Review
Authors: Buvinić Mayra , O'Donnell Megan 
Published: July 2018

AbstractEvidence shows that women face additional constraints because of their gender that affect their economic performance. A review of recent evaluation research demonstrates the types of gender-related constraints women face and the role that economic empowerment interventions can play in overcoming them, especially if they incorporate aspects of smart design, increasing their development impact. The evidence suggests that financial services and training programs are not gender-neutral and that specific design features can yield more positive economic outcomes for women by helping them overcome gender-related constraints. These features include savings and “Graduation” programs that increase women's economic independence, self-reliance and self-control, and the practice of repeated micro-borrowing that increases financial risk-taking and choice. “Smart” design also includes high-quality business management and jobs skills training, and stipends and other incentives in these training programs that address women's and young women's additional time burdens and childcare demands. Peer support may also help to increase financial risk-taking and confidence in business decisions. However, when social norms are too restrictive, and women are prevented from doing any paid work, no design will be smart enough. Subjective economic empowerment appears to be an important intermediate outcome for women that should be promoted and more reliably and accurately measured. Lastly, whenever possible, results should be sex-disaggregated and reported for individuals as well as households.
The Nucleome of Developing Murine Rod Photoreceptors
Authors: Diri Issam Al , Valentine Marc , Xu Beisi , Putnam Daniel , Griffiths Lyra , Lupo Marybeth , Norrie Jackie , Zhang Jiakun , Johnson Dianna , Easton John , Shao Ying , Honnell Victoria , Frase Sharon , Miller Shondra , Stewart Valerie , Chen Xiang , Dyer Michael A. 
Published: July 2018

AbstractThe nuclei of rod photoreceptors in mice and other nocturnal species have an unusual inverted chromatin structure: the heterochromatin is centrally located to help focus light and improve photosensitivity. To better understand this unique nuclear organization, we performed ultra-deep Hi-C analysis on murine retina at 3 stages of development and on purified rod photoreceptors. Predicted looping interactions from the Hi-C data were validated with fluorescence in situ hybridization (FISH). We discovered that a subset of retinal genes that are important for retinal development, cancer, and stress response are localized to the facultative heterochromatin domain. We also used machine learning to develop an algorithm based on our chromatin Hidden Markov Modeling (chromHMM) of retinal development to predict heterochromatin domains and study their dynamics during retinogenesis. FISH data for 264 genomic loci were used to train and validate the algorithm. The integrated data were then used to identify a developmental stage– and cell type-specific core regulatory circuit super-enhancer (CRC-SE) upstream of the Vsx2 gene, which is required for bipolar neuron expression. Deletion of the Vsx2 CRC-SE in mice led to the loss of bipolar neurons in the retina.
Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling
Authors: Nir Guy , Farabella Irene , Estrada Cynthia Pérez , Ebeling Carl G. , Beliveau Brian J. , Sasaki Hiroshi M. , Lee Soun H. , Nguyen Son C. , McCole Ruth B. , Chattoraj Shyamtanu , Erceg Jelena , Abed Jumana AlHaj , Martins Nuno M. C. , Nguyen Huy Q. , Hannan Mohammed A. , Russell Sheikh , Durand Neva C. , Rao Suhas S.P. , Kishi Jocelyn Y. , Soler-Vila Paula , Di Pierro Michele , Onuchic José N. , Callahan Steven , Schreiner John , Stuckey Jeff , Yin Peng , Aiden Erez Lieberman , Marti-Renom Marc A. , Wu C.-ting 
Published: July 2018

AbstractChromosome structure is thought to be crucial for proper functioning of the nucleus. Here, we present a method for visualizing chromosomal DNA at super-resolution and then integrating Hi-C data to produce three-dimensional models of chromosome organization. We begin by applying Oligopaint probes and the single-molecule localization microscopy methods of OligoSTORM and OligoDNA-PAINT to image 8 megabases of human chromosome 19, discovering that chromosomal regions contributing to compartments can form distinct structures. Intriguingly, our data also suggest that homologous maternal and paternal regions may be differentially organized. Finally, we integrate imaging data with Hi-C and restraint-based modeling using a method calledintegrativemodeling ofgenomicregions (IMGR) to increase the genomic resolution of our traces to 10 kb.One Sentence SummarySuper-resolution genome tracing, contact maps, and integrative modeling enable 10 kb resolution glimpses of chromosome folding.
The molecular signatures of compatible and incompatible pollination
Authors: Kodera Chie , Just Jérémy , Da Rocha Martine , Larrieu Antoine , Riglet Lucie , Legrand Jonathan , Rozier Frédérique , Gaude Thierry , Fobis-Loisy Isabelle 
Published: July 2018

AbstractFertilization in flowering plants depends on the early contact and recognition of pollen grains by the receptive papilla cells of the stigma. To identify the associated molecular pathways, we developed a transcriptomic analysis based on single nucleotide polymorphisms (SNPs) present in twoArabidopsis thalianaaccessions, one used as female and the other as male. We succeeded in distinguishing 80 % of transcripts according to their parental origins and drew up a catalog of genes whose expression is modified after pollen-stigma interaction. Global analysis of our data reveals that pattern-triggered immunity (PTI)-associated transcripts are upregulated after compatible pollination. From our analysis, we predicted the activation of the Mitogen-activated Protein Kinase 3 on the female side after compatible pollination, which we confirmed through expression and mutant analysis. Our work defines the molecular signatures of compatible and incompatible pollination, highlights the active status of incompatible stigmas, and unravels a new MPK3-dependent cell wall feature associated with stigma-pollen interaction.
Monkey Features Location Identification Using Convolutional Neural Networks
Authors: Labuguen (P) Rollyn , Gaurav Vishal , Blanco Salvador Negrete , Matsumoto Jumpei , Inoue Kenichi , Shibata Tomohiro 
Published: July 2018

AbstractUnderstanding animal behavior in its natural habitat is a challenging task. One of the primary step for analyzing animal behavior is feature detection. In this study, we propose the use of deep convolutional neural network (CNN) to locate monkey features from raw RGB images of monkey in its natural environment. We train the model to identify features such as the nose and shoulders of the monkey at about 0.01 model loss.
Quantitative comparison of the anterior-posterior patterning system in the embryos of fiveDrosophilaspecies
Authors: Wunderlich Zeba , Fowlkes Charless C. , Eckenrode Kelly B. , Bragdon Meghan D. J. , Abiri Arash , DePace Angela H. 
Published: July 2018

AbstractComplex spatiotemporal gene expression patterns direct the development of the fertilized egg into an adult animal. Comparisons across species show that, in spite of changes in the underlying regulatory DNA sequence, developmental programs can be maintained across millions of years of evolution. Reciprocally, changes in gene expression can be used to generate morphological novelty. Distinguishing between changes in regulatory DNA that lead to changes in gene expression and those that do not is therefore a central goal of evolutionary developmental biology. Quantitative, spatially-resolved measurements of developmental gene expression patterns play a crucial role in this goal, enabling the detection of subtle phenotypic differences between species and the development of computations models that link the sequence of regulatory DNA to expression patterns. Here we report the generation of two atlases of cellular resolution gene expression measurements for the primary anterior-posterior patterning genes inDrosophila simulansandDrosophila virilis. By combining these data sets with existing atlases for three otherDrosophilaspecies, we detect subtle differences in the gene expression patterns and dynamics driving the highly conserved axis patterning system and delineate inter-species differences in the embryonic morphology. These data sets will be a resource for future modeling studies of the evolution of developmental gene regulatory networks.
MOVIE: Multi-Omics Visualization of Estimated contributions
Authors: McCabe Sean D. , Lin Dan-Yu , Love Michael I. 
Published: July 2018

AbstractSummaryThe growth of multi-omics datasets has given rise to many methods for identifying sources of common variation across data types. The unsupervised nature of these methods makes it difficult to evaluate their performance. We present MOVIE, Multi-Omics Visualization of Estimated contributions, as a framework for evaluating the degree of overfitting and the stability of unsupervised multi-omics methods. MOVIE plots the contributions of one data type against another to produce contribution plots, where contributions are calculated for each subject and each data type from the results of each multi-omics method. The usefulness of MOVIE is demonstrated by applying existing multi-omics methods to permuted null data and breast cancer data from The Cancer Genome Atlas. Contribution plots indicated that principal components-based Canonical Correlation Analysis overfit null data, while Sparse multiple Canonical Correlation Analysis and Multi-Omics Factor Analysis provided stable results with high specificity for both the real and permuted null datasets.AvailabilityMOVIE is available as an R package at https://github.com/mccabes292/movieContactmilove@email.unc.eduSupplementary informationSupplementary data are available at Bioinformatics online.
Migration rather than proliferation transcriptomic signatures are strongly associated with breast cancer patient survival
Authors: Nair Nishanth Ulhas , Das Avinash , Rogkoti Vasiliki-Maria , Fokkelman Michiel , Marcotte Richard , de Jong Chiaro G. , Lee Joo Sang , Meilijson Isaac , Hannenhalli Sridhar , Neel Benjamin G. , van de Water Bob , Le Dévédec Sylvia E. , Ruppin Eytan 
Published: July 2018

AbstractThe efficacy of prospective cancer treatments is routinely estimated by in vitro cell-line proliferation screens. However, it is unclear whether tumor aggressiveness and patient survival are influenced more by the proliferative or the migratory properties of cancer cells. To address this question, we experimentally measured proliferation and migration phenotypes across more than 40 breast cancer cell-lines. Based on the latter, we built and validated individual predictors of breast cancer proliferation and migration levels from the cells’ transcriptomics. We then apply these predictors to estimate the proliferation and migration levels of more than 1000 TCGA breast cancer tumors. Reassuringly, both estimates increase with tumor’s aggressiveness, as qualified by its stage, grade, and subtype. However, predicted tumor migration levels are significantly more strongly associated with patient survival than the proliferation levels. We confirm these finding by conducting siRNA knock-down experiments on the highly migratory MDA-MB-231 cell lines and deriving gene knock-down based proliferation and migration signatures. We show that cytoskeletal drugs might be more beneficial in patients with high predicted migration levels. Taken together, these results testify to the importance of migration levels in determining patient survival.
Dietary long-chain omega-3 fatty acids are related to impulse control and anterior cingulate function in adolescents
Authors: Darcey Valerie L. , McQuaid Goldie A. , Fishbein Diana H. , VanMeter John W. 
Published: July 2018

AbstractImpulse control, an emergent function modulated by the prefrontal cortex (PFC), helps to dampen risky behaviors during adolescence. Influences on PFC maturation during this period may contribute to variations in impulse control. Availability of omega-3 fatty acids, an essential dietary nutrient integral to neuronal structure and function, may be one such influence. This study examined whether intake of energy-adjusted long-chain omega-3 fatty acids (eicosapentaenoic acid (EPA) + docosahexaenoic acid (DHA)) was related to variation in impulse control and PFC activity during performance of an inhibitory task in adolescents (n= 87; 51.7% female, mean age 13.3+1.1 years) enrolled in a longitudinal neuroimaging study. Intake of DHA+EPA was assessed using a food frequency questionnaire and adjusted for total energy intake. Inhibitory control was assessed using caregiver rating scale (BRIEF Inhibit subscale) and task performance (false alarm rate) on a Go/No-Go task performed during functional MRI. Reported intake of long-chain omega-3 was positively associated with caregiver ratings of adolescent ability to control impulses (p=0.017) and there was a trend for an association between intake and task-based impulse control (p=0.072). Furthermore, a regression of BOLD response within PFC during successful impulse control (Correct No-Go versus Incorrect NoGo) with energy-adjusted DHA+EPA intake revealed that adolescents reporting lower intakes display greater activation in the dorsal anterior cingulate, potentially suggestive of a possible lag in cortical development. The present results suggest that dietary omega-3 fatty acids are related to development of both impulse control and function of the dorsal anterior cingulate gyrus in normative adolescent development. Insufficiency of dietary omega-3 fatty acids during this developmental period may be a factor which hinders development of behavioral control.
Plasticity in Escherichia coli cell wall metabolism promotes fitness and mediates intrinsic antibiotic resistance across environmental conditions
Authors: Mueller Elizabeth A , Levin Petra Anne 
Published: July 2018

ABSTRACTAlthough the peptidoglycan cell wall is an essential structural and morphological feature of most bacterial cells, the extracytoplasmic enzymes involved in its synthesis are frequently dispensable under standard culture conditions. By modulating a single growth parameter—extracellular pH—we discovered a subset of these so-called “redundant” enzymes in Escherichia coli are required for maximal fitness across pH environments. Among these pH specialists are the class A penicillin binding proteins PBP1 a and PBP1 b; defects in these enzymes attenuate growth in alkaline and acidic conditions, respectively. Genetic, biochemical, and cytological studies demonstrate that synthase activity is required for cell wall integrity across a wide pH range, and differential activity across pH environments significantly alters intrinsic resistance to cell wall active antibiotics. Together, our findings reveal previously thought to be redundant enzymes are instead specialized for distinct environmental niches, thereby ensuring robust growth and cell wall integrity in a wide range of conditions.
Analysis of the impact of molecular motions on the efficiency of XL-MS and the distance restraints in hybrid structural biology
Authors: Svetlov Vladimir , Nudler Evgeny 
Published: July 2018

AbstractCovalent cross-link mapping by mass spectrometry (XL-MS) is rapidly becoming the most widely used method of hybrid structural biology. We investigated the impact of incremental variations of cross-linker length have on the depth of XL-MS interrogation of protein-protein complexes, and assessed the role molecular motions in solution play in generation of cross-link-derived distance restraints. Supplementation of a popular NHS-ester cross-linker, DSS, with 2 reagents shorter or longer by CH2-CH2, increased the number of non-reductant cross-links by ~50%. Molecular dynamics simulations of these cross-linkers revealed 3 individual, partially overlapping ranges of motion, consistent with partially overlapping sets of cross-links formed by each reagent. Similar simulations elucidated protein fold-specific ranges of motions for the reactive and backbone atoms from rigid and flexible target domains. Together these findings create a quantitative framework for generation of cross-linker- and protein fold-specific distance restraints for XL-MS-guided protein-protein docking.
Gene cluster conservation identifies melanin and perylenequinone biosynthesis pathways in multiple plant pathogenic fungi
Authors: Ebert Malaika K. , Spanner Rebecca E. , Jonge Ronnie de , Smith David J. , Holthusen Jason , Secor Gary A. , Thomma Bart P.H.J. , Bolton Melvin D. 
Published: July 2018

SummaryPerylenequinones are a family of structurally related polyketide fungal toxins with nearly universal toxicity. These photosensitizing compounds absorb light energy which enables them to generate reactive oxygen species that damage host cells. This potent mechanism serves as an effective weapon for plant pathogens in disease establishment. The sugar beet pathogenCercospora beticolasecretes the perylenequinone cercosporin during infection. We have shown recently that the cercosporin toxin biosynthesis(CTB)gene cluster is present in several other phytopathogenic fungi, prompting the search for biosynthetic gene clusters (BGCs) of structurally similar perylenequinones in other fungi. Here, we report the identification of the elsinochrome and phleichrome BGCs ofElsinoё fawcettiiandCladosporium phlei,respectively, based on gene cluster conservation with theCTBand hypocrellin BGCs. Furthermore, we show that previously reported BGCs for elsinochrome and phleichrome are involved in melanin production. Phylogenetic analysis of the corresponding melanin polyketide synthases (PKSs) and alignment of melanin BGCs revealed high conservation between the established and newly identifiedC. beticola, E. fawcettii,andC. phleimelanin BGCs. Mutagenesis of the identified perylenequinone and melanin PKSs inC. beticolaandE. fawcettiicoupled with mass spectrometric metabolite analyses confirmed their roles in toxin and melanin production.Originality and significance statementGenes involved in secondary metabolite (SM) production are often clustered together to form biosynthetic pathways. These pathways frequently have highly conserved keystone enzymes which can complicate allocation of a biosynthetic gene cluster (BGC) to the cognate SM. In our study, we utilized a combination of comparative genomics, phylogenetic analyses and biochemical approaches to reliably identify BGCs for perylenequinone toxins and DHN-melanin in multiple plant pathogenic fungi. Furthermore, we show that earlier studies that aimed to identify these perylenequinone pathways were misdirected and actually reported DHN-melanin biosynthetic pathways. Our study outlines a reliable approach to successfully identify fungal SM pathways.