bluuebunny/crossref_metadata_2025_split huggingface dataset:
Divergent cytosine DNA methylation patterns in single‐cell, soybean root hairs
Authors: Hossain Md Shakhawat , Kawakatsu Taiji , Kim Kyung Do , Zhang Ning , Nguyen Cuong T. , Khan Saad M. , Batek Josef M. , Joshi Trupti , Schmutz Jeremy , Grimwood Jane , Schmitz Robert J. , Xu Dong , Jackson Scott A. , Ecker Joseph R. , Stacey Gary 
Published: January 2017

Summary

Chromatin modifications, such as cytosine methylation of DNA, play a significant role in mediating gene expression in plants, which affects growth, development, and cell differentiation. As root hairs are single‐cell extensions of the root epidermis and the primary organs for water uptake and nutrients, we sought to use root hairs as a single‐cell model system to measure the impact of environmental stress.

We measured changes in cytosine DNA methylation in single‐cell root hairs as compared with multicellular stripped roots, as well as in response to heat stress.

Differentially methylated regions (DMRs) in each methylation context showed very distinct methylation patterns between cell types and in response to heat stress. Intriguingly, at normal temperature, root hairs were more hypermethylated than were stripped roots. However, in response to heat stress, both root hairs and stripped roots showed hypomethylation in each context, especially in the CHH context. Moreover, expression analysis of mRNA from similar tissues and treatments identified some associations between DMRs, genes and transposons.

Taken together, the data indicate that changes in DNA methylation are directly or indirectly associated with expression of genes and transposons within the context of either specific tissues/cells or stress (heat).
Arabidopsis phosphoinositide‐specific phospholipase C 4 negatively regulates seedling salt tolerance
Authors: Xia Keke , Wang Bo , Zhang Jiewei , Li Yuan , Yang Hailian , Ren Dongtao 
Published: January 2017

AbstractPrevious physiological and pharmacological studies have suggested that the activity of phosphoinositide‐specific phospholipase C (PI‐PLC) plays an important role in regulating plant salt stress responses by altering the intracellular Ca2+ concentration. However, the individual members of plant PLCs involved in this process need to be identified. Here, the function of AtPLC4 in the salt stress response of Arabidopsis seedlings was analysed. plc4 mutant seedlings showed hyposensitivity to salt stress compared with Col‐0 wild‐type seedlings, and the salt hyposensitive phenotype could be complemented by the expression of native promoter‐controlled AtPLC4. Transgenic seedlings with AtPLC4 overexpression (AtPLC4 OE) exhibited a salt‐hypersensitive phenotype, while transgenic seedlings with its inactive mutant expression (AtPLC4m OE) did not exhibit this phenotype. Using aequorin as a Ca2+ indicator in plc4 mutant and AtPLC4 OE seedlings, AtPLC4 was shown to positively regulate the salt‐induced Ca2+ increase. The salt‐hypersensitive phenotype of AtPLC4 OE seedlings was partially rescued by EGTA. An analysis of salt‐responsive genes revealed that the transcription of RD29B, MYB15 and ZAT10 was inversely regulated in plc4 mutant and AtPLC4 OE seedlings. Our findings suggest that AtPLC4 negatively regulates the salt tolerance of Arabidopsis seedlings, and Ca2+ may be involved in regulating this process.
European Knowledge Neighbourhood: Knowledge Production in EU Neighbouring Countries and Intensity of the Relationship with EU Countries
Authors: Autant‐Bernard Corinne , Chalaye Sylvie , Gagliardini Elisa , Usai Stefano 
Published: January 2017

AbstractThis study aims to analyse the creation of knowledge in the European neighbourhood and the diffusion of knowledge among EU countries and European neighbouring countries (ENCs). We first collate different indicators of knowledge production and diffusion in order to characterise the main feature of ENCs. In this respect, we contribute not only with an overview of potential knowledge interactions between EU and ENCs, but also suggest original ways to account for the different facets of knowledge diffusion. We use these indicators to assess the efficiency of ENC and EU in their use of knowledge resources, relying on data envelopment analysis (DEA). Contrary to the rare DEA studies in the field, inputs are both internal and external. The results show that, despite their weakness, ENCs may benefit from their orientation towards the EU for access to external knowledge, with some of them successfully turning their rare knowledge resources into knowledge creation and innovation.
EVIDENCIAS RESPECTO A LA MEDIACIÓN PENAL EN LA NORMA EUROPEA
Authors: Soler-Noguera Irene , Iglesias-Ortuño Emilia 
Published: January 2017

<p>El presente artículo plantea como objetivo principal de investigación conocer la normativa vigente en mediación penal de los países pertenecientes a la Unión Europea, para estudiar y comparar los rasgos característicos de esta normativa entre los países europeos. Para este fin se ha utilizado una metodología de investigación cualitativa basada en el análisis documental por categorías con el software MaxQDA para comparar las diversas legislaciones seleccionadas. Los países estudiados han sido Alemania, Austria, Bélgica, Finlandia, Francia, Hungría, Italia, Luxemburgo, Polonia, Portugal y República Checa. Los hallazgos han sido que la normativa específica en esta materia (que aparece sobre todo en Códigos Penales y Procesales más que en leyes autónomas) tiene muy poco tiempo de desarrollo, está fundamentada para delitos menos graves y hay muy poca fundamentación teórica de la mediación penal en las leyes. La sistematización de la legislación por categorías con ayuda de un programa informático ha permitido construir una visión general de la mediación penal en Europa muy útil para su desarrollo y sobre todo para darle visibilidad a esta práctica restaurativa.</p>
Draft Genome Sequence of a
Chitinophaga
Strain Isolated from a Lignocellulose Biomass-Degrading Consortium
Authors: Kishi Luciano T. , Lopes Erica M. , Fernandes Camila C. , Fernandes Gabriela C. , Sacco Lais P. , Carareto Alves Lucia M. , Lemos Eliana G. M. 
Published: January 2017

ABSTRACT

Chitinophaga
comprises microorganisms capable of degrading plant-derived carbohydrates, serving as a source of new tools for the characterization and degradation of plant biomass. Here, we report the draft genome assembly of a
Chitinophaga
strain with 8.2 Mbp and 7,173 open reading frames (ORFs), isolated from a bacterial consortium that is able to degrade lignocellulose.
Complete Genome Sequence of a Potential Novel
Bacillus
sp. Strain, FJAT-18017, Isolated from a Potato Field
Authors: Liu Guo-Hong , Liu Bo , Wang Jie-Ping , Che Jian-Mei , Chen Qian-Qian 
Published: January 2017

ABSTRACT

Bacillus
sp. strain FJAT-18017 was isolated from a potato field in Xinjiang, China. This paper is the first report, to our knowledge, to demonstrate the fully sequenced and completely annotated genome of
Bacillus
sp. FJAT-18017. The genome size is 5,265,521 bp. The average G+C content was 42.42%.
Draft Genome Sequence of
Microbacterium
sp. Strain Alg239_V18, an Actinobacterium Retrieved from the Marine Sponge
Spongia
sp
Authors: Karimi Elham , Gonçalves Jorge M. S. , Reis Margarida , Costa Rodrigo 
Published: January 2017

ABSTRACT

Here, we describe the draft genome sequence of
Microbacterium
sp. strain Alg239_V18, an actinobacterium retrieved from the marine sponge
Spongia
sp. Genome annotation revealed a vast gene repertoire involved in antibiotic and heavy metal-resistance, and a versatile carbohydrate assimilation metabolism with potential for chitin utilization.
Draft Genome Sequence of
Desulfovibrio
BerOc1, a Mercury-Methylating Strain
Authors: Goñi Urriza Marisol , Gassie Claire , Bouchez Oliver , Klopp Christophe , Guyoneaud Rémy 
Published: January 2017

ABSTRACT

Desulfovibrio
BerOc1 is a sulfate-reducing bacterium isolated from the Berre lagoon (French Mediterranean coast). BerOc1 is able to methylate and demethylate mercury. The genome size is 4,081,579 bp assembled into five contigs. We identified the
hgcA
and
hgcB
genes involved in mercury methylation, but not those responsible for mercury demethylation.
First Complete Genome Sequence of Haemophilus influenzae Serotype a
Authors: Iskander Mariam , Hayden Kristy , Van Domselaar Gary , Tsang Raymond 
Published: January 2017

ABSTRACT

Haemophilus influenzae
is an important human pathogen that primarily infects small children. In recent years,
H. influenzae
serotype a has emerged as a significant cause of invasive disease among indigenous populations. Here, we present the first complete whole-genome sequence of
H. influenzae
serotype a.
Genomic Epidemiology of Penicillin-Nonsusceptible Pneumococci with Nonvaccine Serotypes Causing Invasive Disease in the United States
Authors: Andam Cheryl P. , Mitchell Patrick K. , Callendrello Alanna , Chang Qiuzhi , Corander Jukka , Chaguza Chrispin , McGee Lesley , Beall Bernard W. , Hanage William P. 
Published: January 2017

ABSTRACT

Conjugate vaccination against seven pneumococcal serotypes (PCV7) reduced disease prevalence due to antibiotic-resistant strains throughout the 2000s. However, diseases caused by resistant nonvaccine type (NVT) strains increased. Some of these emerging strains were derived from vaccine types (VT) that had changed their capsule by recombination. The introduction of a vaccine targeting 13 serotypes (PCV13) in 2010 has led to concern that this scenario will repeat itself. We generated high-quality draft genomes from 265 isolates of NVT pneumococci not susceptible to penicillin (PNSP) in 2009 and compared them with the genomes of 581 isolates from 2012 to 2013 collected by the Active Bacterial Core surveillance (ABCs) of the Centers for Disease Control and Prevention (CDC). Of the seven sequence clusters (SCs) identified, three SCs fell into a single lineage associated with serogroup 23, which had an origin in 1908 as dated by coalescent analysis and included isolates with a divergent 23B capsule locus. Three other SCs represented relatively deep-branching lineages associated with serotypes 35B, 15A, and 15BC. In all cases, the resistant clones originated prior to 2010, indicating that PNSP are at present dominated by descendants of NVT clones present before vaccination. With one exception (15BC/ST3280), these SCs were related to clones identified by the Pneumococcal Molecular Epidemiology Network (PMEN). We conclude that postvaccine diversity in NVT PNSP between 2009 and 2013 was driven mainly by the persistence of preexisting strains rather than through
de novo
adaptation, with few cases of serotype switching. Future surveillance is essential for documenting the long-term dynamics and resistance of NVT PNSP.
Utility of social media and crowd-sourced data for pharmacovigilance: a scoping review protocol
Authors: Tricco Andrea C , Zarin Wasifa , Lillie Erin , Pham Ba , Straus Sharon E 
Published: January 2017

IntroductionAdverse events associated with medications are under-reported in postmarketing surveillance systems. A systematic review of published data from 37 studies worldwide (including Canada) found the median under-reporting rate of adverse events to be 94% in spontaneous reporting systems. This scoping review aims to assess the utility of social media and crowd-sourced data to detect and monitor adverse events related to health products including pharmaceuticals, medical devices, biologics and natural health products.Methods and analysisOur review conduct will follow the Joanna Briggs Institute scoping review methods manual. Literature searches were conducted in MEDLINE, EMBASE and the Cochrane Library from inception to 13 May 2016. Additional sources included searches of study registries, conference abstracts, dissertations, as well as websites of international regulatory authorities (eg, Food and Drug Administration (FDA), the WHO, European Medicines Agency). Search results will be supplemented by scanning the references of relevant reviews. We will include all publication types including published articles, editorials, websites and book sections that describe use of social media and crowd-sourced data for surveillance of adverse events associated with health products. Two reviewers will perform study selection and data abstraction independently, and discrepancies will be resolved through discussion. Data analysis will involve quantitative (eg, frequencies) and qualitative (eg, content analysis) methods.DisseminationThe summary of results will be sent to Health Canada, who commissioned the review, and other relevant policymakers involved with the Drug Safety and Effectiveness Network. We will compile and circulate a 1-page policy brief and host a 1-day stakeholder meeting to discuss the implications, key messages and finalise the knowledge translation strategy. Findings from this review will ultimately inform the design and development of a data analytics platform for social media and crowd-sourced data for pharmacovigilance in Canada and internationally.Registration detailsOur protocol was registered prospectively with the Open Science Framework (https://osf.io/kv9hu/).
Immunohistochemical Phenotype of Breast Cancer during 25-Year Follow-up of the Royal Marsden Tamoxifen Prevention Trial
Authors: Detre Simone I. , Ashley Susan , Mohammed Kabir , Smith Ian E. , Powles Trevor J. , Dowsett Mitch 
Published: January 2017

Abstract
The randomized, double-blinded Royal Marsden Tamoxifen Breast Cancer Prevention Trial in healthy high-risk women started in 1986 and is still blinded. Eligible participants (n = 2,471) were randomly assigned to tamoxifen (20 mg/d) or placebo for 8 years. Analysis in 2006 showed a 30% risk reduction of estrogen receptor (ER)-positive invasive breast cancer mostly in the posttreatment period. Biomarker analysis in this population may identify any subgroup-specific preventive effects tamoxifen. After a median follow-up of 18.4 years, 242 patients had developed invasive cancer, 134 on placebo and 108 on tamoxifen. From these, 180 tissue blocks were available and ER, progesterone receptor (PgR), Ki67, HER2, and EGFR were immunohistochemically analyzed. A 32% reduction in ER+ and PgR+ invasive cancers resulted after 8 years of treatment. Quantitative levels of ER and PgR were lower in the tamoxifen-treated group, significantly so for ER (P = 0.001). These lower ER levels were restricted to the posttreatment period (P = 0.018). Among the ER+ group, there was a similar proportional decrease in PgR+ and PgR− tumors by tamoxifen. The median levels of Ki67 were similar in both arms. The numbers of HER2-positive and EGFR-positive cancers were higher in the tamoxifen arm but not significantly so. In conclusion, the preventive effects of tamoxifen result in reduced ER-positive but not ER-negative tumors and reduced ER expression in the ER-positive cases largely confined to the posttreatment period. Overall reductions in PgR expression are explained by lower frequency of ER-positive cases. Impact on Ki67, HER2, and EGFR was modest. Cancer Prev Res; 10(3); 171–6. ©2017 AACR.
Combined Beamforming with Orthogonal Space Time Block Code for MIMO-OFDM with Simple Feedback
Authors: M. Abd Elkader Hala , M. Abdel-Hamid Gamal , El-Dien Adly Tag , A. Nassif Asmaa 
Published: January 2017

<p>In this paper, we introduce a proposed scheme to enhance the performance of orthogonal space time block code (OSTBC) with four time slots and two antennas by combing OSTBC with random beamforming to can use it in the downlink transmission for a mobile system. Multiple-input multiple-output orthogonal frequency-division multiplexing (MIMO-OFDM) system has been recognized as one of the most promising techniques to achieve a good service and increase data rate in the next generation (4&amp;5G) broadband wireless communications. So, we apply Space time block code (STBC) for MIMO-OFDM system with linear decoding. Also, we perform STBC with beamforming for MIMO-OFDM system to improve the performance of a system. Simulation results show that the beamforming improves bit error rate (BER) performance of OSTBC and STBC-OFDM for different types of modulation and diversity.</p>
Query Optimization Using Fuzzy Logic in Integrated Database
Authors: Susana Susana , Suharjito Suharjito 
Published: January 2017

<p>Query optimization in integrated database can’t be separated from data processing method. In order to have faster query response time, a method to optimize queries is required. One of many methods that can be used for query optimization is using fuzzy logic with Tsukamoto inference system. Value set on each variable is defined membership functions and Tsukamoto inference system used in determining these rules or the terms of query results, then apply it into query method or query line structure. The application of fuzzy logic inference systems with Tsukamoto can accelerate query response time, and will have more significant difference when the amount of selected data is greater.</p>
Disparities in the Use of Seizure Medications After Intracerebral Hemorrhage
Authors: Naidech Andrew M. , Toledo Paloma , Prabhakaran Shyam , Holl Jane L. 
Published: January 2017

Background and Purpose—
We investigated potential disparities in the use of prophylactic seizure medications in patients with intracerebral hemorrhage.

Methods—
Review of multicenter electronic health record (EHR) data with simultaneous prospective data recording. EHR data were retrieved from HealthLNK, a multicenter EHR repository in Chicago, Illinois, from 2006 to 2012 (multicenter cohort). Additional data were prospectively coded (single-center cohort) from 2007 through 2015.

Results—

The multicenter cohort comprised 3422 patients from 4 HealthLNK centers. Use of levetiracetam varied by race/ethnicity (
P
=0.0000008), with whites nearly twice as likely as blacks to be administered levetiracetam (odds ratio: 1.71; 95% confidence interval, 1.43–2.05;
P
<0.0001). In the single-center cohort (n=450), hematoma location, older age, depressed consciousness, larger hematoma volume, no alcohol abuse, and race/ethnicity were associated with levetiracetam administration (
P
≤0.04). Whites were nearly twice as likely as blacks to receive levetiracetam (odds ratio: 1.9; 95% confidence interval, 1.25–2.89;
P
=0.002); however, the association was confounded by history of hypertension, higher blood pressure on admission, and deep hematoma location. Only hematoma location was independently associated with levetiracetam administration (
P
<0.00001), rendering other variables, including race/ethnicity, nonsignificant.

Conclusions—
Although multicenter EHR data showed apparent racial/ethnic disparities in the use of prophylactic seizure medications, a more complete single-center cohort found the apparent disparity to be confounded by the clinical factors of hypertension and hematoma location. Disparities in care after intracerebral hemorrhage are common; however, administrative data may lead to the discovery of disparities that are confounded by detailed clinical data not readily available in EHRs.
Evaluation of Three Influenza Neuraminidase Inhibition Assays for Use in a Public Health Laboratory Setting during the 2011–2012 Influenza Season
Authors: Murtaugh William , Mahaman Lalla , Healey Benjamin , Peters Heather , Anderson Barbara , Tran Mandy , Ziese Marci , Carlos Maria Paz 
Published: January 2017

Objectives. We evaluated the implementation of three commericially available neuraminidase inhibition assays in a public health laboratory (PHL) setting. We also described the drug susceptibility patterns of human influenza A and B circulating in Maryland during the 2011–2012 influenza season. Methods. From January to May 2012, 169 influenza virus isolates were tested for phenotypic susceptibility to oseltamivir, zanamivir, and peramivir using NA-Fluor™, NA-Star®, and NA-XTD™ concurrently. A 50% neuraminidase inhibitory concentration (IC50) value was calculated to determine drug susceptibility. We used the standard deviation based on the median absolute deviation of the median analysis to determine the potential for reduced drug susceptibility. We evaluated each assay for the use of resources in high- and low-volume testing scenarios. Results. One of the 25 2009 influenza A (H1N1) pandemic isolates tested was resistant to oseltamivir and peramivir, and sensitive to zanamivir, on all three platforms. Eighty-two influenza A (H3N2) and 62 B isolates were sensitive to all three drugs in all three assays. For a low-volume scenario, NA-Star and NA-XTD took 120 minutes to complete, while NA-Fluor required 300 minutes to complete. The lowest relative cost favored NA-Star. In a high-volume scenario, NA-Fluor had the highest throughput. Reagent use was most efficient when maximizing throughput. Cost efficiency from low- to high-volume testing improved the most for NA-Star. Conclusions. Our evaluation showed that both chemiluminescent and fluorescent neuraminidase inhibition assays can be successfully implemented in a PHL setting to screen circulating influenza strains for neuraminidase inhibitor resistance. For improved PHL influenza surveillance, it may be essential to develop guidelines for phenotypic drug-resistance testing that take into consideration a PHL's workload and available resources.
Trends and Differences among Three New Indicators of HIV Infection Progression
Authors: An Qian , Song Ruiguang , Hernandez Angela , Hall H. Irene 
Published: January 2017

Objective. This study proposes three indicators of, and assesses the disparities and trends in, the risk of HIV infection progression among people living with diagnosed HIV infection in the United States. Methods. Using data reported to national HIV surveillance through June 2012, we calculated the AIDS diagnosis hazard, HIV (including AIDS) death hazard, and AIDS death hazard for people living with diagnosed HIV infection for each calendar year from 1997 to 2010. We also calculated a stratified hazard in 2010 by age, race/ethnicity, mode of transmission, region of residence at diagnosis, and year of diagnosis. Results. The risk of HIV infection progression among people living with diagnosed HIV infection decreased significantly from 1997 to 2010. The risks of progression to AIDS and death in 2010 were higher among African Americans and people of multiple races, males exposed through injection drug use (IDU) or heterosexual contact, females exposed through IDU, people residing in the South at diagnosis, and people diagnosed in 2009 compared with white individuals, men who have sex with men, females with infection attributed to heterosexual contact, those residing in the Northeast, and those diagnosed in previous years, respectively. People aged 15–29 years had the highest AIDS diagnosis hazard in 2010. Conclusion. Continued efforts are needed to ensure early HIV diagnosis as well as initial linkage to and continued engagement in HIV medical care among all people living with HIV. Targeted interventions are needed to improve healthcare and supportive services for those with worse health outcomes.