bluuebunny/crossref_metadata_2025 huggingface dataset:
Electrothermally actuated moving contact line dynamics over chemically patterned surfaces with resistive heaters
Authors: Kunti Golak , Bhattacharya Anandaroop , Chakraborty Suman
Published: June 2018

In this paper, we explore the moving contact line dynamics of two Newtonian immiscible fluids over substrates patterned with two different alternative chemical patches. The bulk fluid motion is actuated using electrothermal kinetics where the thermal field is generated by incorporating resistive heaters on the substrate. The electrothermal forces, which arise from the local gradient in electrical conductivity and permittivity, strongly depend on the local temperature and potential distributions. The thermal field and the potential distribution can be modulated by altering the heater characteristics and electrode patterning. The contact line motion and its intricate physics can be effectively tuned by altering the geometrical parameters of the heaters and electrode arrangement. Further, a comparison is executed between conventional electrothermal and heater-assisted electrothermal processes. The interfacial dynamics of the immiscible binary fluids is greatly affected by the present electrothermal mechanism and shows advantages over the conventional electrothermal process. The results presented here are effective for developing various smart devices involving multiphase flow dynamics within an electrokinetic paradigm.
Decoupling the influence of surface structure and intrinsic wettability on boiling heat transfer
Authors: Dai Xianming , Wang Pengtao , Yang Fanghao , Li Xiaochuan , Li Chen
Published: June 2018

Surface structure and intrinsic wettability are both important for boiling heat transfer. While superhydrophilic micro, nano, and hierarchical surfaces are widely used for boiling enhancement, in which the surface structure and intrinsic wettability usually couple together. This study aims to decouple their influences on boiling heat transfer. Copper meshes are utilized as the microporous structures, and conformal superhydrophilic films of TiO2 are deposited by atomic layer deposition (ALD). Although ALD coatings for boiling have been done on flat surfaces, this study separates the influence of surface structure from that of intrinsic wettability on a three-dimensional microporous surface. By comparing two and four layer meshes, we show that the surface structure has no obvious influence on the critical heat flux (CHF), but can significantly enhance the heat transfer coefficient (HTC). The intrinsic superhydrophilicity dramatically increases the CHF due to the fast rewetting of dryout regions. Our conclusion is that fast rewetting is critical to increase the CHF, while large surface areas are vital to enhance the HTC.
Upstream and downstream multipactor of dielectric window by electromagnetic PIC simulations
Authors: Wang Huihui , Liu Laqun , Liu Dagang , Meng Lin
Published: June 2018

By using the electromagnetic Particle-In-Cell method, the multipactor of the dielectric window on the upstream side is observed directly even without presetting extra normal electric fields and compared to that on the downstream side. This paper shows: First, with the initial emission of electrons to provide extra normal electric fields, the secondary electron avalanche is much faster than that on the downstream side. Second, even without the initial emission of electron to provide extra normal electric fields, the secondary electron avalanche occurs on the upstream side, while it is nowhere to be found on the downstream side.
Electronic structure and ferromagnetic properties of Zn vacancies in ZnO screw dislocations: First-principles calculations
Authors: Wu Jingjing , Long Fei , Tang Biyu , Tang Xin
Published: June 2018

First principle calculation, based on density functional theory, is applied to study the configuration and electronic structure of ZnO screw dislocations along [0001] and [112¯0]. O-O bonds can be found in the core of dislocations along [0001], which induces an occupied energy level in forbidden band. The dislocations along [0001] also facilitate the formation and accumulation of Zn vacancies, due to the stress relief in dislocations. Moreover, the dislocations are periodic and continuous, and can mediate the ferromagnetic coupling between Zn vacancies. The antibonding state of O-O bonds around Zn vacancies is responsible for the ferromagnetic state, which is a kind of d0 ferromagnetism. The result also gives us a new view to think the origin of d0 ferromagnetism in ZnO.
Expansion of a mildly relativistic hot pair cloud into an electron-proton plasma
Authors: Dieckmann M. E. , Alejo A. , Sarri G.
Published: June 2018

The expansion of a charge-neutral cloud of electrons and positrons with the temperature 1 MeV into an unmagnetized ambient plasma is examined with a 2D particle-in-cell simulation. The pair outflow drives solitary waves in the ambient protons. Their bipolar electric fields attract electrons of the outflowing pair cloud and repel positrons. These fields can reflect some of the protons, thereby accelerating them to almost an MeV. Ion acoustic solitary waves are thus an efficient means to couple energy from the pair cloud to protons. The scattering of the electrons and positrons by the electric field slows down their expansion to a nonrelativistic speed. Only a dilute pair outflow reaches the expansion speed expected from the cloud's thermal speed. Its positrons are more energetic than its electrons. In time, an instability grows at the front of the dense slow-moving part of the pair cloud, which magnetizes the plasma. The instability is driven by the interaction of the outflowing positrons with the protons. These results shed light on how magnetic fields are created and ions are accelerated in pair-loaded astrophysical jets and winds.
SpliceRover: interpretable convolutional neural networks for improved splice site prediction
Authors: Zuallaert Jasper , Godin Fréderic , Kim Mijung , Soete Arne , Saeys Yvan , De Neve Wesley
Published: June 2018

Motivation

During the last decade, improvements in high-throughput sequencing have generated a wealth of genomic data. Functionally interpreting these sequences and finding the biological signals that are hallmarks of gene function and regulation is currently mostly done using automated genome annotation platforms, which mainly rely on integrated machine learning frameworks to identify different functional sites of interest, including splice sites. Splicing is an essential step in the gene regulation process, and the correct identification of splice sites is a major cornerstone in a genome annotation system.

Results

In this paper, we present SpliceRover, a predictive deep learning approach that outperforms the state-of-the-art in splice site prediction. SpliceRover uses convolutional neural networks (CNNs), which have been shown to obtain cutting edge performance on a wide variety of prediction tasks. We adapted this approach to deal with genomic sequence inputs, and show it consistently outperforms already existing approaches, with relative improvements in prediction effectiveness of up to 80.9% when measured in terms of false discovery rate. However, a major criticism of CNNs concerns their ‘black box’ nature, as mechanisms to obtain insight into their reasoning processes are limited. To facilitate interpretability of the SpliceRover models, we introduce an approach to visualize the biologically relevant information learnt. We show that our visualization approach is able to recover features known to be important for splice site prediction (binding motifs around the splice site, presence of polypyrimidine tracts and branch points), as well as reveal new features (e.g. several types of exclusion patterns near splice sites).

Availability and implementation

SpliceRover is available as a web service. The prediction tool and instructions can be found at http://bioit2.irc.ugent.be/splicerover/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Predicting miRNA–disease association based on inductive matrix completion
Authors: Chen Xing , Wang Lei , Qu Jia , Guan Na-Na , Li Jian-Qiang
Published: June 2018

Motivation

It has been shown that microRNAs (miRNAs) play key roles in variety of biological processes associated with human diseases. In Consideration of the cost and complexity of biological experiments, computational methods for predicting potential associations between miRNAs and diseases would be an effective complement.

Results

This paper presents a novel model of Inductive Matrix Completion for MiRNA–Disease Association prediction (IMCMDA). The integrated miRNA similarity and disease similarity are calculated based on miRNA functional similarity, disease semantic similarity and Gaussian interaction profile kernel similarity. The main idea is to complete the missing miRNA–disease association based on the known associations and the integrated miRNA similarity and disease similarity. IMCMDA achieves AUC of 0.8034 based on leave-one-out-cross-validation and improved previous models. In addition, IMCMDA was applied to five common human diseases in three types of case studies. In the first type, respectively, 42, 44, 45 out of top 50 predicted miRNAs of Colon Neoplasms, Kidney Neoplasms, Lymphoma were confirmed by experimental reports. In the second type of case study for new diseases without any known miRNAs, we chose Breast Neoplasms as the test example by hiding the association information between the miRNAs and Breast Neoplasms. As a result, 50 out of top 50 predicted Breast Neoplasms-related miRNAs are verified. In the third type of case study, IMCMDA was tested on HMDD V1.0 to assess the robustness of IMCMDA, 49 out of top 50 predicted Esophageal Neoplasms-related miRNAs are verified.

Availability and implementation

The code and dataset of IMCMDA are freely available at https://github.com/IMCMDAsourcecode/IMCMDA.

Supplementary information

Supplementary data are available at Bioinformatics online.
Reward-Driven Arousal Impacts Preparation to Perform a Task via Amygdala–Caudate Mechanisms
Authors: Watanabe Noriya , Bhanji Jamil P , Ohira Hideki , Delgado Mauricio R
Published: June 2018

Preparing for a challenging task can increase physiological arousal, in particular when potential incentives are large (e.g., a solo musical performance in front of an audience). Here, we examine how potential reward and its influence on arousal, measured by pupil dynamics, are represented in the brain while preparing for a challenging task. We further ask how neural representations during preparation relate to actual performance. Trials resulting in performance failure were characterized by increased pupil dilation as a function of increasing reward magnitude during preparation. Such failure trials were also associated with activation of the right amygdala representing pupil dilation, and the left caudate representing reward magnitude. Notably, increases in functional connectivity between amygdala and caudate preceded performance failure. These findings highlight increased connectivity between neural regions representing reward and arousal in circumstances where reward-driven arousal impairs performance.
Playing and Being in Georges Perec
Authors: Kemp Anna
Published: June 2018

In his brief account of his own psychoanalysis, Georges Perec describes the psychoanalytic encounter as a game. But what kind of a game is it, and how is it played? On the one hand Perec’s writing presents analysis as an often frustrating, puzzle-solving exercise in which the patient and analyst — like Perec’s notorious puzzle-fiends Percival Bartlebooth and Gaspard Winckler — are locked in intimate and exhausting combat. Such games express Perec’s ambivalent relationship to the psychoanalytic other who, while promising self-knowledge and healing, also threatens to reduce the specificity of his experience to the ‘quincaillerie anonyme’ of the Freudian handbook. However, Perec’s writing also articulates another kind of game — one that chimes with D. W. Winnicott’s understanding of psychoanalysis as a form of creative play. While the closed structures of many Perecquian games give expression to the fraught dynamics of a psychoanalytic encounter characterized by anxiety and suspicion, Perec’s work also elaborates more open and flexible literary games that foster the playful creativity that, in Winnicott’s account, is necessary to feeling alive and real. Such games produce an enabling framework that allows Perec’s autobiographical subject to better approach ‘ce qu[’il] cherche’ and cautiously to imagine connections with others.
High-quality assembly of the reference genome for scarlet sage, Salvia splendens, an economically important ornamental plant
Authors: Dong Ai-Xiang , Xin Hai-Bo , Li Zi-Jing , Liu Hui , Sun Yan-Qiang , Nie Shuai , Zhao Zheng-Nan , Cui Rong-Feng , Zhang Ren-Gang , Yun Quan-Zheng , Wang Xin-Ning , Maghuly Fatemeh , Porth Ilga , Cong Ri-Chen , Mao Jian-Feng
Published: June 2018

Background

Salvia splendens Ker-Gawler, scarlet or tropical sage, is a tender herbaceous perennial widely introduced and seen in public gardens all over the world. With few molecular resources, breeding is still restricted to traditional phenotypic selection, and the genetic mechanisms underlying phenotypic variation remain unknown. Hence, a high-quality reference genome will be very valuable for marker-assisted breeding, genome editing, and molecular genetics.

Findings

We generated 66 Gb and 37 Gb of raw DNA sequences, respectively, from whole-genome sequencing of a largely homozygous scarlet sage inbred line using Pacific Biosciences (PacBio) single-molecule real-time and Illumina HiSeq sequencing platforms. The PacBio de novo assembly yielded a final genome with a scaffold N50 size of 3.12 Mb and a total length of 808 Mb. The repetitive sequences identified accounted for 57.52% of the genome sequence, and 54,008 protein-coding genes were predicted collectively with ab initio and homology-based gene prediction from the masked genome. The divergence time between S. splendens and Salvia miltiorrhiza was estimated at 28.21 million years ago (Mya). Moreover, 3,797 species-specific genes and 1,187 expanded gene families were identified for the scarlet sage genome.

Conclusions

We provide the first genome sequence and gene annotation for the scarlet sage. The availability of these resources will be of great importance for further breeding strategies, genome editing, and comparative genomics among related species.
Consistent decreased activity in the putamen in Parkinson's disease: a meta-analysis and an independent validation of resting-state fMRI
Authors: Wang Jue , Zhang Jia-Rong , Zang Yu-Feng , Wu Tao
Published: June 2018

Background

Resting-state functional magnetic resonance imaging (RS-fMRI) has frequently been used to investigate local spontaneous brain activity in Parkinson's disease (PD) in a whole-brain, voxel-wise manner. To quantitatively integrate these studies, we conducted a coordinate-based (CB) meta-analysis using the signed differential mapping method on 15 studies that used amplitude of low-frequency fluctuation (ALFF) and 11 studies that used regional homogeneity (ReHo). All ALFF and ReHo studies compared PD patients with healthy controls. We also performed a validation RS-fMRI study of ALFF and ReHo in a frequency-dependent manner for a novel dataset consisting of 49 PD and 49 healthy controls.

Findings

Decreased ALFF was found in the left putamen in PD by meta-analysis. This finding was replicated in our independent validation dataset in the 0.027–0.073 Hz band but not in the conventional frequency band of 0.01–0.08 Hz.

Conclusions

Findings from the current study suggested that decreased ALFF in the putamen of PD patients is the most consistent finding. RS-fMRI is a promising technique for the precise localization of abnormal spontaneous activity in PD. However, more frequency-dependent studies using the same analytical methods are needed to replicate these results.

Trial registration: NCT NCT03439163. Registered 20 February 2018, retrospectively registered.
Long-read sequencing and de novo genome assembly of Ammopiptanthus nanus, a desert shrub
Authors: Gao Fei , Wang Xue , Li Xuming , Xu Mingyue , Li Huayun , Abla Merhaba , Sun Huigai , Wei Shanjun , Feng Jinchao , Zhou Yijun
Published: June 2018

Background

Ammopiptanthus nanus is a rare broad-leaved shrub that is found in the desert and arid regions of Central Asia. This plant species exhibits extremely high tolerance to drought and freezing and has been used in abiotic tolerance research in plants. As a relic of the tertiary period, A. nanus is of great significance to plant biogeographic research in the ancient Mediterranean region. Here, we report a draft genome assembly using the Pacific Biosciences (PacBio) platform and gene annotation for A. nanus.

Findings

A total of 64.72 Gb of raw PacBio sequel reads were generated from four 20-kb libraries. After filtering, 64.53 Gb of clean reads were obtained, giving 72.59× coverage depth. Assembly using Canu gave an assembly length of 823.74 Mb, with a contig N50 of 2.76 Mb. The final size of the assembled A. nanus genome was close to the 889 Mb estimated by k-mer analysis. The gene annotation completeness was evaluated using Benchmarking Universal Single-Copy Orthologs; 1,327 of the 1,440 conserved genes (92.15%) could be found in the A. nanus assembly. Genome annotation revealed that 74.08% of the A. nanus genome is composed of repetitive elements and 53.44% is composed of long terminal repeat elements. We predicted 37,188 protein-coding genes, of which 96.53% were functionally annotated.

Conclusions

The genomic sequences of A. nanus could be a valuable source for comparative genomic analysis in the legume family and will be useful for understanding the phylogenetic relationships of the Thermopsideae and the evolutionary response of plant species to the Qinghai Tibetan Plateau uplift.
Equilibrated flux a posteriori error estimates in $L^2(H^1)$-norms for high-order discretizations of parabolic problems
Authors: Ern Alexandre , Smears Iain , Vohralík Martin
Published: June 2018

We consider the a posteriori error analysis of fully discrete approximations of parabolic problems based on conforming $hp$-finite element methods in space and an arbitrary order discontinuous Galerkin method in time. Using an equilibrated flux reconstruction we present a posteriori error estimates yielding guaranteed upper bounds on the $L^2(H^1)$-norm of the error, without unknown constants and without restrictions on the spatial and temporal meshes. It is known from the literature that the analysis of the efficiency of the estimators represents a significant challenge for $L^2(H^1)$-norm estimates. Here we show that the estimator is bounded by the $L^2(H^1)$-norm of the error plus the temporal jumps under the one-sided parabolic condition $h^2 \lesssim \tau $. This result improves on earlier works that required stronger two-sided hypotheses such as $h \simeq \tau $ or $h^2\simeq \tau $; instead, our result now encompasses practically relevant cases for computations and allows for locally refined spatial meshes. The constants in our bounds are robust with respect to the mesh and time-step sizes, the spatial polynomial degrees and the refinement and coarsening between time steps, thereby removing any transition condition.
Measures, drivers and effects of green employment: evidence from US local labor markets, 2006–2014
Authors: Vona Francesco , Marin Giovanni , Consoli Davide
Published: June 2018

This paper explores the nature and the key empirical regularities of green employment in US local labor markets in 2006–2014. The main methodological novelty consists of a new measure of green employment based on the task content of occupations. Descriptive analysis reveals that green employment is pro-cyclical, highly skilled, commands a 4% wage premium and is geographically concentrated. Green employment dynamics positively correlates with local green subsidies within the American Recovery and Reinvestment Act, local green knowledge, and resilience to the great recession. Finally, we find that one additional green job is associated with 4.2 (2.2 in the crisis period) new local jobs in non-tradable non-green activities.
Somatotopy and Organization of Spinothalamic Tracts in the Human Cervical Spinal Cord
Authors: Vedantam Aditya , Bruera Eduardo , Hess Kenneth R , Dougherty Patrick M , Viswanathan Ashwin
Published: June 2018

BACKGROUND

Understanding spinothalamic tract anatomy may improve lesioning and outcomes in patients undergoing percutaneous cordotomy.

OBJECTIVE

To investigate somatotopy and anatomical organization of spinothalamic tracts in the human cervical spinal cord.

METHODS

Patients with intractable cancer pain undergoing cordotomy underwent preoperative and postoperative quantitative sensory testing for sharp pain and heat pain on day 1 and 7 after cordotomy. Intraoperative sensory stimulation was performed with computed tomography (CT) imaging to confirm the location of the radiofrequency electrode during cordotomy. Postoperative magnetic resonance (MR) imaging was performed to define the location of the lesion.

RESULTS

Twelve patients were studied, and intraoperative sensory stimulation combined with CT imaging revealed a somatotopy where fibers from the legs were posterolateral to fibers from the hand. Sharpness detection thresholds were significantly elevated in the area of maximum pain on postoperative day 1 (P = .01). Heat pain thresholds for all areas were not elevated significantly on postoperative day 1, or postoperative day 7. MR imaging confirmed that the cordotomy lesion was in the anterolateral quadrant, and in this location the lesion had a sustained effect on sharp pain but a transient impact on heat pain.

CONCLUSION

In the high cervical spinal cord, spinothalamic fibers mediating sharp pain for the arms are located ventromedial to fibers for the legs, and these fibers are spatially distinct from fibers that mediate heat pain.
Venous Thromboembolism in Patients With Spontaneous Intracerebral Hemorrhage: A Multicenter Study
Authors: Ding Dale , Sekar Padmini , Moomaw Charles J , Comeau Mary E , James Michael L , Testai Fernando , Flaherty Matthew L , Vashkevich Anastasia , Worrall Bradford B , Woo Daniel , Osborne Jennifer
Published: June 2018

BACKGROUND

Patients with spontaneous intracerebral hemorrhage (ICH) are predisposed to venous thromboembolic (VTE) complications, such as deep vein thrombosis and pulmonary embolism.

OBJECTIVE

To evaluate, in a multicenter, retrospective cohort study, the rate of VTE complications in ICH patients during acute hospitalization, identify potential risk factors, and assess their association with functional outcome.

METHODS

We retrospectively analyzed prospectively collected data from 19 centers and 41 sites that participated in the Ethnic/Racial Variations of Intracerebral Hemorrhage study, from August 2010 to February 2016. We compared ICH patients with VTE complications to those without VTE complications. Statistical analyses were performed to determine predictors of VTE complications and poor outcome (modified Rankin Scale ≥ 4) at discharge and 3-mo follow-up.

RESULTS

Of the 2902 ICH patients who were eligible for analysis, 87 (3.0%) had VTE complications: 57 (2.0%) had only deep vein thrombosis, 19 (0.7%) had only pulmonary embolism, and 11 (0.4%) had both. In the multivariable logistic regression analysis, a prior history of VTE (odds ratio [OR] = 6.8; P < .0001), intubation (OR = 4.0; P < .0001), and presence of IVH (OR = 1.8; P = .0157) were independent predictors of VTE complications. After controlling for ICH volume and location, IVH, age, and presenting Glasgow Coma Scale, the occurrence of VTE complications was an independent predictor of poor outcome at discharge (OR = 2.9; P = .002) and 3-mo follow-up (OR = 2.1; P = .02).

CONCLUSION

Although VTE complications are uncommon after ICH, they are associated with significantly worse outcomes. Further studies will be needed to determine the optimal treatment regimen for the prevention and treatment of VTE complications in ICH patients.
Microsurgical Clipping of Ruptured Distal Posterior Inferior Cerebellar Artery Aneurysm: 3-Dimensional Operative Video
Authors: Wainberg Ricardo Chmelnitsky , da Costa Marcos Devanir Silva , Hernández Yair A Ugalde , Caramanti Ricardo Lourenço , Alves Filho César Augusto Ferreira , Palmiero Helbert , Saick Ricardo Pagung , Chaddad-Neto Feres
Published: June 2018

The distal posterior inferior cerebellar artery (PICA) is a rare site of aneurysm formation. Only small case series and case reports regarding surgical treatment are found in the literature.

The PICA is divided into 5 segments (anterior medullary, lateral medullary, tonsilomedullary, telovelotonsillary, and cortical), and the distal ones represent the most complex, due to anatomic variations. We present a case of a 69-yr-old female patient who has suffered from a sudden and intense occipital headache, associated with nausea and vomiting. CT scan showed intraventricular hemorrhage, and further investigation with MRI and MR Angiography revealed a small distal PICA aneurysm, at the superior part of the medial aspect of the left cerebellar tonsil. Digital angiography has demonstrated the aneurysm at the tonsilomedullary segment of the PICA. In this 3-dimensional video, the authors show the microsurgical clipping of a saccular distal PICA aneurysm in the close relation to a choroidal branch, performed by median suboccipital craniotomy. Step-by-step of the dissection, relevant surrounding anatomy and aneurysm clipping is demonstrated. The patient signed the Institutional Consent Form, which allows the use of his/her images and videos for any type of medical publications in conferences and/or scientific articles.
Loop-Mediated Isothermal Amplification for the Diagnostic Detection of Meloidogyne chitwoodi and M. fallax
Authors: Zhang Lei , Gleason Cynthia
Published: June 2018

Meloidogyne chitwoodi is a root-knot nematode that parasitizes a broad range of plants. In the Pacific Northwest (PNW) of the United States, M. chitwoodi is a major potato pest. The nematodes infect roots and tubers; blemishes caused by the nematodes on the tubers significantly affect potato marketability. M. chitwoodi is a quarantine pathogen by many regulatory agencies, limiting potato trade opportunities when it is present. A loop-mediated isothermal amplification (LAMP) assay was developed to amplify the intergenic spacer (IGS2)-18S region of the ribosomal rDNA of M. chitwoodi. Using the LAMP assay, we could detect the presence of M. chitwoodi from infected Washington State soil samples. The LAMP primers showed specificity for DNA from M. chitwoodi and the closely related species M. fallax. There was no cross reaction of the LAMP primers with DNA from tropical nematodes M. incognita, M. arenaria, and M. javanica, or the Northern root-knot nematode M. hapla. The LAMP assays can be completed within 45 min, and they were 100 times more sensitive in nematode detection than conventional PCR. The LAMP assay will facilitate detection of potato nematodes M. chitwoodi and M. fallax. Knowledge of potato nematodes, particularly M. chitwoodi in PNW soils, will aid management decisions.
Temporal Dynamics of Fusarium virguliforme Colonization of Soybean Roots
Authors: Wang Jie , Jacobs Janette L. , Roth Mitchell G. , Chilvers Martin I.
Published: June 2018

Soybean sudden death syndrome (SDS) caused by Fusarium virguliforme is one of the most yield limiting soybean diseases in the United States. SDS disease symptoms include root rot and foliar symptoms induced by fungal toxins. Soybean cultivar resistance is one of the most effective SDS disease management options, but no cultivar displays complete resistance. Soybean SDS foliar symptoms are the primary phenotype used to screen and breed for SDS resistance. Root rot or root colonization measures are seldom utilized, partly due to the lack of convenient and accurate methods for quantification of F. virguliforme. In this study, greenhouse and field experiments were conducted to determine the temporal dynamics of F. virguliforme colonization of soybean roots using quantitative real-time PCR (qPCR). The infection coefficient (IC), or ratio of F. virguliforme DNA to soybean DNA, was determined in soybean cultivars with different SDS foliar resistance ratings. In greenhouse experiments, F. virguliforme was detected in all cultivars 7 days after planting (DAP), with a peak in IC at 14 DAP. All soybean cultivars developed SDS foliar symptoms, but F. virguliforme soybean root colonization levels did not significantly correlate with SDS foliar symptom severity. In field experiments, SDS foliar symptoms developed among soybean cultivars in alignment with provided foliar resistance ratings; however, the F. virguliforme IC were not significantly different between SDS foliar symptomatic and asymptomatic cultivars. F. virguliforme was detected in all cultivars at the first sample collection point 25 DAP (V3 vegetative growth stage), and the IC increased throughout the season, peaking at the last sample collection point 153 DAP (postharvest). Collectively, appearance and disease severity ratings of SDS foliar symptoms were not associated with F. virguliforme quantity in roots, suggesting a need to include F. virguliforme root colonization in breeding efforts to screen soybean germplasm for F. virguliforme root infection resistance. The findings also demonstrates root colonization of the pathogen on nonsymptomatic soybean cultivars leading to persistence of the pathogen in the field, and possible hidden yield loss.
Nanopore Sequencing as a Surveillance Tool for Plant Pathogens in Plant and Insect Tissues
Authors: Bronzato Badial Aline , Sherman Diana , Stone Andrew , Gopakumar Anagha , Wilson Victoria , Schneider William , King Jonas
Published: June 2018

Plant pathogens are constantly emerging and spreading into new areas and there are often limited postdiagnosis treatment options for infection, making surveillance key to their control. Here we present results from a study testing the efficacy of a portable nanopore-based massively parallel sequencing (MPS) technology for use in the detection of diverse plant pathogens in selected samples. The Oxford MinION device was coupled with whole transcriptome amplification (WTA) to sequence the metatranscriptome of plant and insect tissues infected with either Candidatus Liberibacter asiaticus or plum pox virus. Results showed that this methodology is useful for detecting unsuspected viral and bacterial pathogens in plant and insect tissues. The percentage of generated reads assigned to plum pox virus was 95% from infected tissue and 3% from the viruliferous insect, Myzus persicae. Diaphorina citri sequencing led to 22% of the reads mapping as Ca. L. asiaticus. Plum pox virus and Ca. L. asiaticus were detected in both tissue and insect samples near the beginning of each sequencing run, demonstrating the capability of this methodology to obtain results rapidly. This approach also proved the capability of this system to determine the major components of the insect vector’s microbiome and the specific strain of small-genome, high-titer pathogens.
Transgenic Expression ofEFRandBs2Genes for Field Management of Bacterial Wilt and Bacterial Spot of Tomato
Authors: Kunwar Sanju , Iriarte Fanny , Fan Qiurong , Evaristo da Silva Eduardo , Ritchie Laura , Nguyen Nghi Song , Freeman Joshua H. , Stall Robert E. , Jones Jeffrey B. , Minsavage Gerald V. , Colee James , Scott Jay W. , Vallad Gary E. , Zipfel Cyril , Horvath Diana , Westwood Jack , Hutton Samuel F. , Paret Mathews L.
Published: June 2018

Field trials were conducted at two locations in Florida to evaluate transgenic tomato expressing the ELONGATION FACTOR TU RECEPTOR (EFR) gene from Arabidopsis thaliana, the Bs2 gene from pepper, or both Bs2 and EFR (Bs2/EFR) for managing bacterial wilt caused by Ralstonia solanacearum and bacterial spot caused by Xanthomonas perforans. Expression of EFR or Bs2/EFR in the susceptible genotype Fla. 8000 significantly reduced bacterial wilt incidence (50 to 100%) and increased total yield (57 to 114%) relative to lines expressing only Bs2 or the nontransformed Fla. 8000 control, although the marketable yield was not significantly affected. Following harvest, surviving symptomatic and nonsymptomatic plants were assessed for colonization by R. solanacearum. There were no significant differences in the population at the lower stem. Interestingly, in the middle stem, no bacteria could be recovered from EFR or Bs2/EFR lines but viable bacterial populations were recovered from Bs2 and nontransformed control lines at 102to 105CFU/g of stem tissue. In growth-chamber experiments, the EFR transgenic tomato lines were found to be effective against seven different R. solanacearum strains isolated from the southeastern United States, indicating utility across the southeastern United States. In all of the bacterial spot trials, EFR and Bs2/EFR lines had significantly reduced disease severity (22 to 98%) compared with the Fla. 8000 control. The marketable and total yield of Bs2/EFR were significantly higher (43 to 170%) than Fla. 8000 control in three of four field trials. These results demonstrate for the first time the potential of using the EFR gene for field management of bacterial wilt and bacterial spot diseases of tomato.
Examining trends in the diversity of the U.S. National Institutes of Health participating and funded workforce
Authors: Nikaj Silda , Roychowdhury Deepshikha , Lund P. Kay , Matthews Marguerite , Pearson Katrina
Published: June 2018

Here, we use recent U.S. National Institutes of Health (NIH) data to document trends in the NIH‐funded workforce over time. Consistent with previous studies that were initiated by NIH, we find that the number of scientists funded on competing R01‐equivalent (R01 Eq.) and research project grants (RPGs) increased 2–5% per year between 2009 and 2016. Primary beneficiaries of this growth were experienced investigators (Exps), whereas the share of funding awarded to early‐stage investigators (ESIs) and new investigators (NIs) declined. The decline occurred even after NIH instituted the New and Early‐Stage Investigator policy in 2009. When we evaluate the investigator pool, we find that women and racial and ethnic minorities represent a higher percentage of NIs and ESIs relative to Exps. Thus, trends of diminishing support for NIs and ESIs may negatively impact the diversity of the current and future biomedical research workforce. We find some recent gains among women and Hispanics as part of the applicant and awardee pool for both R01 Eq. and RPGs, but significant, large gaps persist among nationally underrepresented racial minorities. Our findings suggest a need to prioritize investments and support of ESIs and NIs, groups in which women and racial and ethnic minorities represent a larger proportion of the applicant pool, to enhance diversity in the NIH‐funded workforce.—Nikaj, S., Roychowdhury, D., Lund, P. K., Matthews, M., Pearson, K. Examining trends in the diversity of the U.S. National Institutes of Health participating and funded workforce. FASEB J. 32, 6410–6422 (2018). www.fasebj.org
The soluble extracellular domain of E‐cadherin interferes with EPEC adherence via interaction with the Tir:intimin complex
Authors: Login Frédéric H. , Jensen Helene H. , Pedersen Gitte A. , Amieva Manuel R. , Nejsum Lene N.
Published: June 2018

Enteropathogenic Escherichia coli (EPEC) causes watery diarrhea when colonizing the surface of enterocytes. The translocated intimin receptor (Tir):intimin receptor complex facilitates tight adherence to epithelial cells and formation of actin pedestals beneath EPEC. We found that the host cell adherens junction protein E‐cadherin (Ecad) was recruited to EPEC microcolonies. Live‐cell and confocal imaging revealed that Ecad recruitment depends on, and occurs after, formation of the Tir:intimin complex. Combinatorial binding experiments using wild‐type EPEC, isogenic mutants lacking Tir or intimin, and E. coli expressing intimin showed that the extracellular domain of Ecad binds the bacterial surface in a Tir:intimin‐dependent manner. Finally, addition of the soluble extracellular domain of Ecad to the infection medium or depletion of Ecad extracellular domain from the cell surface reduced EPEC adhesion to host cells. Thus, the soluble extracellular domain of Ecad may be used in the design of intervention strategies targeting EPEC adherence to host cells.—Login, F. H., Jensen, H. H., Pedersen, G. A., Amieva, M. R., Nejsum, L. N. The soluble extracellular domain of E‐cadherin interferes with EPEC adherence via interaction with the Tir:intimin complex. FASEB J. 32, 6860–6868 (2018). www.fasebj.org
Pressure Injury Risk Factors in Critical Care Patients: A Descriptive Analysis
Authors: Cox Jill , Roche Sharon , Murphy Virginia
Published: June 2018

BACKGROUND:

Pressure injury (PI) development in the critical care population is multifactorial. Despite the application of evidence-based prevention strategies, PIs do occur and may be unavoidable in some patients.

OBJECTIVES:

To describe the risk factors associated with PI development in a sample of medical-surgical intensive care unit patients and determine whether these risk factors were congruent with the risk factors proposed in the work of the National Pressure Ulcer Advisory Panel on unavoidable PIs.

METHODS:

A retrospective, descriptive design was used to determine the PI risk factors present in a sample of 57 critically ill patients admitted to the medical-surgical intensive care unit for more than 24 hours and who acquired a PI during their admission.

RESULTS:

The most frequently identified risk factors were immobility (n = 57 [100%]), septic shock (n = 31 [54%]), vasopressor use (n = 37 [65%]), head-of-bed elevation greater than 30° (n = 53 [93%]), sedation (n = 50 [87.7%]), and mechanical ventilation for more than 72 hours (n = 46 [81%]). The most common PI location was the sacrum (n = 32 [56%]), and the most common stage reported was deep-tissue PI (n = 39 [68%]). The mean number of days to PI development was reported at 7.5 (SD, 7.2) days.

CONCLUSIONS:

Results of this descriptive study were congruent with the literature surrounding the clinical situations that predispose patients to unavoidable PIs. While the implementation of aggressive PI prevention strategies is essential to reducing PI rates, it is important to recognize that in certain populations, such as the critically ill, exposure to certain risk factors may potentially escalate PI risk beyond the scope of prevention and result in an unavoidable PI. Recognizing these risk factors is significant in the journey to differentiate PIs that result from a lack of preventive care from those that may be prevention immune.
Prophylactic Seizure Medication and Health-Related Quality of Life After Intracerebral Hemorrhage
Authors: Naidech Andrew M. , Beaumont Jennifer , Muldoon Kathryn , Liotta Eric M. , Maas Matthew B. , Potts Matthew B. , Jahromi Babak S. , Cella David , Prabhakaran Shyam , Holl Jane L.
Published: June 2018

Objectives:

Prophylactic levetiracetam is currently used in ~40% of patients with intracerebral hemorrhage, and the potential impact of levetircetam on health-related quality of life is unknown. We tested the hypothesis that prophylactic levetiracetam is independently associated with differences in cognitive function health-related quality of life.

Design:

Patients with intracerebral hemorrhage were enrolled in a prospective cohort study. We performed mixed models for T-scores of health-related quality of life, referenced to the U.S. population at 50 ± 10, accounting for severity of injury and time to follow-up.

Setting:

Academic medical center.

Patients:

One-hundred forty-two survivors of intracerebral hemorrhage.

Interventions:

None.

Measurements and Main Results:

T-scores of Neuro-Quality of Life Cognitive Function v2.0 was the primary outcome, whereas Neuro-Quality of Life Mobility v1.0 and modified Rankin Scale (a global functional scale) were secondary measures. We prospectively documented if prophylactic levetiracetam was administered and retrieved administration data from the electronic health record. Patients who received prophylactic levetiracetam had worse cognitive function health-related quality of life (T-score 5.1 points lower; p = 0.01) after adjustment for age (p = 0.3), National Institutes of Health Stroke Scale (p < 0.000001), lobar hematoma (p = 0.9), and time of assessment; statistical models controlling for prophylactic levetiracetam and the Intracerebral Hemorrhage Score, a global measure of intracerebral hemorrhage severity, yielded similar results. Lower T-scores of cognitive function health-related quality of life at 3 months were correlated with more total levetiracetam dosage (p = 0.01) and more administered doses of levetiracetam in the hospital (p = 0.03). Patients who received prophylactic levetiracetam were more likely to have a lobar hematoma (27/38 vs 19/104; p < 0.001), undergo electroencephalography monitoring (15/38 vs 21/104; p = 0.02), but not more likely to have clinical seizures (4/38 vs 7/104; p = 0.5). Levetiracetam was not independently associated with the modified Rankin Scale scores or mobility health-related quality of life (p > 0.1).

Conclusions:

Prophylactic levetiracetam was independently associated with lower cognitive function health-related quality of life at follow-up after intracerebral hemorrhage.
Juvenile-Onset Early-Stage Mycosis Fungoides–Associated Follicular Mucinosis: A Case Report
Authors: Incel Uysal Pinar , Bozdogan Onder , Atilan Ahmet , Yalcin Basak
Published: June 2018

We report a juvenile case of mycosis fungoides with prominent follicular mucinosis (FM). The patient was a 9-year old boy who presented with a 2-month history of enlarging alopecic patch with fine scales on the scalp. Dermatologic examination revealed orange-tan slightly palpable plaques with follicular prominence on his trunk. The patient and his family were not aware of these asymptomatic truncal plaques. Histopathologic examination of both—scalp and trunk—lesions revealed folliculotropic lymphocytic infiltration with mucin. Immunohistochemical study showed that lymphocytic infiltration was CD4 dominant. Flow cytometry analyses of peripheral blood were normal. Any abnormal populations and Sézary cells were not observed on blood smear. Polymerase chain reaction testing showed monoclonality for the T-cell receptor4-ɤ gene. Our patient had the clinical and histopathological diagnosis of follicular mycosis fungoides–associated follicular mucinosis.
Associations Between Disruptive Behavior Problems, Parenting Factors, and Sleep Problems Among Young Children
Authors: Coto Jennifer , Garcia Alexis , Hart Katie C. , Graziano Paulo A.
Published: June 2018

Objective:

To examine within an at-risk/clinical sample of preschool-aged children with externalizing problems: (1) which disruptive behavior and attention disorder symptoms (i.e., inattention, hyperactivity/impulsivity, and oppositionality/aggression) and (2) what aspects of parenting (e.g., discipline practices or stress) are related to children's sleep problems (e.g., sleep habit and night waking problems).

Method:

The sample consisted of 148 children (meanage = 5.06 years, 82% male) with at-risk/clinically elevated levels of externalizing behavior problems and their primary caregiver. As part of a larger study, parents reported on their stress and parenting practices and their children's behavioral and sleep functioning. Positive and negative parenting behaviors (“do” and “don't” skills, respectively) were also observed during a 15-minute parent-child interaction during play.

Results:

Oppositionality/aggression was the only disruptive behavior and attention disorder symptom associated with more sleep habit problems. Higher levels of inconsistent discipline and “don't” skills were also associated with more sleep habit problems. Within a combined model, an interaction emerged such that the association between “don't” skills and elevated sleep habit problems was only evident at low levels of inconsistent discipline. In terms of night waking problems, there was only an association with parenting stress, whereas the other parenting factors and disruptive behavior and attention disorder symptoms were unrelated.

Conclusion:

Although the directionality of our associations cannot be ascertained because of the cross-sectional nature of our study, these findings, nevertheless, highlight the importance of parenting factors (e.g., inconsistent discipline and parenting stress) when considering sleep difficulties in young children with disruptive behavior and attention disorders.
Air Pollution Exposure During Pregnancy and Symptoms of Attention Deficit and Hyperactivity Disorder in Children in Europe
Authors: Forns Joan , Sunyer Jordi , Garcia-Esteban Raquel , Porta Daniela , Ghassabian Akhgar , Giorgis-Allemand Lise , Gong Tong , Gehring Ulrike , Sørensen Mette , Standl Marie , Sugiri Dorothee , Almqvist Catarina , Andiarena Ainara , Badaloní Chiara , Beelen Rob , Berdel Dietrich , Cesaroni Giulia , Charles Marie-Aline , Eriksen Kirsten Thorup , Estarlich Marisa , Fernandez Mariana F. , Forhan Anne , Jaddoe Vincent W.V. , Korek Michal , Lichtenstein Paul , Lertxundi Aitana , Lopez-Espinosa Maria-Jose , Markevych Iana , de Nazelle Audrey , Raaschou-Nielsen Ole , Nieuwenhuijsen Mark , Pérez-Lobato Rocío , Philippat Claire , Slama Rémy , Tiesler Carla M.T. , Verhulst Frank C. , von Berg Andrea , Vrijkotte Tanja , Nybo Andersen Anne-Marie , Heude Barbara , Krämer Ursula , Heinrich Joachim , Tiemeier Henning , Forastiere Francesco , Pershagen Göran , Brunekreef Bert , Guxens Mònica
Published: June 2018

Background:

Exposure to air pollution during pregnancy may increase attention-deficit/hyperactivity disorder (ADHD) symptoms in children, but findings have been inconsistent. We aimed to study this association in a collaborative study of eight European population-based birth/child cohorts, including 29,127 mother–child pairs.

Methods:

Air pollution concentrations (nitrogen dioxide [NO2] and particulate matter [PM]) were estimated at the birth address by land-use regression models based on monitoring campaigns performed between 2008 and 2011. We extrapolated concentrations back in time to exact pregnancy periods. Teachers or parents assessed ADHD symptoms at 3–10 years of age. We classified children as having ADHD symptoms within the borderline/clinical range and within the clinical range using validated cutoffs. We combined all adjusted area-specific effect estimates using random-effects meta-analysis and multiple imputations and applied inverse probability-weighting methods to correct for loss to follow-up.

Results:

We classified a total of 2,801 children as having ADHD symptoms within the borderline/clinical range, and 1,590 within the clinical range. Exposure to air pollution during pregnancy was not associated with a higher odds of ADHD symptoms within the borderline/clinical range (e.g., adjusted odds ratio [OR] for ADHD symptoms of 0.95, 95% confidence interval [CI] = 0.89, 1.01 per 10 µg/m3 increase in NO2 and 0.98, 95% CI = 0.80, 1.19 per 5 µg/m3 increase in PM2.5). We observed similar associations for ADHD within the clinical range.

Conclusions:

There was no evidence for an increase in risk of ADHD symptoms with increasing prenatal air pollution levels in children aged 3–10 years. See video abstract at, http://links.lww.com/EDE/B379.