bluuebunny/crossref_metadata_2025 huggingface dataset:
Confronting Epistemological Racism, Decolonizing Scholarly Knowledge: Race and Gender in Applied Linguistics
Authors: Kubota Ryuko
Published: May 2019

Recent scholarship in sociolinguistics and language education has examined how race and language intersect each other and how racism influences linguistic and educational practices. While racism is often conceptualized in terms of individual and institutional injustices, a critical examination of another form of racism—epistemological racism—problematizes how racial inequalities influence our knowledge production and consumption in academe. Highlighting the importance of the intersectional nature of identity categories, this conceptual article aims to draw scholars’ attention on how epistemological racism marginalizes and erases the knowledge produced by scholars in the Global South, women scholars of color, and other minoritized groups. In today’s neoliberal culture of competition, scholars of color are compelled to become complicit with white Euro-American hegemonic knowledge, further perpetuating the hegemony of white knowledge while marginalizing women scholars of color. Valorizing non-European knowledge and collectivity as an alternative framework also risks essentialism and male hegemony. Conversely, the ethics promoted by black feminism emphasizes a personal ethical commitment to antiracism. Epistemological antiracism invites scholars to validate alternative theories, rethink our citation practices, and develop critical reflexivity and accountability.
cloudSPAdes: assembly of synthetic long reads using de Bruijn graphs
Authors: Tolstoganov Ivan , Bankevich Anton , Chen Zhoutao , Pevzner Pavel A
Published: May 2019

Motivation

The recently developed barcoding-based synthetic long read (SLR) technologies have already found many applications in genome assembly and analysis. However, although some new barcoding protocols are emerging and the range of SLR applications is being expanded, the existing SLR assemblers are optimized for a narrow range of parameters and are not easily extendable to new barcoding technologies and new applications such as metagenomics or hybrid assembly.

Results

We describe the algorithmic challenge of the SLR assembly and present a cloudSPAdes algorithm for SLR assembly that is based on analyzing the de Bruijn graph of SLRs. We benchmarked cloudSPAdes across various barcoding technologies/applications and demonstrated that it improves on the state-of-the-art SLR assemblers in accuracy and speed.

Availability and implementation

Source code and installation manual for cloudSPAdes are available at https://github.com/ablab/spades/releases/tag/cloudspades-paper.

Supplementary Information

Supplementary data are available at Bioinformatics online.
CytoPacq: a web-interface for simulating multi-dimensional cell imaging
Authors: Wiesner David , Svoboda David , Maška Martin , Kozubek Michal
Published: May 2019

Motivation

Objective assessment of bioimage analysis methods is an essential step towards understanding their robustness and parameter sensitivity, calling for the availability of heterogeneous bioimage datasets accompanied by their reference annotations. Because manual annotations are known to be arduous, highly subjective and barely reproducible, numerous simulators have emerged over past decades, generating synthetic bioimage datasets complemented with inherent reference annotations. However, the installation and configuration of these tools generally constitutes a barrier to their widespread use.

Results

We present a modern, modular web-interface, CytoPacq, to facilitate the generation of synthetic benchmark datasets relevant for multi-dimensional cell imaging. CytoPacq poses a user-friendly graphical interface with contextual tooltips and currently allows a comfortable access to various cell simulation systems of fluorescence microscopy, which have already been recognized and used by the scientific community, in a straightforward and self-contained form.

Availability and implementation

CytoPacq is a publicly available online service running at https://cbia.fi.muni.cz/simulator. More information about it as well as examples of generated bioimage datasets are available directly through the web-interface.

Supplementary information

Supplementary data are available at Bioinformatics online.
Active Case Finding for Malaria: A 3-Year National Evaluation of Optimal Approaches to Detect Infections and Hotspots Through Reactive Case Detection in the Low-transmission Setting of Eswatini
Authors: Hsiang Michelle S , Ntshalintshali Nyasatu , Kang Dufour Mi-Suk , Dlamini Nomcebo , Nhlabathi Nomcebo , Vilakati Sibonakaliso , Malambe Calsile , Zulu Zulisile , Maphalala Gugu , Novotny Joseph , Murphy Maxwell , Schwartz Alanna , Sturrock Hugh , Gosling Roly , Dorsey Grant , Kunene Simon , Greenhouse Bryan
Published: May 2019

Background

Reactive case detection (RACD) is a widely practiced malaria elimination intervention whereby close contacts of index cases receive malaria testing to inform treatment and other interventions. However, the optimal diagnostic and operational approaches for this resource-intensive strategy are not clear.

Methods

We conducted a 3-year prospective national evaluation of RACD in Eswatini, a malaria elimination setting. Loop-mediated isothermal amplification (LAMP) was compared to traditional rapid diagnostic testing (RDT) for the improved detection of infections and for hotspots (RACD events yielding ≥1 additional infection). The potential for index case–, RACD-, and individual-level factors to improve efficiencies was also evaluated.

Results

Among 377 RACD events, 10 890 participants residing within 500 m of index cases were tested. Compared to RDT, LAMP provided a 3-fold and 2.3-fold higher yield to detect infections (1.7% vs 0.6%) and hotspots (29.7% vs 12.7%), respectively. Hotspot detection improved with ≥80% target population coverage and response times within 7 days. Proximity to the index case was associated with a dose-dependent increased infection risk (up to 4-fold). Individual-, index case–, and other RACD-level factors were considered but the simple approach of restricting RACD to a 200-m radius maximized yield and efficiency.

Conclusions

We present the first large-scale national evaluation of optimal RACD approaches from a malaria elimination setting. To inform delivery of antimalarial drugs or other interventions, RACD, when conducted, should utilize more sensitive diagnostics and clear context-specific operational parameters. Future studies of RACD’s impact on transmission may still be needed.
Behavioral and Physiological Resistance to Desiccation in Spotted Wing Drosophila (Diptera: Drosophilidae)
Authors: Fanning Philip D , Johnson Anne E , Luttinen Benjamin E , Espeland Elizabeth M , Jahn Nolan T , Isaacs Rufus
Published: May 2019

With a high surface to volume ratio, small organisms must carefully regulate their internal water status. Spotted-wing drosophila, Drosophila suzukii (Matsumura), is an invasive frugivorous insect distributed across a wide range of geographical regions that can have periods of dry and hot weather, suggesting that this species has strategies to avoid stressful environments and reduce water loss. It also survives winter as an adult fly, indicating that it has adaptations to the low air humidity of this season. To determine the importance of water stress to D. suzukii, we studied their survival in environments of low humidity, which was manipulated using Drierite, and their survival and water loss in response to desiccation. Survival of both sexes was lower in drier conditions, and while female winter morph D. suzukii had higher mortality early on, remaining flies were able to survive longer in the drier conditions than the summer morphs. A bioassay method was adapted from Enjin et al. (2016) using 48-well plates to videotape the location of flies and quantify their behavioral responses to humidity. Male and female D. suzukii avoided dry conditions within the bioassay system, but only when there was at least 25% differential between humidity extremes. This response was observed for both summer and winter morphs of D. suzukii and our results provide guidance for attempts to manipulate crop environments to reduce the economic impact of this pest.
Oral anticoagulation in patients with non-valvular atrial fibrillation and a CHA2DS2-VASc score of 1: a current opinion of the European Society of Cardiology Working Group on Cardiovascular Pharmacotherapy and European Society of Cardiology Council on Stroke
Authors: Sulzgruber Patrick , Wassmann Sven , Semb Anne Grete , Doehner Wolfram , Widimsky Petr , Gremmel Thomas , Kaski Juan Carlos , Savarese Gianluigi , Rosano Giuseppe M C , Borghi Claudio , Kjeldsen Keld , Torp-Pedersen Christian , Schmidt Thomas Andersen , Lewis Basil S , Drexel Heinz , Tamargo Juan , Atar Dan , Agewall Stefan , Niessner Alexander
Published: May 2019

Oral anticoagulation in patients presenting with non-valvular atrial fibrillation and a CHA2DS2-VASc score of 1 (CHA2DS2-VASc of 2 in women) remains a challenging approach in clinical practice. Therapeutic decisions need to balance the individual benefit of reducing thromboembolic risk against the potential harm due to an increase in bleeding risk in this intermediate risk patient population. Within the current opinion statement of the European Society of Cardiology working group of cardiovascular pharmacotherapy and the European Society of Cardiology council on stroke the currently available evidence on the anti-thrombotic management in patients presenting with a CHA2DS2-VASc of 1 is summarized. Easily applicable tools for a personalized refinement of the individual thromboembolic risk in patients with atrial fibrillation and a CHA2DS2-VASc score of 1 that guide clinicians through the question whether to anticoagulate or not are provided.
A microanalysis of trade finance: German bank entry and coffee exports in Brazil, 1880–1913
Authors: Kisling Wilfried
Published: May 2019

The trade-finance nexus has enjoyed increasing interest in recent economic studies, but empirical evidence is scarce and studies from a historical perspective seem missing. This study analyses the effect of German bank entry on Brazilian coffee exports between 1880 and 1913 using firm-level data. I create an original data set on the yearly quantities of exported coffee and the credit received from the German Brasilianische Bank für Deutschland by export houses in Brazil. Using a difference-in-difference approach, I find that Brasilianische eased previously existing credit constraints, and that companies financed by Brasilianische exported significantly more than those that were not.
Prediction of ventricular arrhythmias in patients with a spontaneous Brugada type 1 pattern: the key is in the electrocardiogram
Authors: Delinière Antoine , Baranchuk Adrian , Giai Joris , Bessiere Francis , Maucort-Boulch Delphine , Defaye Pascal , Marijon Eloi , Le Vavasseur Olivier , Dobreanu Dan , Scridon Alina , Da Costa Antoine , Delacrétaz Etienne , Kouakam Claude , Eschalier Romain , Extramiana Fabrice , Leenhardt Antoine , Burri Haran , Winum Pierre François , Taieb Jérôme , Bouet Jérôme , Fauvernier Mathieu , Rosianu Horia , Carabelli Adrien , Duband Benjamin , Chevalier Philippe
Published: May 2019

Aims

There is currently no reliable tool to quantify the risks of ventricular fibrillation or sudden cardiac arrest (VF/SCA) in patients with spontaneous Brugada type 1 pattern (BrT1). Previous studies showed that electrocardiographic (ECG) markers of depolarization or repolarization disorders might indicate elevated risk. We aimed to design a VF/SCA risk prediction model based on ECG analyses for adult patients with spontaneous BrT1.

Methods and results

This retrospective multicentre international study analysed ECG data from 115 patients (mean age 45.1 ± 12.8 years, 105 males) with spontaneous BrT1. Of these, 45 patients had experienced VF/SCA and 70 patients did not experience VF/SCA. Among 10 ECG markers, a univariate analysis showed significant associations between VF/SCA and maximum corrected Tpeak–Tend intervals ≥100 ms in precordial leads (LMaxTpec) (P < 0.001), BrT1 in a peripheral lead (pT1) (P = 0.004), early repolarization in inferolateral leads (ER) (P < 0.001), and QRS duration ≥120 ms in lead V2 (P = 0.002). The Cox multivariate analysis revealed four predictors of VF/SCA: the LMaxTpec [hazard ratio (HR) 8.3, 95% confidence interval (CI) 2.4–28.5; P < 0.001], LMaxTpec + ER (HR 14.9, 95% CI 4.2–53.1; P < 0.001), LMaxTpec + pT1 (HR 17.2, 95% CI 4.1–72; P < 0.001), and LMaxTpec + pT1 + ER (HR 23.5, 95% CI 6–93; P < 0.001). Our multidimensional penalized spline model predicted the 1-year risk of VF/SCA, based on age and these markers.

Conclusion

LMaxTpec and its association with pT1 and/or ER indicated elevated VF/SCA risk in adult patients with spontaneous BrT1. We successfully developed a simple risk prediction model based on age and these ECG markers.
A Morphological Integration Perspective on the Evolution of Dimorphism among Sexes and Social Insect Castes
Authors: Friedman Nicholas R , Remeš Vladimír , Economo Evan P
Published: May 2019

Many species have evolved alternate phenotypes, thus enabling individuals to conditionally produce phenotypes that are favorable for reproductive success. Examples of this phenomenon include sexual dimorphism, alternative reproductive strategies, and social insect castes. While the evolutionary functions and developmental mechanisms of dimorphic phenotypes have been studied extensively, little attention has focused on the evolutionary covariance between each phenotype. We extend the conceptual framework and methods of morphological integration to hypothesize that dimorphic traits tend to be less integrated between sexes or social castes. In the case of social insects, we describe results from our recent study of an ant genus in which workers have major and minor worker castes that perform different behavioral repertoires in and around the nest. In the case of birds, we describe a new analysis of a family of songbirds that exhibits plumage coloration that can differ greatly between males and females, with apparently independent changes in each sex. Ant head shape, which is highly specialized in each worker caste, was weakly integrated between worker castes, whereas thorax shape, which is more monomorphic, was tightly integrated. Similarly, in birds, we found a negative association between dimorphism and the degree of integration between sexes. We also found that integration decreased in fairy wrens (Malurus) for many feather patches that evolved greater dichromatism. Together, this suggests that the process of evolving increased dimorphism results in a decrease in integration between sexes and social castes. We speculate that once a mechanism for dimorphism evolves, that mechanism can create independent variation in one sex or caste upon which selection may act.
Predicting residual feed intake status using rumen microbial profiles in ewe lambs1
Authors: Ellison Melinda J , Conant Gavin C , Lamberson William R , Austin Kathleen J , van Kirk Edward , Cunningham Hannah C , Rule Daniel C , Cammack Kristi M
Published: May 2019

Including feed efficiency as a trait for selection has gained interest in the sheep industry because it can result in reduced feed inputs or improve stocking rates, both of which translate into increased profitability for the producer. It is of interest whether the feed efficiency status of a testing population of sheep could be predicted using rumen microbial profiles associated with divergent feed efficiency status in a training population of sheep. Two populations of ewes were fed the same diet, and each group was evaluated for feed efficiency. A total of 20 animals in the testing population were selected for prediction assessment using feed efficiency, including the 6 top-ranked, the 6 bottom-ranked, and 8 middle-ranked ewes stratified over the distribution. Rumen fluid samples were collected and DNA was extracted for sequencing. Using a rumen microbial profile associated with diverging feed efficiency created from the training population, multiple discriminant analyses were performed using the DISCRIM procedure of SAS to determine the probability of correctly identifying lambs in the testing population as low, medium, or high feed efficiency using their microbial profiles. A profile of 6 rumen microbial species were used to correctly (P < 0.001) predict all testing population ewes into their actual feed efficiency status. A regression analysis using the same microbial profile was used to predict feed efficiency values, which were strongly correlated (r = 0.71; P < 0.001) with actual feed efficiency values. These results indicate that specific rumen microbial species may play a role in feed efficiency, and that a microbial profile could be used to rank sheep for feed efficiency.
Fused Colonies of the Formosan Subterranean Termite (Blattodea: Rhinotermitidae) for Laboratory Experiments
Authors: Lee Sang-Bin , Mullins Aaron , Aguilera-Olivares Daniel , Chouvenc Thomas , Su Nan-Yao
Published: May 2019

Laboratory studies of Coptotermes formosanus Shiraki (Blattodea: Rhinotermitidae) often employ the use of field-collected foraging populations of individuals as defined colonies. The biological relevance of this practice is often called into question, because these colonies lack a full composition of reproductive castes and brood, which may have physiological and behavioral consequences. Rearing intact laboratory colonies can be done; however, it is time-consuming and labor-intensive. The artificial fusion of field-collected foraging populations with a young, laboratory-reared incipient colony may provide whole, intact colonies for laboratory research. The current study measures survivorship of fused colonies using laboratory-reared complete incipient colonies ranging in age from 0 to 5 mo, fused with 100 workers and 10 soldiers from field-collected populations of different colonial origin. Results indicate that 60% of colony fusion was successful when the incipient colony introduced is 5 mo of age. This method of colony fusion will provide researchers with intact colonies using minimal resources.
EVALUATING THE COMPETITION EFFECTS OF UBER’S ENTRY INTO THE BRAZILIAN INCUMBENT CAB-HAILING APP SEGMENT
Authors: Resende Guilherme Mendes , Lima Ricardo Carvalho de Andrade
Published: May 2019

This paper assesses the competition effects of Uber’s entry into the incumbent cab-hailing app segment in Brazil. Using a monthly panel data set (from 2014 to 2016) covering the Brazilian municipalities and a difference-in-differences estimator, we show that Uber’s entry into the market resulted in an average reduction of 56.8 percent in the number of rides from cab-hailing apps in the cities where the platform operates. The magnitude of this effect suggests that Uber has had a clearly disruptive effect on the incumbent sector. We also found significant spatial heterogeneity in the competition effects of the platform when comparing the markets of the capitals of the North and Northeast regions (where Uber entered late) with the capitals of the South, Southeast, and Central West regions (where Uber entered early). Only in the second group of municipalities, we found that Uber’s entry caused a reduction in taxi fares (reduction of 12.1 percent). This indicates that the cab-hailing app sector reacted to Uber’s entry by offering discounts in fares after a longer period of exposure to a competitive environment.
Pension Reforms and Public Sector Turnover
Authors: Gorina Evgenia , Hoang Trang
Published: May 2019

Over the past decade, many states have reformed their retirement systems by reducing benefit generosity, tightening retirement provisions, introducing non-defined-benefit (DB) plan options and even replacing DB plans with defined-contribution plans. Many of these reforms have affected post-employment benefits that public workers will receive when they retire. Have these reforms also affected the attractiveness of public sector employment? To answer this question, we use state-level data from 2002 to 2015 and examine the relationship between state pension reforms and public employee turnover following the reforms. We find that employee responsiveness to the reforms was tangible and that it differed by reform type and worker education. These results are important because the design of public retirement benefits will continue to influence the ability of the public sector to recruit and retain high-quality workforce.
Structure and expansion law of H ii regions in structured molecular clouds
Authors: Zamora-Avilés Manuel , Vázquez-Semadeni Enrique , González Ricardo F , Franco José , Shore Steven N , Hartmann Lee W , Ballesteros-Paredes Javier , Banerjee Robi , Körtgen Bastian
Published: May 2019

We present radiation-magnetohydrodynamic simulations aimed at studying evolutionary properties of H ii regions in turbulent, magnetized, and collapsing molecular clouds formed by converging flows in the warm neutral medium. We focus on the structure, dynamics, and expansion laws of these regions. Once a massive star forms in our highly structured clouds, its ionizing radiation eventually stops the accretion (through filaments) towards the massive star-forming regions. The new overpressured H ii regions push away the dense gas, thus disrupting the more massive collapse centres. Also, because of the complex density structure in the cloud, the H ii regions expand in a hybrid manner: they virtually do not expand towards the densest regions (cores), while they expand according to the classical analytical result towards the rest of the cloud, and in an accelerated way, as a blister region, towards the diffuse medium. Thus, the ionized regions grow anisotropically, and the ionizing stars generally appear off-centre of the regions. Finally, we find that the hypotheses assumed in standard H ii-region expansion models (fully embedded region, blister-type, or expansion in a density gradient) apply simultaneously in different parts of our simulated H ii regions, producing a net expansion law (R∝ tα, with α in the range of 0.93–1.47 and a mean value of 1.2 ± 0.17) that differs from any of those of the standard models.
Joint Maximum Likelihood of Phylogeny and Ancestral States Is Not Consistent
Authors: Shaw David A , Dinh Vu C , Matsen Frederick A
Published: May 2019

Maximum likelihood estimation in phylogenetics requires a means of handling unknown ancestral states. Classical maximum likelihood averages over these unknown intermediate states, leading to provably consistent estimation of the topology and continuous model parameters. Recently, a computationally efficient approach has been proposed to jointly maximize over these unknown states and phylogenetic parameters. Although this method of joint maximum likelihood estimation can obtain estimates more quickly, its properties as an estimator are not yet clear. In this article, we show that this method of jointly estimating phylogenetic parameters along with ancestral states is not consistent in general. We find a sizeable region of parameter space that generates data on a four-taxon tree for which this joint method estimates the internal branch length to be exactly zero, even in the limit of infinite-length sequences. More generally, we show that this joint method only estimates branch lengths correctly on a set of measure zero. We show empirically that branch length estimates are systematically biased downward, even for short branches.
Xenograft-based, platform-independent gene signatures to predict response to alkylating chemotherapy, radiation, and combination therapy for glioblastoma
Authors: Zhao Shuang G , Yu Menggang , Spratt Daniel E , Chang S Laura , Feng Felix Y , Kim Michelle M , Speers Corey W , Carlson Brett L , Mladek Ann C , Lawrence Theodore S , Sarkaria Jann N , Wahl Daniel R
Published: May 2019

Background

Predictive molecular biomarkers to select optimal treatment for patients with glioblastoma and other cancers are lacking. New strategies are needed when large randomized trials with correlative molecular data are not feasible.

Methods

Gene signatures (GS) were developed from 31 orthotopic glioblastoma patient-derived xenografts (PDXs), treated with standard therapies, to predict benefit from radiotherapy (RT-GS), temozolomide (Chemo-GS), or the combination (ChemoRT-GS). Independent validation was performed in a heterogeneously treated clinical cohort of 502 glioblastoma patients with overall survival as the primary endpoint. Multivariate Cox analysis was used to adjust for confounding variables and evaluate interactions between signatures and treatment.

Results

PDX models recapitulated the clinical heterogeneity of glioblastoma patients. RT-GS, Chemo-GS, and ChemoRT-GS were correlated with benefit from treatment in the PDX models. In independent clinical validation, higher RT-GS scores were associated with increased survival only in patients receiving RT (P = 0.0031, hazard ratio [HR] = 0.78 [0.66–0.92]), higher Chemo-GS scores were associated with increased survival only in patients receiving chemotherapy (P < 0.0001, HR = 0.66 [0.55–0.8]), and higher ChemoRT-GS scores were associated with increased survival only in patients receiving ChemoRT (P = 0.0001, HR = 0.54 [0.4–0.74]). RT-GS and ChemoRT-GS had significant interactions with treatment on multivariate analysis (P = 0.0009 and 0.02, respectively), indicating that they are bona fide predictive biomarkers.

Conclusions

Using a novel PDX-driven methodology, we developed and validated 3 platform-independent molecular signatures that predict benefit from standard of care therapies for glioblastoma. These signatures may be useful to personalize glioblastoma treatment in the clinic and this approach may be a generalizable method to identify predictive biomarkers without resource-intensive randomized trials.
The Relationship of Varenicline Agonism of α4β2 Nicotinic Acetylcholine Receptors and Nicotine-Induced Dopamine Release in Nicotine-Dependent Humans
Authors: McCaul Mary E , Wand Gary S , Kuwabara Hiroto , Dannals Robert F , Wong Dean , Xu Xiaoqiang
Published: May 2019

Introduction

Cigarette smoking continues to be one of the most important behavioral causes of morbidity and mortality in the world. Varenicline, an α4β2 nicotinic acetylcholine receptor (nAChR) partial agonist, has been shown to increase smoking quit rates compared with nicotine-based products. This human laboratory, double-blind, placebo-controlled study examined varenicline and placebo effects on α4β2-nAChRs occupancy, nicotine-induced change in [11C]raclopride non-displaceable binding potential (BPND), and behavioral measures of cigarette smoking, nicotine craving, and withdrawal.

Methods

Current nicotine dependent daily smokers (N = 17) were randomized to varenicline 1 mg twice daily or placebo for 13 days. Using positron emission tomography), we characterized α4β2-nAChRs occupancy using [18F]AZAN and dopamine receptor binding using [11C]raclopride as well as behavioral measures of cigarettes smoked, craving, and nicotine withdrawal.

Results

Varenicline compared with placebo resulted in significant reductions in [18F]AZAN BPND in multiple brain regions including thalamus, midbrain, putamen, and ventral striatum. Following administration of a controlled-dose nicotine cigarette, dopamine release was significantly suppressed in the ventral striatum in the varenicline-treated compared with the placebo group. There was a significant relationship between α4β2-nAChRs BPND measured in thalamus during the [18F]AZAN scan and nicotine-induced change in raclopride BPND in the ventral striatum.

Conclusion

This is the first human study to demonstrate a direct relationship between the extent of varenicline occupancy of α4β2-nAChRs and the magnitude of dopamine release following nicotine use.

Implications

It has remained unclear how nicotinic receptor blockade through partial agonist medications such as varenicline promotes smoking cessation. One hypothesized mechanism is downstream dampening of the mesolimbic reward dopamine system. For the first time in human smokers, we observed a direct relationship between the extent of varenicline blockade of α4β2-nACh nicotinic receptors and the magnitude of dopamine release following smoking. This has mechanistic and therapeutic implications for improving smoking cessation interventions.
Anatomic Considerations for Injection of the Lateral Atlanto-Axial Joint
Authors: McNabney Charis , Chavda Anesh , Alabsi Hatim , Sellers Stephanie L , Murphy Darra T , Fenton David
Published: May 2019

Objective

We aimed to define the potential complications of intra-articular steroid injections into the lateral C1-2 articulations and safety margins to the relevant structures.

Methods

A total of 488 contrast-enhanced computed tomography angiogram (CTA) “arch to vertex” studies were retrospectively reviewed for theoretical intersection of the vertebral artery or thecal sac and distance of the named structures from the anticipated/theoretical trajectory of injection into the lateral C1-C2 joint.

Results

Patients were 60.4±15.8 years old and 55.5% male. In total, seven vertebral arteries and 11 thecal sac theoretical intersections were found. In cases without a direct intersection, the distance from the trajectory (range) was 0.71±0.18 (0.22–1.44) cm to the vertebral artery and 0.6±0.22 (0.14–1.8) cm to the thecal sac.

Conclusions

Although injection of steroid into the lateral C1-C2 articulation for pain management has historically been reported to carry risk of severe complications due to close proximity and location variability of surrounding structures, our study quantifies the potential risk of such injections. Further, our analysis suggests that preprocedural imaging should be considered.
Applying Prospect Theory to Participation in a CAPI/Web Panel Survey
Authors: Lynn Peter
Published: May 2019

Prospect theory states that the influential power of avoiding negative outcomes is stronger than that of achieving positive outcomes. In a survey context, this theory has been tested with respect to not only participation in a CATI survey, but also giving consent to data linkage in CATI surveys. No study, however, has tested the theory with respect to participation in a CAPI or web survey. This study does so in a mixed-mode panel context; it also tests the moderating effects of time-in-panel, response history, and mode protocol. Results show that the framing of the survey participation request influences participation propensity in a way consistent with prospect theory, but only for relatively recent panel entrants. The opposite effect is found for long-term panel participants. No difference is found between mode protocols.
1Book / Media Theory
Authors: Hyun Trina
Published: May 2019

In 2018, scholarship in book/media theory sketched the ways in which books embody time, shape our experience of time, and live in time. In particular, authors examine the book as a material object that resists being placed in a cohesive, progressive history (Whitney Trettien, Deidre Lynch, Michelle Sizemore, John Plotz), and that bends and textures linear temporality through the experience of reading (Christina Lupton). This review also discusses new theoretical discourses surrounding the material book, including new materialism (Jonathan Senchyne), the digital notion of ‘interactivity’ (The Multigraph Collective), and the concept of rarity (David McKitterick). Recurring through many of the works this year is a call to reconsider our definitions of the book and the archive, as scholars peer into the less well-known, cut-and-paste world of scrapbooks. This chapter is structured under the following headings: 1. The Time of Reading; 2. Books in Time; 3. Books in History; 4. Bookish Agencies.
Identification of lncRNAs Responsive to Infection byPlasmodiophora brassicaein Clubroot-Susceptible and -ResistantBrassica napusLines Carrying Resistance Introgressed from Rutabaga
Authors: Summanwar Aarohi , Basu Urmila , Rahman Habibur , Kav Nat
Published: May 2019

Clubroot disease, caused by Plasmodiophora brassicae Woronin, is a major threat to the production of Brassica’ crops. Resistance to different P. brassicae pathotypes has been reported in the A genome, chromosome A08; however, the molecular mechanism of this resistance, especially the involvement of long noncoding RNAs (lncRNAs), is not understood. We have used a strand-specific lncRNA-Seq approach to catalog lncRNAs from the roots of clubroot-susceptible and -resistant Brassica napus lines. In total, 530 differentially expressed (DE) lncRNAs were identified, including 88% of long intergenic RNAs and 11% natural antisense transcripts. Sixteen lncRNAs were identified as target mimics of the microRNAs (miRNAs) and eight were identified as the precursors of miRNAs. KEGG pathway analysis of the DE lncRNAs showed that the cis-regulated target genes mostly belong to the phenylpropanoid biosynthetic pathway (15%) and plant–pathogen interactions (15%) while the transregulated target genes mostly belong to carbon (18%) and amino acid biosynthesis pathway (19%). In all, 24 DE lncRNAs were identified from chromosome A08, which is known to harbor a quantitative trait locus conferring resistance to different P. brassicae pathotypes; however, eight of these lncRNAs showed expression only in the resistant plants. These results could form the basis for future studies aimed at delineating the roles of lncRNAs in plant–microbe interactions.
Carbendazim Resistance of Fusarium graminearum From Henan Wheat
Authors: Liu Shengming , Fu Liuyuan , Wang Shuan , Chen Jinpeng , Jiang Jia , Che Zhiping , Tian Yuee , Chen Genqiang
Published: May 2019

Fusarium head blight, also called scab, is caused by Fusarium graminearum and is one of the most important destructive diseases of wheat. The frequency of carbendazim resistance in 1,132 isolates of F. graminearum recovered from fields in different regions of Henan Province in 2016, 2017, and 2018 was determined. A total of 31 F. graminearum isolates resistant to carbendazim were detected, including 30 moderately resistant isolates and one highly resistant isolate. The frequency of resistance of F. graminearum isolates to carbendazim was 2.7%. The range of effective concentration (EC50) values of 1,101 sensitive isolates and 30 moderately resistant isolates was 0.08 to 0.98 μg ml−1 and 2.73 to 13.28 μg ml−1, respectively. The mean ± SD EC50 value was 0.55 ± 0.13 μg ml−1 and 5.61 ± 2.58 μg ml−1, respectively. The EC50 value of the highly resistant isolate was 21.12 μg ml−1. Point mutation types of the carbendazim-resistant isolates were characterized by cloning the β2-tubulin gene of 31 resistant isolates. Three point mutation types at amino acids F167Y, E198Q, and E198L in the β2-tubulin gene of resistant isolates were identified. Among 31 resistant isolates, the frequency of point mutation types in F167Y, E198Q, and E198L of the β2-tubulin gene was 71.0, 25.8, and 3.2%, respectively. The data indicate that F. graminearum has developed resistance to carbendazim in Henan Province, and single point mutations at amino acid F167Y were the predominant type of mutation detected.
Ready-to-Eat Salad Crops: A Plant Pathogen’s Heaven
Authors: Gullino Maria Lodovica , Gilardi Giovanna , Garibaldi Angelo
Published: May 2019

The ready-to-eat salad sector, also called fresh-cut or bagged salads, is a fast-growing segment of the fresh-food industry. The dynamism and specialization of this sector, together with the lack of adequate crop rotation, the globalization of the seed market, and climate change, are the main causes of the development of many new diseases that cause severe production losses. Newly detected diseases of the most important crops grown (lettuce, wild and cultivated rocket, lamb’s lettuce, chicory, endive, basil, spinach, and Swiss chard) are critically discussed. The management of these diseases represents a formidable challenge, since few fungicides are registered on these minor-use crops. An interesting feature of the ready-to-eat salad sector is that most crops are grown under protection, often in soilless systems, which provide an environment helpful to the implementation of innovative control methods. Current trends in disease management are discussed, with special focus on the most sustainable practices.
Development of the Automated Primer Design Workflow Uniqprimer and Diagnostic Primers for the Broad-Host-Range Plant Pathogen Dickeya dianthicola
Authors: Karim Shaista , McNally R. Ryan , Nasaruddin Afnan S. , DeReeper Alexis , Mauleon Ramil P. , Charkowski Amy O. , Leach Jan E. , Ben-Hur Asa , Triplett Lindsay R.
Published: May 2019

Uniqprimer, a software pipeline developed in Python, was deployed as a user-friendly internet tool in Rice Galaxy for comparative genome analyses to design primer sets for PCRassays capable of detecting target bacterial taxa. The pipeline was trialed with Dickeya dianthicola, a destructive broad-host-range bacterial pathogen found in most potato-growing regions. Dickeya is a highly variable genus, and some primers available to detect this genus and species exhibit common diagnostic failures. Upon uploading a selection of target and nontarget genomes, six primer sets were rapidly identified with Uniqprimer, of which two were specific and sensitive when tested with D. dianthicola. The remaining four amplified a minority of the nontarget strains tested. The two promising candidate primer sets were trialed with DNA isolated from 116 field samples from across the United States that were previously submitted for testing. D. dianthicola was detected in 41 samples, demonstrating the applicability of our detection primers and suggesting widespread occurrence of D. dianthicola in North America.
Predicting Soybean Yield and Sudden Death Syndrome Development Using At-Planting Risk Factors
Authors: Roth Mitchell G. , Noel Zachary A. , Wang Jie , Warner Fred , Byrne Adam M. , Chilvers Martin I.
Published: May 2019

In the United States, sudden death syndrome (SDS) of soybean is caused by the fungal pathogen Fusarium virguliforme and is responsible for important yield losses each year. Understanding the risk of SDS development and subsequent yield loss could provide growers with valuable information for management of this challenging disease. Current management strategies for F. virguliforme use partially resistant cultivars, fungicide seed treatments, and extended crop rotations with diverse crops. The aim of this study was to develop models to predict SDS severity and soybean yield loss using at-planting risk factors to integrate with current SDS management strategies. In 2014 and 2015, field studies were conducted in adjacent fields in Decatur, MI, which were intensively monitored for F. virguliforme and nematode quantities at-planting, plant health throughout the growing season, end-of-season SDS severity, and yield using an unbiased grid sampling scheme. In both years, F. virguliforme and soybean cyst nematode (SCN) quantities were unevenly distributed throughout the field. The distribution of F. virguliforme at-planting had a significant correlation with end-of-season SDS severity in 2015, and a significant correlation to yield in 2014 (P < 0.05). SCN distributions at-planting were significantly correlated with end-of-season SDS severity and yield in 2015 (P < 0.05). Prediction models developed through multiple linear regression showed that F. virguliforme abundance (P < 0.001), SCN egg quantity (P < 0.001), and year (P < 0.01) explained the most variation in end-of-season SDS (R2 = 0.32), whereas end-of-season SDS (P < 0.001) and end-of-season root dry weight (P < 0.001) explained the most variation in soybean yield (R2 = 0.53). Further, multivariate analyses support a synergistic relationship between F. virguliforme and SCN, enhancing the severity of foliar SDS. These models indicate that it is possible to predict patches of SDS severity using at-planting risk factors. Verifying these models and incorporating additional data types may help improve SDS management and forecast soybean markets in response to SDS threats.
Enhancement of optical force acting on vesicles via the binding of gold nanoparticles
Authors: Tani Yumeki , Kaneta Takashi
Published: May 2019

Here we found that gold nanoparticles (AuNPs) enhance the optical force acting on vesicles prepared from phospholipids via hydrophobic and electrostatic interactions. A laser beam was introduced into a cuvette filled with a suspension of vesicles and it accelerated them in its propagation direction via a scattering force. The addition of the AuNPs exponentially increased the velocity of the vesicles as their concentration increased, but polystyrene particles had no significant impact on velocity in the presence of AuNPs. To elucidate the mechanism of the increased velocity, the surface charges in the vesicles and the AuNPs were controlled; the surface charges of the vesicles were varied via the use of anionic, cationic and neutral phospholipids, whereas AuNPs with positive and negative charges were synthesized by coating with citrate ion and 4-dimethylaminopyridine, respectively. All vesicles increased the velocity at different degrees depending on the surface charge. The vesicles were accelerated more efficiently when their charges were opposite those of the AuNPs. These results suggested that hydrophobic and electrostatic interactions between the vesicles and the AuNPs enhanced the optical force. By accounting for the binding constant between the vesicles and the AuNPs, we proposed a model for the relationship between the concentration of the AuNPs and the velocity of the vesicles. Consequently, the increased velocity of the vesicles was attributed to the light scattering that was enhanced when AuNPs were adsorbed onto the vesicles.
Methodology to calculate interfacial tension under electric field using pendent drop profile analysis
Authors: Mhatre Sameer , Simon Sébastien , Sjöblom Johan
Published: May 2019

In this paper, we present a methodology to calculate interfacial tension of a water–oil interface under an electric field. The Young–Laplace equation, conventionally used to estimate surface/interfacial tension in axisymmetric drop shape analysis (ADSA), is modified to include electrostatic effects. The solution needs normal component of the Maxwell stress at the interface which is calculated separately by solving the Laplace equation for electric potential. The optimized fitting between the resulting theoretical profile and the experimentally obtained profile results into Bond number which is used to calculate the apparent value of interfacial tension. The algorithm can process a large number of drop profiles in one go. The methodology can be applied in the ADSA studies for adsorption dynamics where a drop is held for a long time while surface active molecules are allowed to adsorb. The method discussed in this paper will help the future studies in adsorption dynamics at fluid interfaces under electric field and the resulting interfacial property evolution.
Membrane analogy for multi-material bars under torsion
Authors: Galuppi Laura , Royer-Carfagni Gianni
Published: May 2019

Prandtl's membrane analogy for the torsion problem of prismatic homogeneous bars is extended to multi-material cross sections. The linear elastic problem is governed by the same equations describing the deformation of an inflated membrane, differently tensioned in regions that correspond to the domains hosting different materials in the bar cross section, in a way proportional to the inverse of the material shear modulus. Multi-connected cross sections correspond to materials with vanishing stiffness inside the holes, implying infinite tension in the corresponding portions of the membrane. To define the interface constrains that allow to apply such a state of prestress to the membrane, a physical apparatus is proposed, which can be numerically modelled with a two-dimensional mesh implementable in commercial finite-element model codes. This approach presents noteworthy advantages with respect to the three-dimensional modelling of the twisted bar.
Serum IgE and IgG reactivity to Aspergillus recombinant antigens in patients with cystic fibrosis
Authors: Alghamdi Nada S. , Barton Richard , Wilcox Mark , Peckham Daniel
Published: May 2019

Purpose.The diagnosis of aspergillosis in cystic fibrosis (CF) patients remains a challenge due to overlapping features of both diseases. This is further complicated by inconsistent antibody reactivity to the currently used crude antigen, which has led a more focused evaluation of the efficacy of IgE response to a number of pureAspergillus fumigatusrecombinant proteins in patients with CF and asthma. In this study, we dissected the IgE and IgG responses to multipleA. fumigatusrecombinant antigens in CF patients with differentAspergillusdiseases.

Methodology.Serum IgE and IgG antibodies were measured in 12 CF patients with allergic bronchopulmonary aspergillosis (ABPA), 12 withAspergillussensitization (AS) and 12 withAspergillusbronchitis (AB) against recombinant antigens Asp f1, f2, f3, f4 and f6.

Results.The ABPA group showed significantly greater IgE reactivity to Asp f1, f2, f3 and f4 compared to patients with AS. Patients with AB expressed higher IgG positivity to Asp f1 and Asp f2 compared with those with ABPA. There were very low IgE antibody levels against all recombinant antigens in patients with AS. Aspf1 IgG reactivity in ABPA patients correlated with positive culture.

Conclusion.The use of multiple recombinant antigens may improve the diagnostic accuracy in CF complicated with ABPA or AB. Asp f1 reactivity may relate to the presence of actively growingAspergillusspp., which might be a useful marker for guiding antifungal therapy in ABPA.
Missense mutations in the MLKL ‘brace’ region lead to lethal neonatal inflammation in mice and are present in high frequency in humans
Authors: Hildebrand Joanne M. , Kauppi Maria , Majewski Ian J. , Liu Zikou , Cox Allison , Miyake Sanae , Petrie Emma J. , Silk Michael A. , Li Zhixiu , Tanzer Maria C. , Young Samuel N. , Hall Cathrine , Garnish Sarah E. , Corbin Jason , Stutz Michael D. , Gangatirkar Pradnya , Josefsson Emma C. , Rigbye Kristin , Anderton Holly , Rickard James A. , Tripaydonis Anne , Sheridan Julie , Scerri Thomas S. , Czabotar Peter A. , Zhang Jian-Guo , Allison Cody C. , Pellegrini Marc , Tannahill Gillian M. , Hatchell Esme C. , Willson Tracy A. , Stockwell Dina , de Graaf Carolyn A. , Collinge Janelle , Hilton Adrienne , Silke Natasha , Spall Sukhdeep K. , Chau Diep , Athanasopoulos Vicki , Metcalf Donald , Laxer Ronald M. , Bassuk Alexander G. , Darbro Benjamin W. , Fiatarone Singh Maria A. , Vlahovich Nicole , Hughes David , Kozlovskaia Maria , Ascher David B. , Warnatz Klaus , Venhoff Nils , Thiel Jens , Blum Stefan , Reveille John , Hildebrand Michael S. , Vinuesa Carola G. , McCombe Pamela , Brown Matthew A. , Kile Ben T. , McLean Catriona , Bahlo Melanie , Masters Seth L. , Nakano Hiroyasu , Ferguson Polly J. , Murphy James M. , Alexander Warren S. , Silke John
Published: May 2019

We have isolated a mouse strain with a single missense mutation in the gene encoding MLKL, the essential effector of necroptotic cell death. The resulting substitution lies within the two-helix ‘brace’ and confers constitutive, RIPK3 independent, killing activity to MLKL. Mice homozygous forMlklD139Vdevelop lethal inflammation within days of birth, implicating the salivary glands and pericardium as hotspots for necroptosis and inflammatory infiltration. The normal development ofMlklD139Vhomozygotes until birth, and the absence of any overt phenotype in heterozygotes provides importantin vivoprecedent for the capacity of cells to clear activated MLKL. These observations offer an important insight into the potential disease-modulating roles of three common humanMLKLpolymorphisms that encode amino acid substitutions within or adjacent to the brace region. Compound heterozygosity of these variants is found at up to 12-fold the expected frequency in patients that suffer from a pediatric autoinflammatory disease, CRMO.