bluuebunny/crossref_metadata_2025 huggingface dataset:
Inter-Modular Linkers play a crucial role in governing the biosynthesis of non-ribosomal peptides
Authors: Farag Sherif , Bleich Rachel M , Shank Elizabeth A , Isayev Olexandr , Bowers Albert A , Tropsha Alexander
Published: February 2019

Motivation

Non-ribosomal peptide synthetases (NRPSs) are modular enzymatic machines that catalyze the ribosome-independent production of structurally complex small peptides, many of which have important clinical applications as antibiotics, antifungals and anti-cancer agents. Several groups have tried to expand natural product diversity by intermixing different NRPS modules to create synthetic peptides. This approach has not been as successful as anticipated, suggesting that these modules are not fully interchangeable.

Results

We explored whether Inter-Modular Linkers (IMLs) impact the ability of NRPS modules to communicate during the synthesis of NRPs. We developed a parser to extract 39 804 IMLs from both well annotated and putative NRPS biosynthetic gene clusters from 39 232 bacterial genomes and established the first IMLs database. We analyzed these IMLs and identified a striking relationship between IMLs and the amino acid substrates of their adjacent modules. More than 92% of the identified IMLs connect modules that activate a particular pair of substrates, suggesting that significant specificity is embedded within these sequences. We therefore propose that incorporating the correct IML is critical when attempting combinatorial biosynthesis of novel NRPS.

Availability and implementation

The IMLs database as well as the NRPS-Parser have been made available on the web at https://nrps-linker.unc.edu. The entire source code of the project is hosted in GitHub repository (https://github.com/SWFarag/nrps-linker).

Supplementary information

Supplementary data are available at Bioinformatics online.
Unbiased approximations of products of expectations
Authors: Lee A , Tiberi S , Zanella G
Published: February 2019

We consider the problem of approximating the product of $n$ expectations with respect to a common probability distribution $\mu$. Such products routinely arise in statistics as values of the likelihood in latent variable models. Motivated by pseudo-marginal Markov chain Monte Carlo schemes, we focus on unbiased estimators of such products. The standard approach is to sample $N$ particles from $\mu$ and assign each particle to one of the expectations; this is wasteful and typically requires the number of particles to grow quadratically with the number of expectations. We propose an alternative estimator that approximates each expectation using most of the particles while preserving unbiasedness, which is computationally more efficient when the cost of simulations greatly exceeds the cost of likelihood evaluations. We carefully study the properties of our proposed estimator, showing that in latent variable contexts it needs only ${O} (n)$ particles to match the performance of the standard approach with ${O}(n^{2})$ particles. We demonstrate the procedure on two latent variable examples from approximate Bayesian computation and single-cell gene expression analysis, observing computational gains by factors of about 25 and 450, respectively.
Focal TLR4 activation mediates disturbed flow-induced endothelial inflammation
Authors: Qu Dan , Wang Li , Huo Mingyu , Song Wencong , Lau Chi-Wai , Xu Jian , Xu Aimin , Yao Xiaoqiang , Chiu Jeng-Jiann , Tian Xiao Yu , Huang Yu
Published: February 2019

Aims

Disturbed blood flow at arterial branches and curvatures modulates endothelial function and predisposes the region to endothelial inflammation and subsequent development of atherosclerotic lesions. Activation of the endothelial Toll-like receptors (TLRs), in particular TLR4, contributes to vascular inflammation. Therefore, we investigate whether TLR4 can sense disturbed flow (DF) to mediate the subsequent endothelial inflammation.

Methods and results

En face staining of endothelium revealed that TLR4 expression, activation, and its downstream inflammatory markers were elevated in mouse aortic arch compared with thoracic aorta, which were absent in Tlr4mut mice. Similar results were observed in the partial carotid ligation model where TLR4 signalling was activated in response to ligation-induced flow disturbance in mouse carotid arteries, and such effect was attenuated in Tlr4mut mice. DF in vitro increased TLR4 expression and activation in human endothelial cells (ECs) and promoted monocyte-EC adhesion, which were inhibited in TLR4-knockdown ECs. Among endogenous TLR4 ligands examined as candidate mediators of DF-induced TLR4 activation, fibronectin containing the extra domain A (FN-EDA) expressed by ECs was increased by DF and was revealed to directly interact with and activate TLR4.

Conclusion

Our findings demonstrate the indispensable role of TLR4 in DF-induced endothelial inflammation and pinpoint FN-EDA as the endogenous TLR4 activator in this scenario. This novel mechanism of vascular inflammation under DF condition may serve as a critical initiating step in atherogenesis.
Is small cusp size a limitation for aortic valve repair?†
Authors: Komiya Tatsuhiko , Shimamoto Takeshi , Nonaka Michihito , Matsuo Takehiko
Published: February 2019

OBJECTIVES

We sought to investigate cusp size limitations for valve repair in patients with aortic regurgitation (AR).

METHODS

Preoperative computed tomography was performed in 105 patients. Cusp geometric height (GH) and annulus size were measured. Mean patient age was 60.7 ± 13.7 years. Mean GH of 3 cusps was used in the analysis. Annulus cusp mismatch was graded using predicted coaptation length. Patients were categorized by mean GH into group S (GH <16 mm; n = 35) or L (GH ≥16 mm; n = 70).

RESULTS

Preoperative mean GH was 17.1 ± 2.3 mm. GH and body height were significantly correlated (r = 0.61). Intraoperative mean GH (18.8 ± 2.2 mm) was larger than preoperative mean GH (P < 0.0001). However, postoperative (17.1 ± 2.0 mm) and preoperative mean GH did not differ. Moderate AR was not present on predischarge echocardiography. Mild AR was observed in 51% and 17% of patients in groups S and L, respectively (P = 0.006). During follow-up, moderate or severe AR was observed in 14% and 10% of patients in groups S and L, respectively (P = 0.74). Two patients in group S required reoperation for a regurgitant valve. Twenty (83%) and 15 (21%) patients in groups S and L, respectively, had severe annulus cusp mismatch before surgery. Annulus cusp mismatch resolved in most patients in group L postoperatively, whereas more than half the patients in group S still had severe mismatch.

CONCLUSIONS

Small cusp size (GH <16 mm) is not necessarily a contraindication in aortic valve repair. However, most patients in this group had annulus cusp mismatch. Root replacement or secure annulus plication is mandatory to correct annulus cusp mismatch.
Cost–utility analysis of minimally invasive surgery for lung cancer: a randomized controlled trial
Authors: Bendixen Morten , Kronborg Christian , Jørgensen Ole Dan , Andersen Claus , Licht Peter Bjørn
Published: February 2019

OBJECTIVES:

Minimally invasive video-assisted thoracic surgery (VATS) was first introduced in the early 1990s. For decades, numerous non-randomized studies demonstrated advantages of VATS over thoracotomy with lower morbidity and shorter hospital stay, but only recently did a randomized trial document that VATS results in lower pain scores and better quality of life. Opposing arguments for VATS have always been increased costs and concerns about oncological adequacy. In this paper, we aim to investigate the cost-effectiveness of VATS.

METHODS:

The study was designed as a cost–utility analysis of the first 12 months following surgery and was performed together with a clinical randomized controlled trial of VATS versus thoracotomy for lobectomy of stage 1 lung cancer during a 6-year period (2008–2014). All health-related expenses were retrieved from a national database (Statistics Denmark) including hospital readmissions, outpatient clinic visits, prescription medication costs, consultations with general practitioners, specialists, physiotherapists, psychologists and chiropractors.

RESULTS:

One hundred and three VATS patients and 103 thoracotomy patients were randomized. Mean costs per patient operated by VATS were 103 108 Danish Kroner (Dkr) (€13 818) and 134 945 Dkr (€18 085) by thoracotomy, making the costs for VATS 31 837 Dkr (€4267) lower than thoracotomy (P < 0.001). The difference in quality-adjusted life years gained over 52 weeks of follow-up was 0.021 (P = 0.048, 95% confidence interval −0.04 to −0.00015) in favour of VATS. The median duration of the surgical procedure was shorter after thoracotomy (79 vs 100 min; P < 0.001). The mean length of hospitalization was shorter following VATS (4.8 vs 6.7 days; P = 0.027). The use of other resources was not significantly different between groups. The costs of resources were lower in the VATS group. This difference was primarily due to reduced costs of readmissions (VATS 29 247 Dkr vs thoracotomy 51 734 Dkr; P < 0.001) and costs of outpatient visits (VATS 51 412 Dkr vs thoracotomy 61 575 Dkr; P = 0.012).

CONCLUSIONS:

VATS is a cost-effective alternative to thoracotomy following lobectomy for stage 1 lung cancer. Economical outcomes as measured by quality-adjusted life years were significantly better and overall costs were lower for VATS.

Clinical Trial Registration Number:

NCT01278888.
The Effects of Recognition of Foreign Education for Newly Arrived Immigrants
Authors: Tibajev Andrey , Hellgren Carina
Published: February 2019

We analyze the effects of formal recognition of foreign higher education on employment probabilities and earnings for newly arrived immigrants in Sweden. Prior research has found that immigrants have lower returns on education if it was acquired in the country of origin than if it was acquired in the host country. One reason for this is that foreign credentials work poorly as productivity signals and risk-averse employers avoid employees with credentials they do not fully understand. A formal recognition statement can help overcome this problem by providing credible information about the foreign education, thus reducing uncertainty. Data consists of immigrants who, within the first ten years of residence in Sweden, had their foreign degree formally recognized during 2007–2011. Using fixed effects regressions, we estimate the treatment effect of official recognition to be 4.4 percentage points higher probability of being employed, and 13.9 log points higher wage for those with employment. We also find considerable treatment effect heterogeneity across subcategories of immigrants from different regions of origin, with different reasons for immigration and who obtained recognition during different economic conditions. Our conclusions are that the mechanism of employer uncertainty is real, and that recognition does reduce it. But as the signal of foreign education becomes better, other mechanisms such as human capital transferability problems and quality differences, and the ability to use foreign human capital, become more salient, leading to heterogeneous effects.
Increase of internalized mental health symptoms among adolescents during the last three decades
Authors: Blomqvist Ida , Henje Blom Eva , Hägglöf Bruno , Hammarström Anne
Published: February 2019

Background

Previous studies suggest an overall increase of adolescent mental health symptoms globally since the 1980s until today, especially an increase of internalizing symptoms in girls. Due to methodological limitations of these studies, further studies are warranted to obtain a more solid knowledgebase.

Methods

This study was cross-sectional and compared two separate but geographically identical groups of adolescents in a middle-sized industrial municipality in Northern Sweden at two time-points [(i) 1981, n = 1083, (505 girls, 577 boys), response rate 99.7%; (ii) 2014, n = 682, (338 girls, 344 boys), response rate 98.3%]. All students in their last year of compulsory school were included. The same self-report questionnaire, consisting of four sub-scales (functional somatic-, anxiety-, depressive symptoms and conduct problems), was used at both occasions. Data were analyzed with descriptive statistics, two-way ANOVA and general linear model.

Results

Symptoms of anxiety and depression and functional somatic symptoms, increased among both boys and girls from 1981 until 2014 (P < 0.001 for all subscales), and the increase of these symptoms was higher in girls. Conduct problems were significantly higher in boys in 1981 and decreased over time so that in 2014 there was no longer a significant difference between boys and girls regarding conduct problems (P = 0.286).

Conclusion

In this population-based study spanning over 30 years, both girls and boys showed increasing internalizing problems, while conduct problems decreased. To halt this trend, we need a deeper understanding of the impact of the major societal changes that have occurred during the last three decades.
Development and genomic elucidation of hybrid yeast with improved glucose-xylose co-fermentation at high temperature
Authors: Lin Yuping , Cai Yanqing , Guo Yufeng , Li Xin , Qi Xianni , Qi Qi , Wang Qinhong
Published: February 2019

Enhanced capability of co-fermenting glucose and xylose at high temperature is highly desirable for yeast application in second-generation bioethanol production. Here, we obtained hybrid strains with improved glucose-xylose co-fermentation properties at high temperature by combining genome shuffling and adaptive evolution. Genome resequencing of these strains suggested predominantly inherited genetic information from one parental strain Spathaspora passalidarum SP rather than the other parental strain Saccharomyces cerevisiae ScY01, possibly due to that the CUG codon system of S. passalidarum might have systematically eliminated most of the functional proteins from S. cerevisiae through misfolding. Compared to SP, one-copy loss of a 146-kb fragment was found in the hybrid strain and regained after being evolved for a while, whereas one-copy loss of an 11-kb fragment was only found after being evolved for a longer time. Besides, the genes affected by nonsynonymous variants were also identified, especially the mutation S540F in the endoplasmic reticulum chaperon Kar2. Structural prediction indicated that S540F might change the substrate binding activity of Kar2, and thus play a role in preventing protein aggregation in yeast at high temperature. Our results illustrated genomic alterations during this process and revealed some genomic factors that might be involved to determine yeast thermotolerance.
FSH3 mediated cell death is dependent on NUC1 in Saccharomyces cerevisiae
Authors: Gowsalya Ramachandran , Ravi Chidambaram , Kannan Muthukumar , Nachiappan Vasanthi
Published: February 2019

Family of Serine Hydrolases (FSH) members FSH1, FSH2 and FSH3 in Saccharomyces cerevisiae share conserved sequences with the human candidate tumor suppressor OVCA2. In this study, hydrogen peroxide (H2O2) exposure increased the expression of both mRNA and protein levels of FSH3 in wild-type (WT) yeast cells. The deletion of FSH3 improved the yeast growth rate under H2O2-induction as compared to WT control cells. The overexpression of FSH3 in WT yeast cells caused an apoptotic phenotype, including accumulation of reaction oxygen species, decreased cell viability and cell death. The double deletions fsh1Δ fsh2Δ, fsh1Δ fsh3Δ and fsh2Δ fsh3Δ displayed increased growth compared to WT cells. However, the overexpression of FSH3 effectively inhibited cell growth in all double deletions. Moreover, the overexpression of FSH3 in cells lacking NUC1 did not cause any growth defect in the presence or absence of H2O2. Our results suggest that FSH3 induced apoptosis of yeast in a NUC1 dependent manner.
Assessing the effects of climate change on US West Coast sablefish productivity and on the performance of alternative management strategies
Authors: Haltuch Melissa A , A’mar Z Teresa , Bond Nicholas A , Valero Juan L
Published: February 2019

US West Coast sablefish are economically valuable, with landings of 11.8 million pounds valued at over $31 million during 2016, making assessing and understanding the impact of climate change on the California Current (CC) stock a priority for (1) forecasting future stock productivity, and (2) testing the robustness of management strategies to climate impacts. Sablefish recruitment is related to large-scale climate forcing indexed by regionally correlated sea level (SL) and zooplankton communities that pelagic young-of-the-year sablefish feed upon. This study forecasts trends in future sablefish productivity using SL from Global Climate Models (GCMs) and explores the robustness of harvest control rules (HCRs) to climate driven changes in recruitment using management strategy evaluation (MSE). Future sablefish recruitment is likely to be similar to historical recruitment but may be less variable. Most GCMs suggest that decadal SL trends result in recruitments persisting at lower levels through about 2040 followed by higher levels that are more favorable for sablefish recruitment through 2060. Although this MSE suggests that spawning biomass and catches will decline, and then stabilize, into the future under both HCRs, the sablefish stock does not fall below the stock size that leads to fishery closures.
Accurate estimation of fish length in single camera photogrammetry with a fiducial marker
Authors: Monkman Graham G , Hyder Kieran , Kaiser Michel J , Vidal Franck P
Published: February 2019

Videogrammetry and photogrammetry are increasingly being used in marine science for unsupervised data collection. The camera systems employed are complex, in contrast to “consumer” digital cameras and smartphones carried by potential citizen scientists. However, using consumer cameras in photogrammetry will introduce unknown length estimation errors through both the image acquisition process and lens distortion. This study presents a methodology to achieve accurate 2-dimensional (2-D) total length (TL) estimates of fish without specialist equipment or proprietary software. Photographs of fish were captured with an action camera using a background fiducial marker, a foreground fiducial marker and a laser marker. The geometric properties of the lens were modelled with OpenCV to correct image distortion. TL estimates were corrected for parallax effects using an algorithm requiring only the initial length estimate and known fish morphometric relationships. Correcting image distortion decreased RMSE by 96% and the percentage mean bias error (%MBE) by 50%. Correcting for parallax effects achieved a %MBE of −0.6%. This study demonstrates that the morphometric measurement of different species can be accurately estimated without the need for complex camera equipment, making it particularly suitable for deployment in citizen science and other volunteer-based data collection endeavours.
Decellularization as a method to reduce calcification in bovine pericardium bioprosthetic valves
Authors: Collatusso Claudinei , Roderjan João Gabriel , de Noronha Lucia , Klosowski Allyson , Suss Paula Hansen , Guarita-Souza Luiz César , Costa Francisco Diniz Affonso da
Published: February 2019

OBJECTIVES

Decellularization is an alternative method for processing biological tissues with decreased antigenicity and resistance to calcification. The aim of this study was to characterize the properties of decellularized (dCell) bovine pericardium fixed with 0.1% glutaraldehyde (GA) and to evaluate outcomes of bioprosthetic valves constructed with this tissue when implanted in the mitral position of juvenile sheep.

METHODS

Bioprosthetic mitral valves were constructed with fresh bovine pericardium fixed in 0.5% GA (control group) or dCell bovine pericardium fixed in 0.1% GA (study group). Before implantation, samples were submitted to histological (haematoxylin–eosin, Movat and 4′,6-diamidino-2-phenylindole), biochemical (residual deoxyribonucleic acid and α-gal epitopes) and biomechanical characterization. Valves were implanted (n = 8 in each group) as a mitral valve replacement for 180 days in sheep and explants were re-evaluated histologically and for calcification with radiological studies and calcium content determination.

RESULTS

Unimplanted dCell pericardia exhibited a well-preserved extracellular matrix with absence of cells, a 77% reduction in deoxyribonucleic acid levels and with no detectable α-gal epitopes. When compared to controls, they had lower ultimate tensile strength (7.3 ± 5.4 vs 10.2 ± 3.0 mPa, P = 0.04) and greater percentage elongation in the longitudinal direction (29 ± 6.5% vs 23.8 ± 5.1%, P = 0.02). After 180 days in mitral position, dCell valves showed pliable leaflets without macroscopic signs of calcification. Histologically, dCell leaflets had intact collagen fibres, better tissue remodelling and a significant 89% reduction in calcium content.

CONCLUSIONS

This study demonstrates that bioprosthetic valves constructed with dCell bovine pericardium fixed in low GA concentration were resistant to calcification and may thereby improve long-term durability of the tissue.
Outlier detection for questionnaire data in biobanks
Authors: Sakurai Rieko , Ueki Masao , Makino Satoshi , Hozawa Atsushi , Kuriyama Shinichi , Takai-Igarashi Takako , Kinoshita Kengo , Yamamoto Masayuki , Tamiya Gen
Published: February 2019

Background

Biobanks increasingly collect, process and store omics with more conventional epidemiologic information necessitating considerable effort in data cleaning. An efficient outlier detection method that reduces manual labour is highly desirable.

Method

We develop an unsupervised machine-learning method for outlier detection, namely kurPCA, that uses principal component analysis combined with kurtosis to ascertain the existence of outliers. In addition, we propose a novel regression adjustment approach to improve detection, namely the regression adjustment for data by systematic missing patterns (RAMP).

Result

Application to epidemiological record data in a large-scale biobank (Tohoku Medical Megabank Organization, Japan) shows that a combination of kurPCA and RAMP effectively detects known errors or inconsistent patterns.

Conclusions

We confirm through the results of the simulation and the application that our methods showed good performance. The proposed methods are useful for many practical analysis scenarios.
A self-correcting variable-metric algorithm framework for nonsmooth optimization
Authors: Curtis Frank E , Robinson Daniel P , Zhou Baoyu
Published: February 2019

An algorithm framework is proposed for minimizing nonsmooth functions. The framework is variable metric in that, in each iteration, a step is computed using a symmetric positive-definite matrix whose value is updated as in a quasi-Newton scheme. However, unlike previously proposed variable-metric algorithms for minimizing nonsmooth functions, the framework exploits self-correcting properties made possible through Broyden–Fletcher–Goldfarb–Shanno-type updating. In so doing, the framework does not overly restrict the manner in which the step computation matrices are updated, yet the scheme is controlled well enough that global convergence guarantees can be established. The results of numerical experiments for a few algorithms are presented to demonstrate the self-correcting behaviours that are guaranteed by the framework.
State Delegations and the Influence of COP Decisions
Authors: Goodwin Edward J
Published: February 2019

This article concerns the likelihood that decisions adopted at conferences of the parties (COPs) to multilateral environmental agreements will influence the behaviour of States Parties. Relying upon a theory emphasising the importance of rational persuasion of decisions and the legitimacy of decision-making processes, this article explains how choices concerning the preparation of delegates and then participation of delegations at plenary meetings of the parties to environmental treaties might enhance the likelihood of those decisions having a positive effect upon the actions of States Parties. This is done using a case study of the UK delegation to a meeting of the parties to the 1971 Ramsar Convention on Wetlands of International Importance. That case study also provides examples of potentially positive modalities adopted by the UK, while also revealing suspected concerns for the future surrounding retention of experienced delegates and the impact of Brexit.
The Epidemiology of Cancer Among Homeless Adults in Metropolitan Detroit
Authors: Holowatyj Andreana N , Heath Elisabeth I , Pappas Lisa M , Ruterbusch Julie J , Gorski David H , Triest Jeffrey A , Park Hyo K , Beebe-Dimmer Jennifer L , Schwartz Ann G , Cote Michele L , Schwartz Kendra L
Published: February 2019

Background

Homeless individuals suffer and die disproportionately from chronic diseases and disorders. We describe the epidemiology of cancer among homeless persons in metropolitan Detroit.

Methods

A retrospective cohort study was performed using 1973–2014 data from the Metropolitan Detroit Cancer Surveillance System, a population-based cancer registry and member of the National Institutes of Health-National Cancer Institute’s Surveillance, Epidemiology, and End Results program. Homeless adults were identified through address at diagnosis listed as a homeless shelter, hospital, or supplemental field indicating homelessness. Age-adjusted, sex-specific proportional incidence ratios (PIR) compared cancer incidence proportions by primary tumor site of homeless patients to the nonhomeless referent population. Kaplan-Meier curves depicted unadjusted survival differences in a propensity score matched sample. Differences in 10-year survival were assessed using the score test with a sandwich estimator accounting for matched cluster effects. Statistical tests were two-sided.

Results

A total of 388 individuals experienced homelessness at first primary invasive cancer diagnosis. Statistically significantly higher proportions of respiratory system (PIR = 1.51; 95% confidence interval = 1.28 to 1.79) and female genital system (PIR = 1.83; 95% confidence interval = 1.31 to 2.55) cancers were observed among homeless men and women, respectively. Homeless persons had poorer overall and cancer-reported survival compared with a propensity score matched referent population (median: overall survival, 20.0 vs 38.0 months, respectively, P < .001; cancer-reported survival, 38.0 vs 64.0 months, respectively, P  < .001).

Conclusion

Disparities in disease burden exist between adults who are experiencing homelessness compared with the nonhomeless population at cancer diagnosis. These findings provide clinically relevant information to understand the cancer burden in this medically underserved population and suggest an urgent need to develop cancer prevention and intervention programs to reduce disparities and improve the health of homeless persons.
A Prospective Examination of Child Avoidance Coping and Parental Coping Assistance After Pediatric Injury: A Mixed-Methods Approach
Authors: Jones Alyssa C , Kassam-Adams Nancy , Ciesla Jeffrey A , Barakat Lamia P , Marsac Meghan L
Published: February 2019

Objective

Millions of children experience injuries annually, and avoidance coping increases risk of negative emotional and physical outcomes after injury. Little is known about how children select avoidance coping strategies. Parents may help their children cope with an injury by encouraging or discouraging the use of specific strategies, such as avoidance coping. The present study examined parental influence of child use of avoidance coping post-injury.

Methods

Children ages 8–13 (65% male; 50% White) hospitalized for pediatric injury and their parents (N = 96 child-parent dyads) participated in an interview and discussion task about coping at baseline, and then completed coping/coping assistance measures at three time points: T1 (within 2 weeks post-injury), T2 (6-weeks post-injury), and T3 (12-weeks post-injury).

Results

When presented with an ambiguous situation in the observational interview and discussion task, the number of avoidance coping solutions offered by children independently as well as during a discussion with their parent predicted the child’s ultimate avoidance versus non-avoidance coping choice. The number of avoidance coping solutions offered by parents did not predict children’s final choice to use avoidance coping. Longitudinal data suggest that parent encouragement of avoidance coping predicted child avoidance coping within the first 6-weeks post-trauma.

Conclusions

Our study suggests that child avoidance coping is multifaceted and may result from both parent encouragement as well as independent decisions by children. Future research may explore additional factors that influence child avoidance coping, outside of parental suggestion, in response to trauma exposure.
Digital nudges and dark patterns: The angels and the archfiends of digital communication
Authors: Özdemir Şebnem
Published: February 2019

Nudging is simply guiding people behaviors by the use of user-interface and design elements in digital environments. Today, many decisions are made in online environments. Gaining insights about digital nudging can greatly help communicators, policy makers, and designers lead users to make the most desirable choice for them and/or for the wealth of the society as well. Digital nudges can be used in many digital environments like e-mail, SMS, push notifications, mobile apps, social media, gamification, e-commerce, e-government, location services, corporate digital information systems, and many other digital interfaces that include any kind of decision-making processes. This study is a descriptive study and more of a qualitative nature and aims to identify the digital nudging concept, dark patterns, and usage of digital nudges in real-life applications. It also proposes a brief digital nudging process schema to be used for designing behavioral digital interventions.
Comparing approximate methods for mock catalogues and covariance matrices II: power spectrum multipoles
Authors: Blot Linda , Crocce Martin , Sefusatti Emiliano , Lippich Martha , Sánchez Ariel G , Colavincenzo Manuel , Monaco Pierluigi , Alvarez Marcelo A , Agrawal Aniket , Avila Santiago , Balaguera-Antolínez Andrés , Bond Richard , Codis Sandrine , Dalla Vecchia Claudio , Dorta Antonio , Fosalba Pablo , Izard Albert , Kitaura Francisco-Shu , Pellejero-Ibanez Marcos , Stein George , Vakili Mohammadjavad , Yepes Gustavo
Published: February 2019

We study the accuracy of several approximate methods for gravitational dynamics in terms of halo power spectrum multipoles and their estimated covariance matrix. We propagate the differences in covariances into parameter constraints related to growth rate of structure, Alcock–Paczynski distortions, and biasing. We consider seven methods in three broad categories: algorithms that solve for halo density evolution deterministically using Lagrangian trajectories (ICE–COLA, pinocchio, and peakpatch), methods that rely on halo assignment schemes on to dark matter overdensities calibrated with a target N-body run (halogen, patchy), and two standard assumptions about the full density probability distribution function (Gaussian and lognormal). We benchmark their performance against a set of three hundred N-body simulations, running similar sets of approximate simulations with matched initial conditions, for each method. We find that most methods reproduce the monopole to within $5{{\ \rm per\ cent}}$, while residuals for the quadrupole are sometimes larger and scale dependent. The variance of the multipoles is typically reproduced within $10{{\ \rm per\ cent}}$. Overall, we find that covariances built from approximate simulations yield errors on model parameters within $10{{\ \rm per\ cent}}$ of those from the N-body-based covariance.
Predictors of Epileptic Seizures and Ability to Work in Supratentorial Cavernous Angioma Located Within Eloquent Brain Areas
Authors: Zanello Marc , Goodden John R , Colle Henry , Wager Michel , Hamer Philip C De Witt , Smits Anja , Bello Lorenzo , Tate Matthew , Spena Giannantonio , Bresson Damien , Capelle Laurent , Robles Santiago Gil , Sarubbo Silvio , Rydenhag Bertil , Martino Juan , Meyer Bernhard , Fontaine Denys , Reyns Nicolas , Schichor Christian , Metellus Philippe , Colle David , Robert Erik , Noens Bonny , Muller Peter , Rossi Marco , Nibali Marco Conti , Papagno Costanza , Galbarritu Lara , de Gopegui Edurne Ruiz , Chioffi Franco , Bucheli Carlos , Krieg Sandro M , Wostrack Maria , Yusupov Natan , Visser Victoria , Baaijen Johannes C , Roux Alexandre , Dezamis Edouard , Mandonnet Emmanuel , Corns Robert , Duffau Hugues , Pallud Johan
Published: February 2019

BACKGROUND

The postoperative outcomes and the predictors of seizure control are poorly studied for supratentorial cavernous angiomas (CA) within or close to the eloquent brain area.

OBJECTIVE

To assess the predictors of preoperative seizure control, postoperative seizure control, and postoperative ability to work, and the safety of the surgery.

METHODS

Multicenter international retrospective cohort analysis of adult patients benefitting from a functional-based surgical resection with intraoperative functional brain mapping for a supratentorial CA within or close to eloquent brain areas.

RESULTS

A total of 109 patients (66.1% women; mean age 38.4 ± 12.5 yr), were studied. Age >38 yr (odds ratio [OR], 7.33; 95% confidence interval [CI], 1.53-35.19; P = .013) and time to surgery > 12 mo (OR, 18.21; 95% CI, 1.11-296.55; P = .042) are independent predictors of uncontrolled seizures at the time of surgery. Focal deficit (OR, 10.25; 95% CI, 3.16-33.28; P < .001) is an independent predictor of inability to work at the time of surgery. History of epileptic seizures at the time of surgery (OR, 7.61; 95% CI, 1.67-85.42; P = .003) and partial resection of the CA and/or of the hemosiderin rim (OR, 12.02; 95% CI, 3.01-48.13; P < .001) are independent predictors of uncontrolled seizures postoperatively. Inability to work at the time of surgery (OR, 19.54; 95% CI, 1.90-425.48; P = .050), Karnofsky Performance Status ≤ 70 (OR, 51.20; 95% CI, 1.20-2175.37; P = .039), uncontrolled seizures postoperatively (OR, 105.33; 95% CI, 4.32-2566.27; P = .004), and worsening of cognitive functions postoperatively (OR, 13.71; 95% CI, 1.06-176.66; P = .045) are independent predictors of inability to work postoperatively.

CONCLUSION

The functional-based resection using intraoperative functional brain mapping allows safe resection of CA and the peripheral hemosiderin rim located within or close to eloquent brain areas.
Clinicopathological and Prognostic Characteristics in Extra-Axial Chordomas: An Integrative Analysis of 86 Cases and Comparison With Axial Chordomas
Authors: Lv Guo-Hua , Zou Ming-Xiang , Liu Fu-Sheng , Zhang Yi , Huang Wei , Ye An , Zhang Qian-Shi , Wang Xiao-Bin , Li Jing , Jiang Yi , She Xiao-Ling
Published: February 2019

BACKGROUND

Currently, clinical characteristics and prognostic factors of extra-axial chordoma (EAC) remain poorly understood.

OBJECTIVE

To characterize clinicopathological characteristics in a large EAC cohort and investigate their correlation with survival. We also attempted to compare these outcomes with axial chordoma (AC).

METHODS

Medline and Embase searches (from inception to February 28, 2018) were conducted to identify eligible studies as per predefined criteria. The local database at our center was also retrospectively reviewed to include additional patients.

RESULTS

Forty-three studies from the literature and 86 patients from our local institute were identified, resulting in a total of 86 EAC patients and 75 AC patients for analysis. Overall, EAC had similar characteristics to AC, except for having higher CAM5.2 expression, common lobular growth pattern, and better prognosis. Whereas wide surgical resection was consistently associated with favorable survival in both EAC and AC cohorts on univariate analyses, most parameters showed differential prognostic implications between the 2 groups. Significant prognostic factors for local recurrence-free survival on multivariate analysis included type of surgery in both cohorts and tumor Brachyury expression and adjuvant radiotherapy in AC cohort. Multivariate analysis of overall survival demonstrated that type of surgery, tumor Brachyury expression, and duration of symptoms were significant predictors in the AC cohort, whereas none of the analyzed parameters were predictive of overall survival for the EAC group.

CONCLUSION

These data suggest potentially distinct biological behaviors between EAC and AC and may provide useful information to better understand the prognostic characteristics and improve the outcome prediction of EAC patients.
Association Between Tumor Compartment Volumes, the Incidence of Pretreatment Seizures, and Statin-Mediated Protective Effects in Glioblastoma
Authors: Henker Christian , Kriesen Thomas , Scherer Moritz , Glass Änne , von Deimling Andreas , Bendszus Martin , Weber Marc-André , Herold-Mende Christel , Unterberg Andreas , Piek Jürgen
Published: February 2019

BACKGROUND

Seizures are a common initial symptom of malignant brain tumors such as glioblastoma (GBM). However, why some of these tumors are epileptogenic and others never trigger seizures remains controversial.

OBJECTIVE

To identify potential clinical and radiological features of epileptogenic tumors and the effect of initial seizures on survival.

METHODS

The analyzed patient cohort was retrospectively compiled (bicentric), only isocitrate dehydrogenase wild-type GBMs were included. Volumetric assessment was performed on pretreatment magnetic resonance imaging with the aid of a semi-automated 3D measurement (tumor, necrosis, and edema volume). Two ratios were calculated, reflecting the proportion of peritumoral edema and necrosis (NTR) toward the tumor volume. For overall survival analyses, only patients after a surgical resection (residual tumor volume <2 cm3) followed by standard radiation and chemotherapy were included.

RESULTS

Pretreatment seizures occurred in 33% of cases (n = 224), younger patients (≤60 yr) were predominantly affected (P = .022). All measured volumes were inversely correlated with the onset of seizures (P = .001). In multivariate analyses, the total tumor volume and the NTR were considerably smaller within epileptogenic GBMs (P = .050, P = .019, respectively). A positive statin intake was associated with significantly lesser seizure (P = .007, odds ratio 4.94). Neither the occurrence of seizures nor the intake of statins had an impact on OS (P = .357, P = .507, respectively).

CONCLUSION

The size and amount of necrosis was significantly smaller in epileptogenic GBMs, maybe owed to the fact that these tumors were clinically detected at an earlier stage of their growth. Furthermore, the intake of statins was associated with a decreased occurrence of pretreatment seizures.
Lumboperitoneal and Ventriculoperitoneal Shunting for Idiopathic Intracranial Hypertension Demonstrate Comparable Failure and Complication Rates
Authors: Azad Tej D , Zhang Yi , Varshneya Kunal , Veeravagu Anand , Ratliff John K , Li Gordon
Published: February 2019

BACKGROUND

Idiopathic intracranial hypertension results in increased intracranial pressure leading to headache and visual loss. This disease frequently requires surgical intervention through lumboperitoneal (LP) or ventriculoperitoneal (VP) shunting.

OBJECTIVE

To compare postoperative outcomes between LP and VP shunts, including failure and complication rates.

METHODS

A retrospective analysis was conducted using a national administrative database (MarketScan) to identify idiopathic intracranial hypertension (IIH) patients who underwent LP or VP shunting from 2007 to 2014. Multivariate logistic and Cox regressions were performed to compare rates of shunt failure and time to shunt failure between LP and VP shunts while controlling for demographics and comorbidities.

RESULTS

The analytic cohort included 1082 IIH patients, 347 of whom underwent LP shunt placement at index hospitalization and 735 of whom underwent VP shunt placement. Rates of shunt failure were similar among patients with LP and VP shunt (34.6% vs 31.7%; P = .382). Among patients who experienced shunt failure, the mean number of shunt failures was 2.1 ± 1.6 and was similar between LP and VP cohorts. Ninety-day readmission rates, complication rates, and costs did not differ significantly between LP and VP shunts. Patients who experienced more than two shunt failures tended to have an earlier time to first shunt failure (hazard ratio 1.41; 95% confidence interval 1.08-1.85; P = .013).

CONCLUSION

These findings suggest that LP and VP shunts may have comparable rates of shunt failure and complication. Regardless of shunt type, earlier time to first shunt failure may be associated with multiple shunt failures.
Breadwinner Models Revisited: How a Couple’s Combined Work Histories Influence the Retirement Transition
Authors: Komp-Leukkunen Kathrin
Published: February 2019

As populations age, policymakers seek to stabilize pensions systems by encouraging late retirement and discouraging early economic inactivity. This study takes a novel approach to exploring an individual’s retirement transition into pension or early economic inactivity, locating individual choices in relation to their breadwinner status. It explores gender and country differences in Dutch, Spanish, and Swedish life-history data, which show that men who work less than their partners and dual earners retire into pension. Breadwinner status is particularly relevant in the Netherlands and for early retirement.
Using STACK to support student learning at masters level: a case study
Authors: Lowe T W , Mestel B D
Published: February 2019

The development of six online quizzes to support students’ study of an introductory mathematics masters module at The Open University is described and their use evaluated. The quizzes were implemented using the STACK online e-assessment system, which is powered by a computer-algebra engine. Evaluation of student feedback and an initial quantitative study of the effect of engaging with the quizzes on the final examinations marks suggest that further development of e-assessment at mathematics masters level is warranted.
Effect of Tillage and Cultivar on Plant Population, Sudden Death Syndrome, and Yield of Soybean in Iowa
Authors: Kandel Yuba R. , Leandro Leonor F. S. , Mueller Daren S.
Published: February 2019

Conservation tillage has become a common practice of soybean farming in the Midwestern United States owing to the benefits of soil and moisture conservation. Field trials were established in a field with a history of sudden death syndrome (SDS; caused by Fusarium virguliforme) in Iowa in 2011 and evaluated for five consecutive years to determine the impact of tillage on SDS and yield. The experiment was laid out in a split-split-plot design with four replicates. The main plot factor was tillage (no-till both crops, no-till corn and chisel plow soybean, and disc corn and chisel plow soybean), and each main plot was divided into subplots of corn or soybeans (in a 2-year rotation). Each subplot was again divided into two subsubplots, in which two soybean cultivars, moderately susceptible (MS) and moderately resistant (MR) to SDS, were planted each year. Root rot and SDS disease index (FDX) differed among years, because some years were more favorable for the disease than the others. However, tillage did not affect any parameters, including yield, in any year (P > 0.05). Cultivar effect was significant for each parameter occasionally. When significant, the MR cultivar had lower root rot and FDX and greater yield than the MS cultivar. These data suggest planting resistant cultivars can be an effective management tactic, but tillage does not help for SDS management.
Trends in Occurrence, Distribution, and Population Densities of Plant-Parasitic Nematodes in the Pacific Northwest of the United States from 2012 to 2016
Authors: Zasada Inga A. , Kitner Megan , Wram Catherine , Wade Nadine , Ingham Russell E. , Hafez Saad , Mojtahedi Hassan , Chavoshi Sam , Hammack Nancy
Published: February 2019

The Pacific Northwest (PNW) of the United States (Idaho, Oregon, and Washington) is a diverse agricultural production area with over 400 different commodities grown in the region. Plant-parasitic nematodes are a constraint to the production of many of these commodities. Soil sample data from 2012 to 2016 were obtained from nematode diagnostic laboratories in the region to assess trends in occurrence, population densities, and distribution of plant-parasitic nematodes in the PNW. A total of 38,022 unique data points were analyzed. The number of plant-parasitic nematode samples processed in the PNW by diagnostic laboratories has significantly increased from 2012 to 2016. Fifteen genera of plant-parasitic nematodes were identified by diagnostic laboratories, with 86% of the samples in the PNW containing at least one plant-parasitic nematode genus. These laboratories provide a valuable service to agriculture in the PNW. Additionally, they serve as a rich source of information on plant-parasitic nematode distribution, occurrence, and abundance that, when analyzed, provides an empirical basis upon which to interpret individual grower reports and make management recommendations.
Is Exploitation Competition Involved in a Multitrophic Strategy for the Biocontrol of Fusarium Head Blight?
Authors: Sarrocco Sabrina , Valenti Fabio , Manfredini Sara , Esteban Pilar , Bernardi Rodolfo , Puntoni Grazia , Baroncelli Riccardo , Haidukowski Miriam , Moretti Antonio , Vannacci Giovanni
Published: February 2019

Trichoderma gamsii T6085 was used in combination with a Fusarium oxysporum isolate (7121) in order to evaluate, in a multitrophic approach, their competitive ability against F. graminearum, one of the main causal agents of Fusarium head blight (FHB) on wheat. The two antagonists and the pathogen were coinoculated on two different natural substrates, wheat and rice kernels. Both T6085 and 7121, alone and coinoculated, significantly reduced the substrate colonization and mycotoxin production by the pathogen. The two antagonists did not affect each other. Using a metabolic approach (Biolog), we investigated whether exploitation competition could explain this antagonistic activity. The aim was to define whether the three fungi coexist or if one isolate nutritionally dominates another. Results obtained from Biolog suggest that no exploitative competition occurs between the antagonists and the pathogen during the colonization of the natural substrates. Interference competition was then preliminarily evaluated to justify the reduction in the pathogen’s growth and to better explain mechanisms. A significant reduction of F. graminearum growth was observed when the pathogen grew in the cultural filtrates of T. gamsii T6085, both alone and cocultured with F. oxysporum 7121, thus suggesting the involvement of secondary metabolites. As far as we know, this is the first time that an ecological study has been performed to explain how and which kind of competition could be involved in a multitrophic biocontrol of FHB.