bluuebunny/crossref_metadata_2025_split huggingface dataset:
cloudSPAdes: assembly of synthetic long reads using de Bruijn graphs
Authors: Tolstoganov Ivan , Bankevich Anton , Chen Zhoutao , Pevzner Pavel A 
Published: May 2019

Abstract

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

Abstract

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

Abstract

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

AbstractWith 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

Abstract
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

Abstract
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

Abstract

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

Abstract
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

AbstractIncluding 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

AbstractLaboratory 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

Abstract
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

AbstractOver 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

Abstract
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

AbstractMaximum 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.