bluuebunny/crossref_metadata_2025 huggingface dataset:
A Feeding Adaptation of the Jaw Articulation in New World Jays (Corvidae)
Authors: Zusi Richard L.
Published: October 2019

The jaw articulation of most endemic New World jays (Corvidae) has a condyle of the quadrate and an opposing cotyla of the lower jaw not found in other birds. They also have well-developed meatic articular facets of the quadrate and cranium. The tip of the rhamphotheca of the lower mandible is chisel shaped. These and other features constitute a functional unit, the buttress complex, that braces the partially opened lower jaw and enhances its use as a chisel. The buttress complex stabilizes the lower jaw by anchoring the jaw on the quadrate and reducing torque on the quadrate during pounding. A hypothesis of pounding with the lower mandible was confirmed by field observations of Aphelocoma coerulescens coerulescens, which stabs acorns with the lower mandible and then tears off the shell using both mandibles. This may be an unusually effective method of peeling acorns, and it differs from the techniques used by Garrulus and Pica. The origin of the complex may not be associated with acorn eating. A slight modification of the jaw articulation in Cyanolyca probably represents the evolutionary precursor of the buttress complex. The distribution of the complex in the Corvidae suggests that Cyanolyca is the sister group of other endemic New World jays. Gymnorhinus is related to the New World jays, not to Nucifraga. An example of convergent evolution is provided by Hemignathus wilsoni (Drepanidinae).
Genetic Variation in Piciform Birds: Monophyly and Generic and Familial Relationships
Authors: Lanyon Scott M. , Zink Robert M.
Published: October 2019

Inter and intrafamilial relationships within the New World Piciformes were examined through an electrophoretic analysis of 20 protein-coding loci (19 of which varied between taxa). One individual from each of 26 species representing 25 genera and 5 families was analyzed; Monotus momota (Coraciiformes, Momotidae) was used as an outgroup. Although levels of genetic differentiation were high (the mean Nei's unbiased distance was 1.07), the data proved useful for phylogenetic inference. The jackknife technique was used to estimate the robustness of phylogenetic hypotheses. At the interfamilial level, the results suggest the following groupings: [[[(Bucconidae) (Galbulidae)]{(Picidae)[(Capitonidae) (Ramphastidae)]}]]. These results were consistent with hypotheses of familial relationships proposed by two recent cladistic analyses of morphological character complexes (Simpson and Cracraft 1981, Swierczewski and Raikow 1981). Our data challenge the currently accepted monophyly of the Piciformes, however, in much the same way as do DNA-DNA hybridization data. Agreement among independently derived hypotheses of interfamilial relationships suggests confidence in our knowledge of evolutionary patterns among piciform taxa. Hypotheses of intrafamilial relationships, some of which agreed with morphological patterns obtained in other studies, were presented. This study shows that starch-gel electrophoresis may be useful at higher taxonomic levels.
Annual Reproductive Yield in the Cooperative Pygmy Nuthatch (Sitta pygmaea)
Authors: Sydeman William J. , Güntert Marcel , Balda Russell P.
Published: October 2019

We studied cooperative-breeding Pygmy Nuthatches (Sitta pygmaea) for 4 yr in northern Arizona. Breeding units contained 2-5 birds. Helpers were found at about 30% of all nests. All helpers that later bred on the study area were male. Helpers were mostly yearlings, and offspring or siblings of the birds that they aided, but often aided at least one unrelated breeder. Breeding units with helpers produced significantly more young than those without helpers. Breeding units in habitats with the greatest floral diversity and structural maturity fledged significantly more young than those in other habitats. Habitat did not influence the effect of helpers. Year effects increased the strength of the relationship between helpers and annual reproductive output. Previous breeding experience and pair-bond duration were not related to reproductive success. Total brood loss, although rare, was responsible for the difference in reproductive output among pairs with and without helpers and between habitats.

Breeding birds with helpers benefit by an increase in direct fitness. The advantage to the helpers is not clear but may be an increase in indirect fitness associated with aiding relatives. Helpers may benefit directly, however, by sharing roosting cavities on a group territory thereby enhancing overwinter survival.
Dominance Relationships in Harems of Female Red-Winged Blackbirds
Authors: Roberts Laurel B. , Searcy William A.
Published: October 2019

We investigated the factors determining dominance in aggressive encounters between female Red-winged Blackbirds (Agelaius phoeniceus) resident on territories of single males. Three male territories were observed, with harems of 5, 5, and 3 females. Feeding platforms were placed on the territories to increase the sample of observable encounters between residents. Order of settlement on the territory was strongly related to dominance; in 19 of 23 dyads the earlier settler won the majority of encounters. Proximity to the nest at the encounter site was also related to dominance; in 30 of 45 dyads the female closer to her nest won the majority of interactions. The effect of proximity on dominance also was shown experimentally by moving the platforms from near one nest to near another, which caused the dominance relationships between the pairs of females to reverse. In a partial correlation analysis, both order of settlement and proximity to nest correlated independently with the percentage of encounters won within dyads. Size, age, and nesting stage were not related to dominance.
Breeding Biology of the Puerto Rican Sharp-Shinned Hawk (Accipiter Striatus Venator)
Authors: Delannoy Carlos A. , Cruz Alexander
Published: October 2019

We studied the breeding biology of the Sharp-shinned Hawk (Accipiter striatus venator ) in Maricao forest of western Puerto Rico from 1978 to 1985. Sharp-shinned Hawks are year-round residents and establish nesting territories only during the breeding season, which coincides with the dry and beginning of the wet seasons. Nesting sites were occupied in December and January every year and reoccupancy rates were 50% or higher. Prolonged and intense territorial conflicts between mated and unmated males were common. The onset of egg-laying was in late March or early April approximately 3-4 months after occupancy of nesting sites. Laying of first clutches peaked in early April and spanned 38 days (n = 19 clutches). Laying of second clutches occurred irregularly and spanned 55 days (n = 8 clutches). Females renested only after the initial clutch or brood was lost. The incubation period was 32 days (n = 13 clutches), similar to the duration reported in temperate North America. Nestling females attained larger asymptotic mass than males, but the latter grew faster; although the slopes of the regression lines were statistically homogeneous. Males fledged at an average age of 28.2 days and females at 32.1 days. Young were slightly heavier than adults at fledging, but the wing chord and tail lengths were approximately 50% shorter than those of adults. Fledging occurred at the peak of prey abundance. The breeding cycle in Puerto Rico was approximately 2 months longer than that recorded in Oregon and Utah. The time that elapsed from occupancy of nesting sites to egg laying accounted for the differences. Juveniles departed from nesting sites when prey was still abundant but delivery rates had declined considerably. A total of 105 eggs was laid in 40 nests (average clutch size 2.6), of which 63% hatched and 47% of the nestlings fledged. A total of 0.8 young fledged per breeding attempt. Overall nest success was 29%, 36% (n = 33 nests) in first nesting attempts and 0% in second nesting attempts (n = 9 nests). Most reproductive losses in 28 nests resulted from nestling mortality from Philornis sp. (Diptera, Muscidae) (n = 9) and desertion of clutches (n = 11). Fecundity and reproductive success was lower in Puerto Rico than in Oregon, Utah, and Wyoming. Despite low reproductive success in Maricao forest, the breeding population did not decline during our study.
On the Origin of Darwin's Finches
Authors: Baptista Luis F. , Trail Pepper W.
Published: October 2019

We critically reviewed recent attempts to identify the ancestor of Darwin's finches (Emberizidae, "Geospizinae"), and summarized new information on taxa that have been suggested as sister groups of the geospizines, specifically the emberizines Tiaris, Melanospiza, and Volatinia. Reproductive behaviors and displays are conservative among Darwin's finches, and have been neglected in discussions of the ancestry of the group. We concentrate on these characters. We found that Tiaris and Melanospiza share a large number of apparently derived epigamic behaviors with the geospizines, none of which are exhibited by Volatinia.
WASPS: web-assisted symbolic plasmid synteny server
Authors: Badel Catherine , Da Cunha Violette , Catchpole Ryan , Forterre Patrick , Oberto Jacques
Published: October 2019

Motivation

Comparative plasmid genome analyses require complex tools, the manipulation of large numbers of sequences and constitute a daunting task for the wet bench experimentalist. Dedicated plasmid databases are sparse, only comprise bacterial plasmids and provide exclusively access to sequence similarity searches.

Results

We have developed Web-Assisted Symbolic Plasmid Synteny (WASPS), a web service granting protein and DNA sequence similarity searches against a database comprising all completely sequenced natural plasmids from bacterial, archaeal and eukaryal origin. This database pre-calculates orthologous protein clustering and enables WASPS to generate fully resolved plasmid synteny maps in real time using internal and user-provided DNA sequences.

Availability and implementation

WASPS queries befit all current browsers such as Firefox, Edge or Safari while the best functionality is achieved with Chrome. Internet Explorer is not supported. WASPS is freely accessible at https://archaea.i2bc.paris-saclay.fr/wasps/.

Supplementary information

Supplementary data are available at Bioinformatics online.
RNAIndel: discovering somatic coding indels from tumor RNA-Seq data
Authors: Hagiwara Kohei , Ding Liang , Edmonson Michael N , Rice Stephen V , Newman Scott , Easton John , Dai Juncheng , Meshinchi Soheil , Ries Rhonda E , Rusch Michael , Zhang Jinghui
Published: October 2019

Motivation

Reliable identification of expressed somatic insertions/deletions (indels) is an unmet need due to artifacts generated in PCR-based RNA-Seq library preparation and the lack of normal RNA-Seq data, presenting analytical challenges for discovery of somatic indels in tumor transcriptome.

Results

We present RNAIndel, a tool for predicting somatic, germline and artifact indels from tumor RNA-Seq data. RNAIndel leverages features derived from indel sequence context and biological effect in a machine-learning framework. Except for tumor samples with microsatellite instability, RNAIndel robustly predicts 88–100% of somatic indels in five diverse test datasets of pediatric and adult cancers, even recovering subclonal (VAF range 0.01–0.15) driver indels missed by targeted deep-sequencing, outperforming the current best-practice for RNA-Seq variant calling which had 57% sensitivity but with 14 times more false positives.

Availability and implementation

RNAIndel is freely available at https://github.com/stjude/RNAIndel.

Supplementary information

Supplementary data are available at Bioinformatics online.
iATC-NRAKEL: an efficient multi-label classifier for recognizing anatomical therapeutic chemical classes of drugs
Authors: Zhou Jian-Peng , Chen Lei , Guo Zi-Han
Published: October 2019

Motivation

The anatomical therapeutic chemical (ATC) classification system plays an increasingly important role in drug repositioning and discovery. The correct identification of classes in each level of such system that a given drug may belong to is an essential problem. Several multi-label classifiers have been proposed in this regard. Although they provided satisfactory performance, the feature extraction procedures were still rough. More refined features may further improve the predicted quality.

Results

In this article, we provide a novel multi-label classifier, called iATC-NRAKEL, to predict drug ATC classes in the first level. To obtain more informative drug features, we employed the drug association information in STITCH and KEGG, which was organized by seven drug networks. The powerful network embedding algorithm, Mashup, was adopted to extract informative drug features. The obtained features were fed into the RAndom k-labELsets (RAKEL) algorithm with support vector machine as the basic classification algorithm to construct the classifier. The 10-fold cross-validation of the benchmark dataset with 3883 drugs showed that the accuracy and absolute true were 76.56 and 74.51%, respectively. The comparison results indicated that iATC-NRAKEL was much superior to all previous reported classifiers. Finally, the contribution of each network was analyzed.

Availability and implementation

The codes of iATC-NRAKEL are available at https://github.com/zhou256/iATC-NRAKEL.
RRM adjacent TARDBP mutations disrupt RNA binding and enhance TDP-43 proteinopathy
Authors: Chen Han-Jou , Topp Simon D , Hui Ho Sang , Zacco Elsa , Katarya Malvika , McLoughlin Conor , King Andrew , Smith Bradley N , Troakes Claire , Pastore Annalisa , Shaw Christopher E
Published: October 2019

TDP-43 is a DNA/RNA binding protein, but whether its interactions with RNA are relevant to inclusion formation in ALS is unclear. Chen et al. report that mutated forms of TDP-43 that are unable to bind RNA have an increased tendency to aggregate, and can mediate toxicity by sequestering wild-type TDP-43.
β2-Adrenergic receptor agonists ameliorate the adverse effect of long-term pyridostigmine on neuromuscular junction structure
Authors: Vanhaesebrouck An E , Webster Richard , Maxwell Susan , Rodriguez Cruz Pedro M , Cossins Judith , Wickens James , Liu Wei-wei , Cetin Hakan , Cheung Jonathan , Ramjattan Hayley , Palace Jacqueline , Beeson David
Published: October 2019

The efficacy of anticholinesterase medication may diminish over time. Vanhaesebrouck et al. use an animal model of acetylcholine receptor deficiency syndrome to show that beta-2 adrenergic receptor agonists ameliorate the damage to neuromuscular junction structure caused by prolonged anticholinesterase medication, and thereby counteract the decline in efficacy.
From “Mine” to “Ours”: Gendered Hierarchies of Authorship and the Limits of Taylor Swift’s Paratextual Feminism
Authors: McNutt Myles
Published: October 2019

This article analyzes paratextual strategies deployed by Taylor Swift in her transition from country to pop in the context of her articulation of her authorship as a female songwriter. This was a transition complicated by the gendered hierarchies of pop music, wherein male producers carry significant discursive weight. The article frames the “Voice Memos” included with her 2014 album 1989 as a form of paratextual feminism, reiterating the authenticity she developed as a country star and pushing back against claims her collaboration with male producers like Max Martin and Ryan Tedder threaten her autonomy as a female voice in the music industry. However, the article goes on to consider how these and other paratextual feminisms are inherently tied to neoliberal values of post-feminism, demonstrating that their potential as a gendered critique of the media industries is limited by the lack of actualization within Swift’s broader star text and industry practice.
A Model of Brain Folding Based on Strong Local and Weak Long-Range Connectivity Requirements
Authors: Groden Moritz , Weigand Marvin , Triesch Jochen , Jedlicka Peter , Cuntz Hermann
Published: October 2019

Throughout the animal kingdom, the structure of the central nervous system varies widely from distributed ganglia in worms to compact brains with varying degrees of folding in mammals. The differences in structure may indicate a fundamentally different circuit organization. However, the folded brain most likely is a direct result of mechanical forces when considering that a larger surface area of cortex packs into the restricted volume provided by the skull. Here, we introduce a computational model that instead of modeling mechanical forces relies on dimension reduction methods to place neurons according to specific connectivity requirements. For a simplified connectivity with strong local and weak long-range connections, our model predicts a transition from separate ganglia through smooth brain structures to heavily folded brains as the number of cortical columns increases. The model reproduces experimentally determined relationships between metrics of cortical folding and its pathological phenotypes in lissencephaly, polymicrogyria, microcephaly, autism, and schizophrenia. This suggests that mechanical forces that are known to lead to cortical folding may synergistically contribute to arrangements that reduce wiring. Our model provides a unified conceptual understanding of gyrification linking cellular connectivity and macroscopic structures in large-scale neural network models of the brain.
Effect of Endogenous Clostridioides difficile Toxin Antibodies on Recurrence of C. difficile Infection
Authors: Kelly Ciarán P , Poxton Ian R , Shen Judong , Wilcox Mark H , Gerding Dale N , Zhao Xuemei , Laterza Omar F , Railkar Radha , Guris Dalya , Dorr Mary Beth
Published: October 2019

Background

Endogenous antibodies (eAbs) against Clostridioides (Clostridium) difficile toxins may protect against recurrence of C. difficile infection (rCDI). This hypothesis was tested using placebo group data from MODIFY (Monoclonal Antibodies for C. difficile Therapy) I and II (NCT01241552 and NCT01513239, respectively), global, randomized phase 3 trials that assessed the efficacy and safety of the antitoxin monoclonal antibodies bezlotoxumab and actoxumab in participants receiving antibiotic therapy for CDI.

Methods

A placebo infusion (normal saline) was administered on study day 1. Serum samples were collected on day 1, week 4, and week 12, and eAb-A and eAb-B titers were measured by 2 validated electrochemiluminescence immunoassays. Rates of initial clinical cure and rCDI were summarized by eAb titer category (low, medium, high) at each time point.

Results

Serum eAb titers were available from a total of 773 participants. The proportion of participants with high eAb-A and eAb-B titers increased over time. Rates of initial clinical cure were similar across eAb titer categories. There was no correlation between eAb-A titers and rCDI rate at any time point. However, there was a negative correlation between rCDI and eAb-B titer on day 1 and week 4. rCDI occurred in 22% of participants with high eAb-B titers at baseline compared with 35% with low or medium titers (P = .015).

Conclusions

Higher eAb titers against toxin B, but not toxin A, were associated with protection against rCDI. These data are consistent with the observed efficacy of bezlotoxumab, and lack of efficacy of actoxumab, in the MODIFY trials.

Clinical Trials Registration

NCT01241552 and NCT01513239.
Consensus Report on Shigella Controlled Human Infection Model: Conduct of Studies
Authors: Talaat Kawsar R , Bourgeois A Louis , Frenck Robert W , Chen Wilbur H , MacLennan Calman A , Riddle Mark S , Suvarnapunya Akamol E , Brubaker Jessica L , Kotloff Karen L , Porter Chad K
Published: October 2019

Shigella causes morbidity and mortality worldwide, primarily affecting young children living in low-resource settings. It is also of great concern due to increasing antibiotic resistance, and is a priority organism for the World Health Organization. A Shigella vaccine would decrease the morbidity and mortality associated with shigellosis, improve child health, and decrease the need for antibiotics. Controlled human infection models (CHIMs) are useful tools in vaccine evaluation for early up- or down-selection of vaccine candidates and potentially useful in support of licensure. Over time, the methods employed in these models have become more uniform across sites performing CHIM trials, although some differences in conduct persist. In November 2017, a Shigella CHIM workshop was convened in Washington, District of Columbia. Investigators met to discuss multiple aspects of these studies, including study procedures, clinical and immunological endpoints, and shared experiences. This article serves as a uniform procedure by which to conduct Shigella CHIM studies.
Consensus Report on Shigella Controlled Human Infection Model: Immunological Assays
Authors: Kaminski Robert W , Pasetti Marcela F , Aguilar Ana Older , Clarkson Kristen A , Rijpkema Sjoerd , Bourgeois A Louis , Cohen Dani , Feavers Ian , MacLennan Calman A
Published: October 2019

Moderate to severe diarrhea caused by Shigella is a global health concern due to its substantial contribution to morbidity and mortality in children aged <5 years in low- and middle-income countries. Although antibiotic treatment can be effective, emerging antimicrobial resistance, limited access, and cost affirm the role of vaccines as the most attractive countermeasure. Controlled human infection models (CHIMs) represent a valuable tool for assessing vaccine efficacy and potentially accelerating licensure. Currently, immunological analysis during CHIM studies is customized based on vaccine type, regimen, and administration route. Additionally, differences in type of immunoassays and procedures used limit comparisons across studies. In November 2017, an expert working group reviewed Shigella CHIM studies performed to date and developed consensus guidelines on prioritization of immunoassays, specimens, and collection time points. Immunoassays were ranked into 3 tiers, with antibodies to Shigella lipopolysaccharide (LPS) being the highest priority. To facilitate comparisons across clinical studies, a second workshop was conducted in December 2017, which focused on the pathway toward a recognized enzyme-linked immunosorbent assay (ELISA) to determine serum immunoglobulin G titers against Shigella LPS. The consensus of the meeting was to establish a consortium of international institutions with expertise in Shigella immunology that would work with the National Institute for Biological Standards and Control to establish a harmonized ELISA, produce a reference sera, and identify a reliable source of Shigella LPS for global utilization. Herein we describe efforts toward establishing common procedures to advance Shigella vaccine development, support licensure, and ultimately facilitate vaccine deployment and uptake.
Long-term Persistence of an Extensively Drug-Resistant Subclade of Globally Distributed Pseudomonas aeruginosa Clonal Complex 446 in an Academic Medical Center
Authors: Pincus Nathan B , Bachta Kelly E R , Ozer Egon A , Allen Jonathan P , Pura Olivia N , Qi Chao , Rhodes Nathaniel J , Marty Francisco M , Pandit Alisha , Mekalanos John J , Oliver Antonio , Hauser Alan R
Published: October 2019

Background

Antimicrobial resistance (AMR) is a major challenge in the treatment of infections caused by Pseudomonas aeruginosa. Highly drug-resistant infections are disproportionally caused by a small subset of globally distributed P. aeruginosa sequence types (STs), termed “high-risk clones.” We noted that clonal complex (CC) 446 (which includes STs 298 and 446) isolates were repeatedly cultured at 1 medical center and asked whether this lineage might constitute an emerging high-risk clone.

Methods

We searched P. aeruginosa genomes from collections available from several institutions and from a public database for the presence of CC446 isolates. We determined antibacterial susceptibility using microbroth dilution and examined genome sequences to characterize the population structure of CC446 and investigate the genetic basis of AMR.

Results

CC446 was globally distributed over 5 continents. CC446 isolates demonstrated high rates of AMR, with 51.9% (28/54) being multidrug-resistant (MDR) and 53.6% of these (15/28) being extensively drug-resistant (XDR). Phylogenetic analysis revealed that most MDR/XDR isolates belonged to a subclade of ST298 (designated ST298*) of which 100% (21/21) were MDR and 61.9% (13/21) were XDR. XDR ST298* was identified repeatedly and consistently at a single academic medical center from 2001 through 2017. These isolates harbored a large plasmid that carries a novel antibiotic resistance integron.

Conclusions

CC446 isolates are globally distributed with multiple occurrences of high AMR. The subclade ST298* is responsible for a prolonged epidemic (≥16 years) of XDR infections at an academic medical center. These findings indicate that CC446 is an emerging high-risk clone deserving further surveillance.
Modelling temperature and humidity effects on web performance: implications for predicting orb-web spider (Argiope spp.) foraging under Australian climate change scenarios
Authors: Blamires S J , Sellers W I
Published: October 2019

Lay Summary.

How climate change impacts animal extended phenotypes (EPs) is poorly understood. We modelled how temperature and humidity affects the ability of spider webs to intercept prey. We found humidity had negative effects at the extremes. Temperature, however, likely interacts with humidity to affect web tension and prey retention.
Control of sinus venous valve and sinoatrial node development by endocardial NOTCH1
Authors: Wang Yidong , Lu Pengfei , Jiang Liping , Wu Bingruo , Zhou Bin
Published: October 2019

Aims

Sinus venous valve (SVV) and sinoatrial node (SAN) develop together at the sinoatrial junction during embryogenesis. SVV ensures unidirectional cardiac input and SAN generates sinus rhythmic contraction, respectively; both functions are essential for embryonic survival. We aim to reveal the potential role of endocardial NOTCH signalling in SVV and SAN formation.

Methods and results

We specifically deleted Notch1 in the endocardium using an Nfatc1Cre line. This deletion resulted in underdeveloped SVV and SAN, associated with reduced expression of T-box transcription factors, Tbx5 andTbx18, which are essential for the formation of SVV and SAN. The deletion also led to decreased expression of Wnt2 in myocardium of SVV and SAN. WNT2 treatment was able to rescue the growth defect of SVV and SAN resulted from the Notch1 deletion in whole embryo cultures. Furthermore, the Notch1 deletion reduced the expression of Nrg1 in the SVV myocardium and supplement of NRG1 restored the growth of SVV in cultured Notch1 knockout embryos.

Conclusion

Our findings support that endocardial NOTCH1 controls the development of SVV and SAN by coordinating myocardial WNT and NRG1 signalling functions.
Selective ETA vs. dual ETA/B receptor blockade for the prevention of sunitinib-induced hypertension and albuminuria in WKY rats
Authors: Mirabito Colafella Katrina M , Neves Karla B , Montezano Augusto C , Garrelds Ingrid M , van Veghel Richard , de Vries René , Uijl Estrellita , Baelde Hans J , van den Meiracker Anton H , Touyz Rhian M , Danser A H Jan , Versmissen Jorie
Published: October 2019

Aims

Although effective in preventing tumour growth, angiogenesis inhibitors cause off-target effects including cardiovascular toxicity and renal injury, most likely via endothelin (ET)-1 up-regulation. ET-1 via stimulation of the ETA receptor has pro-hypertensive actions whereas stimulation of the ETB receptor can elicit both pro- or anti-hypertensive effects. In this study, our aim was to determine the efficacy of selective ETA vs. dual ETA/B receptor blockade for the prevention of angiogenesis inhibitor-induced hypertension and albuminuria.

Methods and results

Male Wistar Kyoto (WKY) rats were treated with vehicle, sunitinib (angiogenesis inhibitor; 14 mg/kg/day) alone or in combination with macitentan (ETA/B receptor antagonist; 30 mg/kg/day) or sitaxentan (selective ETA receptor antagonist; 30 or 100 mg/kg/day) for 8 days. Compared with vehicle, sunitinib treatment caused a rapid and sustained increase in mean arterial pressure of ∼25 mmHg. Co-treatment with macitentan or sitaxentan abolished the pressor response to sunitinib. Sunitinib did not induce endothelial dysfunction. However, it was associated with increased aortic, mesenteric, and renal oxidative stress, an effect that was absent in mesenteric arteries of the macitentan and sitaxentan co-treated groups. Albuminuria was greater in the sunitinib- than vehicle-treated group. Co-treatment with sitaxentan, but not macitentan, prevented this increase in albuminuria. Sunitinib treatment increased circulating and urinary prostacyclin levels and had no effect on thromboxane levels. These increases in prostacyclin were blunted by co-treatment with sitaxentan.

Conclusions

Our results demonstrate that both selective ETA and dual ETA/B receptor antagonism prevents sunitinib-induced hypertension, whereas sunitinib-induced albuminuria was only prevented by selective ETA receptor antagonism. In addition, our results uncover a role for prostacyclin in the development of these effects. In conclusion, selective ETA receptor antagonism is sufficient for the prevention of sunitinib-induced hypertension and renal injury.
The Ulcerative Colitis Response Index for Detection of Mucosal Healing in Patients Treated With Anti-tumour Necrosis Factor
Authors: de Bruyn Magali , Ringold Randy , Martens Erik , Ferrante Marc , Van Assche Gert , Opdenakker Ghislain , Dukler Avinoam , Vermeire Séverine
Published: October 2019

Background

Surrogate markers that accurately detect mucosal healing [MH] in patients with ulcerative colitis [UC] are urgently needed. Several stool neutrophil-related proteins are currently used as biomarkers for MH. However, the sensitivity and specificity are not sufficient to avoid unnecessary endoscopic evaluations.

Methods

Novel serum neutrophil-related markers (neutrophil gelatinase B-associated lipocalin and matrix metalloproteinase-9 [NGAL-MMP-9 complex], cathelicidin LL-37 and chitinase 3-like 1 [CHI3L1]), together with C-reactive protein [CRP] and neutrophil counts were studied. Serum samples were obtained from 176 anti-tumour necrosis factor [anti-TNF]-treated UC patients (145 infliximab [IFX] and 31 adalimumab [ADM]) at baseline and after a median of 9.5 weeks. All patients had active disease prior to treatment (Mayo endoscopic subscore [MES] ≥ 2), and MH was defined as MES ≤ 1. Serum was also obtained from 75 healthy controls. Binary logistic regression analysis was used to generate the Ulcerative Colitis Response Index [UCRI]. The performance of individual markers and UCRI was tested with receiver operating characteristic analysis.

Results

All neutrophil-related markers were significantly higher in active UC patients compared to healthy controls. In the IFX cohort, CRP, NGAL-MMP-9, CHI3L1 and neutrophil count decreased significantly after treatment and all marker levels were significantly lower in healers compared to non-healers following IFX. In the ADM cohort, CRP, NGAL-MMP-9, CHI3L1 and neutrophil count decreased significantly only in healers. UCRI [including CRP, CHI3L1, neutrophil count and LL-37] accurately detected MH in both IFX-treated (area under the curve [AUC] = 0.83) and ADM-treated [AUC = 0.79] patients.

Conclusions

The new UCRI index accurately detects MH after treatment with IFX and ADM. This panel is useful for monitoring MH in UC patients under anti-TNF treatment.

Podcast

This article has an associated podcast which can be accessed at https://academic.oup.com/ecco-jcc/pages/podcast
Clarifying the anatomy of common arterial trunk: a clinical study of 70 patients
Authors: Gupta Saurabh Kumar , Aggarwal Abhinav , Shaw Manish , Gulati Gurpreet Singh , Kothari Shyam S , Ramakrishnan Sivasubramanian , Saxena Anita , Devagourou Velayoudam , Talwar Sachin , Sharma Sanjiv , Gupta Neerja , Airan Balram , Anderson Robert H
Published: October 2019

Aims

Anatomic variations in hearts with common arterial trunk are well-known, although there is no large study of living patients. Detailed knowledge of the origins of the pulmonary and coronary arteries is vital for surgical management. We sought to clarify the variations using computed tomography.

Methods and results

We prospectively studied 70 consecutive patients using echocardiography and computed tomography. In 63 (90%) patients, there was aortic dominance, while 7 (10%) had dominance of the pulmonary component. In 27 (43%) patients with aortic dominance, part of the pulmonary segment arose from a truncal valvar sinus. A long confluent pulmonary channel was more common in patients with sinusal origin compared to those with non-sinusal origin of the pulmonary segment (19 vs. 0; P = 0.0005). Close proximity between the orifices of the coronary arteries and the pulmonary component was also more frequent with sinusal origin (21 vs. 6; P < 0.001) with 5 (19%) patients having pulmonary flow obstructed by a truncal valvar leaflet.

Conclusion

Sinusal origin of the pulmonary component is common with aortic dominance, frequently in association with a long confluent pulmonary segment, which may be in close proximity to the origin of a coronary artery. One-fifth of patients with sinusal origin of pulmonary component have a truncal valvar leaflet obstructing the pulmonary orifice. These morpho-anatomic findings have important implications for management.
Pacing therapy in children with isolated complete atrioventricular block: a retrospective study of pacing system survival and pacing-related complications in a national cohort
Authors: Eliasson Håkan , Sonesson Sven-Erik , Salomonsson Stina , Skog Andreasson Amanda , Wahren-Herlenius Marie , Gadler Fredrik
Published: October 2019

Aims

To evaluate pacing system survival and complications to pacemaker (PM) therapy in children with isolated complete atrioventricular block (CAVB).

Methods and results

We performed a nationwide retrospective study of children diagnosed before 15 years of age with isolated CAVB and PM treatment. Between 1983 and 2012, 127 patients underwent PM-implantations at 3.2 (0–17) [median (range)] years and were followed for 11 (0.6–19) years. An endocardial or epicardial PM system was implanted in 72 and 55 patients, respectively. A total of 306 pacing leads (76% steroid-eluting) were implanted. Pacing system survival was significantly affected by age, with a higher risk of a new intervention for children aged <1 month at first implantation. Lead survival of the steroid-eluting leads at 5 and 10 years was 90 and 81%, respectively, with no difference between epicardial and endocardial systems. Complications leading to revision of the pacing system occurred in 24% of the patients. Patients aged <1 month at first PM implantation had a five-fold increased risk for a complication to occur. Dividing the cohort according to year of first procedure showed that those who had their first implantation ≥2002 had fewer complications and also lead- and pacing system survival was better in the later cohort.

Conclusion

Pacing system survival and complications to PM therapy in young patients with isolated CAVB were significantly affected by age, with low age at PM implantation constituting a risk factor. Endocardial and epicardial pacing systems showed no significant differences in performance.
Reduced dose of rivaroxaban and dabigatran vs. vitamin K antagonists in very elderly patients with atrial fibrillation in a nationwide cohort study
Authors: Fauchier Laurent , Blin Patrick , Sacher Frédéric , Dureau-Pournin Caroline , Bernard Marie-Agnès , Lassalle Regis , Droz-Perroteau Cécile , Dallongeville Jean , Moore Nicholas
Published: October 2019

Aims

The real-life benefits and risks of the non-vitamin K antagonist oral anticoagulants for stroke prevention in very elderly patients with atrial fibrillation (AF) are still debated.

Methods and results

Cohorts of new users of rivaroxaban 15 mg, dabigatran 110 mg, or vitamin K antagonists (VKA) for AF ≥85 years old in 2013 or 2014 were identified in the nationwide French claims database and followed-up for 1 year. Cohorts were compared after 1:1 matching using high-dimensional propensity score. Compared to VKA use and considering 1-year cumulative incidences, risk of stroke, and systemic embolism was not different with rivaroxaban use [hazard ratio 1.14, 95% confidence interval (CI): 0.93–1.40] and lower with dabigatran use (0.77, 95% CI: 0.60–0.99), risk of major bleeding was not different with rivaroxaban use (0.91, 95% CI: 0.74–1.11) and with dabigatran use (0.81, 95% CI: 0.64–1.03), risk of all-cause death was borderline to significance lower with rivaroxaban use (0.91, 95% CI: 0.83–1.00), and lower with dabigatran use (0.87, 95% CI: 0.78–0.97). The risk for a composite of all events above was not different with rivaroxaban use (0.96, 95% CI: 0.88–1.04) and lower with dabigatran use (0.87, 95% CI: 0.79–0.96) as compared with VKA use. The risk for the composite of all events was not different with rivaroxaban use as compared with dabigatran use (1.09, 95% CI: 0.97–1.23).

Conclusion

This study shows for the first time in more than 25 000 new real-life anticoagulant users for AF aged ≥85 years a neutral overall benefit-risk of rivaroxaban 15 mg vs. VKA and a favourable overall benefit-risk of dabigatran 110 mg vs. VKA on relevant clinical events.

Study registration

European Medicines Agency EUPAS14567 (www.encepp.eu) and Clinicaltrials.gov id NCT02864758.
Salmonella adapts to plants and their environment during colonization of tomatoes
Authors: Zarkani Azhar A , Schierstaedt Jasper , Becker Marlies , Krumwiede Johannes , Grimm Maja , Grosch Rita , Jechalke Sven , Schikora Adam
Published: October 2019

Humans and animals are considered typical hosts for Salmonella, however, also plants can be colonized. Tomatoes were linked to salmonellosis outbreaks already on several occasions. The aim of this study was, therefore, to establish a comprehensive view on the interaction between Salmonella enterica and tomatoes, and to test the hypothesis that colonization of plants is an interactive process. We assessed the persistence of Salmonella in agricultural soil, the colonization pattern in and on tomatoes, as well as the reciprocal responses of tomatoes to different Salmonella strains and Salmonella to root exudates and tomato-related media. This study revealed that Salmonella can persist in the soil and inside the tomato plant. Additionally, we show that Salmonella strains have particular colonization pattern, although the persistence inside the plant differs between the tested strains. Furthermore, the transcriptome response of tomato showed an up-regulation of several defense-related genes. Salmonella transcriptome analysis in response to the plant-based media showed differentially regulated genes related to amino acid and fatty acid synthesis and stress response, while the response to root exudates revealed regulation of the glyoxylate cycle. Our results indicate that both organisms actively engage in the interaction and that Salmonella adapts to the plant environment.
Genomic characterization of Vibrio parahaemolyticus from Pacific white shrimp and rearing water in Malaysia reveals novel sequence types and structural variation in genomic regions containing the Photorhabdus insect-related (Pir) toxin-like genes
Authors: Yan Chrystine Zou Yi , Austin Christopher M , Ayub Qasim , Rahman Sadequr , Gan Han Ming
Published: October 2019

The Malaysian and global shrimp aquaculture production has been significantly impacted by acute hepatopancreatic necrosis disease (AHPND) typically caused by Vibrio parahaemolyticus harboring the pVA plasmid containing the pirAVp and pirBVp genes, which code for Photorhabdus insect-related (Pir) toxin. The limited genomic resource for V. parahaemolyticus strains from Malaysian aquaculture farms precludes an in-depth understanding of their diversity and evolutionary relationships. In this study, we isolated shrimp-associated and environmental (rearing water) V. parahaemolyticus from three aquaculture farms located in Northern and Central Malaysia followed by whole-genome sequencing of 40 randomly selected isolates on the Illumina MiSeq. Phylogenomic analysis and multilocus sequence typing (MLST) reveal distinct lineages of V. parahaemolyticus that harbor the pirABVp genes. The recovery of pVA plasmid backbone devoid of pirAVp or pirABVp in some V. parahaemolyticus isolates suggests that the toxin genes are prone to deletion. The new insight gained from phylogenomic analysis of Asian V. parahaemolyticus, in addition to the observed genomic instability of pVa plasmid, will have implications for improvements in aquaculture practices to diagnose, treat or limit the impacts of this disease.
Verrucous antral gastritis in relation to Helicobacter pylori infection, nutrition, and gastric atrophy
Authors: Tsuji Naoko , Umehara Yasuko , Takenaka Mamoru , Minami Yasunori , Watanabe Tomohiro , Nishida Naoshi , Kudo Masatoshi
Published: October 2019

Background

There have been few studies in the English literature regarding verrucous gastritis (VG). The present study investigated the clinical and endoscopic features of verrucous antral gastritis, especially focusing on Helicobacter pylori infection, nutrition, and gastric atrophy.

Methods

We performed a retrospective study of patients who underwent routine endoscopy with indigo carmine chromoendoscopy and a comparative study was conducted between VG-positive and VG-negative groups. VG was subdivided into classical and numerous types based on the number and distribution of verrucous lesions. Demographic, clinical, and endoscopic data including body mass index (BMI), serum albumin and cholesterol, gastric atrophy, reflux oesophagitis, Barrett’s oesophagus, and H. pylori status were collected. Univariate and multivariable analyses were performed to identify factors associated with VG.

Results

We analysed the data of 621 patients undergoing routine endoscopy and found that VG (n = 352) was significantly associated with increased BMI (1.12 [1.05–1.18], P < 0.01), reflux esophagitis (1.96 [1.10–3.28], P < 0.01), and H. pylori negativity with or without a history of eradication (9.94 [6.00–16.47] and 6.12 [3.51–10.68], P < 0.001, respectively). Numerous-type (n = 163) VG was associated with both closed- and open-type gastric atrophy (9.9 [4.04–21.37] and 8.10 [3.41–19.24], P < 0.001, respectively). There were no statistical differences between groups regarding age, sex, total cholesterol, albumin, and bile-colored gastric juice.

Conclusions

Verrucous antral gastritis was related to increased BMI, reflux esophagitis, and H. pylori negativity. Numerous-type verrucous lesions were associated with gastric atrophy. These indicate that VG may be a physiological phenomenon due to high gastric acidity, mechanical overload, and vulnerability of background mucosa.
Selection of code width and analysis of influencing factors in multitransient electromagnetic method
Authors: Wang Xianxiang , Deng Juzhi , Ren Jingli
Published: October 2019

The multitransient electromagnetic method (MTEM) uses an m pseudo-random binary sequence (PRBS) as the source waveform, which requires deconvolution to recover the impulse response. To obtain high-precision impulse responses, the frequency bandwidth of a pseudo-random sequence should be consistent with the identified system. Code width is an important parameter of an m pseudo-random sequence which determines the maximum frequency bandwidth of an m pseudo-random sequence. If the code width is too wide, the signal-to-noise ratio of the high-frequency section cannot be guaranteed; if it is too narrow, it will result in wastage of transmission time and energy. Therefore, this study developed a method for selecting an appropriate code width and an empirical formula for calculating the appropriate code width on the basis of relevant numerical simulation results. Then, factors influencing the appropriate code width were investigated through formula derivations and numerical simulations. Results showed that in the uniform half-space, the code width is proportional to the conductivity and square of offset. In the 1-D model, the appropriate code width is still proportional to the conductivity, but no longer to the square of the offset.Thank you very much for your remind.I did not refer to any data bases.
Coda-Q in the 2.5–20 s period band from seismic noise: application to the greater Alpine area
Authors: Soergel D , Pedersen H A , Stehly L , Margerin L , Paul A ,   AlpArray Working Group
Published: October 2019

Coda-Q is used to estimate the attenuation and scattering properties of the Earth. So far focus has been on earthquake data at frequencies above 1 Hz, as the high noise level in the first and second microseismic peak, and possibly lower scattering coefficient, hinder stable measurements at lower frequencies. In this work, we measure and map coda-Q in the period bands 2.5–5 s, 5–10 s and 10–20 s in the greater Alpine region using noise cross-correlations between station pairs, based on data from permanent seismic stations and from the temporary AlpArray experiment. The observed coda-Q for short interstation distances is independent of azimuth so there is no indication of influence of the directivity of the incoming noise field on our measurements. In the 2.5–5 s and 5–10 s period bands, our measurements are self-consistent, and we observe stable geographic patterns of low and high coda-Q in the period bands 2.5–5 s and 5–10 s. In the period band 10–20 s, the dispersion of our measurements increases and geographic patterns become speculative. The coda-Q maps show that major features are observed with high resolution, with a very good geographical resolution of for example low coda-Q in the Po Plain. There is a sharp contrast between the Po Plain and the Alps and Apennines where coda-Q is high, with the exception a small area in the Swiss Alps which may be contaminated by the low coda-Q of the Po Plain. The coda of the correlations is too short to make independent measurements at different times within the coda, so we cannot distinguish between intrinsic and scattering Q. Measurements on more severely selected data sets and longer time-series result in identical geographical patterns but lower numerical values. Therefore, high coda-Q values may be overestimated, but the geographic distribution between high and low coda-Q areas is respected. Our results demonstrate that noise correlations are a promising tool for extending coda-Q measurements to frequencies lower than those analysed with earthquake data.