bluuebunny/crossref_metadata_2025 huggingface dataset:
Reflux-Associated Cholecystopathy
Authors: Muraki Takashi , Memis Bahar , Reid Michelle D. , Uehara Takeshi , Ito Tetsuya , Hasebe Osamu , Okaniwa Shinji , Horigome Naoto , Hisa Takeshi , Mittal Pardeep , Freedman Alexa , Maithel Shishir , Sarmiento Juan M. , Krasinskas Alyssa , Koshiol Jill , Adsay Volkan
Published: June 2017

Pancreaticobiliary maljunction (PBM) is the anomalous union of the main pancreatic duct and common bile duct outside the Oddi-sphincter, allowing the reflux of pancreatic juice to the gallbladder. There is only limited awareness and understanding of the pathologic correlates of this condition, mostly from Japan; this entity is largely unrecognized in the West. In this study, 76 gallbladders from patients with PBM (64 from Japan; 12 from the United States) were analyzed and contrasted with 66 from non-PBM patients. These were predominantly females (54 vs. 22), mean age, 53 (range: 14 to 81). Cholelithiasis was uncommon (16% vs. 80% in non-PBM, P<0.01) whereas cholesterolosis was more common (49% vs. 29%, P=0.02) suggesting an altered chemical milieu. There was a distinctive diffuse mucosal hyperplasia (82% vs. 42%, P<0.01) with markedly elongated folds (mean: 1.1 vs. 0.7 mm, P<0.01) composed of compact villoglandular proliferation, often showing broad-based pushing into muscle, accompanied by prominent and more complex Rokitansky-Aschoff sinus formation (2.0 vs. 1.0/cm, P<0.01) at the base. At the tips, this villiform hyperplasia displayed frequent horizontal bridging of the folds (68% vs. 47%, P=0.01), bulbous dilatation (52% vs. 21%, P<0.01) as well as deposition of a peculiar amyloid-like hyaline material (56% vs. 15%, P<0.01). Despite paucity of inflammation and gallstones, findings attributed to mucosal injury were common including: pyloric gland metaplasia (70% vs. 48%, P=0.01) and intestinal metaplasia (24% vs. 6%, P<0.01). Invasive gallbladder carcinoma was present in 22 (29%) of the cases with 6 of these (27%) arising in association with intracholecystic papillary tubular neoplasm. Five cases had bile duct carcinoma at the time of cholecystectomy and 1 developed it 4 years after. In conclusion, gallbladders with patients with PBM display a distinctive pattern of mucosal hyperplasia with distinguishing features, which in constellation render it a microscopically diagnosable specific entity. We propose to refer to this entity as “reflux-associated cholecystopathy.” Recognition of the pathologic characteristics of this entity is important so that investigation for, as well as treatment and prevention of, PBM-associated complications (biliary tract cancers and pancreatitis) can be instituted. This group also offers a distinct model of carcinogenesis (chemical rather than inflammatory) in the gallbladder for cancer researchers to scrutinize.
Cyclin D1 Is Expressed in Neoplastic Cells of Langerhans Cell Histiocytosis but Not Reactive Langerhans Cell Proliferations
Authors: Shanmugam Vignesh , Craig Jeffrey W. , Hornick Jason L. , Morgan Elizabeth A. , Pinkus Geraldine S. , Pozdnyakova Olga
Published: June 2017

Langerhans cell histiocytosis (LCH) is characterized by frequent activating mutations involving the mitogen-activated protein kinase (MAPK) pathway. Therefore, downstream markers of MAPK pathway activation such as cyclin D1 may be useful as novel diagnostic markers of neoplasia in LCH. The goal of this study was to investigate cyclin D1 expression in LCH and reactive Langerhans cell accumulations using immunohistochemistry on archival tissue. All LCH cases tested (39/39) showed cyclin D1 expression in CD1a/Langerin+ cells. Most cases (22/39; 56%) showed strong cyclin D1 expression in the majority (≥50%) of lesional cells. Only a few cases (6/39; 15%) showed cyclin D1 expression in a small subset (<20%). Nearly all LCH cases (26/27; 96%) showed p-ERK expression by immunohistochemistry, parallel to cyclin D1 expression. CD1a+ Langerhans cells in all cases of florid dermatopathic lymphadenopathy and normal skin were negative for cyclin D1, as demonstrated by CD1a/cyclin D1 double staining. The majority of skin specimens (14/18; 78%) with dermatitis-related changes did not show cyclin D1 expression in the CD1a+ epidermal Langerhans cell aggregates. A minority (4/18; 22%) showed weak cyclin D1 staining in a small subset (5% to 10%) of CD1a+ Langerhans cells. We conclude that cyclin D1 is ubiquitously expressed in LCH, in keeping with the known near universal MAPK activation in this disease. Further, it is not significantly expressed in reactive Langerhans cell proliferations in lymph node or skin. Therefore, cyclin D1 immunohistochemistry may be useful in excluding non-neoplastic mimics of LCH.
Short-Term Peripheral Vasoactive Infusions in Pediatrics: Where Is the Harm?
Authors: Patregnani Jason T. , Sochet Anthony A. , Klugman Darren
Published: June 2017

Objective:

Pediatric shock represents a major cause of morbidity and mortality in the United States. Standardization of treatment such as volume resuscitation and vasoactive administration has resulted in improved patient outcomes. Vasoactives have been anecdotally associated with peripheral IV infiltration and extravasation. There is a paucity of evidence in pediatrics to determine the ideal route of vasoactive infusions and what, if any, risk factors and harm are associated with peripheral IV infiltration and extravasation. We aim to assess the frequency of and risk factors for peripheral IV infiltration and extravasation during peripheral IV vasoactive infusions in children admitted to the PICU.

Design:

A retrospective, cohort study of all children admitted to a PICU from January 2012 to June 2014.

Setting:

Forty-four–bed PICU at Children’s National Health System.

Patients:

All children 0–18 years old receiving a vasoactive infusion through a peripheral IV for a minimum of 1 hour.

Interventions:

None.

Measurements and Main Results:

The primary outcomes of this study were incidence of peripheral IV infiltration and extravasation and resultant tissue injury. Secondary outcomes were peripheral IV characteristics and vasoactive infusion data. One hundred two patients met inclusion criteria. Sixty-two percent (63/102) were admitted with the diagnosis of septic shock. The most commonly used vasoactive agent was dopamine. The median peak Vasoactive Infusion Score was 10 (6–14). Peripheral IV infiltration and extravasation incidence was 2% (2/102) and neither event resulted in injury requiring medical or surgical intervention.

Conclusions:

Vasoactive infusions through peripheral IV in children admitted to the PICU with shock were observed to have a low incidence of peripheral IV infiltration and extravasation and resultant tissue injury. Short-term delivery of vasoactives via peripheral IV catheter in a highly monitored PICU setting appears to be safe.
Symmetry Restoration at Rest after Masseter-to-Facial Nerve Transfer: Is It as Efficient as Smile Reanimation?
Authors: Chen Gang , Wang Wenjin , Wang Wei , Ding Wei , Yang Xianxian
Published: June 2017

Background:

Masseter-to-facial nerve transfer is a highly efficient technique for reanimating paralyzed muscle and has been reported to restore facial symmetry at rest. However, no systematic studies have been performed, and the effects of preoperative droop of the oral commissure on postoperative symmetry at rest have rarely been reported.

Methods:

The authors retrospectively analyzed 35 patients with masseteric-to-facial nerve anastomosis and assessed the quality and quantity of the dynamic recovery and the oral commissure symmetry at rest. The dynamic and static effects were then compared.

Results:

All of the patients’ Terzis scores were increased postoperatively, and over half of the patients presented restored symmetric smiles (Terzis scores of 4 or 5). The postoperative symmetry scale of the oral commissure at rest improved in 18 of 35 patients. Both the mean postoperative altitude difference of oral commissure excursion and the postoperative altitude difference of bilateral oral commissure position were decreased compared with preoperative values. The preoperative symmetry had a significant effect on the postoperative altitude difference of the bilateral oral commissure position. The effects of the dynamic and static symmetry improvements were transformed to a comparable factor α. The dynamic α was significantly greater than the static α.

Conclusions:

Masseter-to-facial nerve transfer is a reliable technique for smile reanimation. However, it has only a limited effect on the improvement of symmetry at rest. Assessing the preoperative symmetry of the oral commissure at rest can be used to predict postoperative outcomes, and patients with severe droop of the oral commissure (symmetry scale grade III or IV) should receive static suspension.
Quantitative Analysis of Iodine Image of Dual-energy Computed Tomography at Rest
Authors: Nakahara Takehiro , Toyama Takuji , Jinzaki Masahiro , Seki Ryotaro , Saito Yuichiro , Higuchi Tetsuya , Yamada Minoru , Arai Masashi , Tsushima Yoshito , Kuribayashi Sachio , Kurabayashi Masahiko
Published: June 2017

Purpose:

Dual-energy computed tomography (DECT) can be used for visual determination of iodine distribution in the myocardium (iodine image); however, the accuracy and reproducibility of the process remains debatable. Because of the low contrast-to-noise ratio of CT, we hypothesized that quantitative measurement may be more accurate for detecting myocardial ischemia. In this study, we evaluated our quantitative method by comparing it with visual analysis using 99mTc-tetrofosmin (TF) stress-rest single-photon emission computed tomography (SPECT) myocardial perfusion imaging (MPI) as the reference standard.

Materials and Methods:

Forty-three patients who had a significant stenosis on cardiac rest DECT and had received 99mTc-TF stress-rest SPECT MPI within 1 month were retrospectively analyzed. The regions of interest were set on iodine images in accordance with the American Heart Association (AHA) 17-segment model (a total of 731 segments). The regions of interest values were divided by the amount of iodine (mg) per unit weight (kg) and defined as perfusion value (perfusion value analysis). All segments were also visually analyzed and receiver operating characteristic curve analysis performed to identify the superior analysis.

Results:

The receiver operating characteristic curve analysis showed that perfusion value analysis is significantly superior to visual analysis [the area under the curve: 0.921 (95% confidence interval, 0.860-0.981) versus 0.685 (95% confidence interval, 0.580-0.791), respectively, P<0.05], with 93.8% sensitivity, 99.1% specificity, 98.9% accuracy, 83.3% positive predictive value, and 99.7% negative predictive value (P<0.01).

Conclusions:

Quantitative analysis of the iodine image of rest DECT, called perfusion value analysis, is more accurate than visual analysis when compared with 99mTc-TF SPECT MPI as the reference standard.
Human to yeast pathway transplantation: cross-species dissection of the adenine de novo pathway regulatory node
Authors: Agmon Neta , Temple Jasmine , Tang Zuojian , Schraink Tobias , Baron Maayan , Chen Jun , Mita Paolo , Martin James A. , Tu Benjamin P. , Yanai Itai , Fenyö David , Boeke Jef D.
Published: June 2017

Pathway transplantation from one organism to another represents a means to a more complete understanding of a biochemical or regulatory process. The purine biosynthesis pathway, a core metabolic function, was transplanted from human to yeast. We replaced the entireSaccharomyces cerevisiaeadenine de novo pathway with the cognate human pathway components. A yeast strain was “humanized” for the full pathway by deleting all relevant yeast genes completely and then providing the human pathway in trans using a neochromosome expressing the human protein coding regions under the transcriptional control of their cognate yeast promoters and terminators. The “humanized” yeast strain grows in the absence of adenine, indicating complementation of the yeast pathway by the full set of human proteins. While the strain with the neochromosome is indeed prototrophic, it grows slowly in the absence of adenine. Dissection of the phenotype revealed that the human ortholog ofADE4, PPAT, shows only partial complementation. We have used several strategies to understand this phenotype, that point toPPAT/ADE4as the central regulatory node. Pathway metabolites are responsible for regulatingPPAT’sprotein abundance through transcription and proteolysis as well as its enzymatic activity by allosteric regulation in these yeast cells. Extensive phylogenetic analysis of PPATs from diverse organisms hints at adaptations of the enzyme-level regulation to the metabolite levels in the organism. Finally, we isolated specific mutations in PPAT as well as in other genes involved in the purine metabolic network that alleviate incomplete complementation byPPATand provide further insight into the complex regulation of this critical metabolic pathway.
Discrete anatomical coordinates for speech production and synthesis
Authors: Assaneo M Florencia , Butavand Daniela Ramirez , Trevisan Marcos A , Mindlin Gabriel B
Published: June 2017

The sounds of all languages are described by a finite set of symbols, which are extracted from the continuum of sounds produced by the vocal organ. How the discrete phonemic identity is encoded in the continuous movements producing speech remains an open question for the experimental phonology. In this work, this question is assessed by using Hall-effect transducers and magnets -mounted on the tongue, lips and jaw- to track the kinematics of the oral tract during the vocalization ofvowel-consonant-vowelstructures. Using athreshold strategy, the time traces of the transducers were converted into discrete motor coordinates unambiguously associated with the vocalized phonemes. Furthermore, the signals of the transducers combined with the discretization strategy were used to drive a low-dimensional vocal model capable of synthesizing intelligible speech. The current work not only addressed a relevant inquiry of the biology of language, but also shows the performance of the experimental technique to monitor the displacement of the main articulators of the vocal tract while speaking. This novel electronic device represents an economic and portable option to the standard system used to study the vocal tract movements.
Phytoplankton functional types: a trait perspective
Authors: Irwin Andrew J , Finkel Zoe V
Published: June 2017

Phytoplankton functional types are groupings of many species into a smaller number of types according to their ecological or biogeochemical role. Models describe phytoplankton functional types by a set of traits that determine their growth rates or fitness. Traits for functional types are often determined from observations on a small number of species under laboratory conditions. Functional types can be composed of a large number of species with very different trait values, so the representation of a type by an average trait value may not be appropriate. A potential solution is to estimate trait values from observations of the aggregate biomass of phytoplankton functional types in natural populations. We report on some recent efforts to extract trait values from time-series data using Bayesian statistical models and discuss some challenges of this approach.
Transfer entropy as a tool for inferring causality from observational studies in epidemiology
Authors: Aziz N. Ahmad
Published: June 2017

Recently Wiener’s causality theorem, which states that one variable could be regarded as the cause of another if the ability to predict the future of the second variable is enhanced by implementing information about the preceding values of the first variable, was linked to information theory through the development of a novel metric called ‘transfer entropy’. Intuitively, transfer entropy can be conceptualized as a model-free measure of directed information flow from one variable to another. In contrast, directionality of information flow is not reflected in traditional measures of association which are completely symmetric by design. Although information theoretic approaches have been applied before in epidemiology, their value for inferring causality from observational studies is still unknown. Therefore, in the present study we use a set of simulation experiments, reflecting the most classical and widely used epidemiological observational study design, to validate the application of transfer entropy in epidemiological research. Moreover, we illustrate the practical applicability of this information theoretic approach to ‘real-world’ epidemiological data by demonstrating that transfer entropy is able to extract the correct direction of information flow from longitudinal data concerning two well-known associations, i.e. that between smoking and lung cancer and that between obesity and diabetes risk. In conclusion, our results provide proof-of-concept that the recently developed transfer entropy method could be a welcome addition to the epidemiological armamentarium, especially to dissect those situations in which there is a well-described association between two variables but no clear-cut inclination as to the directionality of the association.
Mutational sequencing for accurate count and long-range assembly
Authors: Kumar Vijay , Rosenbaum Julie , Wang Zihua , Forcier Talitha , Ronemus Michael , Wigler Michael , Levy Dan
Published: June 2017

We introduce a new protocol, mutational sequencing or muSeq, which randomly deaminates unmethylated cytosines at a fixed and tunable rate. The muSeq protocol marks each initial template molecule with a unique mutation signature that is present in every copy of the template, and in every fragmented copy of a copy. In the sequenced read data, this signature is observed as a unique pattern of C-to-T or G-to-A nucleotide conversions. Clustering reads with the same conversion pattern enables accurate count and long-range assembly of initial template molecules from short-read sequence data. We explore count and low-error sequencing by profiling a 135,000 fragment PstI representation, demonstrating that muSeq improves copy number inference and significantly reduces sporadic sequencer error. We explore long-range assembly in the context of cDNA, generating contiguous transcript clusters greater than 3,000 bp in length. The muSeq assemblies reveal transcriptional diversity not observable from short-read data alone.
Unintended Consequences and the Paradox of Control: Management of Emerging Pathogens with Age-Specific Virulence
Authors: Carran Spencer , Ferrari Matthew , Reluga Timothy
Published: June 2017

We project the long term incidence of Zika virus disease (ZVD) under varying hazards of infection and consider how the age-distribution of disease burden varies between these scenarios. Pathogens with age-structured disease outcomes, such as rubella and Zika virus, require that management decisions consider their impact not only on total disease incidence but also on distribution of disease burden within a population. In some cases, reductions of overall transmission can have the paradoxical effect of increasing the incidence of severe disease despite decreasing the total incidence. This happens because of corresponding increases in the average age of infection. Beginning with the current population structure and demographic rates of Brazil, we project forward total ZVD burden as measured by cases occurring in pregnant women and document the scenarios under which a paradox of control for Zika management emerges. We conclude that while a paradox of control can occur for ZVD, the higher total costs from increasing the average age of infection will only be realized after several decades and vanish under conservative discounting of future costs. This indicates that managers faced with an emerging pathogen should prioritize current disease incidence over potential increases in severe disease outcomes in the endemic state.

Author Summary

The intuitive response to an emerging outbreak is to halt, or at least reduce, transmission. However, in some circumstances, reducing overall transmission and incidence may be counterproductive from a public health perspective as public health interventions affect both the total level and the distribution of disease burden. We consider the scenarios under which reducing transmission of an emerging pathogen such as Zika virus may increase the costs associated with disease in the most vulnerable segments of the population - in this case, reproductive-age women. We conclude that after applying standard discounting rates to future cases, the “paradox of control” vanishes and reducing hazard of infection uniformly reduces the total costs associated with severe disease.
The polyploid state plays a tumor suppressive role in the liver
Authors: Zhang Shuyuan , Zhou Keijin , Luo Xin , Li Lin , Nguyen Liem , Zhang Yu , Tarlow Branden , Siegwart Daniel , Zhu Hao
Published: June 2017

Most cells in the liver are polyploid, but the functional role of polyploidy is unknown. Polyploidization normally occurs through cytokinesis failure and endoreduplication around the time of weaning. To interrogate the function of polyploidy while avoiding irreversible manipulations of essential cell cycle genes, we developed multiple orthogonal mouse models to transiently and potently alter liver ploidy. Premature weaning, as well as in vivo knockdown ofE2f8orAnln, allowed us to toggle between diploid and polyploid states. While there was no impact of ploidy alterations on liver function, metabolism, or regeneration, hyperpolyploid mice suppressed and hyperdiploid mice accelerated tumorigenesis in mutagen and high fat induced models. Mechanistically, the diploid state was more susceptible to Cas9-mediated tumor suppressor loss but was similarly susceptible toMYConcogene activation, indicating that ploidy differentially protected the liver from distinct genomic aberrations. Our work suggests that polyploidy evolved to prevent malignant outcomes of liver injury.
LIONS: Analysis Suite for Detecting and Quantifying Transposable Element Initiated Transcription from RNA-seq
Authors: Babaian Artem , Thompson Richard , Lever Jake , Gagnier Liane , Karimi Mohammad M. , Mager Dixie L.
Published: June 2017

Transposable Elements (TEs) influence the evolution of novel transcriptional networks yet the specific and meaningful interpretation of how TE-initiation events contribute to the transcriptome has been marred by computational and methodological deficiencies. We developedLIONSfor the analysis of paired-end RNA-seq data to specifically detect and quantify TE-initiated transcripts.

Availability

Source code, container, test data and instruction manual are freely available atwww.github.com/ababaian/LIONS.

Contact

ababaian@bccrc.caormahdi.karimi@lms.mrc.ac.ukordmager@bccrc.ca.

Supplementary information

Supplementary data are available at Bioinformatics online.
Simultaneous spike-time locking to multiple frequencies
Authors: Sinz Fabian H. , Sachgau Carolin , Henninger Jörg , Benda Jan , Grewe Jan
Published: June 2017

Phase locking of neural firing is ubiquitously observed in the brain and occurs when neurons fire at a particular phase of a periodic signal. Here we study in detail how spikes of single neurons can simultaneously lock to multiple distinct frequencies at the example of p-type electroreceptor afferents in the electrosensory system of the Gymnotiform weakly electric fishApteronotus leptorhynchus. We identify key elements for multiple frequency locking, study its determining factors and limits, and provide concise mathematical models reproducing our main findings. Our findings provide another example how rate and temporal codes can coexist and complement each other in single neurons, and demonstrate that sensory coding in p-type electroreceptor afferents provides a much richer representation of the sensory environment than commonly assumed. Since the underlying mechanisms are not specific to the electrosensory system, our results could provide the basis for studying multiple-frequency locking in other systems.
Neural stem cells induce the formation of their physical niche during organogenesis
Authors: Seleit Ali , Krämer Isabel , Riebesehl Bea , Ambrosio Elizabeth M. , Stolper Julian S. , Dross Nicolas , Lischik Colin Q. , Centanin Lazaro
Published: June 2017

Most organs rely on stem cells to maintain homeostasis during post-embryonic life. Typically, stem cells of independent lineages work coordinately within mature organs to ensure proper ratios of cell types. Little is known, however, on how these different stem cells locate to forming organs during development. Here we show that neuromasts of the posterior lateral line in medaka are composed of two independent life-long lineages with different embryonic origins. Clonal analysis and 4D imaging revealed a hierarchical organisation with instructing and responding roles: an inner, neural lineage induces the formation of an outer, border cell lineage (nBC) from the skin epithelium. Our results demonstrate that the neural lineage is necessary and sufficient to generate nBCs highlighting self-organisation principles at the level of the entire embryo. We hypothesise that transformation of surrounding tissues plays a major role during the establishment of vertebrate stem cell niches.
Stability-based sorting: The forgotten process behind (not only) biological evolution
Authors: Flegr Jaroslav , Toman Jan
Published: June 2017

Natural selection is considered to be the main process that drives biological evolution. It requires selected entities to originate dependent upon one another by the means of reproduction or copying, and for the progeny to inherit the qualities of their ancestors. However, natural selection is a manifestation of a more generalpersistence principle, whose temporal consequences we propose to name “stability-based sorting” (SBS). Sorting based onstatic stability, i.e., SBS in its strict sense and usual conception, favours characters that increase the persistence of their holders and act on all material and immaterial entities. Sorted entities could originate independently from each other, are not required to propagate and need not exhibit heredity. Natural selection is a specific form of SBS—sorting based ondynamic stability. It requires some form of heredity and is based on competition for the largest difference between the speed of generating its own copies and their expiration. SBS in its strict sense and selection thus have markedly different evolutionary consequences that are stressed in this paper. In contrast to selection, which is opportunistic, SBS is able to accumulate even momentarily detrimental characters that are advantageous for the long-term persistence of sorted entities. However, it lacks the amplification effect based on the preferential propagation of holders of advantageous characters. Thus, it works slower than selection and normally is unable to create complex adaptations. From a long-term perspective, SBS is a decisive force in evolution—especially macroevolution. SBS offers a new explanation for numerous evolutionary phenomena, including broad distribution and persistence of sexuality, altruistic behaviour, horizontal gene transfer, patterns of evolutionary stasis, planetary homeostasis, increasing ecosystem resistance to disturbances, and the universal decline of disparity in the evolution of metazoan lineages. SBS acts on all levels in all biotic and abiotic systems. It could be the only truly universal evolutionary process, and an explanatory framework based on SBS could provide new insight into the evolution of complex abiotic and biotic systems.
Inferring synteny between genome assemblies: a systematic evaluation
Authors: Liu Dang , Hunt Martin , Tsai Isheng. J.
Published: June 2017

Identification of synteny between genomes of closely related species is an important aspect of comparative genomics. However, it is unknown to what extent draft assemblies lead to errors in such analysis. To investigate this, we fragmented genome assemblies of model nematodes to various extents and conducted synteny identification and downstream analysis. We first show that synteny between species can be underestimated up to 40% and find disagreements between popular tools that infer synteny blocks. This inconsistency and further demonstration of erroneous gene ontology enrichment tests throws into question the robustness of previous synteny analysis when gold standard genome sequences remain limited. In addition, determining the true evolutionary relationship is compromised by assembly improvement using a reference guided approach with a closely related species. Annotation quality, however, has minimal effect on synteny if the assembled genome is highly contiguous. Our results highlight the need for gold standard genome assemblies for synteny identification and accurate downstream analysis.

Author summary

Genome assemblies across all domains of life are currently produced routinely. Initial analysis of any new genome usually includes annotation and comparative genomics. Synteny provides a framework in which conservation of homologous genes and gene order is identified between genomes of different species. The availability of human and mouse genomes paved the way for algorithm development in large-scale synteny mapping, which eventually became an integral part of comparative genomics. Synteny analysis is regularly performed on assembled sequences that are fragmented, neglecting the fact that most methods were developed using complete genomes. Here, we systematically evaluate this interplay by inferring synteny in genome assemblies with different degrees of contiguation. As expected, our investigation reveals that assembly quality can drastically affect synteny analysis, from the initial synteny identification to downstream analysis. Importantly, we found that improving a fragmented assembly using synteny with the genome of a related species can be dangerous, as thisa prioriassumes a potentially false evolutionary relationship between the species. The results presented here re-emphasize the importance of gold standard genomes to the science community, and should be achieved given the current progress in sequencing technology.
Kin competition accelerates experimental range expansion in an arthropod herbivore
Authors: Van Petegem Katrien , Moerman Felix , Dahirel Maxime , Fronhofer Emanuel A. , Vandegehuchte Martijn L. , Van Leeuwen Thomas , Wybouw Nicky , Stoks Robby , Bonte Dries
Published: June 2017

With ongoing global change, life is continuously forced to move to novel areas, which leads to dynamically changing species ranges. As dispersal is central to range dynamics, factors promoting fast and distant dispersal are key to understanding and predicting species ranges. During range expansions, genetic variation is depleted at the expanding front. Such conditions should reduce evolutionary potential, while increasing kin competition. Organisms able to recognise relatives may be able to assess increased levels of relatedness at expanding range margins and to increase their dispersal in a plastic manner. Using individual-based simulations and experimental range expansions of a spider mite, we demonstrate that plastic responses to kin structure can be at least as important as evolution in driving range expansion speed. Because recognition of kin or kind is increasingly documented across the tree of life, we anticipate it to be a highly important but neglected driver of range expansions.
Bayesian Comparison of Explicit and Implicit Causal Inference Strategies in Multisensory Heading Perception
Authors: Acerbi Luigi , Dokka Kalpana , Angelaki Dora E. , Ma Wei Ji
Published: June 2017

The precision of multisensory heading perception improves when visual and vestibular cues arising from the same cause, namely motion of the observer through a stationary environment, are integrated. Thus, in order to determine how the cues should be processed, the brain must infer the causal relationship underlying the multisensory cues. In heading perception, however, it is unclear whether observers follow the Bayesian strategy, a simpler non-Bayesian heuristic, or even perform causal inference at all. We developed an efficient and robust computational framework to perform Bayesian model comparison of causal inference strategies, which incorporates a number of alternative assumptions about the observers. With this framework, we investigated whether human observers’ performance in anexplicitcause attribution and animplicitheading discrimination task can be modeled as a causal inference process. In the explicit inference task, all subjects accounted for cue disparity when reporting judgments of common cause, although not necessarily all in a Bayesian fashion. By contrast, but in agreement with previous findings, data from the heading discrimination task only could not rule out that several of the same observers were adopting a forced-fusion strategy, whereby cues are integrated regardless of disparity. Only when we combined evidence from both tasks we were able to rule out forced-fusion in the heading discrimination task. Crucially, findings were robust across a number of variants of models and analyses. Our results demonstrate that our proposed computational framework allows researchers to ask complex questions within a rigorous Bayesian framework that accounts for parameter and model uncertainty.
Underwater hyperspectral classification of deep sea corals exposed to 2-methylnaphthalene
Authors: Letnes Paul Anton , Hansen Ingrid Myrnes , Sandvik Aas Lars Martin , Eide Ingvar , Pettersen Ragnhild , Tassara Luca , Receveur Justine , Floch Stephane le , Guyomarch Julien , Camus Lionel , Bytingsvik Jenny
Published: June 2017

Coral reefs around the world are under threat due to anthropogenic impacts on the environment. It is therefore important to develop methods to monitor the status of the reefs and detect changes in the health condition of the corals at an early stage before severe damage occur. In this work, we evaluate underwater hyperspectral imaging as a method to detect changes in health status of both orange and white color morphs of the coral speciesLophelia pertusa.

Differing health status was achieved by exposing 66 coral samples to the toxic compound 2-methylnaphthalene in concentrations of 0 mg L−1to 3.5 mg L−1. A machine learning model was utilized to classify corals according to lethal concentration (LC) levels LC5 (5 % mortality) and LC25 (25 % mortality), solely based on their reflectance spectra. All coral samples were classified to correct concentration group. This is a first step towards developing a remote sensing technique able to assess environmental impact on deep-water coral habitats over larger areas.
Parent of Origin Effects on Quantitative Phenotypes in a Founder Population
Authors: Mozaffari Sahar V. , DeCara Jeanne M. , Shah Sanjiv J. , Lang Roberto M. , Nicolae Dan L. , Ober Carole
Published: June 2017

The impact of the parental origin of associated alleles in GWAS has been largely ignored. Yet sequence variants could affect traits differently depending on whether they are inherited from the mother or the father. To explore this possibility, we studied 21 quantitative phenotypes in a large Hutterite pedigree. We first identified variants with significant single parent (maternal-only or paternal-only) effects, and then used a novel statistical model to identify variants with opposite parental effects. Overall, we identified parent of origin effects (POEs) on 11 phenotypes, most of which are risk factors for cardiovascular disease. Many of the loci with POEs have features of imprinted regions and many of the variants with POE are associated with the expression of nearby genes. Overall, our results indicate that POEs, which are often opposite in direction, are relatively common in humans, have potentially important clinical effects, and will be missed in traditional GWAS.
Imputation-Based Genomic Coverage Assessments of Current Genotyping Arrays:Illumina HumanCore, OmniExpress, Multi-Ethnic global array and sub-arrays, Global Screening Array, Omni2.5M, Omni5M, and Affymetrix UK Biobank
Authors: Nelson Sarah C. , Romm Jane M. , Doheny Kimberly F. , Pugh Elizabeth W. , Laurie Cathy C.
Published: June 2017

Genotyping arrays have been widely adopted as an efficient means to interrogate variation across the human genome. Genetic variants may be observed either directly, via genotyping, or indirectly, through linkage disequilibrium with a genotyped variant. The total proportion of genomic variation captured by an array, either directly or indirectly, is referred to as “genomic coverage.” Here we use genotype imputation and Phase 3 of the 1000 Genomes Project to assess genomic coverage of several modern genotyping arrays. We find that in general, coverage increases with increasing array density. However, arrays designed to cover specific populations may yield better coverage in those populations compared to denser arrays not tailored to the given population. Ultimately, array choice involves trade-offs between cost, density, and coverage, and our work helps inform investigators weighing these choices and trade-offs.
Evolution and genetics of precocious burrowing behavior inPeromyscusmice
Authors: Metz Hillery C. , Bedford Nicole L. , Pan Linda , Hoekstra Hopi E.
Published: June 2017

A central challenge in biology is to understand how innate behaviors evolve between closely related species. One way to elucidate how differences arise is to compare the development of behavior in species with distinct adult traits. Here, we report thatPeromyscus polionotusis strikingly precocious with regard to burrowing behavior, but not other behaviors, compared to its sister speciesP. maniculatus. InP. polionotus, burrows were excavated as early as 17 days of age, whileP. maniculatusdid not build burrows until 10 days later. Moreover, the well-known differences in burrow architecture between adults of these species—P. polionotusadults excavate long burrows with an escape tunnel, whileP. maniculatusdig short, single-tunnel burrows—were intact in juvenile burrowers. To test whether this juvenile behavior is influenced by early-life environment, pups of both species were reciprocally cross-fostered. Fostering did not alter the characteristic burrowing behavior of either species, suggesting these differences are genetic. In backcross F2hybrids, we show that precocious burrowing and adult tunnel length are genetically correlated, and that a singleP. polionotusallele in a genomic region linked to adult tunnel length is predictive of precocious burrow construction. The co-inheritance of developmental and adult traits indicates the same genetic region—either a single gene with pleiotropic effects, or closely linked genes— acts on distinct aspects of the same behavior across life stages. Such genetic variants likely affect behavioral drive (i.e. motivation) to burrow, and thereby affect both the development and adult expression of burrowing behavior.

Highlights

JuvenileP. polionotusconstruct burrows precociously compared to its sister speciesP. maniculatus

Cross-fostering does not alter species-specific burrowing behavior

A QTL linked to adult tunnel length predicts developmental onset of burrow construction in hybrids

Pleiotropic genetic variant(s) may affect behavioral drive across life stages
Protective radiolucent aluminium oxide coatings for beryllium X-ray optics
Authors: Yurkevich Oksana , Maksimova Ksenia , Goikhman Alexander , Grunin Alexey , Prokopovich Pavel , Tyurin Alexander , Medvedskaya Polina , Lyatun Ivan , Snigireva Irina , Snigirev Anatoly
Published: June 2017

Beryllium, being one of the most transparent materials to X-ray radiation, has become the material of choice for X-ray optics instrumentation at synchrotron radiation sources and free-electron laser facilities. However, there are concerns due to its high toxicity and, consequently, there is a need for special safety regulations. The authors propose to apply protective coatings in order to seal off beryllium from the ambient atmosphere, thus preventing degradation processes providing additional protection for users and prolonging the service time of the optical elements. This paper presents durability test results for Be windows coated with atomic-layer-deposition alumina layers run at the European Synchrotron Radiation Facility. Expositions were performed under monochromatic, pink and white beams, establishing conditions that the samples could tolerate without radiation damage. X-ray treatment was implemented in various environments, i.e. vacuum, helium, nitrogen, argon and dry air at different pressures. Post-process analysis revealed their efficiency for monochromatic and pink beams.
11-[Bis(trimethylsilyl)amino]-2,4-bis(trimethylsilyl)-7,8,9,10-tetrahydro-6H-cyclohepta[1,2-b]quinoline
Authors: Çelik Ísmail , Akkurt Mehmet , Ekiz Makbule , Tutar Ahmet , Ökten Salih , Ersanlı Cem Cüneyt
Published: June 2017

In the title compound, C26H48N2Si4, the cycloheptane ring adopts a chair conformation, while the quinolinyl ring system is almost planar [maximum deviation = 0.040 (3) Å for one of the C atoms carrying a Me3Si group]. In the crystal, in the absence of classical hydrogen bonding, the packing is dominated by van der Waals forces. One of the N-bound trimethylsilyl groups is disordered by rotation about the C—SiMe3bond, and was modelled over two sets of sites in the ratio 0.873 (8):0.127 (8).
An alternative model of pre-hospital care for 999 patients who require non-emergency medical assistance
Authors: Blodgett Joanna M. , Robertson Duncan , Ratcliffe David , Rockwood Kenneth
Published: June 2017

Purpose

With the increasing demand on ambulance services, paramedics are tasked to arrange as much out of hospital care as possible, to develop integrated systems of care and work with hundreds of different providers – all in the 15 minutes allocated for assessment. A UK ambulance trust is navigating and leading much of this work as one of the first trusts to implement a general practitioner referral policy as an alternate to direct conveyance. The paper aims to discuss this issue.

Design/methodology/approach

Here the authors discuss the referral scheme, examine the limited evidence available and discuss what is needed to influence prospective success of implementing this scheme in other trusts.

Findings

Limited evidence for these schemes are described, however there is a clear gap in critical appraisal and methodologically rigorous evidence needed to implement these schemes in other ambulance schemes.

Originality/value

In order to facilitate collaboration of healthcare services and to minimize the burden of increasing numbers of patients, communication and discussion of alternate routes of care is crucial. This viewpoint piece is one of the first to emphasize the potential benefits of such schemes.
An exploration of violence against paramedics, burnout and post-traumatic symptoms in two Australian ambulance services
Authors: Wongtongkam Nualnong
Published: June 2017

Purpose

Violence directed at ambulance paramedics has attracted increasing public attention because of its major negative impact on the physical and psychological well-being of victims and productivity of organisations. The purpose of this paper is to explore the prevalence of violent incidents, contributing factors, burnout and post-traumatic symptoms among paramedics.

Design/methodology/approach

A cross-sectional survey was distributed in two ambulance services in Tasmania and South Australia, with self-administered instruments completed online. In total, 48 respondents completed questionnaires.

Findings

There were no significant differences between sites in timing of violent incidents, consequences of traumatic events or organisation provision. Surprisingly, over 90 per cent of paramedics had not been pushed, slapped, beaten, scratched or spat on in the previous month. There was a statistically significant difference between genders for being yelled at or verbally abused (p=0.02). When considering burnout, female paramedics showed significantly higher levels of emotional exhaustion t(37)=–2.32, p=0.02 and lower levels of career satisfaction than their male counterparts, t(37)=3.32, p=0.00.

Originality/value

Although prevalence rates of violent incidents seemed lower than expected, policy interventions to encourage female paramedics to display their professional identities and steps to enhance well-being and safety while on duty should be considered.
Effects of different temperature regimes on survival of Diaphorina citri and its endosymbiotic bacterial communities
Authors: Hussain Mubasher , Akutse Komivi Senyo , Ravindran Keppanan , Lin Yongwen , Bamisile Bamisope Steve , Qasim Muhammad , Dash Chandra Kanta , Wang Liande
Published: June 2017

The Asian citrus psyllid, Diaphorina citri, is a major pest of citrus and vector of citrus greening (huanglongbing) in Asian. In our field‐collected psyllid samples, we discovered that Fuzhou (China) and Faisalabad (Pakistan), populations harbored an obligate primary endosymbiont Candidatus Carsonella (gen. nov.) with a single species, Candidatus Carsonella ruddii (sp. nov.) and a secondary endosymbiont, Wolbachia surface proteins (WSP) which are intracellular endosymbionts residing in the bacteriomes. Responses of these symbionts to different temperatures were examined and their host survival assessed. Diagnostic PCR assays showed that the endosymbionts infection rates were not significantly reduced in both D. citri populations after 24 h exposure to cold or heat treatments. Although quantitative PCR assays showed significant reduction of WSP relative densities at 40°C for 24 h, a substantial decrease occurred as the exposure duration increased beyond 3 days. Under the same temperature regimes, Ca. C. ruddii density was initially less affected during the first exposure day, but rapidly reduced at 3–5 days compared to WSP. However, the mortality of the psyllids increased rapidly as exposure time to heat treatment increased. The responses of the two symbionts to unfavorable temperature regimes highlight the complex host‐symbionts interactions between D. citri and its associated endosymbionts.
Grazing of leaf‐associated Cercomonads (Protists: Rhizaria: Cercozoa) structures bacterial community composition and function
Authors: Flues Sebastian , Bass David , Bonkowski Michael
Published: June 2017

Preferential food selection in protists is well documented, but we still lack basic understanding on how protist predation modifies the taxonomic and functional composition of bacterial communities. We conducted feeding trials using leaf‐associated cercomonad Cercozoa by incubating them on a standardized, diverse bacterial community washed from plant leaves. We used a shotgun metagenomics approach to investigate the taxonomic and functional changes of the bacterial community after five days protist predation on bacteria. Predation‐induced shifts in bacterial community composition could be linked to phenotypic protist traits. Protist reproduction rate, morphological plasticity and cell speed were most important in determining bacterial community composition. Analyses of co‐occurrence patterns showed less complex correlations between bacterial taxa in the protist‐grazed treatments with a higher proportion of positive correlations than in non‐grazed controls, suggesting that predation reduced the influence of strong competitors. Protist predation influenced 14 metabolic core functions including membrane transport from which type VI secretion systems were in particular upregulated. In view of the functional importance of bacterial communities in the phyllosphere and rhizosphere of plants, a more detailed understanding of predator‐prey interactions, changes in microbial composition and function, and subsequent repercussions on plant performance are clearly required.