bluuebunny/crossref_metadata_2025 huggingface dataset:
A survey to profile conference interpreting practice in China
Authors: Han Chao
Published: October 2016

This report presents findings from an online survey of 140 English/Chinese conference interpreters, conducted as a follow-up of an exploratory diary study (Han 2015), to provide a detailed account of real-life interpreting practice in China. Three main tendencies are identified: a) conference-related materials (mainly programmes and speakers’ scripts/notes) are often received late, leaving little preparation time; b) interpreters do a much wider variety of simultaneous interpreting tasks than previously thought, albeit with varying degrees of frequency; c) difficulties are felt to arise mainly from technical subject matter and terminology, speakers’ delivery (strong accent, speed), and lack of preparation. These findings largely support the diary study results and previous scholarly descriptions.
Metacognition and cognitive control: behavioural adaptation requires conflict experience
Authors: Questienne Laurence , Van Opstal Filip , van Dijck Jean-Philippe , Gevers Wim
Published: October 2016

Cognitive control allows adapting our behaviour to improve performance. A behavioural signature of cognitive control is the Gratton effect. This effect is observed in conflict tasks and indicates smaller congruency effects after incongruent trials than after congruent trials. Metacognitive experience may play a role in this effect: When participants introspect on their conflict experience, the Gratton effect follows the conflict introspection instead of the stimulus congruency. However this Gratton effect could also be triggered by the labelling that the introspective method implies and/or by a misperception of the stimulus conflict. The current study investigated whether the experiential component of the introspection is necessary to trigger cognitive control or whether labelling a trial as conflicting or not can be sufficient. In a priming task, Gratton effects following metacognitive conflict experience and conflict label were contrasted. Replicating earlier reports, results showed that the metacognitive experience of conflict can trigger a Gratton effect. However a conflict label, either generated by the participants themselves or presented to the participants via feedback was not able to induce cognitive control. Results are discussed in light of current theories of cognitive control.
INTEGRATE-neo: a pipeline for personalized gene fusion neoantigen discovery
Authors: Zhang Jin , Mardis Elaine R , Maher Christopher A
Published: October 2016

Motivation

While high-throughput sequencing (HTS) has been used successfully to discover tumor-specific mutant peptides (neoantigens) from somatic missense mutations, the field currently lacks a method for identifying which gene fusions may generate neoantigens.

Results

We demonstrate the application of our gene fusion neoantigen discovery pipeline, called INTEGRATE-Neo, by identifying gene fusions in prostate cancers that may produce neoantigens.

Availability and Implementation

INTEGRATE-Neo is implemented in C ++ and Python. Full source code and installation instructions are freely available from https://github.com/ChrisMaherLab/INTEGRATE-Neo.

Supplementary information

Supplementary data are available at Bioinformatics online.
Effects of elevated pCO2 on crab survival and exoskeleton composition depend on shell function and species distribution: a comparative analysis of carapace and claw mineralogy across four porcelain crab species from different habitats
Authors: Page Tessa M. , Worthington Samantha , Calosi Piero , Stillman Jonathon H.
Published: October 2016

Elevated concentration of carbon dioxide (elevated pCO2) that cause reduced pH is known to influence calcification in many marine taxa, but how elevated pCO2 influences cation composition of mineralized structures is less well studied. To a large extent, the degree to which elevated pCO2 impacts mineralized structures is influenced by physiological adaptation of organisms to environments where low pH is routinely experienced. Here, we test the hypotheses that elevated pCO2 will differently impact the relative concentrations of divalent cations (Ca2+, Mg2+, Sr2+, and Mn2+) in four closely related species of porcelain crabs distributed across intertidal zone gradients. Cation composition of carapace and claw exoskeleton was determined using inductively coupled plasma mass spectrometry following 24-day exposures to pH/pCO2 levels of 8.0/418 and 7.4/1850 µatm during the intermoult period. Reduced pH/elevated pCO2 caused a 13–24% decrease of carapace [Ca2+] across all species, and species-specific responses in carapace and claw [Mg2+], [Sr2+] and [Mn2+] were observed. During a 24-day exposure, reduced pH/elevated pCO2 reduced survival probability in low-intertidal but not mid-intertidal species. Overall, the effect of reduced pH/elevated pCO2 on exoskeleton mineral composition was muted in mid-intertidal species relative to low-intertidal species, indicating that extant adaptation to the variable intertidal zone may lessen the impact of ocean acidification (OA) on maintenance of mineralized structures. Differences in responses to reduced pH/elevated pCO2 among closely related species adds complexity to predictive inferences regarding the effects of OA.
An integrated view of fisheries: tunnelling between silos
Authors: Cochrane Kevern L.
Published: October 2016

Global recognition of the need for an ecosystem approach to fisheries and its subsequent formalization in the 1990s and 2000s were, to me, natural and necessary developments that put a name and a clearer form to an approach that I have been pursuing throughout my career. During that progression, I have drifted from fisheries ecology into stock assessment and provision of advice for marine fisheries management and on to a stimulating mix of geographical areas and fishery themes while working for the Food and Agricultural Organization in Rome, with some detours along the way. My work has focused on supporting the application of scientific knowledge in fisheries and has broadly followed three themes: environmental influences on fish productivity, fisheries management and governance, and the role of politics and policy in fisheries. This paper reviews work on each of those themes and presents some conclusions that I have come to on the challenges and obstacles to sustainable and responsible fisheries. The more difficult of these challenges centre on conflicts between social and economic goals and the long-term need for sustainability. Unsurprisingly, I have not found any simple solutions for them, and hold the view that we can only achieve a sustainable and equitable future if we look at the big picture and address the fundamental causes of these problems.
Discovery of a 0.42-s pulsar in the ultraluminous X-ray source NGC 7793 P13
Authors: Israel G. L. , Papitto A. , Esposito P. , Stella L. , Zampieri L. , Belfiore A. , Rodríguez Castillo G. A. , De Luca A. , Tiengo A. , Haberl F. , Greiner J. , Salvaterra R. , Sandrelli S. , Lisini G.
Published: October 2016

NGC 7793 P13 is a variable (luminosity range ∼100) ultraluminous X-ray source proposed to host a stellar-mass black hole of less than 15 M⊙ in a binary system with orbital period of 64 d and a 18–23 M⊙ B9Ia companion. Within the EXTraS (Exploring the X-ray Transient and variable Sky) project, we discovered pulsations at a period of ∼0.42 s in two XMM–Newton observations of NGC 7793 P13, during which the source was detected at LX ∼ 2.1 × 1039 and 5 × 1039 erg s−1 (0.3–10 keV band). These findings unambiguously demonstrate that the compact object in NGC 7793 P13 is a neutron star accreting at super-Eddington rates. While standard accretion models face difficulties accounting for the pulsar X-ray luminosity, the presence of a multipolar magnetic field with B ∼ few × 1013 G close to the base of the accretion column appears to be in agreement with the properties of the system.
A Revised Host Galaxy Association for GRB 020819B: A High-Redshift Dusty Starburst, Not a Low-Redshift Gas-Poor Spiral
Authors: Perley Daniel A. , Krühler Thomas , Schady Patricia , Michałowski Michał J. , Thöne Christina C. , Petry Dirk , Graham John F. , Greiner Jochen , Klose Sylvio , Schulze Steve , Kim Sam
Published: October 2016

The purported spiral host galaxy of GRB 020819B at z = 0.41 has been seminal in establishing our view of the diversity of long-duration gamma-ray burst environments: optical spectroscopy of this host provided evidence that GRBs can form even at high metallicities, while millimetric observations suggested that GRBs may preferentially form in regions with minimal molecular gas. We report new observations from VLT (MUSE and X-shooter) which demonstrate that the purported host is an unrelated foreground galaxy. The probable radio afterglow is coincident with a compact, highly star-forming, dusty galaxy at z = 1.9621. The revised redshift naturally explains the apparent nondetection of CO(3-2) line emission at the afterglow site from ALMA. There is no evidence that molecular gas properties in GRB host galaxies are unusual, and limited evidence that GRBs can form readily at super-Solar metallicity.
Testing the Interpersonal Theory of Suicide in Chronic Pain
Authors: Wilson Keith G. , Heenan Adam , Kowal John , Henderson Peter R. , McWilliams Lachlan A. , Castillo Dyana
Published: October 2016

Objective:

The interpersonal theory of suicide offers a conceptual framework for understanding suicidal ideation (SI) that may be applicable to individuals with chronic pain. The theory emphasizes the importance of 2 interpersonal constructs as precursors to SI: perceived burdensomeness (the belief that one has become a burden to others) and thwarted belongingness (a lack of social integration or connection). Our objective was to test the interpersonal theory of suicide in people with chronic pain.

Methods:

Hierarchical regression analysis was used in a cross-sectional study of 282 patients of an interdisciplinary pain clinic. The Beck Scale for Suicide Ideation was the criterion measure of SI, and independent variables included both general and pain-specific predictors.

Results:

After adjusting for other known or putative risk factors related to pain and mental health, perceived burdensomeness significantly predicted SI, whereas thwarted belongingness did not. As expected according to theory, the interaction between perceived burdensomeness and thwarted belongingness was also significant; perceived burdensomeness was a strong predictor of SI at high levels of thwarted belongingness, but only marginally at low levels. Other independent predictors were male sex, number of prior suicide attempts, and hopelessness.

Discussion:

These findings are in line with some, but not all, of the major predictions of the interpersonal theory of suicide. In general, however, they support the relevance of the theory for individuals with chronic pain.
A Randomized Trial of Palliative Care Discussions Linked to an Automated Early Warning System Alert
Authors: Picker David , Dans Maria , Heard Kevin , Bailey Thomas , Chen Yixin , Lu Chenyang , Kollef Marin H.
Published: October 2016

Objective:

To determine whether an Early Warning System could identify patients wishing to focus on palliative care measures.

Design:

Prospective, randomized, pilot study.

Setting:

Barnes-Jewish Hospital, Saint Louis, MO (January 15, 2015, to December 12, 2015).

Patients:

A total of 206 patients; 89 intervention (43.2%) and 117 controls (56.8%).

Interventions:

Palliative care in high-risk patients targeted by an Early Warning System.

Measurements and Main Results:

Advanced directive documentation was significantly greater prior to discharge in the intervention group (37.1% vs 15.4%; p < 0.001) as were first-time requests for advanced directive documentation (14.6% vs 0.0%; p < 0.001). Documentation of resuscitation status was also greater prior to discharge in the intervention group (36.0% vs 23.1%; p = 0.043). There was no difference in the number of patients requesting a change in resuscitation status between groups (11.2% vs 9.4%; p = 0.666). However, changes in resuscitation status occurred earlier and on the general medicine units for the intervention group compared to the control group. The number of patients transferred to an ICU was significantly lower for intervention patients (12.4% vs 27.4%; p = 0.009). The median (interquartile range) ICU length of stay was significantly less for the intervention group (0 [0–0] vs 0 [0–1] d; p = 0.014). Hospital mortality was similar (12.4% vs 10.3%; p = 0.635).

Conclusions:

This study suggests that automated Early Warning System alerts can identify patients potentially benefitting from directed palliative care discussions and reduce the number of ICU transfers.
Transcanalicular Laser-Assisted Dacryocystorhinostomy With Endonasal Augmentation in Primary Nasolacrimal Duct Obstruction: Our Experience
Authors: Goel Ruchi , Nagpal Smriti , Kumar Sushil , Meher Ravi , Kamal Saurabh , Garg Sonam
Published: October 2016

Purpose:

To evaluate and compare the success rate of transcanalicular laser-assisted dacryocystorhinostomy with endonasal augmentation, with and without intubation, in patients suffering from primary acquired nasolacrimal duct obstruction, at 1 year of follow up.

Methods:

A prospective, randomized interventional pilot study was conducted at a tertiary care center, in accordance with the guidelines of Declaration of Helsinki. Sixty eyes of 60 adult patients with primary acquired nasolacrimal duct obstruction were included. The participants were divided randomly into 2 equal groups (A and B-without and with bicanalicular intubation, respectively). An osteotomy was first created using 980 nm diode laser (set at 8W continuous mode) transcanalicularly and then enlarged intranasally using Blakesley’s nasal forceps, followed by bicanalicular silicon intubation in group B patients. The tubes were removed at the end of 8 weeks. The ostium size was assessed endoscopically at 8 weeks and again at the end of follow up, at 1 year. A successful outcome was defined in terms of ostium patency at the end of 1 year. The results were analyzed at the end of a follow up of 1 year, using various statistical tests (p < 0.05).

Results:

The mean age of the patients was 35.3 ± 15.89 years, with 23 male and 37 female patients, the 2 groups having a similar male:female ratio. An overall success rate of 90% was achieved at the end of 1 year with no statistically significant difference between the groups. Postoperative complications like tube displacement and punctal, canalicular injury were more in the intubated group. The average osteotomy size was 8.06 ± 5.4 mm2 at the end of 1 year.

Conclusions:

Transcanalicular laser-assisted dacryocysto rhinostomy, with endonasal augmentation, is a scarless, effective, daycare procedure, for treatment of primary acquired nasolacrimal duct obstruction with no additional advantage offered by silicone intubation.
A Case of Idiopathic Bilateral Hemolacria in an 11-Year-Old Girl
Authors: Sobol Ethan K. , Barmettler Anne
Published: October 2016

An 11-year-old healthy girl was noted to have intermittent, spontaneous, and bilateral hemolacria of 14 months’ duration. Examination and workup failed to identify an organic or psychogenic cause. The patient was expectantly managed with eventual spontaneous resolution. This report draws attention to this unusual and often concerning clinical entity. The case report is in compliance with the Health Insurance Portability and Accountability Act.
Non-Exenteration Management of Sino-Orbital Fungal Disease
Authors: Athavale Dnyaneshwar D. , Jones Robin , O’Donnell Brett A. , Forer Martin , Biggs Nigel
Published: October 2016

Purpose:

To describe the non-exenteration management of sino-orbital fungal infection, a life-threatening condition for which orbital exenteration is generally considered a first-line treatment.

Methods:

A retrospective case series is presented of 7 orbits in 6 consecutive patients admitted and treated at 2 major metropolitan tertiary teaching hospitals in Sydney, New South Wales, Australia.

Results:

Seven orbits in 6 consecutive patients with sino-orbital fungal infection were treated conservatively with surgical debridement and intravenous antifungal agents. Four patients were immunosuppressed and the other 2 patients were otherwise healthy. All presented with pain, proptosis, or loss of vision. Causative organisms found were Mucormycoses, Aspergillus, and Scedosporium prolificans. Exenteration was avoided in all patients as part of their planned management and 5 patients, including 1 with bilateral disease, survived their disease without exenteration. Medical treatment included intravenous liposomal amphotericin B or voriconazole. A single immunosuppressed patient deteriorated and as a last resort, exenteration was performed, but this made no difference to his clinical course and in retrospect could have been avoided as he died of multiple cerebral metastases diagnosed shortly after his deterioration.

Conclusion:

The authors recommend that patients with sino-orbital fungal disease preferably be treated conservatively, without orbital exenteration.
Epigenetic Mediators Between Childhood Socioeconomic Disadvantage and Mid-Life Body Mass Index: The New England Family Study
Authors: Loucks Eric B. , Huang Yen-Tsung , Agha Golareh , Chu Su , Eaton Charles B. , Gilman Stephen E. , Buka Stephen L. , Kelsey Karl T.
Published: October 2016

Objective

Childhood socioeconomic disadvantage is associated with adulthood obesity risk; however, epigenetic mechanisms are poorly understood. This work's objective was to evaluate whether associations of childhood socioeconomic disadvantage with adulthood body mass index (BMI) are mediated by DNA methylation.

Methods

Participants were 141 men and women from the New England Family Study, prospectively followed prenatally through a mean age of 47 years. Epigenomewide DNA methylation was evaluated in peripheral blood and adipose tissue obtained at adulthood, using the Infinium HumanMethylation450K BeadChip. Childhood socioeconomic status (SES) at age 7 years was assessed directly from parents' reports. Offspring adiposity was directly assessed using BMI at a mean age of 47 years. Associations of SES, DNA methylation, and BMI were estimated using least square estimators. Statistical mediation analyses were performed using joint significance test and bootstrapping.

Results

Of CpG sites significant at the 25% false discovery rate level in epigenomewide methylation BMI analyses, 91 sites in men and 71 sites in women were additionally significant for SES-methylation associations (p< .001) in adipose tissue. Many involved genes biologically relevant for development of obesity, including fatty acid synthase, transmembrane protein 88, signal transducer and activator of transcription 3, and neuritin 1. There was no evidence of epigenetic mediation in peripheral blood leukocytes.

Conclusions

DNA methylation at specific genes may be mediators of associations between childhood socioeconomic disadvantage and mid-life BMI in adipose tissue. Findings motivate continued efforts to study if and how childhood socioeconomic disadvantage is biologically embedded at the level of the epigenome in regions etiologically relevant for adiposity.
Surface modification and cellular uptake evaluation of Au-coated Ni
80
Fe
20
nanodiscs for biomedical applications
Authors: Barrera Gabriele , Serpe Loredana , Celegato Federica , Coїsson Marco , Martina Katia , Canaparo Roberto , Tiberto Paola
Published: October 2016

A nanofabrication technique based on self-assembling of polystyrene nanospheres is used to obtain magnetic Ni
80
Fe
20
nanoparticles with a disc shape. The free-standing nanodiscs (NDs) have diameter and thickness of about 630 nm and 30 nm, respectively. The versatility of fabrication technique allows one to cover the ND surface with a protective gold layer with a thickness of about 5 nm. Magnetization reversal has been studied by room-temperature hysteresis loop measurements in water-dispersed free-standing NDs. The reversal shows zero remanence, high susceptibility and nucleation/annihilation fields due to spin vortex formation. In order to investigate their potential use in biomedical applications, the effect of NDs coated with or without the protective gold layer on cell growth has been evaluated. A successful attempt to bind cysteine-fluorescein isothiocyanate (FITC) derivative to the gold surface of magnetic NDs has been exploited to verify the intracellular uptake of the NDs by cytofluorimetric analysis using the FITC conjugate.
Organosilane-functionalization of nanostructured indium tin oxide films
Authors: Pruna R. , Palacio F. , Martínez M. , Blázquez O. , Hernández S. , Garrido B. , López M.
Published: October 2016

Fabrication and organosilane-functionalization and characterization of nanostructured ITO electrodes are reported. Nanostructured ITO electrodes were obtained by electron beam evaporation, and a subsequent annealing treatment was selectively performed to modify their crystalline state. An increase in geometrical surface area in comparison with thin-film electrodes area was observed by atomic force microscopy, implying higher electroactive surface area for nanostructured ITO electrodes and thus higher detection levels. To investigate the increase in detectability, chemical organosilane-functionalization of nanostructured ITO electrodes was performed. The formation of 3-glycidoxypropyltrimethoxysilane (GOPTS) layers was detected by X-ray photoelectron spectroscopy. As an indirect method to confirm the presence of organosilane molecules on the ITO substrates, cyclic voltammetry and electrochemical impedance spectroscopy (EIS) were also carried out. Cyclic voltammograms of functionalized ITO electrodes presented lower reduction-oxidation peak currents compared with non-functionalized ITO electrodes. These results demonstrate the presence of the epoxysilane coating on the ITO surface. EIS showed that organosilane-functionalized electrodes present higher polarization resistance, acting as an electronic barrier for the electron transfer between the conductive solution and the ITO electrode. The results of these electrochemical measurements, together with the significant difference in the X-ray spectra between bare ITO and organosilane-functionalized ITO substrates, may point to a new exploitable oxide-based nanostructured material for biosensing applications. As a first step towards sensing, rapid functionalization of such substrates and their application to electrochemical analysis is tested in this work. Interestingly, oxide-based materials are highly integrable with the silicon chip technology, which would permit the easy adaptation of such sensors into lab-on-a-chip configurations, providing benefits such as reduced size and weight to facilitate on-chip integration, and leading to low-cost mass production of microanalysis systems.
TheE. colimolecular phenotype under different growth conditions
Authors: Caglar Mehmet U. , Houser John R. , Barnhart Craig S. , Boutz Daniel R. , Carroll Sean M. , Dasgupta Aurko , Lenoir Walter F. , Smith Bartram L. , Sridhara Viswanadham , Sydykova Dariya K. , Wood Drew Vander , Marx Christopher J. , Marcotte Edward M. , Barrick Jeffrey E. , Wilke Claus O.
Published: October 2016

Modern systems biology requires extensive, carefully curated measurements of cellular components in response to different environmental conditions. While high-throughput methods have made transcriptomics and proteomics datasets widely accessible and relatively economical to generate, systematic measurements of both mRNA and protein abundances under a wide range of different conditions are still relatively rare. Here we present a detailed, genome-wide transcriptomics and proteomics dataset ofE. coligrown under 34 different conditions. Additionally, we provide measurements of doubling times andin-vivometabolic fluxes through the central carbon metabolism. We manipulate concentrations of sodium and magnesium in the growth media, and we consider four different carbon sources glucose, gluconate, lactate, and glycerol. Moreover, samples are taken both in exponential and stationary phase, and we include two extensive time-courses, with multiple samples taken between 3 hours and 2 weeks. We find that exponential-phase samples systematically differ from stationary-phase samples, in particular at the level of mRNA. Regulatory responses to different carbon sources or salt stresses are more moderate, but we find numerous differentially expressed genes for growth on gluconate and under salt and magnesium stress. Our data set provides a rich resource for future computational modeling ofE. coligene regulation, transcription, and translation.
Transcriptional landscape of cell lines and their tissues of origin
Authors: Lopes-Ramos Camila M. , Paulson Joseph N. , Chen Cho-Yi , Kuijjer Marieke L. , Fagny Maud , Platig John , Sonawane Abhijeet R. , DeMeo Dawn L. , Quackenbush John , Glass Kimberly
Published: October 2016

Cell lines are an indispensable tool in biomedical research and often used as surrogates for tissues. An important question is how well a cell line’s transcriptional and regulatory processes reflect those of its tissue of origin. We analyzed RNA-Seq data from GTEx for 127 paired Epstein-Barr virus transformed lymphoblastoid cell lines and whole blood samples; and 244 paired fibroblast cell lines and skin biopsies. A combination of gene expression and network analyses shows that while cell lines carry the expression signatures of their primary tissues, albeit at reduced levels, they also exhibit changes in their patterns of transcription factor regulation. Cell cycle genes are over-expressed in cell lines compared to primary tissue, and they have a reduction of repressive transcription factor targeting. Our results provide insight into the expression and regulatory alterations observed in cell lines and suggest that these changes should be considered when using cell lines as models.

Highlights

Cell lines differ from their source tissues in gene expression and regulation

Distinct cell lines share altered patterns of cell cycle regulation

Cell cycle genes are less strongly targeted by repressive TFs in cell lines

Cell lines share expression with their source tissue, but at reduced levels
Lowest expressing microRNAs capture indispensable information: identifying cancer types
Authors: Rasnic Roni , Linial Nathan , Linial Michal
Published: October 2016

The primary function of microRNAs (miRNAs) is to maintain cell homeostasis. In cancerous tissues miRNAs’ expression undergo drastic alterations. In this study, we used miRNA expression profiles from The Cancer Genome Atlas (TCGA) of 24 cancer types and 3 healthy tissues, collected from >8500 samples. We seek to classify the cancer’s origin and tissue identification using the expression from 1046 reported miRNAs. Despite an apparent uniform appearance of miRNAs among cancerous samples, we recover indispensable information from lowly expressed miRNAs regarding the cancer/tissue types. Multiclass support vector machine classification yields an average recall of 58% in identifying the correct tissue and tumor types. Data discretization has led to substantial improvement reaching an average recall of 91% (95% median). We propose a straightforward protocol as a crucial step in classifying tumors of unknown primary origin. Our counter-intuitive conclusion is that in almost all cancer types, highly expressing miRNAs mask the significant signal that lower expressed miRNAs provide.
Gene regulatory network inference from single-cell data using multivariate information measures
Authors: Chan Thalia E. , Stumpf Michael P.H. , Babtie Ann C.
Published: October 2016

While single-cell gene expression experiments present new challenges for data processing, the cell-to-cell variability observed also reveals statistical relationships that can be used by information theory. Here, we use multivariate information theory to explore the statistical dependencies between triplets of genes in single-cell gene expression datasets. We develop PIDC, a fast, efficient algorithm that uses partial information decomposition (PID) to identify regulatory relationships between genes. We thoroughly evaluate the performance of our algorithm and demonstrate that the higher order information captured by PIDC allows it to outperform pairwise mutual information-based algorithms when recovering true relationships present in simulated data. We also infer gene regulatory networks from three experimental single-cell data sets and illustrate how network context, choices made during analysis, and sources of variability affect network inference. PIDC tutorials and open-source software for estimating PID are available here:https://github.com/Tchanders/network_inference_tutorials. PIDC should facilitate the identification of putative functional relationships and mechanistic hypotheses from single-cell transcriptomic data.
First report of the East-Central South African Genotype of Chikungunya Virus in Rio de Janeiro, Brazil
Authors: de Souza Thiara Manuele Alves , de Azeredo Elzinandes Leal , da Silva Jéssica Badolato Corrêa , Damasco Paulo Vieira , Santos Carla Cunha , de Paiva Fabienne Petitinga , Nunes Priscila Conrado Guerra , Barbosa Luciana Santos , Cipitelli Márcio da Costa , Chouin-Carneiro Thaís , Faria Nieli Rodrigues da Costa , Nogueira Rita Maria Ribeiro , de Bruycker-Nogueira Fernanda , dos Santos Flavia Barreto
Published: October 2016

Background

Chikungunya virus (CHIKV) is an arbovirus that causes an acute febrile illness characterized by severe and debilitating arthralgia. In Brazil, the Asian and East-Central South African (ECSA) genotypes are circulating in the north and northeast of the country, respectively. In 2015, the first autochthonous cases in Rio de Janeiro, Brazil were reported but until now the circulating strains have not been characterized. Therefore, we aimed here to perform the molecular characterization and phylogenetic analysis of CHIKV strains circulating in the 2016 outbreak occurred in the municipality of Rio de Janeiro.

Methods

The cases analyzed in this study were collected at a private Hospital, from April 2016 to May 2016, during the chikungunya outbreak in Rio de Janeiro, Brazil. All cases were submitted to the Real Time RT-PCR for CHIKV genome detection and to anti-CHIKV IgM ELISA. Chikungunya infection was laboratorially confirmed by at least one diagnostic method and, randomly selected positive cases (n=10), were partially sequenced (CHIKV E1 gene) and analyzed.

Results

The results showed that all the samples grouped in ECSA genotype branch and the molecular characterization of the fragment did not reveal the A226V mutation in the Rio de Janeiro strains analyzed, but a K211T amino acid substitution was observed for the first time in all samples and a V156A substitution in two of ten samples.

Conclusions

Phylogenetic analysis and molecular characterization reveals the circulation of the ECSA genotype of CHIKV in the city of Rio de Janeiro, Brazil and two amino acids substitutions (K211T and V156A) exclusive to the CHIKV strains obtained during the 2016 epidemic, were reported.
Chimeric Genes Revealed in the Polyploidy Fish Hybrids ofCarassius cuvieri(Female) ×Megalobrama amblycephala(Male)
Authors: Hu Fangzhou , Wu Chang , Zhou Yunfan , Wang Shi , Xiao Jun , Wu Yanhong , Xu Kang , Ren Li , Liu Qingfeng , Li Wuhui , Wen Ming , Tao Min , Qin Qinbo , Zhao Rurong , Luo Kaikun , Liu Shaojun
Published: October 2016

The genomes of newly formed natural or artificial polyploids may experience rapid gene loss and genome restructuring. In this study, we obtained tetraploid hybrids (4n=148, 4nJB) and triploid hybrids (3n=124, 3nJB) derived from the hybridization of two different subfamily speciesCarassius cuvieri(♀, 2n = 100, JCC) andMegalobrama amblycephala(♂, 2n = 48, BSB). Some significant morphological and physiological differences were detected in the polyploidy hybrids compared with their parents. To reveal the molecular traits of the polyploids, we compared the liver transcriptomes of 4nJB, 3nJB and their parents. The results indicated high proportion chimeric genes (31 > %) and mutated orthologous genes (17 > %) both in 4nJB and 3nJB. We classified 10 gene patterns within three categories in 4nJB and 3nJB orthologous gene, and characterized 30 randomly chosen genes using genomic DNA to confirm the chimera or mutant. Moreover, we mapped chimeric genes involved pathways and discussed that the phenotypic novelty of the hybrids may relate to some chimeric genes. For example, we found there is an intragenic insertion in the K+ channelkcnk5b, which may be related to the novel presence of the barbels in 4nJB. Our results indicated that the genomes of newly formed polyploids experienced rapid restructuring post-polyploidization, which may results in the phenotypic and phenotypic changes among the polyploidy hybrid offspring. The formation of the 4nJB and 3nJB provided new insights into the genotypic and phenotypic diversity of hybrid fish resulting from distant hybridization between subfamilies.
The fitness ofPseudomonas aeruginosaquorum sensing signal cheats is influenced by the diffusivity of the environment
Authors: Mund Anne , Diggle Stephen P. , Harrison Freya
Published: October 2016

Experiments examining the social dynamics of bacterial quorum sensing (QS) have focused on mutants which do not respond to signals, and the role of QS-regulated exoproducts as public goods. The potential for QS signal molecules to themselves be social public goods has received much less attention. Here, we analyse how signal-deficient (lasI−) mutants of the opportunistic pathogenPseudomonas aeruginosainteract with wild-type cells in an environment where QS is required for growth. We show that when growth requires a ‘private’ intracellular metabolic mechanism activated by the presence of QS signal,lasI−mutants act as social cheats and outcompete signal-producing wild-type bacteria in mixed cultures, because they can use the signals produced by wild type cells. However, reducing the ability of signal molecules to diffuse through the growth medium, results in signal molecules becoming less accessible to mutants, leading to reduced cheating. Our results indicate that QS signal molecules can be considered as social public goods in a way that has been previously described for other exoproducts, but that spatial structuring of populations reduces exploitation by non-cooperative signal cheats.

Importance

Bacteria communicate via signaling molecules to regulate the expression of a whole range of genes. This process, termed quorum sensing (QS), moderates bacterial metabolism in many environmental conditions, from soil and water (where QS-regulated genes influence nutrient cycling) to animal hosts (where QS-regulated genes determine pathogen virulence). Understanding the ecology of QS could therefore yield vital clues as to how we might modify bacterial behaviour for environmental or clinical gains. Here, we demonstrate that QS signals act as shareable public goods. This means that their evolution, and therefore population-level responses to interference with QS, will be constrained by population structure. Further, we show that environmental structure (constraints on signal diffusion) alters the accessibility of QS signals and demonstrates that we need to consider population and environmental structure to help us further our understanding of QS signaling systems.
Potent optogenetic inhibition of behavior with anion channelrhodopsins
Authors: Mohammad Farhan , Stewart James C. , Ott Stanislav , Chlebikova Katarina , Chua Jia Yi , Koh Tong-Wey , Ho Joses , Claridge-Chang Adam
Published: October 2016

Optogenetics employs light exposure to manipulate physiology in genetically modified organisms. There are abundant tools for optogenetic excitation of neuronal activity, but the limitations of current activity photo-inhibitors present an obstacle to demonstrating the necessity of specific neuronal circuits. Here we show that anion channelrhodopsins can be used to specifically and rapidly inhibit a range of systems involved inDrosophilalocomotion, wing expansion, memory retrieval and gustation, demonstrating their broad utility to the circuit analysis of behavior.
normR: Regime enrichment calling for ChIP-seq data
Authors: Helmuth Johannes , Li Na , Arrigoni Laura , Gianmoena Kathrin , Cadenas Cristina , Gasparoni Gilles , Sinha Anupam , Rosenstiel Philip , Walter Jörn , Hengstler Jan G. , Manke Thomas , Chung Ho-Ryun
Published: October 2016

ChIP-seq probes genome-wide localization of DNA-associated proteins. To mitigate technical biases ChIP-seq read densities are normalized to read densities obtained by a control. Our statistical framework “normR” achieves a sensitive normalization by accounting for the effect of putative protein-bound regions on the overall read statistics. Here, we demonstrate normR’s suitability in three studies: (i) calling enrichment for high (H3K4me3) and low (H3K36me3) signal-to-ratio data; (ii) identifying two previously undescribed H3K27me3 and H3K9me3 heterochromatic regimes of broad and peak enrichment; and (iii) calling differential H3K4me3 or H3K27me3-enrichment between HepG2 hepatocarcinoma cells and primary human Hepatocytes. normR is readily available onhttp://bioconductor.org/packages/normr
Striking differences in patterns of germline mutation between mice and humans
Authors: Lindsay Sarah J. , Rahbari Raheleh , Kaplanis Joanna , Keane Thomas , Hurles Matthew E.
Published: October 2016

Recent whole genome sequencing (WGS) studies have estimated that the human germline mutation rate per basepair per generation (∼1.2−10−8)1,2is substantially higher than in mice (3.5-5.4−10−9)3,4, which has been attributed to more efficient purifying selection due to larger effective population sizes in mice compared to humans.5,6,7. In humans, most germline mutations are paternal in origin and the numbers of mutations per offspring increase markedly with paternal age2,8,9and more weakly with maternal age10. Germline mutations can arise at any stage of the cellular lineage from zygote to gamete, resulting in mutations being represented in different proportion and types of cells, with the earliest embryonic mutations being mosaic in both somatic and germline cells. Here we use WGS of multi-sibling mouse and human pedigrees to show striking differences in germline mutation rate and spectra between the two species, including a dramatic reduction in mutation rate in human spermatogonial stem cell (SSC) divisions, which we hypothesise was driven by selection. The differences we observed between mice and humans result from both biological differences within the same stage of embryogenesis or gametogenesis and species-specific differences in cellular genealogies of the germline.
A synchrotron X-ray diffraction deconvolution method for the measurement of residual stress in thermal barrier coatings as a function of depth
Authors: Li C. , Jacques S. D. M. , Chen Y. , Daisenberger D. , Xiao P. , Markocsan N. , Nylen P. , Cernik R. J.
Published: October 2016

The average residual stress distribution as a function of depth in an air plasma-sprayed yttria stabilized zirconia top coat used in thermal barrier coating (TBC) systems was measured using synchrotron radiation X-ray diffraction in reflection geometry on station I15 at Diamond Light Source, UK, employing a series of incidence angles. The stress values were calculated from data deconvoluted from diffraction patterns collected at increasing depths. The stress was found to be compressive through the thickness of the TBC and a fluctuation in the trend of the stress profile was indicated in some samples. Typically this fluctuation was observed to increase from the surface to the middle of the coating, decrease a little and then increase again towards the interface. The stress at the interface region was observed to be around 300 MPa, which agrees well with the reported values. The trend of the observed residual stress was found to be related to the crack distribution in the samples, in particular a large crack propagating from the middle of the coating. The method shows promise for the development of a nondestructive test for as-manufactured samples.
Influence of stress on the properties of Ge nanocrystals in an SiO2 matrix
Authors: Pivac Branko , Dubček Pavo , Popović Jasminka , Dasović Jasna , Bernstorff Sigrid , Radić Nikola , Zavašnik Janez
Published: October 2016

In this work, self-assembled Ge quantum dot (QD) formation in a dielectric matrix is explored. Of particular interest were their structural and optical properties, in order to understand the stress build-up in such a process and its impact on the material properties during processing. To this end, thin films consisting of (Ge + SiO2)/SiO2 multilayers grown by RF magnetron sputtering were deposited at room temperature. Annealing of such films at 873 K in inert N2 atmosphere produced, at the position of the Ge-rich SiO2 layers, a high lateral density (about 1012 cm−2) of Ge QDs with a good crystallinity. SiO2 spacer layers separated the adjacent Ge-rich layers, where the Ge QDs were formed with a diameter of about the size of the (Ge + SiO2) as-deposited layer thickness, and created a good vertical repeatability, confirmed by the appearance of a Bragg sheet in two-dimensional small-angle X-ray scattering patterns. The structural analysis, by wide-angle X-ray diffraction, grazing-incidence small-angle X-ray scattering and transmission electron microscopy, has shown that the described processing of the films induced large compressive stress on the formed QDs. Optical analysis by time-resolved photoluminescence (PL) revealed that the high density of crystalline Ge QDs embedded in the amorphous SiO2 matrix produced a strong luminescence in the visible part of the spectrum at 2–2.5 eV photon energy. It is shown that the decay dynamics in this energy range are very fast, and therefore the transitions that create such PL are attributed to matrix defects present in the shell surrounding the Ge QD surface (interface region with the matrix). The measured PL peak, though wide at its half-width, when analysed in consecutive short spectral segments showed the same decay dynamics, suggesting the same mechanism of relaxation.
MAGNDATA: towards a database of magnetic structures. II. The incommensurate case
Authors: Gallego Samuel V. , Perez-Mato J. Manuel , Elcoro Luis , Tasci Emre S. , Hanson Robert M. , Aroyo Mois I. , Madariaga Gotzon
Published: October 2016

A free web page under the name MAGNDATA, which provides detailed quantitative information on more than 400 published magnetic structures, has been made available at the Bilbao Crystallographic Server (http://www.cryst.ehu.es). It includes both commensurate and incommensurate structures. In the first article in this series, the information available on commensurate magnetic structures was presented [Gallego, Perez-Mato, Elcoro, Tasci, Hanson, Momma, Aroyo & Madariaga (2016). J. Appl. Cryst.
49, 1750–1776]. In this second article, the subset of the database devoted to incommensurate magnetic structures is discussed. These structures are described using magnetic superspace groups, i.e. a direct extension of the non-magnetic superspace groups, which is the standard approach in the description of aperiodic crystals. The use of magnetic superspace symmetry ensures a robust and unambiguous description of both atomic positions and magnetic moments within a common unique formalism. The point-group symmetry of each structure is derived from its magnetic superspace group, and any macroscopic tensor property of interest governed by this point-group symmetry can be retrieved through direct links to other programs of the Bilbao Crystallographic Server. The fact that incommensurate magnetic structures are often reported with ambiguous or incomplete information has made it impossible to include in this collection a good number of the published structures which were initially considered. However, as a proof of concept, the published data of about 30 structures have been re-interpreted and transformed, and together with ten structures where the superspace formalism was directly employed, they form this section of MAGNDATA. The relevant symmetry of most of the structures could be identified with an epikernel or isotropy subgroup of one irreducible representation of the space group of the parent phase, but in some cases several irreducible representations are active. Any entry of the collection can be visualized using the online tools available on the Bilbao server or can be retrieved as a magCIF file, a file format under development by the International Union of Crystallography. These CIF-like files are supported by visualization programs like Jmol and by analysis programs like JANA and ISODISTORT.
Crystal structures of di-μ-bromido-bis{dibromido[η5-2-(dimethylamino)indenyl]zirconium(IV)} and dibromidobis[η5-2-(dimethylamino)indenyl]zirconium(IV)
Authors: Medvedev Michael G. , Borisov Ilya S. , Kulyabin Pavel S. , Izmer Vyatcheslav V. , Kononovich Dmitry S. , Uborsky Dmitry V. , Voskoboynikov Alexander Z.
Published: October 2016

In the title compounds, [Zr2Br6(C11H12N)2], (I) and [ZrBr2(C11H12N)2], (II), the positions of the η5-binding 2-dimethylaminoindenyl units are fixed by intramolecular C—H...Br interactions involving aromatic or dimethylamino H atoms. The binuclear molecule of (I) is located on a general position, while the mononuclear molecule of (II) is situated on a twofold rotation axis. Both ZrIV atoms in (I) are ligated by one cyclopentadienyl (CP) ring and four Br ligands (two bridging, two terminal), while in (II) the ZrIV atom is ligated by two CP rings and two terminal Br ligands. The crystal structures of both (I) and (II) comprise of strands of π–π- and N–π-bonded molecules, which in turn are linked by C—H...Br interactions.
4-[(4-Hydroxymethyl-2H-1,2,3-triazol-2-yl)methyl]-6,8-dimethyl-2H-chromen-2-one
Authors: El-Khatatneh Nasseem , Chandra  , Shamala D. , Shivashankar K. , Mahendra M.
Published: October 2016

In the title compound, C15H15N3O3, the dihedral angle between the triazole ring and coumarin ring system [r.m.s. deviation = 0.040 Å] is 77.40 (6)°. The O atom of the hydroxymethyl group deviates from the triazole ring plane by 1.345 (1) Å. In the crystal, inversion dimers linked by pairs of O—H...O hydrogen bonds generate R
2
2(22) loops; C—H...O and C—H...N interactions link the dimers into a three-dimensional network.
[(Dimethylamino)methyl]dimethylazanium bis(trifluoromethanesulfonyl)amide
Authors: Hummel Michael , Laus Gerhard , Kahlenberg Volker , Schottenberger Herwig
Published: October 2016

The title molecular salt, C5H15N2
+·C2F6NO4S2
−, was obtained by a proton transfer reaction between bis(trifluoromethanesulfonyl)amine and bis(dimethylamino)methane. In the crystal, the ions are linked by N—H...O=S hydrogen bonds, and these units are linked by C—H...O hydrogen bonds, forming sheets parallel to the bc plane. The crystal was refined as a non-merohedral twin with a BASF factor of 0.316 (1).
The selfie phenomenon – consumer identities in the social media marketplace
Authors: Kedzior Richard , Allen Douglas E. , Schroeder Jonathan
Published: October 2016

Purpose

The purpose of this paper is to outline the contributions presented in this special section on the selfie phenomenon and its significance for marketing practice and scholarship.

Design/methodology/approach

The significance of the topic is reviewed and themes related to the selfie phenomenon and marketplace issues are discussed in connection with extant research. The contributions of each paper are briefly highlighted and discussed.

Findings

Although the selfie is a relatively new phenomenon, both marketing practice and scholarship have noticed its prominence in consumer lives and potential for generating marketplace insights. Despite its frequently presumed triviality, the selfie is a multifaceted phenomenon of significance to key marketing areas such as branding, consumer behavior or market research. Possible avenues for future research are outlined.

Originality/value

Key issues relating to research into the selfie phenomenon for marketing scholars are illuminated.