bluuebunny/crossref_metadata_2025_split huggingface dataset:
Haemoproteus paraortalidum n. sp. in captive Black-fronted Piping-guans Aburria jacutinga (Galliformes, Cracidae): high prevalence in a population reintroduced into the wild
Authors: Ferreira-Junior Francisco C. , Angeli Dutra Daniela de , Martins Nelson R.S , Valkiūnas Gediminas , Braga Érika M. 
Published: March 2018

AbstractHaemosporidian parasites of the genus Haemoproteus are widespread and can cause disease and even mortality in birds under natural and captive conditions. The Black-fronted Piping-guan (Aburria jacutinga) is an endangered Neotropical bird of the Cracidae (Galliformes) going through a reintroduction program to avoid extinction. We used microscopic examination and partial cytochrome b DNA sequencing to describe a new Haemoproteus species infecting Black-fronted Piping-guans bred and raised in captivity that were reintroduced into the Atlantic rainforest. Haemoproteus (Parahaemoproteus) paraortalidum n. sp. was detected in the blood of 19 out of 29 examined birds. The new species is distinguished from other haemoproteids due to the shape of gametocytes, which have pointed ends in young stages, and due to the presence of vacuole-like unstained spaces in macrogametocytes and numerous volutin granules both in macro- and microgametocytes. Illustrations of the new species are provided. Phylogenetic inference positioned this parasite in the Parahaemoproteus subgenus clade together with the other two Haemoproteus genetic lineages detected in cracids up to date. We discuss possible implications of the reintroduction of birds infected with haemosporidian parasites into de wild. Treatment of Haemoproteus infections remains insufficiently studied, but should be considered for infected birds before reintroduction to improve host reproductive and survival rates after release.
Rapid, raw-read reference and identification (R4IDs): A flexible platform for rapid generic species ID using long-read sequencing technology
Authors: Parker Joe , Helmstetter Andrew , Crowe James , Iacona John , Devey Dion , Papadopulos Alexander S. T. 
Published: March 2018

AbstractThe versatility of the current DNA sequencing platforms and the development of portable, nanopore sequencers means that it has never been easier to collect genetic data for unknown sample ID. DNA barcoding and meta-barcoding have become increasingly popular and barcode databases continue to grow at an impressive rate. However, the number of canonical genome assemblies (reference or draft) that are publically available is relatively tiny, hindering the more widespread use of genome scale DNA sequencing technology for accurate species identification and discovery. Here, we show that rapid raw-read reference datasets, or R4IDs for short, generated in a matter of hours on the Oxford Nanopore MinION, can bridge this gap and accelerate the generation of useable reference sequence data. By exploiting the long read length of this technology, shotgun genomic sequencing of a small portion of an organism’s genome can act as a suitable reference database despite the low sequencing coverage. These R4IDs can then be used for accurate species identification with minimal amounts of re-sequencing effort (1000s of reads). We demonstrated the capabilities of this approach with six vascular plant species for which we created R4IDs in the laboratory and then re-sequenced, live at the Kew Science Festival 2016. We further validated our method using simulations to determine the broader applicability of the approach. Our data analysis pipeline has been made available as a Dockerised workflow for simple, scalable deployment for a range of uses.
Early-life social environment alters juvenile behavior and neuroendocrine function in a highly social cichlid fish
Authors: Solomon-Lane Tessa K. , Hofmann Hans A. 
Published: March 2018

AbstractEarly-life experiences can shape adult behavior, with consequences for fitness and health, yet fundamental questions remain unanswered about how early-life social experiences are translated into variation in brain and behavior. The African cichlid fish Astatotilapia burtoni, a model system in social neuroscience, is well known for its highly plastic social phenotypes in adulthood. Here, we rear juveniles in either social groups or pairs to investigate the effects of early-life social environments on behavior and neuroendocrine gene expression. We find that both juvenile behavior and neuroendocrine function are sensitive to early-life effects. Behavior robustly co-varies across multiple contexts (open field, social cue investigation, and dominance behavior assays) to form a behavioral syndrome, with pair-reared juveniles towards the end of syndrome that is less active and socially interactive. Pair-reared juveniles also submit more readily as subordinates. In a separate cohort, we measured whole brain expression of stress and sex hormone genes. Expression of glucocorticoid receptor (GR) 1a was elevated in group-reared juveniles, supporting a highly-conserved role for the stress axis mediating early-life effects. The effect of rearing environment on androgen receptor (AR) α and estrogen receptor (ER) α expression was mediated by treatment duration (1 vs. 5 weeks). Finally, expression of corticotropin-releasing factor (CRF) and GR2 decreased significantly over time. Rearing environment also caused striking differences in gene co-expression, such that expression was tightly integrated in pair-reared juveniles, but not group-reared or isolates. Together, this research demonstrates the important developmental origins of behavioral phenotypes and identifies potential behavioral and neuroendocrine mechanisms.
Barcoded oligonucleotides ligated on RNA amplified for multiplex and parallel in-situ analyses
Authors: Iyer Eswar P. R. , Punthambaker Sukanya , Liu Songlei , Jindal Kunal , Farrell Michael , Murn Jernej , Ferrante Thomas , Rudnicki Stewart , Kohman Richie E. , Wassie Asmamaw T. , Goodwin Daniel , Chen Fei , Alon Shahar , Sinha Anubhav , Milanova Denitsa , Aron Liviu , Camplisson Conor , Skrynnyk Alex , Reginato Paul Louis , Conway Nick , Aach John , Yankner Bruce , Boyden Edward S. , Church George M. 
Published: March 2018

AbstractWe present Barcoded Oligonucleotides Ligated On RNA Amplified for Multiplexed and parallel In-Situ analysis (BOLORAMIS), a reverse-transcription (RT)-free method for spatially-resolved, targeted, in-situ RNA identification of single or multiple targets. For this proof of concept, we have profiled 154 distinct coding and small non-coding transcripts ranging in sizes 18 nucleotides in length and upwards, from over 200, 000 individual human induced pluripotent stem cells (iPSC) and demonstrated compatibility with multiplexed detection, enabled by fluorescent in-situ sequencing. We use BOLORAMIS data to identify differences in spatial localization and cell-to-cell expression heterogeneity. Our results demonstrate BOLORAMIS to be a generalizable toolset for targeted, in-situ detection of coding and small non-coding RNA for single or multiplexed applications.
A Comparison of Temporal Response Function Estimation Methods for Auditory Attention Decoding
Authors: Wong Daniel D.E. , Fuglsang Søren A. , Hjortkjær Jens , Ceolini Enea , Slaney Malcolm , Cheveigné Alain de 
Published: March 2018

ABSTRACTThe decoding of selective auditory attention from noninvasive electroencephalogram (EEG) data is of interest in brain computer interface and auditory perception research. The current state-of-the-art approaches for decoding the attentional selection of listeners are based on temporal response functions (TRFs). In the current context, a TRF is a function that facilitates a mapping between features of sound streams and EEG responses. It has been shown that when the envelope of attended speech and EEG responses are used to derive TRF mapping functions, the TRF model predictions can be used to discriminate between attended and unattended talkers. However, the predictive performance of the TRF models is dependent on how the TRF model parameters are estimated. There exist a number of TRF estimation methods that have been published, along with a variety of datasets. It is currently unclear if any of these methods perform better than others, as they have not yet been compared side by side on a single standardized dataset in a controlled fashion. Here, we present a comparative study of the ability of different TRF estimation methods to classify attended speakers from multi-channel EEG data. The performance of the TRF estimation methods is evaluated using different performance metrics on a set of labeled EEG data from 18 subjects listening to mixtures of two speech streams.
Simultaneous B and T cell acute lymphoblastic leukemias in zebrafish driven by transgenic MYC: implications for oncogenesis and lymphopoiesis
Authors: Borga Chiara , Park Gilseung , Foster Clay , Burroughs-Garcia Jessica , Marchesin Matteo , Ahmed Syed T. , Bresolin Silvia , Batchelor Lance , Scordino Teresa , Miles Rodney R. , Kronnie Geertruy te , Regens James L. , Frazer J. Kimble 
Published: March 2018

AbstractPrecursor-B cell acute lymphoblastic leukemia (pre-B ALL) is the most common pediatric cancer, but there are no useful zebrafish pre-B ALL models. We describe the first highly-penetrant zebrafish pre-B ALL, driven by human MYC. Leukemias express B lymphoblast-specific genes and are distinct from T cell ALL (T-ALL)—which these fish also develop. Zebrafish pre-B ALL shares in vivo features and expression profiles with human pre-B ALL, and these profiles differ from zebrafish T-ALL or normal B and T cells. These animals also exhibit aberrant lymphocyte development. As the only robust zebrafish pre-B ALL model and only example where T-ALL also develops, this model can reveal differences between MYC-driven pre-B vs. T-ALL and be exploited to discover novel pre-B ALL therapies.Statement of significanceWe describe the first robust zebrafish pre-B ALL model in MYC-transgenic animals known to develop T-ALL, revealing the only animal model with both human ALL types. We also describe aberrant multi-lineage lymphopoiesis. This powerful system can be used to study MYC-driven leukemogenesis and discover new pre-B ALL targeted therapies.
Distinct and stage-specific contributions of TET1 and TET2 to stepwise cytosine oxidation in the transition from naive to primed pluripotency
Authors: Mulholland Christopher B. , Traube Franziska R. , Parsa Edris , Eckl Eva-Maria , Schönung Maximillian , Modic Miha , Bartoschek Michael D. , Stolz Paul , Ryan Joel , Carell Thomas , Leonhardt Heinrich , Bultmann Sebastian 
Published: March 2018

ABSTRACTThe TET-oxidized cytosine derivatives, 5-hydroxymethylcytosine (5hmC) and 5-formylcytosine (5fC), are considered DNA demethylation intermediates as well as stable epigenetic marks in mammals. We compared modified cytosine and enzyme levels in TET-knockout cells during naive pluripotency exit and found distinct and differentiation-dependent contributions of TET1 and TET2 to 5hmC and 5fC formation. The divergent modified cytosine levels argue for independent consecutive oxidation steps in vivo with broad implications for epigenetic regulation.
Detection of race-specific resistance against Puccinia coronata f. sp. avenae in Brachypodium species
Authors: Omidvar Vahid , Dugyala Sheshanka , Li Feng , Rottschaefer Susan , Miller Marisa E. , Ayliffe Mick , Moscou Matthew J. , Kianian Shahryar F. , Figueroa Melania 
Published: March 2018

AbstractOat crown rust caused by Puccinia coronata f. sp. avenae is the most destructive foliar disease of cultivated oat. Characterization of genetic factors controlling resistance responses to Puccinia coronata f. sp. avenae in non-host species could provide new resources for developing disease protection strategies in oat. We examined symptom development and fungal colonization levels of a collection of Brachypodium distachyon and B. hybridum accessions infected with three North American P. coronata f. sp. avenae isolates. Our results demonstrated that colonization phenotypes are dependent on both host and pathogen genotypes, indicating a role for race-specific responses in these interactions. These responses were independent of the accumulation of reactive oxygen species. Expression analysis of several defense-related genes suggested that salicylic acid and ethylene-mediated signaling, but not jasmonic acid are components of resistance reaction to P. coronata f. sp. avenae. Our findings provide the basis to conduct a genetic inheritance study to examine if effector-triggered immunity contributes to non-host resistance to P. coronata f. sp. avenae in Brachypodium species.
Accounting for location uncertainty in azimuthal telemetry data improves ecological inference
Authors: Gerber Brian D. , Hooten Mevin B. , Peck Christopher P. , Rice Mindy B. , Gammonley James H. , Apa Anthony D. , Davis Amy J. 
Published: March 2018

AbstractCharacterizing animal space use is critical to understand ecological relationships. Despite many decades of using radio-telemetry to track animals and make spatial inference, there are few statistical options to handle these unique data and no synthetic framework for modeling animal location uncertainty and accounting for it in ecological models. We describe a novel azimuthal telemetry model (ATM) to account for azimuthal uncertainty with covariates and propagate location uncertainty into ecological models. We evaluate the ATM with commonly used estimators in several study design scenarios using simulation. We also provide illustra-tive empirical examples, demonstrating the impact of ignoring location uncertainty within home range and resource selection analyses. We found the ATM to have good performance and the only model that has appropriate measures of coverage. Ignoring animal location un-certainty when estimating resource selection or home ranges can have pernicious effects on ecological inference. We demonstrate that home range estimates can be overly confident and conservative when ignoring location uncertainty and resource selection coefficients can lead to incorrect inference and over confidence in the magnitude of selection. Our findings and model development have important implications for interpreting historical analyses using this type of data and the future design of radio-telemetry studies.
Pan-cancer deconvolution of cellular composition identifies molecular correlates of antitumour immunity and checkpoint blockade response
Authors: Chakravarthy Ankur , Furness Andrew , Joshi Kroopa , Ghorani Ehsan , Ford Kirsty , Ward Matthew J , King Emma V , Lechner Matt , Marafioti Teresa , Quezada Sergio , Thomas Gareth J , Feber Andrew , Fenton Tim R 
Published: March 2018

AbstractThe nature and extent of immune cell infiltration into solid tumours are key determinants of therapeutic response. Here, using a novel DNA methylation-based approach to tumour cell fraction deconvolution, we report the integrated analysis of tumour composition and genomics across a wide spectrum of solid cancers. Initially studying head and neck squamous cell carcinoma, we identify two distinct tumour subgroups: ‘immune hot’ and ‘immune cold’, which display differing prognosis, mutation burden, cytokine signalling, cytolytic activity, and oncogenic driver events. We demonstrate the existence of such tumour subgroups pan-cancer, link clonal-neoantigen burden to hot tumours, and show that transcriptional signatures of hot tumours are selectively engaged in immunotherapy responders. We also find that treatment-naive hot tumours are markedly enriched for known immune-resistance genomic alterations and define a catalogue of novel and known mediators of active antitumour immunity, deriving biomarkers and potential targets for precision immunotherapy.
All-optical electrophysiology reveals brain-state dependent changes in hippocampal subthreshold dynamics and excitability
Authors: Adam Yoav , Kim Jeong J. , Lou Shan , Zhao Yongxin , Brinks Daan , Wu Hao , Mostajo-Radji Mohammed A. , Kheifets Simon , Parot Vicente , Chettih Selmaan , Williams Katherine J. , Farhi Samouil L. , Madisen Linda , Harvey Christopher D. , Zeng Hongkui , Arlotta Paola , Campbell Robert E. , Cohen Adam E. 
Published: March 2018

AbstractA technology to record membrane potential from multiple neurons, simultaneously, in behaving animals will have a transformative impact on neuroscience research1. Parallel recordings could reveal the subthreshold potentials and intercellular correlations that underlie network behavior2. Paired stimulation and recording can further reveal the input-output properties of individual cells or networks in the context of different brain states3. Genetically encoded voltage indicators are a promising tool for these purposes, but were so far limited to single-cell recordings with marginal signal to noise ratio (SNR) in vivo4-6. We developed improved near infrared voltage indicators, high speed microscopes and targeted gene expression schemes which enabled recordings of supra- and subthreshold voltage dynamics from multiple neurons simultaneously in mouse hippocampus, in vivo. The reporters revealed sub-cellular details of back-propagating action potentials, correlations in sub-threshold voltage between multiple cells, and changes in dynamics associated with transitions from resting to locomotion. In combination with optogenetic stimulation, the reporters revealed brain state-dependent changes in neuronal excitability, reflecting the interplay of excitatory and inhibitory synaptic inputs. These tools open the possibility for detailed explorations of network dynamics in the context of behavior.
A sexually dimorphic neuroendocrine cascade acts through shared sensory neurons to regulate behavior inC. elegans
Authors: Hilbert Zoë A. , Kim Dennis H. 
Published: March 2018

ABSTRACTSexually dimorphic behaviors are observed in species across the animal kingdom, however the relative contributions of sex-specific and sex-shared nervous systems to such behaviors are not fully understood. Building on our previous work which described the sexually dimorphic expression of a neuroendocrine ligand, DAF-7, and its role in behavioral decision-making inC. elegans(Hilbert and Kim, 2017), we show here that sex-specific expression ofdaf-7is regulated by another neuroendocrine ligand, Pigment Dispersing Factor (PDF-1), which has previously been implicated in regulating male-specific behavior (Barrios et al., 2012). Our analysis revealed that PDF-1 acts sex- and cell-specifically in the ASJ neurons to regulate the expression ofdaf-7and we show that differences in the expression of the PDFR-1 receptor account for the sex-specific effects of this pathway. Our data suggest that modulation of the sex-shared nervous system by neuroendocrine signaling pathways can play a role in shaping sexually dimorphic behaviors.
Automated high-quality reconstruction of metabolic networks from high-throughput data
Authors: Hartleb Daniel , Fritzemeier C. Jonathan , Lercher Martin J. 
Published: March 2018

AbstractWhile new genomes are sequenced at ever increasing rates, their phenotypic analysis remains a major bottleneck of biomedical research. The generation of genome-scale metabolic models capable of accurate phenotypic predictions is a labor-intensive endeavor; accordingly, such models are available for only a small percentage of sequenced species. The standard metabolic reconstruction process starts from a (semi-)automatically generated draft model, which is then refined through extensive manual curation. Here, we present a novel strategy suitable for full automation, which exploits high-throughput gene knockout or nutritional growth data. We test this strategy by reconstructing accurate genome-scale metabolic models for three strains ofStreptococcus, a major human pathogen. The resulting models contain a lower proportion of reactions unsupported by genomic evidence than the most widely usedE. colimodel, but reach the same accuracy in terms of knockout prediction. We confirm the models’ predictive power by analyzing experimental data for auxotrophy, additional nutritional environments, and double gene knockouts, and we generate a list of potential drug targets. Our results demonstrate the feasibility of reconstructing high-quality genome-scale metabolic models from high-throughput data, a strategy that promises to massively accelerate the exploration of metabolic phenotypes.Significance statementReading bacterial genomes has become a cheap, standard laboratory procedure. A genome by itself, however, is of little information value – we need a way to translate its abstract letter sequence into a model that describes the capabilities of its carrier. Until now, this endeavor required months of manual work by experts. Here, we show how this process can be automated by utilizing high-throughput experimental data. We use our novel strategy to generate highly accurate metabolic models for three strains ofStreptococcus, a major threat to human health.
Site-Specific Labelling of Multidomain Proteins by Amber Codon Suppression
Authors: Heil Christina S. , Rittner Alexander , Goebel Bjarne , Beyer Daniel , Grininger Martin 
Published: March 2018

AbstractAmber codon suppression is a powerful tool to site-specifically modify proteins to generate novel biophysical probes. Yet, its application on large and complex multidomain proteins is challenging, leading to difficulties during structural and conformational characterization using spectroscopic methods. The animal fatty acid synthase type I is a 540 kDa homodimer displaying large conformational variability. As the key enzyme ofde novofatty acid synthesis, it attracts interest in the fields of obesity, diabetes and cancer treatment. Substrates and intermediates remain covalently bound to the enzyme during biosynthesis and are shuttled to all catalytic domains by the acyl carrier protein domain. Thus, conformational variability of animal FAS is an essential aspect for fatty acid biosynthesis. We investigate this multidomain protein as a model system for probing amber codon suppression by genetic encoding of non-canonical amino acids. The systematic approach relies on a microplate-based reporter assay of low complexity, that was used for quick screening of suppression conditions. Furthermore, the applicability of the reporter assay is demonstrated by successful upscaling to both full-length constructs and increased expression scale. The obtained fluorescent probes of murine FAS type I could be subjected readily to a conformational analysis using single-molecule fluorescence resonance energy transfer.
Autism Diagnostic Observation Schedule (ADOS) scores in males and females diagnosed with autism: a naturalistic study
Authors: Adamou Marios , Johnson Maria , Alty Bronwen 
Published: March 2018

PurposeMany tools are available for assessing autism in an adult population; however, few have been studied for the effects of gender on diagnostic scores. The purpose of this paper is to evaluate the Autism Diagnostic Observation Schedule (ADOS) assessment for gender bias in a clinical population, specifically whether the ADOS favours a “male-type” of autism.Design/methodology/approachThe ADOS scores of patients referred to an NHS specialist autism assessment service were retrospectively examined for significant gender differences. The combined ADOS scores and diagnostic outcome were grouped by gender for each participant. The data were analysed in SPSS using independentt-tests to look for significant gender differences between combined ADOS scores and diagnostic outcomes.FindingsA significant difference was observed in the mean combined ADOS scores for those participants who later received an autism diagnosis (male=10, female=6,t(13)=3.34,p=10; 0.005). However, no significant difference was observed between mean scores of those who did not receive an autism diagnosis (t(26)=1.21,p=0.237).Originality/valueThe ADOS is a popular assessment used for autism diagnosis. These results provide support for a male gender bias. This could have clinical implications for autism assessment services, whereby lower diagnostic thresholds could be considered for female patients. This could allow more females with autism to receive a diagnosis, and access support services.