tDCS Facilitation of Picture Naming: Item-Specific, Task General, or Neither?

The aim of the present study was to clarify the conditions under which anodal tDCS applied to left hemisphere language sites may facilitate picture naming latencies in healthy young adults. We built upon previous studies by directly testing for item-specific and generalized effects of tDCS through manipulation of item-familiarization and through testing for both online and offline effects of stimulation, in the same paradigm. In addition, we tested for the robustness of these effects by comparing two left hemisphere sites critical for lexical retrieval. Twenty-eight healthy young adults completed two testing sessions receiving either anodal (1.5 mA, 20 min) or sham stimulation (1.5 mA, 30 s) in each session. Half of the participants received tDCS over the left inferior frontal region and the other half over the left posterior superior temporal region. All participants were asked to a name a set of pictures and their response latencies were compared at three time points (before, during, and after the end of stimulation). The stimulus set was constructed so that some items were presented at all time points, some before and after stimulation, and some during stimulation only. A parsimonious linear mixed effects model (LMM) revealed robust repetition priming effects as latencies were reliably faster for previously named items in all conditions. However, active tDCS did not produce any additional facilitation in relation to sham, and even led to slower performance in the IFG group when the stimulated items differed from those tested at baseline and post-test. Our findings add to the present debate about the efficacy of single-session tDCS for modulation of lexical retrieval in healthy young adults. We conclude that future research should take a more systematic, step-wise approach to the application of tDCS to the study of language and that more sensitive experimental paradigms, which include a training element, are more adapted to the study of cognitive processes in populations with optimal levels of cortical excitability

SUBTLEX-CY: A new word frequency database for Welsh

We present SUBTLEX-CY, a new word frequency database created from a 32 million word corpus of Welsh television subtitles. An experiment comprising of a lexical decision task examined SUBTLEX-CY frequency estimates against words with inconsistent frequencies in a much smaller Welsh corpus that is often used by researchers, the Cronfa Electroneg o’r Gymraeg (CEG; Ellis et al., 2001) as well as four other Welsh word frequency databases. Words were selected that were classified as low frequency (LF) in SUBTLEX-CY and high frequency (HF) in CEG and compared to words that were classified as medium frequency (MF) in both SUBTLEX-CY and CEG. Reaction time analyses showed that HF words in CEG were responded to more slowly compared to medium frequency (MF) words, suggesting that SUBTLEX-CY corpus provides a more reliable estimate of Welsh word frequencies. The new Welsh word frequency database that also includes part-of-speech, contextual diversity, and other lexical information is freely available for research purposes on the Open Science Framework repository at https://osf.io/9gkqm/

Contemporary carbon fluxes do not reflect the long-term carbon balance for an Atlantic blanket bog

Peatlands are one of the largest terrestrial stores of carbon. Carbon exchange in peatlands is often assessed solely by measurement of contemporary fluxes; however, these fluxes frequently indicate a much stronger sink strength than that measured by the rate of C accumulation in the peat profile over longer timescales. Here we compare profile-based measurements of C accumulation with the published net ecosystem C balance for the largest peatland area in Britain, the Flow Country of northern Scotland. We estimate the long-term rate of C accumulation to be 15.4 g C m−2 yr−1 for a site where a recent eddy covariance study has suggested contemporary C uptake more than six times greater (99.37 g C m−2 yr−1). Our estimate is supported by two further long-term C accumulation records from nearby sites which give comparable results. We demonstrate that a strong contemporary C sink strength may not equate to a strong long-term sink and explore reasons for this disparity. We recommend that contemporary C sequestration should be viewed in the context of the long-term ecological drivers, such as fires, ecohydrological feedbacks and the changing quality of litter inputs

VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data

<p>Abstract</p> <p>Background</p> <p>The procedural aspects of genome sequencing and assembly have become relatively inexpensive, yet the full, accurate structural annotation of these genomes remains a challenge. Next-generation sequencing transcriptomics (RNA-Seq), global microarrays, and tandem mass spectrometry (MS/MS)-based proteomics have demonstrated immense value to genome curators as individual sources of information, however, integrating these data types to validate and improve structural annotation remains a major challenge. Current visual and statistical analytic tools are focused on a single data type, or existing software tools are retrofitted to analyze new data forms. We present Visual Exploration and Statistics to Promote Annotation (VESPA) is a new interactive visual analysis software tool focused on assisting scientists with the annotation of prokaryotic genomes though the integration of proteomics and transcriptomics data with current genome location coordinates.</p> <p>Results</p> <p>VESPA is a desktop Java™ application that integrates high-throughput proteomics data (peptide-centric) and transcriptomics (probe or RNA-Seq) data into a genomic context, all of which can be visualized at three levels of genomic resolution. Data is interrogated via searches linked to the genome visualizations to find regions with high likelihood of mis-annotation. Search results are linked to exports for further validation outside of VESPA or potential coding-regions can be analyzed concurrently with the software through interaction with BLAST. VESPA is demonstrated on two use cases (<it>Yersinia pestis </it>Pestoides F and <it>Synechococcus </it>sp. PCC 7002) to demonstrate the rapid manner in which mis-annotations can be found and explored in VESPA using either proteomics data alone, or in combination with transcriptomic data.</p> <p>Conclusions</p> <p>VESPA is an interactive visual analytics tool that integrates high-throughput data into a genomic context to facilitate the discovery of structural mis-annotations in prokaryotic genomes. Data is evaluated via visual analysis across multiple levels of genomic resolution, linked searches and interaction with existing bioinformatics tools. We highlight the novel functionality of VESPA and core programming requirements for visualization of these large heterogeneous datasets for a client-side application. The software is freely available at <url>https://www.biopilot.org/docs/Software/Vespa.php</url>.</p

From genotypes to organisms: state-of-the-art and perspectives of a cornerstone in evolutionary dynamics

Understanding how genotypes map onto phenotypes, fitness, and eventually organisms is arguably the next major missing piece in a fully predictive theory of evolution. We refer to this generally as the problem of the genotype-phenotype map. Though we are still far from achieving a complete picture of these relationships, our current understanding of simpler questions, such as the structure induced in the space of genotypes by sequences mapped to molecular structures, has revealed important facts that deeply affect the dynamical description of evolutionary processes. Empirical evidence supporting the fundamental relevance of features such as phenotypic bias is mounting as well, while the synthesis of conceptual and experimental progress leads to questioning current assumptions on the nature of evolutionary dynamics-cancer progression models or synthetic biology approaches being notable examples. This work delves with a critical and constructive attitude into our current knowledge of how genotypes map onto molecular phenotypes and organismal functions, and discusses theoretical and empirical avenues to broaden and improve this comprehension. As a final goal, this community should aim at deriving an updated picture of evolutionary processes soundly relying on the structural properties of genotype spaces, as revealed by modern techniques of molecular and functional analysis

Study protocol for a randomised pilot study of a computer-based, non-pharmacological cognitive intervention for motor slowing and motor fatigue in Parkinson’s disease

Abstract Background Parkinson’s disease (PD) is a chronic, neurodegenerative disorder affecting over 137,000 people in the UK and an estimated five million people worldwide. Treatment typically involves long-term dopaminergic therapy, which improves motor symptoms, but is associated with dose-limiting side effects. Developing effective complementary, non-pharmacological interventions is of considerable importance. This paper presents the protocol for a three-arm pilot study to test the implementation of computer-based cognitive training that aims to produce improvements or maintenance of motor slower and motor fatigue symptoms in people with PD. The primary objective is to assess recruitment success and usability of external data capture devices during the intervention. The secondary objectives are to obtain estimates of variance and effect size for changes in primary and secondary outcome measures to inform sample size calculations and study design for a larger scale trial. Methods The study aims to recruit between 40 and 60 adults with early- to middle-stage PD (Hoehn and Yahr 1–3) from National Health Service (NHS) outpatients’ clinics and support groups across North Wales, UK. Participants will be randomised to receive training over five sessions in either a spatial grid navigation task, a sequential subtraction task or a spatial memory task. Patient-centred outcome measures will include motor examination scores from part 3 of the UPDRS-III and data from movement kinematic and finger tapping tasks. Discussion The results of this study will provide information regarding the feasibility of conducting a larger randomised control trial of non-pharmacological cognitive interventions of motor symptoms in PD. Trial registration ISRCTN, ISRCTN12565492. Registered 4 April 2018—retrospectively registered, in accordance with the WHO Trial Registration Data Set

Near Infrared Fluorescent Nanoparticles Derived from Hyaluronic Acid Improve Tumor Contrast for Image-Guided Surgery.

Tumor tissue that remains undetected at the primary surgical site can cause tumor recurrence, repeat surgery, and treatment strategy alterations that impose a significant patient and healthcare burden. Intraoperative near infrared fluorescence (NIRF) imaging is one potential method to identify remaining tumor by visualization of NIR fluorophores that are preferentially localized to the tumor. This requires development of fluorophores that consistently identify tumor tissue in different patients and tumor types. In this study we examined a panel of NIRF contrast agents consisting of polymeric nanoparticle (NP) formulations derived from hyaluronic acid (HA), with either physically entrapped indocyanine green (ICG) or covalently conjugated Cy7.5. Using orthotopic human breast cancer MDA-MB-231 xenografts in nude mice we identified two lead formulations. One, NanoICGPBA, with physicochemically entrapped ICG, showed 2.3-fold greater tumor contrast than ICG alone at 24 h (p \u3c 0.01), and another, NanoCy7.5100-H, with covalently conjugated Cy7.5, showed 74-fold greater tumor contrast than Cy7.5 alone at 24 h (p \u3c 0.0001). These two lead formulations were then tested in immune competent BALB/c mice bearing orthotopic 4T1 breast cancer tumors. NanoICGPBA showed 2.2-fold greater contrast than ICG alone (p \u3c 0.0001), and NanoCy7.5100-H showed 14.8-fold greater contrast than Cy7.5 alone (p \u3c 0.0001). Furthermore, both NanoICGPBA and NanoCy7.5100-H provided strong tumor enhancement using image-guided surgery in mice bearing 4T1 tumors. These studies demonstrate the efficacy of a panel of HA-derived NPs in delineating tumors in vivo, and identifies promising formulations that can be used for future in vivo tumor removal efficacy studies

A non-synonymous coding change in the CYP19A1 gene Arg264Cys (rs700519) does not affect circulating estradiol, bone structure or fracture

Background The biosynthesis of estrogens from androgens is catalyzed by aromatase P450 enzyme, coded by the CYP19A1 gene on chromosome 15q21.2. Genetic variation within the CYP19A1 gene sequence has been shown to alter the function of the enzyme. The aim of this study is to investigate whether a non-synonymous Arg264Cys (rs700519) single nucleotide polymorphism (SNP) is associated with altered levels of circulating estradiol, areal bone mineral density or fracture. Methods This population- based study of 1,022 elderly Caucasian women (mean age 74.95 ± 2.60 years) was genotyped for the rs700519 SNP were analyzed to detect any association with endocrine and bone phenotypes. Results The genotype frequencies were 997 wildtype (97.6%), 24 heterozygous (2.3%) and 1 homozygous (0.1%). When individuals were grouped by genotype, there was no association between the polymorphism and serum estradiol (wildtype 27.5 ± 16.0; variants 31.2 ± 18.4, P = 0.27). There was also no association seen on hip bone mineral density (wildtype 0.81 ± 0.12; 0.84 ± 0.14 for variants, P = 0.48) or femoral neck bone mineral density (0.69 ± 0.10 for wildtype; 0.70 ± 0.12 for variants, P = 0.54) before or after correction of the data with age, height, weight and calcium therapy. There were also no associations with quantitative ultrasound measures of bone structure (broadband ultrasound attenuation, speed of sound and average stiffness). Conclusions In a cohort of 1,022 elderly Western Australian women, the presence of Arg264Cys (rs700519) polymorphism was not found to be associated with serum estradiol, bone structure or phenotypes

From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics

Understanding how genotypes map onto phenotypes, fitness, and eventually organisms is arguably the next major missing piece in a fully predictive theory of evolution. We refer to this generally as the problem of the genotype-phenotype map. Though we are still far from achieving a complete picture of these relationships, our current understanding of simpler questions, such as the structure induced in the space of genotypes by sequences mapped to molecular structures, has revealed important facts that deeply affect the dynamical description of evolutionary processes. Empirical evidence supporting the fundamental relevance of features such as phenotypic bias is mounting as well, while the synthesis of conceptual and experimental progress leads to questioning current assumptions on the nature of evolutionary dynamics-cancer progression models or synthetic biology approaches being notable examples. This work delves into a critical and constructive attitude in our current knowledge of how genotypes map onto molecular phenotypes and organismal functions, and discusses theoretical and empirical avenues to broaden and improve this comprehension. As a final goal, this community should aim at deriving an updated picture of evolutionary processes soundly relying on the structural properties of genotype spaces, as revealed by modern techniques of molecular and functional analysis.Comment: 111 pages, 11 figures uses elsarticle latex clas

Nanopore native RNA sequencing of a human poly(A) transcriptome

High-throughput complementary DNA sequencing technologies have advanced our understanding of transcriptome complexity and regulation. However, these methods lose information contained in biological RNA because the copied reads are often short and modifications are not retained. We address these limitations using a native poly(A) RNA sequencing strategy developed by Oxford Nanopore Technologies. Our study generated 9.9 million aligned sequence reads for the human cell line GM12878, using thirty MinION flow cells at six institutions. These native RNA reads had a median length of 771 bases, and a maximum aligned length of over 21,000 bases. Mitochondrial poly(A) reads provided an internal measure of read-length quality. We combined these long nanopore reads with higher accuracy short-reads and annotated GM12878 promoter regions to identify 33,984 plausible RNA isoforms. We describe strategies for assessing 3′ poly(A) tail length, base modifications and transcript haplotypes