bluuebunny/crossref_metadata_2025_split huggingface dataset:
Population Dynamics and Evaluation of Alternative Management Strategies for Nonnative Lake Trout in Priest Lake, Idaho
Authors: Ng Elizabeth L. , Fredericks Jim P. , Quist Michael C. 
Published: January 2016

Abstract
Lake Trout Salvelinus namaycush have been introduced widely throughout the western USA to enhance recreational fisheries, but high predatory demand can create challenges for management of yield and trophy fisheries alike. Lake Trout were introduced to Priest Lake, Idaho, during the 1920s, but few fishery-independent data are available to guide current or future management actions. We collected fishery-independent data to describe population dynamics and evaluate potential management scenarios using an age-structured population model. Lake Trout in Priest Lake were characterized by fast growth at young ages, which resulted in young age at maturity. However, adult growth rates and body condition were lower than for other Lake Trout populations. High rates of skipped spawning (&gt;50%) were also observed. Model projections indicated that the population was growing (λ = 1.03). Eradication could be achieved by increasing annual mortality to 0.32, approximately twice the current rate. A protected slot length limit could increase population length-structure, but few fish grew fast enough to exit the slot. In contrast, a juvenile removal scenario targeting age-2 to age-5 Lake Trout maintained short-term harvest of trophy-length individuals while reducing overall population abundance.
Effect of the structure of dietary epoxylignan on its cytotoxic activity: relationship between the structure and the activity of 7,7′-epoxylignan and the introduction of apoptosis by caspase 3/7
Authors: Wukirsari Tuti , Nishiwaki Hisashi , Nishi Kosuke , Sugahara Takuya , Akiyama Koichi , Kishida Taro , Yamauchi Satoshi 
Published: January 2016

Abstract
We compared the cytotoxic activities of dietary epoxylignans and their stereoisomers and found (−)-verrucosin, which is (7S,7′R,8R,8′R)-7,7′-epoxylignan, to be the most cytotoxic epoxylignan against HeLa cells (IC50 = 6.6 μM). On the other hand, the activity was about a factor of 10 less against HL-60. In this research on the relationship between the structure and cytotoxic activity of (−)-verrucosin 13, the 7-(4-methoxyphenyl)-7′-(3,4-dimethoxyphenyl) derivative 60, for which the activity (IC50 = 2.4 μM) is three times greater than (−)-verrucosin 13, was discovered. The induction of apoptosis by caspase 3/7 was observed upon treatment with the (−)-verrucosin derivative.
Spectral mapping of V348 Puppis: spiral arms in the period gap★
Authors: Saito R. K. , Baptista R. 
Published: January 2016

Abstract
We report the analysis of Hubble Space Telescope (HST) UV–optical spectroscopy of the nova-like variable V348 Puppis with eclipse mapping techniques. We measured the eclipse width at disc centre and determined a lower limit on the mass ratio of q &gt; 0.3, with a tight relation between q and the binary inclination i. For 0.31 ≤ q ≤ 0.6, we have 79$_{.}^{\circ}$5 ≤ i ≤ 88$_{.}^{\circ}$2. Simulations with 3D eclipse mapping give no support to the suggestion of self-shielding of the accretion disc of V348 Pup, indicating a geometrically thin disc. Eclipse maps reveal two structures in the accretion disc interpreted as tidally induced spiral arms, which account for 50–60  per cent of the disc flux in the continuum. The uneclipsed component accounts for 30–50  per cent of the light, indicating that a significant fraction of the light comes from a vertically extended disc chromosphere + wind. Its spectrum can be fitted by an isothermal slab of gas with temperature T = 9600 K and column density Σ ∼1010 g cm−2, corresponding to optically thick thermal emission. Superhumps had faded by the epoch of the HST observations; the disc shrank in size while the disc wind flux increased with respect to observations when superhumps were present. This may be explained if the disc wind outflow is the dominant source of angular momentum loss from the accretion disc. Previously observed accretion disc radii of V348 Pup and of two other binaries with large discs are used to derive an empirical expression for the maximum possible disc radius, which implies that superhumps may be found in systems with up to q ≃ 0.7.
Efficient Correction of the Sickle Mutation in Human Hematopoietic Stem Cells Using a Cas9 Ribonucleoprotein Complex
Authors: DeWitt Mark A. , Magis Wendy , Bray Nicolas L. , Wang Tianjiao , Berman Jennifer R. , Urbinati Fabrizia , Muñoz Denise P. , Kohn Donald B. , Walters Mark C. , Carroll Dana , Martin David K. , Corn Jacob E. 
Published: January 2016

AbstractSickle Cell Disease (SCD) is a serious recessive genetic disorder caused by a single nucleotide polymorphism (SNP) in the ß-globin gene (HBB). Sickle hemoglobin polymerizes within red blood cells (RBCs), causing them to adopt an elongated “sickle” shape. Sickle RBCs damage vasculature, leading to severe symptoms, ultimately diminishing patient quality of life and reducing lifespan. Here, we use codelivery of a pre-formed Cas9 ribonucleoprotein complex (RNP) and a singlestranded DNA (ssDNA) oligonucleotide donor to drive sequence replacement at the SCD SNP in human CD34+ hematopoietic stem/progenitor cells (HSPCs). Corrected HSPCs from SCD patients produce less sickle hemoglobin protein and correspondingly increased wild-type hemoglobin when differentiated into erythroblasts. When injected into immunocompromised mice, treated HSPCs maintain editing long-term at therapeutically relevant levels. These results demonstrate that the Cas9 RNP/ssDNA donor approach can mediate efficient HSPC gene editing and could form the basis for treatment of SCD by autologous hematopoietic cell transplantation.
Population-Scale Sequencing Data Enables Precise Estimates of Y-STR Mutation Rates
Authors: Willems Thomas , Gymrek Melissa , Poznik G. David , Tyler-Smith Chris ,   The 1000 Genomes Project Chromosome Y Group, Erlich Yaniv 
Published: January 2016

AbstractShort Tandem Repeats (STRs) are mutation-prone loci that span nearly 1% of the human genome. Previous studies have estimated the mutation rates of highly polymorphic STRs using capillary electrophoresis and pedigree-based designs. While this work has provided insights into the mutational dynamics of highly mutable STRs, the mutation rates of most others remain unknown. Here, we harnessed whole-genome sequencing data to estimate the mutation rates of Y-chromosome STRs (Y-STRs) with 2-6 base pair repeat units that are accessible to Illumina sequencing. We genotyped 4,500 Y-STRs using data from the 1000 Genomes Project and the Simons Genome Diversity Project. Next, we developed MUTEA, an algorithm that infers STR mutation rates from population-scale data using a high-resolution SNP-based phylogeny. After extensive intrinsic and extrinsic validations, we harnessed MUTEA to derive mutation rate estimates for 702 polymorphic STRs by tracing each locus over 222,000 meioses, resulting in the largest collection of Y-STR mutation rates to date. Using our estimates, we identified determinants of STR mutation rates and built a model to predict rates for STRs across the genome. These predictions indicate that the load of de novo STR mutations is at least 75 mutations per generation, rivaling the load of all other known variant types. Finally, we identified Y-STRs with potential applications in forensics and genetic genealogy, assessed the ability to differentiate between the Y-chromosomes of father-son pairs, and imputed Y-STR genotypes.
Transethnic genetic correlation estimates from summary statistics
Authors: Brown Brielin C. ,   Asian Genetic Epidemiology Network-Type 2 Diabetes (AGEN-T2G) Consortium, Ye Chun Jimmie , Price Alkes L. , Zaitlen Noah 
Published: January 2016

abstractThe increasing number of genetic association studies conducted in multiple populations provides unprecedented opportunity to study how the genetic architecture of complex phenotypes varies between populations, a problem important for both medical and population genetics. Here we develop a method for estimating thetransethnic genetic correlation: the correlation of causal variant effect sizes at SNPs common in populations. We take advantage of the entire spectrum of SNP associations and use only summary-level GWAS data. This avoids the computational costs and privacy concerns associated with genotype-level information while remaining scalable to hundreds of thousands of individuals and millions of SNPs. We apply our method to gene expression, rheumatoid arthritis, and type-two diabetes data and overwhelmingly find that the genetic correlation is significantly less than 1. Our method is implemented in a python package calledpopcorn.
Open Hardware: Towards a Fully-Wireless Sub-Cranial Neuro-Implant for Measuring Electrocorticography Signals
Authors: Rotermund David , Pistor Jonas , Hoeffmann Janpeter , Schellenberg Tim , Boll Dmitriy , Tolstosheeva Elena , Gauck Dieter , Stemmann Heiko , Peters-Drolshagen Dagmar , Kreiter Andreas K. , Schneider Martin , Paul Steffen , Lang Walter , Pawelzik Klaus R. 
Published: January 2016

AbstractImplantable neuronal interfaces to the brain are an important keystone for future medical applications. However, entering this field of research is difficult since such an implant requires components from many different areas of technology. Since the complete avoidance of wires is important due to the risk of infections and other long-term problems, means for wireless transmitting data and energy are a necessity which adds to the requirements. In recent literature many high-tech components for such implants are presented with remarkable properties. However, these components are typically not freely available for your system. Every group needs to re-develop their own solution. This raises the question if it is possible to create a reusable design for an implant and its external base-station, such that it allows other groups to use it as a starting point. In this article we try to answer this question by presenting a design based exclusively on commercial off-the-shelf components and studying the properties of the resulting system. Following this idea, we present a fully wireless neuronal implant for simultaneously measuring electrocorticography signals at 128 locations from the surface of the brain. All design files are available as open source.
Logic models to predict continuous outputs based on binary inputs with an application to personalized cancer therapy
Authors: Knijnenburg Theo , Klau Gunnar , Iorio Francesco , Garnett Mathew , McDermott Ultan , Shmulevich Ilya , Wessels Lodewyk 
Published: January 2016

AbstractMining large datasets using machine learning approaches often leads to models that are hard to interpret and not amenable to the generation of hypotheses that can be experimentally tested. Finding ‘actionable knowledge’ is becoming more important, but also more challenging as datasets grow in size and complexity. We present ‘Logic Optimization for Binary Input to Continuous Output’ (LOBICO), a computational approach that infers small and easily interpretable logic models of binary input features that explain a binarized continuous output variable. Although the continuous output variable is binarized prior to optimization, the continuous information is retained to find the optimal logic model. Applying LOBICO to a large cancer cell line panel, we find that logic combinations of multiple mutations are more predictive of drug response than single gene predictors. Importantly, we show that the use of the continuous information leads to robust and more accurate logic models. LOBICO is formulated as an integer programming problem, which enables rapid computation on large datasets. Moreover, LOBICO implements the ability to uncover logic models around predefined operating points in terms of sensitivity and specificity. As such, it represents an important step towards practical application of interpretable logic models.
Read-Based Phasing of Related Individuals
Authors: Garg Shilpa , Martin Marcel , Marschall Tobias 
Published: January 2016

AbstractMotivationRead-based phasing deduces the haplotypes of an individual from sequencing reads that cover multiple variants, while genetic phasing takes only genotypes as input and applies the rules of Mendelian inheritance to infer haplotypes within a pedigree of individuals. Combining both into an approach that uses these two independent sources of information - reads and pedigree - has the potential to deliver results better than each individually.ResultsWe provide a theoretical framework combining read-based phasing with genetic haplotyping, and describe a fixed-parameter algorithm and its implementation for finding an optimal solution. We show that leveraging reads of related individuals jointly in this way yields more phased variants and at a higher accuracy than when phased separately, both in simulated and real data. Coverages as low as 2× for each member of a trio yield haplotypes that are as accurate as when analyzed separately at 15× coverage per individual.Availabilityhttps://bitbucket.org/whatshap/whatshap(branch pedmec)Contactt.marschall@mpi-inf.mpg.de
Expanding perspectives on cognition in humans, animals, and machines
Authors: Gomez-Marin Alex , Mainen Zachary F 
Published: January 2016

AbstractOver the past decade neuroscience has been attacking the problem of cognition with increasing vigor. Yet, what exactlyiscognition, beyond a general signifier of anything seemingly complex the brain does? Here, we briefly review attempts to define, describe, explain, build, enhance and experience cognition. We highlight perspectives including psychology, molecular biology, computation, dynamical systems, machine learning, behavior and phenomenology. This survey of the landscape reveals not a clear target for explanation but a pluralistic and evolving scene with diverse opportunities for grounding future research. We argue that rather than getting to the bottom of it, over the next century, by deconstructing and redefining cognition, neuroscience will and should expand rather than merely reduce our concept of the mind.
Bayesian Inference of Natural Selection from Allele Frequency Time Series
Authors: Schraiber Joshua G. , Evans Steven N. , Slatkin Montgomery 
Published: January 2016

AbstractThe advent of accessible ancient DNA technology now allows the direct ascertainment of allele frequencies in ancestral populations, thereby enabling the use of allele frequency time series to detect and estimate natural selection. Such direct observations of allele frequency dynamics are expected to be more powerful than inferences made using patterns of linked neutral variation obtained from modern individuals. We developed a Bayesian method to make use of allele frequency time series data and infer the parameters of general diploid selection, along with allele age, in non-equilibrium populations. We introduce a novel path augmentation approach, in which we use Markov chain Monte Carlo to integrate over the space of allele frequency trajectories consistent with the observed data. Using simulations, we show that this approach has good power to estimate selection coefficients and allele age. Moreover, when applying our approach to data on horse coat color, we find that ignoring a relevant demographic history can significantly bias the results of inference. Our approach is made available in a C++ software package.
Automated Discrimination of Dicentric and Monocentric Chromosomes by Machine Learning-based Image Processing
Authors: Li Yanxin , Knoll Joan H. , Wilkins Ruth , Flegal Farrah N. , Rogan Peter K. 
Published: January 2016

AbstractDose from radiation exposure can be estimated from dicentric chromosome (DC) frequencies in metaphase cells of peripheral blood lymphocytes. We automated DC detection by extracting features in Giemsa-stained metaphase chromosome images and classifying objects by machine learning (ML). DC detection involves i) intensity thresholded segmentation of metaphase objects, ii) chromosome separation by watershed transformation and elimination of inseparable chromosome clusters, fragments and staining debris using a morphological decision tree filter, iii) determination of chromosome width and centreline, iv) derivation of centromere candidates and v) distinction of DCs from monocentric chromosomes (MC) by ML. Centromere candidates are inferred from 14 image features input to a Support Vector Machine (SVM). 16 features derived from these candidates are then supplied to a Boosting classifier and a second SVM which determines whether a chromosome is either a DC or MC. The SVM was trained with 292 DCs and 3135 MCs, and then tested with cells exposed to either low (1 Gy) or high (2-4 Gy) radiation dose. Results were then compared with those of 3 experts. True positive rates (TPR) and positive predictive values (PPV) were determined for the tuning parameter, σ. At larger σ, PPV decreases and TPR increases. At high dose, for σ= 1.3, TPR = 0.52 and PPV = 0.83, while at σ= 1.6, the TPR = 0.65 and PPV = 0.72. At low dose and σ = 1.3, TPR = 0.67 and PPV = 0.26. The algorithm differentiates DCs from MCs, overlapped chromosomes and other objects with acceptable accuracy over a wide range of radiation exposures.
Divorcing Strain Classification From Species Names
Authors: Baltrus David A. 
Published: January 2016

AbstractConfusion about strain classification and nomenclature permeates modern microbiology. Although taxonomists have traditionally acted as gatekeepers of order, the numbers of and speed at which new strains are identified has outpaced the opportunity for professional classification for many lineages. Furthermore, the growth of bioinformatics and database fueled investigations have placed metadata curation in the hands of researchers with little taxonomic experience. Here I describe practical challenges facing modern microbial taxonomy, provide an overview of complexities of classification for environmentally ubiquitous taxa likePseudomonas syringae, and emphasize that classification and nomenclature need not be the one in the same. A move toward implementation of relational classification schemes based on inherent properties of whole genomes could provide sorely needed continuity in how strains are referenced across manuscripts and data sets.
A Bayesian framework for comparing the structure of spontaneous correlated activity recorded under different conditions
Authors: Cutts Catherine S , Eglen Stephen J 
Published: January 2016

AbstractDistant-dependent correlations in spontaneous retinal activity are thought to be instructive in the development of the retinotopic map and eye-specific segregation maps. Many studies which seek to investigate these correlations and their role in map formation record spontaneous retinal activity from different pheno-types or experimental conditions and compare the distance-dependence of the correlations between different conditions. They seek to demonstrate that these correlations differ significantly, and this analysis is often key to the study’s conclusions. In this work, we assess the methods of inference which have been previously used to investigate this problem and conclude that they are inadequate. We propose a hierarchical Bayesian framework to model distant-dependent correlations in spontaneous retinal activity data and specify a method which uses the data to specify the form of the model. This model allows us to assess the evidence for/against differences in correlations between experimental conditions in a more robust and credible way. We demonstrate the use of this method by applying it to data from two studies of spontaneous retinal activity. We believe however the framework to be rather more general and that it can be used in a wide range of datasets where distance and correlation are substitute for other independent and dependent variables from experiments.
Dendritic trafficking faces physiologically critical speed-precision tradeoffs
Authors: Williams Alex H. , O’Donnell Cian , Sejnowski Terrence , O’Leary Timothy 
Published: January 2016

AbstractNervous system function requires intracellular transport of channels, receptors, mRNAs, and other cargo throughout complex neuronal morphologies. Local signals such as synaptic input can regulate cargo trafficking, motivating the leading conceptual model of neuron-wide transport, sometimes called the “sushi-belt model” (Doyle and Kiebler, 2011). Current theories and experiments are based on this model, yet its predictions are not rigorously understood. We formalized the sushi belt model mathematically, showing how it can achieve arbitrarily complex spatial distributions of cargo in reconstructed morphologies. However, the model also predicts an unavoidable, morphology dependent tradeoff between speed, precision and metabolic efficiency of cargo transport. With experimental estimates of trafficking kinetics, the model predicts delays of many hours or days for modestly accurate and efficient cargo delivery throughout a dendritic tree. These findings challenge current understanding of the efficacy of nucleus-to-synapse trafficking and may explain the prevalence of local biosynthesis in neurons.
The assessment of autism spectrum disorders in adults
Authors: Galanopoulos Anastasios , Robertson Dene , Woodhouse Emma 
Published: January 2016

Purpose– The purpose of this paper is to explore and highlight the main elements of an autism spectrum disorder assessment in adults. It features significant challenges for the clinical teams responsible to undertake the assessment. This paper aims to explain the importance of the wider needs assessment in accordance to the Autism Act and Autism Strategy.Design/methodology/approach– The paper describes the main symptom domains for an ASD diagnosis, according to the two basic diagnostic manuals. It provides compendious summary of the available diagnostic tools and the significant comorbidities people with ASD present with including other neurodevelopmental disorders, mental or physical health problems, challenging behaviour and risk issues.Findings– The paper proposes that all National Health System professionals should be able to recognise possible signs of ASD and accordingly refer individuals for a comprehensive assessment to secondary services. It highlights the importance of a wider needs assessment as part of a broader approach to addressing the needs of those with suspected ASD.Practical implications– The paper aims to improve the gaps which remain in the referral and diagnostic process of people affected by ASD.Social implications– Through a comprehensive assessment the paper aims to improve the educational, social and personal functioning of people with ASD as well as the quality of life of their parents and carers.Originality/value– The paper assembles a wide range of relevant considerations in regards to potential ASD in one place, and can be used to inform a comprehensive understanding of the assessment/diagnosis process.