Reading sentences with a late closure ambiguity: does semantic information help?

Stowe (1989) reported that semantic information eliminates garden paths in sentences with the direct-object vs. subject ambiguity, such as Even before the police stopped the driver was very frightened. Three experiments are presented which addressed some methodological problems in Stowe's study. Experiment 1, using a word-by-word, self-paced reading task with grammaticality judgements, manipulated animacy of the first subject noun while controlling for the plausibility of the transitive action. The results suggest that initial sentence analysis is not guided by animacy. Experiment 2 and 3, using the self-paced task with grammaticality judgements and eye-tracking, varied the plausibility of the direct-object nouns to test revision effects. Plausibility was found to facilitate revision without fully eliminating garden paths, in line with various revision models. The findings support the view of a sentence processing system relying heavily on syntactic information, with semantic information playing a weaker role both in initial analysis and during revision, thus supporting serial, syntax-first models and ranked-parallel models relying on structural criteria

Plasminogen activator‐1 overexpression decreases experimental postthrombotic vein wall fibrosis by a non‐vitronectin‐dependent mechanism

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/108289/1/jth12644.pd

The PDF4LHC report on PDFs and LHC data: Results from Run I and preparation for Run II

The accurate determination of the Parton Distribution Functions (PDFs) of the proton is an essential ingredient of the Large Hadron Collider (LHC) program. PDF uncertainties impact a wide range of processes, from Higgs boson characterisation and precision Standard Model measurements to New Physics searches. A major recent development in modern PDF analyses has been to exploit the wealth of new information contained in precision measurements from the LHC Run I, as well as progress in tools and methods to include these data in PDF fits. In this report we summarise the information that PDF-sensitive measurements at the LHC have provided so far, and review the prospects for further constraining PDFs with data from the recently started Run II. This document aims to provide useful input to the LHC collaborations to prioritise their PDF-sensitive measurements at Run II, as well as a comprehensive reference for the PDF-fitting collaborations.Comment: 55 pages, 13 figure

Population Structure Analyses Provide Insight into the Source Populations Underlying Rural Isolated Communities in Illinois

We have previously hypothesized that relatively small and isolated rural communities may experience founder effects, defined as the genetic ramifications of small population sizes at the time of a community’s establishment. To explore this, we used an Illumina Infinium Omni2.5Exome-8 chip to collect data from 157 individuals from four Illinois communities, three rural and one urban. Genetic diversity estimates of 999,259 autosomal markers suggested that the reduction in heterozygosity due to shared ancestry was approximately 0, indicating a randomly mating population. An eigenanalysis, which is similar to a principal component analysis but ran on a genetic coancestry matrix, conducted in the SNPRelate R package revealed that the majority of these individuals formed one cluster with a few putative outliers obscuring population variation. An additional eigenanalysis on the same markers in a combined data set including the 2,504 individuals in the 1000 Genomes database found that most of the 157 Illinois individuals clustered into one group in close proximity to individuals of European descent. A final eigenanalysis of the Illinois individuals with the 503 individuals of European descent (within the 1000 Genomes Project) revealed two clusters of individuals and likely two source populations; one British and one consisting of multiple European subpopulations. We therefore demonstrate the feasibility of examining genetic relatedness across Illinois populations and assessing the number of source populations using publicly available databases. When assessed, it becomes possible for population structure information to contribute to the understanding of genetic history in rural populations

Computer vision and machine learning for robust phenotyping in genome-wide studies

Traditional evaluation of crop biotic and abiotic stresses are time-consuming and labor-intensive limiting the ability to dissect the genetic basis of quantitative traits. A machine learning (ML)-enabled image-phenotyping pipeline for the genetic studies of abiotic stress iron deficiency chlorosis (IDC) of soybean is reported. IDC classification and severity for an association panel of 461 diverse plant-introduction accessions was evaluated using an end-to-end phenotyping workflow. The workflow consisted of a multi-stage procedure including: (1) optimized protocols for consistent image capture across plant canopies, (2) canopy identification and registration from cluttered backgrounds, (3) extraction of domain expert informed features from the processed images to accurately represent IDC expression, and (4) supervised ML-based classifiers that linked the automatically extracted features with expert-rating equivalent IDC scores. ML-generated phenotypic data were subsequently utilized for the genome-wide association study and genomic prediction. The results illustrate the reliability and advantage of ML-enabled image-phenotyping pipeline by identifying previously reported locus and a novel locus harboring a gene homolog involved in iron acquisition. This study demonstrates a promising path for integrating the phenotyping pipeline into genomic prediction, and provides a systematic framework enabling robust and quicker phenotyping through ground-based systems

New parton distributions in fixed flavour factorization scheme from recent deep-inelastic-scattering data

We present our QCD analysis of the proton structure function $F_2^p(x,Q^2)$ to determine the parton distributions at the next-to-leading order (NLO). The heavy quark contributions to $F_2^i(x,Q^2)$, with $i$ = $c$, $b$ have been included in the framework of the `fixed flavour number scheme' (FFNS). The results obtained in the FFNS are compared with available results such as the general-mass variable-flavour-number scheme (GM-VFNS) and other prescriptions used in global fits of PDFs. In the present QCD analysis, we use a wide range of the inclusive neutral-current deep-inelastic-scattering (NC DIS) data, including the most recent data for charm $F_2^c$, bottom $F_2^b$, longitudinal $F_L$ structure functions and also the reduced DIS cross sections $\sigma_{r,NC}^\pm$ from HERA experiments. The most recent HERMES data for proton and deuteron structure functions are also added. We take into account ZEUS neutral current $e^ \pm p$ DIS inclusive jet cross section data from HERA together with the recent Tevatron Run-II inclusive jet cross section data from CDF and D{\O}. The impact of these recent DIS data on the PDFs extracted from the global fits are studied. We present two families of PDFs, {\tt KKT12} and {\tt KKT12C}, without and with HERA `combined' data sets on $e^{\pm}p$ DIS. We find these are in good agreement with the available theoretical models.Comment: 23 pages, 26 figures and 4 tables. V3: Only few comments and references added in the replaced version, results unchanged. Code can be found at http://particles.ipm.ir/links/QCD.ht

Identification of DNA methylation changes at cis-regulatory elements during early steps of HSC differentiation using tagmentation-based whole genome bisulfite sequencing

Epigenetic alterations during cellular differentiation are a key molecular mechanism which both instructs and reinforces the process of lineage commitment. Within the haematopoietic system, progressive changes in the DNA methylome of haematopoietic stem cells (HSCs) are essential for the effective production of mature blood cells. Inhibition or loss of function of the cellular DNA methylation machinery has been shown to lead to a severe perturbation in blood production and is also an important driver of malignant transformation. HSCs constitute a very rare cell population in the bone marrow, capable of life-long self-renewal and multi-lineage differentiation. The low abundance of HSCs has been a major technological barrier to the global analysis of the CpG methylation status within both HSCs and their immediate progeny, the multipotent progenitors (MPPs). Within this Extra View article, we review the current understanding of how the DNA methylome regulates normal and malignant hematopoiesis. We also discuss the current methodologies that are available for interrogating the DNA methylation status of HSCs and MPPs and describe a new data set that was generated using tagmentation-based whole genome bisulfite sequencing (TWGBS) in order to comprehensively map methylated cytosines using the limited amount of genomic DNA that can be harvested from rare cell populations. Extended analysis of this data set clearly demonstrates the added value of genome-wide sequencing of methylated cytosines and identifies novel important cis-acting regulatory regions that are dynamically remodeled during the first steps of haematopoietic differentiation