julilili42/papers huggingface dataset:
DACCOR–Detection, characterization, and reconstruction of repetitive regions in bacterial genomes
2018-05-29

The reconstruction of genomes using mapping-based approaches with short reads experiences difficulties when resolving repetitive regions. These repetitive regions in genomes result in low mapping qualities of the respective reads, which in turn lead to many unresolved bases. Currently, the reconstruction of these regions is often based on modified references in which the repetitive regions are masked. However, for many references, such masked genomes are not available or are based on repetitive regions of other genomes. Our idea is to identify repetitive regions in the reference genome de novo. These regions can then be used to reconstruct them separately using short read sequencing data. Afterward, the reconstructed repetitive sequence can be inserted into the reconstructed genome. We present the program detection, characterization, and reconstruction of repetitive regions, which performs these steps automatically. Our results show an increased base pair resolution of the repetitive regions in the reconstruction of Treponema pallidum samples, resulting in fewer unresolved bases.
Peri-saccadic perceptual mislocalization is different for upward saccades
2018-05-29

Abstract Saccadic eye movements, which dramatically alter retinal images, are associated with robust peri-movement perceptual alterations. Such alterations, thought to reflect brain mechanisms for maintaining perceptual stability in the face of saccade-induced retinalimage disruptions, are often studied by asking subjects to localize brief stimuli presented around the time of horizontal saccades. However, other saccade directions are not usually explored. Motivated by recently discovered asymmetries in upper and lower visual field representations in the superior colliculus, a structure important for both saccade generation and visual analysis, here we observed significant differences in peri-saccadic perceptual alterations for upward saccades relative to other saccade directions. We also found that, even for purely horizontal saccades, perceptual alterations differ for upper versus lower retinotopic stimulus locations. Our results, coupled with conceptual modeling, suggest that peri-saccadic perceptual alterations might critically depend on neural circuits, like superior colliculus, that asymmetrically represent the upper and lower visual fields.
Runge–Kutta convolution coercivity and its use for time-dependent boundary integral equations
2018-05-29

Abstract A coercivity property of temporal convolution operators is an essential tool in the analysis of time-dependent boundary integral equations and their space and time discretizations. It is known that this coercivity property is inherited by convolution quadrature time discretization based on A-stable multistep methods, which are of order at most 2. Here we study the question as to which Runge–Kutta-based convolution quadrature methods inherit the convolution coercivity property. It is shown that this holds without any restriction for the third-order Radau IIA method, and on permitting a shift in the Laplace domain variable, this holds for all algebraically stable Runge–Kutta methods and hence for methods of arbitrary order. As an illustration the discrete convolution coercivity is used to analyse the stability and convergence properties of the time discretization of a nonlinear boundary integral equation that originates from a nonlinear scattering problem for the linear wave equation. Numerical experiments illustrate the error behaviour of the Runge–Kutta convolution quadrature time discretization.
Peer Review #3 of "DACCOR–Detection, characterization, and reconstruction of repetitive regions in bacterial genomes (v0.2)"
2018-05-29

The reconstruction of genomes using mapping-based approaches with short reads experiences difficulties when resolving repetitive regions.These repetitive regions in genomes result in low mapping qualities of the respective reads, which in turn lead to many unresolved bases.Currently, the reconstruction of these regions is often based on modified references in which the repetitive regions are masked.However, for many references, such masked genomes are not available or are based on repetitive regions of other genomes.Our idea is to identify repetitive regions in the reference genome de novo.These regions can then be used to reconstruct them separately using short read sequencing data.Afterward, the reconstructed repetitive sequence can be inserted into the reconstructed genome.We present the program DACCOR, which performs these steps automatically.Our results show an increased base pair resolution of the repetitive regions in the reconstruction of Treponema pallidum samples, resulting in fewer unresolved bases.
Peer Review #3 of "DACCOR–Detection, characterization, and reconstruction of repetitive regions in bacterial genomes (v0.3)"
2018-05-29

The reconstruction of genomes using mapping-based approaches with short reads experiences difficulties when resolving repetitive regions.These repetitive regions in genomes result in low mapping qualities of the respective reads, which in turn lead to many unresolved bases.Currently, the reconstruction of these regions is often based on modified references in which the repetitive regions are masked.However, for many references, such masked genomes are not available or are based on repetitive regions of other genomes.Our idea is to identify repetitive regions in the reference genome de novo.These regions can then be used to reconstruct them separately using short read sequencing data.Afterward, the reconstructed repetitive sequence can be inserted into the reconstructed genome.We present the program DACCOR, which performs these steps automatically.Our results show an increased base pair resolution of the repetitive regions in the reconstruction of Treponema pallidum samples, resulting in fewer unresolved bases.
Peer Review #1 of "DACCOR–Detection, characterization, and reconstruction of repetitive regions in bacterial genomes (v0.1)"
2018-05-29

The reconstruction of genomes using mapping-based approaches with short reads experiences difficulties when resolving repetitive regions.These repetitive regions in genomes result in low mapping qualities of the respective reads, which in turn lead to many unresolved bases.Currently, the reconstruction of these regions is often based on modified references in which the repetitive regions are masked.However, for many references, such masked genomes are not available or are based on repetitive regions of other genomes.Our idea is to identify repetitive regions in the reference genome de novo.These regions can then be used to reconstruct them separately using short read sequencing data.Afterward, the reconstructed repetitive sequence can be inserted into the reconstructed genome.We present the program DACCOR, which performs these steps automatically.Our results show an increased base pair resolution of the repetitive regions in the reconstruction of Treponema pallidum samples, resulting in fewer unresolved bases.
Peer Review #2 of "DACCOR–Detection, characterization, and reconstruction of repetitive regions in bacterial genomes (v0.3)"
2018-05-29

The reconstruction of genomes using mapping-based approaches with short reads experiences difficulties when resolving repetitive regions.These repetitive regions in genomes result in low mapping qualities of the respective reads, which in turn lead to many unresolved bases.Currently, the reconstruction of these regions is often based on modified references in which the repetitive regions are masked.However, for many references, such masked genomes are not available or are based on repetitive regions of other genomes.Our idea is to identify repetitive regions in the reference genome de novo.These regions can then be used to reconstruct them separately using short read sequencing data.Afterward, the reconstructed repetitive sequence can be inserted into the reconstructed genome.We present the program DACCOR, which performs these steps automatically.Our results show an increased base pair resolution of the repetitive regions in the reconstruction of Treponema pallidum samples, resulting in fewer unresolved bases.
Peer Review #2 of "DACCOR–Detection, characterization, and reconstruction of repetitive regions in bacterial genomes (v0.1)"
2018-05-29

The reconstruction of genomes using mapping-based approaches with short reads experiences difficulties when resolving repetitive regions.These repetitive regions in genomes result in low mapping qualities of the respective reads, which in turn lead to many unresolved bases.Currently, the reconstruction of these regions is often based on modified references in which the repetitive regions are masked.However, for many references, such masked genomes are not available or are based on repetitive regions of other genomes.Our idea is to identify repetitive regions in the reference genome de novo.These regions can then be used to reconstruct them separately using short read sequencing data.Afterward, the reconstructed repetitive sequence can be inserted into the reconstructed genome.We present the program DACCOR, which performs these steps automatically.Our results show an increased base pair resolution of the repetitive regions in the reconstruction of Treponema pallidum samples, resulting in fewer unresolved bases.
Peer Review #2 of "DACCOR–Detection, characterization, and reconstruction of repetitive regions in bacterial genomes (v0.2)"
2018-05-29

The reconstruction of genomes using mapping-based approaches with short reads experiences difficulties when resolving repetitive regions.These repetitive regions in genomes result in low mapping qualities of the respective reads, which in turn lead to many unresolved bases.Currently, the reconstruction of these regions is often based on modified references in which the repetitive regions are masked.However, for many references, such masked genomes are not available or are based on repetitive regions of other genomes.Our idea is to identify repetitive regions in the reference genome de novo.These regions can then be used to reconstruct them separately using short read sequencing data.Afterward, the reconstructed repetitive sequence can be inserted into the reconstructed genome.We present the program DACCOR, which performs these steps automatically.Our results show an increased base pair resolution of the repetitive regions in the reconstruction of Treponema pallidum samples, resulting in fewer unresolved bases.
Finite groups satisfying character degree congruences
2018-05-29

Abstract Let G be a finite group, p a prime and <m:math xmlns:m="http://www.w3.org/1998/Math/MathML"> <m:mrow> <m:mi>c</m:mi> <m:mo>∈</m:mo> <m:mrow> <m:mo stretchy="false">{</m:mo> <m:mn>0</m:mn> <m:mo>,</m:mo> <m:mn>1</m:mn> <m:mo>,</m:mo> <m:mi mathvariant="normal">...</m:mi> <m:mo>,</m:mo> <m:mrow> <m:mi>p</m:mi> <m:mo>-</m:mo> <m:mn>1</m:mn> </m:mrow> <m:mo stretchy="false">}</m:mo> </m:mrow> </m:mrow> </m:math> {c\\in\\{0,1,\\ldots,p-1\\}} . Suppose that the degree of every nonlinear irreducible character of G is congruent to c modulo p . If here <m:math xmlns:m="http://www.w3.org/1998/Math/MathML"> <m:mrow> <m:mi>c</m:mi> <m:mo>=</m:mo> <m:mn>0</m:mn> </m:mrow> </m:math> {c=0} , then G has a normal p -complement by a well known theorem of Thompson. We prove that in the cases where <m:math xmlns:m="http://www.w3.org/1998/Math/MathML"> <m:mrow> <m:mi>c</m:mi> <m:mo>≠</m:mo> <m:mn>0</m:mn> </m:mrow> </m:math> {c\\neq 0} the group G is solvable with a normal abelian Sylow p -subgroup. If <m:math xmlns:m="http://www.w3.org/1998/Math/MathML"> <m:mrow> <m:mi>p</m:mi> <m:mo>≠</m:mo> <m:mn>3</m:mn> </m:mrow> </m:math> {p\\neq 3} then this is true provided these character degrees are congruent to c or to <m:math xmlns:m="http://www.w3.org/1998/Math/MathML"> <m:mrow> <m:mo>-</m:mo> <m:mi>c</m:mi> </m:mrow> </m:math> {-c} modulo p .
Peer Review #3 of "DACCOR–Detection, characterization, and reconstruction of repetitive regions in bacterial genomes (v0.1)"
2018-05-29

The reconstruction of genomes using mapping-based approaches with short reads experiences difficulties when resolving repetitive regions.These repetitive regions in genomes result in low mapping qualities of the respective reads, which in turn lead to many unresolved bases.Currently, the reconstruction of these regions is often based on modified references in which the repetitive regions are masked.However, for many references, such masked genomes are not available or are based on repetitive regions of other genomes.Our idea is to identify repetitive regions in the reference genome de novo.These regions can then be used to reconstruct them separately using short read sequencing data.Afterward, the reconstructed repetitive sequence can be inserted into the reconstructed genome.We present the program DACCOR, which performs these steps automatically.Our results show an increased base pair resolution of the repetitive regions in the reconstruction of Treponema pallidum samples, resulting in fewer unresolved bases.
The advantages of linear concentration–response curves for in vitro bioassays with environmental samples
2018-05-30

Abstract In vitro assays and high-throughput screening (HTS) tools are increasingly being employed as replacements for animal testing, but most concentration–response curves are still evaluated with models developed for animal testing. We argue that application of in vitro assays, particularly reporter gene assays, to environmental samples can benefit from a different approach to concentration–response modeling. First, cytotoxicity often occurs at higher concentrations, especially for weakly acting compounds and in complex environmental mixtures with many components. In these cases, specific effects can be masked by cytotoxicity. Second, for many HTS assays, low effect levels can be precisely quantified because of the low variability of controls in cell-based assays and the opportunity to run many concentrations and replicates when using high-density well-plate formats (e.g., 384 or more wells per plate). Hence, we recommend focusing concentration–response modeling on the lower portion of the concentration–response curve, which is approximately linear. Effect concentrations derived from low–effect level linear concentration–response models facilitate simple derivation of relative effect potencies and the correct application of mixture toxicity models in the calculation of bioanalytical equivalent concentrations. Environ Toxicol Chem 2018;37:2273–2280. © 2018 SETAC Abstract Linear concentration–response curves allow simple description of low-dose effects yet rigorous derivation of bioanalytical equivalent concentrations.
Planform changes and large wood dynamics in two torrents during a severe flash flood in Braunsbach, Germany 2016
2018-05-30

This work presents a post-event survey study, addressing the geomorphic response and large wood budget of two torrents, Grimmbach and Orlacher Bach, in southwestern Germany that were affected by a flash flood on May 29, 2016. During the event, large amounts of wood clogged and damaged a bridge of a cycling path at the outlet of the Grimmbach, while the town of Braunsbach was devastated by discharge and material transported along the Orlacher Bach. The severity of the event in these two small catchments (30.0 km<sup>2</sup> and 5.95 km<sup>2</sup>, respectively) is remarkable in basins with a relatively low average slope (10.7 and 12.0%, respectively). In order to gain a better understanding of the driving forces during this flood event an integrated approach was applied including (i) an estimate of peak discharges, (ii) an analysis of changes in channel width by comparing available aerial photographs before the flood with a post-flood aerial surveys with an Unmanned Aerial Vehicle and validation with field observations, (iii) a detailed mapping of landslides and analysis of their connectivity with the channel network and finally (iv) an analysis of the amounts of large wood recruited and deposited in the channel. The morphological changes in the channels can be explained by hydraulic parameters, such as stream power and unit stream power, and by morphological parameters such as the valley confinement. This is similar for LW recruitment amounts and volume of exported LW since most of it comes from the erosion of the valley floor. The morphological changes and large wood recruitment and deposit are in the range of studied mountain rivers. Both factors thus need to be considered for mapping and mitigating flash flood hazards also in this kind of low range mountains.
Circulating MicroRNA-21 Correlates With Left Atrial Low-Voltage Areas and Is Associated With Procedure Outcome in Patients Undergoing Atrial Fibrillation Ablation
2018-05-30

Background: Atrial fibrosis is a hallmark of arrhythmogenic structural remodeling in patients with persistent atrial fibrillation (AF) and is negatively correlated with procedure outcome in patients undergoing ablation. However, noninvasive methods to determine the extent of atrial fibrosis are limited. Here, we used microRNA (miRNA) expression analysis to detect markers of left atrial low-voltage areas (LVAs) in patients with persistent AF undergoing catheter ablation. Methods: We performed 3-dimensional voltage mapping in 102 patients (average age 62.1±13.1 years, CHA 2 DS 2 -VASc score of 2.3±1.6, LA size 41.5±5.7 mm) undergoing ablation for persistent AF and determined the extent of left atrial low-voltage. LVAs were defined if bipolar electrogram amplitudes were &lt;0.5 mV during sinus rhythm. Before ablation, we obtained a blood sample, isolated miRNAs, and profiled them on a miRCURY LNA Universal RT microRNA PCR Human panel. Results: Sixty-nine miRNAs were identified in all samples, with an average of 123 miRNAs detectable per sample. We found that the serum concentration of miR-21, a miRNA that has been previously linked to cardiac fibrosis development, was strongly associated with the extent of LVAs determined by voltage mapping. We could confirm that LVAs were negatively correlated with ablation success in a 1-year follow-up. In addition, miR-21 serum levels were associated with AF-free survival after catheter ablation. Conclusions: Circulating miR-21 correlates with left atrial LVAs and is associated with procedure outcome in patients with persistent AF undergoing ablation.
Chlorosis as a Developmental Program in Cyanobacteria: The Proteomic Fundament for Survival and Awakening
2018-05-30

Cyanobacteria that do not fix atmospheric nitrogen gas survive prolonged periods of nitrogen starvation in a chlorotic, dormant state where cell growth and metabolism are arrested. Upon nutrient availability, these dormant cells return to vegetative growth within 2-3 days. This resuscitation process is highly orchestrated and relies on the stepwise reinstallation and activation of essential cellular structures and functions. We have been investigating the transition to chlorosis and the return to vegetative growth as a simple model of a cellular developmental process and a fundamental survival strategy in biology. In the present study, we used quantitative proteomics and phosphoproteomics to describe the proteomic landscape of a dormant cyanobacterium and its dynamics during the transition to vegetative growth. We identified intriguing alterations in the set of ribosomal proteins, in RuBisCO components, in the abundance of central regulators and predicted metabolic enzymes. We found O-phosphorylation as an abundant protein modification in the chlorotic state, specifically of metabolic enzymes and proteins involved in photosynthesis. Nondegraded phycobiliproteins were hyperphosphorylated in the chlorotic state. We provide evidence that hyperphosphorylation of the terminal rod linker CpcD increases the lifespan of phycobiliproteins during chlorosis.
Toll-Like Receptor 2 and Lipoprotein-Like Lipoproteins Enhance Staphylococcus aureus Invasion in Epithelial Cells
2018-05-30

Staphylococcus aureus contains a certain subclass of lipoproteins, the so-called lipoprotein-like lipoproteins (Lpl's), that not only represent Toll-like receptor 2 (TLR2) ligands but are also involved in host cell invasion. Here we addressed the question of which factors contribute to Lpl-mediated invasion of epithelial cells and keratinocytes.
WATCHING GRASS GROW- A PILOT STUDY ON THE SUITABILITY OF PHOTOGRAMMETRIC TECHNIQUES FOR QUANTIFYING CHANGE IN ABOVEGROUND BIOMASS IN GRASSLAND EXPERIMENTS
2018-05-30

Abstract. Grassland ecology experiments in remote locations requiring quantitative analysis of the biomass in defined plots are becoming increasingly widespread, but are still limited by manual sampling methodologies. To provide a cost-effective automated solution for biomass determination, several photogrammetric techniques are examined to generate 3D point cloud representations of plots as a basis, to estimate aboveground biomass on grassland plots, which is a key ecosystem variable used in many experiments. Methods investigated include Structure from Motion (SfM) techniques for camera pose estimation with posterior dense matching as well as the usage of a Time of Flight (TOF) 3D camera, a laser light sheet triangulation system and a coded light projection system. In this context, plants of small scales (herbage) and medium scales are observed. In the first pilot study presented here, the best results are obtained by applying dense matching after SfM, ideal for integration into distributed experiment networks.
Control-value appraisals predicting students’ boredom in accounting classes: a continuous-state-sampling approach
2018-05-30

Abstract Background Boredom is a prevalent experience in school. Findings indicate that students are bored in a notable amount of instructional time with negative consequences for learning outcomes. The control-value theory considers control and value appraisals to be important antecedents of boredom. Methods In our study with 95 commercial school ninth graders, we investigated control-value appraisals and students’ boredom over 2 curricular weeks in the subject accounting by means of an experience sampling procedure with equally spaced measurement intervals called Continuous-State-Sampling. The CSSM data design generates a hierarchical data structure. Variability of students’ boredom can be segmented into three components: between times within lessons, between lessons within students and between students. We use multilevel models to address our research questions. Results We found negative associations for control and value appraisals in predicting boredom over time. In addition, the value appraisal moderates the relation between subjective control and boredom: Interested students get bored when lacking time to reflect on subject matter. Our results further revealed that control and value only interact when being conceptualised as state constructs close to the situation. Conclusions The results show that students’ in situ-experiences of boredom are related to personal and situational factors as well as their dynamic interplay.
Digital Rectal Examination and Anoscopy
2018-05-30

A complete physical examination includes a digital rectal examination. If the digital rectal examination is inconclusive, then anoscopy can be used to further examine the anal canal. This video demonstrates both the digital rectal examination and anoscopy.
Mapping the electric field distribution of tightly focused cylindrical vector beams with gold nanorings
2018-05-30

In this paper gold nanorings (NRs) are applied as particularly well-suited sensing elements for mapping the radially symmetric electric fields in the high numerical aperture focus of cylindrical vector beams. The optical properties of gold nanorings are analyzed by a combination of extinction and single particle dark field spectroscopy as well as confocal photoluminescence (PL) imaging. The results are compared to numerical calculations. The in-plane components in the focus of the cylindrical vector beams are estimated through the PL intensity distributions of the NRs. The optimum overlap between the structure and excitation is visualized by a narrow centre spot in the far-field PL scan.