julilili42/papers huggingface dataset:
LATE-BREAKING ABSTRACT: Evaluating blood eosinophils and exacerbation history to predict ICS response in COPD
2016-09-01

<b>Introduction:</b> Inhaled corticosteroids (ICS) are used to reduce the rate of COPD exacerbations (EX). Debate continues over use of blood eosinophils (EOS) to predict ICS response, with some suggesting a cut-off of ≥2% (Pascoe S et al. Lancet Respir Med 2015;3:435–42). In the WISDOM study (NCT00975195), this response was driven by patients with higher EOS levels (≥4% or ≥300 cells/μL) [Watz H et al. Lancet Respir Med 2016;4:390–8]. <b>Aim:</b> We analysed WISDOM data stratified by prior EX and EOS levels to determine if the ICS responder group could be better specified. <b>Methods:</b><i>Post hoc</i> analysis of the rate of moderate/severe EX after complete ICS withdrawal using a negative binomial regression model to estimate EX rate according to number of prior EX (&lt;2 and ≥2, estimated based on the number of courses of antibiotics or steroids in the past year) and EOS subgroups. <b>Results:</b> High EOS counts (≥400 cells/μL) were associated with increased EX rate after complete ICS withdrawal only in patients with ≥2 prior EX (Figure). <b>Conclusions:</b> Withdrawal of ICS only increased the rate of EX in patients with both raised EOS (≥400 cells/μL) and a history of frequent EX. In patients who do not meet these criteria, ICS may not be as effective as is commonly assumed. <b>Funding:</b> Boehringer Ingelheim.
Performance Analysis of CoDel and PIE for Saturated TCP Sources
2016-09-01

In the recent years, the bufferbloat phenomenon was observed which is mainly due to oversized unmanaged buffers in the Internet. This triggered a new discussion of active queue management (AQM) algorithms in the IETF. "Controlled Delay" (CoDel) and "Proportional Integral controller Enhanced" (PIE) are considered as an alternative to "Random Early Detection" (RED). Their intention is both to take advantage of large buffers for occasional bursts and to limit queueing delays most of the time. Moreover, they are able to cope with varying bandwidth. In this paper, we study the performance of CoDel, PIE, and CoDel-ACT, which is an effective modification of CoDel that leads to better performance than CoDel in our studies. We experiment with saturated TCP sources and a fixed-bandwidth bottleneck link and focus on the delay-limiting phase of the algorithms. We investigate the impact of configuration parameters and traffic load on link utilization and queueing delay. We study the timely evolution of queuing delays and drop patterns, and point out significant differences among the algorithms. In particular, we show that CoDel's drop behavior changes over time and may lead to underutilization.
jLISP: An Open, Modular, and Extensible Java-Based LISP Implementation
2016-09-01

LISP is a standardized overlay protocol implementing the locator/identifier split for the Internet. Multiple extensions exist, e.g., for NAT traversal, traffic engineering, etc. Existing LISP implementations are mostly platform-specific, hard to extend or they are closed source. In this work we present a Java-based implementation for LISP which is open source, modular, and features a plugin mechanism that enables simple integration of new functionality. It provides behavior for LISP nodes, infrastructure nodes, and various extensions, it is easily portable, can be run on various operating systems and platforms, in particular on Android smartphones. The demo illustrates LISP-based communication including the extensions mentioned above. In addition, the extensibility is demonstrated by a plugin for a statistics application.
Generation of optic atrophy 1 patient-derived induced pluripotent stem cells (iPS-OPA1-BEHR) for disease modeling of complex optic atrophy syndromes (Behr syndrome)
2016-09-01

Human skin fibroblasts were isolated from a 48-year-old patient carrying compound heterozygous mutations (c.610+364G>A and c.1311A>G) in OPA1, responsible for early onset optic atrophy complicated by ataxia and pyramidal signs (Behr syndrome; OMIM #210000). Fibroblasts were reprogrammed using episomal plasmids carrying hOCT4, hSOX2, hKLF4, hL-MYC and hLIN28. The generated transgene-free line iPS-OPA1-BEHR showed no additional genomic aberrations, maintained the disease-relevant mutations, expressed important pluripotency markers and was capable to differentiate into cells of all three germ layers in vitro. The generated iPS-OPA1-BEHR line might be a useful platform to study the pathomechanism of early onset complicated optic atrophy syndromes.
An extension of a convergence theorem for Markov chains arising in population genetics
2016-09-01

Abstract An extension of a convergence theorem for sequences of Markov chains is derived. For every positive integer N let ( X N ( r )) r be a Markov chain with the same finite state space S and transition matrix Π N = I + d N B N , where I is the unit matrix, Q a generator matrix, ( B N ) N a sequence of matrices, lim N ℩∞ c N = lim N →∞ d N =0 and lim N →∞ c N ∕ d N =0. Suppose that the limits P ≔lim m →∞ ( I + d N Q ) m and G ≔lim N →∞ P B N P exist. If the sequence of initial distributions P X N (0) converges weakly to some probability measure μ, then the finite-dimensional distributions of ( X N ([ t ∕ c N )) t ≥0 converge to those of the Markov process ( X t ) t ≥0 with initial distribution μ, transition matrix P e t G and lim N →∞ ( I + d N Q + c N B N ) [ t ∕ c N ]
Exploring the temporal dynamics of attentional reallocations with the multiple object tracking paradigm
2016-09-01

The dynamic environment of human observers requires continuous reallocations of visual attention in order to compensate for location changes of the attended objects. Particularly, situations with reduced spatial distance between targets and other objects in the display are crucial for keeping track of the target objects. In the present experiments, we explored how the temporal dynamics of such moments of reduced spacing affects the reallocation of visual attention. We asked participants to track four targets among indistinguishable distractors. Hereby, we manipulated whether target and distractor objects moved at a constant speed or whether their actual speed followed a sine wave profile. The variable speed oscillated around the constant speed thus maintaining average speed as well as travelled distance and average spatial proximity. The critical difference between the experimental conditions was that the durations of the events of spatial interference were more variable with variable speed profiles than with constant speed profiles. Particularly, the accelerations and decelerations of the variable speed profiles induced brief events of spatial interference at high object speeds as well as long events of spatial interference at slow object speeds. The overall duration of the events of interference, however, was indistinguishable between the conditions with variable and constant speed profiles. We observed inferior tracking performance with variable speed profiles relative to constant speed profiles (Experiments 1a and 1b). When we increased the number of pairs of targets and distractors moving with a variable speed profile (Experiment 2), performance declined continuously. Remarkably, tracking performance also declined when only distractors moved at variable speeds, suggesting that the dynamic changes in inter-object spacing rather than the variable speed impairs tracking (Experiment 3). In sum, our results provide evidence for a flexible allocation of the attentional resource toward targets suffering spatial interference by demonstrating the temporal constraints of the reallocation process. Meeting abstract presented at VSS 2016
Reducing the central fixation bias: The influence of scene preview
2016-09-01

Models that aim at predicting fixation locations of observers in a natural scene can be based on assumptions on bottom up processes, top down processes, and systematic eye movement tendencies. Among the best predictors of fixation locations in an image is the distance of an image location from the image center. Because this central fixation bias (Tatler, 2007) is independent of image content, initial fixation position, screen or eye position, it is a very strong nuisance factor for scene viewing experiments under laboratory conditions. Scene preview from as short as 75 ms has been shown (Vo & Henderson, 2010) to influence saccade target selection effectively. Thus, a short scene preview might alter eye guidance during initial fixations and result in a reduced central fixation bias. In a scene viewing experiment, we manipulated the initial fixation position to keep the eyes for a certain amount of time fixated on one location before they were allowed to explore the scene freely for five seconds. As a result, we found that the central fixation bias was reduced for all pretrial fixation times from 125 ms to 1000 ms compared to a control group without scene preview. There were no systematic differences between the different pretrial fixation times. Our results have important practical implications for the evaluation of models of visual attention, since controlled initial fixation durations reduce attentional capture of the stimulus and, therefore, the central fixation bias. Meeting abstract presented at VSS 2016
The #Dress phenomenon an empirical investigation into the role of the background.
2016-09-01

The #TheDress phenomenon refers to a dichotomy in colour perception, which is specific to the foto of a blue&black dress, namely that most observers judge its colours as either blue/black or white/gold. Hypotheses explaining the phenomenon include individual variations of information pocessing at sensory as well as cognitive stages. In particular it has been proposed that the lack of/ambiguity in background information leads observers to different conclusions about the illuminant and the light field. We will present result of matching experiments involving the presentations of the real blue/black dress, mounted on differently colour backgrounds and under the illuminations of two slide projectors, thereby mimicking the ambiguity of the photo. The results identify the use of information from the background as a source for the observed individual differences. The results are discussed in the context of the aquisition, the content and the use of scene knowledge. Meeting abstract presented at VSS 2016
Efficient selection of VANET messages for series vehicles
2016-09-01

In Vehicular Ad-hoc Networks (VANETs) communication among vehicles enables new advanced driver assistance systems. Cooperative Awareness Messages (CAMs) are so frequently exchanged that deployable electronic control units will not be powerful enough to process them all. Thus, most relevant CAMs need to be selected for processing. In this paper, we give an overview of relevance estimation function (REFs) for CAMs that assign them a relevance value based on metadata.We describe and evaluate an efficient message buffer and selection mechanism for most relevant CAMs. It efficiently decreases the relevance of buffered CAMs over time. We evaluate the results of the mechanism with regards to selection probability and message waiting time under realistic conditions. Furthermore, we study the runtime of various REFs using a prototypical implementation on a hardware evaluation platform. The results show that the proposed algorithms are feasible on close-to-production hardware as they quickly process most relevant CAMs.
Identification of factors associated with exacerbation risk in severe COPD: Multivariate analysis of the WISDOM study
2016-09-01

<b>Introduction:</b> Treatment management and patient outcomes could be improved by identifying patients with severe COPD who are at increased risk of exacerbations. <b>Aim:</b> To identify factors associated with exacerbation risk using a multivariate analysis of data from the WISDOM study. <b>Methods:</b> In WISDOM (NCT00975195; 12-month, randomised, parallel-group study), patients with severe to very severe COPD and a history of exacerbations received 18 μg tiotropium, 100 μg salmeterol and 1000 μg fluticasone propionate daily for 6 weeks, then continued or reduced inhaled corticosteroids (ICS) for 12 weeks. This <i>post hoc</i> multivariate analysis of time to first moderate or severe exacerbation used a stepwise selection process for candidate variables. <b>Results:</b> For the overall study period, the analysis was based on 2291 patients. Factors associated with a significantly increased risk of exacerbation were taking ICS at screening and ≥2 previous courses of antibiotics or steroids (Figure). Higher baseline FEV<sub>1</sub>, GOLD C vs GOLD D and taking xanthines at screening were associated with a significantly decreased risk of exacerbation. A backwards elimination variable selection process confirmed these results. <b>Conclusions:</b> Several factors were significantly associated with exacerbation risk in WISDOM. An increased risk was found in patients with prior ICS treatment and an exacerbation history. <b>Funding:</b> Boehringer Ingelheim.
In vivogenome editing using nuclease-encoding mRNA corrects SP-B deficiency
2016-09-01

Genome editing using site-specific endonucleases (SSE) holds great potential to repair disease-causing genes. In this study we offer a promising approach to deliver SSEs as nuclease-encoded, chemically modified mRNA (nec-mRNA) together with a repair template to correct the lung disease Surfactant Protein-B (SP-B) deficiency while simultaneously reducing SSE-induced off-target effects. To assess the potential of mRNA-encoded nucleases to create site specific double-strand breaks (DSBs), we evaluated a panel of 15 transcription activator-like effector nucleases (TALENs) and 36 Zink-Finger nucleases (ZFNs) for non-homologous end-joining (NHEJ) and also tested for the integration of a promoter template by homology-directed repair (HDR) <i>in vitro</i>. In addition we compared different mRNA modifications to assess immunoreactions against nec-mRNA. Finally, we co-administered intratracheally nec-mRNA with the repair template to SP-B deficient mice and evaluated the survival and promoter integration efficacy. Compared to plasmid-DNA, delivery of mRNA-encoded nucleases resulted in more frequent induction of DSBs (<i>P</i> &lt; 0.05) and HDR (<i>P</i> &lt; 0.05) <i>in vitro</i>. While being only transiently expressed, incorporation of modified nucleosides into nec-mRNA and complexation into nanoparticles (NPs) increased mRNA expression levels (<i>P</i> &lt; 0.001) <i>in vivo</i>. Also, no immune activation was observed. Importantly, delivery of nec-mRNA-NP to SP-B deficient mice lead to prolonged survival rates compared with matched control groups (<i>P</i> &lt; 0.001). In-out PCRs confirmed successful gene manipulation. In conclusion, we have shown that delivery of nec-mRNA-NP together with a repair template results in successful, site-specific genome editing <i>in vivo</i>.
Some observations on the psychophysics of Deep Neural Networks
2016-09-01

Deep convolutional neural networks (DNNs) are currently very popular, drawing interest for their high performance on object classification tasks. Additionally, they are being examined for purported parallels between their hierarchical features and those found in systems of biological vision (e.g. Yamins etal., 2014). Human vision has been studied extensively by psychophysics using simple grating stimuli, and many experimental results can be accommodated within a model where linear filters are followed by point-wise non-linearities as well as non-linear interactions between filters (Goris et al., 2013). However, two of the most striking failures of current spatial vision models are their inability to account for the contrast-modulation experiments by Henning et al. (1975) and the plaid-masking experiments by Derrington and Henning (1989). Googlenet and Alexnet are two DNNs performing well on object recognition. We ran contrast-modulated and plaid-masking stimuli through the networks and extracted the layer activations. Since these networks are fully deterministic, we designed an optimal linear decoder around the assumption of late, zero-mean additive noise, where the variance of the noise was calibrated to match human performance on contrast detection experiments. Unlike human observers, neither Alexnet nor Googlenet show any trace in any of their layers of masking by contrast-modulated gratings. Worse still, adding the contrast-modulated mask strongly facilitated detection. Using plaid-masks, Googlenet again showed strong facilitation. Alexnet, on the other hand, shows plaid-masking effects at least qualitatively similar to those found in human observers. However, this was only true for the last layers, the "object" layers, not the early layers. Strong claims that DNNs mirror the human visual system appear premature. Not only do the DNNs fail to show the masking effects found in human observers, different DNNs were found to behave wildly differently to simple stimuli. Meeting abstract presented at VSS 2016
Konfrontation, Kooperation oder Kooptation.
2016-09-01

The establishment of a Commission for the Disposal of High-Level Radioactive Waste by the state puts the anti-nuclear movement into a new situation. In the past, the relationship between the movement and the institutions of the state was mainly characterized by confrontation. But the establishment of a Repository Search Committee changed the situation and raised the question of cooperation. Using the hegemony theory, the article analyses the developments and conflicts between the movement and the state in the case of the search process for a nuclear waste repository. Thereby the article mainly focuses on dynamics inside the anti-nuclear movement and the relationship between the different fraction of the movement and the state.
A Tailored Approach to the Treatment of a Patient with a Severe Dynamic Manifestation of Rosacea: A Case Report
2016-09-01

Rosacea is a chronic inflammatory disease that can manifest as a spectrum of symptoms including erythema, inflammatory lesions, edema, and telangiectasia. Treatment decisions need to be adapted to reflect the nature and severity of the different symptoms present. In this report, we discuss the case of a female patient diagnosed with severe, inflamed papulopustular rosacea (PPR) presenting with a large number of inflammatory lesions and severe background erythema. This patient responded well to a treatment regimen consisting of a short course of antibiotics in combination with a corticosteroid, followed by monotherapy with isotretinoin to reduce the inflammation. Brimonidine gel, used as needed, was then added to isotretinoin to target the remaining background erythema. This case of severe PPR required a combinatorial treatment regimen to effectively target all symptoms present. The patient continued to apply topical metronidazole throughout the different treatment regimens prescribed over the course of almost 1 year. Use of topical metronidazole helped to repair and protect the skin barrier, which minimized the occurrence of dermatological adverse events when topical treatments were used. We conclude that in patients with severe disease and an important inflammatory component, a rapid response can be obtained with a multimodal, tailored approach that also includes treatment to repair and protect the skin barrier.
Investigating the influence of personal BMI on own body size perception in females using self-avatars
2016-09-01

Previous research has suggested that inaccuracies in own body size estimation can largely be explained by a known error in perceived magnitude, called contraction bias (Cornelissen, Bester, Cairns, Tovée & Cornelissen, 2015). According to this, own body size estimation is biased towards an average reference body, such that individuals with a low body mass index (BMI) should overestimate their body size and high BMI individuals should underestimate their body size. However, previous studies have mainly focused on self-body size evaluation of patients suffering from anorexia nervosa. In this study, we tested healthy females varying in BMI to investigate whether personal body size influences accuracy of body size estimation and sensitivity to weight changes, reproducing a scenario of standing in front of a full length mirror. We created personalized avatars with a 4D full-body scanning system that records participants' body geometry and texture, and altered the weight of the avatars based on a statistical body model. In two psychophysical experiments, we presented the stimuli on a stereoscopic, large-screen immersive display, and asked participants to respond to whether the body they saw was their own. Additionally, we used several questionnaires to assess participants' self-esteem, eating behavior, and their attitudes towards their body shape and weight. Our results show that participants, across the range of BMI, veridically perceived their own body size, contrary to what is suggested by the contraction bias hypothesis. Interestingly, we found that BMI influenced sensitivity to weight changes in the positive direction, such that people with higher BMIs were more willing to accept bigger bodies as their own. BMI did not influence sensitivity to weight changes in the negative direction. Meeting abstract presented at VSS 2016
Generation of induced pluripotent stem cells (iPSCs) from a hereditary spastic paraplegia patient carrying a homozygous R486C mutation in CYP7B1 (SPG5)
2016-09-01

Skin fibroblasts were obtained from a 47-year-old hereditary spastic paraplegia patient carrying a homozygous mutation R486C in CYP7B1 (Cytochrome P450, Family 7, Subfamily B, Polypeptide 1), responsible for causing hereditary spastic paraplegia type 5 (SPG5). Induced pluripotent stem cells (iPSCs) were generated by transfection with episomal plasmids carrying hOCT4, hSOX2, hKLF4, hL-MYC and hLIN28. The generated line iPS-SPG5-R486C was transgene-free, retained the specific mutation with no additional genomic aberrations, expressed pluripotency markers and was able to differentiate into cells of all germ layers in vitro. The generated iPS-SPG5-R486C line may be a useful resource for disease modelling of SPG5.
A data-driven procedure to determine the bunching window: An application to the Netherlands
2016-09-01

This paper presents empirical evidence on taxpayers' responsiveness to taxation by estimating the compensated elasticity of taxable income with respect to the net-of-tax rate in the Netherlands. Applying the bunching approach introduced by Saez (2010), we fi nd clear evidence of bunching behaviour at the thresholds of the Dutch tax schedule with a precise estimated elasticity of 0.023 at the upper threshold. In line with the literature, we fi nd much larger estimates for women and self-employed individuals. We also identify signi cant bunching behaviour for individuals in paid employment which we attribute to tax deductions for couples. This paper adds to the literature on bunching by proposing the use of information criteria to determine the counterfactual model, and by the development of an intuitive, data-driven procedure to determine the bunching window.