julilili42/papers huggingface dataset:
Space in numerical and ordinal information: A common construct?
2017-12-21

Space is markedly involved in numerical processing, both explicitly in instrumental learning and implicitly in mental operations on numbers. Besides action decisions, action generations, and attention, the response-related effect of numerical magnitude or ordinality on space is well documented in the Spatial-Numerical Associations of Response Codes (SNARC) effect. Here, right- over left-hand responses become relatively faster with increasing magnitude positions. However, SNARC-like behavioral signatures in non-numerical tasks with ordinal information were also observed and inspired new models integrating seemingly spatial effects of ordinal and numerical metrics. To examine this issue further, we report a comparison between numerical SNARC and ordinal SNARC-like effects to investigate group-level characteristics and individual-level deductions from generalized views, i.e., convergent validity. Participants solved order-relevant (before/after classification) and order-irrelevant tasks (font color classification) with numerical stimuli 1-5, comprising both magnitude and order information, and with weekday stimuli, comprising only ordinal information. A small correlation between magnitude- and order-related SNARCs was observed, but effects are not pronounced in order-irrelevant color judgments. On the group level, order-relevant spatial-numerical associations were best accounted for by a linear magnitude predictor, whereas the SNARC effect for weekdays was categorical. Limited by the representativeness of these tasks and analyses, results are inconsistent with a single amodal cognitive mechanism that activates space in mental processing of cardinal and ordinal information alike. A possible resolution to maintain a generalized view is proposed by discriminating different spatial activations, possibly mediated by visuospatial and verbal working memory, and by relating results to findings from embodied numerical cognition.
Planning and self-control, but not working memory, directly predict multiplication performance in adults
2017-12-21

Empirical evidence suggests that working memory (WM) is closely related to arithmetic performance. WM, which is the ability to monitor and update recent information, underlies various cognitive processes and behaviors including planning, self-regulation, and self-control. However, only a few studies have examined whether WM uniquely explains variance in arithmetic performance when other WM-related domain-general factors are taken into account. In this study, we examined whether WM explains unique variance in arithmetic performance when planning, self-regulation, and self-control are considered as well. We used the Tower of London task as a measure of planning, self-rated reports as a measure of self-regulation and self-control, and WM measures, to test which of these domain-general functions predicts complex multiplication performance. Results showed that planning predicted multiplication accuracy and self-control predicted response time, while WM and self-regulation did not predict complex multiplication performance. Although WM was not a direct predictor of multiplication performance, it possibly exerted its influence as part of planning ability. We suggest that complex multiplication is not predicted by WM per se, but rather by WM-related general cognitive and behavioral factors, namely self-control and the planning component of executive functions.
The sensitivity of natural language to the distinction between class nouns and role nouns
2017-12-21

This paper argues that language makes a distinction among individual count nouns between class nouns (e.g., man) and role nouns (e.g., judge). This is reflected in the effects of class nouns vs. role nouns in three positions: (i) the complement of as in restrictive role as-phrases, (ii) the descriptive content of definite descriptions in a certain type of logical argument, and (iii) the predicative expression in German copular clauses. To capture the sensitivity to this distinction formally, I introduce a domain of roles D_r and a type-shifting operator PLAY , which connects D_r to the domain of individuals D_e . Using these tools, I propose analyses of the contrasts arising in (i)–(iii) that account for the observed sensitivity to role nouns.
Identification of Protein Complexes Associated with the Usher Syndrome 2C and Epilepsy-Associated Protein VLGR1 Applying Affinity Proteomics
2017-12-21

Authors aimed to identify novel VLGR1-associated protein networks to shed light on its integration into signaling pathways and the cellular compartments in which VLGR1 functions using high-resolution affinity proteomics based on tandem affinity purifications (TAPs).
Magnitude estimation is influenced by social power
2017-12-21

The action-specific perception account suggests that how people perceive the environment depends on their ability to act on it, assuming that estimation is influenced by inter-individual traits, but also by situated states. Moreover, several studies revealed that social power affects basic cognitive processes and even influences the way we perceive the physical environment. In the present study, we examined whether social power also influences estimation performance of spatial magnitudes (i.e., line estimation). Participants estimated the line length of a given number in an increase and a decrease condition, after (low versus high) social power had been manipulated between participants via role assignment. In the increase condition, low-power participants overestimated line lengths, whereas such a bias was not observed for high-power participants. In contrast, the power manipulation did not affect performance in the decrease condition, suggesting that proportion-judgement strategies might have been applied here, thereby reducing the overall bias in line estimations. Our findings support the notion that social power has an impact on the perception of the physical environment and that perception can depend on personal as well as situational factors. Moreover, the present research suggests that high (compared to low) social power may help people to overcome biases in overestimating magnitudes.
Cover Image, Volume 9, Issue 1
2017-12-21

The cover image, by Dierk Niessing et al., is based on the Focus Article mRNA transport in fungal top models , DOI: 10.1002/wrna.1453 . Image Credit: CEPLAS ‐ Cluster of Excellence on Plant Sciences image
Bryophyte-dominated biological soil crusts mitigate soil erosion in an early successional Chinese subtropical forest
2017-12-22

Abstract. This study investigated the development of biological soil crusts (biocrusts) in an early successional subtropical forest plantation and their impact on soil erosion. Within a biodiversity and ecosystem functioning experiment in southeast China (biodiversity and ecosystem functioning (BEF) China), the effect of these biocrusts on sediment delivery and runoff was assessed within micro-scale runoff plots under natural rainfall, and biocrust cover was surveyed over a 5-year period. Results showed that biocrusts occurred widely in the experimental forest ecosystem and developed from initial light cyanobacteria- and algae-dominated crusts to later-stage bryophyte-dominated crusts within only 3 years. Biocrust cover was still increasing after 6 years of tree growth. Within later-stage crusts, 25 bryophyte species were determined. Surrounding vegetation cover and terrain attributes significantly influenced the development of biocrusts. Besides high crown cover and leaf area index, the development of biocrusts was favoured by low slope gradients, slope orientations towards the incident sunlight and the altitude of the research plots. Measurements showed that bryophyte-dominated biocrusts strongly decreased soil erosion, being more effective than abiotic soil surface cover. Hence, their significant role in mitigating sediment delivery and runoff generation in mesic forest environments and their ability to quickly colonise soil surfaces after disturbance are of particular interest for soil erosion control in early-stage forest plantations.
Dioptric defocus maps across the visual field for different indoor environments
2017-12-22

One of the factors proposed to regulate the eye growth is the error signal derived from the defocus in the retina and actually, this might arise from defocus not only in the fovea but the whole visual field. Therefore, myopia could be better predicted by spatio-temporally mapping the 'environmental defocus' over the visual field. At present, no devices are available that could provide this information. A 'Kinect sensor v1' camera (Microsoft Corp.) and a portable eye tracker were used for developing a system for quantifying 'indoor defocus error signals' across the central 58° of the visual field. Dioptric differences relative to the fovea (assumed to be in focus) were recorded over the visual field and 'defocus maps' were generated for various scenes and tasks.
Expanded Haemodialysis Therapy of Chronic Haemodialysis Patients Prevents Calcification and Apoptosis of Vascular Smooth Muscle Cells in vitro
2017-12-22

&lt;b&gt;&lt;i&gt;Background:&lt;/i&gt;&lt;/b&gt; Vascular calcification is a common phenomenon in patients with chronic kidney disease and strongly associated with increased cardiovascular mortality. Vascular calcification is an active process mediated in part by inflammatory processes in vascular smooth muscle cells (VSMC). These could be modified by the insufficient removal of proinflammatory cytokines through conventional high-flux (HF) membranes. Recent trials demonstrated a reduction of inflammation in VSMC by use of dialysis membranes with a higher and steeper cut-off. These membranes caused significant albumin loss. Therefore, the effect of high retention Onset (HRO) dialysis membranes on vascular calcification and its implications in vitro&lt;i&gt;&lt;/i&gt; was evaluated. &lt;b&gt;&lt;i&gt;Methods:&lt;/i&gt;&lt;/b&gt; In the PERCI II trial, 48 chronic dialysis patients were dialyzed using HF and HRO dialyzers and serum samples were collected. Calcifying VSMC were incubated with the serum samples. Calcification was determined using alizarin red staining (AZR) and determination of alkaline phosphatase (ALP) activity. Furthermore, apoptosis was evaluated, and release of matrix Gla protein (MGP), osteopontin (OPN) and growth differentiation factor 15 (GDF-15) were measured in cell supernatants. &lt;b&gt;&lt;i&gt;Results:&lt;/i&gt;&lt;/b&gt; Vascular calcification in vitro was significantly reduced by 24% (ALP) and 36% (AZR) after 4 weeks of HRO dialysis and by 33% (ALP) and 48% (AZR) after 12 weeks of dialysis using HRO membranes compared to HF dialysis. Apoptosis was significantly lower in the HRO group. The concentrations of MGP and OPN were significantly elevated after incubation with HF serum compared to HRO serum and healthy controls. Similarly, GDF-15 release in the supernatant was elevated after incubation with HF serum, an effect significantly ameliorated after treatment with HRO medium. &lt;b&gt;&lt;i&gt;Conclusions:&lt;/i&gt;&lt;/b&gt; Expanded haemodialysis therapy reduces the pro-calcific potential of serum from dialysis patients in vitro&lt;i&gt;.&lt;/i&gt; With a markedly reduced albumin filtration compared to high cut-off dialysis, use of the HRO dialyzers may possibly provide a treatment option for chronic dialysis patients to reduce the progression of vascular calcification.
Staphylococcus aureuswall teichoic acid is a pathogen-associated molecular pattern that is recognized by langerin (CD207) on skin Langerhans cells
2017-12-22

Abstract Staphylococcus aureus is a major cause of skin and soft tissue infections and aggravator of the inflammatory skin disease atopic dermatitis (AD). Epicutaneous exposure to S. aureus induces Th17 responses through skin Langerhans cells (LCs), which paradoxically contribute to host defense but also to AD pathogenesis. The underlying molecular mechanisms of the association between S. aureus and skin inflammation are poorly understood. Here, we demonstrate that human LCs directly interact with S. aureus through the pattern-recognition receptor langerin (CD207). Human, but not mouse, langerin interacts with S. aureus through the conserved β- N -acetylglucosamine (GlcNAc) modifications on wall teichoic acid (WTA), thereby discriminating S. aureus from other staphylococcal species. Importantly, the specific S. aureus WTA glycoprofile strongly influences the level of Th1-and Th17-polarizing cytokines that are produced by in vitro generated LCs. Finally, in a murine epicutaneous infection model, S. aureus induced a more pronounced influx of inflammatory cells and pro-inflammatory cytokine transcripts in skin of human langerin transgenic mice compared to wild-type mice. Our findings provide molecular insight into the unique pro-inflammatory capacities of S. aureus in relation to inflammatory skin disease.
Interrupted Growth to Manipulate Phase Separation in DIP:C60 Organic Semiconductor Blends
2017-12-22

We studied the influence of periodic growth interruptions during codeposition of diindenoperylene (DIP) and buckminsterfullerene (C60) in an equimolar mixing ratio. DIP and C60 are known to phase-separate when codeposited, but the details and, in particular, the length scales depend on kinetic factors. Using X-ray scattering and atomic force microscopy, we demonstrate that the phase separation mechanism is in fact influenced by growth interruptions, with more pronounced effects if the deposition rates are low. For high deposition rates, growth interruptions have no appreciable effect. We discuss our proof-of-concept investigation in the context of the relevant processes and their time scales.
The bovine alveolar macrophage DNA methylome is resilient to infection withMycobacterium bovis
2017-12-22

Abstract DNA methylation is pivotal in orchestrating gene expression patterns in various mammalian biological processes. Perturbation of the bovine alveolar macrophage (bAM) transcriptome, due to Mycobacterium bovis ( M. bovis ) infection, has been well documented; however, the impact of this intracellular pathogen on the bAM epigenome has not been determined. Here, whole genome bisulfite sequencing (WGBS) was used to assess the effect of M. bovis infection on the bAM DNA methylome. The methylomes of bAM infected with M. bovis were compared to those of non-infected bAM 24 hours post-infection (hpi). No differences in DNA methylation (CpG or non-CpG) were observed. Analysis of DNA methylation at proximal promoter regions uncovered &gt;250 genes harbouring intermediately methylated (IM) promoters (average methylation of 33–66%). Gene ontology analysis, focusing on genes with low, intermediate or highly methylated promoters, revealed that genes with IM promoters were enriched for immune-related GO categories; this enrichment was not observed for genes in the high or low methylation groups. Targeted analysis of genes in the IM category confirmed the WGBS observation. This study is the first in cattle examining genome-wide DNA methylation at single nucleotide resolution in an important bovine cellular host-pathogen interaction model, providing evidence for IM promoter methylation in bAM.
Efficacy and Safety of Fosmidomycin–Piperaquine as Nonartemisinin-Based Combination Therapy for Uncomplicated Falciparum Malaria: A Single-Arm, Age De-escalation Proof-of-Concept Study in Gabon
2017-12-23

This is the first report of the use of the combination fosmidomycin-piperaquine. The combination appeared to have high efficacy and be safe and well tolerated despite observed transient changes in electrocardiogram with prolongation of the QT interval. Clinical Trials Registration. NCT02198807.
European Early Pleistocene biogeography and ecology based on the mammal record: Case studies and preliminary syntheses
2017-12-24

The European Quaternary has for a long time attracted the interest of specialists around the world, not only because of its fascinating mammal record, including iconic taxa such as mammoths, giant deer, bisons, wolfs, saber- tooth cats, etc., but also because of the observed direct link between turnovers in the synthesis of consecutive mammal palaeocommunities and global climatic oscillations. Initial interest was focused on the Middle and Late Pleistocene, the period with an ever-increasing contrast between the glacial and interglacials. However, it soon became clear that the lower part of the Pleistocene (considered to start at ∼1.8 Ma at that time) was a pivotal period during which the later and modern European mammal fauna largely emerged through successive events of migration, origina- tion and extinction. Most of the modern Eurasian genera and many of the modern species lineages became clearly morphologically recognizable by the end of the Early Pleis- tocene.
Friedreich and dominant ataxias: quantitative differences in cerebellar dysfunction measurements
2017-12-26

Background Sensitive outcome measures for clinical trials on cerebellar ataxias are lacking. Most cerebellar ataxias progress very slowly and quantitative measurements are required to evaluate cerebellar dysfunction. Methods We evaluated two scales for rating cerebellar ataxias: the Composite Cerebellar Functional Severity (CCFS) Scale and Scale for the Assessment and Rating of Ataxia (SARA), in patients with spinocerebellar ataxia (SCA) and controls. We evaluated these scales for different diseases and investigated the factors governing the scores obtained. All patients were recruited prospectively. Results There were 383 patients with Friedreich’s ataxia (FRDA), 205 patients with SCA and 168 controls. In FRDA, 31% of the variance of cerebellar signs with the CCFS and 41% of that with SARA were explained by disease duration, age at onset and the shorter abnormal repeat in the FXN gene. Increases in CCFS and SARA scores per year were lower for FRDA than for SCA (CCFS index: 0.123±0.123 per year vs 0.163±0.179, P&lt;0.001; SARA index: 1.5±1.2 vs 1.7±1.7, P&lt;0.001), indicating slower cerebellar dysfunction indexes for FRDA than for SCA. Patients with SCA2 had higher CCFS scores than patients with SCA1 and SCA3, but similar SARA scores. Conclusions Cerebellar dysfunction, as measured with the CCFS and SARA scales, was more severe in FRDA than in patients with SCA, but with lower progression indexes, within the limits of these types of indexes. Ceiling effects may occur at late stages, for both scales. The CCFS scale is rater-independent and could be used in a multicentre context, as it is simple, rapid and fully automated. Trial registration number ClinicalTrials.gov: NCT02069509 .
Recurrence of Spontaneous Pneumothorax Is Not Associated with Allegedly Risk-Prone Lifestyle Conduct
2017-12-26

In our study, none of the supposed "classic" lifestyle-associated risk factors for PNTX recurrence after VATS proved to be a significant threat. Postoperative patient behavior might not be constrained by overcautious medical advice.
The Time of Teaching in the Global South: Networking Pedagogy and the Teaching of Caribbean poetry (with an example from Derek Walcott)
2017-12-26

This article asks about the time(-space) of teaching as a creative process. In order to address this issue, it turns to the teaching of a particular poetic form, that of the sonnet, which it reads as an exemplification of creative constraint as an apprenticeship in enabling networks. In order to exemplify that process of spatial constraint revealing itself as enabling creative networking, it turns to a sonnet by the Caribbean poet Derek Walcott in which the natural environment as a network of sites of distributed agency is foregrounded asthe instantiation of creative networking. In all three instances (teaching the sonnet as genre via a specific example from Walcott’s oeuvre), what counts is the network, in which agency is distributed/dispersed, and creativity consists of connectivity with other nodes on the network so as to interact with them.
Denotational validation of higher-order Bayesian inference
2017-12-27

We present a modular semantic account of Bayesian inference algorithms for probabilistic programming languages, as used in data science and machine learning. Sophisticated inference algorithms are often explained in terms of composition of smaller parts. However, neither their theoretical justification nor their implementation reflects this modularity. We show how to conceptualise and analyse such inference algorithms as manipulating intermediate representations of probabilistic programs using higher-order functions and inductive types, and their denotational semantics. Semantic accounts of continuous distributions use measurable spaces. However, our use of higher-order functions presents a substantial technical difficulty: it is impossible to define a measurable space structure over the collection of measurable functions between arbitrary measurable spaces that is compatible with standard operations on those functions, such as function application. We overcome this difficulty using quasi-Borel spaces, a recently proposed mathematical structure that supports both function spaces and continuous distributions. We define a class of semantic structures for representing probabilistic programs, and semantic validity criteria for transformations of these representations in terms of distribution preservation. We develop a collection of building blocks for composing representations. We use these building blocks to validate common inference algorithms such as Sequential Monte Carlo and Markov Chain Monte Carlo. To emphasize the connection between the semantic manipulation and its traditional measure theoretic origins, we use Kock's synthetic measure theory. We demonstrate its usefulness by proving a quasi-Borel counterpart to the Metropolis-Hastings-Green theorem.
Changes in the cyclotron line energy on short and long timescales in V 0332+53
2017-12-27

We present the results of the pulse-amplitude-resolved spectroscopy of the accreting pulsar V 0332+53 using the NuSTAR observations of the source in 2015 and 2016. We investigate the dependence of the energy of the cyclotron resonant scattering feature (CRSF) as a function of X-ray luminosity on timescales comparable with the spin period of the pulsar within individual observations, and the behavior on longer timescales within and between the two observed outbursts. We confirm that in both cases the CRSF energy is negatively correlated with flux at luminosities higher than the critical luminosity and is positively correlated at lower luminosities. We also confirm the recently reported gradual decrease in the line energy during the giant outburst in 2015. Using the NuSTAR data, we find that this decrease was consistent with a linear decay throughout most of the outburst, and flattened or even reversed at the end of the 2015 outburst, approximately simultaneously with the transition to the subcritical regime. We also confirm that by the following outburst in 2016 the line energy rebounded to previous values. The observed behavior of the CRSF energy with time is discussed in terms of changes in the geometry of the CRSF forming region caused by changes in the effective magnetospheric radius.
Prognostic significance of cytogenetic heterogeneity in patients with newly diagnosed multiple myeloma
2017-12-27

Key Points Clonal heterogeneity detected by iFISH is common in newly diagnosed MM. Treatment with bortezomib overcomes the negative impact of high-risk cytogenetic abnormalities if no further subclones are detected.