julilili42/papers huggingface dataset:
Stimulus expectation prolongs rather than shortens perceived duration: Evidence from self-generated expectations.
2017-05-08

Previous studies have suggested that unexpected stimuli are perceived as being longer than expected ones (e.g., the temporal oddball effect). These studies manipulated stimulus expectation mostly via stimulus repetitions and stimulus probabilities. However, these manipulations might affect duration judgments not only through the modulation of stimulus expectation. Therefore, the present study introduces a novel paradigm to isolate the effect of stimulus expectation on perceived duration from repetition and probability effects. In 2 experiments, participants vocalized which of 2 possible stimuli they expected in each trial immediately before stimulus presentation (self-generated expectations). Following stimulus presentation, participants performed a temporal bisection task on the duration of the presented stimuli. For both color (Experiment 1) and shape stimuli (Experiment 2), longer perceived durations were observed when stimulus expectations were fulfilled rather than violated. These results contrast with previous studies from which it has been concluded that stimulus expectation shortens perceived duration. Instead, the findings are rather in line with the idea that higher level stimulus expectation enhances stimulus processing and thus prolongs subjective duration (Matthews & Gheorghiu, 2016). Importantly, this also challenges the assumption that higher level stimulus expectation is a key mechanism driving the temporal oddball effect. (PsycINFO Database Record
Non-invasive <em>In Vivo</em> Fluorescence Optical Imaging of Inflammatory MMP Activity Using an Activatable Fluorescent Imaging Agent
2017-05-08

This paper describes a non-invasive method for imaging matrix metalloproteinases (MMP)-activity by an activatable fluorescent probe, via in vivo fluorescence optical imaging (OI), in two different mouse models of inflammation: a rheumatoid arthritis (RA) and a contact hypersensitivity reaction (CHR) model. Light with a wavelength in the near infrared (NIR) window (650 - 950 nm) allows a deeper tissue penetration and minimal signal absorption compared to wavelengths below 650 nm. The major advantages using fluorescence OI is that it is cheap, fast and easy to implement in different animal models. Activatable fluorescent probes are optically silent in their inactivated states, but become highly fluorescent when activated by a protease. Activated MMPs lead to tissue destruction and play an important role for disease progression in delayed-type hypersensitivity reactions (DTHRs) such as RA and CHR. Furthermore, MMPs are the key proteases for cartilage and bone degradation and are induced by macrophages, fibroblasts and chondrocytes in response to pro-inflammatory cytokines. Here we use a probe that is activated by the key MMPs like MMP-2, -3, -9 and -13 and describe an imaging protocol for near infrared fluorescence OI of MMP activity in RA and control mice 6 days after disease induction as well as in mice with acute (1x challenge) and chronic (5x challenge) CHR on the right ear compared to healthy ears.
Novel homozygous mutation in the SPATA7 gene causes autosomal recessive retinal degeneration in a consanguineous German family
2017-05-08

Retinitis pigmentosa (RP) is the term for a heterogeneous group of inherited eye disorders in which abnormalities of the photoreceptors or the retinal pigment epithelium lead to progressive vision ...
Interacting Learning Processes during Skill Acquisition: Learning to control with gradually changing system dynamics
2017-05-08

ABSTRACT There is increasing evidence that sensorimotor learning under real-life conditions relies on a composition of several learning processes. Nevertheless, most studies examine learning behaviour in relation to one specific learning mechanism. In this study, we examined the interaction between reward-based skill acquisition and motor adaptation to changes of object dynamics. Thirty healthy subjects, split into two groups, acquired the skill of balancing a pole on a cart in virtual reality. In one group, we gradually increased the gravity, making the task easier in the beginning and more difficult towards the end. In the second group, subjects had to acquire the skill on the maximum, most difficult gravity level. We hypothesized that the gradual increase in gravity during skill acquisition supports learning despite the necessary adjustments to changes in cart-pole dynamics. We found that the gradual group benefits from the slow increment, although overall improvement was interrupted by the changes in gravity and resulting system dynamics, which caused short-term degradations in performance and timing of actions. In conclusion, our results deliver evidence for an interaction of reward-based skill acquisition and motor adaptation processes, which indicates the importance of both processes for the development of optimized skill acquisition schedules.
Thyroid Autoimmunity: Role of Anti-thyroid Antibodies in Thyroid and Extra-Thyroidal Diseases
2017-05-09

Autoimmune diseases have a high prevalence in the population, and autoimmune thyroid disease (AITD) is one of the most common representatives. Thyroid autoantibodies are not only frequently detected in patients with AITD but also in subjects without manifest thyroid dysfunction. The high prevalence raises questions regarding a potential role in extra-thyroidal diseases. This review summarizes the etiology and mechanism of AITD and addresses prevalence of antibodies against thyroid peroxidase, thyroid-stimulating hormone receptor (TSHR), and anti-thyroglobulin and their action outside the thyroid. The main issues limiting the reliability of the conclusions drawn here include problems with different specificities and sensitivities of the antibody detection assays employed, as well as potential confounding effects of altered thyroid hormone levels, and lack of prospective studies. In addition to the well-known effects of TSHR antibodies on fibroblasts in Graves' disease (GD), studies speculate on a role of anti-thyroid antibodies in cancer. All antibodies may have a tumor-promoting role in breast cancer carcinogenesis despite anti-thyroid peroxidase antibodies having a positive prognostic effect in patients with overt disease. Cross-reactivity with lactoperoxidase leading to induction of chronic inflammation might promote breast cancer, while anti-thyroid antibodies in manifest breast cancer might be an indication for a more active immune system. A better general health condition in older women with anti-thyroid peroxidase antibodies might support this hypothesis. The different actions of the anti-thyroid antibodies correspond to differences in cellular location of the antigens, titers of the circulating antibodies, duration of antibody exposure, and immunological mechanisms in GD and Hashimoto's thyroiditis.
The Genomic History Of Southeastern Europe
2017-05-09

Abstract Farming was first introduced to southeastern Europe in the mid-7 th millennium BCE – brought by migrants from Anatolia who settled in the region before spreading throughout Europe. To clarify the dynamics of the interaction between the first farmers and indigenous hunter-gatherers where they first met, we analyze genome-wide ancient DNA data from 223 individuals who lived in southeastern Europe and surrounding regions between 12,000 and 500 BCE. We document previously uncharacterized genetic structure, showing a West-East cline of ancestry in hunter-gatherers, and show that some Aegean farmers had ancestry from a different lineage than the northwestern Anatolian lineage that formed the overwhelming ancestry of other European farmers. We show that the first farmers of northern and western Europe passed through southeastern Europe with limited admixture with local hunter-gatherers, but that some groups mixed extensively, with relatively sex-balanced admixture compared to the male-biased hunter-gatherer admixture that prevailed later in the North and West. Southeastern Europe continued to be a nexus between East and West after farming arrived, with intermittent genetic contact from the Steppe up to 2,000 years before the migration that replaced much of northern Europe’s population.
Quantifying Angular Correlations between the Atomic Lattice and the Superlattice of Nanocrystals Assembled with Directional Linking
2017-05-09

We show that the combination of X-ray scattering with a nanofocused beam and X-ray cross correlation analysis is an efficient way for the full structural characterization of mesocrystalline nanoparticle assemblies with a single experiment. We analyze several hundred diffraction patterns at individual sample locations, that is, individual grains, to obtain a meaningful statistical distribution of the superlattice and atomic lattice ordering. Simultaneous small- and wide-angle X-ray scattering of the same sample location allows us to determine the structure and orientation of the superlattice as well as the angular correlation of the first two Bragg peaks of the atomic lattices, their orientation with respect to the superlattice, and the average orientational misfit due to local structural disorder. This experiment is particularly advantageous for synthetic mesocrystals made by the simultaneous self-assembly of nanocrystals and surface-functionalization with conductive ligands. While the structural characterization of such materials has been challenging so far, the present method now allows correlating the mesocrystalline structure with optoelectronic properties.
The Beaker Phenomenon and the Genomic Transformation of Northwest Europe
2017-05-09

Bell Beaker pottery spread across western and central Europe beginning around 2750 BCE before disappearing between 2200–1800 BCE. The mechanism of its expansion is a topic of long-standing debate, with support for both cultural diffusion and human migration. We present new genome-wide ancient DNA data from 170 Neolithic, Copper Age and Bronze Age Europeans, including 100 Beaker-associated individuals. In contrast to the Corded Ware Complex, which has previously been identified as arriving in central Europe following migration from the east, we observe limited genetic affinity between Iberian and central European Beaker Complex-associated individuals, and thus exclude migration as a significant mechanism of spread between these two regions. However, human migration did have an important role in the further dissemination of the Beaker Complex, which we document most clearly in Britain using data from 80 newly reported individuals dating to 3900–1200 BCE. British Neolithic farmers were genetically similar to contemporary populations in continental Europe and in particular to Neolithic Iberians, suggesting that a portion of the farmer ancestry in Britain came from the Mediterranean rather than the Danubian route of farming expansion. Beginning with the Beaker period, and continuing through the Bronze Age, all British individuals harboured high proportions of Steppe ancestry and were genetically closely related to Beaker-associated individuals from the Lower Rhine area. We use these observations to show that the spread of the Beaker Complex to Britain was mediated by migration from the continent that replaced &gt;90% of Britain’s Neolithic gene pool within a few hundred years, continuing the process that brought Steppe ancestry into central and northern Europe 400 years earlier.
Origins of bond and spin order in rare-earth nickelate bulk and heterostructures
2017-05-09

We analyze the charge- and spin response functions of rare-earth nickelates\\nRNiO3 and their heterostructures using random-phase approximation in a two-band\\nHubbard model. The inter-orbital charge fluctuation is found to be the driving\\nmechanism for the rock-salt type bond order in bulk RNiO3, and good agreement\\nof the ordering temperature with experimental values is achieved for all RNiO3\\nusing realistic crystal structures and interaction parameters. We further show\\nthat magnetic ordering in bulk is not driven by the spin fluctuation and should\\nbe instead explained as ordering of localized moments. This picture changes for\\nlow-dimensional heterostructures, where the charge fluctuation is suppressed\\nand overtaken by the enhanced spin instability, which results in a\\nspin-density-wave ground state observed in recent experiments. Predictions for\\nspectroscopy allow for further experimental testing of our claims.\\n
Recapitulation of a progenitor-like transcriptional profile in pancreatic carcinogenesis is initiated by the epigenetic modifier Ring1b.
2017-05-09

The development of the pancreatic ductal adenocarcinoma (PDAC) is hallmarked by extensive changes in the transcriptional program of acinar cells. Early precancerous lesions, such as acinar-to-ductal metaplasia (ADM), primarily express pancreatic progenitor genes, whereas differentiation genes are repressed. Given that inflammation-triggered acinar-to-ductal metaplasia (ADM) occurs in the absence of genetic mutations, the high cellular plasticity of acinar cells and the changes in their transcriptional profile likely depend on epigenetic modifications. Even the expression of oncogenic Kras at an adult stage requires the induction of a progenitor-like ADM status for the initiation of pancreatic cancer. By analyzing an in vitro carcinogenesis model, we have previously shown that the epigenetic remodeler Ring1b, the catalytic subunit of the Polycomb repressor complex 1, is reactivated in pancreatic carcinogenesis and contributes to the epigenetic silencing of acinar cell fate genes. Overall, we hypothesize that Ring1b establishes a progenitor-like epigenetic profile during ADM formation resulting in acinar gene silencing and an enhanced susceptibility towards oncogenic Kras-mediated cell transformation.
A Genome-Wide Association Study of IVGTT-Based Measures of First-Phase Insulin Secretion Refines the Underlying Physiology of Type 2 Diabetes Variants
2017-05-10

Understanding the physiological mechanisms by which common variants predispose to type 2 diabetes requires large studies with detailed measures of insulin secretion and sensitivity. Here we performed the largest genome-wide association study of first-phase insulin secretion, as measured by intravenous glucose tolerance tests, using up to 5,567 individuals without diabetes from 10 studies. We aimed to refine the mechanisms of 178 known associations between common variants and glycemic traits and identify new loci. Thirty type 2 diabetes or fasting glucose–raising alleles were associated with a measure of first-phase insulin secretion at P &amp;lt; 0.05 and provided new evidence, or the strongest evidence yet, that insulin secretion, intrinsic to the islet cells, is a key mechanism underlying the associations at the HNF1A, IGF2BP2, KCNQ1, HNF1B, VPS13C/C2CD4A, FAF1, PTPRD, AP3S2, KCNK16, MAEA, LPP, WFS1, and TMPRSS6 loci. The fasting glucose–raising allele near PDX1, a known key insulin transcription factor, was strongly associated with lower first-phase insulin secretion but has no evidence for an effect on type 2 diabetes risk. The diabetes risk allele at TCF7L2 was associated with a stronger effect on peak insulin response than on C-peptide–based insulin secretion rate, suggesting a possible additional role in hepatic insulin clearance or insulin processing. In summary, our study provides further insight into the mechanisms by which common genetic variation influences type 2 diabetes risk and glycemic traits.
Causality and Causal Reasoning in Natural Language
2017-05-10

This chapter provides a combined overview of theoretical and psycholinguistic approaches to causality in language. The chapter’s main phenomenological focus is on causal relations as expressed intra-clausally by verbs (e.g., break, open) and between sentences by discourse markers (e.g., because, therefore). Special attention is given to implicit causality verbs that are argued to trigger expectations of explanations to occur in subsequent discourse. The chapter also discusses linguistic expressions that do not encode causation as such, but that seem to be dependent on a causal model for their adequate evaluation, such as counterfactual conditionals. The discussion of the phenomena is complemented by an overview of important aspects of their cognitive processing as revealed by psycholinguistic experimentation.
African nonhuman primates are infected with the yaws bacteriumTreponema pallidumsubsp.pertenue
2017-05-10

Abstract Treponema pallidum subsp. pertenue ( TPE ) is the causative agent of yaws. The disease was subject to global eradication efforts in the mid 20 th century but reemerged in West Africa, Southern Asia, and the Pacific region. Despite its importance for eradication, detailed data on possible nonhuman disease reservoirs are missing. A number of African nonhuman primates (NHPs) have been reported to show skin ulcerations suggestive of treponemal infection in humans. Furthermore antibodies against Treponema pallidum ( TP ) have been repeatedly detected in wild NHP populations. While genetic studies confirmed that NHPs are infected with TP strains, subspecies identification was only possible once for a strain isolated in 1966, pinpointing the involvement of TPE . We therefore collected a number of recently isolated simian TP strains and determined eight whole genome sequences using hybridization capture or long-range PCR combined with next-generation sequencing. These new genomes were compared with those of known human TP isolates. Our results show that naturally occurring simian TP strains circulating in three African NHP species all cluster with human TPE strains and show the same genomic structure as human TPE strains. These data indicate that humans are not the exclusive host for the yaws bacterium and that a One Health approach is required to achieve sustainable eradication of human yaws.
Patent breadth as effective barrier to market entry
2017-05-10

Firms protecting their invention by a patent have the legal right to exclude competitors from using the patented matter. However, despite patent protection, competitors could enter the market by ‘inventing around’. Provided that inventing around becomes more difficult the broader a patent is, the strength of protection against market entry increases in patent breadth. Building on a theoretical benchmark formalizing the relationship between varying patent breadth and the threat of market entry, our empirical analysis supports the prediction that inventors perceive broad patents as effective market entry barriers.
From Earlier to Later Hominins
2017-05-10

Abstract More than fifty years ago researchers recognised that microscopic patterns of wear on tooth enamel surfaces record information about ingestive behaviours and diets. Various methods of analysis have since been developed and applied to detect subtle dietary differences amongst extant and extinct species, and to differentiate short-term and seasonal variations in diet. This chapter provides a historical overview of methods of dental microwear analysis and their applications to non-human primates and fossil hominins. We consider in detail microwear texture analysis, wherein scanning confocal profilometry and scale-sensitive fractal analysis are used as tools for 3D characterization of microwear features. Studies employing this technique on a broad range of taxa, including hominins, attest to its efficacy, and provide insights into diets of extinct forms. We also for the first time compare microwear textures of Plio-Pleistocene species with those of Neanderthals to consider variation in diet between earlier and more recent fossil hominins.
Habitual exercise levels are associated with cerebral amyloid load in presymptomatic autosomal dominant Alzheimer's disease
2017-05-11

Abstract Introduction The objective of this study was to evaluate the relationship between self‐reported exercise levels and Alzheimer's disease (AD) biomarkers, in a cohort of autosomal dominant AD mutation carriers. Methods In 139 presymptomatic mutation carriers from the Dominantly Inherited Alzheimer Network, the relationship between self‐reported exercise levels and brain amyloid load, cerebrospinal fluid (CSF) Aβ 42, and CSF tau levels was evaluated using linear regression. Results No differences in brain amyloid load, CSF Aβ 42 , or CSF tau were observed between low and high exercise groups. Nevertheless, when examining only those already accumulating AD pathology (i.e., amyloid positive), low exercisers had higher mean levels of brain amyloid than high exercisers. Furthermore, the interaction between exercise and estimated years from expected symptom onset was a significant predictor of brain amyloid levels. Discussion Our findings indicate a relationship exists between self‐reported exercise levels and brain amyloid in autosomal dominant AD mutation carriers.
Neonatal myeloid derived suppressor cells show reduced apoptosis and immunosuppressive activity upon infection with Escherichia coli
2017-05-11

Susceptibility to infection during the neonatal period and reduced control of inflammation in neonates are attributed to immunosuppression persisting from fetal life. Myeloid‐derived suppressor cells (MDSCs) are immature myeloid progenitors with suppressive activity and increased numbers in cord blood. We hypothesized that MDSCs contribute to innate host defence in neonates, paralleled by anti‐inflammatory signalling.Phagocytic activity, infection induced apoptosis, expression of B‐cell lymphoma (Bcl)‐2 family proteins, production of reactive oxygen species (ROS), cytokine production and T‐cell suppression of neonatal granulocytic‐MDSCs (G‐MDSCs) after infection with Escherichia coli ( E. coli ) were compared to neonatal autologous mature polymorphonuclear leukocytes (PMNs). Phagocytic activity of G‐MDSCs upon infection with E. coli was equal to that of mature PMNs, however, apoptosis of G‐MDSCs was decreased. G‐MDSCs showed enhanced Bcl‐2‐expression and lower ROS production compared to PMNs. Inhibition of Bcl‐2 reduced apoptosis rates of G‐MDSCs to that of mature PMNs. Induction of anti‐inflammatory transforming growth factor beta (TGF‐β) was enhanced, while pro‐inflammatory IL‐8 decreased in G‐MDSCs compared to PMNs. Infected G‐MDSCs strongly suppressed proliferation of T cells. We show a direct role of G‐MDSCs for anti‐bacterial host defence. Prolonged survival and anti‐inflammatory capacity suggest that G‐MDSCs are important for immune‐regulation after bacterial infection.
First‐trimester ultrasound screening for trisomy 21 based on maternal age, fetal nuchal translucency, and different methods of ductus venosus assessment
2017-05-11

Abstract Objective To examine whether combining the dichotomous assessment of the a‐wave and the ductus venosus (DV) pulsatility index for veins (PIV) measurement improves first‐trimester screening performance. Methods Retrospective study performed at the University Hospital of Tuebingen based on singleton pregnancies that underwent first‐trimester screening including DV flow assessment. In each case, the risk of trisomy 21 was calculated based on maternal age, fetal nuchal translucency, and DV flow either as dichotomous classification of the a‐wave, as measurement of the DV PIV, or both. Results There were 5280 euploid fetuses and 127 fetuses with trisomy 21. The DV a‐wave was reversed in 2.3% and 66.1% in the euploid and trisomy 21 cases, respectively. The DV PIV measurements were above the 95th percentile in 8.3% and 77.2% the euploid and trisomy 21 cases, respectively. For a false positive rate of 3%, the detection rate for trisomy 21 based on maternal age, fetal NT, and DV flow is about 87% irrespective of whether DV is examined as a continuous or dichotomous variable. The combination of both resulted in a small decrease at 3% false positive rate. Conclusion Assessment of the DV a‐wave and the DV PIV result in similar DRs. Combining these two approaches does not appear to improve their individual screening performance. © 2017 John Wiley &amp; Sons, Ltd.