julilili42/papers huggingface dataset:
Texture Fields: Learning Texture Representations in Function Space
2019-10-01

In recent years, substantial progress has been achieved in learning-based reconstruction of 3D objects. At the same time, generative models were proposed that can generate highly realistic images. However, despite this success in these closely related tasks, texture reconstruction of 3D objects has received little attention from the research community and state-of-the-art methods are either limited to comparably low resolution or constrained experimental setups. A major reason for these limitations is that common representations of texture are inefficient or hard to interface for modern deep learning techniques. In this paper, we propose Texture Fields, a novel texture representation which is based on regressing a continuous 3D function parameterized with a neural network. Our approach circumvents limiting factors like shape discretization and parameterization, as the proposed texture representation is independent of the shape representation of the 3D object. We show that Texture Fields are able to represent high frequency texture and naturally blend with modern deep learning techniques. Experimentally, we find that Texture Fields compare favorably to state-of-the-art methods for conditional texture reconstruction of 3D objects and enable learning of probabilistic generative models for texturing unseen 3D models. We believe that Texture Fields will become an important building block for the next generation of generative 3D models.
Adverse events during a disorder‐specific psychotherapy compared to a nonspecific psychotherapy in patients with chronic depression
2019-10-01

Abstract Objectives A recent trial comparing Cognitive Behavioral Analysis System of Psychotherapy (CBASP) and supportive psychotherapy in chronic depression found CBASP to be more effective in treating depressive symptoms. We aimed to evaluate adverse events that occurred during this trial. Materials and Method A randomized trial of chronically depressed outpatients was performed. The treatment included 32 sessions of CBASP or supportive psychotherapy. Therapists asked patients about adverse events and their intensity in each session using a standardized checklist. We analyzed the mean number of (severe) adverse events per patient up to Session 32 with gamma frailty recurrent event models. Results Two hundred and sixty patients were included in the analyses (66% female, mean age 45 years). Patients in the supportive psychotherapy group reported less severe adverse events in general, and less severe adverse events related to personal life and to occupational life than patients in the CBASP group. Less adverse events related to suicidal thoughts were reported in the CBASP compared with the supportive psychotherapy group. Conclusions Differences in the adverse events profile may be explained by the treatment elements. Adverse events related to personal and occupational life for example might be considered a necessary and expected yet temporary adverse treatment outcome of an effective CBASP treatment.
Multicenter Tract-Based Analysis of Microstructural Lesions within the Alzheimer’s Disease Spectrum: Association with Amyloid Pathology and Diagnostic Usefulness
2019-10-01

Diffusion changes as determined by diffusion tensor imaging are potential indicators of microstructural lesions in people with mild cognitive impairment (MCI), prodromal Alzheimer's disease (AD), and AD dementia. Here we extended the scope of analysis toward subjective cognitive complaints as a pre-MCI at risk stage of AD. In a cohort of 271 participants of the prospective DELCODE study, including 93 healthy controls and 98 subjective cognitive decline (SCD), 45 MCI, and 35 AD dementia cases, we found reductions of fiber tract integrity in limbic and association fiber tracts in MCI and AD dementia compared with controls in a tract-based analysis (p < 0.05, family wise error corrected). In contrast, people with SCD showed spatially restricted white matter alterations only for the mode of anisotropy and only at an uncorrected level of significance. DTI parameters yielded a high cross-validated diagnostic accuracy of almost 80% for the clinical diagnosis of MCI and the discrimination of Aβ positive MCI cases from Aβ negative controls. In contrast, DTI parameters reached only random level accuracy for the discrimination between Aβ positive SCD and control cases from Aβ negative controls. These findings suggest that in prodromal stages of AD, such as in Aβ positive MCI, multicenter DTI with prospectively harmonized acquisition parameters yields diagnostic accuracy meeting the criteria for a useful biomarker. In contrast, automated tract-based analysis of DTI parameters is not useful for the identification of preclinical AD, including Aβ positive SCD and control cases.
The Influences of Adherence to Tamoxifen and CYP2D6 Pharmacogenetics on Plasma Concentrations of the Active Metabolite (Z)‐Endoxifen in Breast Cancer
2019-10-01

Tamoxifen efficacy in breast cancer is suspected to depend on adherence and intact drug metabolism. We evaluated the role of adherence behavior and pharmacogenetics on the formation rate of (Z)‐endoxifen. In 192 Brazilian patients, we assessed plasma levels of tamoxifen and its metabolites at 3, 6, and 12 months of treatment (liquid‐chromatography tandem mass spectrometry), adherence behavior (Morisky, Green, and Levine medication adherence scale), and cytochrome P450 2D6 (CYP2D6) and other pharmacogene polymorphisms (matrix‐assisted laser‐desorption‐ionization time of flight) mass spectrometry, real‐time polymerase chain reaction). Adherence explained 47% of the variability of tamoxifen plasma concentrations ( P &lt; 0.001). Although CYP2D6 alone explained 26.4%, the combination with adherence explained 40% of (Z)‐endoxifen variability at 12 months ( P &lt; 0.001). The influence of low adherence to not achieving relevant (Z)‐endoxifen levels was highest in patients with noncompromised CYP2D6 function (relative risk 3.65; 95% confidence interval 1.48–8.99). As a proof‐of‐concept, we demonstrated that (Z)‐endoxifen levels are influenced both by patient adherence to tamoxifen and CYP2D6, which is particularly relevant for patients with full CYP2D6 function.
On a direct description of pseudorelativistic Nelson Hamiltonians
2019-10-01

Abstract interior-boundary conditions allow for the direct description of the domain and the action of Hamiltonians for a certain class of ultraviolet-divergent models in quantum field theory. This method, which comes without the need for renormalization, was recently applied to the nonrelativistic Nelson model. Here, we demonstrate the flexibility of the novel approach by applying it to two relativistic variants of Nelson’s model. The existence of Hamiltonians for these models was shown using renormalization techniques by Eckmann [Commun. Math. Phys. 18, 247 (1970); J. Math. Phys. 15, 190 (1974)]. However, many important properties, such as the domain and the action of the Hamiltonian, were not known. We construct the Hamiltonians for such models via abstract boundary conditions, describing their action explicitly for the first time. In addition, we obtain a detailed characterization of their domain.
Drug-induced chromatin accessibility changes associate with sensitivity to liver tumor promotion
2019-10-01

Liver cancer susceptibility varies amongst humans and between experimental animal models because of multiple genetic and epigenetic factors. The molecular characterization of such susceptibilities has the potential to enhance cancer risk assessment of xenobiotic exposures and disease prevention strategies. Here, using DNase I hypersensitivity mapping coupled with transcriptomic profiling, we investigate perturbations in cis -acting gene regulatory elements associated with the early stages of phenobarbital (PB)-mediated liver tumor promotion in susceptible versus resistant mouse strains (B6C3F1 versus C57BL/6J). Integrated computational analyses of strain-selective changes in liver chromatin accessibility underlying PB response reveal differential epigenetic regulation of molecular pathways associated with PB-mediated tumor promotion, including Wnt/β-catenin signaling. Complementary transcription factor motif analyses reveal mouse strain–selective gene regulatory networks and a novel role for Stat, Smad, and Fox transcription factors in the early stages of PB-mediated tumor promotion. Mapping perturbations in cis -acting gene regulatory elements provides novel insights into the molecular basis for susceptibility to xenobiotic-induced rodent liver tumor promotion and has the potential to enhance mechanism-based cancer risk assessments of xenobiotic exposures.
Turritelline mass accumulations from the Lower Miocene of southern Germany: implications for tidal currents and nutrient transport within the North Alpine Foreland Basin
2019-10-01

The mass occurrence of turritelline gastropod shells from the Lower Miocene of southern Germany allows for detailed studies of their palaeoecology, transport mechanisms, preservation potentials and the reconstruction of nutrient regimes. Changes in the fabric of the gastropod‐dominated beds are used to reconstruct a generally deepening environment corresponding to the Lower Miocene transgression within the Upper Molasse Sea of the North Alpine Foreland Basin. The sedimentary succession ranges from chaotically arranged, densely packed and near‐shore transported; wave‐influenced deposits showing bimodal shell orientations; more widely dispersed shells showing a uni‐directional orientation; and dispersed shells showing diverse orientations. The shells often show damage to the apex and aperture though it is not clear whether this is due to predation events, pagurisation or abrasion due to transport. An outstanding feature is the replacement of aragonite shells by calcite leading to internal vugs as well as modulating the outer shell surface morphology. The high density of turritelline gastropods indicates a nutrient‐rich palaeoenvironment at the northern edge of the Molasse Sea.
GPS tracking and population genomics suggest itinerant breeding across drastically different habitats in the Phainopepla
2019-10-01

Abstract Migratory birds generally divide the annual cycle between discrete breeding and nonbreeding ranges. Itinerant breeders, however, reproduce twice at different geographic locations, migrating between them. This unusual flexibility in movement ecology and breeding biology suggests that some species can rapidly modulate the conflicting physiological and behavioral traits required for migration and reproduction. The Phainopepla (Phainopepla nitens), a songbird of the southwestern USA, has long been suspected to breed first in desert habitats in spring, then migrate to woodland habitats to breed again in summer. However, direct evaluation of movement and gene flow among individuals breeding in different locations has previously been logistically intractable. We deployed GPS tags on free-flying Phainopeplas in southern California, all of which migrated to hypothesized woodland breeding habitats after desert breeding (an average distance of 232 km). GPS data also revealed previously unknown fall and spring stopover sites. Population genomic analyses revealed no genetic differentiation among desert and woodland breeding populations, indicating significant movement and gene flow across the region. Finally, we used random forest analyses to quantify substantial environmental differences among temporal stages. Our results provide direct evidence that individual Phainopeplas do indeed move between 2 drastically different breeding habitats in the same year, representing a rare and extreme example of life-history flexibility.
Computational historical linguistics
2019-10-01

Abstract Computational approaches to historical linguistics have been proposed for half a century. Within the last decade, this line of research has received a major boost, owing both to the transfer of ideas and software from computational biology and to the release of several large electronic data resources suitable for systematic comparative work. In this article, some of the central research topics of this new wave of computational historical linguistics are introduced and discussed. These are automatic assessment of genetic relatedness , automatic cognate detection , phylogenetic inference and ancestral state reconstruction . They will be demonstrated by means of a case study of automatically reconstructing a Proto-Romance word list from lexical data of 50 modern Romance languages and dialects. The results illustrate both the strengths and the weaknesses of the current state of the art of automating the comparative method.
Development of a specific IgY-based ELISA for prothymosin alpha, a bioactive polypeptide with diagnostic and therapeutic potential
2019-10-01

Prothymosin alpha (ProTα) is a highly conserved polypeptide (109 amino acids in humans) with diagnostic and therapeutic potential; ProTα exerts intra- and extra-cellular biological functions associated with cell proliferation, apoptosis and immune regulation, while it has been suggested to act as a damage-associated molecular pattern (DAMP) or alarmin. In this work, chicken polyclonal anti-ProTα antibodies that had been developed several years ago were immunochemically evaluated and proven to retain immunoreactivity for ProTα, with remarkable thermal and pH stability. Moreover, the antibodies showed practically no cross-reactivity with a series of ProTα-fragments, eventually intracellularly produced -such as ProTα[1-28] (also known as Tα1) and ProTα[100-109], which exert <i>per se</i> biological activity and might be present in biological samples along with the intact molecule, being therefore highly specific for whole-length ProTα. Based on the above antibodies (IgYs-3<i>e</i>), a highly specific competitive ProTα-ELISA with well-studied analytical characteristics (intra- and inter-assay CVs: ≤5% and ≤12%, respectively, limit of detection: 2.1 ng/mL, recovery: 88-104%) was developed. The new ProTα-ELISA was applied to the analysis of supernatants of HeLa cells driven to necrosis; intact ProTα was measured in cell culture supernatants, at levels that seemed to depend on % cell necrosis.
Vagus nerve stimulation increases vigor to work for rewards
2019-10-01

Abstract Interoceptive feedback transmitted via the vagus nerve plays a vital role in motivation by tuning actions according to physiological needs. Whereas vagus nerve stimulation (VNS) reinforces actions and enhances dopamine transmission in animals, motivational effects elicited by VNS in humans are still largely elusive. Here, we applied non-invasive transcutaneous auricular VNS (taVNS) on the left or the right ear using a randomized cross-over design (vs. sham). During stimulation, 81 healthy participants had to exert effort to earn food or monetary rewards. We reasoned that taVNS enhances motivation and tested whether it does so by increasing prospective benefits (i.e., vigor) or reducing costs of action (i.e., maintenance) compared to sham stimulation. In line with preclinical studies, taVNS generally enhanced invigoration of effort ( p = .004, Bayes factor, BF 10 = 7.34), whereas stimulation on the left side primarily facilitated vigor for food rewards (left taVNS: Stimulation × Reward Type, p =.003, BF 10 = 11.80). In contrast, taVNS did not affect effort maintenance ( p s ≥ .09, BF 10 &lt; 0.52). Critically, during taVNS, vigor declined less steeply with decreases in wanting (Δ b = −.046, p = .031) indicating a boost in the drive to work for rewards. Collectively, our results suggest that taVNS enhances reward-seeking by boosting vigor, not effort maintenance and that the side of the stimulation affects generalization beyond food reward. We conclude that taVNS may enhance the pursuit of prospective rewards which may pave new avenues for treatment of motivational deficiencies.
On completeness and parametricity in the realizability semantics of System F
2019-10-01

We investigate completeness and parametricity for a general class of realizability semantics for System F defined in terms of closure operators over sets of -terms. This class includes most semantics used for normalization theorems, as those arising from Tait's saturated sets and Girard's reducibility candidates. We establish a completeness result for positive types which subsumes those existing in the literature, and we show that closed realizers satisfy parametricity conditions expressed either as invariance with respect to logical relations or as dinaturality. Our results imply that, for positive types, typability, realizability and parametricity are equivalent properties of closed normal -terms.
P2714Time-dependent myocardial necrosis in patients suffering from ST-elevation myocardial infarction without angiographic collateral flow visualized by cardiac magnetic resonance imaging
2019-10-01

Abstract Background Acute complete occlusion of a coronary artery results in progressive ischemia, moving from the endocardium to the epicardium (“wavefront”). Dependent on time-to-reperfusion and collateral flow, myocardial infarction (MI) will manifest, with transmural MI portending poor prognosis. Late gadolinium enhancement cardiac magnetic resonance (LGE-CMR) imaging can detect MI with high diagnostic accuracy. Primary percutaneous coronary intervention (PCI) is the preferred reperfusion strategy in patients with STEMI &lt;12 hours of symptom onset. Purpose We sought to visualize time-dependent necrosis in a ST-segment elevation myocardial infarction (STEMI) population by LGE-CMR. Methods STEMI patients with: single-vessel disease, complete occlusion with Thrombolysis in Myocardial Infarction (TIMI) score 0, absence of collateral flow (Rentrop score 0) and symptom onset &lt;12 hours were consecutively enrolled. By LGE-CMR, area at risk (AAR) and infarct size (IS), myocardial salvage index (MSI), transmurality index, and transmurality grade (0–50%, 51–75%, 76–100%) were determined. Results 164 patients (54±11 years, 80% male) were included. Receiver-operating-characteristic (ROC)-curve (area under the curve [AUC] = 0.81) indicating transmural necrosis revealed the best diagnostic cut-off for a symptom-to-balloon time of 121 minutes, i.e. patients with &gt;121 minutes demonstrated increased IS, transmurality index, transmurality grade (all p-values &lt;0.01), and decreased MSI (p&lt;0.001) vs. patients with symptom-to-balloon times ≤121 minutes. Conclusions In myocardial infarction with no residual antegrade, and no collateral flow, immediate reperfusion is vital. A symptom-to-balloon time of &gt;121 minutes causes a high grade of transmural necrosis. In the present, pure STEMI population, time to reperfusion to salvage myocardium was less than suggested by current guidelines.
P4730Underweight is associated with unfavourable short- and long-term outcomes after MitraClip therapy: a body mass index derived subgroup analysis of the German Transcatheter Mitral Valve Interventions (
2019-10-01

Abstract Background Underweight and obesity represent classical risk factors for patients undergoing cardiac surgery or interventional treatment. The multicentre German Transcatheter Mitral Valve Interventions (TRAMI) registry comprises a large and prospectively enrolled real-world cohort of patients treated by MitraClip implantation. Aims The current analysis examines the impact of underweight, overweight and obesity on intra-hospital, short and long-term outcomes in patients treated by MitraClip therapy. Methods and results From 08/2010 until 07/2013, 799 patients (age 75.3±8.6 years, male gender 60.7%, median logistic EuroSCORE 20% [12; 31], functional mitral regurgitation (MR): 69.3%) were prospectively enrolled into the multicentre, industry-independent German Transcatheter Mitral Valve Interventions registry. Patients were stratified according to body mass index (BMI) into four groups: BMI&lt;20 kg/m2 (underweight, n=49), BMI 20.0 to &lt;25.0 kg/m2 (normal weight, n=293), BMI 25.0 to &lt;30.0 kg/m2 (overweight, n=296) and BMI≥30 kg/m2 (obese, n=132). Procedure and radiation time were comparable among all groups. Significant increased rates of procedural failure (12.2% vs. 2.1 [normal weight], p&lt;0.001), transfusion/bleeding (20.8% vs. normal weight: 5.6%, obesity: 7.0%, p&lt;0.01), sepsis or multiorgan failure and low cardiac output failure were found for underweight patients only. Kaplan-Meier survival curves demonstrated inferior survival for underweight patients, but comparable outcomes for all other patients (global log rank test, p&lt;0.01). Multivariable Cox-regression analysis (adjusted for age, gender, creatinine≥1.5mg/dl, diabetes, left ventricular ejection fraction&lt;30% and chronic obstructive pulmonary disease) confirmed underweight (as compared to normal weight) as an independent risk factor of death (hazard ratio [HR]: 1.58, 95%-confidence interval (CI): 1.01–2.46, p=0.044) and overweight as protective against death (HR: 0.71; 95%-CI: 0.55–0.93; p=0.011). Conclusion Underweight patients are exposed to increased rates of procedural failure, bleeding and low cardiac output as well as increased short- and long-term mortality rates when undergoing MitraClip implantation and should therefore be carefully discussed within the heart team. Acknowledgement/Funding The TRAMI registry has been supported by proprietary means of IHF. Additional funding is provided by “Deutsche Herzstiftung” and a grant from Abbott.
A Minimalistic Hydrolase Based on Co-Assembled Cyclic Dipeptides
2019-10-01

This paper describes minimalistic cyclic dipeptides acting as esterase-mimicks in a self-assembled hydrogel state. It demonstrates that cyclic dipeptides could have acted as enzyme-precursors on a primordial earth and hence be important for abiogenesis.
Model evaluation in computational historical linguistics
2019-10-01

Abstract This is a reply to the comments by Hammarström et al. (This volume) and List (This volume) on the target article Computational Historical Linguistics (This volume). There I proposed several methodological principles for research in Computational Historical Linguistics pertaining to suitable techniques for model fitting and model evaluation. Hammarström et al. debate the usefulness of these principles, and List proposes a novel evaluation measure specifically aimed at the task of proto-form reconstruction. This reply will focus on the role of model evaluation in our field.
Statistics of white dwarf properties in intermediate polars
2019-10-01

Abstract Many intermediate polars are hard X-ray sources. The theory of their hard X-ray radiation is well developed and allows us to determine white dwarf masse in this kind of cataclysmic variables. Here we present the results of determination the masses of 35 white dwarfs in the intermediate polars observed by observatories NuSTAR (10 sources) and Swift/BAT (25 sources). The corresponding mass accrerion rates and the luminosity function were also derived due to accurate distance to the sources well known now after Gaia DR2.