julilili42/papers huggingface dataset:
Learning 3D Shape Completion Under Weak Supervision
2018-10-29

Abstract We address the problem of 3D shape completion from sparse and noisy point clouds, a fundamental problem in computer vision and robotics. Recent approaches are either data-driven or learning-based: Data-driven approaches rely on a shape model whose parameters are optimized to fit the observations; Learning-based approaches, in contrast, avoid the expensive optimization step by learning to directly predict complete shapes from incomplete observations in a fully-supervised setting. However, full supervision is often not available in practice. In this work, we propose a weakly-supervised learning-based approach to 3D shape completion which neither requires slow optimization nor direct supervision. While we also learn a shape prior on synthetic data, we amortize, i.e., learn , maximum likelihood fitting using deep neural networks resulting in efficient shape completion without sacrificing accuracy. On synthetic benchmarks based on ShapeNet (Chang et al. Shapenet: an information-rich 3d model repository, 2015. arXiv:1512.03012 ) and ModelNet (Wu et al., in: Proceedings of IEEE conference on computer vision and pattern recognition (CVPR), 2015) as well as on real robotics data from KITTI (Geiger et al., in: Proceedings of IEEE conference on computer vision and pattern recognition (CVPR), 2012) and Kinect (Yang et al., 3d object dense reconstruction from a single depth view, 2018. arXiv:1802.00411 ), we demonstrate that the proposed amortized maximum likelihood approach is able to compete with the fully supervised baseline of Dai et al. (in: Proceedings of IEEE conference on computer vision and pattern recognition (CVPR), 2017) and outperforms the data-driven approach of Engelmann et al. (in: Proceedings of the German conference on pattern recognition (GCPR), 2016), while requiring less supervision and being significantly faster.
Measurement of negative and depressive symptoms: Discriminatory relevance of affect and expression
2018-10-29

Abstract There is conceptual overlap between negative and depressive symptoms: Mainly the ‘avolition’ factor of negative symptoms also encompasses main symptoms of depression. However, whereas in depression mood is low, mainly anticipatory anhedonia can be found in negative symptoms. Moreover, patients with schizophrenia (SCZ) show greater expressive deficits than those with Major Depressive Episode (MDE). We investigated if measures of depressive and negative symptoms differentiate SCZ subjects, subjects with MDE, and healthy controls (HC). 21 SCZ, 22 MDE, and 25 HC subjects were examined with a rater assessment and a self-rating for negative symptoms (Clinical Assessment Interview for Negative Symptoms (CAINS); Motivation and Pleasure – Self-Report (MAP-SR)) and depressive symptoms (Hamilton Rating Scale for Depression (HAMD-17); Beck Depression Inventory (BDI)). All measures differentiated the psychiatric samples from HC (all p’s &lt; 0.01). The ratings of depressive symptoms (HAMD-17, BDI) and rater assessment of negative symptoms (CAINS) – specifically its sub scale measuring expressive deficits – managed to discriminate between subjects with schizophrenia and those with MDE (SCZ &gt; MDE &gt; HC for negative, MDE &gt; SCZ &gt; HC for depressive symptoms, all p’s &lt; 0.05). The self-rating of negative symptoms (MAP-SR) did not. To differentiate negative symptoms and depression clinicians might look for (self-)reported low mood and observer-rated reduction in speech as well as in gestures and facial expression. Reduced expression and moderate levels of depression point towards a negative syndrome, whereas mostly unimpaired expression and high scores of self-reported depressive symptoms are more likely to indicate a depressive syndrome.
Synthesis and Characterization of Novel Polyol Esters of Undecylenic Acid As Ecofriendly Lubricants
2018-10-29

Abstract Three novel esters of undecylenic acid (UA) were synthesized using the following polyols: linear diglycerol (DG), pentaerythritol monomethylether (PEME), and trimethyloltoluene (TMT). They were characterized through density, viscosity, thermo‐oxidative stability, melting point (m.p.), miscibility with mineral oils, and toxicity to evaluate their potential as ecofriendly lubricants. Trimethylolpropane (TMP) triundecylenate was also synthesized and characterized as a reference ester. Esters’ densities were in the range 0.93–0.97 g cm −3 . The PEME ester showed a kinematic viscosity of 25.2 cSt at 40°C, only slightly higher than that of TMP ester (24.7 cSt), both of them near the ISO VG 22 class, while DG and TMT esters were near the ISO VG 32 class, with viscosities of 28.3 and 37.1 cSt, respectively. PEME and TMT esters were similar in thermo‐oxidative stability and more stable than their corresponding oleate esters. The m.p. of TMT ester was remarkedly low (−54°C), showing its potential for very cold temperature applications. TMT ester was found to be nontoxic against Artemia salina (LC 50 &gt; 1000 μg mL −1 ), an initial indication of nontoxicity of UA esters in aquatic media. The synthesized esters showed potential to be applied as ecofriendly lubricants.
Psychotherapeutic Group Intervention for Traumatized Male Refugees Using Imaginative Stabilization Techniques—A Pilot Study in a German Reception Center
2018-10-29

<b>Background:</b> Due to persecution, human rights violations and armed conflicts, the prevalence of post-traumatic stress disorder (PTSD) is high in refugee populations. Previous studies indicate that trauma-focused treatments are highly effective in treating PTSD in refugees. However, these approaches rely on the stability of the therapeutic setting, treatment continuity, and safe housing. Although early treatment of PTSD is recommended, these requirements are not met in reception centers. Therefore, we conducted a pilot study to examine the effect of imaginative stabilization techniques derived from psychodynamic psychotraumatology therapy for the early stabilization of traumatized refugees in a reception center. <b>Methods:</b> From May 2017 to April 2018, 86 imaginative stabilization group therapy sessions have taken place. A sample of 43 out of 46 traumatized refugees completed self-report questionnaires assessing PTSD, depression, and anxiety symptoms prior to attending open imaginative stabilization group therapy sessions. Furthermore, participants filled in self-report questionnaires on distress and emotional state (valence/arousal/dominance) before and after each session. After having participated in four consecutive sessions, a sub-group of 17 participants completed a follow-up assessment of PTSD, depression, and anxiety symptoms. Follow-up interviews were conducted with 25 participants 2 weeks after their last session attendance to explore self-practice habits post intervention. <b>Results:</b> The pre-post-intervention comparison of scores indicated a significant reduction of distress (<i>z</i> = -3.35, <i>p</i> < 0.001, <i>r</i> = -0.51) and an improvement of affective reports for valence (<i>z</i> = -4.79, <i>p</i> < 0.001, <i>r</i> = -0.82) and dominance (<i>z</i> = -3.89, <i>p</i> < 0.001, <i>r</i> = -0.59), whereas arousal scores were not affected. We found a significant reduction of anxiety symptoms (<i>z</i> = -2.04, <i>p</i> < 0.05, <i>r</i> = -0.49), whereas PTSD and depression scores remained unchanged. Follow-up interviews revealed that 80% of the participants continued to practice the imaginative stabilization techniques after redistribution to other accommodation. <b>Conclusion:</b> The results indicate that imaginative stabilization techniques are a promising and feasible approach to treat refugees in unstable reception center settings. In regular imaginative stabilization group therapy sessions, we were able to reduce the participants' distress and anxiety symptoms while strengthening their internal resources and increasing their emotional stability.
Nicotine Enhances Staphylococcus epidermidis Biofilm Formation by Altering the Bacterial Autolysis, Extracellular DNA Releasing, and Polysaccharide Intercellular Adhesin Production
2018-10-29

<i>Staphylococcus epidermidis</i> is a common bacterial colonizer of human skin and mucous membranes, yet it has emerged as an important nosocomial pathogen largely due to its ability to form biofilms. Tobacco smoke has been demonstrated as a contributor to various infection diseases by improving the biofilm formation of multiple bacterial species; however, the association between tobacco smoke and <i>S. epidermidis</i> biofilm is still unclear. In this study, we tested the effect of nicotine, one of the most active components of tobacco, on <i>S. epidermidis</i> biofilm formation, and we studied the underlying mechanisms. Our results showed that nicotine promoted the biofilm formation of <i>S. epidermidis</i> 1457 strain (SE1457) and enhanced its initial attachment to a polyethylene surface as well as polysaccharide intercellular adhesin (PIA) production. In addition, an increased extracellular DNA release and a higher autolysis rate of SE1457 was detected after nicotine treatment, which was consistent with the increased ratio of dead cells in nicotine-treated SE1457 biofilm observed with confocal laser-scanning microscopy. Furthermore, the effect of nicotine on several autolysis-related and biofilm-related gene knockout mutants of SE1457 was tested. It showed that in <i>ΔsaeRS, ΔlytSR</i>, and <i>ΔsceD</i>, nicotine induced increase in biofilm formation was similar to that in SE1457; but in <i>ΔarlRS, ΔatlE</i>, and <i>ΔicaC</i>, the effect was obviously impaired. Consistently, the increase of the bacterial autolysis rate in <i>ΔarlRS</i> and <i>ΔatlE</i> induced by nicotine was not as significant as that in SE1457. Meanwhile, the growth inhibition of nicotine on SE1457 was observed, and it was much less on <i>ΔarlRS</i> and restored by the <i>arlRS</i> complementation. The <i>arlRS</i> transcription in SE1457 was inhibited by nicotine during cultivation as indicated by a promoter reporter assay using green fluoresent protein. Taken together, our study indicates that nicotine improves <i>S. epidermidis</i> biofilm formation by promoting its initial attachment and intercellular accumulation; the <i>arlRS, atlE</i>, and <i>ica</i> genes mediating bacterial autolysis and PIA production play an important role in this process.
Evidential strength of intonational cues and rational adaptation to (un-)reliable intonation
2018-10-29

Intonation plays an integral role in comprehending spoken language. It is also remarkably variable, often exhibiting only probabilistic mappings between form and function. Despite this apparent uncertainty, listeners can rapidly integrate intonational information to predictively map a given pitch accent onto the speaker's likely referential intentions. We use manual response dynamics (mouse-tracking) to investigate two questions: (i) whether listeners draw predictive inferences from the presence and absence of an intonational marking and (ii) whether and how listeners adapt their online interpretation of intonational cues when these are reliable or stochastically unreliable. We formulate a novel Bayesian model of rational predictive cue integration and explore predictions derived under a concrete link hypothesis relating a quantitative notion of evidential strength of a cue to the moment in time, relative to the unfolding speech signal, at which mouse trajectories finally turn towards the eventually selected option. In order to capture rational belief updates after concrete observations of a speaker's behavior, we formulate and explore an extension of this model that includes the listener's hierarchical beliefs about the speaker's likely production behavior. Our results are compatible with the assumption that listeners rapidly and rationally integrate all available intonational information, that they expect reliable intonational information initially, and that they adapt these initial expectations gradually during exposition to unreliable input.
Spatial context effects at different scales: A formal model for egocentric contexts in two- and three-dimensional space
2018-10-29

Spatial context effects are a topic in many scientific disciplines. This paper examines which conceptual steps are necessary for determining the extension, or the appropriate scale, of relevant spatial environments when contexts can be analytically disaggregated into context elements. Adequate models of scale need to specify not only the distance-dependent relevance of context elements but also their distribution and an adequate combination. In this way, it becomes possible to understand why non-monotonic patterns in scale-related context effects have been repeatedly found in spite of common assumptions of distance decay in relevance. In many cases, a distance-related maximum of (aggregate) context relevance can be expected, so that there is an “optimal” range for the measurement of context effects. It is also important to distinguish between applications in two- and three-dimensional space. This general model helps to specify the steps necessary for the determination of spatial context patterns and to identify unrealistic assumptions.
Curiosity carry-over effect
2018-10-29

Curiosity is a powerful source of motivation and allows us to explore and acquire knowledge without relying on extrinsic incentives. So far, studies have mostly focused on the curiosity felt towards a specific object. Using a paradigm that sequentially activates curiosity on a trial-by-trial basis with trivia questions, we showed that the curiosity of one trial carries over to the next trial, even if each trial presents completely independent information. This carry-over effect was observed both when curiosity was measured through self-reports and a behavioral task (i.e. willingness-to-pay task). The results were also replicated when participants’ curiosity was not resolved, eliminating the role of general positive emotions. Theoretical implication of this carry-over effect was discussed.
BRI1 controls vascular cell fate in the Arabidopsis root through RLP44 and phytosulfokine signaling
2018-10-30

Significance Cell-fate determination and cellular behavior in plants rely mainly on positional information and intercellular communication. A plethora of cues are perceived by surface receptors and integrated into an adequate cellular output. Here, we show that the small receptor-like protein RLP44 acts as an intermediary to connect the receptors for two well-known signaling molecules, brassinosteroid and phytosulfokine, to control cell fate in the root vasculature. Furthermore, we show that the brassinosteroid receptor has functions that are independent from the responses to its hormone ligands and reveal that phytosulfokine signaling promotes procambial cell identity. These results provide a mechanistic framework for the integration of multiple signaling pathways at the plasma membrane by shifting associations of receptors in multiprotein complexes.
Molecular Fingerprinting of On–Off Direction-Selective Retinal Ganglion Cells Across Species and Relevance to Primate Visual Circuits
2018-10-30

The ability to detect moving objects is an ethologically salient function. Direction-selective neurons have been identified in the retina, thalamus, and cortex of many species, but their homology has remained unclear. For instance, it is unknown whether direction-selective retinal ganglion cells (DSGCs) exist in primates and, if so, whether they are the equivalent to mouse and rabbit DSGCs. Here, we used a molecular/circuit approach in both sexes to address these issues. In mice, we identify the transcription factor Satb2 (special AT-rich sequence-binding protein 2) as a selective marker for three RGC types: On–Off DSGCs encoding motion in either the anterior or posterior direction, a newly identified type of Off-DSGC, and an Off-sustained RGC type. In rabbits, we find that expression of Satb2 is conserved in On–Off DSGCs; however, it has evolved to include On–Off DSGCs encoding upward and downward motion in addition to anterior and posterior motion. Next, we show that macaque RGCs express Satb2 most likely in a single type. We used rabies virus-based circuit-mapping tools to reveal the identity of macaque Satb2-RGCs and discovered that their dendritic arbors are relatively large and monostratified. Together, these data indicate Satb2-expressing On–Off DSGCs are likely not present in the primate retina. Moreover, if DSGCs are present in the primate retina, it is unlikely that they express Satb2. SIGNIFICANCE STATEMENT The ability to detect object motion is a fundamental feature of almost all visual systems. Here, we identify a novel marker for retinal ganglion cells encoding directional motion that is evolutionarily conserved in mice and rabbits, but not in primates. We show in macaque monkeys that retinal ganglion cells (RGCs) that express this marker comprise a single type and are morphologically distinct from mouse and rabbit direction-selective RGCs. Our findings indicate that On–Off direction-selective retinal neurons may have evolutionarily diverged in primates and more generally provide novel insight into the identity and organization of primate parallel visual pathways.
On the inference speed and video-compression robustness of DeepLabCut
2018-10-30

Pose estimation is crucial for many applications in neuroscience, biomechanics, genetics and beyond. We recently presented a highly efficient method for markerless pose estimation based on transfer learning with deep neural networks called DeepLabCut. Current experiments produce vast amounts of video data, which pose challenges for both storage and analysis. Here we improve the inference speed of DeepLabCut by up to tenfold and benchmark these updates on various CPUs and GPUs. In particular, depending on the frame size, poses can be inferred offline at up to 1200 frames per second (FPS). For instance, 278 × 278 images can be processed at 225 FPS on a GTX 1080 Ti graphics card. Furthermore, we show that DeepLabCut is highly robust to standard video compression (ffmpeg). Compression rates of greater than 1,000 only decrease accuracy by about half a pixel (for 640 × 480 frame size). DeepLabCut’s speed and robustness to compression can save both time and hardware expenses.
Refolding and in vitro characterization of human papillomavirus 16 minor capsid protein L2
2018-10-30

Abstract The minor capsid protein L2 of papillomaviruses exhibits multiple functions during viral entry including membrane interaction. Information on the protein is scarce, because of its high tendency of aggregation. We determined suitable conditions to produce a functional human papillomavirus (HPV) 16 L2 protein and thereby provide the opportunity for extensive in vitro analysis with respect to structural and biochemical information on L2 proteins and mechanistic details in viral entry. We produced the L2 protein of high-risk HPV 16 in Escherichia coli as inclusion bodies and purified the protein under denaturing conditions. A successive buffer screen resulted in suitable conditions for the biophysical characterization of 16L2. Analytical ultracentrifugation of the refolded protein showed a homogenous monomeric species. Furthermore, refolded 16L2 shows secondary structure elements. The N-terminal region including the proposed transmembrane region of 16L2 shows alpha-helical characteristics. However, overall 16L2 appears largely unstructured. Refolded 16L2 is capable of binding to DNA indicating that the putative DNA-binding regions are accessible in refolded 16L2. Further the refolded protein interacts with liposomal membranes presumably via the proposed transmembrane region at neutral pH without structural changes. This indicates that 16L2 can initially interact with membranes via pre-existing structural features.
Keratinocyte Growth Factor Modified Messenger RNA Accelerating Cell Proliferation and Migration of Keratinocytes
2018-10-30

Keratinocyte growth factor (KGF) plays a central role in wound healing as it induces cell proliferation and motility. The use of growth factors such as KGF is therefore viewed as a promising approach in wound therapy, although effective application remains a major problem because of inactivation and the resulting short half-life of applied growth factors in wound beds. Therefore, the rational of this study was to develop and investigate an innovative strategy to improve wound healing using an in vitro-transcribed modified KGF messenger RNA (mRNA). After transfection of cells, we evaluated the effects of the produced KGF protein on cell migration and reepithelialization of keratinocytes using a scratch assay. The results demonstrate that KGF-mRNA-transfected cells exhibited a high KGF protein release that is sufficient to significantly improve reepithelialization in the performed scratch assays. Transfection with growth factor mRNA therefore seems to be a promising therapeutic strategy, especially for difficult wounds, as it leads to a temporary increase of growth factor expression in the treated wound area without interfering with the DNA of the nucleus, as seen in gene therapeutic applications.
Self-assessment of negative symptoms – Critical appraisal of the motivation and pleasure – Self-report's (MAP-SR) validity and reliability
2018-10-30

We found that the MAP-SR is adequate to assess anhedonia but is less suitable when assessing motivation. Therefore, we propose using the "pleasure and hedonic activity scale" to cover the "anhedonia" subdomain. We think the "motivation" part of the instrument requires reconstruction.
Infectious Entry of Merkel Cell Polyomavirus
2018-10-30

Abstract Merkel Cell Polyomavirus (MCPyV) is a small, non-enveloped tumor virus associated with an aggressive form of skin cancer, the Merkel cell carcinoma (MCC). MCPyV infections are highly prevalent in the human population with MCPyV virions being continuously shed from human skin. However, the precise host cell tropism(s) of MCPyV remains unclear: MCPyV is able to replicate within a subset of dermal fibroblasts, but MCPyV DNA has also been detected in a variety of other tissues. However, MCPyV appears different from other polyomaviruses as it requires sulfated polysaccharides such as heparan sulfates and/or chondroitin sulfates for initial attachment. Like other polyomaviruses, MCPyV engages sialic acid as a (co-receptor). To explore the infectious entry process of MCPyV, we analyzed the cell biological determinants of MCPyV entry into A549 cells, a highly transducible lung carcinoma cell line, in comparison to well-studied simian virus 40 and a number of other viruses. Our results indicate that MCPyV enters cells via caveolar/lipid raft-mediated endocytosis but not macropinocytosis, clathrin-mediated endocytosis or glycosphingolipid-enriched carriers. The viruses internalized in small endocytic pits that led the virus to endosomes and from there to the endoplasmic reticulum (ER). Similar to other polyomaviruses, trafficking required microtubular transport, acidification of endosomes, and a functional redox environment. To our surprise, the virus was found to acquire a membrane envelope within endosomes, a phenomenon not reported for other viruses. Only minor amounts of viruses reached the ER, while the majority was retained in endosomal compartments suggesting that endosome-to-ER trafficking is a bottleneck during infectious entry. Importance MCPyV is the first polyomavirus directly implicated in the development of an aggressive human cancer, the Merkel Cell Carcinoma (MCC). Although MCPyV is constantly shed from healthy skin, MCC incidence increases among aging and immunocompromised individuals. To date, the events connecting initial MCPyV infection and subsequent transformation still remain elusive. MCPyV differs from other known polyomaviruses concerning its cell tropism, entry receptor requirements, and infection kinetics. In this study, we examined the cellular requirements for endocytic entry as well as the subcellular localization of incoming virus particles. A thorough understanding of the determinants of the infectious entry pathway and the specific biological niche will benefit prevention of virus-derived cancers such as MCC.