julilili42/papers huggingface dataset:
MorphVAE: Generating Neural Morphologies from 3D-Walks using a Variational Autoencoder with Spherical Latent Space
2021-06-15

Abstract For the past century, the anatomy of a neuron has been considered one of its defining features: The shape of a neuron’s dendrites and axon fundamentally determines what other neurons it can connect to. These neurites have been described using mathematical tools e.g. in the context of cell type classification, but generative models of these structures have only rarely been proposed and are often computationally inefficient. Here we propose M orph VAE, a sequence-to-sequence variational autoencoder with spherical latent space as a generative model for neural morphologies. The model operates on walks within the tree structure of a neuron and can incorporate expert annotations on a subset of the data using semi-supervised learning. We develop our model on artificially generated toy data and evaluate its performance on dendrites of excitatory cells and axons of inhibitory cells of mouse motor cortex (M1) and dendrites of retinal ganglion cells. We show that the learned latent feature space allows for better cell type discrimination than other commonly used features. By sampling new walks from the latent space we can easily construct new morphologies with a specified degree of similarity to their reference neuron, providing an efficient generative model for neural morphologies.
Natural and cryptic peptides dominate the immunopeptidome of atypical teratoid rhabdoid tumors
2021-06-15

A bstract Atypical teratoid/rhabdoid tumors (AT/RT) are highly aggressive CNS-tumors of infancy and early childhood. Hallmark is the surprisingly simple genome with inactivating mutations or deletions in the SMARCB1 gene as the oncogenic driver. Nevertheless, AT/RTs are infiltrated by immune cells and even clonally expanded T cells. However, it is unclear, which epitopes T-cells might recognize on AT/RT cells. Here, we report a comprehensive MS-based analysis of naturally presented HLA-class-I and class-II ligands on 23 AT/RTs. Comparative HLA ligandome analysis of the HLA-ligandome revealed 55 class-I and 139 class-II tumor-exclusive peptides. No peptide originated from the SMARCB1-region. In addition, 61 HLA-class I tumor-exclusive peptide sequences derived from non-canonically translated proteins. Combination of peptides from natural and cryptic class I and class II origin gave optimal representation of tumor cell compartments. Substantial overlap existed with the cryptic immunopeptidome of glioblastomas but no concordance was found with extracranial tumors. More than 80% of AT/RT-exclusive peptides were able to successfully prime CD8 + T-cells, whereas naturally occurring memory responses in AT/RT-patients could only be detected for class-II epitopes. Interestingly, &gt;50% of AT/RT-exclusive class-II ligands were also recognized by T-cells from glioblastoma patients but not from healthy donors. These findings highlight that AT/RTs, potentially paradigmatic for other pediatric tumors with a low mutational load, present a variety of highly immunogenic HLA-class-I and class-II peptides from canonical as well as non-canonical protein sources. Inclusion of such cryptic peptides into therapeutic vaccines would enable an optimized mapping of the tumor cell surface, thereby reducing the likelihood of immune evasion. One Sentence Summary The HLA-ligandome of atpyical teratoid-rhabdoid tumors contains immunogenic, tumor-exclusive peptides derived from natural and cryptic source proteins.
Learning-based Camera Relocalization with Domain Adaptation via Image-to-Image Translation
2021-06-15

Camera relocalization is promising for robot navigation; however, the lack of sufficient reference images and challenging shifts of conditions limit its further application. This paper proposes a learning-based three-step pipeline that applies spatial information features for camera relocalization problems. We first introduce a frustum intersection over union (IoU) to represent the image pair's spatial similarity. This representation is used to train an image retrieval model to find nearest neighbor candidates for query images. A spatial sample consensus (SPASAC) operation is then deployed to filter the outliers in the candidates. Afterward, a relative camera pose regressor is used with the valid candidates to predict every query image's absolute pose. Besides, we introduce two implementations of image-to-image translation networks for camera relocalization to increase the number of synthetic reference images and challenging night-to-day localization performance. Experiments show that our method can estimate camera poses across different domains and outperforms related methods in four benchmarks. Specifically, the experiments on the Tuebingen Buildings dataset demonstrate the robustness of our approach when localizing UAV-captured images with highspeed movement and large viewpoint variation.
Crafting Idiosyncrasies. Early Social Complexity, Ivory and Identity-Making in Copper Age Iberia
2021-06-15

As a raw material, ivory has been used to manufacture a wide range of objects, normally associated with sumptuous material culture. In this article we explore the role played by ivory and ivory artefacts among early complex societies, and particularly its importance in the definition of identities among emergent elites. To this end, we make a thorough examination of the evidence from Copper Age Iberia, focusing on the mega-site of Valencina, in southern Spain. This site has provided what to date is the largest assemblage of prehistoric ivory in western Europe, with an estimated total of 8.8 kg, including finely crafted artefacts of unrivalled beauty and sophistication. Our study looks carefully at the technological, morphological and contextual dimensions of Copper Age ivory. As a result, we contend that the broad morphological variability together with the technological uniformity of this assemblage suggest that, while belonging to a common technological tradition, objects were deliberately crafted as unique and unrepeatable so that they could be used to create and maintain socio-cultural idiosyncrasies and ideological legitimation.
Counting tropical rational space curves with cross-ratio constraints
2021-06-15

Abstract This is a follow-up paper of Goldner (Math Z 297(1–2):133–174, 2021), where rational curves in surfaces that satisfy general positioned point and cross-ratio conditions were enumerated. A suitable correspondence theorem provided in Tyomkin (Adv Math 305:1356–1383, 2017) allowed us to use tropical geometry, and, in particular, a degeneration technique called floor diagrams . This correspondence theorem also holds in higher dimension. In the current paper, we introduce so-called cross-ratio floor diagrams and show that they allow us to determine the number of rational space curves that satisfy general positioned point and cross-ratio conditions. The multiplicities of such cross-ratio floor diagrams can be calculated by enumerating certain rational tropical curves in the plane.
Information and Communication Technologies for Development (ICT4D) critique
2021-06-16

This paper reconstructs the major points of criticism of both research and practice of Information and Communication Technologies for/and Development (ICT4D/ICTD). Since ICT4D/ICTD was established both as a stream in development work and as an academic field of study, numerous critical reflections on its norms, theories, methods, and consequences were published. This paper provides a first comprehensive compilation and synthesis of what the authors term ICT4D critique. The authors recount criticism about the modus operandi of ICT4D research, the alleged weakness of theories and lack of quality, research gaps, and the politics of ICT4D research. They further recite criticism of the neoliberal orientation of ICT4D practice, the lack of user-centric projects, Eurocentrism and techno-optimism, and the lack of ethical reflection in the field. This paper is intended to serve as a resource and point of reference for students, researchers, and practitioners, in particular those who are new to the field.
Mantle sources and magma evolution in Europe's largest rare earth element belt (Gardar Province, SW Greenland): New insights from sulfur isotopes
2021-06-16

This work is a contribution to the HiTech AlkCarb project and was funded by the European Union's Horizon 2020 research and innovation programme under grant agreement No. 689909. W.H. also acknowledges support from a UKRI Future Leaders Fellowship (MR/S033505/1). A.J.B. is funded by the NERC National Environment Isotope Facility award (NE/S011587/1) and the Scottish Universities Environmental Research Centre.
Adapting the Pore Size of Individual, 3D-Printed CPC Scaffolds in Maxillofacial Surgery
2021-06-16

Three dimensional (3D) printing allows additive manufacturing of patient specific scaffolds with varying pore size and geometry. Such porous scaffolds, made of 3D-printable bone-like calcium phosphate cement (CPC), are suitable for bone augmentation due to their benefit for osteogenesis. Their pores allow blood-, bone- and stem cells to migrate, colonize and finally integrate into the adjacent tissue. Furthermore, the pore size affects the scaffold’s stability. Since scaffolds in maxillofacial surgery have to withstand high forces within the jaw, adequate mechanical properties are of high clinical importance. Although many studies have investigated CPC for bone augmentation, the ideal porosity for specific indications has not been defined yet. We investigated 3D printed CPC cubes with increasing pore sizes and different printing orientations regarding cell migration and mechanical properties in comparison to commercially available bone substitutes. Furthermore, by investigating clinical cases, the scaffolds’ designs were adapted to resemble the in vivo conditions as accurately as possible. Our findings suggest that the pore size of CPC scaffolds for bone augmentation in maxillofacial surgery necessarily needs to be adapted to the surgical site. Scaffolds for sites that are not exposed to high forces, such as the sinus floor, should be printed with a pore size of 750 μm to benefit from enhanced cell infiltration. In contrast, for areas exposed to high pressures, such as the lateral mandible, scaffolds should be manufactured with a pore size of 490 μm to guarantee adequate cell migration and in order to withstand the high forces during the chewing process.
No evidence for a specific vitamin D deficit in benign paroxysmal positional vertigo
2021-06-16

Abstract Background and purpose The aim was to investigate whether there is a difference in serum 25‐hydroxyvitamin D (25(OH)D) concentration between patients with benign paroxysmal positional vertigo (BPPV), patients with other vestibular diseases and patients with other neurological non‐vestibular diseases presenting in a tertiary neurological academic outpatient clinic. Methods The serum 25(OH)D concentration was measured in 680 patients (368 male, mean age ± SD 58 ± 17 years, 661 Caucasian) without vitamin D supplementation. 158 patients had BPPV; 221 had other vestibular diseases (including 122 with peripheral vestibular disorders, such as unilateral vestibulopathy or Ménière's disease; 46 with central vestibular disorders, such as vestibular migraine or cerebellar dizziness; 53 with functional dizziness); and 301 patients with other neurological non‐vestibular diseases. Results There was no significant difference in the serum 25(OH)D concentration between patients with BPPV (mean ± SD 23.4 ± 9.4 ng/ml) and those with other vestibular disorders (24.9 ± 10.1 ng/ml, p = 0.324). Patients with other neurological disorders had even lower concentrations (21.4 ± 10.6 ng/ml) than patients with BPPV ( p &lt; 0.005), patients with other vestibular disorders ( p &lt; 0.005) and all patients with vestibular disorders (24.9 ± 10.1 ng/ml, p &lt; 0.005). Conclusion Our analysis does not support the theory of a specific relationship between serum 25(OH)D concentration and the occurrence of BPPV or other vestibular disorders.
A distributed saccade-associated network encodes high velocity conjugate and monocular eye movements in the zebrafish hindbrain
2021-06-16

Abstract Saccades are rapid eye movements that redirect gaze. Their magnitudes and directions are tightly controlled by the oculomotor system, which is capable of generating conjugate, monocular, convergent and divergent saccades. Recent studies suggest a mainly monocular control of saccades in mammals, although the development of binocular control and the interaction of different functional populations is less well understood. For zebrafish, a well-established model in sensorimotor research, the nature of binocular control in this key oculomotor behavior is unknown. Here, we use the optokinetic response and calcium imaging to characterize how the developing zebrafish oculomotor system encodes the diverse repertoire of saccades. We find that neurons with phasic saccade-associated activity (putative burst neurons) are most frequent in dorsal regions of the hindbrain and show elements of both monocular and binocular encoding, revealing a mix of the response types originally hypothesized by Helmholtz and Hering. Additionally, we observed a certain degree of behavior-specific recruitment in individual neurons. Surprisingly, calcium activity is only weakly tuned to saccade size. Instead, saccade size is apparently controlled by a push–pull mechanism of opposing burst neuron populations. Our study reveals the basic layout of a developing vertebrate saccade system and provides a perspective into the evolution of the oculomotor system.
Shifts in growth, but not differentiation, foreshadow the formation of exaggerated forms under chicken domestication
2021-06-16

Domestication provides an outstanding opportunity for biologists to explore the underpinnings of organismal diversification. In domesticated animals, selective breeding for exaggerated traits is expected to override genetic correlations that normally modulate phenotypic variation in nature. Whether this strong directional selection affects the sequence of tightly synchronized events by which organisms arise (ontogeny) is often overlooked. To address this concern, we compared the ontogeny of the red junglefowl (RJF) ( Gallus gallus ) to four conspecific lineages that underwent selection for traits of economic or ornamental value to humans. Trait differentiation sequences in embryos of these chicken breeds generally resembled the representative ancestral condition in the RJF, thus revealing that early ontogeny remains highly canalized even during evolution under domestication. This key finding substantiates that the genetic cost of domestication does not necessarily compromise early ontogenetic steps that ensure the production of viable offspring. Instead, disproportionate beak and limb growth (allometry) towards the end of ontogeny better explained phenotypes linked to intense selection for industrial-scale production over the last 100 years. Illuminating the spatial and temporal specificity of development is foundational to the enhancement of chicken breeds, as well as to ongoing research on the origins of phenotypic variation in wild avian species.
Oncological validation of bone turnover markers c-terminal telopeptide of type I collagen (1CTP) and peptides n-terminal propeptide of type I procollagen (P1NP) in patients with prostate cancer and bone metastases
2021-06-16

The present study confirms that increased levels of 1CTP and P1NP concentrations are associated with presence of metastatic disease in the bone. Moreover, these markers are able to predict clinical course in PC patients with bone metastases. The potential use of these markers for treatment selection in advanced PC remains to be determined.
TüEyeQ, a rich IQ test performance data set with eye movement, educational and socio-demographic information
2021-06-16

Abstract We present the TüEyeQ data set - to the best of our knowledge - the most comprehensive data set generated on a culture fair intelligence test (CFT 20-R), i.e., an IQ Test, consisting of 56 single tasks, taken by 315 individuals aged between 18 and 30 years. In addition to socio-demographic and educational information, the data set also includes the eye movements of the individuals while taking the IQ test. Along with distributional information we also highlight the potential for predictive analysis on the TüEyeQ data set and report the most important covariates for predicting the performance of a participant on a given task along with their influence on the prediction.
Texture characterization of some large hailstones with an automated technique
2021-06-16

Abstract Hailstone structures have been studied for over a century, but so far mainly by manual optical means. This paper presents new texture and microstructure data (i.e. crystal lattice orientations, grain sizes and shapes) measured with an Automatic Ice Texture Analyzer, which gives access to high spatial and angular resolutions. The hailstones show two main characteristics: (1) they are structured with several concentric layers composed of alternating fine equiaxed grains and coarse elongated and radially oriented grains, and (2) they show two texture types with c -axes oriented either parallel or perpendicular to the radial direction. Such textures are compared with the ones observed in lake S1 and S2 ices, respectively. The S1 texture type (with c -axes parallel to the columnar crystals that grew in the radial direction) may result from epitaxial growth from a polycrystalline embryo, while the S2 texture ( c -axes in the plane perpendicular to the column direction) may result from the growth from an embryo made of a few crystals with mainly one crystallographic orientation. Our novel high-resolution maps and measurements of both microstructure and texture may help to shed new light on the long-term discussion on the growth mechanisms of large hailstones.
A compact low-power gaze gesture sensor based on laser feedback interferometry for smart glasses
2021-06-16

The integration of gaze gesture sensors in next-generation smart glasses will improve usability and enable new interaction concepts. However, consumer smart glasses place additional requirements to gaze gesture sensors, such as a low power consumption, high integration capability and robustness to ambient illumination. We propose a novel gaze gesture sensor based on laser feedback interferometry (LFI), which is capable to measure the rotational velocity of the eye as well as the sensors distance towards the eye. This sensor delivers a unique and novel set of features with an outstanding sample rate allowing to not only predict a gaze gesture but also to anticipate it. To take full advantage of the unique sensor features and the high sampling rate, we propose additionally a novel gaze gesture classification algorithm based on single sample. At a mean F1-score of 93.44 performance at a negative latency between gaze gesture input and command execution.
A new adaptive procedure for estimating perceptual thresholds: the effects of observer bias and its correction
2021-06-16

Abstract Adaptive threshold estimation procedures sample close to a subject’s perceptual threshold by dynamically adapting the stimulation based on the subject’s performance. Yet, perceptual thresholds not only depend on the observers’ sensory capabilities but also on any bias in terms of their expectations and response preferences, thus distorting the precision of the threshold estimates. Using the framework of signal detection theory (SDT), independent estimates of both, an observer’s sensitivity and internal processing bias can be delineated from threshold estimates. While this approach is commonly available for estimation procedures engaging the method of constant stimuli (MCS), correction procedures for adaptive methods (AM) are only scarcely applied. In this article, we introduce a new AM that takes individual biases into account, and that allows for a bias-corrected assessment of subjects’ sensitivity. This novel AM is validated with simulations and compared to a typical MCS-procedure, for which the implementation of bias correction has been previously demonstrated. Comparing AM and MCS demonstrates the viability of the presented AM. Besides its feasibility, the results of the simulation reveal both, advantages, and limitations of the proposed AM. The procedure has considerable practical implications, in particular for the design of shaping procedures in sensory training experiments, in which task difficulty has to be constantly adapted to an observer’s performance, to improve training efficiency.
Human leucocyte antigen G (HLA-G) and its murine homologue Qa-2 protect from pregnancy loss
2021-06-16

Abstract During pregnancy, the maternal immune system has to balance tightly between protection against pathogens and tolerance towards a semi-allogeneic organism. Dysfunction of this immune adaptation can lead to severe complications such as pregnancy loss, preeclampsia or fetal growth restriction. The MHC-Ib molecule HLA-G is well known to mediate immunological tolerance. However, no in-vivo studies have yet demonstrated a beneficial role of HLA-G for pregnancy success. Myeloid derived suppressor cells (MDSC) are suppressively acting immune cells accumulating during pregnancy and mediating maternal-fetal tolerance. Here, we analyzed the impact of Qa-2, the murine homologue to HLA-G, on pregnancy outcome in vivo . We demonstrate that lack of Qa-2 led to intrauterine growth restriction and increased abortion rates especially in late pregnancy accompanied by changes in uterine gene expression, altered spiral artery remodeling and protein aggregation in trophoblast cells indicating a preeclampsia-like phenotype. Furthermore, lack of Qa-2 caused decreased accumulation of MDSC and impaired MDSC function. Lastly, we show that application of sHLA-G reduced abortion rates in Qa-2 deficient mice by inducing MDSC. Our results highlight the importance of an interaction between HLA-G and MDSC for pregnancy success and the therapeutic potential of HLA-G for the treatment of immunological pregnancy complications.
Contracting Institutions and Firm Integration Around the World
2021-06-16

Firm integration is fundamentally shaped by contractual frictions. But do better contracting institutions, reducing these frictions, induce firms to be more or less deeply integrated? To address this question, this paper exploits unique micro data on ownership shares across more than 200,000 firm pairs worldwide, including domestic and cross-border ownership links. We uncover a new stylized fact: Firms choose higher ownership shares in subsidiaries located in countries with better contracting institutions. We develop a Property-Rights Theory of the multinational firm featuring partial ownership that rationalizes this pattern and guides our econometric analysis. The estimations demonstrate that better contracting institutions favor deeper integration, in particular in relationship-specific industries.
Plant “helper” immune receptors are Ca 2+ -permeable nonselective cation channels
2021-06-17

Calcium signaling for host cell death In response to microbial pathogens, some plants kill off their own cells to limit further spread of infection. The Toll/Interleukin-1 receptor/Resistance class of nucleotide-binding leucine-rich repeat receptors (known as TNLs) function in plants as immune receptors. These TNLs work together with a dedicated set of helper proteins. Jacob et al. reveal the structure of one of these helpers known as NRG1 (N REQUIREMENT GENE 1). The structure resembles a known animal cation channel. The authors demonstrate that helper NLRs directly control calcium ion influx to initiate host cell death, providing a mechanism for TNL outputs. Science , abg7917, this issue p. 420