Miracle-dz/UniFAR-FTUs huggingface dataset:
From point samples to surfaces - on meshing and alternatives

© 2018 International Society for Photogrammetry and Remote Sensing. All rights reserved. Terrestrial laser scanners deliver a dense point-wise sampling of an object's surface. For many applications a surface-like reconstruction is required. The most typical example is the visualization of the scanned data. Traditional approaches use meshing algorithms to reconstruct and triangulate the surface represented by the points. Especially in cultural heritage, where complex objects with delicate structures are recorded in highly detailed scans, this process is not without problems. Often long and tedious manual clean-up procedures are required to achieve satisfactory results. After summarizing our experience with current meshing technology we therefore explore alternative approaches for surface reconstruction. An alternative approach presented within this paper is point splatting. We have developed an algorithm to compute a suitable surfel representation directly from the raw laser scanner data. This results in a speedy and fully automated procedure for surface reconstruction. The properties of the different approaches for surface reconstruction are discussed considering a practical example from the field of cultural heritage. The Panagia Kera in Kritsa near Agios Nikolaos on the island of Crete was chosen as a suitable example.
Dynamic Analysis of Neural Encoding by Point Process Adaptive Filtering

Neural receptive fields are dynamic in that with experience, neurons change their spiking responses to relevant stimuli. To understand how neural systems adapt the irrepresentations of biological information, analyses of receptive field plasticity from experimental measurements are crucial. Adaptive signal processing, the well-established engineering discipline for characterizing the temporal evolution of system parameters, suggests a framework for studying the plasticity of receptive fields. We use the Bayes' rule Chapman-Kolmogorov paradigm with a linear state equation and point process observation models to derive adaptive filters appropriate for estimation from neural spike trains. We derive point process filter analogues of the Kalman filter, recursive least squares, and steepest-descent algorithms and describe the properties of these new fil-ters. We illustrate our algorithms in two simulated data examples. The first is a study of slow and rapid evolution of spatial receptive fields in hippocampal neurons. The second is an adaptive decoding study in which a signal is decoded from ensemble neural spiking activity as the recep-tive fields of the neurons in the ensemble evolve. Our results provide a paradigm for adaptive estimation for point process observations and suggest a practical approach for constructing filtering algorithms to track neural receptive field dynamics on a millisecond timescale.
Multiscale geometric analysis of turbulence by curvelets

In this paper, after a brief review of curvelets and their relation to classical wavelet transform, multiscale geometric analysis is systematically applied to turbulent flows in two and three dimensions. The analysis is based on the constrained minimization of a total variation functional representing the difference between the data and its representation in the curvelet space. Constrained multiscale minimization results in a minimum loss of the geometric flow features and the extraction of the coherent structures with their edges and geometry properly preserved, which is significant for turbulence modeling. The effectiveness of curvelet analysis compared to the wavelet transform is demonstrated for both two- and three-dimensional turbulent flows.
Arabidopsis KINETOCHORE NULL2 Is an Upstream Component for Centromeric Histone H3 Variant cenH3 Deposition at Centromeres[W]

This work finds that Arabidopsis KINETOCHORE NULL2 (KNL2) colocalizes with the centromere histone variant cenH3. Characterization of knl2 mutants showed reduction of cenH3 deposition at centromeres, abnormalities of mitosis and meiosis, seed abortion, and alterations in DNA methylation. The centromeric histone H3 variant cenH3 is an essential centromeric protein required for assembly, maintenance, and proper function of kinetochores during mitosis and meiosis. We identified a KINETOCHORE NULL2 (KNL2) homolog in Arabidopsis thaliana and uncovered features of its role in cenH3 loading at centromeres. We show that Arabidopsis KNL2 colocalizes with cenH3 and is associated with centromeres during all stages of the mitotic cell cycle, except from metaphase to mid-anaphase. KNL2 is regulated by the proteasome degradation pathway. The KNL2 promoter is mainly active in meristematic tissues, similar to the cenH3 promoter. A knockout mutant for KNL2 shows a reduced level of cenH3 expression and reduced amount of cenH3 protein at chromocenters of meristematic nuclei, anaphase bridges during mitosis, micronuclei in pollen tetrads, and 30% seed abortion. Moreover, knl2 mutant plants display reduced expression of suppressor of variegation 3-9 homologs2, 4, and 9 and reduced DNA methylation, suggesting an impact of KNL2 on the epigenetic environment for centromere maintenance.
Choreographing lived experience: dance, feelings and the storytelling body

Although narrative-based research has been central to studies of illness experience, the inarticulate, sensory experiences of illness often remain obscured by exclusively verbal or textual inquiry. To foreground the body in our investigation of subjective and intersubjective aspects of eating disorders, we—a medical anthropologist and a contemporary dance choreographer—designed a collaborative project, in which we studied the experiences of women who had eating disorders, through eight weeks of integrating dance practice-based, discussion-based and interview-based research. Grounded in the participants’ own reflections on choreographing, dancing and watching others perform solos about their eating disordered experiences, our analysis examines the types of knowledge the participants used in choreographing their dance works, and the knowledge that they felt the dance enabled them to convey. We find that the participants consistently spoke of feeling as guiding their choreographic processes; they also said the experiences they conveyed through their dance works were centred in feelings, rather than in practices or events. Through dance, the participants said they could communicate experiences that would have remained unspoken otherwise. Yet, notably, dance practice also enabled participants to begin defining and describing their experiences verbally. We suggest, therefore, that through engaging participants in contemporary dance practice, we can begin to identify and address embodied experiences of illness and recovery that may be silenced in speech or writing alone.
Boundary states for supertubes in flat spacetime and Gödel universe

We construct boundary states for supertubes in the flat spacetime. The T-dual objects of supertubes are moving spiral D1-branes (D-helices). Since we can obtain these D-helices from the usual D1-branes via null deformation, we can construct the boundary states for these moving D-helices in the covariant formalism. Using these boundary states, we calculate the vacuum amplitude between two supertubes in the closed string channel and read the open string spectrum via the open closed duality. We find there are critical values of the energy for on-shell open strings on the supertubes due to the non-trivial stringy correction. We also consider supertubes in the type IIA G? del universe in order to use them as probes of closed timelike curves. This universe is the T-dual of the maximally supersymmetric type IIB PP-wave background. Since the null deformations of D-branes are also allowed in this PP-wave, we can construct the boundary states for supertubes in the type IIA G? del universe in the same way. We obtain the open string spectrum on the supertube from the vacuum amplitude between supertubes. As a consequence, we find that the tachyonic instability of open strings on the supertube, which is the signal of closed time like curves, disappears due to the stringy correction.
Action Possibility Judgments of People with Varying Motor Abilities Due to Spinal Cord Injury

Predictions about one's own action capabilities as well as the action capabilities of others are thought to be based on a simulation process involving linked perceptual and motor networks. Given the central role of motor experience in the formation of these networks, one's present motor capabilities are thought to be the basis of their perceptual judgments about actions. However, it remains unknown whether the ability to form these action possibility judgments is affected by performance related changes in the motor system. To determine if judgments of action capabilities are affected by long-term changes in one's own motor capabilities, participants with different degrees of upper-limb function due to their level (cervical vs. below cervical) of spinal cord injury (SCI) were tested on a perceptual-motor judgment task. Participants observed apparent motion videos of reciprocal aiming movements with varying levels of difficulty. For each movement, participants determined the shortest movement time (MT) at which they themselves and a young adult could perform the task while maintaining accuracy. Participants also performed the task. Analyses of MTs revealed that perceptual judgments for participant's own movement capabilities were consistent with their actual performance- people with cervical SCI had longer judged and actual MTs than people with below cervical SCI. However, there were no between-group differences in judged MTs for the young adult. Although it is unclear how the judgments were adjusted (altered simulation vs. threshold modification), the data reveal that people with different motor capabilities due to SCI are not completely biased by their present capabilities and can effectively adjust their judgments to estimate the actions of others.
Depth edge based trilateral filter method for stereo matching

Recently, trilateral filter based method is more accurate than other local stereo matching methods on Middlebury benchmark. The boundary strength term is the key part of this method, which is computed from a color edge map. In this paper, we prove that boundary strength term, computed from a depth edge map, produces more accurate results. Then, we propose a depth edge detection technique to obtain an accurate depth edge map and present a depth edge based trilateral filter method. The experimental evaluation on the Middlebury benchmark shows that the proposed method outperforms the original trilateral filter method and also other local methods.
Reasoning, problem solving, and decision processes: the problem space as a fundamental category

The notion of a problem space is well known in the area of problem solving research, both in cognitive psychology and artificial intelligence. The Problem Space Hypothesis is enunciated that the scope of problem spaces is to be extended to all symbolic cognitive activity. The paper is devoted to explaining the nature of this hypothesis and describing some of its potential implications, with no attempt at a critical marshalling of the evidince pro and con. Two examples are used, one a typical problem solving activity (the Tower of Hanoi) and the other syllogistic reasoning. The latter is an example where the search behavior typical of problem spaces is not clearly in evidence, so it provides a useful area to explore the extension of the concept. A focal issue used in the paper is the origin of the numerous flow diagrams that serve as theories of how subjects behave in tasks in the psychological laboratory. Hypothesis these flow diagrams derive from the interaction of the task environment and the problem space.
Participation et adaptation des organisations au changement institutionnel : les organisations agricoles au Costa Rica face aux politiques de libéralisation

La these se positionne par rapport aux debats portant sur la place des producteurs agricoles dans le contexte des politiques de liberalisation, et se propose de reflechir plus particulierement au role des organisations. L’approche theorique mobilisee est celle du changement institutionnel, qui ouvre de facon large le spectre de l’economie, par la prise en compte des concepts de modeles mentaux et de dependance au sentier notamment. Un travail long d’enquetes, mene aupres d’organisations agricoles intervenant au sein de quatre filieres agricoles au Costa Rica (cafe, lait, haricot et ananas) a permis la realisation de notre recherche. Les donnees recueillies ont ete analysees au travers de descriptions analytiques (trajectoires et comportements strategiques des organisations), d’analyses textuelles (modeles mentaux des organisations) et de modelisations comprehensives du comportement. Nous montrons que les organisations peuvent contribuer efficacement au maintien ou a l’insertion des producteurs agricoles sur des marches dynamiques, au travers des deux principaux leviers d’action que constituent la participation aux processus d’elaboration des politiques et la commercialisation de produits agricoles (transformes ou non). La reussite des organisations, s’inscrit toutefois dans une logique de dependance au sentier, et depend notamment de leurs modeles mentaux. Notre these plaide ainsi pour une integration accrue des phenomenes historiques et cognitifs dans l’analyse economique, garante d’une meilleure comprehension de la complexite des phenomenes observes de maniere contemporaine.
The Impact of Preoperative Hip Heterotopic Ossification Extent on Recurrence in Patients with Head and Spinal Cord Injury: A Case Control Study

Background The preoperative Heterotopic Ossification (HO) extent is usually one of the main used criteria to predict the recurrence before excision. Brooker et al built a radiologic scale to assess this pre operative extent around the hip. The aim of this study is to investigate the relationship between the recurrence risk after hip HO excision in Traumatic Brain Injury (TBI) and Spinal Cord Injury (SCI) patients and the preoperative extent of HO. Methodology/Principal Findings A case control study including TBI or SCI patients following surgery for troublesome hip HO with (case, n = 19) or without (control, n = 76) recurrence. Matching criteria were: sex, pathology (SCI or TBI) and age at the time of surgery (+/−4.5 years). For each etiology (TBI and SCI), the residual cognitive and functional status (Garland classification), the preoperative extent (Brooker status), the modified radiological and functional status (GCG-BD classification), HO localization, side, mean age at the CNS damage, mean delay for the first HO surgery, and for the case series, the mean operative delay for recurrence after the first surgical intervention were noted. Conclusions/Significance The median delay for first HO surgery was 38.6 months (range 4.5 to 414.5;) for the case subgroup and 17.6 months (range 5.7 to 339.6) for the control group. No significant link was found between recurrence and operative delay (p = 0.51); the location around the joint (0.07); the Brooker (p = 0.52) or GCG-BD status (p = 0.79). Including all the matching factors, no significant relationship was found between the recurrence HO risk and the preoperative extent of troublesome hip HO using Brooker status (OR = 1.56(95% CI: 0.47–5.19)) or GCG-BD status (OR class 3 versus 2 = 0.67(95% CI: 0.11–4.24) and OR class 4 versus 2 = 0.79(95%CI: 0.09–6.91)). Until the pathophysiology of HO development is understood, it will be difficult to create tools which can predict HO recurrence.
Heat shock protein 70 (hsp70) as an emerging drug target.

Heat shock protein 70 (Hsp70) is a molecular chaperone that is expressed in response to stress. In this role, Hsp70 binds to its protein substrates and stabilize them against denaturation or aggregation until conditions improve.1 In addition to its functions during a stress response, Hsp70 has multiple responsibilities during normal growth; it assists in the folding of newly synthesized proteins,2, 3 the subcellular transport of proteins and vesicles,4 the formation and dissociation of complexes,5 and the degradation of unwanted proteins.6, 7 Thus, this chaperone broadly shapes protein homeostasis by controlling protein quality control and turnover during both normal and stress conditions.8 Consistent with these diverse activities, genetic and biochemical studies have implicated it in a range of diseases, including cancer, neurodegeneration, allograft rejection and infection. This review provides a brief review of Hsp70 structure and function and then explores some of the emerging opportunities (and challenges) for drug discovery. Hsp70 is Highly Conserved Members of the Hsp70 family are ubiquitously expressed and highly conserved; for example, the major Hsp70 from Escherichia coli, termed DnaK, is approximately 50% identical to human Hsp70s.9 Eukaryotes often express multiple Hsp70 family members with major isoforms found in all the cellular compartments: Hsp72 (HSPA1A) and heat shock cognate 70 (Hsc70/HSPA8) in the cytosol and nucleus, BiP (Grp78/HSPA5) in the endoplasmic reticulum and mtHsp70 (Grp75/mortalin/HSPA9) in mitochondria. Some of the functions of the cytosolic isoforms, Hsc70 and Hsp72, are thought to be redundant, but the transcription of Hsp72 is highly responsive to stress and Hsc70 is constitutively expressed. In the ER and mitochondria, the Hsp70 family members are thought to fulfill specific functions and have unique substrates, with BiP playing key roles in the folding and quality control of ER proteins and mtHsp70 being involved in the import and export of proteins from the mitochondria. For the purposes of this review, we will often use Hsp70 as a generic term to encompass the shared properties of the family members.
Abstract Dialectical Frameworks

In this paper we introduce dialectical frameworks, a powerful generalization of Dung-style argumentation frameworks where each node comes with an associated acceptance condition. This allows us to model different types of dependencies, e.g. support and attack, as well as different types of nodes within a single framework. We show that Dung's standard semantics can be generalized to dialectical frameworks, in case of stable and preferred semantics to a slightly restricted class which we call bipolar frameworks. We show how acceptance conditions can be conveniently represented using weights respectively priorities on the links and demonstrate how some of the legal proof standards can be modeled based on this idea.
Annotating Semantic Relations Combining Facts and Opinions

As part of the Statement Map project, we are constructing a Japanese corpus annotated with the semantic relations bridging facts and opinions that are necessary for online information credibility evaluation. In this paper, we identify the semantic relations essential to this task and discuss how to efficiently collect valid examples from Web documents by splitting complex sentences into fundamental units of meaning called "statements" and annotating relations at the statement level. We present a statement annotation scheme and examine its reliability by annotating around 1,500 pairs of statements. We are preparing the corpus for release this winter.
Sound-based distributional models

Following earlier work in multimodal distributional semantics, we present the first results of our efforts to build a perceptually grounded semantic model. Rather than using images, our models are built on sound data collected from freesound.org. We compare three models: one bag-of-words model based on user-provided tags, a model based on audio features, using a ‘bag-of-audio-words’ approach and a model that combines the two. Our results show that the models are able to capture semantic relatedness, with the tag-based model scoring higher than the sound-based model and the combined model. However, capturing semantic relatedness is biased towards language-based models. Future work will focus on improving the sound-based model, finding ways to combine linguistic and acoustic information, and creating more reliable evaluation data.
Expression and Biological Activity of the Cystine Knot Bioinsecticide PA1b (Pea Albumin 1 Subunit b)

The PA1b (Pea Albumin 1, subunit b) peptide is an entomotoxin extract from Legume seeds with lethal activity on several insect pests, such as mosquitoes, some aphids and cereal weevils. This 37 amino-acid cysteine-rich peptide has been, until now, obtained by biochemical purification or chemical synthesis. In this paper, we present our results for the transient production of the peptide in Nicotiana benthamiana by agro-infiltration, with a yield of about 35 µg/g of fresh leaves and maximum production 8 days after infiltration. PA1b is part of the PA1 gene which, after post-translational modifications, encodes two peptides (PA1b and PA1a). We show that transforming tobacco with the PA1b cDNA alone does not result in production of the toxin and, in fact, the entire cDNA is necessary, raising the question of the role of PA1a. We constructed a PA1-cassette, allowing for the quick “cut/paste” of different PA1b mutants within a conserved PA1 cDNA. This cassette enabled us to produce the six isoforms of PA1b which exist in pea seeds. Biological tests revealed that all the isoforms display similar activity, with the exception of one which is inactive. The lack of activity in this isoform led us to conclude that the amphiphilic nature of the peptide is necessary for activity. The possible applications of this expression system for other cysteine-rich biomolecules are discussed.
Strong Locally Testable Codes with Relaxed Local Decoders

Locally testable codes (LTCs) are error-correcting codes that admit very efficient codeword tests. An LTC is said to be strong if it has a proximity-oblivious tester, that is, a tester that makes only a constant number of queries and rejects non-codewords with a probability that depends solely on their distance from the code. Locally decodable codes (LDCs) are complementary to LTCs. While the latter allow for highly efficient rejection of strings that are far from being codewords, LDCs allow for highly efficient recovery of individual bits of the information that is encoded in strings that are close to being codewords. Constructions of strong-LTCs with nearly-linear length are known, but the existence of a constant-query LDC with polynomial length is a major open problem. In an attempt to bypass this barrier, Ben-Sasson et al. (SICOMP 2006) introduced a natural relaxation of local decodability, called relaxed-LDCs. This notion requires local recovery of nearly all individual information-bits, yet allows for recovery-failure (but not error) on the rest. Ben-Sasson et al. constructed a constant-query relaxed-LDC with nearly-linear length (i.e., length k1+α for an arbitrarily small constant α > 0, where k is the dimension of the code). This work focuses on obtaining strong testability and relaxed decodability simultaneously. We construct a family of binary linear codes of nearly-linear length that are both strong-LTCs (with one-sided error) and constant-query relaxed-LDCs. This improves upon the previously known constructions, which either obtain only weak LTCs or require polynomial length. Our construction heavily relies on tensor codes and PCPs. In particular, we provide strong canonical PCPs of proximity for membership in any linear code with constant rate and relative distance. Loosely speaking, these are PCPs of proximity wherein the verifier is proximity oblivious (similarly to strong-LTCs) and every valid statement has a unique canonical proof. Furthermore, the verifier is required to reject non-canonical proofs (even for valid statements). As an application, we improve the best known separation result between the complexity of decision and verification in the setting of property testing.