Miracle-dz/UniFAR-FTUs huggingface dataset:
Indoor localization by denoising autoencoders and semi-supervised learning in 3D simulated environment

Robotic mapping and localization methods are mostly dominated by using a combination of spatial alignment of sensory inputs, loop closure detection, and a global fine-tuning step. This requires either expensive depth sensing systems, or fast computational hardware at run-time to produce a 2D or 3D map of the environment. In a similar context, deep neural networks are used extensively in scene recognition applications, but are not yet applied to localization and mapping problems. In this paper, we adopt a novel approach by using denoising autoencoders and image information for tackling robot localization problems. We use semi-supervised learning with location values that are provided by traditional mapping methods. After training, our method requires much less run-time computations, and therefore can perform real-time localization on normal processing units. We compare the effects of different feature vectors such as plain images, the scale invariant feature transform and histograms of oriented gradients on the localization precision. The best system can localize with an average positional error of ten centimeters and an angular error of four degrees in 3D simulation.
Trie Indexes for Efficient XML Query Evaluation

As the number of applications that rely on XML data increases, so does the need for performing efficient XML query evaluation. A critical part of the solution involves providing new techniques for designing XML indexes and lookup algorithms. In this paper, we leverage the results of our research on coupling the partitions induced by fragments of XPath algebra and those induced by the structural properties of an XML document to lead the design of the N[k] and P[k]-Trie indexes for XML. We present the rationale behind our approach, and detail the structure of the indexes, their features, and algorithms for evaluating XPath queries with index-only plans. We show that the P[k]-Trie indexes are capable of answering XPath queries with arbitrarily complicated predicates using index-only plans and improving query performance in orders of magnitude over the A[k]-index.
A Generic Scheme for Secure Data Sharing in Cloud

Working in various service models ranging from SaaS, PaaS, to IaaS, cloud computing is a new revolution in IT, and could reshape the business model of how the IT industry works today. Storage services are a fundamental component of the cloud computing paradigm. By exploiting the storage services, users outsource their data to the cloud so as to enjoy the reduced upfront maintenance and capital costs. However, a security challenge associated with data outsourcing is how to prevent data abuses by the cloud. It has been commonly accepted that data encryption offers a good solution to this problem. With data encryption, an issue arises when the data owner who outsourced the data wants to revoke some data consumers' access privileges, which normally involves key re-distribution and data re-encryption. In this work, we propose a generic scheme to enable fine-grained data sharing over the cloud, which does not require key-redistribution and data re-encryption whatsoever. The main primitives we make use of are attribute-based/predicate encryption and proxy re-encryption, but our construction is not restricted to any specific scheme of its kind. Our scheme has a number of advantages over other similar proposals in the literature.
The Early Result of Whole Pelvic Radiotherapy and Stereotactic Body Radiotherapy Boost for High-Risk Localized Prostate Cancer

Purpose: The rationale for hypofractionated radiotherapy in the treatment of prostate cancer is based on the modern understanding of radiobiology and advances in stereotactic body radiotherapy (SBRT) techniques. Whole-pelvis irradiation combined with SBRT boost for high-risk prostate cancer might escalate biologically effective dose without increasing toxicity. Here, we report our 4-year results of SBRT boost for high-risk localized prostate cancer. Methods and Materials: From October 2009 to August 2012, 41 patients newly diagnosed, high-risk or very high-risk (NCCN definition) localized prostate cancer were treated with whole-pelvis irradiation and SBRT boost. The whole pelvis dose was 45 Gy (25 fractions of 1.8 Gy). The SBRT boost dose was 21 Gy (three fractions of 7 Gy). Ninety percent of these patients received hormone therapy. The toxicities of gastrointestinal (GI) and genitourinary (GU) tracts were scored by Common Toxicity Criteria Adverse Effect (CTCAE v3.0). Biochemical failure was defined by Phoenix definition. Results: Median follow-up was 42 months. Mean PSA before treatment was 44.18 ng/ml. Mean PSA level at 3, 6, 12, 18, and 24 months was 0.94, 0.44, 0.13, 0.12, and 0.05 ng/ml, respectively. The estimated 4-year biochemical failure-free survival was 91.9%. Three biochemical failures were observed. GI and GU tract toxicities were minimal. No grade 3 acute GU or GI toxicity was noted. During radiation therapy, 27% of the patient had grade 2 acute GU toxicity and 12% had grade 2 acute GI toxicity. At 3 months, most toxicity scores had returned to baseline. At the last follow-up, there was no grade 3 late GU or GI toxicity. Conclusions: Whole-pelvis irradiation combined with SBRT boost for high-risk localized prostate cancer is feasible with minimal toxicity and encouraging biochemical failure-free survival. Continued accrual and follow-up would be necessary to confirm the biochemical control rate and the toxicity profiles.
Can the viability of a nonunion be evaluated using SPECT/CT? A preliminary retrospective study.

INTRODUCTION The importance of the vitality of a nonunion is crucial for the planning of the reconstructive procedure. Purpose of the present study is to analyze the role of single photon emission computed tomography (SPECT) in diagnosing and planning the treatment of atrophic nonunions in the upper and lower extremity. PATIENTS AND METHODS This study examined retrospectively the SPECT/CT scans of 10 patients (mean age = 44.5 ± 16.5 years, 9 males/1 female, 4 tibia/4 femur/1 radius/1 fibula) who underwent surgical exploration for suspected avital pseudarthrosis. Surgical and histopathological findings were compared with the radiologists' findings to assess the sensitivity and specificity of SPECT in diagnosing avital nonunions. The average interval from the osteosynthesis until their SPECT scan was 18 months. All surgical findings have been documented electronically in the hospital computer system. Results of the radiologist's reading were then compared with surgical exploration and histopathological findings and specifity and sensitivity was calculated. RESULTS There were 4 vital and 6 nonvital pseudarthroses. SPECT scans identified all the vital pseudarthroses and 3 of the 6 nonvital pseudarthroses. The sensitivity of SPECT in diagnosing non-vital atrophic nonunions is 50% and the specifity 100%. CONCLUSIONS SPECT/CT scan is a test with a low sensitivity but good specificity that excludes infection and confirms nonviability of the nonunion site. However, we shall wait for larger pool of research results in order to incorporate this test in routine clinical use.
Automatic real-world assembly of machine-designed structures

Several approaches have been presented which allow robots to build structures to adapt themselves or their environments. To autonomously build these structures, a design must be made, from which instructions for the fabrication process can be derived. For a constrained fabrication process, e.g. considering the limited range of a robot, this transfer can be cumbersome. We present a local building process based on a sequence of two distinct operations, which implicitly encodes the shape of a structure. Given this encoding, the structure can readily be built with a real-world robotic system. We show automatic design of structures reaching out of the robot's range and fulfilling stability and strength constraints using an evolutionary design algorithm. The final design can then be built with a robotic arm from wooden cubes and hot melt adhesives. We demonstrate the whole process including the construction of a structure from more than thirty cubes with our real-world setup. We expect that automatic design and construction can further improve the physical adaptability of robotic systems.
An Arabidopsis Homolog of Yeast ATG6/VPS30 Is Essential for Pollen Germination1[W]

Yeast (Saccharomyces cerevisiae) Atg6/Vps30 is required for autophagy and the sorting of vacuolar hydrolases, such as carboxypeptidase Y. In higher eukaryotes, however, roles for ATG6/VPS30 homologs in vesicle sorting have remained obscure. Here, we show that AtATG6, an Arabidopsis (Arabidopsis thaliana) homolog of yeast ATG6/VPS30, restored both autophagy and vacuolar sorting of carboxypeptidase Y in a yeast atg6/vps30 mutant. In Arabidopsis cells, green fluorescent protein-AtAtg6 protein localized to punctate structures and colocalized with AtAtg8, a marker protein of the preautophagosomal structure. Disruption of AtATG6 by T-DNA insertion resulted in male sterility that was confirmed by reciprocal crossing experiments. Microscopic analyses of AtATG6 heterozygous plants (AtATG6/atatg6) crossed with the quartet mutant revealed that AtATG6-deficient pollen developed normally, but did not germinate. Because other atatg mutants are fertile, AtAtg6 likely mediates pollen germination in a manner independent of autophagy. We propose that Arabidopsis Atg6/Vps30 functions not only in autophagy, but also plays a pivotal role in pollen germination.
Regulation of glycerol kinase by enzyme IIIGlc of the phosphoenolpyruvate:carbohydrate phosphotransferase system

Wild-type glycerol kinase of Escherichia coli is inhibited by both nonphosphorylated enzyme IIIGlc of the phosphoenolpyruvate:carbohydrate phosphotransferase system and fructose 1,6-diphosphate. Mutant glycerol kinase, resistant to inhibition by fructose 1,6-diphosphate, was much less sensitive to inhibition by enzyme IIIGlc. The difference between the wild-type and mutant enzymes was even greater when inhibition was measured in the presence of both enzyme IIIGlc and fructose 1,6-diphosphate. The binding of enzyme IIIGlc to glycerol kinase required the presence of the substrate glycerol.
Effects of APOE, APOB and LDLR variants on serum lipids and lack of association with xanthelasma in individuals from Southeastern Brazil

Xanthelasma might be a clinical manifestation of dyslipidemia, a recognized risk factor for coronary artery disease. We investigated the association of apolipoprotein E (APOE HhaI), apolipoprotein B (APOB XbaI and Ins/Del) and LDL receptor (LDLR AvaII and HincII) gene polymorphisms with lipid profiles in 100 Brazilians with xanthelasma and 100 controls. Allele frequencies were similar in both groups. APOE, APOB and LDLR genotypes were not correlated with differences in the serum lipid profile. In individuals with xanthelasma, the APOB D allele was associated with less chance of having increased LDL-cholesterol (O.R. = 0.16, CI95% = 0.03-0.94, p = 0.042). In the control group, the APOB X+ allele was associated with less chance of having both increased total cholesterol (O.R. = 0.16, CI95% = 0.03-0.78, p = 0.023) and increased LDL-cholesterol (O.R. = 0.10, CI95% = 0.02-0.60, p = 0.012). Moreover, there was a significantly higher frequency of control individuals (68%) with elevated serum triglyceride levels, compared to patients (48%, p = 0.008). On the other hand, triglyceride levels in controls also seemed to be influenced by all other gene polymorphisms studied, an effect that might be enhanced by environmental factors.
Identifying relevant medical reports from an assorted report collection using the multinomial naïve Bayes classifier and the UMLS

A patient’s electronic medical record contains a large number of medical reports and imaging studies. Identifying the relevant information in order to make a diagnosis can be a time consuming process that can easily overwhelm the physician. Summarizing key clinical information for physicians evaluating brain tumor patients is an ongoing research project at our institution. Notably, identifying documents associated with brain tumor is an important step in collecting the data relevant for summarization. Current electronic medical record systems lack meta-information which is useful in structuring heterogeneous medical information. Thus, identifying reports relevant to a particular task cannot be easily retrieved from a structured database. This necessitates content analysis methods for identifying relevant reports. This paper reports a system designed to identify brain-tumor related reports from an assorted collection of clinical reports. A large collection of clinical reports was obtained from our university hospital database. A domain expert manually annotated the documents classifying them into `related’ and ùnrelated’ categories. A multinomial naïve Bayes classifier was trained to use word level and UMLS concept level features from the reports to identify brain tumor related reports from the assorted collection. The system was trained on 90% and tested on 10% of the manually annotated corpus. A ten-fold cross validation is reported. Performance of the system was best (f-score 94.7) when the system was trained using both word level and UMLS concept level features. Using UMLS concepts improved classifier accuracy.
Evaluation of Retinoids for Induction of the Redundant Gene ABCD2 as an Alternative Treatment Option in X-Linked Adrenoleukodystrophy

X-linked adrenoleukodystrophy (X-ALD), the most common peroxisomal disorder, is a clinically heterogeneous disease that can manifest as devastating inflammatory cerebral demyelination (CALD) leading to death of affected males. Currently, the only curative treatment is allogeneic hematopoietic stem cell transplantation (HSCT). However, HSCT is only effective when performed at an early stage because the inflammation may progress for eighteen months after HSCT. Thus, alternative treatment options able to immediately halt the progression are urgently needed. X-ALD is caused by mutations in the ABCD1 gene, encoding the peroxisomal membrane protein ABCD1, resulting in impaired very long-chain fatty acid metabolism. The related ABCD2 protein is able to functionally compensate for ABCD1-deficiency both in vitro and in vivo. Recently, we demonstrated that of the cell types derived from CD34+ stem cells, predominantly monocytes but not lymphocytes are metabolically impaired in X-ALD. As ABCD2 is virtually not expressed in these cells, we hypothesize that a pharmacological up-regulation of ABCD2 should compensate metabolically and halt the inflammation in CALD. Retinoids are anti-inflammatory compounds known to act on ABCD2. Here, we investigated the capacity of selected retinoids for ABCD2 induction in human monocytes/macrophages. In THP-1 cells, 13-cis-retinoic acid reached the highest, fivefold, increase in ABCD2 expression. To test the efficacy of retinoids in vivo, we analyzed ABCD2 mRNA levels in blood cells isolated from acne patients receiving 13-cis-retinoic acid therapy. In treated acne patients, ABCD2 mRNA levels were comparable to pre-treatment levels in monocytes and lymphocytes. Nevertheless, when primary monocytes were in vitro differentiated into macrophages and treated with 13-cis-retinoic acid, we observed a fourfold induction of ABCD2. However, the level of ABCD2 induction obtained by retinoids alone is probably not of therapeutic relevance for X-ALD. In conclusion, our results suggest a change in promoter accessibility during macrophage differentiation allowing induction of ABCD2 by retinoids.
Analysis and Experiments of a Haptic Telemanipulation Environment for a Microrobot Driven by Centripetal Forces

This paper presents the analytical and experimental results on a new haptic telemanipulation environment for microrobot control. The proposed environment is comprised of a 5DOF force feedback mechanism, acting as the master, and a 2DOF microrobot, acting as the slave. The fact that the slave microrobot is driven by two centripetal force vibration micromotors makes the presented telemanipulation environment exceptional and challenging. The unique characteristics and challenges that arise during the haptic micromanipulation of the specific device are described and analyzed. The developed solutions are presented and discussed. Several experiments show that, regardless of the disparity between the master and slave, the proposed environment facilitates functional and simple microrobot control during micromanipulation operations. DOI: 10.1115/1.2988385
Temporal Interval Reasoning with CLP( Q )

Temporal reasoning is an important aspect of common-sense reasoning. The SUMO upper ontology incorporates Allen’s in(cid:13)uential axiomatization of temporal relations, but without reasoning capabilities. We propose a re(cid:12)nement of the SUMO temporal ontology, implemented in CLP( Q ), a Constraint Logic Programming system over the domain of rational numbers.
Quantization of Filter Bank Frame Expansions Through Moving Horizon Optimization

This paper describes a novel approach to quantization in oversampled filter banks. The new technique is based on moving horizon optimization, does not rely on an additive white noise quantization model and allows stability to be explicitly enforced in the associated nonlinear feedback loop. Moreover, the quantization structure proposed here includes SigmaDelta and linear predictive subband quantizers as a special case and, in general, outperforms them.
RECON: A remotely controlled drone for roads safety

The RECON project is an unmanned aerial vehicle (UAV), which is automated to monitor, analyze, inspect, and intervene in bridges, roads, residential areas, etc. RECON is controlled using data acquisition devices from National Instruments and programmed under LabVIEW. The system is prepared to make a stable journey, communicate, deliver, and intervene and assist. RECON is ubiquitous; the software is web-enabled so that the user can control it using smart phones, tablets, laptops and other computing devices. The system provides a true pervasive computing experience. This paper presents the system organization, architecture, programming application, evaluation and analysis of the proposed system.
Acquiring Predicate-Argument Mapping Information from Multilingual Texts

This paper discusses automatic acquisition of predicate-argument mapping information from multilingual texts. The lexicon of our NLP system abstracts the language-dependent portion of predicate-argument mapping information from the core meaning of verb senses (i.e. semantic concepts as defined in the knowledge base). We represent this mapping information in terms of cross-linguistically generalized mapping types called situation types and word sense-specific idiosyncrasies. This representation has enabled us to automatically acquire predicate-argument mapping information, specifically situation types and idiosyncrasies, for verbs in English, Spanish, and Japanese texts.
Trachipleistophora extenrec n. sp. a New Microsporidian (Fungi: Microsporidia) Infecting Mammals

ABSTRACT. A new microsporidian Trachipleistophora extenrec n. sp. was isolated from a muscle lesion of the streaked tenrec Hemicentetes semispinosus Cuvier, 1798 (Mammalia, Tenrecidae), an insectivore endemic to Madagascar. The spores isolated from the tenrec were infectious to severe combined immunodeficient (SCID) mice by intramuscular injection. Material obtained from muscular lesions in mice was used for the parasite description. All developmental stages of the microsporidian were covered by a dense coat, which during sporogony changed into the sporophorous vesicle wall. Eight, 16, 32, or more spores were formed inside the sporophorous vesicle as the result of the division by plasmotomy and sequential fission of a multinucleate sporogonial plasmodium. Spores were ovoid, 4.7 × 2.8 μm in size, had a large posterior vacuole, and had an isofilar polar tube with 15–16 coils. Although the fine structure and the developmental pattern of the organism were in some respects similar to the genus Vavraia, molecular phylogeny based on the gene sequences of the small subunit rRNA and RNA polymerase subunit II indicated that the organism belongs to the genus Trachipleistophora. The diagnostic characters of the genera Trachipleistophora and Vavraia are discussed as well as the discrepancies between the phylogenies of these two microsporidian genera based on morphology and molecules.
Regularization on Image Patches: a linear reconstruction from manifold embedding

Inspired by the recent low dimension manifold model (LDMM)[1], which achieves high performance in imaging inpainting,we consider regularization on image patches from their low dimensional embedding. We provide a framework for patch-based signal decomposition by frames generated from the embedding coordinates and from patch bases in a convolution form. For any given embedding of patches (or more generally a set of data points in high dimensional space), the energy concentration of the coefficients of such frames characterizes the optimal patch basis, with respect to which the linear reconstruction from the embedding of the image has minimum error. This leads to a weighted `2−regularization on coefficients in the decomposition of an image with respect to this optimal frame; we use this to extend the original LDMM to a re-weighted LDMM that achieves better inpainting results. Our framework can be generalized to the setting of a union of local embedding, and we show that the state-of-the-art denoising algorithm BM3D fits in our framework.
The Solution Structures of Two Human IgG1 Antibodies Show Conformational Stability and Accommodate Their C1q and FcγR Ligands*

Background: The human IgG1 antibody subclass is the most abundant one and is widely used in therapeutic applications. Results: Ultracentrifugation and x-ray/neutron scattering, together with atomistic modeling, revealed asymmetric concentration-independent IgG1 solution structures. Conclusion: The complement and receptor Fc binding sites are not hindered by the Fab regions, explaining its full activity. Significance: These solution structures clarify IgG1 activity and its therapeutic applications. The human IgG1 antibody subclass shows distinct properties compared with the IgG2, IgG3, and IgG4 subclasses and is the most exploited subclass in therapeutic antibodies. It is the most abundant subclass, has a half-life as long as that of IgG2 and IgG4, binds the FcγR receptor, and activates complement. There is limited structural information on full-length human IgG1 because of the challenges of crystallization. To rectify this, we have studied the solution structures of two human IgG1 6a and 19a monoclonal antibodies in different buffers at different temperatures. Analytical ultracentrifugation showed that both antibodies were predominantly monomeric, with sedimentation coefficients s20,w0 of 6.3–6.4 S. Only a minor dimer peak was observed, and the amount was not dependent on buffer conditions. Solution scattering showed that the x-ray radius of gyration Rg increased with salt concentration, whereas the neutron Rg values remained unchanged with temperature. The x-ray and neutron distance distribution curves P(r) revealed two peaks, M1 and M2, whose positions were unchanged in different buffers to indicate conformational stability. Constrained atomistic scattering modeling revealed predominantly asymmetric solution structures for both antibodies with extended hinge structures. Both structures were similar to the only known crystal structure of full-length human IgG1. The Fab conformations in both structures were suitably positioned to permit the Fc region to bind readily to its FcγR and C1q ligands without steric clashes, unlike human IgG4. Our molecular models for human IgG1 explain its immune activities, and we discuss its stability and function for therapeutic applications.