Miracle-dz/UniFAR-FTUs huggingface dataset:
Enhancement of median nerve regeneration by mesenchymal stem cells engraftment in an absorbable conduit: improvement of peripheral nerve morphology with enlargement of somatosensory cortical representation

We studied the morphology and the cortical representation of the median nerve (MN), 10 weeks after a transection immediately followed by treatment with tubulization using a polycaprolactone (PCL) conduit with or without bone marrow-derived mesenchymal stem cell (MSC) transplant. In order to characterize the cutaneous representation of MN inputs in primary somatosensory cortex (S1), electrophysiological cortical mapping of the somatosensory representation of the forepaw and adjacent body parts was performed after acute lesion of all brachial plexus nerves, except for the MN. This was performed in ten adult male Wistar rats randomly assigned in three groups: MN Intact (n = 4), PCL-Only (n = 3), and PCL+MSC (n = 3). Ten weeks before mapping procedures in animals from PCL-Only and PCL+MSC groups, animal were subjected to MN transection with removal of a 4-mm-long segment, immediately followed by suturing a PCL conduit to the nerve stumps with (PCL+MSC group) or without (PCL-Only group) injection of MSC into the conduit. After mapping the representation of the MN in S1, animals had a segment of the regenerated nerve processed for light and transmission electron microscopy. For histomorphometric analysis of the nerve segment, sample size was increased to five animals per experimental group. The PCL+MSC group presented a higher number of myelinated fibers and a larger cortical representation of MN inputs in S1 (3,383 ± 390 fibers; 2.3 mm2, respectively) than the PCL-Only group (2,226 ± 575 fibers; 1.6 mm2). In conclusion, MSC-based therapy associated with PCL conduits can improve MN regeneration. This treatment seems to rescue the nerve representation in S1, thus minimizing the stabilization of new representations of adjacent body parts in regions previously responsive to the MN.
Continuous tracking within and across camera streams

This paper presents a new approach for continuous tracking of moving objects observed by multiple, heterogeneous cameras. Our approach simultaneously processes video streams from stationary and pan-tilt-zoom cameras. The detection of moving objects from moving camera streams is performed by defining an adaptive background model that takes into account the camera motion approximated by an affine transformation. We address the tracking problem by separately modeling motion and appearance of the moving objects using two probabilistic models. For the appearance model, multiple color distribution components are proposed for ensuring a more detailed description of the object being tracked. The motion model is obtained using a Kalman filter (KF) process, which predicts the position of the moving object. The tracking is performed by the maximization of a joint probability model. The novelty of our approach consists in modeling the multiple trajectories observed by the moving and stationary cameras in the same KF framework. It allows deriving a more accurate motion measurement for objects simultaneously viewed by the two cameras and an automatic handling of occlusions, errors in the detection and camera handoff. We demonstrate the performances of the system on several video surveillance sequences.
Abnormal Crowd Behavior Detection Using Topological Methods

In this paper we present a novel framework for abnormal behavior detection in crowded scenes. For this purpose, the theory of topological simplification on the dense field is extended to the sparse particle motion field, which is used to describe the dynamics of the crowd. We propose two new methods for analysis of boundary point structure and extraction of critical point from the particle motion field. Both methods can be used to describe the global topological structure of the crowd motion, which is the kernel idea of our work. Various types of abnormal behaviors, including crowd formation/dispersal, crowds splitting/merging, can be detected by monitoring the changes of the topological structure. The advantage of our method is that each kind of abnormal event can be described as a specific topological structure change, therefore we do not need a complex classifier to detect these anomalies. Experiments are conducted on known datasets and results show that our method is effective in detecting and locating these kinds of abnormal behaviors.
Unfolding of the bacterial nucleoid both in vivo and in vitro as a result of exposure to camphor

Both prokaryotic and eukaryotic cells are sensitive to killing by camphor; however, the mechanism by which camphor kills has not been elucidated. We report here that camphor unfolds the nucleoid of Escherichia coli and that unfolding does not require DNA replication, translation, or cell division. We show that exposure of isolated nucleoids to camphor results in unfolding of the chromosome.
Retroviral Vector Targeting to Human Immunodeficiency Virus Type 1-Infected Cells by Receptor Pseudotyping

ABSTRACT We report the generation of retroviral vectors based on Moloney murine leukemia virus that specifically transduce cells infected with T-cell-tropic human immunodeficiency virus type 1 (HIV-1). This vector was pseudotyped with T-cell-tropic HIV-1 receptors CD4 and CXCR4. We demonstrate that transduction is contingent upon HIV-1 gp120 and gp41 expression.
Tumor cell lysates as immunogenic sources for cancer vaccine design

Autologous dendritic cells (DCs) loaded with tumor-associated antigens (TAAs) are a promising immunological tool for cancer therapy. These stimulate the antitumor response and immunological memory generation. Nevertheless, many patients remain refractory to DC approaches. Antigen (Ag) delivery to DCs is relevant to vaccine success, and antigen peptides, tumor-associated proteins, tumor cells, autologous tumor lysates, and tumor-derived mRNA have been tested as Ag sources. Recently, DCs loaded with allogeneic tumor cell lysates were used to induce a potent immunological response. This strategy provides a reproducible pool of almost all potential Ags suitable for patient use, independent of MHC haplotypes or autologous tumor tissue availability. However, optimizing autologous tumor cell lysate preparation is crucial to enhancing efficacy. This review considers the role of cancer cell-derived lysates as a relevant source of antigens and as an activating factor for ex vivo therapeutic DCs capable of responding to neoplastic cells. These promising therapies are associated with the prolonged survival of advanced cancer patients.
Avidin is a promising tag for fusion proteins produced in baculovirus-infected insect cells.

The baculovirus expression vector system (BEVS) has become one of the most versatile and powerful eukaryotic systems for recombinant protein expression. We have constructed a novel baculovirus transfer vector (pbacAVs+C) which allows for the efficient production, detection, and single-step purification of the desired molecule as a secretion-compatible avidin fusion protein in insect cells. It also enables fast construction of the baculoviruses by site-specific transposition in Escherichia coli. To demonstrate the power of this vector, we report here on the production of immunologically intact hevein, a major cysteine-rich latex allergen, as avidin fusion protein. Our results indicate that avidin is a stable and versatile tag in the BEVS. It retains its extraordinarily high biotin-binding activity and also enables independent folding of the fusion partner. The versatility with which avidin fusion proteins can be detected, purified, and immobilized is the basis for the use of our system as a useful alternative in eukaryotic fusion protein production.
Identification of novel oligodendroglioma‐associated candidate tumor suppressor genes in 1p36 and 19q13 using microarray‐based expression profiling

Loss of heterozygosity (LOH) on chromosomal arms 1p and 19q is the most common genetic alteration in oligodendroglial tumors and associated with response to radio‐ and chemotherapy as well as favorable prognosis. Using microsatellite analysis, we previously identified the chromosomal regions 1p36.22‐p36.31 and 19q13.3, as candidate tumor suppressor gene regions being commonly deleted in these tumors. To identify genes within these regions that are downregulated in oligodendroglial tumors with LOH 1p/19q, we performed cDNA microarray‐based RNA expression profiling of 35 gliomas with known allelic status on 1p and 19q, including 7 oligodendrogliomas and 8 diffuse astrocytomas of World Health Organization (WHO) grade II, as well as 14 anaplastic oligodendrogliomas and 6 anaplastic oligoastrocytomas of WHO grade III. The microarrays used for expression profiling carried ∼7,000 gene‐specific cDNAs, with complete coverage of the genes located in 1p36.13‐p36.31 and 19q13.2‐q13.33. Microarray analysis identified 8 genes from these regions (MGC4399, SRM, ICMT, RPL18, FTL, ZIN, FLJ10781 and DBP), which all showed significantly lower expression in 1p/19q‐deleted gliomas when compared to gliomas without 1p/19q losses. Quantitative real‐time reverse transcription‐PCR analyses were performed for the MGC4399, ICMT and RPL18 genes and confirmed the microarray findings. In addition, we found that the cytosolic phospholipase A2 (PLA2G4C) gene at 19q13.3 demonstrated significantly lower expression in anaplastic oligodendrogliomas (WHO grade III) when compared to well‐differentiated oligodendrogliomas (WHO grade II). Taken together, our study provides a set of interesting novel candidate genes that may play important roles in the pathogenesis of oligodendroglial tumors. © 2006 Wiley‐Liss, Inc.
Containing a Confused Deputy on x86: A Survey of Privilege Escalation Mitigation Techniques

The weak separation between user- and kernelspace in modern operating systems facilitates several forms of privilege escalation. This paper provides a survey of protection techniques, both cutting-edge and time-tested, used to prevent common privilege escalation attacks. The techniques are compared against each other in terms of their effectiveness, their performance impact, the complexity of their implementation, and their impact on diversification techniques such as ASLR. Overall the literature provides a litany of disjoint techniques, each of which trades some performance cost for effectiveness against a particular isolated threat. No single technique was found to effectively mitigate all known and potential attack vectors with reasonable performance cost overhead.
A Progressive and Cell Non-Autonomous Increase in Striatal Neural Stem Cells in the Huntington's Disease R6/2 Mouse

Neural stem and progenitor cells are located in the subependyma of the adult forebrain. An increase in adult subependymal cell proliferation is reported after various kinds of brain injury. We demonstrate an expansion of neural precursor cells in the postnatal subependyma in a murine genetic disease model of Huntington's disease (HD), the R6/2 mouse. We used the in vitro neurosphere assay as an index of the number of neural stem cells in vivo and to assess proliferation kinetics in vitro and in vivo bromodeoxyuridine labeling to assess the progenitor cell population and their fates. Disease progression in this model leads to an increase in the numbers of neural stem cells in the adult striatal subependyma. This increase is produced cell non-autonomously by events in the R6/2 brains as the mice become increasingly symptomatic. Once the neural stem cell increase is induced in vivo, it is maintained during in vitro passaging of neural stem cells, but the neural stem cell increase is not reproduced during in vitro passaging of neural stem cells from presymptomatic R6/2 mice. In addition, we show that some of the R6/2 neural progenitor cells show a change from their normal migration destiny toward the olfactory bulb. Instead, some of these cells migrate into the striatum, one of the main affected areas in HD. Our findings demonstrate that HD damage recruits precursor cells in two ways: expansion of neural stem cells and altered migration of progenitor cells.
Rapid 3D printing of anatomically accurate and mechanically heterogeneous aortic valve hydrogel scaffolds

The aortic valve exhibits complex three-dimensional (3D) anatomy and heterogeneity essential for the long-term efficient biomechanical function. These are, however, challenging to mimic in de novo engineered living tissue valve strategies. We present a novel simultaneous 3D printing/photocrosslinking technique for rapidly engineering complex, heterogeneous aortic valve scaffolds. Native anatomic and axisymmetric aortic valve geometries (root wall and tri-leaflets) with 12–22 mm inner diameters (ID) were 3D printed with poly-ethylene glycol-diacrylate (PEG-DA) hydrogels (700 or 8000 MW) supplemented with alginate. 3D printing geometric accuracy was quantified and compared using Micro-CT. Porcine aortic valve interstitial cells (PAVIC) seeded scaffolds were cultured for up to 21 days. Results showed that blended PEG-DA scaffolds could achieve over tenfold range in elastic modulus (5.3±0.9 to 74.6±1.5 kPa). 3D printing times for valve conduits with mechanically contrasting hydrogels were optimized to 14 to 45 min, increasing linearly with conduit diameter. Larger printed valves had greater shape fidelity (93.3±2.6, 85.1±2.0 and 73.3±5.2% for 22, 17 and 12 mm ID porcine valves; 89.1±4.0, 84.1±5.6 and 66.6±5.2% for simplified valves). PAVIC seeded scaffolds maintained near 100% viability over 21 days. These results demonstrate that 3D hydrogel printing with controlled photocrosslinking can rapidly fabricate anatomical heterogeneous valve conduits that support cell engraftment.
Fast scene text localization by learning-based filtering and verification

This paper proposes a new method for fast text localization in natural scene images by combining learning-based region filtering and verification in a coarse-to-fine strategy. In each pyramid layer, a boosted region filter is used to extract candidate text regions, which are segmented into candidate text lines by multi-orientation projection analysis. A polynomial classifier with combined features is used to verify patches of candidate text lines for removing non-texts. The remaining text patches over all pyramid layers are grouped into text lines based on their spatial relationships. The text lines are further refined and partitioned into words by connected component analysis. Experimental results show that the proposed method provides competitive localization performance at high speed.
The Via Lactea INCITE simulation: Galactic dark matter substructure at high resolution

It is a clear and unique prediction of the cold dark matter paradigm of cosmological structure formation that galaxies form hierarchically and are embedded in massive, extended dark halos teeming with self-bound substructure, or 'subhalos. ' The amount and spatial distribution of subhalos around their host provide unique information and clues on the galaxy assembly process and the nature of the dark matter. Here we present results from the Via Lactea INCITE simulation, a one billion particle, one million CPU-hour simulation of the formation and evolution of a galactic dark matter halo and its substructure population.
A Convex Programming Model for Protein Structure Prediction

Motivation: Distance geometry methods provide a mechanism to produce atom coordinates based on distance measurements taken from such sources as protein nuclear magnetic resonance spectroscopy experiments. Traditional methods suffice when accurate distance measurements are available but it is unclear effectively well they handle noisy distance measurements. Results: We introduce the concept of convex prediction and convex design which are combined in Domo, a novel method to solve the coordinate realization problem. On a benchmark of 124 proteins, Domo produces coordinate estimates which are statistically superior to standard distance geometry techniques with a very competitive computational cost. One may interpret convex prediction as a rough potential energy model for protein structures. We investigate the robustness of convex prediction for its applications to full ab initio protein structure estimation. Availability: Software developed for this study is available at http://bioinfo.cs. umn.edu/supplements/eccb2010 along with supplementary material.
SATEComp : a Tool for in Silico Analysis of Transposable Elements

components in living beings and are involved in several fundamental processes. Due to the amount and variety of this type of molecule, the manual identification of TEs can be a very hard task. The Group of Bioinformatics of Rio Claro has developed SATEComp, a computational system aimed at identifying putative TEs in biological sequences and helping in the analysis of the results. SATEComp uses three strategies in order to identify TEs (BLAST, RepeatMasker and Keyword searches) that can be used in different combinations, giving the users the flexibility to plan their own work strategy. The system allows the TE identification to be done either locally or remotely, all accomplished automatically. The results can be seen in several types of interfaces and formats provided by the system. SATEComp can drastically reduce the amount of data to be analyzed manually.
MuSS-bits: sensor-display blocks for deaf people to explore musical sounds

Hearing loss makes learning a musical instrument a challenging task. Prior work suggests that a universal sensory substitution system that works uniformly across all deaf users may not exist given the diversity within the deaf community. In this paper, we present Music Sensory Substitution (MuSS) Bits, wireless sensor-display pairs that enable exploration of musical sound as well as customization of visual and vibrotactile feedback to cater to individual requirements and preferences. MuSS-Bits are portable, easy to deploy on the user's body, on an instrument, or in the environment, and provide real-time feedback. We review existing music sensory substitution systems, discuss the design space for MuSS-Bits, present details of a prototypical implementation and illustrate interaction possibilities including initial user reactions.
Image compression algorithm based on Hilbert Scanning of Embedded quadTrees: An introduction of the Hi-SET coder

In this work we present an effective and computationally simple algorithm for image compression based on Hilbert Scanning of Embedded quadTrees (Hi-SET). It allows to represent an image as an embedded bitstream along a fractal function. Embedding is an important feature of modern image compression algorithms, in this way Salomon in [1, pg. 614] cite that another feature and perhaps a unique one is the fact of achieving the best quality for the number of bits input by the decoder at any point during the decoding. Hi-SET possesses also this latter feature. Furthermore, the coder is based on a quadtree partition strategy, that applied to image transformation structures such as discrete cosine or wavelet transform allows to obtain an energy clustering both in frequency and space. The coding algorithm is composed of three general steps, using just a list of significant pixels. The implementation of the proposed coder is developed for gray-scale and color image compression. Hi-SET compressed images are, on average, 6.20dB better than the ones obtained by other compression techniques based on the Hilbert scanning. Moreover, Hi-SET improves the image quality in 1.39dB and 1.00dB in gray-scale and color compression, respectively, when compared with JPEG2000 coder.
Effect of Opening on Behavior of Raft Foundations Resting on Different Types of Sand Soil

In this paper, the elasto – plastic finite element analysis is carried out using the three-dimensional PLAXIS program to study the effect of opening position and type of soil on behavior ofraft foundations under columns loads. The analysis has been done for raft foundations with middle, edge, and corner opening positions and the results are obtained for three different types of soil which are loose sand, medium dense sand and dense sand soil. The effect of opening positions and type of soilon behavior of raft foundations is presented in graphical form and it is discussed.
Relating taxonomies with regulations

Increasingly, taxonomies are being developed for a wide variety of industrial domains and specific applications within those domains. These industry or application specific taxonomies attempt to represent the vocabularies commonly used by the practitioners. These formal representations have the potential to automate information retrieval, facilitate interoperability and improve decision making. Decisions made must comply with existing government regulations and codes of practices, which are not always known to the industry practitioners. Although regulations and codes are now in digital forms and are often available online, it remains difficult to search for relevant regulatory information that are applicable to particular decisions. As industry practitioners, unlike legal practitioners, are familiar with one or more industry-specific taxonomies but not necessarily regulatory organization systems, it would be desirable to relate regulations with existing industry-specific taxonomies. The mapping from a single taxonomy to a single regulation is a trivial keyword matching task. In this paper, we examine techniques to map a single taxonomy to multiple regulations, as well as to map multiple taxonomies to a single regulation. Those techniques include cosine similarity, Jaccard coefficient and market-basket analysis. These techniques provide a metric that measures the similarity between concepts from different taxonomies. Preliminary evaluations of the three metrics are performed using examples from the building industry. These examples illustrate the potential regulatory benefits from the mapping between various taxonomies and regulations.
Chromosome 14 familial Alzheimer’s disease: the clinical and neuropathological characteristics of a family with a leucine→serine (L250S) substitution at codon 250 of the presenilin 1 gene

BACKGROUND Seven affected members are described from a kindred with autosomal dominant familial Alzheimer’s disease associated with a novel mutation in the presenilin 1 (PS1) gene on chromosome 14 that results in a leucine to serine substitution at codon 250 (L250S). METHOD Clinical information on the pedigree was collected directly from family members including affected members and their carers and also from hospital records. RESULTS Detailed clinical information was available on five members. All had an early age at onset with a median age of 52 (95% confidence interval (95% CI) 49.4–54.9). Age at onset varied between 49 and 56 years, with duration of illness varying between six years and 15 years. Myoclonus, depression, and psychosis were features of this pedigree; seizures were not reported. CONCLUSIONS PS1 L250S familial Alzheimer’s disease is an early onset form of Alzheimer’s disease with clinical features similar to other reported familial Alzheimer’s disease pedigrees, except that seizures were absent.