Miracle-dz/UniFAR-FTUs huggingface dataset:
MicroRNAs in Heart Failure: Is the Picture Becoming Less miRky?

With 550 000 new cases diagnosed annually and $37 billion spent per year,1 heart failure (HF) with reduced ejection fraction is one of the largest contributors to disease burden and healthcare expenditure in the United States. Despite significant progress in the treatment of HF2,3 with medications, the prognosis of HF remains dismal, with a mortality rate of 42% at 5 years after diagnosis. Therefore, understanding the underlying molecular pathways in the transition from established cardiovascular disease to HF may spur the development of novel biomarkers and therapeutic targets. The heart responds to stressors such as hypoxia (in myocardial infarction [MI]), increased wall stress (in valvular heart disease), and neurohormonal/metabolic stress (in diabetes mellitus and hypertension) by cardiomyocyte hypertrophy and fibrosis. Although initially compensatory for increased wall stress or myocyte loss, the molecular pathways that underlie pathological hypertrophy are ultimately maladaptive, recapitulating further hypertrophy, contractile dysfunction, apoptosis, and fibrosis. The progression to HF is associated with a characteristic cascade of altered intracellular signaling and gene expression, representing a final common pathway to ultimate decompensation. The various signaling pathways that underlie pathological hypertrophy and the progression to HF have been the subject of intense investigation and are summarized in multiple review publications.4–9. More recently, considerable attention has been paid to microRNAs (miRNAs), a novel biological control mechanism with the ability to regulate entire molecular networks by complex feedback and feed-forward mechanisms. Several reviews have summarized recent findings implicating miRNAs in cardiac development and disease.10,11 In the past few years, the discovery of circulating miRNAs has led to their investigation as biomarkers and mediators of cell–cell communication. This review focuses on recent developments detailing the role of miRNAs in the pathogenesis of HF, their potential role as biomarkers, and their use as …
3D human posture estimation using the HOG features from monocular image

In this paper, we propose a method to estimate the 3D human posture from monocular image without using the markers. A 3D human body is expressed by a multi-joint model, and a set of the joint angles describes a posture. The proposed method estimates the posture using histograms of oriented gradients(HOG) feature vectors that can express the shape of the object in the input image obtained from monocular camera. In addition, the feature dimension of the background region is reduced for reliability by principal component analysis (PCA) computed at every block of HOG. The joint angles in human multi-joint model are estimated by linear regression analysis applied to its feature vector extracted from the input image. As a result of comparison experiment with the shape contexts features, the RMS error was reduced by about 5.35 degrees.
Markerless human motion capture: An application of simulated annealing and Fast Marching Method

Research into optical markerless human motion capture has attracted significant attention. However, the complexity of the human anatomy, ambiguities introduced by lacking full-perspective view data and noises involved in data processing make human motion capture a non-convex, multi-modal optimisation problem in high dimensional space. The proposed method incorporates an isotropic distance map calculated by Fast Marching Method with simulated annealing to efficiently explore the high dimensional space in the probabilistically important directions. This allows simulated annealing to relax the fitness test criteria and work in an incremental fashion, reducing the likelihood of being trapped in local minima. Moreover, instead of using a slow annealing schedule, the annealing progress is controlled by accounting for the shape of the importance distribution, thereby leading to an effective exploration and fast convergence. To improve robustness of tracking, Fast Marching Method is utilised to smooth noisy silhouette images. Finally, several experiments show the efficiency of the proposed method.
Low-level laser-assisted liposculpture: clinical report of 700 cases.

BACKGROUND Suction-assisted lipoplasty has limitations, particularly in dealing with fibrous areas such as the back, sides, and male chest, or when secondary lipoplasty is performed. OBJECTIVE The use of low-level laser-assisted lipoplasty was evaluated in a series of 700 cases. METHODS After adequate infiltration was obtained in all targeted body areas, a 635-nm electric diode laser was applied to the targeted areas for 6 to 12 minutes, depending on the specific area, to liquefy the fat, which was extracted immediately after laser treatment. RESULTS Excellent aesthetic results, including an improved silhouette contour, smooth abdominal surface, and good skin retraction, were obtained in 95% of cases. Postoperative recovery was rapid, and complications were minimal. CONCLUSIONS Low-level laser-assisted lipoplasty can be a valuable adjunctive tool for the performance of lipoplasty. (Aesthetic Surg J 2002;22:451-455.).
Transient and Stable GFP Expression in Germ Cells by the vasa Regulatory Sequences from the Red Seabream (Pagrus major)

Primordial germ cells (PGCs) are the precursors of gametes responsible for genetic transmission to the next generation. They provide an ideal system for cryopreservation and restoration of biodiversity. Recently, considerable attention has been raised to visualize, isolate and transplant PGCs within and between species. In fish, stable PGC visualization in live embryo and individual has been limited to laboratory fish models such as medaka and zebrafish. One exception is the rainbow trout, which represents the only species with aquaculture importance and has GFP-labeled germ cells throughout development. PGCs can be transiently labeled by embryonic injection of mRNA containing green fluorescence protein gene (GFP) and 3'-untranslated region (3'-UTR) of a maternal germ gene such as vasa, nos1, etc. Stable PGC labeling can be achieved through production of transgenic animals by some transcriptional regulatory sequences from germ genes, such as the vasa promoter and 3'-UTR. In this study, we reported the functional analyses of the red seabream vasa (Pmvas) regulatory sequences, using medaka as a model system. It was showed that injection of GFP-Pmvas3'UTR mRNA was able to label medaka PGCs during embryogenesis. Besides, we have constructed pPmvasGFP transgenic vector, and established a stable transgenic medaka line exhibiting GFP expression in germ cells including PGCs, mitotic and meiotic germ cells of both sexes, under control of the Pmvas transcriptional regulatory sequences. It is concluded that the Pmvas regulatory sequences examined in this study are sufficient for germ cell expression and labeling.
Amdb: a visual access method development tool

The development process for access methods (AMs) in database systems is complex and tedious. Amdb is a graphical tool that facilitates the design and tuning process for height-balanced tree-structured AMs. Central to amdb's user interface is a suite of graphical views that visualize the entire search tree, paths and subtrees within the tree, and data contained in the tree. These views animate search tree operations in order to visualize the behavior of an access method. Amdb provides metrics that characterize the performance of queries, the tree structure, and the structure-shaping aspects of an AM implementation. The visualizations can be used to browse the performance metrics in the context of the tree structure. The combination of these features allows a designer to locate the sources of performance loss reported by the metrics and investigate causes for those deficiencies.
Characterization of Niobium Carbide Layers Produced in Ductile Cast Iron Using Thermo-Reactive Treatments

Ductile cast irons are materials with good ductility and toughness, but they are susceptible to high wear rates since they have low hardness. One way to increase their wear resistance is through thermo-reactive diffusion treatments (TRD), in which carbide layers are produced on the surface of the material. In this study, two ductile cast irons (with and without the addition of copper) were treated in a salt bath composed of borax, ferroniobium (16 wt.%) and aluminum (3 wt.%) at 1000°C for 4 h. The XRD and micro-hardness analysis indicated that NbC layers were produced with hardness values higher than 2000 HV. Two methods were used to examine the adherence of the layer to the substrate. In the first method, indentations were performed using Rockwell C scale (VDI 3198). The second method used Vickers micro-hardness indentations (loads 100, 200, and 300 gf) at the interface layer/substrate. In both tests, the layers showed good adhesion to substrates. The 3198 VDI test also showed that the NbC layer produced good toughness. The results of micro-adhesive and micro-abrasive wear tests showed that the layer was very effective in increasing wear resistance.
Automated Acquisition of Cryo Electron Micrographs Using Leginon

Molecular microscopy is one of the most important structural approaches in cell biological investigations and can provide insight into complex biological questions that no other technique can provide. Currently, the technique typically requires the acquisition of very large numbers of transmission electron micrographs from frozen hydrated specimens using low dose techniques. The field is constrained by manual data acquisition methods that are slow, labor-intensive and result in a very low percentage of suitable images. We have developed a system, called Leginon, for automatically acquiring images from a transmission electron microscope. Our first prototype of this system demonstrated that we could acquire 1000 high magnification images per day from negatively stained catalase crystals. We have now extended this system to acquire low dose images of specimens embedded in vitreous ice. Methods: Specimens were prepared on Quantifoil grids using techniques which have been described previously. The Leginon system uses a Philips CM200 TEM and a Gatan MSC CCD camera and is controlled by the emScope software library. The overall acquisition protocol requires (i) obtaining a low magnification image [660x] of a grid square from a Quantifoil grid (fig. 1a); (ii) automatically identifying holes containing ice of suitable thickness; (iii) acquiring an intermediate magnification image [6600x] of the identified hole (fig. 1b); (iv) identifying features of interest within the hole; (v) focusing at high magnification [38,000x] and finally (vi) acquiring a high magnification image (fig 1c,d).
Development of JavaScript-based deep learning platform and application to distributed training

Deep learning is increasingly attracting attention for processing big data. Existing frameworks for deep learning must be set up to specialized computer systems. Gaining sufficient computing resources therefore entails high costs of deployment and maintenance. In this work, we implement a matrix library and deep learning framework that uses JavaScript. It can run on web browsers operating on ordinary personal computers and smartphones. Using JavaScript, deep learning can be accomplished in widely diverse environments without the necessity for software installation. Using GPGPU from WebCL framework, our framework can train large scale convolutional neural networks such as VGGNet and ResNet. In the experiments, we demonstrate their practicality by training VGGNet in a distributed manner using web browsers as the client.
Algorithm 603: COLROW and ARCECO: FORTRAN Packages for Solving Certain Almost Block Diagonal Linear Systems by Modified Alternate Row and Column Elimination

In the numerical solution of boundary-value problems for ordinary differential equations, hnear systems with a partmular block structure are encountered. In this paper two packages of FORTRAN subroutines, COLROW and ARCECO, which use alternate row and column elimination for solving such systems, as discussed by Varah, are described Varah's procedure is stable, and introduces no fillin, tha t is, reqmres no additional storage To improve its efficiency, use is made of the fact tha t after each sequence of eliminations a reducible matrix is obtained. In addition, the packages presented treat systems with a more general structure than those considered by Varah. The results of numerical experiments, which demonstrate the effectiveness of the new packages and their superiority over a prevmusly pubhshed code, on a suitably restrmted class of problems, are presented
ARH1 of Saccharomyces cerevisiae: A new essential gene that codes for a protein homologous to the human adrenodoxin reductase

A yeast gene was found in which the derived protein sequence has similarity to human and bovine adrenodoxin reductase (Nobrega, F. G., Nobrega, M. P. and Tzagoloff, A. (1992). EMBO J. 11, 3821–3829; Lacour, T. and Dumas, B. (1996). Gene 174, 289–292), an enzyme in the mitochondrial electron transfer chain that catalyses in mammals the conversion of cholesterol into pregnenolone, the first step in the synthesis of all steroid hormones. It was named ARH1 (Adrenodoxin Reductase Homologue 1) and here we show that it is essential. Rescue was possible by the yeast gene, but failed with the human gene. Supplementation was tried without success with various sterols, ruling out its involvement in the biosynthesis of ergosterol. Immunodetection with a specific polyclonal antibody located the gene product in the mitochondrial fraction. Consequently ARH1p joins the small group of gene products that affect essential functions carried out by the organelle and not linked to oxidative phosphorylation. © 1998 John Wiley & Sons, Ltd.
The major outer membrane protein of Acidovorax delafieldii is an anion-selective porin

The major outer membrane protein (Omp34) of Acidovorax delafieldii (formerly Pseudomonas delafieldii) was purified to homogeneity and was characterized biochemically and functionally. The polypeptide has an apparent molecular weight (Mr) of 34,000, and it forms stable oligomers at pH 9.0 in the presence of 10% octylpolyoxyethylene or 2% lithium dodecyl sulfate below 70 degrees C. The intact protein has a characteristic secondary structure composition, as revealed by Fourier transforming infrared spectroscopy (about 60% beta sheet). These features and the amino acid composition are typical for porins. The purified Omp34 is associated with 1 to 2 mol of lipopolysaccharide per mol of the monomer. Pore-forming activity was demonstrated with lipid bilayer experiments. Single-channel and selectivity measurements showed that the protein forms highly anion-selective channels. The unusual dependence of the single-channel conductance on salt concentration suggests that the porin complexes bear positive surface charges, accumulating negatively charged counterions at the pore mouth.
The efficacy of various bone augmentation procedures for dental implants: a Cochrane systematic review of randomized controlled clinical trials.

PURPOSE To test (a) whether and when bone augmentation procedures are necessary and (b) which is the most effective augmentation technique for specific clinical indications. Trials were divided into 3 categories: (1) major vertical or horizontal bone augmentation (or both); (2) implants placed in extraction sockets; (3) fenestrated implants. MATERIALS AND METHODS An exhaustive search was conducted for all randomized controlled clinical trials (RCTs) comparing different techniques and materials for augmenting bone for implant treatment reporting the outcome of implant therapy at least to abutment connection. No language restriction was applied. The last electronic search was conducted on October 1, 2005. RESULTS Thirteen RCTs of 30 potentially eligible trials reporting the outcome of 332 patients were suitable for inclusion. Six trials evaluated techniques for vertical and/or horizontal bone augmentation. Four trials evaluated techniques of bone grafting for implants placed in extraction sockets, and 3 trials evaluated techniques to treat fenestrated implants. CONCLUSIONS Major bone grafting procedures of extremely resorbed mandibles may not be justified. Bone substitutes may replace autogenous bone for sinus lift procedures of extremely atrophic sinuses. Both guided bone regeneration procedures and distraction osteogenesis can be used to augment bone vertically, but it is unclear which is the most efficient. It is unclear whether augmentation procedures are needed at immediate single implants placed in fresh extraction sockets; however, sites treated with barrier + Bio-Oss showed a higher position of the gingival margin than sites treated with barriers alone. More bone was regenerated around fenestrated implants with nonresorbable barriers than without barriers; however, it remains unclear whether such bone is of benefit to the patient. Bone morphogenetic proteins may enhance bone formation around implants grafted with Bio-Oss, but there was no reliable evidence supporting the efficacy of other active agents, such as platelet-rich plasma, in conjunction with implant treatment.
Performance and Design of Turbo Codes on Rayleigh Fading Channels

Fading in wireless environments is a major obstacle to reliable communications. In order to mitigate the e ects of fading, channel coding is often employed. In this thesis, the performance and design of the channel coding technique, turbo codes, [1] is examined over Rayleigh fading channels. The thesis considers coherent BPSK signaling over both time-correlated and fully-interleaved Rayleigh, slow-fading channels with additive noise. The performance analysis begins with simulation results for typical turbo schemes in regions of low signal-to-noise. The e ects of block length, turbo decoder iterations, channel side information and channel correlation are examined. For regions of higher signal-to-noise, an average upper bound is developed and applied to a variety of fading conditions. The bound serves to illustrate the achievable performance of turbo codes and the e ects of block length and constituent encoder choice in the performance of turbo codes. Following from the performance analysis, this thesis outlines criteria for optimizing turbo codes for fading channels. In this analysis, design criteria are developed for the turbo interleaver on both fully-interleaved and correlated channels. For time-correlated channels, alternative interleaving schemes are proposed and studied through simulations. i
Ultra Wideband Preliminaries

“Ultra-wideband technology holds great promise for a vast array of new applications that have the potential to provide significant benefits for public safety, businesses and consumers in a variety of applications such as radar imaging of objects buried under the ground or behind walls and shortrange, high-speed data transmission”[FCC,2002] This quote focuses the level of importance of UWB technology as its applications are various. The FCC outlined possible applications of this technology such as imaging systems, ground penetrating radar (GPR) systems, wall-imaging systems, through-wall imaging systems, medical systems, surveillance systems, vehicular radar systems and communications and measurements systems. The spectrum allocation for UWB is in the range from 1.99 GHz10.6 GHz, 3.1 GHz10.6 GHz, or below 960 MHz depending on the particular application [FCC,2002]. The global interest in this technology is huge especially in communications environment due to the potential delivery of ultra high speed data transmission, coexistence with existing electrical systems (due to the extremely low power spectrum density) with low power consumption using a low cost one-chip implementation. There are many advantages and benefits of UWB systems as shown in Table 1 over narrowband technologies. Therefore, with the approval of FCC regulations for UWB, several universities and companies have jumped into the realm of UWB research [Nokia, 2006].
Visual scene recognition with biologically relevant generative models

This research focuses on developing visual object categorization methodologies that are based on machine learning techniques and biologically inspired generative models of visual scene recognition. Modelling the statistical variability in visual patterns, in the space of features extracted from them by an appropriate low level signal processing technique, is an important matter of investigation for both humans and machines. To study this problem, we have examined in detail two recent probabilistic models of vision: a simple multivariate Gaussian model as suggested by (Karklin & Lewicki, 2009) and a restricted Boltzmann machine (RBM) proposed by (Hinton, 2002). Both the models have been widely used for visual object classification and scene analysis tasks before. This research highlights that these models on their own are not plausible enough to perform the classification task, and suggests Fisher kernel as a means of inducing discrimination into these models for classification power. Our empirical results on standard benchmark data sets reveal that the classification performance of these generative models could be significantly boosted near to the state of the art performance, by drawing a Fisher kernel from compact generative models that computes the data labels in a fraction of total computation time. We compare the proposed technique with other distance based and kernel based classifiers to show how computationally efficient the Fisher kernels are. To the best of our knowledge, Fisher kernel has not been drawn from the RBM before, so the work presented in the thesis is novel in terms of its idea and application to vision problem.
Characterization of a (2R,3R)-2,3-Butanediol Dehydrogenase from Rhodococcus erythropolis WZ010

The gene encoding a (2R,3R)-2,3-butanediol dehydrogenase from Rhodococcus erythropolis WZ010 (ReBDH) was over-expressed in Escherichia coli and the resulting recombinant ReBDH was successfully purified by Ni-affinity chromatography. The purified ReBDH in the native form was found to exist as a monomer with a calculated subunit size of 37180, belonging to the family of the zinc-containing alcohol dehydrogenases. The enzyme was NAD(H)-specific and its optimal activity for acetoin reduction was observed at pH 6.5 and 55 °C. The optimal pH and temperature for 2,3-butanediol oxidation were pH 10 and 45 °C, respectively. The enzyme activity was inhibited by ethylenediaminetetraacetic acid (EDTA) or metal ions Al3+, Zn2+, Fe2+, Cu2+ and Ag+, while the addition of 10% (v/v) dimethyl sulfoxide (DMSO) in the reaction mixture increased the activity by 161.2%. Kinetic parameters of the enzyme showed lower Km values and higher catalytic efficiency for diacetyl and NADH in comparison to those for (2R,3R)-2,3-butanediol and NAD+. The activity of acetoin reduction was 7.7 times higher than that of (2R,3R)-2,3-butanediol oxidation when ReBDH was assayed at pH 7.0, suggesting that ReBDH-catalyzed reaction in vivo might favor (2R,3R)-2,3-butanediol formation rather than (2R,3R)-2,3-butanediol oxidation. The enzyme displayed absolute stereospecificity in the reduction of diacetyl to (2R,3R)-2,3-butanediol via (R)-acetoin, demonstrating its potential application on the synthesis of (R)-chiral alcohols.