Miracle-dz/UniFAR-FTUs huggingface dataset:
Nitric Oxide Production by the Human Intestinal Microbiota by Dissimilatory Nitrate Reduction to Ammonium

The free radical nitric oxide (NO) is an important signaling molecule in the gastrointestinal tract. Besides eukaryotic cells, gut microorganisms are also capable of producing NO. However, the exact mechanism of NO production by the gut microorganisms is unknown. Microbial NO production was examined under in vitro conditions simulating the gastrointestinal ecosystem using L-arginine or nitrate as substrates. L-arginine did not influence the microbial NO production. However, NO concentrations in the order of 90 ng NO-N per L feed medium were produced by the fecal microbiota from nitrate. 15N tracer experiments showed that nitrate was mainly reduced to ammonium by the dissimilatory nitrate reduction to ammonium (DNRA) pathway. To our knowledge, this is the first study showing that gastrointestinal microbiota can generate substantial amounts of NO by DNRA and not by the generally accepted denitrification or L-arginine pathway. Further work is needed to elucidate the exact role between NO produced by the gastrointestinal microbiota and host cells.
Spectral Subtraction Steered by Multi-Step Forward Linear Prediction For Single Channel Speech Dereverberation

A speech signal captured by a distant microphone is generally smeared by reverberation, which severely degrades automatic speech recognition (ASR) performance. In this paper, we propose a novel dereverberation method utilizing multi-step forward linear prediction. It precisely estimates and suppresses the late reflections, which constitute a major cause of ASR performance degradation. Our experimental results showed that the proposed method can improve ASR performance significantly even without using special adaptation methods such as multi-condition acoustic model training
Automatic Detection and Classification of Pole-Like Objects in Urban Point Cloud Data Using an Anomaly Detection Algorithm

Detecting and modeling urban furniture are of particular interest for urban management and the development of autonomous driving systems. This paper presents a novel method for detecting and classifying vertical urban objects and trees from unstructured three-dimensional mobile laser scanner (MLS) or terrestrial laser scanner (TLS) point cloud data. The method includes an automatic initial segmentation to remove the parts of the original cloud that are not of interest for detecting vertical objects, by means of a geometric index based on features of the point cloud. Vertical object detection is carried out through the Reed and Xiaoli (RX) anomaly detection algorithm applied to a pillar structure in which the point cloud was previously organized. A clustering algorithm is then used to classify the detected vertical elements as man-made poles or trees. The effectiveness of the proposed method was tested in two point clouds from heterogeneous street scenarios and measured by two different sensors. The results for the two test sites achieved detection rates higher than 96%; the classification accuracy was around 95%, and the completion quality of both procedures was 90%. Non-detected poles come from occlusions in the point cloud and low-height traffic signs; most misclassifications occurred in man-made poles adjacent to trees.
Interprocedural compilation of Fortran D for MIMD distributed-memory machines

Algorithms exist for compiling Fortran D for MIMD (multiple-instruction multiple-data) distributed-memory machines, but they are significantly restricted in the presence of procedure calls. The authors present interprocedural analysis, optimization, and code generation algorithms for Fortran D that limit compilation to only one pass over each procedure. This is accomplished by collecting summary information after edits, and then compiling procedures in reverse topological order to propagate necessary information. Delaying instantiation of the computation partition, communication, and dynamic data decomposition is key to enabling interprocedural optimization. Recompilation analysis preserves the benefits of separate compilation. Empirical results show that interprocedural optimization is crucial in achieving acceptable performance for a common application. <<ETX>>
Yeast Reveal a “Druggable” Rsp5/Nedd4 Network that Ameliorates α-Synuclein Toxicity in Neurons

From Yeast to Therapeutic? Yeast has shown some promise as a model system to generate lead compounds that could have therapeutic potential for the cellular problems associated with neurodegenerative diseases. Along these lines, Tardiff et al. (p. 979, published online 24 October) and Chung et al. (p. 983, published online 24 October) describe the results of multiple screens in yeast that lead to the identification of a potential therapeutic compound to combat the cytotoxic affect of α-synuclein accumulation. The compound was able to reverse the pathological hallmarks of Parkinson's disease in cultured neurons derived from patients with α-synuclein–induced Parkinson's disease dementia. Screening in yeast yields an effective therapeutic for Parkinson’s patient–derived neuronal stem cells. α-Synuclein (α-syn) is a small lipid-binding protein implicated in several neurodegenerative diseases, including Parkinson’s disease, whose pathobiology is conserved from yeast to man. There are no therapies targeting these underlying cellular pathologies, or indeed those of any major neurodegenerative disease. Using unbiased phenotypic screens as an alternative to target-based approaches, we discovered an N-aryl benzimidazole (NAB) that strongly and selectively protected diverse cell types from α-syn toxicity. Three chemical genetic screens in wild-type yeast cells established that NAB promoted endosomal transport events dependent on the E3 ubiquitin ligase Rsp5/Nedd4. These same steps were perturbed by α-syn itself. Thus, NAB identifies a druggable node in the biology of α-syn that can correct multiple aspects of its underlying pathology, including dysfunctional endosomal and endoplasmic reticulum–to-Golgi vesicle trafficking.
Development of Lateral Flow Assay Based on Size-Controlled Gold Nanoparticles for Detection of Hepatitis B Surface Antigen

In this study, we developed lateral flow assay (LFA) biosensors for the detection of hepatitis B surface antigens using well-controlled gold nanoparticles (AuNPs). To enhance colorimetric signals, a seeded growth method was used for the preparation of size-controlled AuNPs with a narrow size distribution. Different sizes of AuNPs in the range of 342–137.8 nm were conjugated with antibodies and then optimized for the efficient detection of LFA biosensors. The conjugation stability was investigated by UV-vis spectroscopy of AuNP dispersion at various pH values and concentrations of antibody. Based on optimized conjugation conditions, the use of 42.7 ± 0.8 nm AuNPs exhibited superior performance for the detection of LFAs relative to other sizes of AuNPs.
Transcriptomic response of sea urchin larvae Strongylocentrotus purpuratus to CO2-driven seawater acidification

SUMMARY Ocean acidification from the uptake of anthropogenic CO2 is expected to have deleterious consequences for many calcifying marine animals. Forecasting the vulnerability of these marine organisms to climate change is linked to an understanding of whether species possess the physiological capacity to compensate for the potentially adverse effects of ocean acidification. We carried out a microarray-based transcriptomic analysis of the physiological response of larvae of a calcifying marine invertebrate, the purple sea urchin, Strongylocentrotus purpuratus, to CO2-driven seawater acidification. In lab-based cultures, larvae were raised under conditions approximating current ocean pH conditions (pH 8.01) and at projected, more acidic pH conditions (pH 7.96 and 7.88) in seawater aerated with CO2 gas. Targeting expression of ∼1000 genes involved in several biological processes, this study captured changes in gene expression patterns that characterize the transcriptomic response to CO2-driven seawater acidification of developing sea urchin larvae. In response to both elevated CO2 scenarios, larvae underwent broad scale decreases in gene expression in four major cellular processes: biomineralization, cellular stress response, metabolism and apoptosis. This study underscores that physiological processes beyond calcification are impacted greatly, suggesting that overall physiological capacity and not just a singular focus on biomineralization processes is essential for forecasting the impact of future CO2 conditions on marine organisms. Conducted on targeted and vulnerable species, genomics-based studies, such as the one highlighted here, have the potential to identify potential `weak links' in physiological function that may ultimately determine an organism's capacity to tolerate future ocean conditions.
A novel semi-fragile forensic watermarking scheme for remote sensing images

A semi-fragile watermarking scheme for multiple band images is presented. We propose to embed a mark into remote-sensing images applying a tree-structured vector quantization approach to the pixel signatures, instead of processing each band separately. The signature of the multi- or hyperspectral image is used to embed the mark into it in order to detect any significant modification of the original image. The image is segmented into three-dimensional blocks and a tree-structured vector quantizer (TSVQ) is built for each block. These trees are manipulated using an iterative algorithm until the resulting block satisfies a required criterion which establishes the embedded mark. The method is shown to be able to preserve the mark under lossy compression (above a given threshold) but, at the same time, it detects possibly forged blocks and their position in the whole image.
Restoring focus in photographs : extraction of the point-spread function

Out-of-focus images are the bane of the modern photographer. While error in exposure, cropping, and color can often be easily fixed in post-processing, errors in focus are not so simple to erase. The most common approach to dealing with an out-of-focus image is to use a tool like “unsharp mask,” which increases the apparent sharpness of the photo but does not correct the fundamental focusing mistake. This is because the unsharp mask procedure increases the acutance (essentially, the edge contrast) instead of reversing the blur. Fortunately, a technique that applies deconvolution can recover the latent sharp image from the observed blurry picture. Formally, we can represent the captured (blurred) image B with the equation
The Universality of NBTI Relaxation and its Implications for Modeling and Characterization

As of date many NBTI models have been published which aim to successfully capture the essential physics. As such, these models have mostly focused on the stress phase. The relaxation phase, on the other hand, has not received as much attention, possibly because of the contradictory results published so far. Particularly noteworthy are the very long relaxation tails of almost logarithmic nature, which cannot be successfully described by the reaction-diffusion model. The authors argue that understanding the nature of the relaxation phase could hold the key to unraveling the underlying NBTI mechanism. In particular, the authors stipulate that the relaxation phase follows a universal relaxation law, demonstrate the valuable consequences resulting therefrom, and use this universality to classify presently available NBTI models.
eNOS Protects from Atherosclerosis Despite Relevant Superoxide Production by the Enzyme in apoE−/− Mice

Background All three nitric oxide synthase (NOS) isoforms are expressed in atherosclerotic plaques. NOS enzymes in general catalyse NO production. However, under conditions of substrate and cofactor deficiency, the enzyme directly catalyse superoxide formation. Considering this alternative chemistry, the effects of NOS on key events in spontaneous hyperlipidemia driven atherosclerosis have not been investigated yet. Here, we evaluate how endothelial nitric oxide synthase (eNOS) modulates leukocyte/endothelial- (L/E) and platelet/endothelial- (P/E) interactions in atherosclerosis and the production of nitric oxide (NO) and superoxide by the enzyme. Principal Findings Intravital microscopy (IVM) of carotid arteries revealed significantly increased L/E-interactions in apolipoproteinE/eNOS double knockout mice (apoE−/−/eNOS−/−), while P/E-interactions did not differ, compared to apoE−/−. eNOS deficiency increased macrophage infiltration in carotid arteries and vascular cell adhesion molecule-1 (VCAM-1) expression, both in endothelial and smooth muscle cells. Despite the expression of other NOS isoforms (inducible NOS, iNOS and neuronal NOS, nNOS) in plaques, Electron Spin Resonance (ESR) measurements of NO showed significant contribution of eNOS to total circulating and vascular wall NO production. Pharmacological inhibition and genetic deletion of eNOS reduced vascular superoxide production, indicating uncoupling of the enzyme in apoE−/− vessels. Conclusion Overt plaque formation, increased vascular inflammation and L/E- interactions are associated with significant reduction of superoxide production in apoE−/−/eNOS−/− vessels. Therefore, lack of eNOS does not cause an automatic increase in oxidative stress. Uncoupling of eNOS occurs in apoE−/− atherosclerosis but does not negate the enzyme's strong protective effects.
International Perspectives

18 glaucoma today July/august 2013 In this edition of Glaucoma Today’s “International Perspectives” column, Scott D. Lawrence, MD, and Donald L. Budenz, MD, MPH, identify issues that differentiate SubSaharan Africa (SSA) from other less developed nations in relation to glaucoma care. This region of Africa has one of the lowest numbers of ophthalmologists per capita globally and has a higher prevalence and severity of glaucoma than other developing countries. Drs. Lawrence and Budenz point out the need for innovative screening strategies and novel therapeutic concepts. An introductory course in a school of public health would ask students the following question: How would you spend $1 million on health care in SSA? Unlike other developing nations, far more eye diseases are competing for each dollar. Most countries in SSA are not only concerned with cataract blindness but must address other diseases such as trachoma and river blindness as well. Add to that the cost of expensive therapies for systemic diseases such as malnutrition, malaria, and AIDS. Taking all of this into account, it is hard to imagine how to balance the million-dollar budget. Self-sufficiency is the cornerstone of long-term success. The development of centers of excellence within SSA, whereby ophthalmologists train others for subspecialty care, is crucial. A matter that will need to be addressed is how and where to develop an initial center of excellence in SSA. I hope you enjoy this edition of “International Perspectives” and that this and the articles that follow broaden your perspective on glaucoma care around the world. —Alan L. Robin, MD, section editor
Isolated primate primordial follicles require a rigid physical environment to survive and grow in vitro.

BACKGROUND In vitro follicle growth is a promising fertility preservation strategy in which ovarian follicles are cultured to produce mature and fertilization-competent oocytes. However, in primates, there has been limited success with in vitro follicle growth starting from primordial and primary follicles because adequate isolation methods and culture strategies have not been established. Understanding how to use primordial follicles for fertility preservation has significant implications because these follicles are the most abundant in the ovary, are found in all females and are fairly resistant to cryopreservation and chemotherapeutics. METHODS In the primate ovary, primordial follicles are concentrated near the collagen-rich ovarian cortex. To obtain these follicles, we separated the ovarian cortex prior to enzymatic digestion and enriched the primordial follicle concentration by using a novel double filtration system. To test the hypothesis that a rigid physical environment, as found in vivo, is optimal for survival, primordial follicles were cultured in different concentrations of alginate for up to 6 days. Follicle survival and morphology were monitored throughout the culture. RESULTS We found that primate ovarian tissue can be maintained for up to 24 h at 4°C without compromising tissue or follicle health. Hundreds of intact and viable primordial follicles were isolated from each ovary independent of animal age. Follicle survival and morphology were more optimal when follicles were cultured in 2% alginate compared with 0.5% alginate. CONCLUSIONS By mimicking the rigid ovarian environment through the use of biomaterials, we have established conditions that support primordial follicle culture. These results lay the foundations for studying the basic biology of primordial follicles in a controlled environment and for using primordial follicles for fertility preservation methods.
reveals subtle variations in the NK cell repertoire Characterization of a novel NKG2D and NKp46 double-mutant mouse

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Laser Actuated Presentation System

We present here a pattern sensitive PowerPoint presentation scheme. The presentation is actuated by simple patterns drawn on the presentation screen by a laser pointer. A specific pattern corresponds to a particular command required to operate the presentation. Laser spot on the screen is captured by a RGB webcam with a red filter mounted, and its location is identified at the blue layer of each captured frame by estimating the mean position of the pixels whose intensity is above a given threshold value. Measured Reliability, Accuracy and Latency of our system are 90%, 10 pixels (in the worst case) and 38 ms respectively.
Real-Time Tracking with On-line Feature Selection

The main idea is to formulate the tracking problem as a binary classification task and to achieve robustness by continuously updating the current classifier of the target object with respect to the current surrounding background. For this purpose we use an on-line AdaBoost feature selection algorithm [1] for tracking. The distinct advantage of the method is its capability of updating a model (classifier) during tracking. This allows on the one hand that a classifier can adapt to any object and on the other hand to handle appearance changes (e.g. out of plane rotations, illumination changes) quite naturally. Moreover, depending on the background the algorithm selects the most discriminating features for tracking resulting in stable tracking results. By using fast computable features (e.g. Haar wavelets, integral orientation histograms, local binary patterns) the algorithm runs in real-time (more than 20 fps using a standard 1.6 GHz PC with 512 MB RAM). The main innovation of the proposed tracking approach is an on-line AdaBoost algorithm [1] which allows efficient updating of a classifier and makes an on-line selection of tracking features feasible. The principle of the tracking approach with a classifier is depicted in Figure 1. Since we are
Communication issues in distributed multisensory robotics

The EU funded project ViewFinder aims at integrating mobile robots into a command and control network. These robots will be equipped with numerous perception sensors producing a lot of data that would have to be exchanged between different computers on the robots or over a wireless link. This paper presents the communication requirements of the ViewFinder project and reviews possible technical solutions. It describes and compares two software packages, namely CoRoBA and Mailman, that are used in the project. Results of communication performance of standard Wi-Fi and Wimax systems in typical ViewFinder environments are reported. Finally tailored solutions for solving communication issues are proposed.
Code Clone Analysis Method for Practical Refactoring Support

Recently, code clone has been regarded as one of factors that make software maintenance more diﬃcult. A code clone is a code fragment in a source code that is identical or similar to another. For example, if we modify a code fragment which has code clones, it is necessary to consider whether we have to modify each of its code clones. There are two ways of maintenance support for code clones. One is to comprehend and manage code clones, and the other is to remove them. For the former support, we have developed code clone analysis environment Gemini . For the latter support, several methods have proposed. But, it is diﬃcult to apply them to industrial software because of various reasons such as high time complexity. In this paper, we propose a method that detects refactoring-oriented code clone in practical use time. And, we develop a characterization of code clones by some metrics, which suggest how to remove them. Then, we develop refactoring support tool Cancer . We expect Cancer can support software maintenance more eﬀectively.
Warm dark matter versus bumpy power spectra

In this paper we explore the differences between a warm dark matter (WDM) model and a cold dark matter (CDM) model where the power on a certain scale is reduced by introducing a narrow negative feature (‘dip’). This dip is placed in a way so as to mimic the loss of power in the WDM model: both models have the same integrated power out to the scale where the power of the dip model rises to the level of the unperturbed CDM spectrum again. Using N-body simulations we show that some of the large-scale clustering patterns of this new model follow more closely the usual CDM scenario while simultaneously suppressing small-scale structures (within galactic haloes) even more efficiently than WDM. The analysis in the paper shows that the new Dip model appears to be a viable alternative to WDM, but it is based on different physics. Where WDM requires the introduction of a new particle species, the Dip model is based on a non-standard inflationary period. If we are looking for an alternative to the currently challenged standard ΛCDM structure formation scenario, neither the ΛWDM nor the new Dip model can be ruled out based on the analysis presented in this paper. They both make very similar predictions and the degeneracy between them can only be broken with observations yet to come.
Ieee Copyright Notice Active Visual 3d Perception

Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE. Abstract This paper deals with the 3D structure estimation of a set of geometrical primitives in an active vision context. Our method is based on the structure from controlled motion approach which consists in constraining the camera motion in order to obtain an optimal estimation of the 3D structure of a geometrical primitive. Since this approach involves to focus on the considered primitive, we present a method for connecting up many estimations. We have developed perceptual strategies able to perform a succession of optimal estimation. A scene exploration process centered on current visual 2D information and the structure of the previously studied primitives is presented. It allows us to have an optimal estimation of each primitive of a scene composed of cylinders, segments and polygons.