Miracle-dz/UniFAR-FTUs huggingface dataset:
Impact of Genotypic Studies on Mycobacterial Taxonomy: the New Mycobacteria of the 1990s

SUMMARY The advancement of genetic techniques has greatly boosted taxonomic studies in recent years. Within the genus Mycobacterium, 42 new species have been detected since 1990, most of which were grown from clinical samples. Along with species for which relatively large numbers of strains have been reported, some of the new species of mycobacteria have been detected rarely or even only once. From the phenotypic point of view, among the new taxa, chromogens exceed nonchromogens while the numbers of slowly and rapidly growing species are equivalent. Whereas conventional identification tests were usually inconclusive, an important role was played by lipid analyses and in particular by high-performance liquid chromatography. Genotypic investigations based on sequencing of 16S rRNA gene have certainly made the most important contribution. The investigation of genetic relatedness led to the redistribution of the species previously included in the classically known categories of slow and rapid growers into new groupings. Within slow growers, the intermediate branch related to Mycobacterium simiae and the cluster of organisms related to Mycobacterium terrae have been differentiated; among rapid growers, the group of thermotolerant mycobacteria has emerged. The majority of species are resistant to isoniazid and, to a lesser extent, to rifampin. Many of the new species of mycobacteria are potentially pathogenic, and there are numerous reports of their involvement in diseases. Apart from disseminated and localized diseases in immunocompromised patients, the most frequent infections in immunocompetent people involve the lungs, skin, and, in children, cervical lymph nodes. The awareness of such new mycobacteria, far from being a merely speculative exercise, is therefore important for clinicians and microbiologists.
The Cytokine IL-1β Activates IFN Response Factor 3 in Human Fetal Astrocytes in Culture 1

The cytokine IL-1β is a major activator of primary human fetal astrocytes in culture, leading to the production of a wide range of cytokines and chemokines important in the host defense against pathogens. IL-1β, like TLR4, signals via the MyD88/IL-1βR-associated kinase-1 pathway linked to activation of NF-κB and AP-1. Recent studies have shown that TLR4 also signals independently of MyD88, resulting in the activation of IFN regulatory factor 3 (IRF3), a transcription factor required for the production of primary antiviral response genes such as IFN-β. Using a functional genomics approach, we observed that IL-1β induced in astrocytes a group of genes considered to be IFN-stimulated genes (ISG), suggesting that IL-1β may also signal via IRF3 in these cells. We now show, using real-time PCR, that in astrocytes IL-1β induces the expression of IFN-β, IRF7, CXCL10/IFN-γ-inducible protein-10, and CCL5/RANTES. Chemokine expression was confirmed by ELISA. We also show that IL-1β induces phosphorylation and nuclear translocation of IRF3 and delayed phosphorylation of STAT1. The dependency of IFN-β, IRF7, and CXCL10/IFN-γ-inducible protein-10 gene expression on IRF3 was confirmed using a dominant negative IRF3-expressing adenovirus. The robust induction by IL-1β of additional ISG noted on the microarrays, such as STAT1, 2′5′-oligoadenylate synthetase 2, and ISG15, also supports an active signaling role for IL-1β via this pathway in human fetal astrocytes. These data are the first to show that IL-1β, in addition to TLRs, can stimulate IRF3, implicating this cytokine as an activator of genes involved in innate antiviral responses in astrocytes.
Chronic Labile Hypertension Produced by Lesions of the Nucleus Tractus Solitarii in the Cat

SUMMARY. Bilateral electrolytic-lesions of the nucleus tractus solitarii (NTS) were made at the level of the obex in seven cats. Within 1 hour the mean arterial pressure (MAP) rose to a maximum of 144 mm Hg (141% of control), and by 7 hours heart rate reached a peak of 236 beats/min (148% of control). The barore-ceptor reflexes were abolished. After 24 hours the arterial pressure became extremely labile, with variations of 80–100 mm Hg observed. The lability occurred spontaneously and during behaviors that were self-initiated or elicited by environmental stimuli. The MAP in the lesion group was 144 mm Hg (180% of control) during the day, and 96 mm Hg (120% of control) at night. The lability, measured by the standard deviation, during the day in the lesion group was 4 times greater than in the control group and at night there were no differences. The heart rate of the lesion group was always higher than that of the control group but the lability of both groups was the same. We conclude that lesions of the NTS produced labile hypertension, probably by disinhibition of sympathetic activity through central interruption of the baroreceptor reflexes. The higher, more labile arterial pressures during the day may be caused by uninhibited increases in sympathetic activity elicited by environmental stimuli that are present during the day and absent at night. The daily variation of pressure may also be caused by somatomotor activity or by a daily rhythm of sympathetic activity which is unmasked by the lesions.
Myocardial perfusion

Noninvasive cardiac magnetic resonance (CMR) imaging has progressed rapidly over the past few years and will most likely become an integral part of the diagnostic workup of patients with known or suspected coronary artery disease (CAD). In this article the rationale for using perfusion‐CMR is discussed, followed by a summary of current state‐of‐the‐art perfusion‐CMR techniques that addresses pharmacological stress, monitoring, pulse sequences, and doses of contrast media (CM) for first‐pass studies. In the second part, unresolved aspects of perfusion‐CMR, such as the lack of fully established and validated imaging protocols, are discussed. The optimum pulse sequence parameters, required cardiac coverage, analysis algorithms, criteria for data quality, and other aspects remain to be defined. Furthermore, since expertise in perfusion‐CMR is not yet widely available, training of physicians and technicians to perform perfusion‐CMR according to recognized standards is an important future requirement. In the last part of the review, some ideas are proposed to improve the management of patients with known or suspected CAD. This involves making a shift from a “reactive” strategy, in which patients are typically approached when they are symptomatic, to an “active” strategy, in which perfusion‐CMR is performed for early detection of high‐risk patients so that revascularizations can be performed before potentially deadly infarcts occur. An ideal test for such an active strategy would be highly accurate, reliable, safe (and thus repeatable), and affordable. Large multicenter trials have shown that in experienced centers perfusion‐CMR is reliable and repeatable, and it is hoped that future studies will demonstrate its cost‐effectiveness as well. J. Magn. Reson. Imaging 2006. © 2006 Wiley‐Liss, Inc.
Reduction of abdominal pressure in patients with ascites reduces gastroesophageal reflux.

The effect of the reduction of intra-abdominal pressure on the lower esophageal sphincter pressure (LESP) and the 24-hour pH monitoring were studied in 16 patients with ascites before and after paracentesis. LESP did not change (P > 0.05) with the reduction of intra-abdominal pressure (before paracentesis: 17.48 mmHg and postparacentesis: 18.67 mmHg). The results were divided into two groups according to the achieved reduction in intra-abdominal pressure group A were those in who the reduction was greater than 70% and B consisted of those a reduction of less than 70%. LESP did not change even when results for each group were considered separately (P > 0.05): group A (before: 15.60 mmHg; after: 18.09 mmHg); group B (before: 23.09 mmHg; after: 20.40 mmHg). However the 24-h pH monitoring showed pathological reflux in patients with ascites that was reduced with the paracentesis (P < 0.05; total number of reflux episodes before paracentesis was 520.26, and after, 136.26). All pH-monitoring parameters were statistically different (P < 0.05) before and after the reduction of intra-abdominal pressure for group A but not for group B. LESP does not change significantly (P > 0.05) when the intra-abdominal pressure is significantly reduced (P < 0.05). Patients with ascites showed gastroesophageal reflux. Intra-abdominal pressure reduction greater than 70% lead to a significant reduction in gastroesophageal reflux.
Sink Status and Photosynthetic Rate of the Leaflet Galls Induced by Bystracoccus mataybae (Eriococcidae) on Matayba guianensis (Sapindaceae)

The galling insect Bystracoccus mataybae (Eriococcidae) induces green and intralaminar galls on leaflets of Matayba guianensis (Sapindaceae), and promotes a high oxidative stress in host plant tissues. This biotic stress is assumed by the histochemical detection of hydrogen peroxide, a reactive oxygen species (ROS), whose production alters gall physiology. Thus, we hypothesize that high levels of nutrients are accumulated during gall development in response to a local maintenance of photosynthesis and to the galling insect activity. Moreover, the maintenance of low levels of photosynthesis may guarantee O2 production and CO2 consumption, as well as may avoid hypoxia and hypercarbia in gall tissues. To access the photosynthesis performance, the distribution of chlorophyllous tissues and the photochemical and carboxylation rates in gall tissues were analyzed. In addition, histochemical tests for hydrogen peroxide and phenolic derivatives were performed to confirm the biotic stress, and set the possible sites where stress dissipation occurs. The contents of sugars and nitrogen were evaluated to quantify the gall sink. Currently, we assume that the homeostasis in gall tissues is ruptured by the oxidative stress promoted by the galling insect activity. Thus, to supply the demands of gall metabolism, the levels of water-soluble polysaccharides and starch increase in gall tissues. The low values of maximum quantum efficiency of PSII (Fv/Fm) indicate a low photosynthetic performance in gall tissues. In addition, the decrease of PSII operating efficiency, (F’m–F’)/F’m, and Rfd (instantaneous fluorescence decline ratio in light, to measure tissue vitality) demonstrate that the tissues of B. mataybae galls are more susceptible to damage caused by stressors than the non-galled tissues. Thus, the high oxidative stress in gall developmental sites is dissipated not only by the accumulation of phenolic derivatives in the protoplast, but also of lignins in the walls of neoformed sclereids.
A Neural Network With Logical Reasoning Based on Auxiliary Inputs

This paper describes a neural network design using auxiliary inputs, namely the indicators, that act as the hints to explain the predicted outcome through logical reasoning, mimicking the human behavior of deductive reasoning. Besides the original network input and output, we add an auxiliary input that reflects the specific logic of the data to formulate a reasoning process for cross-validation. We found that one can design either meaningful indicators, or even meaningless ones, when using such auxiliary inputs, upon which one can use as the basis of reasoning to explain the predicted outputs. As a result, one can formulate different reasonings to explain the predicted results by designing different sets of auxiliary inputs without the loss of trustworthiness of the outcome. This is similar to human explanation process where one can explain the same observation from different perspectives with reasons. We demonstrate our network concept by using the MNIST data with different sets of auxiliary inputs, where a series of design guidelines are concluded. Later, we validated our results by using a set of images taken from a robotic grasping platform. We found that our network enhanced the last 1–2% of the prediction accuracy while eliminating questionable predictions with self-conflicting logics. Future application of our network with auxiliary inputs can be applied to robotic detection problems such as autonomous object grasping, where the logical reasoning can be introduced to optimize robotic learning.
Biogas Upgrading by Pressure Swing Adsorption

Biogas is a raw gaseous stream produced by anaerobic decomposition of organic matter. The main component of biogas is methane, reason why this stream is considered to be a renewable source of energy and fuel. The most positive aspects of biogas rely on its worldwide decentralized production and on the environmental benefits of avoiding methane emissions to atmosphere while using bio-methane it to replace fossil fuels. In order to use the energy obtained in biogas, its production should be controlled. The production of biogas from organic matter is a complex process involving many different bacterial groups. In a simple way, the entire biogas conversion from organic matter can be divided into four steps (Gavala et al., 2003; Demirbas et al., 2011): 1. Hydrolisis: complex organic molecules are hydrolyzed into smaller units (sugars, amino-acids, alcohols, fatty acids, etc. 2. Acidogenese: acidogenic bacteria further break down the molecules into volatile fatty acids, NH3, H2S and H2. 3. Acetanogese: the acetanogens transform the molecules into CO2, H2 and mainly acetic acid. 4. Metanogese: at the end of the process, the methanogenic archaea transform the H2 and acetic acid molecules into a mixture of CO2, CH4 and water. These production steps can be controlled in reactors (digesters) or are naturally occurring in landfills that can be optimized for collection of biogas (see www.epa.gov/lmop). The digesters can operate in mesophilic and thermophilic modes, which means that the biogas is generated at 293-313 K and 323-333 K, respectively (Gavala et al., 2003). Biogas generation in landfills mainly operates in psychrophilic conditions (285-290 K) (Monteiro et al., 2011). Biogas main constituents are methane, carbon dioxide, sulphur compounds (H2S, siloxanes), water and minor contaminants (O2, N2, ammonia, chlorine, fluorines, etc) (Wellinger, 2009; Pettersson and Wellinger, 2009, www.epa.gov/lmop). The final composition of biogas is variable and strongly depends on the source of organic matter (Pettersson and Wellinger, 2009). Major sources of biogas production are landfills, waste-water treatment plants, manure fermentation and fermentation of energy crops. The composition of the biogas obtained from these sources is given in Table 1. For comparison, the composition and properties of natural gas are included in Table 1. The methane content vary strongly due to the different kind of molecules processed: i.e, fat has a much higher bio-methane yield than carbohydrates. The biogas yield of cereal residues is also high (around 200 m3 CH4/ton)
Construction of a Transplantable Tissue-Engineered Artificial Peritoneum

Background: Peritoneal defects lead to serious postoperative problems. Thus the development of physiological material to cover peritoneal defects is very desirable. Aim: The aim of this study was to develop a transplantable artificial peritoneum. Method: The artificial peritoneum consisted of collagen gel, fibroblasts, and mesothelial cells, and histological features were analyzed. The artificial peritoneum at the site of a peritoneal defect in the rat was transplanted to the abdominal wall. Results: Histological examination revealed that the artificial peritoneum consisted of a flat mesothelial monolayer upon a stromal matrix. All transplanted artificial peritoneums adapted well to the host and prevented severe adhesion. Conclusion: Our artificial peritoneum may be a useful transplantable bioengineered material for repair of surgical peritoneal defects.
Steroidogenic factor-1 binding and transcriptional activity of the cholesterol side-chain cleavage promoter in rat granulosa cells.

The cholesterol side-chain cleavage cytochrome P450 (CYP11A; P450scc) gene is expressed in rat ovarian follicles in response to gonadotropins (FSH/LH) and cAMP. To identify functional regions within the rat P450scc promoter, 894 basepairs (bp) of 5'-flanking sequence and 5'-deletions (at -379, -101, -73, and -38 bp) were linked to the human GH reporter gene and transfected into cultured rat granulosa cells. cAMP inducibility of the rat promoter was localized to a region (between -73/-38 bp) that contains one of two AGGT/CC/TA motifs, designated SCC1 (-51/-43 bp) and SCC2 (-79/-71 bp), within the rat promoter. One of the nuclear proteins in granulosa cells that binds to SCC1 was identified as the orphan receptor, steroidogenic factor-1 (SF-1). In contrast, multiple protein-DNA complexes formed with SCC2, only one of which was clearly identified as SF-1. Nuclear extract binding was sequence specific; SCC1 bound SF-1 more strongly than did SCC2. Thus, the two AGGT/CC/TA motifs of the rat promoter appear to differ structurally and functionally. Furthermore, because the expression of SF-1 mRNA precedes hormonal/cAMP induction of P450scc mRNA and is not regulated in vitro by cAMP, the functional role of SF-1 in transcriptional regulation of the P450scc gene, including its induction by cAMP, is not entirely clear and is probably dependent on other factors and/or the modification (phosphorylation? ) of SF-1.
Improving Task Performance through High Level Shared Control of Multiple Robots with a Context Aware Human-Robot Interface

In multi-robot control, robots need the ability to perform well in the absence of valid human input. This paper describes a shared control scheme for multiple robots where control can be traded between human and autonomous agents on the fly, reducing the negative effect of robots requiring attention while the user's attention is devoted elsewhere. The control approach is a hybrid of traded control where the control is traded between the human and autonomous agents and coordinated control where high level human user commands are mapped to low level implementation under partial control of the autonomous system. An allocation authority decides whether the user or autonomous agent is controlling the robot at a given time based on a command context. This allocation authority control scheme is compared to a coordinated control scheme in a multi-robot soccer domain. The results demonstrate that an allocation authority approach produces improved task performance and may have generalizable applicability. Specifically in the context of robotic soccer, the proposed control scheme was shown to have 18.5% more possession and 8.2% more territory than traded control while also reducing mental demands on users.
Gain-scheduled H-infinity observer design for nonlinear stochastic systems with time-delay and actuator saturation

In this paper, we propose a method for designing continuous gain-scheduled robust H∞ observer on a class of extended stochastic nonlinear systems subject to time delay and actuator saturation. Initially, gradient linearization procedure is applied to describe such extended nonlinear systems into several model-based linear systems. Next, a robust linear H∞ observer is designed to such linear stochastic models. Subsequently, a convex hull set is investigated and sufficient condition is derived in terms of feedback observer to determine whether a given initial condition belongs to an ellipsoid invariant set. Finally, continuous gain-scheduled approach is employed to design continuous nonlinear observers on the entire extended nonlinear jump system. A simulation example is given to illustrate the effectiveness of developed techniques.
Efficient modeling of travel in networks with time-varying link speeds

This paper investigates exact and approximate methods for estimating time-minimizing vehicular movements in road network models where link speeds vary over time. The assumptions made about network conditions recognize the intrinsic relationship between speed and travel duration and are substantiated by elementary methods to obtain link travel duration. The assumptions also imply a condition of FIFO consistency, which (as shown by work of Kaufman and Smith) justifies the use of Dijkstra's algorithm for path-finding purposes. The paper describes several adaptations of the Dijkstra algorithm, including new variants that are addressed specifically to the dynamic conditions mentioned above. Computational tests indicate that these procedures will be useful for scheduling, modeling, and other purposes, when applied to networks of substantial size. © 2000 John Wiley & Sons, Inc.
Efficient distribution of fragmented sensor data for obfuscation

The inherent nature of unattended sensors makes these devices most vulnerable to detection, exploitation, and denial in contested environments. Physical access is often cited as the easiest way to compromise any device or network. A new mechanism for mitigating these types of attacks developed under the Assistant Secretary of Defense for Research and Engineering, ASD(R&E) project, “Smoke Screen in Cyberspace”, was previously demonstrated in a live, over-the-air experiment. Smoke Screen encrypts, slices up, and disburses redundant fragments of files throughout the network. This paper describes enhancements to the disbursement of the file fragments routing improving the efficiency and time to completion of fragment distribution by defining the exact route, fragments should take to the destination. This is the first step in defining a custom protocol for the discovery of participating nodes and the efficient distribution of fragments in a mobile network. Future work will focus on the movement of fragments to avoid traffic analysis and avoid the collection of the entire fragment set that would enable an adversary to reconstruct the original piece of data.
Glucose Starvation Alters Heat Shock Response, Leading to Death of Wild Type Cells and Survival of MAP Kinase Signaling Mutant

A moderate heat shock induces Neurospora crassa to synthesize large quantities of heat shock proteins that are protective against higher, otherwise lethal temperatures. However, wild type cells do not survive when carbohydrate deprivation is added to heat shock. In contrast, a mutant strain defective in a stress-activated protein kinase does survive the combined stresses. In order to understand the basis for this difference in survival, we have determined the relative levels of detected proteins in the mutant and wild type strain during dual stress, and we have identified gene transcripts in both strains whose quantities change in response to heat shock or dual stress. These data and supportive experimental evidence point to reasons for survival of the mutant strain. By using alternative respiratory mechanisms, these cells experience less of the oxidative stress that proves damaging to wild type cells. Of central importance, mutant cells recycle limited resources during dual stress by undergoing autophagy, a process that we find utilized by both wild type and mutant cells during heat shock. Evidence points to inappropriate activation of TORC1, the central metabolic regulator, in wild type cells during dual stress, based upon behavior of an additional signaling mutant and inhibitor studies.