Miracle-dz/UniFAR-FTUs huggingface dataset:
End-Product Control of Carbon Metabolism in Culture-Grown Sugar Beet Plants (Molecular and Physiological Evidence on Accelerated Leaf Development and Enhanced Gene Expression)

Sugar beet (Beta vulgaris L.) seedlings were grown on media containing 90 to 300 mM sucrose or glucose. Compared to controls, sugar-grown plants had higher growth rate, photosynthesis, and leaf sugar levels. The steady-state level of transcripts increased significantly for the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) (rbcS) and the cytosolic fructose-1,6-bisphosphatase and moderately for the Rubisco large subunit (rbcL). The transcript level of sucrose phosphate synthase remained unchanged. Fructose-1,6-bisphosphatase and Rubisco activities did not change in the presence of sugars, but that of sucrose phosphate synthase increased (44 and 90% under selective and nonselective assay conditions, respectively). Accelerated leaf development was indicated by (a) autoradiograms of leaves that showed that sucrose loading occurred earlier, (b) export capacity that also occurred earlier but, after about 2 weeks, differences were not detectable, and (c) sucrose synthase activity that declined significantly. Several conclusions emerged: (a) response was nonosmotic and gene and sugar specific, (b) sugars caused accelerated leaf development and sink-to-source transition, (c) enhanced gene expression was due to advanced leaf development, and (d) whereas Rubisco and cytosolic fructose-1,6-bisphosphatase genes were sugar repressed in mature leaves of greenhouse-grown plants, they were unaffected in mature, culture-grown leaves. To our knowledge, these data provide the first evidence in higher plants that, depending on the physiological/developmental context of leaves, sugars lead to differential regulation of the same gene.
An Integrated Pipeline of Open Source Software Adapted for Multi-CPU Architectures: Use in the Large-Scale Identification of Single Nucleotide Polymorphisms

The large amounts of EST sequence data available from a single species of an organism as well as for several species within a genus provide an easy source of identification of intra- and interspecies single nucleotide polymorphisms (SNPs). In the case of model organisms, the data available are numerous, given the degree of redundancy in the deposited EST data. There are several available bioinformatics tools that can be used to mine this data; however, using them requires a certain level of expertise: the tools have to be used sequentially with accompanying format conversion and steps like clustering and assembly of sequences become time-intensive jobs even for moderately sized datasets. We report here a pipeline of open source software extended to run on multiple CPU architectures that can be used to mine large EST datasets for SNPs and identify restriction sites for assaying the SNPs so that cost-effective CAPS assays can be developed for SNP genotyping in genetics and breeding applications. At the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), the pipeline has been implemented to run on a Paracel high-performance system consisting of four dual AMD Opteron processors running Linux with MPICH. The pipeline can be accessed through user-friendly web interfaces at http://hpc.icrisat. cgiar.org/PBSWeb and is available on request for academic use. We have validated the developed pipeline by mining chickpea ESTs for interspecies SNPs, development of CAPS assays for SNP genotyping, and confirmation of restriction digestion pattern at the sequence level.
Anisotropic Point Set Surfaces

Point Set Surfaces define smooth surfaces from regular samples based on weighted averaging of the points. Because weighting is done based on a spatial scale parameter, point set surfaces apply basically only to regular samples. We suggest to attach individual weight functions to each sample rather than to the location in space. This extends Point Set Surfaces to irregular settings, including anisotropic sampling adjusting to the principal curvatures of the surface. In particular, we describe how to represent surfaces with ellipsoidal weight functions per sample. Details of deriving such a representation from typical inputs and computing points on the surface are discussed.
Nuclear Medicine: Flare Response versus Disease Progression in Patients with Non-small Cell Lung Cancer Flare Response versus Disease Progression in Patients with Non-small Cell Lung Cancer

We present a case report of a patient with metastatic non-small cell lung cancer (NSCLC) who had a series of fluorine-18 fluorodeoxyglucose positron emission tomography/computed tomography (18F-FDG PET/CT) scans for assessment of response to treatment. A restaging 18F-FDG PET/CT scan after six cycles showed increased FDG activity in the bone lesions with reduced activity in the lung and liver lesions. The increased bone activity was considered to be due to flare phenomenon rather than metastasis. A short interval follow up scan after 1 month was advised to confirm this interpretation but this repeat scan showed disease relapse. Although the flare phenomenon does exist, caution should be exercised in attributing increased tracer uptake in the lesions in patients with adenocarcinoma of lung and especially those who have received erlotinib during the course of their treatment. Distinguishing the 'flare phenomenon' and 'disease progression' is at times difficult but is important since misdiagnosis may result in an unnecessary delay in patient management. A 59-year-old male presented to his general practitioner with hoarseness of voice, reduced appetite and right hip and left shoulder pain. In addition, he complained of mild exertional dyspnoea but had no other significant chest symptoms. Chest radiography showed a mass in the upper lobe of the left lung and the baseline CT scan demonstrated a 3 cm spiculated mass and satellite nodules in the same lobe. Multiple metastatic lesions were found in the liver. In addition mediastinal and left hilar lymph node metastases were noted [Figures 1, 2]. Subsequent magnetic resonance imaging (MRI) of the spine confirmed bone metastases within the spine, sacrum and proximal femora [Figure 3]. The baseline 18F-FDG PET/CT scan showed intense uptake in the 3 cm mass in the upper lobe of the left lung, mediastinal nodes, left hilar nodes and multiple liver and bone lesions [Figure 4]. Chemotherapy (cisplatin and pemetrexed) and palliative radiotherapy were commenced after biopsy of the left scapular mass which showed an adenocarcinoma that demonstrated positive immuno-staining for CK7 (cytokeratin 7) and TTF1 (thyroid transcription factor-1) compatible with primary lung carcinoma [Figure 5]. A follow-up 18F-FDG PET/CT scan after two cycles of chemotherapy showed a significant reduction in tracer avidity with mild uptake in the left upper lobe lung mass (maximum standardised uptake value (SUVmax) 3.2; previously 20.4) and multiple bone lesions (SUVmax 3.6; previously 8.4). No uptake was seen in the mediastinal nodes, left hilar nodes or liver lesions. After …
GIS and Public Health

This Special Issue on GIS and public health is the result of a highly selective process, which saw the participation of some 20 expert peer-reviewers and led to the acceptance of one half of the high-quality submissions received over the past year. Many threads link these papers to each other and, indeed, to our original call for papers, but the element that most clearly emerges from these works is the inextricable connection between public health and the environment. Indeed, GIS analysis of public health simply cannot disregard the geospatial dimension of environmental resources and risks. What consistently emerges from these analyses is that current geospatial research can only scratch the surface of the complex interactions of spatial resources, risks, and public health. In today’s world, or at least in the developed world, researchers and practitioners can count on virtually endless data, on inexpensive computational power, and on seamless connectivity. In this research environment, these papers point to the need for improved analytical tools, covering concepts, representation, modeling and reliability. These works are important contributions that help us to identify what advances in geospatial analysis can better address the complex interactions of public health with our physical and cultural environment, and bridge research and practice, so that geospatial analyses can inform public health policy making. [. ]
gyrA mutations in quinolone-resistant isolates of the fish pathogen Aeromonas salmonicida

gyrA mutations in quinolone-resistant isolates of Aeromonas salmonicida have been detected by using PCR to amplify the quinolone resistance-determining region of gyrA and subsequent cloning and sequencing of PCR products. Comparison of nucleotide and derived amino acid sequences of PCR products from quinolone-susceptible and -resistant bacteria revealed a serine 83-to-isoleucine substitution in the gyrase A protein of resistant isolates. One of the resistant isolates differed from the other by a two- to fourfold-higher MIC of the fluoroquinolone enrofloxacin and carried an additional alanine 67-to-glycine substitution, which may contribute to the higher level of resistance.
Uncertainty Increases the Reliance on Affect in Decisions

How do psychological states of uncertainty influence the way people make decisions? We propose that such states increase the reliance on affective inputs in judgments and decisions. In accord with this proposition, results from six studies show that the priming of uncertainty (vs. certainty) consistently increases the effects of a variety of affective inputs on consumers’ judgments and decisions. Primed uncertainty is shown to amplify the effects of the pleasantness of a musical soundtrack (study 1), the attractiveness of a picture (study 2), the appeal of affective attributes (studies 3 and 4), incidental mood states (study 6), and even incidental states of disgust (study 5). Moreover, both negative and positive uncertainty increase the influence of affect in decisions (study 4). The results additionally show that the increased reliance on affective inputs under uncertainty does not necessarily come at the expense of a reliance on descriptive attribute information (studies 2 and 5), and that the increased reliance on affect under uncertainty is distinct from a general reliance on heuristic or peripheral cues (study 6). The phenomenon may be due to uncertainty threatening the self, thereby encouraging a reliance on inputs that are closer to the self and have high subjective validity.
EEG-based driver fatigue detection using hybrid deep generic model

Classification of electroencephalography (EEG)-based application is one of the important process for biomedical engineering. Driver fatigue is a major case of traffic accidents worldwide and considered as a significant problem in recent decades. In this paper, a hybrid deep generic model (DGM)-based support vector machine is proposed for accurate detection of driver fatigue. Traditionally, a probabilistic DGM with deep architecture is quite good at learning invariant features, but it is not always optimal for classification due to its trainable parameters are in the middle layer. Alternatively, Support Vector Machine (SVM) itself is unable to learn complicated invariance, but produces good decision surface when applied to well-behaved features. Consolidating unsupervised high-level feature extraction techniques, DGM and SVM classification makes the integrated framework stronger and enhance mutually in feature extraction and classification. The experimental results showed that the proposed DBN-based driver fatigue monitoring system achieves better testing accuracy of 73.29 % with 91.10 % sensitivity and 55.48 % specificity. In short, the proposed hybrid DGM-based SVM is an effective method for the detection of driver fatigue in EEG.
Coronary stent patency: dual-energy multidetector CT assessment in a pilot study with anthropomorphic phantom.

PURPOSE To prospectively evaluate, by optimizing image acquisition and introducing alternative image postprocessing techniques, dual-energy multidetector computed tomography (CT) for depiction of the lumens of coronary artery stents placed in a moving anthropomorphic heart phantom. MATERIALS AND METHODS Four coronary stents (2, 3, 4, and 5 mm) were examined at 64-section dual-energy multidetector CT by using a dual-detector "double-decker" imager with stacked high- and low-energy detector arrays, 0.67-mm section thickness, and 32 x 0.625-mm collimation. Simultaneous high- and low-energy data sets were acquired at 80 and 140 kVp and at 400 mAs. Cardiac motion was simulated in a moving anthropomorphic heart phantom. Stents were imaged longitudinally and axially with the phantom at rest and with it in motion. Use of an enhancement algorithm based on high- and low-energy absorption profiles was proposed. Stent lumen depiction and stent mesh delineation were quantified in terms of contrast-to-noise ratio (CNR) and kurtosis (kappa), respectively. Image quality was analyzed at univariate general linear model analysis in which peak voltage and data enhancement algorithm were dependent factors and stent orientation and cardiac motion were independent factors. RESULTS Analysis of CNR and kappa revealed an interdependency between CNR and kappa and stent diameter: The CNR and kappa of smaller stents increased significantly when these stents were imaged at lower peak voltages in the axial plane and with the enhancement algorithm applied to the 80-kVp data sets (P < .001). The CNR and kappa of larger stents increased significantly when these stents were imaged at higher peak voltages in the longitudinal plane, and imaging of these stents benefited from the enhancement algorithm being applied to the 140-kVp data sets (P < .001). CONCLUSION Dual-energy multidetector CT performed with optimized acquisition parameters and alternative image postprocessing led to enhanced coronary stent lumen depiction to an extent beyond that achieved with single-energy multidetector CT.
Maintenance and regulation of extracellular volume and the ion environment in Drosophila larval nerves

In mammals and insects, paracellular blood barriers isolate the nervous system from the rest of the animal. Glia and accessory cells of the nervous system use pumps, channels, cotransporters, and exchangers collectively to maintain the extracellular ion environment and osmotic balance in the nervous system. At present, the molecular mechanisms that regulate this process remain unclear. In humans, loss of extracellular ion and volume regulation in the nervous system poses serious health threats. Drosophila is a model genetic organism with a proven track record for uncovering molecular mechanisms relevant to human health and disease. Here, we review what is known about extracellular ion and volume regulation in larval abdominal nerves, present some new data about the impact of neural activity on the extracellular environment, and relate the findings to mammalian systems. Homologies have been found at the level of morphology, physiology, molecular mechanisms, and mutant phenotypes. The Fray‐Ncc69 module regulates extracellular volume in larval nerves. Genetic rescue experiments with the mammalian orthologs prove this module has a direct correlate in humans. This and other molecular homologies, together with the similar physiological needs, suggest that uncovering the molecular mechanisms of ion and volume regulation in larval nerves will likely provide significant insights into this process in mammalian systems. © 2011 Wiley‐Liss, Inc.
Superior Colliculus Cell Responses Related to Eye Movements in Awake Monkeys

Single cell responses were recorded from the superior colliculus of awake monkeys trained to move their eyes. A class of cells that discharged before eye movements was found in the intermediate and deep layers of the colliculus. The response of the cells was most vigorous before saccadic eye movements within a particular range of directions. These cells had no visual receptive fields, and visually guided eye movements were not necessary for their discharge, since they responded in total darkness before spontaneous eye movements and vestibular nystagmus.
Lipopolysaccharides Impair Insulin Gene Expression in Isolated Islets of Langerhans via Toll-Like Receptor-4 and NF-κB Signalling

Background Type 2 diabetes is characterized by pancreatic β-cell dysfunction and is associated with low-grade inflammation. Recent observations suggest that the signalling cascade activated by lipopolysaccharides (LPS) binding to Toll-Like Receptor 4 (TLR4) exerts deleterious effects on pancreatic β-cell function; however, the molecular mechanisms of these effects are incompletely understood. In this study, we tested the hypothesis that LPS alters insulin gene expression via TLR4 and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) in islets. Methodology/Principal Findings A 24-h exposure of isolated human, rat and mouse islets of Langerhans to LPS dose-dependently reduced insulin gene expression. This was associated in mouse and rat islets with decreased mRNA expression of pancreas-duodenum homebox-1 (PDX-1) and mammalian homologue of avian MafA/l-Maf (MafA). Accordingly, LPS exposure also decreased glucose-induced insulin secretion. LPS repression of insulin, PDX-1 and MafA expression, as well as its inhibition of insulin secretion, were not observed in islets from TLR4-deficient mice. LPS inhibition of β-cell gene expression in rat islets was prevented by inhibition of the NF-κB pathway, but not the p38 mitogen-activated protein kinase (p38 MAPK) pathway. Conclusions/Significance Our findings demonstrate that LPS inhibit β-cell gene expression in a TLR4-dependent manner and via NF-κB signaling in pancreatic islets, suggesting a novel mechanism by which the gut microbiota might affect pancreatic β-cell function.
The Single T65S Mutation Generates Brighter Cyan Fluorescent Proteins with Increased Photostability and pH Insensitivity

Cyan fluorescent proteins (CFP) derived from Aequorea victoria GFP, carrying a tryptophan-based chromophore, are widely used as FRET donors in live cell fluorescence imaging experiments. Recently, several CFP variants with near-ultimate photophysical performances were obtained through a mix of site-directed and large scale random mutagenesis. To understand the structural bases of these improvements, we have studied more specifically the consequences of the single-site T65S mutation. We find that all CFP variants carrying the T65S mutation not only display an increased fluorescence quantum yield and a simpler fluorescence emission decay, but also show an improved pH stability and strongly reduced reversible photoswitching reactions. Most prominently, the Cerulean-T65S variant reaches performances nearly equivalent to those of mTurquoise, with QY = 0.84, an almost pure single exponential fluorescence decay and an outstanding stability in the acid pH range (pK1/2 = 3.6). From the detailed examination of crystallographic structures of different CFPs and GFPs, we conclude that these improvements stem from a shift in the thermodynamic balance between two well defined configurations of the residue 65 hydroxyl. These two configurations differ in their relative stabilization of a rigid chromophore, as well as in relaying the effects of Glu222 protonation at acid pHs. Our results suggest a simple method to greatly improve numerous FRET reporters used in cell imaging, and bring novel insights into the general structure-photophysics relationships of fluorescent proteins.
Rate-monotonic scheduling on uniform multiprocessors

Each processor in a uniform multiprocessor machine is characterized by a speed or computing capacity, with the interpretation that a job executing on a processor with speed s for t time units completes (s /spl times/ t) units of execution. The scheduling of systems of periodic tasks on uniform multiprocessor platforms using the rate-monotonic scheduling algorithm is considered here. A simple, sufficient test is presented for determining whether a given periodic task system will be successfully scheduled by algorithm upon a particular uniform multiprocessor platform-this test generalizes earlier results concerning rate-monotonic scheduling upon identical multiprocessor platforms.
Role of Conformational Motions in Enzyme Function: Selected Methodologies and Case Studies

It is now common knowledge that enzymes are mobile entities relying on complex atomic-scale dynamics and coordinated conformational events for proper ligand recognition and catalysis. However, the exact role of protein dynamics in enzyme function remains either poorly understood or difficult to interpret. This mini-review intends to reconcile biophysical observations and biological significance by first describing a number of common experimental and computational methodologies employed to characterize atomic-scale residue motions on various timescales in enzymes, and second by illustrating how the knowledge of these motions can be used to describe the functional behavior of enzymes and even act upon it. Two biologically relevant examples will be highlighted, namely the HIV-1 protease and DNA polymerase β enzyme systems.
Enhancing Brassinosteroid Signaling via Overexpression of Tomato (Solanum lycopersicum) SlBRI1 Improves Major Agronomic Traits

Brassinosteroids (BRs) play important roles in plant growth, development, and stress responses through the receptor, Brassinosteroid-insensitive 1 (BRI1), which perceives BRs and initiates BR signaling. There is considerable potential agricultural value in regulating BR signaling in crops. In this study, we investigated the effects of overexpressing the tomato (Solanum lycopersicum) BRI1 gene, SlBRI1, on major agronomic traits, such as seed germination, vegetative growth, fruit ethylene production, carotenoid accumulation, yield, and quality attributes. SlBRI1 overexpression enhanced the endogenous BR signaling intensity thereby increasing the seed germination rate, lateral root number, hypocotyl length, CO2 assimilation, plant height, and flower size. The transgenic plants also showed an increase in fruit yield and fruit number per plant, although the mean weight of individual fruit was reduced, compared with wild type. SlBRI1 overexpression also promoted fruit ripening and ethylene production, and caused an increase in levels of carotenoids, ascorbic acid, soluble solids, and soluble sugars during fruit ripening. An increased BR signaling intensity mediated by SlBRI1 overexpression was therefore positively correlated with carotenoid accumulation and fruit nutritional quality. Our results indicate that enhancing BR signaling by overexpression of SlBRI1 in tomato has the potential to improve multiple major agronomic traits.