Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic Characterization of Natural Gases: ABSTRACT

An empirical model is presented in which the origin of most natural gases can be deduced from compositional variations in the gases. The genetic characterization is performed using the C2+ composition of the gases, the 13C concentration in methane (^dgr13C1) and ethane (^dgr13C2), as well as the deuterium concentration in methane ^dgrD. Three diagrams are designed in which C2+, ^dgr13D, and ^dgr13C2 are plotted versus ^dgr13C1. In these three diagrams, compositional fields can be defined for primary gases, i.e., those gases for which compositional changes are due to processes occurring during their formation (biogenic and thermogenic associated and nonassociated gases, respectively). Secondary gases result from mixing processes after formation of gases. The variability of natural gases can be described by (and reduced to) predominantly various mixing processes of primary gases. Two types of migration of gases can be recognized: shallow migration where thermogenic gases are stripped of C2+ or become mixed with biogenic gases, and deep migration where deep dry gases become mixed with gases from more immature sources. Case histories will be presented to demonstrate the applicability of the model. End_of_Article - Last_Page 546------------
Long-term changes in total ozone column content and its association with stratospheric temperature over two neighbouring tropical Asian stations

This paper focuses on the long-term declining change in total ozone column (TOC) derived from satellite measurements over a 25 year period over two neighbouring tropical Asian sites, Karachi, and Mt Abu. A strong declining trend was observed in TOC at both sites, with a significance level of over 95% and a higher magnitude of 4 to 10 DU per decade in September to December and a weak statistical significance level of below 85% and a lower magnitude of 2 to 4 DU per decade in pre-monsoon months. However, during the monsoon months, a small declining trend of about 1 DU per decade was observed, but this variation is statistically insignificant. Further, the long-term changes in TOC exhibit seasonal dependence with a more negative change of 10 DU per decade in winter over Karachi and 7 DU per decade over Mt Abu. The consequence of such a net long-term declining change in TOC as high as 10 DU per decade is expected to have serious environmental implications due to an overall increase in ground-level solar UV radiation of 18% over the normal values in the tropics. In order to identify some plausible causes of this depletion trend in ozone concentration with stratospheric temperature and solar activity, it is clear that there is a strong relationship between the seasonal dependence of the long-term declining trend of TOC on air temperature at 10 mb or stratospheric cooling. At the same time, there is a less significant long-term variation in TOC due to altered solar activity levels.
Reductions in all-cause, cancer, and coronary mortality in statin-treated patients with heterozygous familial hypercholesterolaemia: a prospective registry study

Aims To examine the changes in coronary, all-cause, and cancer mortality in patients with heterozygous familial hypercholesterolaemia (FH) before and after lipid-lowering therapy with statins. Methods and results A total of 3382 patients (1650 men) aged <80 years were recruited from 21 lipid clinics in the United Kingdom and followed prospectively between 1980 and 2006 for 46 580 person-years. There were 370 deaths, including 190 from coronary heart disease (CHD) and 90 from cancer. The standardized mortality ratio (compared with the population in England and Wales) was calculated before and from 1 January 1992. In patients aged 20–79 years, CHD mortality fell significantly by 37% (95% CI = 7–56) from 3.4- to 2.1-fold excess. Primary prevention resulted in a 48% reduction in CHD mortality from 2.0-fold excess to none, with a smaller reduction of nearly 25% in patients with established disease. Coronary mortality was reduced more in women than in men. In patients without known CHD at registration, all-cause mortality from 1992 was 33% (21–43), lower than in the general population, mainly due to a 37% (21–50) lower risk of fatal cancer. Conclusion The results emphasize the importance of early identification of FH and treatment with statins.
Ischemic Brain Edema Following Middle Cerebral Artery Occlusion in Baboons: Relationship Between Regional Cerebral Water Content and Blood Flow at 1 to 2 Hours

The relationship between increase in water content in ischemic brain and levels of regional blood flow has been studied in 11 primates. Flows were recorded using the method of hydrogen (2-minute) clearance, from a total of 128 electrodes in cortex and white matter, and a gradation of ischemia was produced by middle cerebral occlusion transorbitally. The flows were reduced in the area of densest ischemia from control levels of 42.0 ± 12.0 ml/ lOOg/min to 7.0 ± 5.4 ml/ lOOg/min, with lesser decreases over the remainder of the ischemic hemisphere. Water content was measured in cortex and white matter, in regions topographically related to those of flow measurements, by densitometric assessment using precalibrated kerosene/bromobenzine columns. The average water content of cortex in regions remote from ischemia was 797.4 ± 5.8 mg/gm and in white matter 708.5 ± 8.2 mg/gm. Significant increases in water content (comparing corresponding regions of the two hemispheres) of up to 11.4 ± 7.5 mg/gm were demonstrated in the most ischemic cortical areas. A gradient of water increase was evident in the ischemic hemisphere, increases in water content being greatest in the opercular zone and least in the parasagittal area. Significant differences in white matter water content between the 2 hemispheres were demonstrated only in the most densely ischemic areas in the current experiments where ischemia was limited to 93 ± 20 mins in the 11 animals without reperfusion. The relationship between ischemic density and water content increase showed that significant increases in water content occurred in regions where terminal flows had been below 20 ml/lOOg/min, indicating that accumulation of water in ischemic brain begins at flow values comparable to those associated with the failure of synaptic transmission, higher than those associated with failure of the ionic pump of the cell. Possible pathophysiological mechanisms are discussed.
Gallium Maltolate Treatment Eradicates Pseudomonas aeruginosa Infection in Thermally Injured Mice

ABSTRACT Gallium (Ga) is a semimetallic element that has demonstrated therapeutic and diagnostic-imaging potential in a number of disease settings, including cancer and infectious diseases. Gallium's biological actions stem from its ionic radius being almost the same as that of ferric iron (Fe3+), whereby it can replace iron (Fe) in Fe3+-dependent biological systems, such as bacterial and mammalian Fe transporters and Fe3+-containing enzymes. Unlike Fe3+, ionic gallium (Ga3+) cannot be reduced, and when incorporated, it inactivates Fe3+-dependent reduction and oxidation processes that are necessary for bacterial and mammalian cell proliferation. Most pathogenic bacteria require Fe for growth and function, and the availability of Fe in the host or environment can greatly enhance virulence. We examined whether gallium maltolate (GaM), a novel formulation of Ga, had antibacterial activity in a thermally injured acute infection mouse model. Dose-response studies indicated that a GaM dose as low as 25 mg/kg of body weight delivered subcutaneously was sufficient to provide 100% survival in a lethal P. aeruginosa-infected thermally injured mouse model. Mice treated with 100 mg/kg GaM had undetectable levels of Pseudomonas aeruginosa in their wounds, livers, and spleens, while the wounds of untreated mice were colonized with over 108P. aeruginosa CFU/g of tissue and their livers and spleens were colonized with over 105P. aeruginosa CFU/g of tissue. GaM also significantly reduced the colonization of Staphylococcus aureus and Acinetobacter baumannii in the wounds of thermally injured mice. Furthermore, GaM was also therapeutically effective in preventing preestablished P. aeruginosa infections at the site of the injury from spreading systemically. Taken together, our data suggest that GaM is potentially a novel antibacterial agent for the prevention and treatment of wound infections following thermal injury.
A trapped double bond-photoisomerization intermediate in a bacterial photoreceptor

Abbreviations ASU asymmetric unit BV, PCB, PVB (bilin compounds serving as chromophores) biliverdin Ixα, phycocyanobilin, phycoviolobilin CAPSO N-cyclohexyl-2-hydroxyl-3-aminopropanesulfonic acid CBCR cyanobacteriochrome GAF (protein domain) cGMP-specific phosphodiesterases adenylyl cyclases and FhlA IMAC immobilized metal-affinity chromatography MR molecular replacement PAS (protein domain) Per-Arnt-Sim PHY (protein domain) phytochrome-specific Pfr, Pg, Pr far red-, green-, and red-absorbing states of phytochromes and CBCRs Summary The GAF3 domain of cyanobacteriochrome Slr1393 (Synechocystis PCC6803) with an in vivo assembled phycocyanobilin (PCB) chromophore has been crystallized in parental state (1.8 Å) and photoproduct state (1.86 Å), identified by 15-Z and 15-E chromophore configuration. Comparison of both structures for the same protein allows precise determination of structural changes after photo-activation. The chromophore photoisomerization causes an outward movement and partial helix formation of a formerly unstructured loop. A tryptophan residue located in this loop, in π-π stacking distance to PCB in the dark state, moves away by 14 Å opening the binding cleft for the entry of water molecules. Also the in vitro assembled protein (chromophore addition to apo-protein) has been crystallized (1.6 Å resolution). Most importantly, an intermediate structure was solved (2.1 Å) with the protein in photoproduct conformation and the chromophore already isomerized into the parental 15-Z configuration, thereby giving insight into chromophore-initiated conformational protein changes. Impact Statement This manuscript presents crystal structures of a photochromic protein in both states, before (1.6 Å) and after (1.9 Å) the light induced photochemical event with sufficient resolution to allow detailed description of conformational changes of chromophore and protein. The light driven reaction, double bond photoisomerization of a covalently bound bilin chromophore is presented here for the first time. Our results allow determining the impact of the chromophore photochemistry on the protein conformation. In addition, we succeeded in trapping an intermediate carrying the chromophore already in isomerized state with the protein still in unchanged conformation. Absorption spectra of this intermediate clearly demonstrate a color change, thus allowing conclusion that the absorption of phytochromes is predominantly determined by the chromophore conformation alone with only moderate effect of the surrounding protein. Authors’ Contributions XX, KHZ, and WG designed the experiment. XX generated the protein. AH performed crystallization trials, collected the X-ray diffraction data and solved the structure. All authors contributed in preparing the manuscript.
Simultaneous MRI acquisition of blood volume, blood flow, and blood oxygenation information during brain activation

Simultaneous acquisition of complementary functional hemodynamic indices reflecting different aspects of brain activity would be a valuable tool for functional brain‐imaging studies offering enhanced detection power and improved data interpretation. As such, a new MRI technique is presented that is able to achieve concurrent acquisition of three hemodynamic images based primarily on the changes of cerebral blood volume, blood flow, and blood oxygenation, respectively, associated with brain activation. Specifically, an inversion recovery pulse sequence has been designed to measure VASO (vascular space occupancy), ASL (arterial spin labeling) perfusion, and BOLD (blood‐oxygenation‐level‐dependent) signals in a single scan. The MR signal characteristics in this sequence were analyzed, and image parameters were optimized for the simultaneous acquisition of these functional images. The feasibility and efficacy of the new technique were assessed by brain activation experiments with visual stimulation paradigms. Experiments on healthy volunteers showed that this technique provided efficient image acquisition, and thus higher contrast‐to‐noise ratio per unit time, compared with conventional techniques collecting these functional images separately. In addition, it was demonstrated that the proposed technique was able to be utilized in event‐related functional MRI experiments, with potential advantages of obtaining accurate transient information of the activation‐induced hemodynamic responses. Magn Reson Med 52:1407–1417, 2004. Published 2004 Wiley‐Liss, Inc.
Evidence for a SAL1-PAP Chloroplast Retrograde Pathway That Functions in Drought and High Light Signaling in Arabidopsis[C][W][OA]

This work describes a chloroplast-to-nucleus retrograde signaling pathway involving SAL1, a chloroplast and mitochondrial enzyme that degrades the phosphonucleotide 3′-phosphoadenosine 5′-phosphate (PAP). In the absence of SAL1 or in response to drought and high light, PAP accumulates and can move between the chloroplast and the nucleus, where it inhibits exoribonucleases, thereby inducing stress-responsive genes. Compartmentation of the eukaryotic cell requires a complex set of subcellular messages, including multiple retrograde signals from the chloroplast and mitochondria to the nucleus, to regulate gene expression. Here, we propose that one such signal is a phosphonucleotide (3′-phosphoadenosine 5′-phosphate [PAP]), which accumulates in Arabidopsis thaliana in response to drought and high light (HL) stress and that the enzyme SAL1 regulates its levels by dephosphorylating PAP to AMP. SAL1 accumulates in chloroplasts and mitochondria but not in the cytosol. sal1 mutants accumulate 20-fold more PAP without a marked change in inositol phosphate levels, demonstrating that PAP is a primary in vivo substrate. Significantly, transgenic targeting of SAL1 to either the nucleus or chloroplast of sal1 mutants lowers the total PAP levels and expression of the HL-inducible ASCORBATE PEROXIDASE2 gene. This indicates that PAP must be able to move between cellular compartments. The mode of action for PAP could be inhibition of 5′ to 3′ exoribonucleases (XRNs), as SAL1 and the nuclear XRNs modulate the expression of a similar subset of HL and drought-inducible genes, sal1 mutants accumulate XRN substrates, and PAP can inhibit yeast (Saccharomyces cerevisiae) XRNs. We propose a SAL1-PAP retrograde pathway that can alter nuclear gene expression during HL and drought stress.
Synaptotagmin IV is necessary for the maturation of secretory granules in PC12 cells

In neuroendocrine PC12 cells, immature secretory granules (ISGs) mature through homotypic fusion and membrane remodeling. We present evidence that the ISG-localized synaptotagmin IV (Syt IV) is involved in ISG maturation. Using an in vitro homotypic fusion assay, we show that the cytoplasmic domain (CD) of Syt IV, but not of Syt I, VII, or IX, inhibits ISG homotypic fusion. Moreover, Syt IV CD binds specifically to ISGs and not to mature secretory granules (MSGs), and Syt IV binds to syntaxin 6, a SNARE protein that is involved in ISG maturation. ISG homotypic fusion was inhibited in vivo by small interfering RNA–mediated depletion of Syt IV. Furthermore, the Syt IV CD, as well as Syt IV depletion, reduces secretogranin II (SgII) processing by prohormone convertase 2 (PC2). PC2 is found mostly in the proform, suggesting that activation of PC2 is also inhibited. Granule formation, and the sorting of SgII and PC2 from the trans-Golgi network into ISGs and MSGs, however, is not affected. We conclude that Syt IV is an essential component for secretory granule maturation.
Recurrent Mossy Fibers Establish Aberrant Kainate Receptor-Operated Synapses on Granule Cells from Epileptic Rats

Glutamatergic mossy fibers of the hippocampus sprout in temporal lobe epilepsy and establish aberrant synapses on granule cells from which they originate. There is currently no evidence for the activation of kainate receptors (KARs) at recurrent mossy fiber synapses in epileptic animals, despite their important role at control mossy fiber synapses. We report that KARs are involved in ongoing glutamatergic transmission in granule cells from chronic epileptic but not control animals. KARs provide a substantial component of glutamatergic activity, because they support half of the non-NMDA receptor-mediated excitatory drive in these cells. KAR-mediated EPSCKAs are selectively generated by recurrent mossy fiber inputs and have a slower kinetics than EPSCAMPA. Therefore, in addition to axonal rewiring, sprouting of mossy fibers induces a shift in the nature of glutamatergic transmission in granule cells that may contribute to the physiopathology of the dentate gyrus in epileptic animals.
Accelerating the Multilayer Perceptron Learning with the Davidon Fletcher Powell Algorithm

In this paper, the Davidon Fletcher Powell (DFP) algorithm for nonlinear least squares is proposed to train multilayer perceptron (MLP). Applied on both a single output layer perceptron and MLP, we find that this algorithm is faster than the Marquardt-Levenberg (ML) algorithm known as the fastest algorithm used to train MLP until now. The number of iterations required by DFP algorithm to converge is less than about 50% of what is required by the ML algorithm. Interpretations of these results are provided in the paper.
Quantitative relations between risk, return and firm size

We analyze —for a large set of stocks comprising four financial indices— the annual logarithmic growth rate R and the firm size, quantified by the market capitalization MC. For the Nasdaq Composite and the New York Stock Exchange Composite we find that the probability density functions of growth rates are Laplace ones in the broad central region, where the standard deviation σ(R), as a measure of risk, decreases with the MC as a power law σ(R)∼(MC)- β. For both the Nasdaq Composite and the S&P 500, we find that the average growth rate ⟨R⟩ decreases faster than σ(R) with MC, implying that the return-to-risk ratio ⟨R⟩/σ(R) also decreases with MC. For the S&P 500, ⟨R⟩ and ⟨R⟩/σ(R) also follow power laws. For a 20-year time horizon, for the Nasdaq Composite we find that σ(R) vs. MC exhibits a functional form called a volatility smile, while for the NYSE Composite, we find power law stability between σ(r) and MC.
Sensitivity of CT colonography for nonpolypoid colorectal lesions interpreted by human readers and with computer-aided detection.

OBJECTIVE The purpose of our study was to determine the sensitivity of CT colonography (CTC) interpreted by human readers and with computer-aided detection (CAD) for genuinely nonpolypoid colorectal lesions, defined as 2 mm or less in lesion height at colonoscopy. MATERIALS AND METHODS A computerized database search for a 33-month period found 21 patients who had undergone both colonoscopy and CTC and who had a total of 23 genuinely nonpolypoid colorectal lesions: eight adenomas (9-30 mm in width), 10 stage Tis or T1 adenocarcinomas (10-25 mm), and five nonadenomatous lesions (8-20 mm). CTC was performed using a cathartic preparation and fecal tagging and was interpreted by experienced readers in a blinded manner using a primary 3D method and with CAD. RESULTS The sensitivities of human readers for nonpolypoid adenomatous lesions (i.e., both adenomas and adenocarcinomas), adenocarcinomas, and nonadenomatous lesions were 66.7% (12/18), 90% (9/10), and 0% (0/5), respectively. Sensitivities were 55.6% (10/18), 90% (9/10), and 0% (0/5) for CAD. A 10-mm stage T1 adenocarcinoma was missed by a human reader on blinded review but was detected with CAD. Both human readers and CAD yielded significantly higher sensitivity for adenomatous lesions than for nonadenomatous lesions (p = 0.014 and 0.046, respectively) and for adenocarcinomas than for noncancerous lesions (p = 0.003 and 0.0001, respectively). CONCLUSION CTC showed a high sensitivity for nonpolypoid stage Tis and T1 adenocarcinomas 10 mm or greater in width despite the limited overall sensitivity for nonpolypoid adenomatous lesions, when performed using cathartic preparation and fecal tagging.
Information geometric analysis of phase transitions in complex patterns: the case of the Gray-Scott reaction–diffusion model

The Fisher–Rao metric from information geometry is related to phase transition phenomena in classical statistical mechanics. Several studies propose to extend the use of information geometry to study more general phase transitions in complex systems. However, it is unclear whether the Fisher–Rao metric does indeed detect these more general transitions, especially in the absence of a statistical model. In this paper we study the transitions between patterns in the Gray-Scott reaction–diffusion model using Fisher information. We describe the system by a probability density function that represents the size distribution of blobs in the patterns and compute its Fisher information with respect to changing the two rate parameters of the underlying model. We estimate the distribution non-parametrically so that we do not assume any statistical model. The resulting Fisher map can be interpreted as a phase-map of the different patterns. Lines with high Fisher information can be considered as boundaries between regions of parameter space where patterns with similar characteristics appear. These lines of high Fisher information can be interpreted as phase transitions between complex patterns.
Estimation of Ambient Air Quality in Delhi

For decades, it has been well known that air pollution causes adverse health effects on humans (Thurston et al., 1989, Shandilya and Khare, 2012). Since the late 1980s, epidemiological studies were published relating the mortality and morbidity to the ambient levels of fine particles without showing the expected results (Borja-Aburto et al., 1997). Most emphasis was then given to the particles with an aerodynamic diameter smaller than 10μm (PM10) particularly to the class of the fine particulates. A special study carried out by United Nations Sources (UNECE, 1979) shows that the frequency of finding a particle of diameter range 2-4m is 27.5%, which is higher in an overall range of 1-12m, so the danger of the fine particulates of diameter ranges 2-4m is higher than the danger by any particle which may lie in the range of 4-12m. Therefore, there is a rising awareness about further fine fraction i.e., particles with an aerodynamic diameter smaller than 2. 5μm (PM2.5). Aerosols, which originate directly from the sources, are termed as “Primary aerosols”. There may be the conversion of gaseous matter into the particulate due to many Physico-Chemical reactions. Such types of particulates are known as “Secondary Aerosols” (Perkins, 1974, Shandilya et al., 2009).