Miracle-dz/UniFAR-FTUs huggingface dataset:
Mutational analysis of RsrA, a zinc‐binding anti‐sigma factor with a thiol–disulphide redox switch

In the Gram‐positive bacterium, Streptomyces coelicolor A3(2), expression of the thioredoxin system is modulated by a sigma factor called σR in response to changes in the cytoplasmic thiol–disulphide status, and the activity of σR is controlled post‐translationally by an anti‐sigma factor, RsrA. In vitro, the anti‐sigma factor activity of RsrA, which contains seven cysteines, correlates with its thiol–disulphide redox status. Here, we investigate the function of RsrA in vivo. A constructed rsrA null mutant had very high constitutive levels of disulphide reductase activity and σR‐dependent transcription, confirming that RsrA is a negative regulator of σR and a key sensor of thiol–disulphide status. Targeted mutagenesis revealed that three of the seven cysteines in RsrA (C11, C41 and C44) were essential for anti‐sigma factor activity and that a mutant RsrA protein containing only these three cysteines was active and still redox sensitive in vivo. We also show that RsrA is a metalloprotein, containing near‐stoichiometric amounts of zinc. On the basis of these data, we propose that a thiol–disulphide redox switch is formed between two of C11, C41 and C44, and that all three residues play an essential role in anti‐sigma factor activity in their reduced state, perhaps by acting as ligands for zinc. Unexpectedly, rsrA null mutants were blocked in sporulation, probably as a consequence of an increase in the level of free σR.
Modern Heterozoan Carbonates from a Eutrophic Tropical Shelf (Mauritania)

Abstract Heterozoan or foramol production is typical in extratropical carbonate sedimentary systems. However, under mesotrophic to eutrophic conditions, heterozoan carbonates also form in tropical settings, but such heterozoan tropical sedimentary systems are poorly understood. Nevertheless, distinction between tropical and extratropical heterozoan carbonates in ancient successions is crucial for accurate paleoenvironmental and paleoclimate reconstructions. Here, surficial Holocene and Pleistocene sediments of the northern Mauritanian shelf are studied as an example of a tropical eutrophic carbonate depositional system (11 μg·L−1 Chl-a [chlorophyll-a]). Upwelling nutrient-rich waters push onto the wide Mauritanian shelf, where they can warm up to in excess of 25°C. This condition favors production of heterozoan carbonates dominated by bivalves and foraminifers, even in this tropical setting. In addition, sediments are provided by eolian input from the desertic hinterland. The resulting sediments are carbonate and mixed carbonate–siliciclastic facies, in which the carbonates are characterized by a mixture of tropical and cosmopolitan taxa. Benthic photosynthetic biota are absent while suspension-feeding organisms are dominant. This foramol grain association on a shelf scale is reminiscent of cool-water carbonates, therefore recognition of warm-water heterozoan carbonates relies on key taxa related to tropical waters within the biota assemblages associated with a highly productive environment.
Some basic stress diffusion solutions for fluid‐saturated elastic porous media with compressible constituents

This is a study of the formulation, some basic solutions, and applications of the Biot linearized quasistatic elasticity theory of fluid-infiltrated porous materials. Whereas most previously solved problems are based on idealizing the fluid and solid constituents as separately incompressible, full account is taken here of constituent compressibility. Previous studies are reviewed and the Biot constitutive equations relating strain and fluid mass content to stress and pore pressure are recast in terms of new material parameters, more directly open to physical interpretation as the Poisson ratio and induced pore pressure coefficient in undrained deformation. Different formulations of the coupled deformation/diffusion field equations and their analogues in coupled thermoelasticity are discussed, and a new formulation with stress and pore pressure as basic variables is presented that leads, for plane problems, to a convenient complex variable representation of solutions. The problems solved include those of the suddenly introduced edge dislocation and concentrated line force and of the suddenly pressurized cylindrical and spherical cavity. The dislocation solution is employed to represent that for quasi-static motions along a shear fault, and a discussion is given, based on fracture mechanics models for fault propagation, of phenomena involving coupled behavior between the rupturing solid and its pore fluid, which could serve to stabilize a fault against rapid spreading. Also, the solution for a pressurized cylindrical cavity leads to a time-dependent stress field near the cavity wall, and its relevance to time effects in the inception of hydraulic fractures from boreholes, or from drilled holes in laboratory specimens, is discussed. Various limiting cases are identified, and numerical values of the controlling porous media elastic parameters are given for several rocks.
Which laboratory variable is related with time trial performance time in the Tour de France?

Objective: To investigate the relationship between several physiological variables that can be easily obtained during cycle ergometer gradual testing (for example, peak power output (Wpeak), Vo2max, or ventilatory threshold (VT)) and actual (>50 km) time trials (TT) time performance during the Tour de France. Methods: We collected data in professional cyclists from the first TT of the 1998 Tour de France (TT1, 58 km distance; n = 6 cyclists) and the first (TT2, 56.5 km; n = 5) and second TT of the 1999 Tour de France (TT3, 57 km; n = 5). Results: A negative relationship was found between power output (W) at VT (VTWatt) and TT final time (s) in TT1 (r = −0.864; p = 0.026; standard error of estimate (SEE) of 73 s; and 95% confidence limits (95% CL) −0.98; −0.18), TT2 (r = −0.77; p = 0.27; SEE of 139 s; and 95% CL −0.98; 0.35), and TT3 (r = −0.923; p = 0.025; SEE of 94 s; and 95% CL −1.00; −0.22). Conclusions: Actual performance in long TT during the Tour de France (>50 km distance, performed after at least 1–2 weeks of continuous competition), in which some cumulative fatigue inevitably occurs, is related, at least in part, to the power output that elicits the VT. No other routine physiological variable (for example, Vo2max or Wpeak) is related to performance in this type of event.
Mirando el Desarrollo Económico de Chile: una Comparación Internacional

This paper examines the relative position of Chile in time and compared with other emerging and industrial economies, through various economic development indicators, particularly over the past two decades. It provides a descriptive analysis, without exploring causalities or testing hypotheses on the economic growth of the country. This analysis reveals the strengths and weaknesses that serve as the base for growth policy discussion. The comparison of economic development indicators shows that Chile is relatively strong in macroeconomic stability, quality of institutions, commercial and financial integration, and in the progress of other structural reforms that are manifested in its well-developed capital market and private sector involvement in production. However, when it comes to quality of education, efforts made in technological innovation, infrastructure quality and quantity, and some social indicators, its performance is poor.
Αlpha-Synuclein as a Mediator in the Interplay between Aging and Parkinson’s Disease

Accumulation and misfolding of the alpha-synuclein protein are core mechanisms in the pathogenesis of Parkinson’s disease. While the normal function of alpha-synuclein is mainly related to the control of vesicular neurotransmission, its pathogenic effects are linked to various cellular functions, which include mitochondrial activity, as well as proteasome and autophagic degradation of proteins. Remarkably, these functions are also affected when the renewal of macromolecules and organelles becomes impaired during the normal aging process. As aging is considered a major risk factor for Parkinson’s disease, it is critical to explore its molecular and cellular implications in the context of the alpha-synuclein pathology. Here, we discuss similarities and differences between normal brain aging and Parkinson’s disease, with a particular emphasis on the nigral dopaminergic neurons, which appear to be selectively vulnerable to the combined effects of alpha-synuclein and aging.
An Empirical Study of Different Approaches for Protein Classification

Many domains would benefit from reliable and efficient systems for automatic protein classification. An area of particular interest in recent studies on automatic protein classification is the exploration of new methods for extracting features from a protein that work well for specific problems. These methods, however, are not generalizable and have proven useful in only a few domains. Our goal is to evaluate several feature extraction approaches for representing proteins by testing them across multiple datasets. Different types of protein representations are evaluated: those starting from the position specific scoring matrix of the proteins (PSSM), those derived from the amino-acid sequence, two matrix representations, and features taken from the 3D tertiary structure of the protein. We also test new variants of proteins descriptors. We develop our system experimentally by comparing and combining different descriptors taken from the protein representations. Each descriptor is used to train a separate support vector machine (SVM), and the results are combined by sum rule. Some stand-alone descriptors work well on some datasets but not on others. Through fusion, the different descriptors provide a performance that works well across all tested datasets, in some cases performing better than the state-of-the-art.
Detection and correction of adjacency effects in hyperspectral airborne data of coastal and inland waters: the use of the near infrared similarity spectrum

A method for the detection and correction of water pixels affected by adjacency effects is presented. The approach is based on the comparison of spectra with the near infrared (NIR) similarity spectrum. Pixels affected by adjacency effects have a water-leaving reflectance spectrum with a different shape to the reference spectrum. This deviation from the similarity spectrum is used as a measure for the adjacency effect. Secondly, the correspondence with the NIR similarity spectrum is used to quantify and to correct for the contribution of the background radiance during atmospheric correction. The advantage of the approach is that it requires no a priori assumptions on the sediment load or related reflectance values in the NIR and can therefore be applied to turbid waters. The approach is tested on hyperspectral airborne data (Compact Airborne Spectrographic Imager (CASI), Airborne Hyperspectral Scanner (AHS)) acquired above coastal and inland waters at different flight altitudes and under varying atmospheric conditions. As the NIR similarity spectrum forms the basis of the approach, the method will fail for water bodies for which this similarity spectrum is no longer valid.
Air Pollution and Cardiovascular Mortality in Kerman from 2006 to 2011

Air pollution is one of the problems in major world cities that endanger the health of the inhabitants of these cities. Air pollution may cause increased death from cardiovascular diseases. This study was carried out in Kerman, Iran. Data about cardiovascular mortality was inquired from the Kerman city Health Authority and air pollution data was inquired from the Kerman Environmental Protection Agency from 2006 to 2011. The concentration of seven pollutants SO2, NO2, O3, CO, PM10, NOX NO, is measured daily in Kerman. The relation between mortality from cardiovascular diseases and air pollution was analyzed by using correlation and negative binomial regression. Statistical analysis showed that the only significant correlation observed was between ozone and female cardiovascular mortality (r = 0.31). With increase in ozone, the number of female cardiovascular deaths increased as well. But in both crude and adjusted negative binomial regression increase in pollutants was not associated with increased incidence of cardiovascular deaths. There was not a significant relation between air pollution and cardiovascular death in Kerman. More studies in cities with higher levels of pollutants are needed to assess the effects of pollutants on cardiovascular mortality.
Statistical French Dependency Parsing: Treebank Conversion and First Results

We first describe the automatic conversion of the French Treebank (Abeillé and Barrier, 2004), a constituency treebank, into typed projective dependency trees. In order to evaluate the overall quality of the resulting dependency treebank, and to quantify the cases where the projectivity constraint leads to wrong dependencies, we compare a subset of the converted treebank to manually validated dependency trees. We then compare the performance of two treebank-trained parsers that output typed dependency parses. The first parser is the MST parser (Mcdonald et al., 2006), which we directly train on dependency trees. The second parser is a combination of the Berkeley parser (Petrov et al., 2006) and a functional role labeler: trained on the original constituency treebank, the Berkeley parser first outputs constituency trees, which are then labeled with functional roles, and then converted into dependency trees. We found that used in combination with a high-accuracy French POS tagger, the MST parser performs a little better for unlabeled dependencies (UAS=90.3% versus 89.6%), and better for labeled dependencies (LAS=87.6% versus 85.6%).
Initial investigation of signal capture techniques for objective measurement of spatial impression considering head movement

In a previous study it was discovered that listeners normally make head movements attempting to evaluate source width and envelopment as well as source location. To accommodate this finding in the development of an objective measurement model for spatial impression, two capturing models were introduced and designed in this research, based on binaural technique: 1) rotating Head And Torso Simulator (HATS), and 2) a sphere with multiple microphones. As an initial study, measurements of interaural time difference (ITD), level difference (ILD) and cross-correlation coefficient (IACC) made with the HATS were compared with those made with a sphere containing two microphones. The magnitude of the differences was judged in a perceptually relevant manner by comparing them with the just-noticeable differences (JNDs) of these parameters. The results showed that the differences were generally not negligible, implying the necessity of enhancement of the sphere model, possibly by introducing equivalents of the pinnae or torso. An exception was the case of IACC, where the reference of JND specification affected the perceptual significance of its difference between the two models.
Wild-Type ApoA-I and the Milano Variant Have Similar Abilities to Stimulate Cellular Lipid Mobilization and Efflux

Objective—The present study is a comparative investigation of cellular lipid mobilization and efflux to lipid-free human apoA-I and apoA-IMilano, reconstituted high-density lipoprotein (rHDL) particles containing these proteins and serum isolated from mice expressing human apoA-I or apoA-IMilano. Methods and Results—Cholesterol and phospholipid efflux to these acceptors was measured in cell systems designed to assess the contributions of ATP-binding cassette A1 (ABCA1), scavenger receptor type BI (SRBI), and cellular lipid content to cholesterol and phospholipid efflux. Acceptors containing the Milano variant of apoA-I showed no functional increase in lipid efflux in all assays when compared with wild-type apoA-I. In fact, in some systems, acceptors containing the Milano variant of apoA-I promoted significantly less efflux than the acceptors containing wild-type apoA-I (apoA-Iwt). Additionally, intracellular cholesteryl ester hydrolysis in macrophage foam cells was not different in the presence of either apoA-IMilano or apoA-Iwt. Conclusion—Collectively these studies suggest that if the Milano variant of apoA-I offers greater atheroprotection than wild-type apoA-I, it is not attributable to greater cellular lipid mobilization.
Primary Magmas at the Volcanic Front of the NE Japan Arc: Coeval Eruption of Crustal Low-K Tholeiitic and Mantle-derived Medium-K Calc-Alkaline Basalts at Azuma Volcano

It has long been thought that the low-K tholeiitic (TH) and medium-K calc-alkaline (CA) lavas in the NEJapan arc were produced by fractional crystallization from mantle-derived basalt magmas, and that the latter formed from mixing of mafic and felsic magmas, both derived from a common primaryTH basalt through fractionation. An alternative view was recently proposed on the basis of Sr isotope microanalysis of plagioclase phenocrysts from the Zao volcano, suggesting that (1) the low-K TH basaltic andesites formed by melting of lower crustal amphibolite and that (2) the medium-K CA basalts to andesites formed by mixing of mantle-derived basalt and crustal TH melts.To investigate further the origin of the ‘primary’ low-K TH and medium-K CA basalts, we investigated basalts and andesites from Azuma volcano. Azuma is a Quaternary eruption center at the volcanic front in the NE Japan arc that has erupted two types of basalt: (1) radiogenic-Sr (Sr/ Sr1⁄4 0·7058^0·7062) low-K TH basalt lavas without evidence of magma mixing and assimilation; (2) unradiogenic-Sr (Sr/Sr1⁄4 0·7039^0·7041) medium-K CA basalt lavas with subtle evidence for magma mixing. Associated intermediate lavas are voluminous and are all (3) mildly radiogenic-Sr (Sr/ Sr1⁄4 0·7044^0·7055) medium-K andesites, all of which have CA affinities with evidence for rigorous magma mixing but no crustal assimilation. The low-K TH basalt has an isotopic composition similar to that of crustal granitoids beneath Azuma and has a composition indicating that it potentially formed from a high-degree lower crustal amphibolite melt.The medium-KCA basalt has a basaltic groundmass with Mg-rich olivine (Fo89) and calcic plagioclase phenocrysts (An90) and the most unradiogenic Sr (Sr/ Sr1⁄4 0·7037^0·7038), suggesting that it originated from a primary mantle melt. Major and trace element microanalysis of the basaltic groundmass indicates that the primary magma composition is close to high-K. We conclude that the mantle-derived basalt at Azuma is the result of a highto medium-K magma that was later mixed with a low-K TH basalt melt from the amphibolitic lower crust to form medium-K CA basalts and andesites. This supports the view of a lower crustal origin of the low-KTH basalts and simultaneously requires a reappraisal of the origin of the across-arc variation in K contents of the mantle-derived primary arc basalts, as the highto medium-K CA basalt is geochemically fairly similar to the high-K rear-arc basalt in the NE Japan arc.
Clonal Origin of Metastatic Testicular Teratomas

Purpose: Testicular teratomas in adult patients are histologically diverse tumors that frequently coexist with other germ cell tumor (GCT) components. These mixed GCTs often metastasize to retroperitoneal lymph nodes where multiple GCT elements are frequently present in the same metastatic lesion. Neither the genetic relationships among the different components in metastatic lesions nor the relationships between primary and metastatic GCT components have been elucidated. Experimental Design: We examined metastases from 31 patients who underwent primary retroperitoneal lymph node dissection for metastatic testicular GCT. All patients had metastatic mature teratoma with one or more other GCT components. This study included a total of 72 metastatic GCT components and 16 primary GCT components from 31 patients. Genomic DNA samples from each component were prepared from formalin-fixed, paraffin-embedded tissue sections using laser-assisted microdissection. Loss of heterozygosity (LOH) assays for seven microsatellite polymorphic markers on chromosomes 1p36 (D1S1646), 9p21 (D9S171 and IFNA), 9q21 (D9S303), 13q22-q31 (D13S317), 18q22 (D18S543), and 18q21 (D18S60) were done to assess clonality. Results: Twenty-nine of 31 (94%) cases showed allelic loss in one or more components of the metastatic GCTs. Twenty-nine of 31 mature teratomas showed allelic loss in at least one of seven microsatellite polymorphic markers analyzed. The frequency of allelic loss in informative cases of metastatic mature teratoma was 27% (8 of 30) with D1S1646, 34% (10 of 29) with D9S171, 37% (10 of 27) with IFNA, 27% (8 of 30) with D9S303, 46% (13 of 28) with D13S317, 26% (7 of 27) with D18S543, and 36% (10 of 28) with D18S60. Completely concordant allelic loss patterns between the mature teratoma and all of the other metastatic GCT components were seen in 26 of 29 cases in which the mature teratoma component showed LOH. Nearly identical allelic loss patterns were seen in the three remaining cases. In six cases analyzed, LOH patterns of each metastatic component were compared with each GCT component of the primary testicular tumor. In all six cases, each primary and metastatic component showed an identical pattern of allelic loss. Conclusion: Our data support the common clonal origin of metastatic mature teratomas with other components of metastatic testicular GCTs and with each component of the primary tumor.
“My Curiosity was Satisfied, but not in a Good Way”: Predicting User Ratings for Online Recipes

In this paper, we develop an approach to automatically predict user ratings for recipes at Epicurious.com, based on the recipes’ reviews. We investigate two distributional methods for feature selection, Information Gain and Bi-Normal Separation; we also compare distributionally selected features to linguistically motivated features and two types of frameworks: a one-layer system where we aggregate all reviews and predict the rating vs. a two-layer system where ratings of individual reviews are predicted and then aggregated. We obtain our best results by using the two-layer architecture, in combination with 5 000 features selected by Information Gain. This setup reaches an overall accuracy of 65.60%, given an upper bound of 82.57%.
The January 30, 1989 Arctic polar stratospheric clouds (PSC) event - Evidence for a mechanism of dehydration

In-situ particle measurements made aboard the NASA ER-2 in the Arctic on 890130 (YYMMDD) show Type 1 PSC particles over much of the flight, with instances of embedded Type 2 PSCs. The Type 2 particles were observed at temperatures warmer than the local frost-point temperature of water; extended up to the upper size cutoff of the instrument ({approximately}24 {mu}m diameter); and are shown to contain too large a volume to be primarily NAT. Based on measured vertical temperature profiles, the authors conclude that the Type 2 particles observed on this day were formed above the aircraft in a region where saturation with respect to ice was achieved and were sufficiently large to have fallen into the path of the ER-2. Although, the amount of material in the particles, expressed as water, is small by comparison to the total (vapor + aerosol) water concentration, the flux of water from the falling particles is of sufficient magnitude, if sustained, to lead to dehydration of the source region. These observations verify the mechanism for dehydration of polar vortex air masses by precipitation of ice particles.