Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome-wide Analysis of the Response to Cell Wall Mutations in the Yeast Saccharomyces cerevisiae*

Perturbations of the yeast cell wall trigger a repair mechanism that reconfigures its molecular structure to preserve cell integrity. To investigate this mechanism, we compared the global gene expression in five mutant strains, each bearing a mutation (i.e. fks1, kre6, mnn9, gas1, and knr4 mutants) that affects in a different manner the cell wall construction. Altogether, 300 responsive genes were kept based on high stringency criteria during data processing. Functional classification of these differentially expressed genes showed a substantial subset of induced genes involved in cell wall construction and an enrichment of metabolic, energy generation, and cell defense categories, whereas families of genes belonging to transcription, protein synthesis, and cellular growth were underrepresented. Clustering methods isolated a single group of ∼80 up-regulated genes that could be considered as the stereotypical transcriptional response of the cell wall compensatory mechanism. The in silico analysis of the DNA upstream region of these co-regulated genes revealed pairwise combinations of DNA-binding sites for transcriptional factors implicated in stress and heat shock responses (Msn2/4p and Hsf1p) with Rlm1p and Swi4p, two PKC1-regulated transcription factors involved in the activation genes related to cell wall biogenesis and G1/S transition. Moreover, this computational analysis also uncovered the 6-bp 5′-AGCCTC-3′ CDRE (calcineurin-dependent response element) motif in 40% of the co-regulated genes. This motif was recently shown to be the DNA binding site for Crz1p, the major effector of calcineurin-regulated gene expression in yeast. Taken altogether, the data presented here lead to the conclusion that the cell wall compensatory mechanism, as triggered by cell wall mutations, integrates three major regulatory systems: namely the PKC1-SLT2 mitogen-activated protein kinase-signaling module, the “global stress” response mediated by Msn2/4p, and the Ca2+/calcineurin-dependent pathway. The relative importance of these regulatory systems in the cell wall compensatory mechanism is discussed.
Analysis of models for induced gas flow in the unsaturated zone

Accurate description of induced gas flow in an unsaturated zone is indispensable for characterizing the unsaturated zone. Hantush's approximation and a finite difference approximation of the leakage term are frequently employed in modeling the induced gas flow in an unsaturated zone underlying a leaky confining layer. However, no studies have been conducted on the errors that result from these approximations. This study presents a physically more rigorous model based on mass conservation in both the upper leaky confining layer and the lower permeable layer (the unsaturated zone). Flow in the upper layer is assumed to be vertical, and in the lower layer, it is two‐dimensionally axisymmetric, with gas pressure and flux continuity at the interface of the two layers. A new steady state solution for a well with a finite radius and two new transient solutions for a well with an infinitely small radius and with a finite radius are developed for this rigorous model. In addition, another new transient solution is derived using the finite difference approximation of the leakage term for the same problem. The developed solutions are compared with previous approximate solutions. Results indicate that Hantush's approximation overestimates the gas pressure at shallower depths and underestimates it at deeper depths under the condition of gas injection. This error changes with the hydrogeological parameters and well configurations. The finite difference approximation works reasonably well under the usual field conditions. Neglecting the well radius for a small radius well does not induce much error.
Seismic Hazard Analysis for Kuala Lumpur, Malaysia

In the past, probabilistic seismic hazard analysis (PSHA) has been performed by researchers to assess the level of seismic hazard in Kuala Lumpur, Malaysia and its vicinity. However, the peak ground acceleration (PGA) values obtained are high due to unsuitable ground motion prediction equation (GMPE). This article is divided into two parts: development of a suitable GMPE and the PSHA for this region. Two main sources have been identified as the contributors to earthquake hazard in Peninsular Malaysia, namely the Sumatra strike-slip fault and Sumatra subduction zone. For the subduction zone, nine recorded large earthquake events are analyzed and regression analysis is performed to obtain a new GMPE for this region. In performing PSHA, the strike-slip fault is divided into 14 zones based on the individual fault segments, while the subduction is divided into 4 zones. Historical earthquakes of this region are collected, processed, and segregated according to the zones. PSHA has been conducted by modeling the source seismicity using Gutenberg-Richter and characteristic earthquake models. The developed GMPE has been used along with other attenuation models: Megawati and Pan [2010] and component attenuation model (CAM) by Balendra et al. [2002] for subduction; and Sadigh et al. [1997] and CAM for strike-slip fault. The peak ground accelerations in Kuala Lumpur for 10% and 2% probability of exceedances in 50 years are found to be 16.5 gal and 23.4 gal, respectively. From deaggregation analysis, the main contributor for the 10% probability of exceedance in 50 years is found to be a 7.5 Mw earthquake at 300 km, originating from the strike slip fault. Finally, the design response spectrum for Kuala Lumpur is developed for rock sites, which would be amplified further by local soil profile.
Separating the thermal fingerprints of lava flows and simultaneous lava fountaining using ground‐based thermal camera and SEVIRI measurements

During effusive eruptions, thermal satellite monitoring has proved well suited to map the thermal flux from lava flows. However, during lava fountaining events, thermal contributions from active flows and from the fountain itself cannot be separated in low resolution satellite data. Here using photogrammetry and atmospheric modeling techniques, we compare radiance estimates from long‐range ground‐based thermal camera data (from which the fountain can be excluded) with those from SEVIRI satellite images for a fountaining event at Mount Etna (12 August 2011). The radiant heat flux determined from the ground‐based camera showed similar behavior to values retrieved from Spinning Enhanced Visible and Infrared Imager (SEVIRI); thus the SEVIRI signal is interpreted to be dominated by the lava flows, with minimal contribution from the fountain. Furthermore, by modeling the cooling phase of each pixel inundated by lava, the mean thickness and lava volume (~2.4 × 106 m3) derived from camera images are comparable with those calculated from SEVIRI (~2.8 × 106 m3).
VARIATIONS IN CALDERA DEVELOPMENT IN THE TERTIARY VOLCANIC FIELD

Calderas, 4–30 km in diameter, are the major igneous centers of Trans-Pecos Texas. Twelve calderas occur in two north-northwest-trending belts. Eight, including two in adjacent Chihuahua, occur in a western alkali-calcic belt. Four are in an eastern alkalic belt. Additional calderas are probably associated with two major ash-flow sheets in the eastern belt. Sources exist for all major tuffs of Trans-Pecos, other than these two, so additional calderas are unlikely. All calderas were formed between 38 and 28 Ma ago. The two calderas in Chihuahua were formed 30 and 28 Ma ago and show significant differences in composition and eruptive style from the earlier calderas. Calderas are underlain by individual magma chambers that were active for no more than about 1 Ma. The caldera cycle in Texas is highly variable. Minor volcanism commonly occurred before ash-flow tuff eruption and caldera collapse. Tumescence occurred in at most two calderas. Ash-flow eruption and collapse were simultaneous in all calderas, as shown by thick, intracaldera tuffs that are interbedded with breccias shed from caldera walls. Collapse occurred along discrete fracture systems in most of the western calderas but along hinge zones in the eastern calderas and at least part of the two young calderas in Chihuahua. Sedimentation within calderas was minor. Preresurgent volcanism ranged from minor to extensive and was best developed in the western calderas, all of which show some form of resurgence. No eastern calderas were resurgent. Resurgence is expressed in many ways in western calderas, but only a few fit the classic model. Ring-fracture volcanism was irregularly developed. Hydrothermal alteration and ore deposition were abundant and spatially and genetically related to calderas in the western alkali-calcic belt. Alteration and ore deposition were minor to nonexistent in the eastern alkalic belt.
Evidence of impacts from rising temperature on inflows to the Murray‐Darling Basin

The 2001–2007 Australian drought was the hottest on record with inflows to Australia's longest river system, the Murray‐Darling, reaching an historical low. Here we examine the relative importance of rising temperature and decreasing rainfall over its catchment, the Murray Darling Basin (MDB). Although annual‐total inflow is more sensitive to rainfall over the southern MDB, where rainfall since 2001, has been the lowest on record, this alone can not explain the observed inflow decline. A relationship exists between inflow variations and fluctuations of temperature not associated with rainfall in the austral winter and spring: a rise of 1°C leads to an approximate 15% reduction in the climatological annual inflow. Our results provide strong evidence that rising temperatures due to the enhanced greenhouse effect have a strong impact on southern Australia's water resources, in addition to any reduction in rainfall, and project a long‐term decline in inflows to this river system as the greenhouse effect continues.
Experimental investigation of shock metamorphic effects in a metapelitic granulite: The importance of shock impedance contrast between components

Shock recovery experiments were performed at 12.5, 25, 34, 40, and 56 GPa at 25 °C, and at 18 and 25 GPa at 400 °C, on a high‐grade, migmatitic, garnet‐cordierite metapelite from the Etivé aureole, Scotland. Objectives for this study were to (1) characterize shock effects in a complex polymineralic rock with a significant proportion of hydrous ferromagnesian minerals, both as a function of variable shock pressure and preshock temperature, and (2) to explore the effects of shock impedance contrast between component minerals on the respective abundances and distribution of these features. At any shock pressure, the order of decreasing intensity of shock metamorphic effects in component phases is: cordierite (Crd)→biotite (Bt)→plagioclase (Pl)→K‐feldspar (Kfs)→quartz (Qtz)→garnet (Grt)→orthopyroxene (Opx). Samples shocked to pressures below 40 GPa (25 °C) were typically characterized by marked heterogeneous distribution of shock effects on both intragranular and intergranular scales. Shock heterogeneity is mainly attributed to shock impedance contrast between contiguous phases, and manifests as shock amplification locally where shock impedance contrast is greatest, and shock suppression where impedance contrast is least. The heterogeneous distribution of shock metamorphic effects in both experiments and natural rocks is a signature of extreme disequilibrium at the submillimeter scale. The heterogeneous distribution of shock metamorphic effects mitigates against the use of shock effects in minerals exclusively as regional shock pressure barometers, and ought to be augmented by additional constraints on shock pressure from numerical models.
Regulation of photosynthetic activity of crop species subjected to abiotic environmental stresses

This thesis aimed to study regulations of photosynthetic activity of plants under two of the most important abiotic stresses: water stress and salt stress. We mainly focused on the physiological and biochemical mechanisms that regulate growth and productivity under limiting conditions, in order to acquire a better understanding of the complex defense responses of plants to environmental abiotic stresses, which represent the greatest global constraints for agriculture. In order to tackle such broad aim, an integrated approach was necessary. This study was carried out on some specific crops with the peculiar purpose to test cultivars that are tolerant to drought or salinity used under harsh environments. Although abiotic stresses have been largely studied for tomato, pepper and grape species, the specific behavior of many local and typical cultivars and landraces to cope with drought and salinity problems is still new. Hence, the general aim of this work was pursued through three main experimental activities, illustrated in chapters 2-4. Chapter 2 focuses on two typical long-storage tomato landraces grown in greenhouse under extreme (gs< 0.01mol m-2 s-1) water stress conditions ; chapter 3 focuses on two pepper cultivars - grown in a soilless system differently behaving under severe (15.6 dS m-1) long-term salt stress conditions; chapter 4 focuses on a wine grape cultivar, typical in Southern Italy, grown in two soils with contrasting hydrological properties for retaining water.
Constraints on Cumulus Parameterization from Simulations of Observed MJO Events

AbstractTwo recent activities offer an opportunity to test general circulation model (GCM) convection and its interaction with large-scale dynamics for observed Madden–Julian oscillation (MJO) events. This study evaluates the sensitivity of the Goddard Institute for Space Studies (GISS) GCM to entrainment, rain evaporation, downdrafts, and cold pools. Single Column Model versions that restrict weakly entraining convection produce the most realistic dependence of convection depth on column water vapor (CWV) during the Atmospheric Radiation Measurement MJO Investigation Experiment at Gan Island. Differences among models are primarily at intermediate CWV where the transition from shallow to deeper convection occurs. GCM 20-day hindcasts during the Year of Tropical Convection that best capture the shallow–deep transition also produce strong MJOs, with significant predictability compared to Tropical Rainfall Measuring Mission data. The dry anomaly east of the disturbance on hindcast day 1 is a good predictor o.
Post-socialist urban growth of Bucharest, Romania – a change detection analysis on Landsat imagery (1984–2010)

In this study, Bucharest, the capital city of Romania was selected as a case study. Based on time series of Landsat TM imagery and statistical data, an analysis on urban growth from 1984 to 2010 was performed, using an integrated approach of remote sensing and GIS techniques. The land cover data were validated by CORINE Land Cover maps. The results revealed that rapid urban growth of the Bucharest region led to accelerated land use conversion from cropland to built-up land. The processes of deindustrialization in the core city and industrialization to the ring road represent other driving factors for spatiotemporal pattern of built-up land. The paper will discuss these processes and their impact on economic growth and residential suburbanization of the studied region.
Altered mineral uptake into fresh arc magmas: insights from U–Th isotopes of samples from Andean volcanoes under differential crustal stress regimes

Abstract Uranium–thorium (U–Th) isotope compositions of whole rocks, groundmasses and minerals from mafic to intermediate Andean arc magmas were determined to assess the influence of crustal stress on rates of pre-eruptive crystallization and the significance of crystal uptake. Volcanoes investigated include Lascar in the central Andes, situated in a compressional regime, and Callaqui and Lonquimay in the southern Andes, situated in a transtensional regime. In the southern Andes, Calbuco volcano, which experienced variations in the local stress field due to volcano unloading triggered by large debris avalanches, was also targeted. In U–Th equiline space, whole rock and groundmass coincide in each studied sample, and are close to secular equilibrium or in slight U-excess. No isochronal relationships are displayed by the mineral separates, although many are out of secular equilibrium. Further, (234U/238U) activity ratios of some mineral separates from the southern Andes are in disequilibrium and vary significantly between different phases of individual rock samples. The combined data indicate that many crystals are foreign to the melts they are carried in, and that some mineral phases have experienced incipient weathering before their incorporation into the melt. Using Calbuco as an example, we speculate that volcano loading may affect secondary alteration processes at depth.
Tree Matching Problems with Applications to Structured Text Databases

A venturi scrubber for the scrubbing of an inlet gas stream with a scrubbing liquid or slurry, to remove gaseous or vaporous components from the gas stream, or to remove entrained solid particulate or discrete liquid droplet (fog or mist) constituents, and thereby to prevent air pollution and/or to recover the component or constituent. The venturi scrubber has an adjustable throat characterized by the provision of structure to adjust the cross-sectional dimension of the gas passage at or adjacent to the throat section. The structure includes at least one movable baffle at the periphery of the gas passage, and a container. The container is disposed external to and contiguous with the baffle, and a controlled amount of a fluid is passed into the container so that the internal fluid pressure within the container, and resultant volumetric dimension of the container, and thereby also the resultant displacement of the baffle relative to the periphery of the throat section, are adjustable in proportion to a change in the flow rate of the inlet gas stream.
Welfare state expenditures and the redistribution of well-being: Children, elders, and others in comparative perspective

This paper describes the size, nature, and redistributive effects of welfare state expenditures in ten advanced industrialized nations and relates these differences across nations to disparities in the economic well-being of country populations as a whole and three (mutually exclusive and exhaustive) sub-groups: children (and their families); elders; and childless adult households. Data from the Organization for Economic Cooperation and Development (OECD) are used to describe differences in the size and nature of welfare states. The OECD health, welfare and education benefits data are combined with micro data on household incomes from the Luxembourg Income Study (LIS) to assess their distribution and finance across the income distribution in ten countries. The results indicate a wide range of differences in levels of economic resources and support, within as well as between, nations and groups. Counting in kind benefits at government cost substantially reduces cross national differences in market and cash disposable incomes, but does not eliminate them. But the results are very sensitive to how inkind benefits, especially health insurance, are measured and valued and call into question the extra-ordinarily high US expenditures on health care.
Les formes fluviales d’une rivière en gorge, le Chassezac (Cévennes, France)

La dynamique fluviale des vallees en gorge du rebord cevenol du Massif central est encore mal connue. L’etude des formations alluviales periglaciaires et actuelles dans le bassin du Chassezac (Cevennes) permet de retracer l’evolution des talwegs depuis la derniere periode froide. On peut ainsi montrer qu’on est passe d’un lit wurmien remblaye et caracterise par des ecoulements tres competents et une dynamique de tressage a un fond de gorge ou alternent des secteurs rocheux et des bancs caillouteux qui traduisent un deficit sedimentaire. La repartition longitudinale de ces formes alluviales, infeodee a celle des vestiges periglaciaires comme leur composition granulometrique tres grossiere, pose le probleme de la mobilite de la charge de fond actuelle. L’etude lichenometrique des unites alluviales permet de determiner la relation liant la taille des particules aux puissances specifiques necessaires a leur mise en mouvement. On peut alors prolonger la courbe enveloppe de la mobilite pour des blocs dont le diametre est compris entre 100 cm et 230 cm, valeurs absentes de la litterature jusqu’ici, et montrer en meme temps que seuls les debits exceptionnels (superieurs a 2 500 m3/s) sont morphogenes a l’Holocene.
Gypsum facies transitions in basin-marginal evaporites: middle Miocene (Badenian) of west Ukraine

In the middle Miocene Badenian gypsum basin of the Carpathian Foredeep, west Ukraine, three main zones of gypsum development occur in the peripheral parts of the basin. Zone I consists entirely of stromatolitic gypsum formed in a nearshore zone. Zone II is located more basinward and is characterized by stromatolitic gypsum in the lower part of the section, overlain by a sabre gypsum unit. Zone III occurs in still more basinward areas and is characterized by giant gypsum intergrowths (or secondary nodular gypsum pseudomorphs of these) in the lowermost part, overlain by stromatolitic gypsum, sabre gypsum and then by clastic gypsum units. Correlation between these facies and zones has been achieved using lithological marker beds and surfaces. Of particular importance for correlation is a characteristic marker bed (usually 20–40 cm thick) of cryptocrystalline massive gypsum occurring in zones II and III. The marker was not distinguished in zone I, possibly because this bed is older than the entire gypsum section of that zone. These new results strongly suggest that the deposition of giant gypsum intergrowth facies and stromatolitic gypsum facies was coeval. In some sections of zones I and II, limestone intercalations have been recorded within the upper part of the gypsum sections. Considerable scatter of the δ18O and δ13C values of these limestones indicates variable diagenetic overprints of marine carbonates, but a marine provenance of the limestones is confirmed by microfacies analysis. Some of the limestones are coeval with an intercalation of gypsarenitic, mostly laminated gypsum occurring in the sabre gypsum unit of zones II and III. Badenian gypsum formed in extremely shallow-water to subaerial environments on broad, very low relief areas of negligible brine depth, which could be affected by rapid transgressions. Stable isotope (δ34S, δ18O) studies of the gypsum demonstrate that the sulphate was of sea-water origin or was derived from dissolution of Miocene marine evaporites. Investigations of individual inclusions in the gypsum indicate decreased water salinity when compared with modern marine-derived, calcium sulphate-saturated water. Groundwater influences are indicated by high calcium sulphate contents of the brines in the evaporite basin. The chemical composition of Badenian waters was thus a mixture of relic sea water (depleted in NaCl), groundwater (enriched in calcium sulphate) and surface run-off.
Turbulent bottom Ekman boundary layer measured over a continental shelf

An acoustic Doppler current profiler was deployed in summer and autumn in 2007–2009 at two stations on the East China Sea shelf. Clear velocity spirals that basically correspond to theoretical Ekman spirals were identified for both mean and tidal currents. From these spirals and the corresponding Ekman equation, we estimated the time‐averaged eddy viscosity (μ) profiles. The estimated μ was largest (2–3 × 10−3 m2 s−1) around 5 m from the bottom and decreased almost exponentially with height. A qualitatively similar profile of the eddy diffusivity was also inferred from the acoustic Doppler current profiler data and microstructure profiler data. The flux Richardson number was estimated as 0.11 ± 0.10 ∼ 0.46 ± 0.17, indicating relatively large buoyancy contribution to the turbulent kinetic energy budget.