Miracle-dz/UniFAR-FTUs huggingface dataset:
Chromatin determinants impart camptothecin sensitivity

Camptothecin‐induced locking of topoisomerase 1 on DNA generates a physical barrier to replication fork progression and creates topological stress. By allowing replisome rotation, absence of the Tof1/Csm3 complex promotes the conversion of impending topological stress to DNA catenation and causes camptothecin hypersensitivity. Through synthetic viability screening, we discovered that histone H4 K16 deacetylation drives the sensitivity of yeast cells to camptothecin and that inactivation of this pathway by mutating H4 K16 or the genes SIR1‐4 suppresses much of the hypersensitivity of tof1∆ strains towards this agent. We show that disruption of rDNA or telomeric silencing does not mediate camptothecin resistance but that disruption of Sir1‐dependent chromatin domains is sufficient to suppress camptothecin sensitivity in wild‐type and tof1∆ cells. We suggest that topoisomerase 1 inhibition in proximity of these domains causes topological stress that leads to DNA hypercatenation, especially in the absence of the Tof1/Csm3 complex. Finally, we provide evidence of the evolutionarily conservation of this mechanism.
Four Decades of Progress in Monitoring and Modeling of Processes in the Soil-Plant- Atmosphere System: Applications and Challenges Wireless Sensor Network deployment for monitoring soil moisture dynamics at the field scale

We describe the deployment of a Wireless Sensor Network (WSN), composed of 135 soil moisture and 27 temperature sensors, in an apple tree orchard of about 5000 m 2 , located in the municipality of Cles, a small town in the Alpine region, northeastern Italy. The orchard is divided into three parcels each one subjected to a different irrigation schedule. The objective of the present work is to monitor soil moisture dynamics in the top soil to a detail, in both space and time, suitable to analyze the interplay between soil moisture dynamics and plant physiology. The deployment consists of 27 locations (verticals) connected by a multi hop WSN, each one equipped with 5 soil moisture sensors deployed at the depths of 10, 20, 30, 50 and 80 cm, and a temperature sensor at the depth of 20 cm. The proposed monitoring system is based on totally independent sensor nodes, which allow both real time and historic data management and are connected through an input/output interface to a WSN platform. Meteorological data are monitored by a weather station located at a distance of approximately 100 m from the experimental site. Great care has been posed to calibration of the capacitance sensors, both in the laboratory, with soil samples, and on site, after deployment, in order to minimize the noise caused by small oscillations in the input voltage and uncertainty in the calibrat * ion curves. In this work we report the results of a preliminary analysis on the data collected during the growing season 2009. We observed that the WSN greatly facilitates the collection of detailed measurements of soil moisture, thereby increasing the amount of information useful for exploring hydrological processes, but they should be used with care since the accuracy of collected data depends critically on the capability of the system to maintain constant the input voltage and on the reliability of calibration curves. Finally, we studied the spatial and temporal distribution of soil moisture in all the irrigated parcels, and explored how different irrigation schedules influence
High-pressure melting of carbonaceous chondrite

Phase equilibria of carbonaceous chondrite and phase density relations at high pressure govern a simple model for solidification of an initially molten chondritic Earth. The solidification can be described by differentiation stages, each characterized by a particular, experimentally predicted, petrologic process that dominates the distribution of chemical components during a specific evolution interval. The stages, though expressed here as discrete events for simplicity, may actually be overlapping segments in the cooling and crystallization continuum of Earth formation. We focus on five important differentiation stages of a chondritic Earth in the following chronological order: (1) sulfide liquid-silicate liquid immiscibility leading to protocore formation; (2) magnesiowustite fractionation at the base of the early mantle; (3) perovskite flotation and fractionation in the midmantle; (4) olivine flotation in the shallow mantle; and (5) garnet flotation in the prototransition zone. Compositional layering produced by the five experimentally predicted differentiation stages obeys mass balance and is consistent with a shallow mantle source for peridotite xenoliths, a transition zone rich in garnet at ∼540 km, a lower mantle with a superchondritic Si/Mg, and a core of Fe-Ni-S-O.
Aqua{6,6′-dimethoxy-2,2′-[ethane-1,2-diylbis(nitrilomethylidyne)]diphenolato}(4-hydroxybenzoato)manganese(III)

The title compound, [Mn(C18H18N2O4)(C7H5O3)(H2O)], was synthesized by a template reaction of ethane-1,2-diamine and 3-methoxysalicylaldehyde in presence of manganese(II) 4-hydroxybenzoate. The Jahn–Teller-distorted manganese(III) centre has an octahedral geometry. Extensive O—H⋯O hydrogen-bonding interactions generate a two-dimensional sheet structure parallel to (103).
Songbird communities in a pyrogenic habitat mosaic

Wildfires play a key role in shaping the boreal forest landscape, yet the response of wildlife to the patchy mosaics they create is poorly understood. We studied songbirds 5–6 years post-fire in a large burn (9600 ha) in the boreal mixed wood forest of north-eastern Alberta. In the spring of 1995 and 1996 we estimated abundance of songbirds in four areas, each with four replicate sites: unburned patches within the fire (Isolates); burned patches (Burns); patches that had been clear-cut prior to burning by wildfire (Cut-Burns); and the unburned, continuous forest adjacent to the burn (Peripherals). We also sampled shrub-based arthropods with sweep-nets at each site. To investigate the role of Isolates, we compared them to Peripherals and to Burns. We compared Cut-Burns to Burns to examine the effect of logging prior to burning. In general, Isolates supported higher numbers of species and individuals than Peripherals, mainly due to higher numbers of aerial-foraging birds. Isolates and Burns had similar species richness and abundance, but Burns supported more aerial foragers while Isolates had more foliage gleaners. Cut-Burns generally supported fewer individuals than Burns, in particular fewer shrub-nesters, aerial foragers, and neotropical migrants. More bird species reached their highest densities in Burns than in any other area. Songbird species richness and abundance were positively related to dry arthropod biomass, with Burns and Isolates having the highest arthropod biomass. These patterns indicated that, 5–6 years post-burn, the patchy mosaic created by this wildfire supported more species than the mature forest surrounding the fire. Clear-cut logging prior to burning resulted in a diminished songbird community compared to that found in burned stands.
Prospects for Advancing Tuberculosis Control Efforts through Novel Therapies

Background Development of new, effective, and affordable tuberculosis (TB) therapies has been identified as a critical priority for global TB control. As new candidates emerge from the global TB drug pipeline, the potential impacts of novel, shorter regimens on TB incidence and mortality have not yet been examined. Methods and Findings We used a mathematical model of TB to evaluate the expected benefits of shortening the duration of effective chemotherapy for active pulmonary TB. First, we considered general relationships between treatment duration and TB dynamics. Next, as a specific example, we calibrated the model to reflect the current situation in the South-East Asia region. We found that even with continued and rapid progress in scaling up the World Health Organization's DOTS strategy of directly observed, short-course chemotherapy, the benefits of reducing treatment duration would be substantial. Compared to a baseline of continuing DOTS coverage at current levels, and with currently available tools, a 2-mo regimen introduced by 2012 could prevent around 20% (range 13%–28%) of new cases and 25% (range 19%–29%) of TB deaths in South-East Asia between 2012 and 2030. If effective treatment with existing drugs expands rapidly, overall incremental benefits of shorter regimens would be lower, but would remain considerable (13% [range 8%–19%] and 19% [range 15%–23%] reductions in incidence and mortality, respectively, between 2012 and 2030). A ten-year delay in the introduction of new drugs would erase nearly three-fourths of the total expected benefits in this region through 2030. Conclusions The introduction of new, shorter treatment regimens could dramatically accelerate the reductions in TB incidence and mortality that are expected under current regimens—with up to 2- or 3-fold increases in rates of decline if shorter regimens are accompanied by enhanced case detection. Continued progress in reducing the global TB burden will require a balanced approach to pursuing new technologies while promoting wider implementation of proven strategies.
The NAC-like gene ANTHER INDEHISCENCE FACTOR acts as a repressor that controls anther dehiscence by regulating genes in the jasmonate biosynthesis pathway in Arabidopsis

ANTHER INDEHISCENCE FACTOR (AIF), a NAC-like gene, was identified in Arabidopsis. In AIF:GUS flowers, β-glucuronidase (GUS) activity was detected in the anther, the upper parts of the filaments, and in the pollen of stage 7–9 young flower buds; GUS activity was reduced in mature flowers. Yellow fluorescent protein (YFP)+AIF-C fusion proteins, which lacked a transmembrane domain, accumulated in the nuclei of the Arabidopsis cells, whereas the YFP+AIF fusion proteins accumulated in the membrane and were absent in the nuclei. Further detection of a cleaved AIF protein in flowers revealed that AIF needs to be processed and released from the endoplasmic reticulum in order to function. The ectopic expression of AIF-C caused a male-sterile phenotype with indehiscent anthers throughout flower development in Arabidopsis. The presence of a repressor domain in AIF and the similar phenotype of indehiscent anthers in AIF-C+SRDX plants suggest that AIF acts as a repressor. The defect in anther dehiscence was due to the down-regulation of genes that participate in jasmonic acid (JA) biosynthesis, such as DAD1/AOS/AOC3/OPR3/OPCL1. The external application of JA rescued the anther indehiscence in AIF-C and AIF-C+SRDX flowers. In AIF-C+VP16 plants, which are transgenic dominant-negative mutants in which AIF is converted to a potent activator via fusion to a VP16-AD motif, the anther dehiscence was promoted, and the expression of DAD1/AOS/AOC3/OPR3/OPCL1 was up-regulated. Furthermore, the suppression of AIF through an antisense strategy resulted in a mutant phenotype similar to that observed in the AIF-C+VP16 flowers. The present data suggest a role for AIF in controlling anther dehiscence by suppressing the expression of JA biosynthesis genes in Arabidopsis.
Effect of soluble Jagged1-mediated inhibition of Notch signaling on proliferation and differentiation of an adipocyte progenitor cell model

Adipose tissue development is dependent on multiple signaling mechanisms and cell-cell interactions that regulate adipogenesis, angiogenesis and extracellular remodeling. The Notch signaling pathway is an important cell-fate determinant whose role in adipogenesis is not clearly defined. To address this issue, we examined the effect of inhibition of Notch signaling by soluble-Jagged1 in the 3T3-L1 preadipocyte line. In vitro, soluble-Jagged1 expression in 3T3-L1 cells altered cell morphology, increased the rate of cell proliferation and induced an early transcriptional response to differentiation stimuli. However, these cells did not form mature adipocytes due to their inability to exit the cell-cycle in response to serum-starvation and glucocorticoid-induced cell-cycle arrest. In contrast, subcutaneous allografts of soluble-Jagged1 cells formed larger fat pads containing lipid-filled adipocytes with improved neovascularization compared with controls. Since adipogenesis is tightly associated with angiogenesis, we evaluated the influence of soluble-Jagged1 on endothelial cells by culturing them in cell-free conditioned media from preadipocytes. Soluble Jagged1-mediated inhibition of Notch signaling increased levels of secreted cytokines, potentially contributing to the improved cell growth and proliferation observed in these cultures. Our findings demonstrate an initial requirement of Notch signaling inactivation for preadipocyte cell commitment and support the hypothesis that cell-to-cell crosstalk between the preadipocytes and endothelial cells is required for neovascularization and remodeling of the tissue to promote hyperplasia and hypertrophy of differentiating adipocytes.
Optimal locations for absolute gravity measurements and sensitivity of GRACE observations for constraining glacial isostatic adjustment on the northern hemisphere

SUMMARY Gravity rate of change is an important quantity in the investigation of glacial isostatic adjustment (GIA). However, measurements with absolute and relative gravimeters are laborious and time-consuming, especially in the vast GIA-affected regions of high latitudes with insufficient infrastructure. Results of the Gravity Recovery And Climate Experiment (GRACE) satellite mission have thus provided tremendous new insight as they fully cover those areas. To better constrain the GIA model (i.e. improve the glaciation history and Earth parameters) with new gravity data, we analyse the currently determined errors in gravity rate of change from absolute gravity (AG) and GRACE measurements in North America and Fennoscandia to test their sensitivity for different ice models, lithospheric thickness, background viscosity and lateral mantle viscosity variations. We provide detailed sensitivity maps for these four parameters and highlight areas that need more AG measurements to further improve our understanding of GIA. The best detectable parameter with both methods in both regions is the sensitivity to ice model changes, which covers large areas in the sensitivity maps. Also, most of these areas are isolated from sensitive areas of the other three parameters. The latter mainly overlap with ice model sensitivity and each other. Regarding existing AG stations, more stations are strongly needed in northwestern and Arctic Canada. In contrast, a quite dense network of stations already exists in Fennoscandia. With an extension to a few sites in northwestern Russia, a complete station network is provided to study the GIA parameters. The data of dense networks would yield a comprehensive picture of gravity change, which can be further used for studies of the Earth’s interior and geodynamic processes.
The 2010 slow slip event and secular motion at Kı̄lauea, Hawai‵i, inferred from TerraSAR‐X InSAR data

We present here a small baseline subset (SBAS) algorithm to extract both transient and secular ground deformations on the order of millimeters in the presence of tropospheric noise on the order of centimeters, when the transient is of short duration and known time and the background deformation is smooth in time. We applied this algorithm to study the 2010 slow slip event as well as the secular motion of Kı̄lauea's south flank using 49 TerraSAR‐X images. We also estimate the tropospheric delay variation relative to a given reference pixel using an interferometric synthetic aperture radar (InSAR) SBAS approach. We compare the InSAR SBAS solution for both ground deformation and tropospheric delays with existing GPS measurements and confirm that the ground deformation signal and tropospheric noise in InSAR data are successfully separated. We observe that the coastal region on the south side of the Hilina Pali moves at a higher background rate than the region north side of the Pali. We also conclude that the 2010 slow slip event (SSE) displacement is mainly horizontal and the maximum magnitude of the 2010 SSE vertical component is less than 5 mm.
Global surface wave phase velocity variations

Global Love and Rayleigh wave phase velocity variations from 85 to 250 s are determined using about 30,000 seismograms from earthquakes with M ≥ 6.0. The phases used are G1, R1, G2, and R2 arrivals. The data were obtained from the Chinese Digital Seismic Network, GEOSCOPE, and Global Seismic Network archives for the time period January 1980 to June 1992. All seismograms underwent careful quality control in the time and frequency domains. We consider the inversion damping and model parameterization issues, examining the data statistics and assuming that errors in data and model spaces are Gaussian random distributions with zero mean. It is not stable to invert for a model with resolution higher than about spherical harmonic degree, l = 22, given the path sampling and scatter of our data set, and the low frequency data only warrant expansion up to about l = 12. We find that a block model parameterization, with its local basis functions, has fewer artifacts than a high order spherical harmonic inversion which must be heavily damped. However, spherical harmonic functions provide intrinsically superior recovery of the long-wavelength structure. Our final models involve a hybrid parameterization, in which an initial iteration retrieves the low order spherical harmonic components that are used as an aspherical reference model for performing a final block model inversion. The optimal block size decreases with frequency. This approach exploits the separate attributes of global and local basis functions for resolving different components of the heterogeneity, allows for variable resolution for different frequencies, and provides a natural framework for embedding localized high resolution regional inversions into the global model. We perform inversions both with and without corrections for shallow crustal structure. At the shorter periods the phase velocity maps strongly reflect the surface tectonics, correlating with continental shields, mid-ocean ridges, and tectonically active areas. The tectonic correlation diminishes gradually with period.
2-Isopropyl-6-methyl-4-oxo-3,4-dihydropyrimidin-1-ium 2-carboxy-4,6-dinitrophenolate monohydrate

In the title molecular salt, C8H13N2O+·C7H3N2O7 −·H2O, the pyrimidinium cation is essentially planar, with a maximum deviation of 0.009 (1) Å. The cation undergoes an enol–keto tautomerism during the crystallization. In the crystal, the ion pairs and water molecules are connected via O—H⋯O, N—H⋯O and C—H⋯O hydrogen bonds, forming two-dimensional networks parallel to the bc plane. There is an intramolecular O—H⋯O hydrogen bond in the 3,5-dinitrosalicylate anion, which generates an S(6) ring motif.
Trends in Global and Basin-Scale Runoff over the Late Twentieth Century: Methodological Issues and Sources of Uncertainty

AbstractWhile human influence has been detected in global and regional surface air temperature, detection–attribution studies of direct (i.e., land use and water management) and indirect (i.e., climate related) effects of human activities on land surface hydrology remain a crucial and controversial issue. In the present study, a set of global offline hydrological simulations is performed during the 1960–94 period using the Interactions between Soil, Biosphere, and Atmosphere–Total Runoff Integrating Pathways (ISBA-TRIP) modeling system. In contrast to previous numerical sensitivity studies, the model captures the observed trend in river runoff over most continents without including land use changes and/or biophysical CO2 effects, at least when the comparison is made over 154 large rivers with a minimum amount of missing data. The main exception is northern Asia, where the simulated runoff trend is negative, in line with the prescribed precipitation forcing but in contrast with the observed runoff trend. T.
Hypoxia and Ischemia Promote a Maladaptive Platelet Phenotype

Objective— Reduced blood flow and tissue oxygen tension conditions result from thrombotic and vascular diseases such as myocardial infarction, stroke, and peripheral vascular disease. It is largely assumed that while platelet activation is increased by an acute vascular event, chronic vascular inflammation, and ischemia, the platelet activation pathways and responses are not themselves changed by the disease process. We, therefore, sought to determine whether the platelet phenotype is altered by hypoxic and ischemic conditions. Approach and Results— In a cohort of patients with metabolic and peripheral artery disease, platelet activity was enhanced, and inhibition with oral antiplatelet agents was impaired compared with platelets from control subjects, suggesting a difference in platelet phenotype caused by the disease. Isolated murine and human platelets exposed to reduced oxygen (hypoxia chamber, 5% O2) had increased expression of some proteins that augment platelet activation compared with platelets in normoxic conditions (21% O2). Using a murine model of critical limb ischemia, platelet activity was increased even 2 weeks postsurgery compared with sham surgery mice. This effect was partly inhibited in platelet-specific ERK5 (extracellular regulated protein kinase 5) knockout mice. Conclusions— These findings suggest that ischemic disease changes the platelet phenotype and alters platelet agonist responses because of changes in the expression of signal transduction pathway proteins. Platelet phenotype and function should, therefore, be better characterized in ischemic and hypoxic diseases to understand the benefits and limitations of antiplatelet therapy.
On the Distribution of Climate Change Resulting from an Increase in CO2 Content of the Atmosphere

Abstract A study of the climatic effect of doubling or quadrupling of CO2 in the atmosphere has been continued by the use of a simple general circulation model with a limited computational domain, highly idealized geography, no seasonal variation of insolation, and a simplified interaction between cloud and radiative transfer. The results from the numerical experiments reveal that the response of the model climate to an increase of CO2 content in air is far from uniform geographically. For example, one can identify the high-latitude region of the continent where the runoff rate increases markedly, a zonal belt of decreasing soil moisture around 42° latitude, and a zone of enhanced wetness along the east coast of the subtropical portion of the model continent. The general warming and the increase of moisture content of air, which results from a CO2 increase, contributes to the large reduction of the meridional temperature gradient in the lower model troposphere because of 1) poleward retreat of highly refl.