Miracle-dz/UniFAR-FTUs huggingface dataset:
Vegetation Structure and Soil Properties in Ecuadorian Páramo Grasslands with Different Histories of Burning and Grazing

High-altitude grasslands in the north Andes (páramos) are subject to frequent fires that are usually set by farmers to support traditional cattle-raising systems. Apparently, this practice has caused dramatic changes in the structure and composition of native vegetation, but the mechanisms, magnitude, and direction of these changes still need to be documented for a broader range of conditions. This paper describes the differences in selected soil properties, ground cover, grass tussock structure, and populations of giant Andean rosettes (Espeletia pycnophylla) in four páramo sites in northwestern Ecuador, characterized by contrasting patterns of burning and grazing. The only differences between the soil properties of the sites were the higher pH in the least disturbed site, and the high concentration of P in the more recently burned site. Along the sequence of least impacted to most impacted sites, we observed a decrease in grass tussock cover, and an increase in the amount of bare ground and number of fragments per tussock. In the most undisturbed site tussock coverage was extremely low due to the dominance of shrubs. The density of giant Andean rosettes was higher in the sites with intermediate disturbance regimes, while the mortality of adult stem rosettes was significantly higher at the more recently burned site. The significance of these differences is discussed in the context of the regeneration of páramo vegetation after burning and grazing disturbance.
Homologous recombination-deficient cancers: approaches to improve treatment and patient selection

HR is required to maintain genomic integrity 9 , 12–14 . In line with this notion, homozygous loss of Brca1 or Brca2 leads to the accumulation of DNA breaks and results in activation of p53, which promotes cell cycle arrest and activation of apoptosis and senescence programs 15–18 . As a result, BRCA1 or BRCA2 loss is not tolerated during human or mouse development and leads to embryonic lethality 9,12–14 . Importantly, Brca1 and Brca2 are not only essential in the context of development but also deletion of these genes severely impacts proliferation in vitro, indicating that BRCA1 and BRCA2 are intrinsically essential to cellular viability 12,14,15 In clear contrast, loss of BRCA1 or BRCA2 is tolerated in breast and ovarian cancers affected by BRCA1 or BRCA2 mutations. It remains incompletely understood how these tumor cells remain viable, despite their continuous accumulation of DNA Abstract Loss of BRCA2 affects genome stability and is deleterious for cellular survival. Using a genome-wide genetic screen in near-haploid KBM-7 cells, we show that tumor necrosis factor-alpha (TNFα) signaling is a determinant of cell survival upon BRCA2 inactivation. Specifically, inactivation of the TNF receptor (TNFR1) or its downstream effector SAM68 rescues cell death induced by BRCA2 inactivation. BRCA2 inactivation leads to proinflammatory cytokine production, including TNFα, and increases sensitivity to TNFα. Enhanced TNFα sensitivity is not restricted to BRCA2 inactivation, as BRCA1 or FANCD2 inactivation, or hydroxyurea treatment also sensitizes cells to TNFα. Mechanistically, BRCA2 inactivation leads to cGAS-positive micronuclei and results in a cell-intrinsic interferon response, as assessed by quantitative mass-spectrometry and gene expression profiling, and requires ASK1 and JNK signaling. Combined, our data reveal that micronuclei induced by loss of BRCA2 instigate a cGAS/STING-mediated interferon response, which encompasses rewired TNFα signaling and enhances TNFα
On How Differently the Quasi-harmonic Approximation Works for Two Isostructural Crystals: Thermal Properties of MgO and CaO.

Harmonic and quasi-harmonic thermal properties of two isostructural simple oxides (periclase, MgO, and lime, CaO) are computed with ab initio periodic simulations based on the density-functional-theory (DFT). The more polarizable character of calcium with respect to magnesium cations is found to dramatically aﬀect the validity domain of the quasi-harmonic approximation that, for thermal structural properties (such as temperature dependence of volume, V ( T ), bulk modulus, K ( T ) and thermal expansion coeﬃcient, α ( T )), reduces from [0 K - 1000 K] for MgO to just [0 K - 100 K] for CaO. On the contrary, Thermodynamic properties (such as entropy, S ( T ), and constant-volume speciﬁc heat, C V ( T )) are described reliably at least up to 2000 K and quasi-harmonic constant-pressure speciﬁc heat, C P ( T ) up to about 1000 K in both cases. The eﬀect of the adopted approximation to the exchange-correlation functional of the DFT is here explicitly investigated by considering ﬁve diﬀerent expressions of three diﬀerent classes (local-density approximation, generalized-gradient approximation and hybrids). Computed harmonic thermodynamic properties are found to be almost independent of the adopted functional, whereas quasi-harmonic structural properties are largely aﬀected by the choice of the functional, with diﬀerences that increase as the system becomes softer.
THE PRIVATE SECTOR, URBAN WATER CONSERVATION AND DEVELOPING COUNTRIES: A STAKEHOLDER THEORY-DRIVEN PERSPECTIVE FROM BOTSWANA

ABSTRACT Botswana is a semi-arid and water scarce country with a fast growing urban population. The private sector is an important actor for the urban economy to remain functional and competitive. This has to be supported by adequate water for all sectors of the economy. The contribution of private sector companies in Botswana, whose activities are water dependent to urban water conservation efforts have not been fully documented. This study set out to determine this role. It was found that most companies recognise that water in Botswana is scarce, and some have their own voluntary internal conservation schemes. However, these individual water conservation initiatives are not recognised and incorporated into the wider urban water management system in Botswana.
The thermal state and internal structure of Mars

The evolution and state of the interior of Mars are studied through the use of theoretically calculated thermal history and density models. These models satisfy the constraints of mean density, moment of inertia, and recent volcanism implied by the Mariner 9 photographs. Invoking melting of an Fe-FeS mixture permits initial core formation within the first billion years. At the present time the core radius ranges from about 1300 to 1800 km, depending on composition, and the core is liquid even if the composition is varied from the eutectic. Large-scale differentiation of the silicates occurs in the last 2 b.y. When the mean density is 3.96 g/cm3, the radius is 3389 km, and the moment of inertia factor is 0.377, the density models indicate high mantle densities near 3.74 g/cm3. Thus an FeO content of about 29% is implied, consistent with the production of a low-viscosity magma. Chemical models of the Martian mantle indicate a composition primarily of olivine with about 56% forsterite. In terms of evolutionary history, Mars is probably intermediate between the moon and the earth, its peak of activity being passed in the last billion years.
Relationships between thunderstorms and cloud-to-ground lightning in the United States

Abstract Data from networks of lightning sensors operated during 198689 were employed to perform climatic assessments of cloud-to-ground (CG) flashes, and of the relationship between CG flashes and thunder events, as reported at 62 first-order stations. The average annual CG flash pattern resembles the nation's thunderstorm pattern, with lightning being most frequent at points in the southeast United States (>18 000 flashes in Florida) and least frequent at West Cost stations (< 100 flashes). Flashes in the intermontane area are relatively less than thunderstorms, and greater than 50% of all thunder events there are due to intracloud lightning. An anomalous high in CG frequencies exists from Virginia to New York. Cluster analysis identified ten regions of similar storm activity with several reflecting localized influence (Great Lakes, Florida, the Piedmont, and Arizona). Thunder events provide poor estimates of CG lightning incidence and durations. Cloud-to-ground flash data reveal that 20% (far West) an.
Scatterometer observations of wind variations induced by oceanic islands: Implications for wind-driven ocean circulation

Scatterometer data at 25-km resolution are used to investigate the effects of the Hawaiian and Cabo Verde islands on the mean atmospheric flow. A wake of weak winds, flanked by accelerated winds, appears for each major island of both archipelagos. The resulting wind stress curl displays dipole-like structures, with positive values on the northern side and negative values on the southern side of the lee, extending several island diameters downwind. These curl anomalies reach a magnitude of 2 10‐6 Pa·m‐1 and correspond to Ekman pumping velocities of 3 m·day‐1 for Hawaii and 4 m·day‐1 for Cabo Verde. They spin up cyclonic eddies on the north side and anticyclonic eddies on the south side of the lee of each island. The response of the ocean circulation is investigated using a simple Sverdrup balance. Two counter-rotating Sverdrup gyres are spun up west of the island of Hawaii and extend to the western boundary of the Pacific Ocean. They result in an eastward zonal transport confined between 19° and 20°N. East of 170°W, the surface expression of this transport coincides with the Hawaiian Lee Counter Current. Similar gyres are anticipated to form in the Atlantic Ocean, but remain to be observed. These results suggest that strong mesoscale patterns in the wind field occurring in the lee of high-topography features must be resolved to force global ocean circulation models.
“Bettering Data”: The Role of Everyday Language and Visualization in Critical Novice Data Work

Informed by critical data literacy efforts to promote social justice, this paper uses qualitative methods and data collected during two years of workplace ethnography to characterize the notion of critical novice data work. Specifically, we analyze everyday language used by novice data workers at DataWorks, an organization that trains and employs historically excluded populations to work with community data sets. We also characterize challenges faced by these workers in both cleaning and being critical of data during a project focused on police-community relations. Finally, we highlight novel approaches to visualizing data the workers developed during this project, derived from data cleaning and everyday experience. Findings and discussion highlight the generative power of everyday language and visualization for critical novice data work, as well as challenges and opportunities to foster critical data literacy with novice data workers in the workplace.
Observations of Kelvin‐Helmholtz instability at a cloud base with the middle and upper atmosphere (MU) and weather radars

[1] Using the very high frequency (46.5 MHz) middle and upper atmosphere radar (MUR), Ka band (35 GHz) and X band (9.8 GHz) weather radars, a Kelvin-Helmholtz (KH) instability occurring at a cloud base and its impact on modulating cloud bottom altitudes are described by a case study on 8 October 2008 at the Shigaraki MU Observatory, Japan (34.85°N, 136.10°E). KH braids were monitored by the MUR along the slope of a cloud base gradually rising with time around an altitude of ∼5.0 km. The KH braids had a horizontal wavelength of about 3.6 km and maximum crest-to-trough amplitude of about 1.6 km. Nearly monochromatic and out of phase vertical air motion oscillations exceeding ±3 m s−1 with a period of ∼3 min 20 s were measured by the MUR above and below the cloud base. The axes of the billows were at right angles of the wind and wind shear both oriented east-north-east at their altitude. The isotropy of the radar echoes and the large variance of Doppler velocity in the KH billows (including the braids) indicate the presence of strong turbulence at the Bragg (∼3.2 m) scale. After the passage of the cloud system, the KH waves rapidly damped and the vertical scale of the KH braids progressively decreased down to about 100 m before their disappearance. The radar observations suggest that the interface between clear air and cloud was conducive to the presence of the dynamical shear instability by reducing static stability (and then the Richardson number) near the cloud base. Downward cloudy protuberances detected by the Ka band radar had vertical and horizontal scales of about 0.6–1.1 and 3.2 km, respectively, and were clearly associated with the downward air motions. Observed oscillations of the reflectivity-weighted Doppler velocity measured by the X band radar indicate that falling ice particles underwent the vertical wind motions generated by the KH instability to form the protuberances. The protuberances at the cloud base might be either KH billow clouds or perhaps some sort of mamma. Reflectivity-weighted particle fall velocity computed from Doppler velocities measured by the X band radar and the MUR showed an average value of 1.3 ms−1 within the cloud and in the protuberance environment.
Ecological factors acting on the microfauna in mangrove swamps. The case of foraminiferal assemblages in French Guiana

Abstract Thirty-seven surface sediment samples were collected in January 1999 and July 2000 in the mangrove swamps and mud flats of French Guiana where strong seasonal contrasts occur. Sampling stations were selected to provide information on the foraminiferal assemblages associated with different environmental conditions, on the mud banks and in the mangrove forest. A total of 44 species have been identified. The main parameter acting on the distribution of foraminiferal assemblages is the hydrodynamics of the estuary, characterized by the double influence of coastal water and low-Ca fresh water, with drastic seasonal changes. The coastal end member is dominated by the calcareous species Ammonia tepida, A. parkinsoniana andCribroelphidium spp. , the continental (freshwater) end member is characterized by Miliammina fusca andTrochamminita irregularis . The calcareous species penetrate into the estuary, even into the mangrove forest during the dry season, but totally disappear from the estuary during the rainy season. The second parameter acting on the distribution of foraminiferal assemblages is the vertical elevation that acts indirectly by influencing the time of aerial exposure and the colonization by mangrove trees. Both canopy and litter of the mangrove forest protect the sediment from heating, drying and increases in salinity due to sun and wind. Foraminifera are very rare or absent on the open mud banks affected by mud cracks, but begin to grow as soon as young Avicennia are present. In the mangrove swamps, local conditions influence the composition of the assemblages and the taphonomic processes.
Climatic patterns revealed by pollen and oxygen isotope records across the Matuyama-Brunhes Boundary in the central Mediterranean (southern Italy)

Abstract A c. 50 m thick section located in the Crotone Basin (southern Italy) was investigated using oxygen isotopes, pollen and planktonic foraminifera. The section records two complete transgressive-regressive cycles mainly driven by glacio-eustasy. Biostratigraphy and oxygen isotope chronology indicate that the section spans from Marine Isotope Stage (MIS) 22 (c. 0.87 Ma) to MIS 18.3 (c. 0.73 Ma), thus straddling the Matuyama-Brunhes (M-B) boundary which occurs in the middle of MIS 19. The rich pollen assemblages provide a unique record of the vegetation in the central Mediterranean during the Early-Middle Pleistocene climatic transition. Interglacials are characterized by a mesothermic vegetation similar to the present day, whereas a rain-demanding conifer forest dominates the glacials of MIS 20 and MIS 18. This is unexpected because it is generally considered that during the Pleistocene, glacials in central Mediterranean were characterized by steppe (arid) conditions. By contrast, arid conditions occur during the deglaciations. These results are inconsistent with the widespread practice of linking glacials with arid conditions in the central Mediterranean during Pliocene and Early Pleistocene times. This study emphasizes the need to establish more accurate land-sea correlation.
Microscopic fringe projection system and measuring method

Microscopic fringe projection method based on fringe projection and microscopic imaging was proposed to measure the 3D profile of micro-components, which is fast, accurate and non-contact. The measurement system includes two sets of microscope tubes: one for projecting fringe, and the other for imaging. The sinusoidal fringes generated by the software were projected onto the tested object through the DLP projector. The deformed fringes were captured by the CCD camera. The five-step phase shifting method was used for the phase extraction, and the branch cut algorithm was applied for the phase unwrapping process. After system calibration, a coin was measured to show the applicability of the system.
ElectroEncephaloGraphy robust statistical linear modelling using a single weight per trial

Being able to remove or weigh down the influence of outlier data is desirable for any statistical models. While Magnetic and ElectroEncephaloGraphic (MEEG) data are often averaged across trials per condition, it is becoming common practice to use information from all trials to build statistical linear models. Individual trials can, however, have considerable weight and thus bias inferential results (effect sizes as well as thresholded t/F/p maps). Here, rather than looking for univariate outliers, defined independently at each measurement point, we apply the principal component projection (PCP) method at each channel, deriving a single weight per trial at each channel independently. Using both synthetic data and open EEG data, we show (1) that PCP is efficient at detecting a large variety of outlying trials; (2) how PCP-based weights can be implemented in the context of the general linear model (GLM) with accurate control of type 1 family-wise error rate; and (3) that our PCP-based Weighted Least Square (WLS) approach increases the statistical power of group analyses as well as a much slower Iterative Reweighted Least Squares (IRLS), although the weighting scheme is markedly different. Together, our results show that WLS based on PCP weights derived from whole trial profiles is an efficient method to weigh down the influence of outlier EEG data in linear models. Data availability all data used are publicly available (CC0), all code (simulations and data analyzes) is also available online in the LIMO MEEG GitHub repository (MIT license).
Number of winter precipitation days reconstructed from southwestern tree rings

Abstract The potential of reconstructing the number of winter precipitation days from tree-rings in the southwestern United States is explored in this study. This variable, an alternative to the measure of total precipitation, has not previously been used in dendroclimatic reconstructions. However, it may be a more meaningful measure of seasonal rainfall and indicator of anomalies in atmospheric circulation features than total precipitation in areas such as the arid Southwest, where the distribution of rainfall is spatially variable. The number of precipitation days in the region encompassing southwestern New Mexico and southeastern Arizona was reconstructed for the time period 1702–1983 from a collection of tree-ring chronologies in this area. Results from this study show that tree-ring chronologies explain 71% of the variance in the regional record of the number of precipitation days. The reconstruction is statistically verified and validated with independent data. Tree-ring chronologies in this region .
The Pangenome of Pseudomonas aeruginosa

This review summarizes the most important reports about Pseudomonas aeruginosa pangenome. Pan-genomics has tackled some fundamental concerns in pathogenic bacteria. PATRIC and other databases, store more than 9000 P. aeruginosa genomes. This data mining is an opportunity to develop discoveries related to antibiotic resistance, virulence, pathogenicity, fitness, and evolution, among others. Observing the different pangenomes of P. aeruginosa, it is concluded that this species has an open pangenome, and its accessory genome is larger than the central genome. HGT is one important source for P. aeruginosa genome. In recent years various authors developed P. aeruginosa pangenomes, from works with five genomes to more than 1300 genomes. This last work analyzed 54,272 genes, and they found a short and tiny core genome (only 665 genes). Other research with lesser strains or genomes identified a core genome bigger, almost 20% of the pangenome. Nevertheless, the total work proves that the accessory plus unique genome is larger than the core genome in P. aeruginosa.
Sensitivity of Cloud Liquid Water Content Estimates to the Temperature-Dependent Thermodynamic Phase: A Global Study Using CloudSat Data

AbstractThe main purpose of this study is to underline the sensitivity of cloud liquid water content (LWC) estimates purely to 1) the shape of computationally simplified temperature-dependent thermodynamic phase and 2) the range of subzero temperatures covered to partition total cloud condensate into liquid and ice fractions. Linear, quadratic, or sigmoid-shaped functions for subfreezing temperatures (down to −20° or −40°C) are often used in climate models and reanalysis datasets for partitioning total condensate. The global vertical profiles of clouds obtained from CloudSat for the 4-yr period June 2006–May 2010 are used for sensitivity analysis and the quantitative estimates of sensitivities based on these realistic cloud profiles are provided. It is found that three cloud regimes in particular—convective clouds in the tropics, low-level clouds in the northern high latitudes, and middle-level clouds over the midlatitudes and Southern Ocean—are most sensitive to assumptions on thermodynamic phase. In the.
Prediction of Sediment Concentration in Rivers by Recursive Least-Squares and Linear Minimum Variance Estimators

AbstractPeaks of suspended sediment concentration in rivers appear before peak discharge appears. The observation of discharge is usually done in many rivers for river management, but the suspended sediment concentration is not always observed. The suspended sediment concentration is expressed by a sediment-rating curve over a long period of time. Coefficients in the sediment-rating curve are time varying. The time variation of the suspended sediment concentration is predicted by the sediment-rating curve with the recursive least-squares and the linear minimum variance estimators. Because the sediment-rating curve is linearized by the logarithmic transformation, we can apply the simple linear models such as recursive least-squares and linear minimum variance estimators for the prediction of the suspended sediment concentration. These methods indicate that the coefficients in the sediment-rating curve are time varying. These methods can estimate sediment discharge by identifying the coefficients in the sed.