Miracle-dz/UniFAR-FTUs huggingface dataset:
Visualizing dynamic competence pili and DNA capture throughout the long axis of Bacillus subtilis

ABSTRACT The first step in the process of bacterial natural transformation is DNA capture. Although long hypothesized based on genetics and functional experiments, the pilus structure responsible for initial DNA binding had not yet been visualized for Bacillus subtilis. Here, we visualize functional competence pili in Bacillus subtilis using fluorophore-conjugated maleimide labeling in conjunction with epifluorescence microscopy. In strains that produce pilin monomers within tenfold of wild-type levels, the median length of detectable pili is 300 nm. These pili are retractile and associate with DNA. The analysis of pilus distribution at the cell surface reveals that they are predominantly located along the long axis of the cell. The distribution is consistent with localization of proteins associated with subsequent transformation steps, DNA binding, and DNA translocation in the cytosol. These data suggest a distributed model for B. subtilis transformation machinery, in which initial steps of DNA capture occur throughout the long axis of the cell and subsequent steps may also occur away from the cell poles. IMPORTANCE This work provides novel visual evidence for DNA translocation across the cell wall during Bacillus subtilis natural competence, an essential step in the natural transformation process. Our data demonstrate the existence of natural competence-associated retractile pili that can bind exogenous DNA. Furthermore, we show that pilus biogenesis occurs throughout the cell long axis. These data strongly support DNA translocation occurring all along the lateral cell wall during natural competence, wherein pili are produced, bind to free DNA in the extracellular space, and finally retract to pull the bound DNA through the gap in the cell wall created during pilus biogenesis. This work provides novel visual evidence for DNA translocation across the cell wall during Bacillus subtilis natural competence, an essential step in the natural transformation process. Our data demonstrate the existence of natural competence-associated retractile pili that can bind exogenous DNA. Furthermore, we show that pilus biogenesis occurs throughout the cell long axis. These data strongly support DNA translocation occurring all along the lateral cell wall during natural competence, wherein pili are produced, bind to free DNA in the extracellular space, and finally retract to pull the bound DNA through the gap in the cell wall created during pilus biogenesis.
Validation of rain/no-rain threshold value of cloud liquid water for microwave precipitation retrieval algorithm using CloudSat precipitation product

The rain/no-rain threshold value of cloud liquid water (CLW) is important for the microwave precipitation retrieval algorithms. In our previous study, we proposed a parameterization of rain/no-rain threshold value of CLW as a function of storm height for Global Satellite Mapping of Precipitation (GSMaP) algorithm. In this study, we determine rain/norain threshold value of CLW using CloudSat precipitation product and the cloud liquid water derived from Aqua/AMSRE. The threshold values of CLW from CloudSat precipitation product are lower than 0.5 kg m-2 for GSMaP over all regions. The threshold value of CLW is found at its peak in the Tropics and decreases poleward. The threshold value of cloud liquid water contents computed from threshold value of CLW divided by the zonal mean storm height from PR3A25 is employed on the parameterization of threshold value of CLW. The result shows that GSMaP with new parameterization can detect the shallow rain observed by CloudSat.
Monitoring selective logging in tropical evergreen forests using Landsat: Multitemporal regional analyses in Mato Grosso, Brazil

Abstract Selective logging degrades tropical forests. Logging operations vary in timing, location, and intensity. Evidence of this land use is rapidly obscured by forest regeneration and ongoing deforestation. A detailed study of selective logging operations was conducted near Sinop, State of Mato Grosso, Brazil, one of the key Amazonian logging centers. An 11-yr series of annual Lansdat images (1992–2002) was used to detect and track logged forests across the landscape. A semiautomated method was applied and compared to both visual interpretation and field data. Although visual detection provided precise delineation of some logged areas, it missed many areas. The semiautomated technique provided the best estimates of logging extent that are largely independent of potential user bias. Multitemporal analyses allowed the authors to analyze the annual variations in logging and deforestation, as well as the interaction between them. It is shown that, because of both rapid regrowth and deforestation, evidence .
Parameter estimation of hydraulic properties from one‐step outflow data

The one-step outflow method was presented by Kool et al. (1985a, b) as a fast procedure to estimate unsaturated soil hydraulic properties. Many investigators, however, encountered difficulties obtaining a unique solution to the problem. The purpose of this paper is to evaluate some of the problems related to this method by looking at response surfaces and to make recommendations for improvements in the methodology. The one-step outflow procedure was investigated using synthetic data sets generated for 7.6-cm-diameter by 7.6-cm-high soil cores. A finite difference solution of Richards' equation was used to generate the synthetic data sets. Response surfaces were calculated for the van Genuchten parameters α, n, and Ks for various combinations of matric potential, water content, and outflow data from initially saturated soil cores subjected to a step change in pressure at one of its boundaries. The results clearly show that with outflow data alone, the parameter estimation procedure will have difficulty converging. However, if matric potential data are available for a point in the core at some distance from the outflow boundary, parameter estimation sensitivity is greatly improved. The procedure used was found to be most helpful for determining which auxiliary variables should be measured for parameter estimation from outflow experiments.
Formation of a very thin current sheet in the near-earth magnetotail and the explosive growth phase of substorms

A magnetofrictional method is used to construct two-dimensional MHD equilibria of the Earth's magnetosphere for a given distribution of entropy function (S = pVγ), where p is the plasma pressure and V is the tube volume per unit magnetic flux. It is found that a very thin current sheet with Bz < 0.5nT and thickness < 1000km can be formed in the near-earth magnetotail (x ∼ −8 to −20 Re) during the growth phase of substorm. The tail current sheets are found to become thinner as the entropy or the entropy gradient increases. We suggest that the new “entropy anti-diffusion instability” associated with plasma transport across field lines leads to magnetic field dipolarization and accelerates the formation of thin current sheet, which may explain the observed explosive growth phase of substorms.
Laterally loaded piles in sand: slope effect on P-Y reaction curves

An extensive program of centrifuge tests was undertaken to study the effect of slopes on P-Y curves in dry sand. The paper concerns the method developed in a previous series of centrifuge tests to experimentally determine P-Y curves. Bending-moment curves are fitted by local quintic spline functions through a crossed validation method and then differentiated twice. These experimental P-Y curves are validated by back analysis. The program of tests on piles near slopes is given. It includes studies of the effect of distance to the slope, slope angle, and soil properties. Sample preparation method, model piles, and the lateral-loading device are described. Deflection versus load curves, bending-moment curves, and derived P-Y curves for piles close to slopes are compared to horizontal-ground response. The coefficients that can apply to the P-Y reaction curves of the reference piles (a single pile in horizontal ground) are proposed for use in practice.Key words: pile, slope effets, models, centrifuge, bending .
Time-lapse Changes In Tube And Guided Waves In Cross-well Mallik Experiment

We analyze cross-well seismic data from the Mallik experiment and demonstrate time-lapse changes in tube and guided waves. Although such changes are challenging to interpret, they are generally of a larger magnitude compared to any time-lapse signatures of the first P-wave arrivals reported elsewhere. This suggests better sensitivity of tube and guided waves to small production-related changes and their feasibility for reservoir monitoring.
Variability of UV‐B at four stations in Europe

The variability of solar irradiance in the UV‐B spectral region is studied at four stations operating well‐calibrated spectroradiometers during the period 1991–96. It is confirmed that total ozone is the controlling factor in long‐term changes of solar irradianee below 320 nm received at the ground. This result is supported by the similar long‐term variability under clear sky and all sky conditions during the past five years. The study includes estimates of the amplitude of the annual cycle and estimates of long‐term changes. An important result of this note is, that calculated changes in solar irradiance depend on the length of the observational period and that any speculations on its future changes should be treated always with caution. It is estimated that a 2.7% change per year in solar irradiance at 305 nm at Thessaloniki is a rate that could possibly continue in view of the expected continuation of the ozone decline resulting to an increase of 27% per decade, which is comparable to the amplitude of the annual cycle at that station.
Ozone diurnal variations observed by UARS and their model

Several years of ozone measurements from the Microwave Limb Sounder onboard the Upper Atmosphere Research Satellite are analyzed using a two-dimensional Fourier series in day of year and time of day. Because of limited temporal coverage near local noon, only the diurnal and semidiurnal components are included. Data are investigated in detail at 28°N in the middle stratosphere to lower mesosphere, where the data are considered most reliable. The observations show that ozone is a maximum in the afternoon at 3 mbar and a minimum in the afternoon at 1 mbar and above with a narrow transition zone of reduced diurnal variation in between. This strong dependency on altitude in the transition from a maximum in the afternoon to a minimum in the afternoon, coupled with the small percentage changes in ozone, imposes strict requirements on the data and on the analysis of the data. Comparisons are made with results from a photochemical box model run at 11 levels between 0.46 mbar and 21.5 mbar for 28°N at spring equinox and near the solstices. This is the first time that a data analysis and model comparison of this kind has been made, leading to the identification of relatively small diurnal variations, especially in the transition zone. In the middle stratosphere the model results are in poor agreement with the observations because of the influence of stratospheric dynamics which are neglected in the model runs. In the upper stratosphere the model shows the expected underprediction of absolute ozone amounts, although the percentage change from the midnight value is in excellent agreement with the observations and in particular correctly simulates the diurnal variation in the transition zone between 3 and 1 mbar. Model sensitivity studies are performed to determine the effects of major reaction rate changes and simplified tidal effects.
Fipa cattle in the southwestern highlands of Tanzania: socio-economic roles, traditional management practices and production constraints

This study aimed at determining the socio-economic roles, traditional management practices and production constraints of the Fipa cattle, was conducted in Rukwa region of South-Western Tanzania, using a structured questionnaire. The results indicate that most (90.8 percent) of the respondents depended on crop and livestock production for household income and food security. The Fipa cattle were preferred to other cattle strains by most (91.6 percent) of the farmers owing to their multiple socio-economic functions, adaptive qualities and low management requirements. The Fipa cattle were essentially kept for provision of draught power, income, manure, meat and security against uncertainties. Herded grazing on communal land was practiced by most (99.2 percent) of the farmers all the year-round without any supplementation. However, most (87.5 percent) farmers utilized crop residues in situ during the dry season, after harvesting cereal crops. Kraals made of untreated thorny bushes were the predominant shelters used for Fipa cattle by most (95.8 percent) of the respondents. The majority of respondents mentioned diseases/parasites (94.2 percent) and feed shortages (61.7 percent) during the dry season as the main production constraints. The farmers? preference for Fipa cattle coupled with the multiple roles of the cattle and traditional management practices used by farmers should be used as the entry point for improvement and sustainable utilization of the strain.
Identifying Six Types of Soil Shrinkage Curves from a Large Set of Experimental Data

A typical soil shrinkage curve is S-shaped and composed of four phases termed structural, proportional, residual, and zero shrinkage. However, many studies have not found all four soil shrinkage phases despite investigating the full spectrum of soil moisture content. The objectives of this paper were to determine different soil shrinkage types based on the presence of shrinkage phases and to define relationships between the parameters of different shrinkage types and soil properties. A total of 270 sets of shrinkage data were collected from published (N = 245) and our unpublished work (N = 25), covering a wide range of soil types, sample sizes, and measurement methods. According to the presence of different shrinkage phases, six types of soil shrinkage curves were classified using the shrinkage model proposed by Peng and Horn (2005). Soil shrinkage types generally depended on soil structure, but not on the measurement method. The coefficient of linear extensibility (COLE) had a positive relation with saturated soil bulk density (r = 0.50, P < 0.001), clay content (r = 0.20, P < 0.05), and soil organic carbon (SOC) content (r = 0.46, P < 0.001). This paper is the first to propose six soil shrinkage types that will improve our understanding of the relationship between soil structure and soil water content.
Rock-type controls on downstream changes in clast parameters in sandur systems in Southeast Iceland

ABSTRACT The role of rock type in controlling downstream variation in clast parameters in non-jokulhlaup-affected, Oraefi sandar in Iceland was evaluated. Clast changes in the Svinafellsa are simple, but the effects of tributary sources complicate the clast parameter-distance relationships in the Morsardalur-Kjos system. The behavior of individual rock types must be studied to understand the changes. Both selective sorting and abrasion are taking place, and the relative importance of these processes is evaluated. The volcanic rocks are rounding relatively rapidly, with variation among individual rock types, but there are no significant changes in sphericity and clast form with distance. The compressive strength of the volcanic suite is variable, and significant weathering changes must be takin place during transport from rock face to distal sandur. The influence of such weathering changes on changes in clast parameters needs further research.
Validation of the EBMT risk score in chronic myeloid leukemia in Brazil and allogeneic transplant outcome.

BACKGROUND AND OBJECTIVES The management of chronic myeloid leukemia (CML) has changed radically since the introduction of imatinib therapy. The decision of whether to offer a patient a hematopoietic stem cell transplant (HSCT) must be based on the probability of success of the procedure. The aim of this retrospective analysis of 1,084 CML patients who received an allogeneic HSCT in 10 Brazilian Centers between February 1983 and March 2003 was to validate the EBMT risk score. DESIGN AND METHODS The study population comprised 647 (60%) males and 437 (40%) females, with a median age of 32 years old (range 1 - 59); 898 (83%) were in chronic phase, 146 (13%) were in accelerated phase and 40 (4%) were in blast crisis; 151 (14%) were younger than 20 years old, 620 (57%) were between 20 and 40 and 313 (29%) were older than 40; 1,025 (94%) received an HLA fully matched sibling transplant and only 59 (6%) received an unrelated transplant. In 283 cases (26%) a male recipient received a graft from a female donor. The interval from diagnosis to transplantation was less than 12 months in 223 (21%) cases and greater in 861 (79%). The overall survival, disease-free survival, transplant-related mortality and relapse incidence were 49%, 50%, 45% and 25%, respectively. RESULTS Of the 1084 patients, 179 (17%) had a risk score of 0 or 1, 397 (37%) had a score of 2, 345 (32%) had a score of 3, 135 (12%) had a score of 4 and 28 (2%) a score of 5 or 6. The overall survival (OS) rate in patients with risk scores 0-1 and 2 was similar (58% and 55%, respectively) but significantly better than that in patients with scores 3 or more (score 3 - 44%, 4 - 36 % and 5-6 - 27%, respectively) pp<0.001). Disease-free survival (DFS) and transplant related mortality (TRM) in a patients with a score of 3 or more were 46% and 49%, respectively and the relapse rate beyond score 5-6 was 77%. Disease status had a negative impact on all outcomes (OS, DFS, TRM, and relapse). The OS rate for male recipients of a graft from a female donor was 40% compared to 52% among the other donor-recipient pairs (p=0.004). DFS and TRM were significant for disease phase and female donor-male recipient (p<0.001 and p<0.003, respectively). In our experience, age and interval between diagnosis and transplant did influence OS, DFS, TRM, and relapse rate. INTERPRETATION AND CONCLUSIONS Our results validate the EBMT risk score in the context of a developing country and confirm its usefulness for making point decisions in the imatinib era.
Indonesian throughflow proxy from satellite altimeters and gravimeters

The Indonesian throughflow (ITF) from the Pacific to the Indian Ocean plays an important role in global ocean circulation and climate. Yet, continuous ITF measurement is difficult and expensive. The longest time series of in situ measurements of the ITF to date were taken in the Makassar Strait, the main pathway of the ITF. Here we have demonstrated a plausible approach to derive the ITF transport proxy using satellite altimetry sea surface height (SSH), gravimetry ocean bottom pressure (OBP) data, in situ measurements from the Makassar Strait from 1996 to 1998 and 2004 to 2011, and a theoretical formulation. We first identified the optimal locations of the correlation between the observed ITF transport through the Makassar Strait and the pressure gradients, represented by the SSH and OBP differences between the Pacific and Indian Oceans at a 1° × 1° horizontal resolution. The optimal locations were found centered at 162°E and 11°N in the Pacific Ocean and 80°E and 0° in the Indian Ocean, then were used in the theoretical formulation to estimate the throughflow. The proxy time series follow the observation time series quite well, with the 1993–2011 mean proxy transport of 11.6 ± 3.2 Sv southward, varying from 5.6 Sv during the strong 1997 El Nino to 16.9 Sv during the 2007 La Nina period, which are consistent with previous estimates. The observed Makassar mean transport is 13.0 ± 3.8 Sv southward over 2004–2011, while the SSH proxy (for the same period) gives an ITF mean transport of 13.9 ± 4.1 Sv and the SSH + OBP proxy (for 2004–2010) is 15.8 ± 3.2 Sv.
Asymmetric shallow mantle structure beneath the Hawaiian Swell—evidence from Rayleigh waves recorded by the PLUME network

Author Posting. © The Author(s), 2011. This article is posted here by permission of John Wiley & Sons for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 187 (2011): 1725–1742, doi:10.1111/j.1365-246X.2011. 05238.x.
A suitable vegetation index for quantifying temporal variation of leaf area index (LAI) in semiarid mixed grassland

Determining a suitable vegetation index (VI) is important for accurately quantifying temporal variation in leaf area index (LAI) in semiarid mixed grassland where performances of VI are highly influenced by complex canopy composition, large amounts of dead vegetation, and bare soil. This study investigates the effects of canopy composition on LAI, evaluates the performances of 16 hyperspectral VIs on LAI estimation at each growing stage, and documents the sensitivity of the VIs to green vegetation and the resistance to dead vegetation and bare soil. Finally, the most suitable VI for quantifying LAI temporal variation is determined. The results indicate that dead vegetation accounts for more variation in LAI than does green vegetation. The study also shows that performances of ratio-based, chlorophyll-independent, soil-line-litter-corrected (L-ATSVI), and soil-line-related VIs are more reliable and stable than chlorophyll-corrected VIs and atmospheric resistant vegetation index (SARVI). Normalized difference vegetation index (NDVI), standardized LAI determining index (SLAIDI), and transformed soil-adjusted vegetation index (TSAVI) are the optimum VIs for LAI estimations in the early, maximum, and late growing seasons, respectively. NDVI is the most suitable VI for quantifying temporal variation in LAI during the entire growing season.
Clay Mineral Composition and Geologic Significance of Some Beaufort Sea Sediments

ABSTRACT The less than 2µ fractions of bottom sediments from the Beaufort Sea and Arctic Ocean, were analysed for clay mineral composition. In all of these high latitude sediments, illite is predominant, Chlorite and kaolinite occur in significant amounts and smectite is least abundant. This occurrence of kaolinite is noteworthy. Since the generally accepted view related to marine sediments is that kaolinite is a "low latitude" clay mineral it is suggested that the use of clay minerals in the inference of poleoclimates should be made with great caution.
Observation of the Doubly Charmed Baryon Ξc c

A highly significant structure is observed in the Lambda K-+(c)-pi(+)pi(+) mass spectrum, where the Lambda(+)(c) baryon is reconstructed in the decay mode pK(-)pi(+). The structure is consistent with originating from a weakly decaying particle, identified as the doubly charmed baryon Xi(++)(cc). The difference between the masses of the Xi(++)(cc) and Lambda(+)(c) states is measured to be 1334.94 +/- 0.72(stat.) +/- 0.27(syst.) MeV/c(2), and the Xi(++)(cc) mass is then determined to be 3621.40 +/- 0.72(stat.) +/- 0.27(syst.) +/- 0.14(Lambda(+)(c)) MeV/c(2), where the last uncertainty is due to the limited knowledge of the Lambda(+)(c) mass. The state is observed in a sample of proton-proton collision data collected by the LHCb experiment at a center-of-mass energy of 13 TeV, corresponding to an integrated luminosity of 1.7 fb(-1), and confirmed in an additional sample of data collected at 8 TeV.