Miracle-dz/UniFAR-FTUs huggingface dataset:
It's a Small World: Biogeography and Invasion in the Mouse Intestine

Host associated systems are of particular interest to many microbiologists because invasion of these systems can lead to disease. One important host-associated systems is the intestinal microbiome, but in many studies, including those on pathogenesis, this system is represented by samples from one location (generally the feces or cecum). This body of work was initiated in part because I wondered why a large and diverse ecosystem was being was being represented by samples from only one habitat. The biogeography of living organisms has an impact on landscape ecology studies, including those in the field of invasion ecology. Despite several studies that specifically investigate the biogeography of the intestinal microbiome, there has been a general failure to describe the luminal biogeography of the lower intestinal tract, primarily due to “noise” introduced by inter-subject variation. Herein, the biogeography of the mouse lower intestinal tract was mapped using novel techniques to overcome problems caused by inter-subject variance. These techniques were then used to reveal nuances of invasion in the lower intestine by Clostridium difficile. C. difficile is an invader of the intestinal microbiome that is well-known for its ability to cause disease following antibiotic treatment. I observed large changes with the introduction of antibiotics to this system, resulting in a series of “blooms” of various taxa, most likely an indication of successional changes due to the effects of antibiotics. I also found that without antibiotic treatment, C. difficile, is still associated with changes in the intestinal microbiome. This is an important development, as it suggests that small changes associated with normal colonization by introduced species may be compared with range expansion by the same species. This body of work was primarily done in order to apply ecological theory to microbiome studies and in doing so gave rise to new techniques and new methods of looking at systems. It is my hope that these advances will result in contributions both to investigations of the intestinal microbiome as an ecological system as well as how as it relates to disease.
Noise reduction in remote sensing imagery using data masking and principal component analysis

Noise contamination of remote sensing data is an inherent problem and various techniques have been developed to counter its effects. In multiband imagery, principal component analysis (PCA) can be an effective method of noise reduction. For single images, convolution masking is more suitable. The application of data masking techniques, in association with PCA, can effectively portray the influence of noise. A description is presented of the performance of a developed masking technique in combination with PCA in the presence of simulated additive noise. The technique is applied to Landsat Thematic Mapper (TM) imagery in addition to a test image. Comparisons of the estimated and applied noise standard deviations from the techniques are presented.
Porosity characteristics of Cambrian mudrocks (Oak Ridge, East Tennessee, USA) and their implications for contaminant transport

Abstract Thirty-eight mudrock samples from the Cambrian Conasauga Group were analysed by immersion, helium and mercury porosimetry. The data generated from these techniques include effective porosities, pore throat size distributions and sample densities. The purpose of these analyses was to obtain information required to evaluate the capacity of the Conasauga Group mudrock to retard transport of and to store contaminants on the Oak Ridge Reservation (East Tennessee, USA). Results indicate that the three porosities were 9.90±2.61%, 3.8±0.7% and 8.1±4.3% for immersion (φI), mercury (φHg) and helium porosity (φhe), respectively. These values are considerably higher than those previously reported for these rocks (0.1–3.4%). The φHg values are commonly the smallest of the three. Although the three porosities generally show little change with depth, an expected trend as a result of the maximum burial depth of the Conasauga Group of >4 km, a decrease with depth is seen in some of the coreholes for only φI. Furthermore, inconsistencies between the different porosity types provide an insight into the mudrock pore structure and related geochemical characteristics. For example, they indicate the existence of considerable pore space accessed only through <3 nm pore throats and the possibility of meteoric cement having replaced original diagenetic cement for some mudrock samples, which would lead to a possible instability to immersion with contaminated water. These characteristics have significant implications for the evaluation of the mudrock retardation and storage capacity for contaminants, and the design of remediation measures.
Taxonomy, biostratigraphy and palaeoecology of Choerolophodon (Proboscidea, Mammalia) in the Miocene of SE Europe-SW Asia: implications for phylogeny and biogeography

The Miocene elephantoid Choerolophodon from SE Europe-SW Asia is studied, based on the Greek localities of Thymiana, Axios Valley, Pikermi, Samos and Nikiti-2. Although this genus is well documented in Greece, there is no recent taxonomic study and its biostratigraphy and palaeoecology had never been examined in detail. Three choerolophodont species are recognized in SE Europe–SW Asia: the Middle Miocene C. chioticus (late Orleanian, MN 5), and the Late Miocene C. anatolicus (early Vallesian, MN 9) and C. pentelici (late Vallesian–Turolian, MN 10–MN 13). The latter species is divided into a primitive morph, dated to the late Vallesian and possibly earliest Turolian, and an advanced morph from the Turolian. At the end of the Miocene Choerolophodon disappeared. With respect to the geographical distribution of Choerolophodon, the genus is very well documented in SE Europe–SW Asia but it is unknown from Central, Western and Northern Europe, a fact which is attributed to ecological factors. The phylogenetic relationships of all known choerolophodont species from the Miocene of the Old World are examined using a cladistic analysis, and their proposed biogeography is discussed. Finally, the palaeoecology of Late Miocene Choerolophodon from Northern Greece is studied through a dental microwear analysis, revealing that Choerolophodon foraged mainly on grasses, a type of vegetation widespread in open environments. These palaeoecological results are in agreement with previous environmental reconstructions for the Late Miocene of Greece.
Astronomical constraints on nebular temperatures: Implications for planetesimal formation

Abstract— Motivated by recent observations of T‐Tauri stars and the interpretation of these observations in terms of the properties of circumstellar disks, we derive internal (midplane) temperatures for disks around mature (age ∼1 Ma) T‐Tauri stars. The estimates are obtained by combining published results for disk masses, sizes, accretion rates, and surface temperatures. For 26 stars (for which adequate data are available), we derive midplane temperatures at 1 AU primarily in the range 200–800 K, and 100–400 K at 2.5 AU. It is likely that the solar nebula, at the same stage of evolution, contained planetesimals and objects destined to become meteorite parent bodies. Observations of young stellar objects at earlier stages of evolution (age ∼0.1 Ma) imply that accretion rates were, on the average, at least two orders of magnitude greater than the 10−8 M⊙/year rates typical for mature T‐Tauri stars. Such high values would result in midplane temperatures at or near the silicate vaporization temperature in the terrestrial planet region.
Comparison of three different methods to identify fractional urban signals for improving climate modelling

Urbanization has changed the properties of the Earth’s surface and resulted in modification of the biogeochemical cycle and possible climate feedback at global and regional scales. Such climate effects are especially evident locally over short periods in megacity areas. Climate model simulation and urbanization process analysis are often limited by poor accuracy of land-cover products that largely neglect mixed urban-surface information below certain thresholds. The present study compares three urban land identification methods (fractional cover, overlapping parabolic interpolation, and threshold) used in remote sensing and climate model parameterization with Landsat Thematic Mapper images and Moderate Resolution Imaging Spectroradiometer land-cover data sets in a systematic evaluation. We also analyse deviation induced by scaling effects and its influence on the urban radiation budget to better understand the implications of land-surface parameter deviation on regional climate analysis. A positive linear relationship is found between the spatial scale and urban-area deviation based on combined analysis of the three land identification methods, and deviation trends levelled off with an increase in the spatial scale. Coarse-resolution land-cover products could not capture well the urbanization process indicated by reference data from Beijing between 2000 and 2009, especially in urban fringe areas where major urban expansion was detected. Detailed sub-pixel information was possibly neglected by threshold methods, which resulted in strong deviation between land-cover products and actual conditions. The overlapping parabolic interpolation method used in climate models also produced deviation in surface parameter derivation during nested simulation work. This might further affect model performance at the regional scale and should be considered in climate model simulation.
Road network density correlated with increased lightning fire incidence in the Canadian western boreal forest

This paper quantifies the influence of anthropogenic linear disturbances on fire ignition frequency in the boreal forests of western Canada. Specifically, we tested if linear features increase the frequency of lightning fires, and whether this relationship is affected by spatial resolution. We considered fires that ignited between 1995 and 2002 within a ~67 000 km2 region of boreal mixed-wood forest in north-eastern Alberta where linear features are highly abundant and spatially heterogeneous. We constructed Poisson, Negative Binomial and Zero-Inflated Poisson models at two spatial resolutions (~10 000 and ~2400 ha), including covariates for linear feature densities, forest composition, weather–lightning indices and geography. We found a positive association between lightning fire frequency and road density; this association was consistent at both spatial resolutions. We suggest this occurs owing to increased availability of flammable fine fuels near roads. The effect was attributable neither to increased detectability of fires proximal to roads by human observers, nor to increased lightning strikes due to metallic infrastructure alongside roads or the topographic characteristics of road location. Our results suggest that, in the face of projected road developments in the region, the potential exists for important changes to the regional fire regime. Further research should elucidate the precise mechanisms in order to develop methods for mitigation.
A Smart Utilization MAC (SU-MAC) protocol with power control for ad-hoc wireless networks

Multi-channel medium access control (MAC) protocols have been developed to overcome the contention/collision problems that arise with single channel MAC protocols in ad-hoc wireless networks. In most of the currently available schemes, a single pre-assigned control channel carries all the control packets (RTS/CTS/RES) for data communication. One of the problems identified with this method is that as the number of nodes in a system increases, the throughput drops significantly due to heavy contention on the control channel. Moreover, even if several data channels are available in the system, many of them remain underutilized due to the unavailability of the control channel. This paper presents SU-MAC, a Smart Utilization MAC protocol, that assigns the available multi-channels dynamically. Our protocol combines the control and available data channel bandwidth to send control information and thus avoids blockage of the control channel for long periods. A power control scheme is also used as well to reduce interference and to effectively re-use the available bandwidth. Simulation results show that our SU-MAC protocol is promising in terms of reduced contention at the control channel and improved throughput because of channel re-use.
Major Ion Chemistry and Sensitivity to Acid Precipitation of Sierra Nevada Lakes

Most alpine and subalpine lakes of the Sierra Nevada (California) are very dilute, weakly buffered calcium bicarbonate waters. Seventy-three lakes selected to lie in basins representative of Sierran bedrocks were sampled in the summers of 1981 and 1982 and have a median alkalinity of 50 μeq 1−1 (range 5–1137) and a pH of 7 (range 5.7–9.4). The alkalinity of Sierran lakes cannot be predicted from altitude, basin area, or lake area. The concentrations of sulfate, calcium, or alkalinity in lake waters are positively correlated with the percent areal coverage of volcanic or calcareous rocks in the basins. The lakes are not acidified but are extremely sensitive to increases in acidity of atmospheric precipitation.
First occurrence of the rare 'corundum + quartz' assemblage in the high-grade zone from the Namaqualand Metamorphic Complex, South Africa: evidence for higher-P, T metamorphism?

Abstract We report in this paper the first occurrence of the rare assemblage corundum + quartz in the high-grade metamorphic zone in the core of the Namaqualand Metamorphic Complex (NMC) (South Africa). The magnetite-bearing rocks hosting the corundum-quartz assemblage are very rare, and occur discontinuous bands a few cm wide, associated with diorite, tonalite and anorthosite within quartz- feldspar ± sillimanite ± biotite ± spinel supracrustal rocks extensively intruded by a foliated granite gneiss. The magnetite-bearing rocks are characterized by the presence of abundant crystals of magnetite together with ilmenite, spinel and large (~1 cm in diameter) euhedral crystals of corundum both displaying a sharp contact with magnetite and quartz. However, in some micro-domains, spinel and quartz, as well as corundum and quartz, are separated by a thin corona of sillimanite with or without magnetite. These textural features suggest that the following reactions have taken place: quartz + corundum → sillimanite, and quartz + spinel + O2 → sillimanite + magnetite. These reactions are interpreted as occurring at higher, as yet unknown, P-T conditions than previously estimated for the NMC. Whether corundum and quartz were once in equilibrium is worth investigating, as it could constitute a geothermobarometric assemblage for ultra-high T granulites.
Evaluations of classification and spectral unmixing algorithms using ground based satellite imaging

Abundances of material components in objects are usually computed using techniques such as linear spectral unmixing on individual pixels captured on hyperspectral imaging devices. However, algorithms such as unmixing have many flaws, some due to implementation, and others due to improper choices of the spectral library used in the unmixing (as well as classification). There may exist other methods for extraction of this hyperspectral abundance information. We propose the development of spatial ground truth data from which various unmixing algorithm analyses can be evaluated. This may be done by implementing a three-dimensional hyperpspectral discrete wavelet transform (HSDWT) with a low-complexity lifting method using the Haar basis. Spectral unmixing, or similar algorithms can then be evaluated, and their effectiveness can be measured by how well or poorly the spatial and spectral characteristics of the target are reproduced at full resolution (which becomes single object classification by pixel).
The role of playas in pedogenic gypsum crust formation in the Central Namib Desert: a theoretical model

The formation of Namibia's extensive pedogenic gypsum crusts (CaSO4·2H2O) is interpreted in a new light. It is suggested that gypsum primarily precipitates at isolated points of evaporitic concentration, such as inland playas, and that deflation of evaporitic‐rich gypsum dust from these playas contributes to the formation of pedogenic gypsum duricrusts on the coastal gravel plains of the Namib Desert surrounding these playas. This study establishes the nature, extent and distribution of playas in the Central Namib Desert and provides evidence for playa gypsum deflation and gravel plain deposition. Remote sensing shows the distribution of playas, captures ongoing deflation and provides evidence of gypsum deflation. It is proposed that, following primary marine aerosol deposition, both inland playas and coastal sabkhas generate gypsum which through the process of playa deflation and gravel plain redeposition contributes to the extensive pedogenic crusts found in the Namib Desert region. Copyright © 2001 John Wiley & Sons, Ltd.
Assessment of Residential Rain Barrel Water Quality and Use in Cincinnati, Ohio1

The collection, storage, and reuse of rainwater collected in rain barrels from urban rooftop areas assists municipalities in achieving stormwater management objectives and in some areas also serves as an adjunct resource for domestic water supplies. In this study, rainwater reuse and levels of select microbial indicators were monitored for six residential rain barrels located in the Shepherd Creek watershed of Cincinnati, Ohio. Water from rain barrels typically had poor microbial quality and was used for watering indoor and outdoor plants. Rain barrel water chemistry was slightly acidic, exhibited wide ranges in conductivity, turbidity, and total organic carbon (TOC) concentrations and gave no evidence of the presence of cyanobacterial microcystin toxins. Selected microbial water‐quality indicators indicated that counts of total coliform and enterococci were consistently above U.S. Environmental Protection Agency standards for secondary recreational contact water‐quality standards. Residential rain barrels can provide water appropriate for low‐contact reuses (such as plant watering), although there may be transient periods of high levels of indicator bacteria in the collected water.
Spatial Scaling for Digital Soil Mapping

We describe in this paper, a broad overview of spatial scale concepts and scaling procedures that are specifically relevant for digital soil mapping (DSM). Despite the recent growth and operational status of DSM, one existing and foreseeably growing issue for users of digital soil information is the inequality of spatial scales between what is required and what is actually available to adequately address soil-related questions posed from within and from outside the soil science community. In the absence of conducting new soil survey or not being able to acquire the original legacy soil information (soil point data) as a means of creating user-specified soil information products, spatial scaling provides a useful solution. Spatial scaling for DSM involves changes in map extent, grid-cell resolution, and prediction support. We review in this paper the different forms of spatial scaling, which are described in terms of changes to grid spacing and prediction support. Fine-gridding and coarse-gridding are operations where the grid spacing changes but support remains unchanged. Deconvolution and convolution are operations where the support always changes which may or may not involve changing the grid spacing. While disseveration and conflation operations occur when the support and grid size are equal and both are then changed equally and simultaneously. Some possible and existing pedometric methods are described for implementation of each scaling process, as is an extended example for performing convolution where the support changes yet the resolution remains the same.
On the Matsumoto and Imai human identification scheme

At Eurocrypt'91, Matsumoto and Imai presented a human identification scheme suitable for the human ability of memorising and processing a short secret. It protects against an intruder peeping as a user enters authentication information on a terminal connected to the authentication server. In this paper several attacks are discussed to investigate the security of their scheme. A modified scheme is proposed to avoid these attacks.
Rainfall interception by trees of Pinus radiata, and Eucalyptus viminalis, in a 1300 mm rainfall area of southeastern New South Wales: I. Gross losses and their variability

Interception loss, I, was determined by continuous concurrent measurements of the canopy precipitation balances of a mature seed orchard tree of Pinus radiata, and a dominant tree of Eucalyptus viminalis at a mountainous high rainfall site (900 m a.s.l.) in Tallaganda State Forest of the Upper Shoalhaven Catchment. Approximate canopy storage capacity (Sc) of the pine was 54 l, and that of the eucalypt was 11·3 l. Gross pine I was 26·5 per cent and eucalypt I was 8·3 per cent of total incident rainfall over a period of 18 months, from June 1975 to December 1976. The exponential model that provided the best fit to overall data relating I to gross rainfall (Pg) was of good precision for the pine (r2 = 0·73) but rather poor precision for the eucalypt (r2 = 0·27). A consistent pattern in interception data of the two canopy types suggested that variation in I was related to change in pervasive conditions influencing rates of evaporation from wet canopies during rainfall. Multiple regression analyses confirmed that factors such as rainfall intensity and windspeed explained some of the variation in eucalypt I but little in pine I. Negative eucalypt I and corresponding low values of pine I over a wide range of Pg (up to 20 mm) suggest that capture of wind-borne precipitation (cloud, mist, or fog) had also complicated the canopy precipitation balances.
Separation of a Coastal Current at a Strait Level: Case of the Strait of Sicily

The separation of a coastal current into two branches when encountering a strait, one entering the strait and the other crossing the strait and continuing to flow along the coast, is examined. Analytical solution shows that the strait topography plays a major role in the separation. When the depth of the sill of the strait is shallower than the ocean, double Kelvin waves propagate along the sill discontinuity line and are able to transport energy across the strait. The shallower the sill, the smaller the transport of the surface current entering the strait at the upstream corner and the larger the transport of the current transmitted across the strait. Sensitivity experiments done with a high-resolution primitive equation model confirm this behavior. These considerations explain the separation of the Algerian current into two branches at the Strait of Sicily: one entering the Eastern Mediterranean Sea and the other flowing into the Tyrrhenian Sea.