Miracle-dz/UniFAR-FTUs huggingface dataset:
Landscape-based cumulative effects models for predicting stream response to mountaintop mining in multistressor Appalachian watersheds

We conducted a survey of 170 streams distributed throughout the mountaintop-mining region of West Virginia (USA) and linked stream data to a temporally consistent and comprehensive land-cover data set. We then applied a generalized linear modeling framework and constructed cumulative effects models capable of predicting in-stream response to future surface-mine development within the context of other landuse activities. Predictive models provided precise estimates of specific conductance (model R2 ≤ 0.77 and cross-validated R2 ≤ 0.74), Se (0.74 and 0.70), and benthic macroinvertebrate community composition (0.72 and 0.65). Deletion tests supported the conclusion that stream degradation across the region is the result of complex, but predictable, additive and interactive effects of surface mining, underground mining, and residential development. Furthermore, we found that as stressors other than surface mining are factored out completely, the surface-mining level that results in exceedance of the 300 µS/cm conductivity benchmark increased from 4.4% in the presence of other stressors to 16.6% when only surface mining was present. Last, extrapolating model results to all unsampled stream segments in the region (n = 26,135), we predicted high levels of chemical (33%) and biological (67%) impairment to streams on the current landscape. Of this total impairment, however, <25% could be attributed to surface mining alone. These results underscore the importance of multistressor landuse models for reliable predictions of stream conditions, and the difficulty of interpreting correlations between surface mining and stream impairment without fully accounting for other landuse activities.
Model selection in additive main effect and multiplicative interaction model in durum wheat

The study included data set of 20 durum wheat genotype across 15 rain-fed environments. A combined analysis of variance showed that the genotypes differed significantly for seed yield and GE (year × location) interaction. Cross validations procedure and four various F-tests including FGollob, FRatio, FGH1 and FGH2 are used for testing the GE interaction principal component analysis (IPCA) axes and indicated that two, four, six or seven axes could be significant. According to EV1, D1, AMGE1 and SIPC1 parameters, genotypes G3, G7 and G17 were the most stable genotypes while based on EV4, D4, SIPC4 and AMGE4 parameters, genotype G13 was the most stable genotype. The hierarchical clustering showed that the twenty one studied the AMMI stability parameters and mean yield could be divided into four distinct groups. Group III contains mean yield, SIPC4, SIPC6 and SIPC8 which were computed from four, six or eight IPCAs. In conclusion, G13 (DON-MD 81- 36) was found to be the most stable genotype as well as high mean yield performance (2592.45 kg ha-1) and so is recommended for commercial release in semi-arid areas of Iran. Also, the SIPC-based stability parameters of the AMMI model was found to be useful in detecting the yield stability of the genotypes studied.
Microhabitats in a Forest-Floor Small Mammal Fauna

This study examines microhabitat configurations for 3 small mammal species occupying second—growth mesic forest on Walker Branch Watershed in eastern Tennessee. Small mammal populations were sampled in oak—hickory, chestnut oak and pine forest types, with three 0.36—ha live—trapping grids per forest type. There were 255 total captures for 4 forest—floor species during 9,696 trap nights between 1 May and 16 August 1973. These captures included 2% Blarina brevicauda, 66% Peromyscus leucopus, 5% Ochrotomys nuttalli and 27% Tamias striatus. Blarina was captured most frequently in the pine forest type, Peromyscus and Tamias most frequently in the oak—hickory, and Ochrotomys exclusively in the pine. Twenty—nine variables describing proximate habitat structure were measured at each sample mammal capture site. There were significant overall species differences on 18 of these variables. A subset of variables was identified for each of the 3 most frequently observed species, consisting of only the variables of particular significance for distinguishing the capture sites of that species from those of the other species collectively. Discriminant analysis of these few variables both described the average microhabitat configuration, for a species and indicated the relative importance of each variable for characterizing or describing that configuration, subject to the assumptions of the analysis. The observed differences between species microhabitat configuration are consistent with both the composition by forest type of each species sample and the literature information for each species. Microhabitat segregation among these species is discussed with reference to recent theories of habitat selection, ecological, specialization and resource partitioning in equilibrium faunas.
Genetic Status of Headwater Catfish in Texas and New Mexico: A Perspective from mtDNA and Morphology

Abstract Collections of 231 catfish from 34 localities were surveyed for mtDNA (399 base pairs of cytochrome b) and morphological evidence of headwater catfish Ictalurus lupus in areas of historical occurrence in Texas and New Mexico. The species is of concern for conservation managers, primarily because of the potential for population losses from competition and hybridization with channel catfish I. punctatus. For cytochrome b, there were two deeply divergent (4.8–6.1%) groups, a channel catfish clade of 14 haplotypes (0.8% to 1.3% divergence) and a headwater catfish clade of two haplotypes (1.0% divergence), associated with morphotypes of channel catfish and headwater catfish, respectively. Morphotypes were based on field identification and a canonical discriminant function utilizing external morphology. All specimens from the Nueces River and the main-stem Rio Grande and the Pecos River conformed to morphological and mtDNA expectations for channel catfish. Apparently pure populations of headwater catfi.
Inhibitory effects of nitrate, nitrite, NO and N2O on methanogenesis by Methanosarcina barkeri and Methanobacterium bryantii

In order to elucidate the mechanism of the inhibitory effect of nitrate and its denitrification intermediates nitrite, NO and N2O on methanogenesis in anoxic environments, we tested possible toxic effects of these N-compounds on the methanogenic bacteria Methanosarcina barkeri and Methanobacterium bryantii which are ubiquitous in methanogenic rice field soils. The different N-compounds inhibited H2-dependent methanogenesis by these bacteria to different extents. Nitrate showed the weakest inhibition of methanogenesis in both bacteria, followed by N2O and nitrite for Ms. barkeri, and nitrite and N2O for Mb. bryantii, respectively. In both bacteria, the strongest inhibition was caused by NO. Concentrations of 30 mM nitrate still enabled a CH4 production rate of 25–40% of that before the addition of the N-compound, whereas NO completely inhibited methanogenesis at concentrations ≥0.8–1.7 μM (equivalent to 50–100 Pa NO partial pressure). Removal of NO by replacing the atmosphere with H2/CO2 (8:2) resulted in resumption of methanogenesis only if the bacteria had been treated with NO concentrations ≤0.8 μM (50 Pa). Removal of N2O from the cultures resulted in resumption of methanogenesis if Mb. bryantii had been treated with ≤95 μM N2O (500 Pa) or Ms. barkeri with ≤950 μM N2O (5 kPa). These results show that the denitrification products of nitrate can inhibit CH4 production both reversibly and irreversibly depending on the type of methanogenic bacterium and the applied concentration of the N-compound. In a separate experiment with methanogenic rice field slurries addition of nitrate resulted in immediate inhibition of CH4 production. Nitrate was consumed resulting in the sequential accumulation of nitrite, NO and N2O which were subsequently utilized. Nitrite and N2O reached maximum concentrations that would have been inhibitory in the methanogenic bacterial cultures examined.
Identification of translocations in pea by in situ hybridization with chromosome-specific DNA probes

Biotin-labelled DNA probes for tandemly repeated sequences have been used in in situ hybridization experiments as chromosome-specific markers in pea. Six of the seven chromosome pairs can be marked at single sites in this way. Translocations from a standard karyotype are revealed as chromosomes that have two hybridization sites, rather than one. By probing a tester set of reciprocal translocation (or interchange) lines, some of the markers can be assigned to chromosomes. The method is rapid and simple and, in the absence of well-resolved chromosome bands, provides a means for clarifying some of the problems in pea cytology.Key words: in situ hybridization, translocations, chromosome markers.
Binding of Tat peptides on DOPC and DOPG lipid bilayer membrane studied by molecular dynamics simulations

Cell-penetrating peptides (CPPs) have an ability of internalisation to inner cells through plasma membrane. The plasma membrane and lipid bilayer in experiments contain negatively charged lipids. HIV-1 Tat peptide, which is one of the CPPs, has many arginines with positive charge, and strongly interacts with negatively charged lipids. We investigate the difference between neutral lipids, 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), and negatively charged lipids, 1,2-dioleoyl-sn-glycero-3-[phospho-rac-(1-glycerol)] (DOPG), by all-atom molecular dynamics simulations. We found that the speed of binding of Tat to lipid membrane for DOPC is more than 10 times faster than the speed for DOPG. The Tat peptides bind to the lipid membrane by attractive interaction between arginine in Tat and phosphates in lipids. Comparing the number of phosphates binding to arginine, DOPG gives a larger number than DOPC. The differences indicate the importance of negatively charged lipids for the investigation of the property of CPPs.
Life History Variation in the Spotted Tree Frog, Litoria spenceri (Anura: Hylidae), from Southeastern Australia

Abstract: Knowledge of life history and population demography of threatened amphibians is poor. I used skeletochronology in conjunction with mark–recapture data to examine growth rates, age at maturity, and longevity of the spotted tree frog, Litoria spenceri, a critically endangered Australian species. Ages were reliably determined for 578 individuals across two populations at 335- and 1110-m elevation. Females attained larger body sizes than males and took longer to reach sexual maturity, consistent with most anurans. Males matured at 2 yr and females at 3–4 yr at lower elevations, whereas at higher elevations, males matured at 3–4 yr and females took up to 6 yr to mature, which is slow compared with most anurans. Overall, L. spenceri is long-lived, with a maximum confirmed age of 14 yr. These life history attributes have implications for population dynamics of L. spenceri, which may have markedly different demographic responses to certain threatening processes compared with faster growing, shorter lived species. This study highlights the value and need for more life history and demographic data on threatened species. Generalizations about population demography and dynamics across environmental gradients should be made cautiously.
The effects of drought on water relations and stem shrinkage of Quercus alba

Stem circumference, xylem pressure potential (P), and leaf surface resistance were measured in a dominant forest-grown white oak (Quercus alba L.) tree from the beginning of, through the development of, and to recovery from a major drought in mid-Missouri. Continuous recording of several environmental variables and periodic measurements of soil moisture were made in coordination with the above plant variables. As base P(P measured just before sunrise) and soil moisture decreased, net day-to-day and even week-to-week stem shrinkage was observed. Periodic thunderstorms alleviated soil and plant water deficits and stem circumference recovered. Excellent relationships were noted between soil moisture in the upper 30 cm of a 107-cm profile and either base P or stem circumference.Four clear and 2 cloudy days with rain are presented to illustrate diurnal patterns in the aforementioned variables. The generalized pattern of diurnal fluctuations in stem circumference consisted of early morning shrinkage, which cont.
To Grow or Not to Grow: Optimal Resource Allocation for Daphnia

We constructed a discrete-time model for growth and reproduction of the cladoceran Daphnia and solved it numerically for resource allocation patterns to maximize the intrinsic rate of increase r under various environmental conditions. Conditions modeled include different functional forms for the size dependencies of predation risk and net production. Growth after maturity can maximize r when net production and survival rate increase with body size. The optimal period for growth after maturity increases with the reproductive life span, but the life span need not be long to favor growth. The shape of the net production curve influences the extent to which body size is increased by delaying maturity or by growing after maturity. When net production increases with body size but survival rate does not, growth after maturity is not optimal. However, simultaneous allocation to growth and reproduction can occur in the instar (time step) preceding maturity.
Effects of disturbance intensity on species and functional diversity in a tropical forest

Disturbances are widespread and may affect community assembly, species composition, (functional) diversity and hence ecosystem processes. It remains still unclear to what extent disturbance‐mediated species changes scale‐up to changes in community functional properties, especially for species‐rich tropical forests. A large‐scale field experiment was performed in which the dynamics of 15 000 stems >10 cm in diameter was monitored for 8 years in 44 one‐ha forest plots. Twelve functional effect and response traits were measured for the most dominant tree species. The effects of different intensities of disturbance caused by logging and silvicultural treatments on the species and functional diversity of a Bolivian tropical forest community were evaluated, along with how these changes were driven by underlying demographic processes. Disturbance treatments did not affect species diversity or functional diversity indices based on multiple traits related to primary productivity and decomposition rate. This result suggests that species richness is conserved, and trait variation is maintained, which can buffer the community against environmental change. In contrast, disturbance intensity affected the average plant trait values in the community (the community‐weighted mean) for seven of 12 traits evaluated. At high disturbance intensity, the community had a lower wood density of stem and branches, lower leaf toughness and dry matter content, but higher specific leaf area and leaf N‐ and P concentration, with the value of these traits changing on average 6% over the 8‐year period. The functional spectrum of the community changed, therefore, from ‘slow’, conservative, shade‐tolerant species towards ‘fast’, acquisitive, light‐demanding species. These functional changes in mean trait values may enhance primary productivity and decomposition rate in the short term. Temporal changes in community functional properties were mainly driven by recruitment, and little by mortality or survival. Synthesis. Moderate levels of (logging) disturbance neither affected species diversity nor functional diversity per se in the 8‐year period after logging. Disturbance did, however, change the functional community composition towards ‘fast’ species with more acquisitive traits, thus potentially fuelling primary productivity and nutrient and carbon cycling. In conclusion, tropical forest management may contribute to conserving functional biodiversity of trees while providing forest resources.
Anti-apoptosis effects by Eimeria tenella infection in Madin-Darby bovine kidney cells

Apoptosis is a host defense mechanism that the cell uses to limit production of infectious pathogens. Although many bacteria, viruses and parasites can induce apoptosis in infected cells, some pathogens usually exhibit the ability to suppress the induction of apoptosis in the infected cells. Sophisticated evasion strategies of obligate intracellular parasites, in particular prevention of host cell apoptosis, are necessary to ensure successful replication. To study the ability of Eimeria tenella in this regard, in vitro experiments were performed applying Madin-Darby bovine kidney (MDBK) cells as host cell. We have demonstrated that productive infection of adherent cell lines by E. tenella resulted in an anti-apototic effect. This phenomenon was confirmed using in situ terminal deoxynucleotidyl transferase- mediated (TdT) deoxyuridine triphosphates (dUTP)-fluorescein nick end labeling (TUNEL) assay to detect apoptosis. Therefore, E. tenella could complete its cycle of productive infection while inducing anti-apoptosis in the infected cells. This finding might have implications for the pathobiology of E. tenella and other Eimeria species.
A small, lightweight, and inexpensive “burrowscope” for viewing nest contents of tunnel-nesting birds

Abstract Traditional methods of examining the nest contents of burrow-nesting birds have often been destructive, expensive, and/or limited to large-bodied species. Here we present details of a small, efficient, and inexpensive “burrowscope” designed for examining the nest tunnels of very small birds. The burrowscope consists of a tiny (16 mm × 22 mm) video camera and infrared light-emitting diodes, mounted on the end of flexible conduit (20-mm diameter) that houses a live video feed to a small, hand-held monitor display. In total, the burrowscope is only 22 mm wide at its widest point, weighs approximately 900 g, and was built for less than US $400. The burrowscope was tested in the field and could be used at 99.8% of Rainbow Bee-eater (Merops ornatus) nests and 100% of Spotted Pardalote (Pardalotus punctatus) nests (one of the world's smallest burrow-nesting birds). The accuracy of the burrowscope was evaluated by excavating a nest access hole at a sub-sample of Rainbow Bee-eater nests. The burrowscope enabled precise determination of clutch size at 30 of 30 nests, and brood size at 125 of 127 nests. The equipment could be applied to other organisms, including some invertebrates, reptiles, amphibians, and burrow-nesting mammals.
Response of different decomposer communities to the manipulation of moisture availability: potential effects of changing precipitation patterns

The potential impacts of changes in precipitation patterns associated with global climate change on the relationship between soil community diversity and litter decomposition were investigated. For a period of ca. 5 months, two decomposer communities in litterbags (1000 and 45 μm mesh size) containing spruce litter were subjected to two irrigation treatments: constant and fluctuating (drying/rewetting) moisture conditions. The latter were expected to induce moisture stress on the decomposer communities. The two mesh sizes were used to exclude different faunal components from the decomposer communities. The 1000 μm mesh excluded only the macrofauna, whereas the 45 μm mesh excluded both the macro‐ and mesofauna. In the short‐term perspective of the present study, mesofauna abundance showed no response to imposed fluctuating moisture conditions. Irrespective of the presence of mesofauna, mass loss, microbial biomass and the control mechanisms, regulating carbon mineralization appeared unaffected by fluctuating moisture conditions. The reduction in the functional/structural diversity of the decomposer communities in the 45 μm litterbags resulted in strongly increased Nematoda abundance but it did not alter the response of Nematoda to fluctuating moisture conditions. Processes in the nitrogen (N)‐cycle and mass loss were sensitive indicators of changes in the structural and functional complexity of decomposer communities. However, a negative effect of fluctuating moisture conditions on extractable N was coupled to the presence of mesofauna. Extremes in rainfall patterns, generated by climate change, may have a negative impact on the availability of nutrients, particularly N, for plants. This effect could be amplified by an additional impoverishment in the structural and functional complexity of the respective decomposer communities.
Partial Characterization of Bacteriophages for Clavibacter michiganense subsp. nebraskense

Bacteriophages Clmll, ClmX and ClmXC for Clavibacter (Cl.) michiganense subsp. nebraskense were characterized with respect to biological and physical properties. All phages produced clear plaques on strain CN18-5, the original propagating host. On strain CN76-2, ClmX produced predominantly turbid plaques with a few clear plaques, from which ClmXC was derived. The host range of the three phages was restricted to strains of Cl. michiganense subsp. nebraskense. Adsorption rate constants and burst sizes of the three phages were in the range of 2.9 to 9.4×10-9ml/min and 6 to 19 virions/cell, respectively. All phages were morphologically similar with a hexagonal head about 60nm in width and a flexuous tail approximately 235nm long. The type of nucleic acid was double-stranded DNA. Agarose gel elctrophoresis of restriction endonuclease digests of the phage DNAs indicated that the three phages are similar, but distinguishable in DNA structure. C1mXC was probably a deletion mutant of ClmX.
Enzymic Degradation of Pectic Acid

Pectic acids were not completely hydrolyzed with the preparation of carrot exopolygalacturonase, purified about 280-fold. The degradation limit was found to vary over a wide range according to the source of pectic acid. The value for degradation limit was 56.1% for pectic acid from bast of ramie, whereas it was 6.7% for that from peach flesh.
Comparison of Glycol Methacrylate-and Paraffin-Embedded Tissues for identification of Tritium-Labeled Cells after Emulsion Radioautography

Abstract High resolution radioautographs were obtained from tissue sections embedded in glycol methacrylate (GMA). These sections were of superior quality compared to paraffin-embedded sections and they greatly enhanced the precision by which the number and type of tritium-labeled cells in tissues could be identified. Mice were injected with 3H-thymidine (TdR) (0.5 μCi/gram body wt., 60 Ci/mMole) intraperitoneally and killed one hour later. Samples of spleen, testis, small intestine and distal colon were removed, washed, fixed in 1 % glutaraldehyde-4% formaldehyde, dehydrated, and embedded in GMA. Glycol methacrylate-embedded tissues were sectioned at 2 μm on a JB-4 microtome and floated onto glass slides. Comparable samples of tissue were embedded in paraffin and sectioned at 5 μm. Those sections that were to be used for routine analysis of the number or position of 3H-TdR-labeled cells were prestained by the Feulgen reaction, dipped in Kodak NTB-3 emulsion, exposed for 21 days at 4°C and developed. For .