Miracle-dz/UniFAR-FTUs huggingface dataset:
Surface Quasi-Elastic Light Scattering from an Amphiphilic Graft Copolymer at the Air−Water Interface

Surface quasi-elastic light scattering (SQELS) has been used to obtain the temporal evolution of capillary waves when graft copolymers of polymethyl methacrylate and poly(ethylene oxide) have been spread as monolayers at the air−water interface. The graft copolymers had a polymethyl methacrylate backbone and poly(ethylene oxide) grafts, containing 54 ethylene oxide units. The capillary wave frequency had a maximum at a surface concentration which is unique for each copolymer. At this same concentration the capillary wave damping shows a sharp 3- to 4-fold increase. Graft copolymer composition is the factor determining the surface concentration at which this frequency maximum and increase in damping are observed. Modeling the transverse surface viscoelastic properties as a Maxwell fluid shows that there is a distinctive change in the relaxation time of this mode at this surface concentration. A phase transition takes place, the poly(ethylene oxide) grafts becoming immersed in the subphase to a significant .
Active populations and preserved signals: molecular- and cultivation-based geobiological analyses from microbialites to the marine deep biosphere

Pavilion Lake in British Columbia, Canada is home to modern-day microbialites that are actively growing at multiple depths within the lake. While microbialite morphology changes with depth and previous isotopic investigations suggested a biological role in the formation of these carbonate structures, little is known about their microbial communities. Microbialite samples were first investigated for phototrophic populations using Cyanobacteria-specific primers and 16S rRNA gene cloning. This data was expounded on by high-throughput tagged sequencing analyses of the general bacteria population. Phototrophs and heterotrophs were detected, including species from the recently described Chloroacidobacteria genus, a photoheterotroph that has not been previously observed in microbialite systems. Phototrophs were shown as the most influential contributors to community differences above and below 25 meters, and corresponding shifts in heterotrophic populations were observed at this interface as well. The isotopic composition of carbonate also mirrored this shift in community states. Comparisons to previous studies indicated this population shift may be a consequence of changes in lake chemistry at this depth. Microbial community composition did not correlate with changing microbialite morphology with depth, suggesting something other than community changes may be key to observed variations in microbialite structure.
Activities of Sucrose Catalyzing Enzymes of Cucumber Fruits as Affected by NaC1 Addition to Nutrient Solution

Effects of NaCI addition to the nutrient solution on the activities of acid and neutral invertases (AI and NI) (EC 3.2.1.26) and sucrose synthase (SS) (EC 2.4.1.13) of cucumber (Cucumis sativus L. cv. Asomidori No. 5) fruits were studied. In spring of 1992, cucumber plants were grown with solution culture in a greenhouse. The aeration rate of the solution was kept low. Sixty millimolar NaCI was added to the solution when 10th leaf was expanding. In control fruits, AT activity was fairly constant until 7 d after anthesis. On the day of anthesis, AT activity at 60 mM NaCl tended to be higher than control. At 60 mM NaCI, AT activity tended to be higher in the proximal half than in the distal half of a fruit. In control fruits, SS activity declined as fruits grew. SS activity tended to be lower in fruit at 60 mM NaCI. The developmental changes in the activities of AT and SS tended to be different between pollinated and parthenocarpic fruit. The activity of NI was much lower than those of AT and SS.
The role of pre-mrna secondary structure in gene splicing in saccharomyces cerevisiae

The process of gene splicing, which involves the excision of introns from a pre-mRNA and joining of exons into mature mRNA is one of the essential steps in protein production. Although this process has been extensively studied, it is still not clear how the splice sites are accurately identified and correctly paired across the intron. It is currently believed that identification is accomplished through base-pairing interactions between the splice sites and the spliceosomal snRNAs. However, the relatively conserved sequences at the splice sites are often indistinguishable from similar sequences that are not involved in splicing. This suggests that not only sequence but other features of pre-mRNA may play a role in splicing. A number of authors have studied the effects of pre-mRNA secondary structure on splicing, but these studies are usually limited to one or a small number of genes, and therefore the conclusions are usually gene-specific. This thesis aims to complement previous studies of the role of pre-mRNA secondary structure in splicing by performing a comprehensive computational study of structural characteristics of Saccharomyces cerevisiae introns and their possible role in pre-mRNA splicing. We identify long-range interactions in the secondary structures of all long introns that effectively shorten the distance between the donor site and the branchpoint sequence. The shortened distances are distributed similarly to the branchpoint distances in short yeast introns, which are presumed to be optimal for splicing, and very different from the corresponding distances in random and exonic sequences. We show that in the majority of cases, these stems are conserved among closely related yeast species. Furthermore, we formulate a model of structural requirements for efficient splicing of yeast introns that explains previous splicing studies of the RP51B intron. We also test our model by laboratory experiments, which verify our computational predictions. Finally, we use different computational approaches to identify any structural context at the boundaries or within yeast introns. Our study reveals statistically significant biases, which we use to train machine learning classifiers to distinguish between real and pseudo splice sites.
A Comparison of Two Methods for Estimating Bird Damage to Sunflowers

Template and visual methods of estimating bird damage to sunflower heads were compared in a laboratory test. Both methods provided similar accuracy at low levels of loss, but the visual method was more accurate over the entire spectrum of damage levels. Loss generally was underestimated with the template method and overestimated with the visual method. There was slightly less variation among observers using the template method than among those using the visual method. Time-wise, the visual method was about three times more efficient than the template method and, overall, it appears to be the better assessment method. J. WILDL. MANAGE. 39(4):802-806 Cultivation of sunflowers as a cash crop for the oil seed, confectionary, and bird seed market has increased greatly in the United States in recent years. Maturing sunflower crops are quite vulnerable to damage by birds, especially blackbirds (Agelaius phoeniceus and Quiscalus quiscula). Guarino (1974, unpublished report, Study 45, Work Unit DF-102.3, Denver Wildl. Res. Cent., Denver, Colorado) estimated that 24 percent of the sunflower crop was lost to blackbirds in a 70-km2 area in North Dakota in 1972, and Dolbeer et al. (1974, Prog. Rep., Work Unit P-F-33.10, Patuxent Wildl. Res. Cent., Laurel, Maryland) estimated a 5 to 80 percent loss in 16, 0.8-ha fields in Ohio in 1973. Undoubtedly, future wildlife research and management efforts, such as those done with field corn (Linehan 1967, De Grazio et al. 1969, Stone et al. 1972, Stickley et al. 1972), will be directed toward documenting and reducing bird damage to sunflowers. As a baseline for these endeavors, an objective evaluation of techniques for assessing bird damage to sunflowers needs to be made. This study had two objectives: (1) to summarize data on the accuracy of a template damage-assessment method used in a field study in Ohio in 1973, and (2) to compare, in a controlled laboratory test, the accuracy and efficiency of the template method an a visual method in estimating bird damage to sunflowers. I thank W. J. Francis, C. R. Ingram, A. R. Stickley, Jr., and M. E. Laderach for assistance with laboratory and field work.
PHYLOGENETIC RELATIONSHIPS AMONG ELEVEN YELLOW FLOWERED CAMELLIA SPECIES BASED ON RANDOM AMPLIFIED POLYMORPHIC DNA

Eleven species of yellow flowered Camellia were analyzed using random amplified polymorphic DNA (RAPD) markers. Fourteen decanucleotide primers of arbitrary sequences were selected from 140 primers for DNA amplification. 201 bands were used as markers. Based on the RAPD data, a phenogram has been constructed. The result shows that: (1) C. micrantha and C. fusuiensis are closely related to C. achrysantha; (2) C. chrysanthoides and C. grandis form a monophyletic group with C. xiashiensis; (3) There is a close relationship among C. longzhouensis, C. ptilosperma, C. longruiensis, which form another monophyletic group; (4) C. impressinervis is highly divergent from all the other taxa.
Genetic structure in populations of Rattus sordidus in sugarcane-growing districts of Queensland, Australia

Genetic structure in populations of Rattus sordidus was examined to determine if population substructuring was occurring as a result of differential dispersal of genotypes or habitat preference. Animals were sampled from grasslands, woodlands, and sugarcane fields in high dissection areas (high dissection of sugarcane fields by non-crop habitat) and low dissection (crop monoculture) areas in the Ingham and Mackay sugarcane-growing districts in Queensland, Australia. Data from six polymorphic allozyme loci showed no statistical differences in allele frequencies among populations from the three habitat types, suggesting that sugarcane crops were colonized by a random sample of individuals from the refuge (grassland) populations. Standardized genetic variances and cluster analysis based on genetic distance could not separate samples from high dissection and low dissection areas indicating that the ability of R. sordidus to reach high densities in some crop areas had no genetic basis and individuals within a single sugarcane-growing district formed a panmictic population, probably due to high mobility of the rodents.
New and Interesting Fungi

One of the greatest thrills of the season was the discovery, in Florida, of this long lost species. It was discovered and de? scribed in 1853 by Ravenel, who found it in " damp pine woods " in South Carolina, and its characters are so striking that in spite of the fact that it does not seem to have been reported since his day, it is still retained in our literature, Peck in " Boleti of the United States," and Murrill in North American Flora both listing it.
Analysing species-specific light transmission and related crown characteristics of Pinus sylvestris and Betula pendula using a shoot-level 3D model

This is a first attempt to analyse species-specific light attenuation in mixed boreal forests created by shoot-level 3D tree models. The models are configurations of real individual Scots pine (Pinus sylvestris L.) and silver birch (Betula pendula Roth.) trees grown in mixed-forest stands. We study species-specific differences in radiation transmission by using the ray-casting method. Light transmission was found to be higher in dense birch-dominated stands compared with dense pine-dominated stands because of the higher total foliage area and the higher location of foliage in the pine canopy. Transmission of light per leaf area index (LAI) was nevertheless higher in the pine canopy compared with the birch canopy because of foliage clumping. Especially in clumped canopy, species-specific shoot-level light simulations enable a more realistic estimation of light transmission compared with simpler calculations based on LAI and Beer-Lambert's law. The observed differences in light-transmission characteristics of the studied species may influence the development of target crowns in the neighbourhood. Light attenuation caused by the dense foliage zone in the upper pine canopy could be avoided in dense stands by mixing species with different vertical foliage distributions.
Estimating the green leaf area index of grassland with airborne multispectral scanner data

Remotely sensed radiance recorded in red and near, middle and thermal infrared wavebands is usually correlated with the green leaf area index (GLAI) of a vegetation canopy. Empirical models based upon airborne multispectral scanner data recorded in these wavebands were inverted and the GLAI of grassland was estimated, but to an accuracy of only 18-51% (95% confidence level) for a five-class classification and ± 0.37 ± 0.75 GLAI at a point. Refinement of the methodology by suppression of environmental influences on the remotely sensed data and by allowing for both the asymptote in the empirical model and error in the ground data increased significantly the accuracy of GLAI estimation to 60-88% (95% confidence level) for a five classclassification and ±0.06 ± 0.10 GLAI at a point. It was concluded that future studies of this kind should use red and near infrared radiance; the refined methodology and an improved sampling scheme for the collection of ground data.
A panel of polymorphic microsatellites in the Blue Eared Pheasant (Crossoptilon auritum) developed by cross-species amplification

Bern, Switzerland Abstract Polymorphic microsatellites are among the versatile genetic markers in molecular ecology studies. In contrast to de novo isolation of microsatellites from target species, cross-species amplification is a cost-effective approach for a fast development of microsatellite markers from closely related taxa. In our study, we cross-amplified a panel of polymorphic microsatellite markers for the Blue Eared Pheasant ( Crossoptilon auritum ), a species endemic to China of considerable conservation con-cern. We obtained 11 polymorphic microsatellite markers selected from 112 candidate loci, originally isolated from other Galliforme species. This panel of makers has shown moderate to high levels of polymorphism and include a Z-chromosomal linkage locus. We carried out preliminary analyses of parentage among captive individuals with a known pedigree using this new panel of microsatellites. Our results suggest that the high utility of these markers may be powerful tools for studies in conservation genetics of eared-pheasants and other endangered
Responsiveness of nesting northern goshawks to taped broadcasts of 3 conspecific calls

Because locating nest sites of forest-dwelling raptors is difficult and time-consuming, we determined if broadcasting conspecific vocalizations of northern goshawks (Accipiter gentilis) increased goshawk detectability during the nesting season in northcentral New Mexico (NM) and northcentral Arizona (AZ). We recorded responses of goshawks to an observer who was either broadcasting alarm, wail, or juvenile begging calls, or was not broadcasting at all while walking transects. We sampled 215 transects at 27 goshawk nests during sampling periods associated with courtship, nestling, and fledgling-dependency periods during 1990. Goshawk responses to taped conspecific calls were higher (P = 0.02) than their responses to an observer without a tape
Intensifying ewe productivity

Calculations on the relative efficiencies of cattle, sheep and pigs as meat producers indicate that the main factor limiting the energetic efficiency of sheep meat production is the low average fecundity of the ewe (Blaxter, 1968). Nevertheless with an estimated ‘biological ceiling’ of five lambs per ewe per pregnancy, and a potential mean lambing interval of 6 months (Wilson, 1968), the sheep industry is much further from achieving its biological ceiling than any other form of domestic livestock production. Because these estimates are based on the performance of specific individuals one must question their attainment on a flock basis. Furthermore, even if the necessary technical information were available, its adoption on a commercial scale may be prohibitive on economic grounds. These uncertainties should not deter us from seeking a greater understanding of the basic factors controlling ewe productivity, nor from attempting to integrate this knowledge into existing production systems.
Variations in band reporting rate and implications for kill rate in Greater Snow Geese

We assessed spatial and temporal variation in reporting probability of banded Greater Snow Geese (Chen caerulescens atlantica) shot by hunters in eastern North America and evaluated potential residual biases in kill rate estimation. Adult Greater Snow Geese were marked with reward (value: US\10, \20, \30, \50, and \100) and standard bands (\0, control) in the Canadian Arctic from 2003 to 2005. We used a spatially explicit multinomial model based on 200 direct recoveries from 4256 banded geese to estimate reporting rate and harvest rate. We found that reporting rate for standard bands varied over time whereas harvest rate was higher in Canada than in the U.S. The reporting probability increased from 0.40 ± 0.11 in the first year of the study to 0.82 ± 0.14 and 0.84 ± 0.13 the second and third years, respectively. Overall, these reporting rates are higher than two previous estimates for this population, which leads to lower estimates of kill rate. However, the large annual differences in reporting rates found in this study lead to uncertainty in the estimation of kill rate. We suggest that the increase in reporting rate in the last two year of the study may be due to the dissemination of information among hunters regarding the presence of reward bands on birds, resulting in increased reporting rate for all bands. This raises issues about the need to adequately inform the public in such large-scale studies to avoid undesirable temporal trends over the course of the study. \textcopyright 2014 by the author(s).
On Mussels: Mytilus Californianus as a Prehistoric Resource

The resource utility of Mytilus californianus, one of the most abundant bivalves found in the archaeological record of the west coast of North America and the most common among living intertidal populations has been characterized in variable terms. Experimental evaluation of alternative mussel collection techniques and review of mussel biology reveals that under ideal circumstances this mollusk produces caloric returns comparable to other commodities exploited by range-restricted foragers. Mussels are high in protein, low in carbohydrates, and could contribute to complete diets among highly mobile foragers. Mussels could not be overexploited to extinction, but resource value declines with frequent exploitation, rendering them of less dietary significance in intensified economies.
Evaluating Physical Maps by Clone Location Comparisons

Pairs of large insert clones located in proximity within 384 well storage plates should join contiguous overlapping sets of clones (hereafter contigs) at a predictable frequency. The frequency of clone pairs joining single contigs should be related to distance apart in the plate. Biased frequencies will be caused by errors such as clone contamination, clone duplication, clone insert size variation, and local variations in genome representation. The aim of this study was to detect potential clone contamination errors by biases in the frequencies at which clone pairs that were within the plate, adjacent rows and columns, or neighboring wells joined the same contigs. Simple statistical analyses of three biases in the frequency of pairs of clones coalescing into the same contig were used to identify potential contaminants. Manual editing determined whether the potential contaminants caused gaps or branches within contigs. BAC and YAC contigs of four plants and two animals were examined, including Glycine max (soybean), Arabidopsis thaliana (thrale cress), Oryza sativa (rice), Zea mays (maize), Sorghum bicolor (sorghum), Mus musculus (mouse), and Homo sapiens (human). Clone pairs that formed contigs significantly (0.05 P 0.0001) exceeded expectation with plate pair clones (up to 5-fold, mouse), neighboring clones (up to 3-fold, mouse), and adjacent clones (up to 4-fold, soybean). After manual examination of clone pairs, contigs that contained fewer errors were built.
Role Of O-GlcNAc Transferase In Metabolic Order And Disorder

The O-GlcNAc modification is, akin to phosphorylation, an abundant modification which plays an important role in cellular processes.The addition of OGlcNAc to proteins is regulated by the O-GlcNAc transferase (OGT). This enzyme is ubiquitously expressed in mammals.The human OGT spans approximately 43 kb of genomic DNA, and to date, 3 OGT isoforms have been sequenced (two nuclear and one mitochondrial). In mammals, OGT exist as different isoforms, such as in the rat and the mouse, differing by 30 nucleotides in their N-terminal (exon 2) . In this study, the mouse OGT isoforms were investigated. In addition, the expression of the full OGT transcript and various transcripts was studied by real-time PCR in mouse tissues (liver, heart, kidney, testis, lung, spleen, ear, stomach, intestine, bone, tail and brain). The highest level of full length mouse OGT was found in spleen followed by testis and lung.The human OGT was shown to have highest expression in pancreas.Further investigations showed that mice express both isoforms (one which uses both exon 2A and 2B and one which skips exon 2A and only uses exon 2B). The first isoform showed highest expression in heart and aorta and the second one in liver and lung, suggesting that mouse OGT exists in different isoforms of varying abundance. Post-translational modifications (PTMs) are the major regulators of protein biological functions.PTMs are catalyzed by their respective enzymes which are sequence specific.Depending on the environment and signaling contexts, proteins are modified and instantly functional.In this study, the protein consensus sequences of 4 different modifications were investigated by utilizing the bio-informatic tool MAPRes.This tool mines association rules of a modified residue in peptides.Phosphorylated Ser/Thr/Tyr showed a polar sequence environment withPro at various positions.O-GlcNAc modified Ser/Thr occured in an environment with vicinal Val (-1 position) and Pro (-2 and -3 positions), acetylated Lys occured in a basic environment with a preference for His or Tyr at +1 and Ser at +7 positions. Methylated Lys also showed a preference for basic amino acids, but compared with acetylated Lys, which have a high preference for vicinal Lys, methylated Lys showed a higher preference for Arg. Methylated Arg showed a high preference for Gly both up- and downstream the peptide chain.In addition, the Yin Yang site sequence environment was also investigated and showed that such sites were located in a polar environment with Pro at various positions.These results suggest that Pro is a very important amino acid in the vicinity of modified amino acids.Furthermore the position of Pro could be determinant in deciding whether a residue is phosphorylated, O-GlcNAc modified or both (Yin Yang site).