Miracle-dz/UniFAR-FTUs huggingface dataset:
A phenotypic shift from gastric-intestinal to solely intestinal cell types in intestinal metaplasia in rat stomach following treatment with X-rays

Histological features and genetic changes induced by X-rays in intestinal metaplasia (IM) in rats were assessed by histochemistry and immunohistochemistry. A time course study and a PCR-SSCP analysis were performed. The IMs in rats were classified into two major types according to the cells forming the metaplastic glands. The first (the GI type) had both gastric and intestinal type cells forming the metaplastic glands. The second (the I-sol type) had solely intestinal cells forming the metaplastic glands. This characterization is similar to that used to define human IMs. The occurrence of IMs of the I-sol and GI types in rats gradually increased with time after X-ray irradiation. The number of IMs of the GI type was relatively high at 2 and 4 weeks after X-ray irradiation, and was low thereafter. On the other hand, the number of IMs of the I-sol type was extremely low at 2 weeks after treatment, then increased with time, and reached a maximum at 77 weeks after treatment. In the PCR-SSCP analysis, there were no alterations of the H-ras, K-ras, and p53 genes in the IM glands of rats treated with X-ray irradiation 8 weeks earlier. These observations suggest that the phenotypic change from IMs of the GI type to the I-sol type occurred without ras and p53 gene alterations.
Tree size as a factor influencing leaf emergence and leaf fall in Acacia nigrescens and Combretum apiculatum in the Kruger National Park

In Acacia nigrescens and Combretum apiculatum saplings tended to retain leaves over the dry season, whereas the mature trees generally lost most of their leaves. In Acacia nigrescens the production of new leaves over the dry season was more commonly observed in saplings than in mature trees.
Prevalence and molecular characteristics of rotaviruses from Polish turkey flocks between 2008 and 2011

Abstract Between 2008 and 2011, commercial turkey flocks in Poland were examined for the presence of rotaviruses. Ten faecal swabs from each of 207 turkey flocks (turkeys aged one to 19 weeks) were collected in different regions of the country and tested using a PCR assay that targeted the NSP4 gene. The prevalence of rotavirus was 20.3% in the flocks tested. Phylogenetic analysis revealed a clear division into groups dependent on geographical origin of the analysed viruses. All Polish rotaviruses belonged to the European group. However, they were found to be genetically variable based on the sequence analysis. The most frequently identified rotaviruses belonged to RV-1 subgroup and two of them formed a distinct subgroup of RV-2. Rotaviruses were detected in healthy and enteric turkeys. The observed amino acid changes probably did not affect the group affiliation, nor the pathogenecity of the studied rotavirus strains.
Experimental Impoundments of Prespawning Pacific Herring (Clupea harengus pallasi): Effects of Feeding and Density on Maturation, Growth, and Proximate Analysis

Approximately 3 mo before spawning, Pacific herring (Clupea harengus pallasi) were captured and transferred to experimental netpens and subjected to different holding conditions: high, medium, and low densities; with and without covers; and fed and not fed. Mortality during impoundment was low. There were no detectable effects of density or cover, but feeding accelerated spawning time and promoted gonadal growth. Fed fish had significantly higher somatic weights, gonad weights, and condition factors and significantly lower gonosomale indices than unfed fish. Water content increased in all fish from about 70%, at the beginning, to about 75% when the fish were ripe. Consequently, total body weight increased in all females, and somatic weight decreased, but the decrease was feast in the fed fish. No significant differences in the percentages of total protein and ash in the carcass were found during impoundment, but the levels of fat and free fatty acids showed a progressive decrease. Glycogen levels in the m.
Effect of different sperm concentrations on the post-thaw viability and motility of turkey spermatozoa cryopreserved by the pellet method

Abstract The effects of different prefreezing semen concentrations on post-thawing quality of turkey semen cryopreserved with the pellet method were investigated. Ten pooled semen samples were each divided into 6 subsamples and diluted with Tselutin extender to obtain a final concentration of 0.5, 1, 2, 3, 4 and 5x109/mL respectively. Subsamples were cooled, added with 8% of dimethylacetamide as cryoprotectant and, after 5 minutes of equilibration, seminal aliquots of 80 μL were directly dropped into a liquid nitrogen bath to form frozen pellets. Thawing was performed in few seconds at 75°C. Sperm motility (Accudenz® swim-down test), viability (SyBr-Propidium Iodide staining) and sperm susceptibility to osmotic stress (Hyposmotic-water test) were assessed. Cryopreservation caused an overall loss of sperm quality, however differences in seminal parameters due to the different sperm concentration were observed in turkey spermatozoa after thawing: spermatozoa diluted to 4x109/mL showed significant higher values in mobility, viable and osmotic resistant spermatozoa compared to the other concentrations. This study showed that the post-thaw quality of turkey semen cryopreserved by pellets method was affected differently in relation to prefreezing sperm concentration.
EVALUATION OF TREES AND SHRUBS FOR FORAGE AND FUEL WOOD IN NORTHEAST THAILAND

SUMMARY Seventeen provenances of 14 predominantly leguminous tree and shrub species were evaluated for forage and fuelwood production over a thirty month period at Khon Kaen, Northeast Thailand. When cut at a 1 m height five times during the experimental period, Enterolobium cyclocarpum, Cassia siamea, Gmelina arborea and Leucaena leucocephala gave the highest yields of edible material with accumulated dry matter production of over 2 kg per tree. These same species also gave high yields of woody stem, which has value as firewood in the region. Mortality of the more productive species was low but others, such as Sesbania sesban, S. grandiflora and S. formosa, suffered almost 100% mortality in this monsoonal environment under these management conditions. The leaf of Sesbania sesban was the most digestible of all species with an in vitro dry matter digestibility of 79%. The leaves of all other species except Calliandra calothyrsus had digestibilities greater than 50% with most in the range 60–65%. The crude .
Behavior of the Japanese rock crab ‘Ishigani’Charybdis japonica towards two collapsible baited pots: Evaluation of capture effectiveness

: An underwater camera was used to record the behavior of the crab, Charybdis japonica, towards two baited pots. These were commercial collapsible pots commonly used by Japanese fishermen to catch crabs. One was box shaped with two slit entrances at the ends, while the other was dome shaped and had two open funnel entrances. The pots were placed on the bottom of a pond that was connected to Kagoshima Bay, southern Japan. Underwater video recordings were used to study the different behaviors of the crabs towards the two types of pot. Crabs approached the pot mostly by crawling up current (75%) following the bait odor trail. They made several attempts to enter the pot until they reached the entrance or otherwise they gave up. While the dome-shaped pot allowed the crabs to enter it easily by crawling sideways, the box-shaped pot's tight slit entrances and netting material prevented the crabs from getting in due to entanglement of their spines on the netting. Ingress could only be achieved after several trials and mostly by crawling backwards into the pots. The dome-shaped pot was more efficient (100%) than the box- shaped pot (31%) in catching crabs that came in contact with it.
Carbachol Stimulates Transactivation of Epidermal Growth Factor Receptor and Mitogen-activated Protein Kinase in T84Cells

We have examined the role of tyrosine phosphorylation in regulation of calcium-dependent chloride secretion across T84 colonic epithelial cells. The calcium-mediated agonist carbachol (CCh, 100 μm) stimulated a time-dependent increase in tyrosine phosphorylation of a range of proteins (with molecular masses ranging up to 180 kDa) in T84 cells. The tyrosine kinase inhibitor, genistein (5 μm), significantly potentiated chloride secretory responses to CCh, indicating a role for CCh-stimulated tyrosine phosphorylation in negative regulation of CCh-stimulated secretory responses. Further studies revealed that CCh stimulated an increase in both phosphorylation and activity of the extracellular signal-regulated kinase (ERK) isoforms of mitogen-activated protein kinase. Chloride secretory responses to CCh were also potentiated by the mitogen-activated protein kinase inhibitor, PD98059 (20 μm). Phosphorylation of ERK in response to CCh was mimicked by the protein kinase C (PKC) activator, phorbol myristate acetate (100 nm), but was not altered by the PKC inhibitor GF 109203X (1 μm). ERK phosphorylation was also induced by epidermal growth factor (EGF) (100 ng/ml). Immunoprecipitation/Western blot studies revealed that CCh stimulated tyrosine phosphorylation of the EGF receptor (EGFr) and increased co-immunoprecipitation of the adapter proteins, Shc and Grb2, with the EGFr. An inhibitor of EGFr phosphorylation, tyrphostin AG1478 (1 μm), reversed CCh-stimulated phosphorylation of both EGFr and ERK. Tyrphostin AG1478 also potentiated chloride secretory responses to CCh. We conclude that CCh activates ERK in T84cells via a mechanism involving transactivation of the EGFr, and that this pathway constitutes an inhibitory signaling pathway by which chloride secretory responses to CCh may be negatively regulated.
A new technique to gather 3-D spatial information using a single camera

A new technique using a single camera and shadows to determine 3-D spatial positions of fishes in the laboratory is described. The apparatus consisted of a large aquarium (2.0 x 1.5 x 0.4 m), a wide-angle camera mounted above and two light sources to cast shadows to either side of the fish. Using image analysis and vector mathematics, aquarium objects were plotted within 1.5 cm of their actual location along the x-, y- and z-axis. The technique was also successful in quantifying changes in 3-D spatial pattern of juvenile fish, Atlantic cod Gadus morhua (7.4-8.6 cm standard length, L S ) and cohabitant piscivorous shorthorned sculpin Myoxocephalus scorpinus (12.0-25.8 cm L S ), at these same viewing fields. The new technique should have a wide application, largely because it is potentially less expensive, laborious and invasive than alternative methods for determining 3-D positions of fishes.
The European Community Respiratory Health Survey II

The European Community Respiratory Health Survey (ECRHS) was planned to answer specific questions about the distribution of asthma and health care given for asthma in the European Community. Specifically, the survey is designed to estimate variations in the prevalence of asthma, asthma-like symptoms and airway responsiveness; to estimate variations in exposures to known or suspected risk factors for asthma, and assess to what extent these variations explain the variations in the prevalence of disease; and to estimate differences in the use of medication for asthma. The protocol provides specific instructions on the sampling strategy adopted by the survey teams, as well as providing instructions on the use of questionnaires, the tests for allergy, lung function measurements, tests of airway responsiveness, and blood and urine collection. The principal data collection sheets and questionnaires are provided in the appendices, together with information on coding and quality control. The protocol is published as a reference for those who wish to know more of the methods used in the study, and also to give other groups who wish to collect comparable data access to the detailed methodology.
Intake and digestion in swamp buffaloes and cattle. 2. The comparative response to urea supplements in animals fed tropical grasses

SUMMARY Swamp buffaloes (Bubalus bubalis) and crossbred cattle (B. indicus x B. taurus) were offered two forages in two experiments. In Expt 1, four animals of each species were offered mature Rhodes grass hay (Chloris gayana) with a mineral supplement or with a supplement of minerals and urea (17·6 gN/d). In Expt 2, another group of four buffaloes and four cattle were offered mature spear grass hay( Heteropogon contortus) with mineral supplementation at intervals of 3 h. Four levels of urea (0, 5, 21 and 97 g/day) and 35S-sulphate were continuously infused in four periods. Rhodes grass was consumed in greater amounts by cattle, whereas buffaloes ate more spear grass. Urea supplements increased intake of Rhodes grass by 12% in buffaloes and 22% in cattle, and of spear grass by 34% in buffaloes and 41 % in cattle. Digestibility of cell wall constituents and acid-detergent fibre of spear grass was lower (P < 0·05) in buffaloes than in cattle (417 v. 499; 471 v. 560 g/kg respectively). In Expt 2, dry matter digestibility progressively increased (P < 0·05) from 364 to 408 g/kg with increased urea infusion. Rumen dry matter pool increased by 11–21 % on infusion of 97 g urea/day, compared with no urea. Digestion of ground forages incubated in situ in the rumen was depressed below rumen ammonia levels of 30–60 mg N/l, while digestion of cotton thread was depressed below 60–80 mg N/l (Expt 1) or 150–200 mg N/l (Expt 2). Patterns of N content in cotton thread suggested that more microbes attached in buffaloes and there was subsequently faster detachment than in cattle, particularly with increased urea infusion.
Rapid and Efficient Proteolysis for Protein Analysis by an Aptamer-Based Immobilized Chymotrypsin Microreactor

Efficient protein digestion is a key step for successful mass spectrometry identification. However, traditional in-solution digestion suffers some drawbacks, such as autolysis of protease, long analysis times and lack of control. Recently, specific single-stranded nucleic acids, aptamers, screened from random sequence pools, have been performed high affinity for targets. In this paper, we have developed a novel enzyme reactor, which immobilized chymotrypsin based on aptamer-grafted silica beads. Mixed proteins, which consist of bovine serum albumin, myoglobin, and cytochrome c, were used as samples, to evaluate the digestion performance of the enzymatic reactor. With the use of this novel tool, proteins were digested in 40 min to an extent similar to that achieved with soluble enzyme at 37°C after 16 h. Moreover, enzymatic reactor regeneration was carried out through chymotrypsin elution and re-immobilization. The advanced characteristics of the aptamer-based chymotrypsin reactor demonstrated that aptamers could serve as novel materials for rapid and efficient enzyme immobilization and application in protein studies.
Carboniferous

Abstract Carboniferous geology has developed very rapidly over the past two decades since ideas on sedimentology and new radiometric scales, together with new biostratigraphical schemes based on miospores, conodonts and foraminifera have been synthesized with ideas on plate tectonic processes, climatic changes and oscillations of sea level. The application of the McKenzie model of basin development to the Carboniferous, and the relating of eustatic sea-level changes, which had a profound effect on Carboniferous palaeo-geography, to fluctuations in the size of the Gondwanan ice sheets, have been major factors in the understanding of Carboniferous processes. The Carboniferous evolution of Britain took place to the (present) north of a plate suturing occurring along a line extending from Galicia, through Armorica and the Massif Central to the Vosges, during mid Devonian to early Carboniferous times. In front of this collision zone was the Rheno-Hercynian zone which opened probably during mid Devonian times and which was partly floored by oceanic crust; its closure can be traced through to late Carboniferous times as a series of northwardly directed thrust complexes. To the (present) north of this zone was a foreland on which basins developed on either side of a persistent Wales-London-Brabant High. Studies by Dewey (1982) and Leeder (1982, 1987, 1988) have shown that late Devonian to early Carboniferous extension, involving β factors of up to 2, produced a series of grabens and half-grabens in the Caledonian basement. These developing structures were the dominant control on early Carboniferous sedimentation and produced a sea-bed topography which was
Nature and distribution of rain-forests in New South Wales

Rain-forest has a discontinuous distribution along the coast and adjoining ranges of New South Wales, extending to altitudes of over 4000 ft. Four major subformations can be recognized, along with two other structural forms which may deserve subformation status. The subformations have been defined as tropical, subtropical, temperate, and dry rain-forest. Six floristic alliances and their associations are briefly described. For the widespread development of rain-forest an annual rainfall exceeding 60 in. is required, though rain-forest is found under much lower rainfalls in places favoured by the soil or topography. The Hernicyclia alliance (dry rain-forest) is found in areas showing a distinctly seasonal rainfall distribution, while the Nothofagus alliance (temperate rain-forest) requires cold and very moist conditions. The Castanospermum alliance occurs along creek banks, usually away from the main rain-forest patches, and the Cupaniopsis alliance is found close to the coast, apparently requiring wind-borne supplies of moisture and mineral nutrients for its development. The Argyrodendron (tropical) and Ceratopetalum (subtropical) alliances occur under similar climatic conditions in the north, but with the Ceratopetalum alliance restricted by competition to the less fertile soils. In the south of the State, where climatic sifting has removed many tropical rain-forest species, the Ceratopetalum alliance occurs on the richer soils. The discontinuity of the rain-forest distribution has been brought about by past climatic changes. Human influence has always restricted rain-forest spread, and since European settlement the area of rain-forest in New South Wales has been reduced by about half.
Retinoids Augment Thiazolidinedione PPARγ Activation in Oral Cancer Cells

Background/Aim: Head and neck squamous cell carcinoma affects nearly 500,000 people annually. Augmenting PPARγ functional activation is linked with multiple anti-carcinogenic processes in aerodigestive cell lines and animal models. PPARγ/RXRα heterodimers may be key partners in this activation. Materials and Methods: CA 9-22 and NA cell lines were treated with the PPARγ agonist ciglitazone and/or the RXRα agonist 9-cis-retinoic acid. PPARγ functional activation, cellular proliferation, apoptosis activity, and phenotype were subsequently analyzed. Results: Ciglitazone and 9-cis-retinoic acid independently activated PPARγ and down-regulated the carcinogenic phenotype in vitro. Combination treatment significantly augmented these effects, further decreasing proliferation (p<0.0001), and increasing PPARγ functional activation (p<0.0001), apoptosis (p<0.05), and adipocyte differentiation markers (p<0.0001). Conclusion: The efficacy of the combination of ciglitazone and 9-cis-retinoic acid afforded lowering treatment concentrations while maintaining desired therapeutic outcomes, optimistically supporting the feasibility and practicality of this novel treatment option.
More food, less habitat: how necromass and leaf litter decomposition combine to regulate a litter ant community

1. In brown food webs of the forest floor, necromass (e.g. insect carcasses and frass) falling from the canopy feeds both microbes and ants, with the former decomposing the homes of the latter. In a tropical litter ant community, we added necromass to 1 m2 plots, testing if it added as a net food (increasing ant colony growth and recruitment) or destroyer of habitat (by decomposing leaf litter).
Chapter 13 Jadeitite and other high-pressure metamorphic rocks from the Jade Mines Belt, Tawmaw area, Kachin State, northern Myanmar

The world’s largest jade deposit, containing the highest-quality jade, is exposed in the Pharkant-Tawmaw (also spelled Hparkant or Hpakan and Tawhmaw) Jade Mines Belt, northern Myanmar. This belt is located between latitudes 25° and 26° N and longitudes 96° 12′ and 96° 25′ E in the Myitkyina district (Fig. 13.1). The belt extends in a north–south direction, covering an area of c. 1200 km (Chhibber 1934b). Major jade production sites are located in the Pharkant, Lonkin, Tawmaw, Haungpa and Hwekha areas. In these areas the rock type jadeitite, containing more than 90 vol% of the mineral jadeite, is associated with serpentinites, albitites, lowto medium-grade metamorphic rocks, chlorite schists, garnet–mica schists, graphite schists, glaucophane schists and amphibolites.
Mucus : a new tissue fraction for rapid determination of fish diet switching using stable isotope analysis

Stable isotope analysis of diet switching by fishes often is hampered by slow turnover rates of the tissues analyzed (usually muscle or fins). We examined epidermal mucus as a potentially faster turnover “tissue” that might provide a more rapid assessment of diet switching. In a controlled hatchery experiment, we switched the diet of juvenile steelhead (sea-run rainbow trout, Oncorhynchus mykiss) from a plant-based feed with low δ13C and δ15N to a fish-meal-based diet with higher delta values. We found mucus to provide a significantly more rapid response to diet switching (half-life = 36 days for δ15N, 30 days for δ13C) than muscle tissue (half-life = 94 days for δ15N, 136 days for δ13C), even for growing juvenile fish. Mucus may provide a rapid turnover “tissue” for analysis of diet (or habitat) switching by fish. It has the additional advantage that it may be sampled nonlethally in some fishes, thereby avoiding problems in studying threatened or endangered species. This is the first report of the use of.
The evolutionary potential of developmental instability

Whether or not developmental instability (DI) has evolutionary potential is subject to much debate. Generally, studies fail to detect significant heritability for fluctuating asymmetry (FA), a trait assumed to reflect DI. In addition, between‐trait correlations in FA are low, suggesting that DI is trait‐ rather than individual‐specific. Among the various attempts to explain these patterns, the overall weak correlation between FA and DI at the individual level has received most attention. Presently, the concept of hypothetical repeatability (R) of individual FA allows us to correct for this weak relationship, transforming patterns of FA into unbiased patterns of DI. By applying R to data presented in the literature, we show that heritability of DI remains lower than predicted but between‐trait correlations in DI substantially increase after transformation. We further provide evidence that DI changes from a trait‐ to an individual‐specific property with higher values of R. As increasing hypothetical repeatability might co‐occur with increased environmental or genetic stress, we discuss the potential implications of our results for the study of evolution of stress resistance. From this we conclude that there is an urgent need for studies that compare the evolutionary potential of developmental instability under a variety of stress conditions.