Miracle-dz/UniFAR-FTUs huggingface dataset:
The Blood Island is a Site of Formation of the Primary Embryo Thrombocyte in the Chick Blastoderm

Using the immunohistological technique we inquired at what developmental stage and in which site of chick blastoderm does the embryo thrombocyte (ET) begin to differentiate. An anti‐ET antibody was raised against rabbits by injecting ETs isolated from blood of 10 day chick embryos. By applying the indirect staining method to smear preparations of blood collected from developing embryos it was confirmed that cytoplasm of the ET showed more intense staining than that of the erythroid cell and that the ET population could be distinguished from the erythrocyte population by this antibody. Cells showing the intense staining could be detected first in blood islands of the area opaca vasculosa of stage 9+ blastoderms. These embryo thromboblasts were found singly or in groups of a small number at dorsal periphery of cell clusters in the blood island. The electron microscopy revealed that embryo thromboblasts appeared in the same position in the stage 9+ blastoderm. At stage 10+ or later embryo thromboblasts were also present adhering to the vascular endothelium or free in the vessel lumen. We conclude that ETs start differentiating from primitive mesenchymal cells localized in the blood island of the area opaca vasculosa at stage 9 or earlier, migrate thereafter to vessel lumen, and enter the blood stream.
Opposing fitness consequences of colour pattern in male and female snakes

Local populations of the adder, Vipera berus, are polymorphic for dorsal colour pattern, containing both melanistic (black) and zig‐zag patterned individuals. Colour patterns in snakes influence crypsis and thermoregulatory capacity and therefore may be subjected to natural selection. To find an explanation for the maintenance of this polymorphism I examined temporal and spatial variation in morph frequency, and tested for differential selection among morphs using data from a six year capture‐mark‐recapture study. The data derive from six groups of islands in the Baltic Sea off the Swedish east coast, two mainland localities near the coast, and one inland locality.
Validity of Short and Long Self-Administered Food Frequency Questionnaires in Ranking Dietary Intake in Middle-Aged and Elderly Japanese in the Japan Public Health Center-Based Prospective Study for the Next Generation (JPHC-NEXT) Protocol Area.

Background Longitudinal epidemiological studies require both the periodic update of intake information via repeated dietary survey and the minimization of subject burden in responding to questionnaires. We developed a 66-item Food Frequency Questionnaire (short-FFQ) for the Japan Public Health Center-based prospective Study for the Next Generation (JPHC-NEXT) follow-up survey using major foods from the FFQ developed for the original JPHC Study. For the JPHC-NEXT baseline survey, we used a larger 172-item FFQ (long-FFQ), which was also derived from the JPHC-FFQ. We compared the validity of ranking individuals by levels of dietary consumption by these FFQs among residents of selected JPHC-NEXT study areas. Methods From 2012 to 2013, 240 men and women aged 40-74 years from five areas in the JPHC-NEXT protocol were asked to respond to the long-FFQ and provide 12-day weighed food records (WFR) as reference; 228 also completed the short-FFQ. Spearman's correlation coefficients (CCs) between estimates from the FFQs and WFR were calculated and corrected for intra-individual variation of the WFR. Results Median CC values for energy and 53 nutrients for the short-FFQ for men and women were 0.46 and 0.44, respectively. Respective values for the long-FFQ were 0.50 and 0.43. Compared with the long-FFQ, cross-classification into exact plus adjacent quintiles with the short-FFQ ranged from 68% to 91% in men and 58% to 85% in women. Conclusions Similar to the long-FFQ, the short-FFQ provided reasonably valid measures for ranking middle-aged and elderly Japanese for many nutrients and food groups. The short-FFQ can be used in follow-up surveys in prospective cohort studies aimed at updating diet rank information.
Molecular phylogeny of Indonesian Lymantria Tussock Moths (Lepidoptera: Erebidae) based on CO I gene sequences

Many species of Lymantria are important forestry pests, including L. dispar which is well known distributed from Asia to North America as an invasive species. Like of most other genera of moths, the systematic of this genus is still in dispute, especially on the monophyly and the relationship within this genus due to the fact that genus is very large and varied. This genus was morphologically defined only by a single aphomorphy. To clarify the monophyly of the genus Lymantria, to reveal the phylogenetic relationship among the Indone- sian species, and to establish the genetic characters of Indonesian Lymantria, we analyzed 9 species of Indo- nesian Lymantria involving 33 other species distributed around the world based on nucleotide sequence variation across a 516-bp region in the CO I gene. The results showed that the base composition of this region was a high A+T biased (C: 0.3333). The results also showed that the monophyly of Lymantria was not supported by bootstrap tests at any tree building methods. Indonesian species was distributed into four different groups but the relationship among them was still in dispute. It indicates that relationships among the basal nodes (groups) proposed here were least valid due to the fact that the number of species may not be enough to represent the real number of species in the nature. Moreover CO I gene sequences alone were not able to resolve their relationships at the basal nodes. More investigations were needed by including more species and other genes that the more conserved.
Molecular Cytological Analysis of Cysteine Proteinases from Nodules of Lotus japonicus

Some cysteine proteases are expressed in nodules of leguminous plants. AsNodf32, one of the nodulins of Astragalus sinicus, is a cysteine protease of the papain super family and is expressed strongly in mature nodules. To date, functions of proteinases in the nodules have not been clarified. Homologues of AsNodf32 were identified in the EST library of the model legume Lotus japonicus. The expression of homologous proteinase genes was strongly enhanced in mature nodules. Subcellular localization of one of the L. japonicus proteinases, LjCyp2, was studied using tobacco BY-2 cells. The localization of the LjCyp2-GFP-fusion protein changed depending on the cell growth phase. GFP fluorescence was observed in the cytoplasm of rapidly growing cells while the fluorescence was observed solely in the vacuoles of cells at the stationary phase. Cyclical changes of the localization observed in BY-2 cells may reflect control mechanism of LjCyp2 functions in the nodule.
Effect of Particulates (Dust) on Cotton Growth, Photosynthesis, and Respiration

Wind erosion suspends large quantities of dust in the atmosphere that settle back to the earth's surface and are deposited on plant leaves when wind velocities decrease. The object of this research was to determine the effect of wind-erodible size dust particles on upland cotton [Gossypium hirsutum (L.) ‘Dunn 120’] growth and physiology. Dust ( 15.2 µg m⁻²) resulted in reduced dry weight at 3, 7, and 14 days after application, but dry weight accumulation was not reduced by increasing dust concentration after day 3. The dry weight reduction was due to reduced photosynthesis, 1 and 3 days after dust application, and increased dark respiration, 1, 3, and 7 days after application when dust application rates exceeded 28.6 µg m⁻². This study indicates that particulate deposits can alter cotton growth without physical damage to the plant and without toxic materials present in the dust. However, rapid removal of particulates by wind and rain and low natural deposition rates (1.5 µg m⁻² day⁻¹) indicate that dust deposits on leaves should not be a major problem in cotton production.
Characterization of Maize Sex-Determination Gene Orthologs in Rice ( Oryza Sativa L. Japonica Cv. Nipponbare )

Ensuring food security will be a crucial problem in the coming decades. Heterosis, the phenomenon where hybrid progeny exhibit increased vigor in comparison to their inbred parents, has been exploited to increase agricultural yield in maize (Zea mays) for decades due to its monoecious reproductive state. Unisexuality in maize is genetically controlled due to the concerted action of the Tassel seed1 (ts1), Tassel seed2 (ts2), and Silkless1 (sk1) genes. Orthologs of the Tassel seed genes and sk1 can be found in the rice genome even though rice maintains an ancestral cosexual floral state. This study identified maize sex determination (SD) orthologs in rice, and included subsequent characterization of these orthologs in wild-type and transgenic rice tissues. Rice ts1 (rTs1) was confirmed to be japonica rice MSU-TIGR gene locus LOC_Os04g37430, rice ts2 (rTs2) was confirmed to be locus LOC_Os03g18740, and rice sk1 (rSk1) was confirmed to be LOC_Os04g44354 based on bioinformatic analysis. RT-PCR and multiplexed Taqman qRT-PCR experiments showed that these genes were broadly expressed throughout the plant during vegetative growth in leaves, shoots, and roots, and the rTs1 and rTs2 genes are expressed in inflorescences. Transgenic analysis, using GUS reporter translational fusions, revealed that rTs1 and rTs2 are expressed in leaf vasculature and that rTs2 is expressed in spikelet vasculature, developing anthers, and emerging roots. These results suggest that SD orthologs in rice may be involved in development, specifically with programmed cell death processes, which may involve jasmonic acid signaling.
Successional Change and Resilience of a Very Dry Tropical Deciduous Forest Following Shifting Agriculture

We analyzed successional patterns in a very dry tropical deciduous forest by using 15 plots differing in age after abandonment and contrasted them to secondary successions elsewhere in the tropics. We used multivariate ordination and nonlinear models to examine changes in composition and structure and to estimate forest recovery rates and resilience. A shrub phase characterized early succession (0–3 yr); afterwards, the tree Mimosa acantholoba became dominant. Below its canopy, sprouts and seed‐regenerated individuals of mature forest species slowly accumulated. Canopy height, plant density, and crown cover stabilized in less than 15 yr, whereas species richness, diversity, and basal area continued to increase. The pioneer species group has very low diversity and the long‐lived pioneer phase typical of humid forests is absent; species composition may therefore recover soon as suggested by convergence toward mature forest species composition. The time trend of plant density also differed from humid forests for it lacked its characteristic density decline, presumably because of differences in regeneration mechanisms between very dry and other less water‐stressed forest types. As opposed to the prevailing hypothesis, resilience was not higher than in moister forests, and thus factors other than structure relative simplicity must be accounted for when assessing resilience.
Factors affecting tests for differential pathogenicity in populations of Plasmodiophora brassicae

Factors affecting the use of the European Clubroot Differential (ECD) series for determining the differential pathogenicity of Plasmodiophora brassicae were studied. Replicate tests made with one collection of P. brassicae did not give consistent results. Collections were shown to be heterogeneous for differential pathogenicity. Selection of components of a collection occurred during passage through a range of differential host cultivars. ECD host 06 was shown not to be uniform. There was a linear relationship between the logarithm of spore concentration in the inoculum used in tests and the incidence of disease, and some ECD hosts required a higher concentration of spores than others to give the same incidence of disease. The implications of these findings for the future use of the ECD series are discussed.
The accumulation of heavy metals in plants (Lactuca sativa L., Fragaria vesca L.) after the amelioration of coalmine tailing soils with different organo-mineral amendments

Abstract The investigation was based on two pot experiments with lettuce and strawberry, aiming to assess the uptake of heavy metals (cobalt [Co], chromium [Cr], lead [Pb], cadmium [Cd], nickel [Ni], arsenic [As]) from coalmine tailing soils subjected to different amelioration measures (application of liquid fertilizers combined with different organo-mineral materials – zeolite material, peat material, coal dust and poultry manure processed by flies' worms). The results obtained indicate the problem of high Cr and Ni accumulation in above ground parts of plants (leaves and fruits). The question of Cr mobility within substrates and plants stayed open. Concentrations of Ni and Cr in lettuce and strawberry are below the levels allowed for animal food, but could influence daily human intake. Further work should focus on the mobility of heavy metals within treated tailings and their uptake by different plant species.
The CD3ε Proline-Rich Sequence, and Its Interaction with Nck, Is Not Required for T Cell Development and Function1

The CD3ε proline-rich sequence (PRS) binds to the cytosolic adaptor molecule Nck after TCR ligation. It has been proposed that this interaction is essential for immunological synapse formation and T cell activation. To assess the physiological importance of the CD3ε PRS, we have generated mice that lack this motif (CD3ε.PRSM). Pull-down experiments demonstrated the inability of Nck to bind to the CD3ε PRS in thymocytes from mutant mice after TCR ligation. Surprisingly, no differences were observed in the number and percentage of T cell subsets in the thymus and spleen, and there was no apparent defect in positive or negative selection. Furthermore, the proliferative response of CD3ε. PRSM T cells to staphylococcal enterotoxin B and anti-CD3 Ab was normal. TCR surface expression, constitutive internalization, and Ag-induced down-modulation were also normal. These data suggest that the interaction between the CD3ε PRS and Nck, or any other Src homology 3 domain-containing molecule, is not essential for T cell development and function.
Functional Significance of Bioactive Peptides Derived from Milk Proteins

Bioactive peptides can be defined as protein fragments with potential biological activities. Milk proteins are precursors of many different biologically active peptides. Bioactive peptides from milk proteins are considered potential modulators of various regulatory processes in the body. They mediate physiological functions in cardiovascular, nervous, gastro intestinal and immune systems. The functional significance of bioactivities depends on peptide fragment. Bioactive peptides encrypted in major milk proteins are latent within the sequence of the parent protein molecule. They can be liberated by (i) gastro intestinal digestion of milk, (ii) fermentation of milk with proteolytic starter cultures, and (iii) hydrolysis by proteolytic enzymes. In relation to their mode of action, bioactive peptides may reach target sites at the luminal side of intestinal tract, or after absorption, in peripheral organs. The production, functionalities, and mode of action of bioactive milk peptides as well as latest peptide products and ingredients are reviewed.
Phenolic Content and in vitro Antioxidant Activities of Sweet Orange (Citrus sinensis L.) Fruit Wastes

The phenolic contents and in vitro antioxidant activities of waste components (flavedo, albedo and seed) obtained from Citrus sinensis (orange) fruit were evaluated in this study. Two extracts (ethanol and hydroethanol) were prepared from each sweet orange component. Total phenolic contents were higher in the ethanol seed and albedo extracts (13.05 ± 0.35 and 34.57 ± 0.09 mg gallic acid equivalent/g of extracts, respectively) compared to the hydroethanol extracts (7.88 ± 0.88 and 32.07 ± 0.67 mg gallic acid equivalent/g of extracts, respectively). The hydroethanol flavedo extract however contained significantly higher total phenolics (48.17 ± 1.17 mg gallic acid equivalent/g of extract) compared to the ethanol flavedo extract (12.50 ± 0.50 mg gallic acid equivalent/g of extract). Total flavonoid content ranged from 14.29 ± 0.38 mg quercetin equivalent/g of extract in the ethanol seed extract to 45.79 ± 1.17 mg quercetin equivalent/g of extract in the hydroethanol flavedo extract. DPPH radical scavenging activity testing revealed that the hydroethanol extracts were better inhibitors of the DPPH radical than the ethanol extracts. IC 50 values ranged from 0.18 - 0.23 mg/mL for the hydroethanol extracts and from 0.26 - 0.34 mg/mL for the ethanol extracts. The hydroethanol extract of the flavedo was found to have the best ferric reducing antioxidant potential (FRAP) value (800.30 ± 1.53 µmole Fe(II)/g extract) while the seed extracts contained the lowest FRAP values (329.00 ± 1.53 and 464.30 ± 0.75 µmole Fe(II)/g extract for ethanol and hydroethanol extracts, respectively). Reducing power was observed to be higher in the hydroethanol extracts than the ethanol extracts. Inhibition of lipid peroxidation was highest in the ethanol extract of the flavedo (29.46 ± 0.08 %) and lowest in the seed extract counterpart (8.46 ± 0.15%). Our results suggest that wastes (flavedo, albedo and seeds) generated from sweet orange ( Citrus sinensis ) have biologically important components that may be beneficial to health.
Inland Fishes of California

Preface Acknowledgments Conversion factors Distribution patterns Ecology Change A conservation strategy Identification Key to the Inland Fishes of California Lampreys,Petromyzontidae Sturgeons,Acipenseridae Herrings,Clupeidae Minnows,Cyprinidae Suckers,Catostomidae Bullhead catfishes,Ictaluridae Smelts,Osmeridae Salmon and trout,Salmonidae Pupfishes,Cyprinodontidae Livebearers,Poeciliidae Color plates follow page Killifishes,Fundulidae Silversides,Atherinidae Sculpins,Cottidae Sticklebacks,Gasterosteidae Surfperches,Embiotocidae Striped basses,Moronidae Sunfishes,Centrarchidae Cichlids,Cichlidae Mullets,Mugilidae Perches,Percidae Gobies,Gobiidae References Index
Changes in soil organic carbon, nitrogen, pH and bulk density with the development of larch (Larix gmelinii) plantations in China

Under the government of China's environmental program known as Returning Farmland To Forests (RFTF), about 28 million hectares of farmland have been converted to tree plantation. This has led to a large accumulation of biomass carbon, but less is known about underground carbon‐related processes. One permanent plot (25 years of observation) and four chronosequence plot series comprising 159 plots of larch (Larix gmelinii) plantations in northeastern China were studied. Both methods found significant soil organic carbon (SOC) accumulation (96.4 g C m−2 yr−1) and bulk density decrease (5.7 mg cm−3 yr−1) in the surface soil layer (0–20 cm), but no consistent changes in deeper layers, indicating that larch planting under the RFTF program can increase SOC storage and improve the physical properties of surface soil. Nitrogen depletion (4.1–4.3 g m−2 yr−1), soil acidification (0.007–0.022 pH units yr−1) and carbon/nitrogen (C/N) ratio increase (0.16–0.46 per year) were observed in lessive soil, whereas no significant changes were found in typical dark‐brown forest soil. This SOC accumulation rate (96.4 g m−2 yr−1) can take 39% of the total carbon sink capacity [net ecosystem exchange (NEE)] of larch forests in this region and the total soil carbon sequestration could be 87 Tg carbon within 20 years of plantation by approximating all larch plantations in northeastern China (4.5 Mha), showing the importance of soil carbon accumulation in the ecosystem carbon balance. By comparison with the rates of these processes in agricultural use, the RFTF program of reversing land use for agriculture will rehabilitate SOC, soil fertility and bulk density slowly (< 69% of the depletion rate in agricultural use), so that a much longer duration is needed to rehabilitate the underground function of soil via the RFTF program. Global forest plantations on abandoned farmland or function to protecting farmland are of steady growth and our findings may be important for understanding their underground carbon processes.
Predicting insect phenology across space and time

Many species appear to be undergoing shifts in phenology, arising from climate change. To predict the direction and magnitude of future changes requires an understanding of how phenology depends on climatic variation. Species show large‐scale spatial variation in phenology (affected by differentiation among populations) as well as variation in phenology from year‐to‐year at the same site (affected predominantly by local plasticity). Teasing apart spatial and temporal variation in phenology should allow improved predictions of phenology under climate change. This study is the first to quantify large‐scale spatial and temporal variation in the entire emergence pattern of species, and to test the relationships found by predicting future data. We use data from up to 33 years of permanent transect records of butterflies in the United Kingdom to fit and test models for 15 butterfly species. We use generalized additive models to model spatial and temporal variation in the distribution of adult butterflies over the season, allowing us to capture changes in the timing of emergence peaks, relative sizes of peaks and/or number of peaks in a single analysis. We develop these models using data for 1973–2000, and then use them to predict phenologies from 2001 to 2006. For six of our study species, a model with only spatial variation in phenology is the best predictor of the future, implying that these species have limited plasticity. For the remaining nine species, the best predictions come from a model with both spatial and temporal variation in phenology; for four of these, growing degree‐days have similar effects over space and time, implying high levels of plasticity. The results show that statistical phenology models can be used to predict phenology shifts in a second time period, suggesting that it should be feasible to project phenologies under climate change scenarios, at least over modest time scales.
The new database "Seed oil Fatty Acids" (SOFA)

After more than three years the internet-based database “Seed Oil Fatty Acids” (SOFA) is available again (http://sofa.mri.bund.de) free of charge after registration. This database is a unique collection of information about the fatty acid composition of wild plant seeds. The data were collected from the appropriate pharmaceutical, botanical and chemical literature over a period of more than 40 years. With financial assistance from the German Federal Ministry of Food, Agriculture and Consumer Protection via the lead partner Agency for Renewable Resources (FNR) the new database system based on mySQL and PHP as source language was created. Currently more than 18.000 different tables with about 130.000 individual data sets are searchable from the database. Additionally the database contains about 600 different fatty acids with more than 2.500 synonyms. The search for a defined (e. g. unusual or technically interesting) fatty acid or plant (family, genus, species) which contains this fatty acid is possible online. This search can be done by use of synonyms for the fatty acid (trivial name, systematic name) but also by using substructures of the fatty acid defined by an alpha-numeric delta-notation. It is possible to combine the search for different fatty acids by Boolean operators such as “AND” and “OR”. This paper gives an overview about the application of the different search forms and provides search examples.