Miracle-dz/UniFAR-FTUs huggingface dataset:
Food habits of Barbus luteus in main outfall drain, Iraq

The alimentary canal contents of 360 Barbus luteus caught from MOD between January 2010 to December 2010 were examined. The phyto-plankton, zooplanktons, detritus, diatoms, insects and unidentified digestive food were identified in the alimentary canal of fish. The results of diet analysis showed that the B. luteus was omnivorous. The species of fish tended to consume more plant origin food. The aquatic plants and tissues were the main part of thier food followed by chlorophyta and cyanophyta. The results revealed that the species obtained or fell their food item from the bed of rivers or near to it.
Description of Late-Instars of Bryothinusa koreana Ahn and Jeon (Coleoptera: Staphylinidae: Aleocharinae) by Association of Life Stage Based on DNA Sequence Data

ABSTRACT Late-instars of Bryothinusa koreana Ahn & Jeon are described for the first time based upon DNA sequence data of larvae and adults. Twelve larvae were collected on Geoje Island, Korea, in association with adults of B. koreana. The partial cytochrome oxidase II gene (410 bp) was sequenced from the larvae and from several identified adult Bryothinusa specimens, including B. koreana. The intraspecific p-distances of adult B. koreana were from 0 to 4.44%, and interspecific pairwise distances were 10.77% to 13.47%. The sequence results of the larvae were similar to those of adult B. koreana. Based on these results, the larvae were identified as B. koreana and diagnostic characters of the species are provided, with illustrations of features.
Computational cleaning of noisy 5' end tag sequencing data sets from rare in vivo cells

We present a data filtration and processing pipeline for analysis of nanoCAGE-seq, a variant of the CAGE method allowing for very small amounts of input material, and thus expanding the number of tissue- and cell types available for proteome profiling. For this inherently noisy method, rigorous filter methods, including tag clustering, cluster width and profile filtering, and variance filtering rescue bona fide promoters, allowing for detection of promoter usage, inter-sample promoter switching and detection of new putative promoters. We present result from nanoCAGE from two different studies.
STUDIES OF SOIL FUNGI: III. NEW SPECIES OF CONIOCHAETA, CHAETOMIDIUM, AND THIELAVIA

Descriptions and illustrations are given for three new species of Ascomycetes having colored, one-celled ascospores and isolated from forest soil by J. H. Warcup. Coniochaeta tetraspora Cain sp. nov. has dark spiny hairs on the perithecium. The phialospores and blastospores are typical of the genus. The soil from which it was isolated came from Queensland, Australia. Chaetomidium minutum Cain sp. nov. has short, curved hairs on the globose, nonostiolate perithecia. The soil sample came from N. Queensland, Australia. Thielavia variospora Cain sp. nov. has black, nonostiolate, bare perithecia and was isolated from soil collected in New Guinea.
Screening Lycopersicon accessions for resistance to tomato yellow leaf curl virus: presence of viral DNA and symptom development.

Twenty-three Lycopersicon accessions representing five tomato species were screened for resistance to the tomato yellow leaf curl virus (TYLCV). Plants were grown in a field naturally infested with Bemisia tabaci, the natural vector of this geminiviral disease. The screened genotypes were examined for the presence of viral DNA and symptom development at 2-wk intervals. Tomato cultivars harbored the virus and developed symptoms. Accessions of the wild species L. pimpinellifolium, L. hirsutum, and L. peruvianum showed variance in their response to infection (.)
Habitat correlates of European rabbit (Oryctolagus cuniculus) distribution after the spread of RVHD in Cadiz Province, Spain

European rabbit Oryctolagus cuniculus abundance was evaluated relative to habitat variables within two zones in Cadiz Province (south-east Spain), 2 years after the spread of rabbit viral haemorrhagic disease (RVHD). The study areas were low-lying regions of mixed pasture/agriculture, Mediterranean forest and matorral, west (Zone A) and east (Zone B) of the Sierra de Cadiz mountain chain. A total of 111 sites was selected to sample all existing habitat types. Relative rabbit density in each site was estimated using a pellet count method in one 50 x 2 m transect. Mean pellet densities were 21.05 pellet m in Zone B and significantly lower, 5.85 pellets m in Zone A. Physical variables, such as vegetation characteristics (density, height and patchiness of cover-layer vegetation, etc.), topographical characteristics and human influences, cover-layer vegetation species (woody stemmed shrub species or trees forming dense stands), and ground-layer vegetation species (herbaceous species forming a low-lying layer) were determined within transects. In addition to these variables, soil types, rock type and land form, as well as the presence of aquifers, irrigation, and the proximity of rivers, were determined for each site. Significantly higher pellet densities were found in mixed grassland/matorral and cork oak/matorral than in all other habitats. Pellet density was negatively correlated with density of ground-layer vegetation, while high pellet densities were associated with medium-height ground-layer vegetation (50-100 cm). The presence of Entisols was negatively associated with pellet density. The cover-layer species Pistacia lentiscus, Quercus coccifera, Quercus suber, Opuntia ficus-indica and the ground-layer grasses all showed positive associations with pellet density, while the ground-layer species Echium gaditana and Scorpiurus vermiculatus were negatively associated with pellet density. Multivariate analyses identified the mixed grassland/matorral and cork oak forest/matorral habitats as explaining most of the variation in pellet density. The height of cover-layer vegetation was negatively associated, while Opuntia and table-and/calcareous sandstone were positively associated, with mixed grassland/matorral. Distance from habitation and human impact were negatively associated and Quercus suber was positively associated with cork oak forest/matorral. Comparison with previous studies suggest that the low pellet counts in this study represent very low rabbit densities and the population as a whole appears depleted and fragmented.
The First Step Towards a Decision‐support System for Sugar‐beet Growing: Selection of a Basic Growth Model

Four simulation models were tested for their suitability as a basic growth model in a decision support system for sugar beet growing in The Netherlands. SUCROS and SUBEMO are complex, mechanistic models; LINTUL and PIEteR are relatively simple regression models including causal relationships at a higher level of integration. All four models are dynamic, i.e. they calculate daily development and production rates. The selected model had to be able to predict root and sugar yields accurately and to correct for suboptimal water contents of the soil. It should be possible to include location-specific data and new modules, e.g. for nitrogen fertilization or plant density. Finally, the farmer should be able to collect the required input data easily and cheaply. The tests showed that PIEteR predicted root and sugar yields best, partly because it contained water-balance corrections, based on location-specific soil characteristics. PIEteR could not be applied universally because of its regression character at a high level of integration, but it met the requirements specified.
Promotive Effect of CO2 Enrichment on Plant Growth and Flowering of Eustoma grandiflorum (Raf.) Shinn. under a Winter Culture Regime

Cut Eustoma grandiflorum (Raf.) Shinn. flowers are produced year-round in Japan; however, winter conditions are not favorable for flower production due to low sunlight levels. Here, we investigated the effect of CO2 enrichment after the flower budding stage on the growth and flowering of Eustoma ‘Bolero White’, which were grown under forcing culture for winter shipping. CO2 enrichment increased the fresh weight of plants, in addition to increasing the dry weights of leaves, stems, flower buds and open flowers, and roots. CO2 enrichment also increased the relative growth rate (RGR) by 32%, due to the net assimilation rate (NAR) being stimulated. However, CO2 enrichment had no effect on plant height or the leaf area ratio (LAR). Furthermore, CO2 enrichment increased the total number of flower buds and open flowers, in addition to accelerating flower bud development and the promotion of flowering. During the period of enrichment, the vegetative organs continued to grow in CO2-enriched plants, but not in the control plants. In conclusion, CO2 enrichment promoted flowering and improved the quality of cut flowers (i.e., increasing plant fresh and dry weight and the total number of flower buds and open flowers) of Eustoma under low-sunlight winter conditions.
A predictive model for dormancy loss in Polygonum aviculare L. seeds based on changes in population hydrotime parameters

Changes in population hydrotime parameters were determined during stratification in Polygonum aviculare L. seeds in order to model dormancy loss. Seeds buried in pots were stored at three temperatures (1.6, 7 and 12°C) for 110 d and were exhumed at regular intervals during the storage period. Exhumed seeds were incubated at different water potentials at 15°C and germination time courses were analysed to determine hydrotime parameters. The population mean base water potential (Ψb(50)) decreased concomitantly with seed dormancy, while the hydrotime constant (θH) and the standard deviation of base water potential (θΨb) displayed only minor changes. Based on these results, a model for simulating P. aviculare seed dormancy loss in relation to low temperature was developed. The model employs Ψb(50) as an index of mean seed population dormancy status. While Ψb(50) was allowed to vary as seeds were released from dormancy, θH and θΨb were held constant. Changes in Ψb(50) were related to the time and temperature, using a previously developed thermal stratification time index (Stt), which quantifies the accumulation of thermal time units below a threshold temperature required for dormancy loss to occur. Therefore, Ψb(50) varied in relation to the accumulation of Stt according to time and temperature. Model performance showed acceptable prediction of timing and percentage of germination of seeds buried in irrigated plots, but did not accurately predict germination of seeds exhumed from rain-fed plots. Thus, environmental factors other than temperature could also be involved in the regulation of dormancy status of buried seeds under field conditions.
Chemical basis of differential oviposition by lepidopterous insects

Phytochemical mediators serving as attractants, repellents, stimulants, or deterrents in oviposition behavior of moths and butterflies are reviewed in regard to the chemical mechanism of host selection. Ovipositing females seem generally to utilize plant volatiles as cues for orientation to host plants, and the subsequent contact evaluation of plants by means of less- or non-volatile secondary metabolites is usually of great significance in host recognition. Most lepidopterans appear to be induced to oviposit in response to a single host-specific compound, while extreme synergism of multiple components features the stimulatory system of oviposition enacted by some butterflies. Recent investigations clearly demonstrate that acceptance or rejection of a particular plant by females is regulated not only by the presence or absence of oviposition stimulants but by negative stimuli evoked by co-occurring deterrents. The epideictic pheromones implicated in host assessment by females are also referred to in this review. © 1995 Wiley-Liss, Inc.
Functional properties of caseinate glycoconjugates prepared by controlled heating in the 'dry' state

Glucose, ribose, fructose, lactose, fructo-oligosaccharide (inulin) and a mixture of inulin and fructose were conjugated with caseinate via the Maillard reaction using controlled heating and low water activity conditions in order to improve the functional properties of caseinate for food purposes. Conjugation with ribose and glucose increased the viscosity of caseinate 28-fold over that of the unmodified caseinate control but also produced the most browning. Glycoconjugates of caseinate–fructose reacted at a substrate ratio of 1:0.2 w/w and 60 °C at 67% relative humidity for 48 h increased the viscosity of caseinate 24-fold with less browning. At 80% relative humidity the reaction occurred so rapidly that, within 24 h gels containing darkly coloured particulate matter were produced. Incorporation of inulin at 1:1:0.2 w/w/w caseinate/inulin/fructose prevented formation of gels and produced glycoconjugates having 15-fold the viscosity of unmodified caseinate with minimal browning.
Discriminating the impact of recent human mediated stock transfer from historical gene flow on genetic structure of European grayling Thymallus thymallus L.

Microsatellite markers were first used to partition individuals of European grayling Thymallus thymallus, from the Danube, Rhine and Main, and Elbe drainage systems into subpopulations and to estimate individual immigrant ancestries over the last few generations. Subsequently, the studied populations were 'purged' from recent immigrants and the proportions of evolutionary lineages within the 'purged' populations were re-estimated by applying mtDNA markers. The results confirmed a high level of admixture of the divergent mtDNA lineages (i.e. natural secondary contact) in populations sampled at the contact zones of the drainages. In addition, a substantial amount of introgression was observed for several populations that were known to be affected by stocking of European grayling from different origins.
125I-thrombin binds to clustered receptors on noncoated regions of mouse embryo cell surfaces

We used electron microscope autoradiography (EMAR) to visualize the interaction of 125I-thrombin with its surface receptors on mouse embryo (ME) cells. Autoradiographic grains were spaced over the surface of cells in a periodic nonrandom pattern, indicating 125I-thrombin association with clusters of thrombin receptors. The grain spacing varied slightly from cell to cell, indicating subpopulations of cells with different numbers of thrombin receptors. The average distance between grains on ME cells after binding 125I-thrombin (125 ng/ml) at 37 degrees C was 1.65 +/- 0.49 microns. The average distance between grains on prefixed cells and cells incubated with 125I-thrombin at 4 degrees C was not significantly different from that observed at 37 degrees C. This indicates that thrombin receptors are clustered before thrombin binding and that the thrombin receptor aggregates do not redistribute into large aggregates on the surface of cells subsequent to thrombin binding. The number of grains per cluster also does not change under these three binding conditions. Thus, the number of occupied receptors in each cluster appears to be constant. On the basis of the average grain number and spacing, we estimate that each cluster is approximately 400 nm in diameter containing approximately 550 thrombin-binding sites. These receptor-clusters are not associated with specialized structures or coated regions of the membrane. Additionally, grains observed within cells were not found associated with coated vesicles. Therefore, neither the clustering patterns nor internalization of 125I-thrombin are characteristic of molecules which bind to receptors and are internalized by receptor-mediated endocytosis.
Redefinition of the aphid genus Sitobion Mordvilko (Hemiptera: Aphididae) based on cladistic analyses, with emphasis on North American species

A hypothesis of monophyly for the aphid genus Sitobion is tested using cladistics. A diverse sample of thirty Sitobion species from Africa, Asia, Europe and North America were included, along with six species of Macrosiphum, eight new species similar to some Sitobion, one species of Illinoia, and Dysaphis tulipae (Boyer de Fonscolombe) as outgroup. A matrix of forty‐seven taxa and forty‐eight characters was analysed in paup, resulting in a set of thirty‐nine equally parsimonious cladograms. Despite a high degree of homoplasy in the data, the results show that Sitobion is not a monophyletic group. The endemic North American species, along with two pteridophyte‐feeding species from Europe, clearly belong to a separate lineage from the other Eurasian and African species. The endemic North American species are more closely related to the type species of Macrosiphum and Illinoia than to Sitobion avenae (Fabr.), the type species of Sitobion. Two species are placed as junior synonyms of Sitobion alopecuri (Takahashi): Macrosiphum (Sitobion) salicicornii Richards, syn.n. and Sitobion sylvestri Hille Ris Lambers; syn.n. Twelve species previously listed in Sitobion are placed in Macrosiphum with six new combinations: Macrosiphum adianti (Oestlund);Macrosiphum clydesmithi Robinson, comb.n. ;Macrosiphum cystopteris Robinson;Macrosiphum dryopteridis (Holman), comb.n. ;Macrosiphum equiseti (Holman), comb.n. ;Macrosiphum insularis (Pergande);Macrosiphum lambi Robinson, comb.n. ;Macrosiphum ptericolens Patch;Macrosiphum pteridis Wilson, Macrosiphum rhamni (Clarke);Macrosiphum walkeri Robinson, comb.n. ;Macrosiphum woodsiae Robinson, comb.n. Two synonyms are reinstated as valid species: Macrosiphum occidentalis (Essig) and Macrosiphum pteridis Wilson.
Nucleic Acids Research

three human homeoboxes on chromosome 12 unit ABSTRACTMammalian homeoboxes show a clustered chromosomal organization. In the mouse, at least seven homeoboxes on chromosome 6 and at least six on chromosome 11 identify the murine Hox-1 and Hox-2 loci, respectively. A number of homeoboxes on chromosome 7 define the human HOX-1 locus and homeoboxes on chromosome 17 define the human HOX-2 locus. We studied the genomic organization of three homeobox sequences of the HOX-3 locus on chromosome 12 and analyzed transcripts from this region. Structural characterization and sequencing of several cDNA clones reveal that the three homeobox sequences present in this chromosomal region identify a single transcription unit. Primary transcripts are alternatively processed to give mature messengers with a common 5' noncoding exon encoding different proteins containing one of the three homeodomains.
Detecção molecular e análise filogenética de vírus respiratório sincicial bovino (BRSV) em swabs e tecido pulmonar de bovinos adultos

Bovine respiratory syncytial viruses virus (BRSV) is one of the etiologic agents of pneumonia in young cattle. Few studies have been made aiming detection of the virus in samples collected from adult animals, especially those asymptomatic bovines. However, it is assumed that infections in these groups may occur mostly asymptomatic and this would be an important mechanism for maintaining of BRSV in herds. In this study, the goal was to conduct an analysis of the occurrence of asymptomatic infections by BRSV in lung samples (n=68) and nasal swabs (209) taken from adult animals collected in abattoirs from Southern and Southeastern Brazil respectively, to detect via polymerase chain reaction the occurrence of infected animals in populations of adult cattle. The samples that resulted positive (6) on RT-PCR were subsequently subjected to cutting with restriction enzymes and sequencing for genetic characterization (2 samples). All samples belongs to subgroup B of BRSV, which is reported as the one circulating in Brazil. The results obtained demonstrate that BRSV may be present in samples taken from adult animals, which is in agreement the hypothesis that infections in adults run in a sub-clinical way that may be of importance as a maintenance mechanism of the virus in bovine herds.
Modeling of Discontinuous Relationships in Biology with Censored Regression

Discontinuous relationships between variables are common in biological data. Discontinuities can sometimes give the appearance of curvilinearity, which suggests the data should be analyzed with nonlinear models. Here we show that often a more meaningful analysis can be obtained with censored regression techniques. In a censoring model all points below (or above) a certain threshold are observed only by the value of the threshold (e.g., a baseline temperature). We illustrate the method with an example from plant reproductive biology: plant reproductive mass is never negative but becomes positive only after some "capacity" to flower reaches a threshold. The vegetative mass at which the threshold is reached and the relationship between reproductive mass and vegetative mass above the threshold are estimated from data. Using censored regression with real and simulated data shows that apparent curvilinearity suggested by models that do not account for censoring can be an artifact.
New Device Measures Atmospheric Isocyanic Acid

Isocyanic acid (chemically HNCO), a contaminant linked to cataracts and heart disease, has for the first time been measured in the atmosphere.1 The discovery was made by researchers at the National Oceanic and Atmospheric Administration (NOAA) who designed a new detection system to measure HNCO in environments where conventional methods could not previously detect it. Study leader James Roberts and colleagues developed a specialized negative-ion proton-transfer chemical ionization mass spectrometer to measure organic acids emitted by wildfires2 [look for more information on health effects of wildfires in the September 2011 issue of EHP]. They tested the instrument on brush and tree branches burned in a test chamber, which generated levels of HNCO reaching 600 ppbv. Next they used the device on air samples collected in Boulder, Colorado, during the 2010 Fourmile Canyon wildfire and ambient air samples collected in downtown Los Angeles, California. These samples yielded HNCO concentrations up to 200 pptv and 100 pptv, respectively. No wildfires were burning near Los Angeles at the time, so “we assume isocyanic acid came from vehicle exhaust or photochemical reactions known to make it,” Roberts says. The investigators also observed HNCO in laboratory samples of cigarette smoke but noted “the levels were too high for us to quantify with the . instrument configured in the ambient measurement mode. ” Drawing on a surrogate pyrolysis study that found nearly all the urea in tobacco decomposes to HNCO during burning,3 the researchers calculated mainstream cigarette smoke may contain 40–140 ppmv HNCO.1 Urea is added to cigarettes to enhance flavor. Urea is also used in selective catalytic reduction systems to break down toxic nitrogen oxides (NOX) in diesel exhaust into nitrogen and water. Roberts wants to measure HNCO emitted by these systems, which the European Union mandates for heavy-duty diesel trucks; a similar law is pending in California.4 “In trying to solve the problem of NOX we could be increasing HNCO,” Roberts says. The health effects of chronic exposure to environmental HNCO are unknown, although Roberts and colleagues note the concentrations they measured in smoke “cause carbamylation at physiologically significant levels. ”1 In carbamylation, cyanate binds the amino acid lysine in proteins to form homocitrulline. Stanley Hazen, section head of Preventive Cardiology and Rehabilitation at the Cleveland Clinic, found that high blood levels of homocitrulline are a strong predictor of heart disease, especially in smokers, offering a possible mechanism linking smoking to atherosclerosis.5 “We assumed the exogenous source of cyanate in our study was smoking,” Hazen says. Now Roberts’ study suggests HNCO from air pollution also may increase cardiovascular disease risk. “Any degree of carbamylation has potential to be harmful,” Hazen says, although the levels required to raise cardiac and other health risks remain to be determined.