Miracle-dz/UniFAR-FTUs huggingface dataset:
The intracellular behaviour of Burkholderia cenocepacia in murine macrophages

Burkholderia cenocepacia is an opportunistic pathogen causing life-threatening infections in cystic fibrosis and other immunocompromised patients. The bacterium survives within macrophages by interfering with typical endocytic trafficking, resulting in delayed maturation of a B. cenocepacia-containing phagosome. We hypothesize that B. cenocepacia alters gene expression after internalization by macrophages, inducing genes involved in intracellular survival and host adaptation. Furthermore, we hypothesize that specialized bacterial secretion systems are involved in the interactions between intracellular bacteria and macrophages. In this work, we characterize later-stage infection of macrophages by B. cenocepacia, showing replication within an acidified endosomal compartment suggestive of a phagolysosome. We examine differential gene expression by intracellular B. cenocepacia using selective capture of transcribed sequences (SCOTS) with both competitive enrichment and microarray analysis. We identified 766 genes differentially regulated in intracellular bacteria, of which 329 were induced and 437 repressed. Affected genes are involved in all aspects of cellular life, including information storage and processing, cellular processes and signalling, and metabolism; in general, intracellular gene expression demonstrates a pattern of environmental sensing, bacterial response, and metabolic adaptation to the phagosomal environment. Deletion of various SCOTS-identified genes affects B. cenocepacia entry into macrophages and intracellular replication, as well as host-directed cytotoxicity and spread to neighbouring cells. Expression of secretion system genes is
Euphausiids of the world ocean

This interactive and beautifully illustrated CD-ROM contains an up-to-date taxonomic reference work on the order of Euphausiacea, from the Scripps Institution of Oceanography. Detailed information on all 86 species and higher taxa is given, including full systematic descriptions, taxonomy, biogeography, references, colour photographs and drawings. The database also includes unique information on larval development of 40 species. Two types of fully illustrated, computer-assisted identification keys provide quick and easy access to species information. The distribution information is stored in an interactive geographic information system, allowing fast geographic searches or comparisons of distribution patterns. The entire text is hyperlinked, and a reference database contains all the principal literature for the euphausiids.
Soil seed bank and regeneration of a Calluna vulgaris community after forest clearing

SUMMARY After tree cutting of a margin of a deciduous forest (Querceto petraeae-Betuletum) on acid gravel deposits in South-Limburg, The Netherlands, a Calluna vulgaris community re-established as a result of germination from the soil seed bank. The greater part of the extensive seed bank of Calluna probably originated from heathland vegetation, which was present on the site until half a century ago. The number of viable seeds of Calluna present in the soil samples varied tremendously in time and space. The maximal density found was c. 300 seeds per dm2 to a depth of 20 cm. From a viewpoint of nature preservation, it is important to estimate the feasibility of re-creating former plant communities based upon the seed bank in the soil.
Agro - tourism Management Cruise along the Garden, Khlong Mahasawat, Phutthamonthon District, Nakhonpathom Province

This study is quality research and quantity research. Aims were to study tourist satisfaction to agricultural tourism and to study agricultural tourism management on a cruise to see the gardens along the Khlong Maha Sawat at Phtthamonthon District, Nakhon Pathom Province. Sampling group used in quality research consisted of farmer group representative, lotus farmers, Maha Sawat farmer group representatives, Kaow Tung House and tourism entrepreneur representatives (tourism cruises), in depth interview. The samples used in quantitative research was Thai tourist traveling on a cruise to see the gardens along the Khlong Maha Sawat for 400 people by the questionnaires data collected that confident value as Alpha Coefficient for . 951. Statistics used data analysis such as frequency, percentage, mean, standard deviation, t-test, One-Way ANOVA Studying result found that most represents traveling on a cruise to see the gardens along the Khlong Maha Sawat because life style of farmer and natural to find the traveling information on internet/ website/ social. Mostly impressed activities such visiting Na-Bua, orchid garden, fruit garden/ mixed farming and Maha Sawat Agricultural Housewife Group respectively, in the future would come to travel again and suggest other to travel Tourist satisfied agricultural tourism, traveling on a cruise to garden at Khlong Maha Sawat at Phtthamonthon District, Nakhon Pathom Province. Overview of highest income, sort by average such as tourist attraction, service rate/ financial, service, other facilities and access to tourist attraction respectively. Tourist was sex, age, education level, occupation and different average income a month, agricultural tourist satisfaction, traveling on a cruise to garden at Maha Sawat Canal, Phtthamonthon District, Nakhon Pathom Province, overview and income were different.
Limnotrachelobdella sinensis, a leech associated with mortality in a wild population of Japanese crucian carp Carassius cuvieri in Korea.

Mortality occurred in Japanese crucian carp Carassius cuvieri in a reservoir in Chungnam Province, Korea, in March 2002. Moribund fish showed severe anemia in the gills and piscicolid leeches that were identified as Trachelobdella sp. were reported as the cause of the mortality. Re-examination of the preserved leech specimens reveals that they are not Trachelobdella sp. but Limnotrachelobdella sinensis. The external morphology of the specimens is described. This finding represents the second record of L. sinensis in Korea. The impact of infestation by L. sinensis on a host is discussed in relation to fish mortality.
Carbohydrates : synthetic methods and applications in medicinal chemistry

Part 1 Synthetic methods of carbohydrate by chemicals: efficient reaction channels from mono-and disaccharides to enaniopure building blocks and exploitation of their application profiles, F.W. Lichtenthaler stereocontrolled synthesis of C-glycosides, S. Czernecki glycals in palladium-mediated C-glycosal bond formation, G.D. Davis Jr new apsects of glycosylation reactions, Richard R. Schmidt radical functionalization of the anomeric centre of carbohydrates and synthetic applications, G. Decostes improvements in the synthesis of trehalose-based bacterial lipids, Anderson A.K. Datta et al from sugars to morpholines, spiro-acetals and alkaloids, L. Hough and A.C. Richardson synthesis of antibiotic hygromycon A and its derivatives, Noritaka Chida and Seiichiro Ogawa synthesis of biologically active pseudo-oligosaccharides, T. Suami. Part 2 Synthetic methods of carbohydrate by enzyme: combined classical and chemoenzymatic glycosylations, R. Stiller and J. Thiem synthesis of oligosaccharides related to plant, vertebrate and bacterial, cell-wall glycans, V. Pozsgay malto-oligosaccharides as starting materials for synthesis of bioactive compounds, H. Kuzuhara and N. Sakairi. Part 3 Synthetic and biological studies on sialic acid: systematic synthesis of gangliosides toward the elucidation and biomedical application of their biological functions, A. Hasegawa and M. Kiso synthesis of biologically active sialo-compunds, K. Ikeda and K. Achiwa sialic acid derivatives as glyco-lipoid, H. Ogura synthesis of sialic acid analogues and their behaviour toward the enzymes of the sialic acid metabolism as well as the hemagglutinin X-31 of influenza A virus, A. Zbiral sialic acids regulate cellular and molecular recognition, R. Schauer. Part 4 Functional and biological studies of glycoconjugate: new strategies in the synthesis of beta-D-galacto-oligosaccharides - a synthetic heptasaccharide reveals the "groove-binding" character of a monoclonal antibody, T. Zieglaer et al cell surface carbohydrates - their involvement in cell adhesion chemical and enzymatic methods for the depolymerization and modification of heparin, R.J. Lindhardt.
State Legitimacy and Sector of Employment

Based on Social Identity Theory (SIT), this paper analyzes whether state employees (in-group) have higher state legitimacy beliefs than employees working in the private sector (out-group). Using the fifth and the sixth waves of the World Values Survey and using a legitimacy measure that is based on Norris (1999), multi-level analyses provide evidence in favor of our hypothesis. State employees show significantly higher state legitimacy beliefs than employees working in the private sector. However, it remains unclear whether this effect is driven by social comparisons (SIT) or is simply a result of labor market selection mechanisms.
Food and feeding of Greenland halibut (Reinhardtius hippoglossoides, Walbaum) in the Barents sea and east Greenland waters

Abstract This report describes the diet of Greenland halibut (Reinhardtius hippoglossoides, Walbaum) on the continental slope in the western Barents Sea (1992-1994) and on the shelf outside East Greenland (1991). The proportion of empty stomachs was high: for many predator length groups more than 80 %. There was a decreasing percentage of empty stomachs with increasing predator length. Cephalopods, and especially Gonatus fabricii, was the most important prey category for Greenland halibut at East Greenland in 1991 as well as in the Barents Sea in 1992 and 1994. In the Barents Sea in 1993, however, indeterminable fish remains and herring were the most important prey categories. Herring and blue whiting were the most important species of fish prey in the Barents Sea. It was impossible to identify the fish remains at East Greenland. The potential of stomach data in further ecological investigations and management of Greenland halibut is discussed.
Status and biology of the spawning population of Red Rock Lakes Arctic grayling

The population of lacustrine Arctic grayling (Thymallus arcticus), historically large in Red Rock Lakes, Montana, has declined substantially in recent years. The goal of this study was to determine the current status of the Red Rock Lakes grayling and provide the biological basis for directing management and future restoration efforts of this native population. The spawning population of Arctic grayling in Red Rock Lakes system was monitored during the springs and summers of 1994 and 1995. A cross-channel weir was installed in both years in Red Rock Creek, the primary spawning tributary for these fish, in an attempt to capture all migrants. In both years, grayling began their spawning migrations prior to ice-off of the Upper Lake, while flows were increasing and daily mean temperatures were near 6.0 C. The peak of upstream movement occurred 4-11 May in 1994 and 14-23 May in 1995. Stream residency for adult grayling captured on both upstream and downstream migration averaged 17.7 d (sd 11.3) for females and 34.8 d (sd 10.2) for males and were significantly different (p<.001). Total numbers of spawners captured in Red Rock Creek were 241 in 1994 and 85 in 1995. Only 20 (8.3%) of the grayling captured in 1994 were recaptured in 1995. Average lengths, weights, and condition factors were greater in 1994. Females outnumbered males in the spawning runs by a ratio of 1.8 to 1.0 in 1994 and 2.1 to 1.0 in 1995. Red Rock grayling mature at ages II and III. A shift in age structure was observed between the 2 years. Spawning runs were composed of ages II-VII in 1994 and ages II-VI in 1995. Ages II-III made up 27 and 63 percent of the runs while ages V+ made up 51 and 15 percent of the runs in 1994 and 1995, respectively. In 1994, a weir was also installed in Odell Creek, another historically important spawning tributary. Only 12 grayling were captured from this stream. During the study, no grayling were observed in any of the other 10 historic spawning tributaries for this population. Fry emigration was monitored in Red Rock Creek in 1994. Age-O grayling first appeared in the stream approximately 32 d after initial spawning activity and resided in the stream 10-15 d before emigration. Mean lengths ranged from 12.3 mm at swim-up to 28.5 mm on the last day of stream residence. STATUS AND BIOLOGY OF THE SPAWNING POPULATION OF RED ROCK LAKES ARCTIC GRAYLING
Statistical Methods for Human Microbiome Data Analysis

STATISTICAL METHODS FOR HUMAN MICROBIOME DATA ANALYSIS Jun Chen Hongzhe Li, PhD The human microbiome is the totality of the microbes, their genetic elements and the interactions they have with surrounding environments throughout the human body. Studies have implicated the human microbiome in health and disease. Two central themes of human microbiome studies are to identify potential factors influencing the microbiome composition, and to define the relationship between microbiome features and biological or clinical outcomes. With the development of next generation sequencing technologies, the human microbiome composition can be interrogated using high-throughput DNA sequencing. One strategy sequences the bacterial 16S ribosomal RNA gene for species identification. These 16S sequences are usually clustered into Operational Taxonomic Units (OTUs). Analysis of such OTU data raises several important statistical challenges, including taking into account the phylogenetic relationship among OTUs and modeling high-dimensional overdispersed count data. This dissertation presents three statistical methods developed specifically for 16S data analysis centering around the two themes. To test the association between overall microbiome composition and a covariate/an outcome, a testing procedure based on a generalized UniFrac distance was developed. The generalized UniFrac distance corrects the unduly weighting of classic UniFrac distances on either highly abundant or rare lineages, and was shown to be more powerful than the classic UniFracs. Under the framework of canonical correlation analysis (CCA), a structure-constrained sparse CCA was proposed to select the OTUs and their correlated covariates. A phylogenetic structure-constrained penalty function was imposed to induce certain smoothness on the linear coefficients according to the OTU phylogenetic relationship. Structure-constrained sparse CCA performed much better than sparse CCA in selecting relevant OTUs. Finally, a sparse Dirichlet-multinomial
The role of epigenetics in the rat mammary gland

Epigenetics plays an important role in carcinogenesis with heritable changes in DNA methylation and histone modifications intricately linked to the initiation, promotion, and progression of cancer. Evidence shows that a number of chemical and physical agents can induce epigenetic changes during carcinogenesis. Two such agents, estrogen and ionizing radiation, are generally recognized as being carcinogenic. Yet the epigenetic repercussions of these carcinogens remain relatively unknown. More importantly, the combined effect of these carcinogens has never been addressed in vivo from an epigenetic standpoint. Therefore, we focused on the effect of estrogen and ionizing radiation applied separately or in conjunction. We have found that the exposure to estrogen, either alone or in combination with radiation, induced pronounced morphological alterations, which was paralleled by modifications to the epigenomic landscape in the mammary gland. The results obtained from these rodent models can potentially be extrapolated to humans.
Changes in soil properties under tree species

A study was conducted to study the effects of ber (Ziziphus mauritiana Lamk), drumstick (Moringa olerifera Lam), karonda (Carissa congesta Wt.) and khejri (Prosopis cineraria L. Druce) on the physical and chemical properties of soil at different depths (0–15, 15–30, 30–45 and 45–60 cm). The increase in the porosity and water-holding capacity and decrease in the bulk density (of subsurface soils) in the sites under plantations were marginal, when compared to open sites. There was slight decrease in the pH of soil under vegetated area, whereas no appreciable change in EC was observed. There was an appreciable increase in the organic carbon (0.04 to 0.13%) and available nitrogen content (69 to 100 kg/ha) in the sites under vegetation. Fruit plants, particularly ber and drumstick growing in the arid region indicated the process of deposition of bases such as Ca and Mg in the surface layers from lower strata. Overall results showed that exchangeable cations such as Ca, Mg, and Na and available P and K have depicted a poor potential activity in the maintenance of fertility which is affected by the young nature of plantation. The increase/decrease of soil properties due to the influence of plantation was more in surface (0–15 cm) and subsurface (15–30 cm) than in the sub-surface layers of 30–45 and 45–60 cm. The results obtained from the physical and chemical analyses indicated that among the four different fruit plantations, ber recorded substantial improvement and maintenance in soil fertility followed by drumstick. The nutrient return through litter fall followed the order K > N > Ca in Z. mauritiana and M. olerifera and N > Ca > K, Ca > N > K in C. congesta and cineraria respectively. The soils belong to the order Entisol and the calcareous pH is well adopted for the plantation of these fruit trees.
Invertebrate surveys for conservation

Preface. Acknowledgements. 1: Introduction. Invertebrates in conservation. 2: Approaches to invertebrate surveys: posing the questions. 3: Sampling invertebrates: terrestrial environments. 4: Sampling invertebrates: aquatic environments. 5: Assessing use of sampling methods. 6: Processing and interpreting invertebrate samples. 7: Taxonomy and target groups for conservation studies. 8: Monitoring and evaluation of status. 9: Alternatives to species conservation. 10: Involving people in invertebrate conservation. References. Index
Influence of nitrogen doses on growth and green pod yield parameters of French bean varieties during kharif season under subtropical area of Jammu Region.

A field study was conducted to assess the effect of nitrogen doses on growth and parameters of French bean varieties during kharif 2006–07 and 2007–08.Three level (180 kg/ha, 120 kg/ha and 80 kg/ha) of nitrogen doses were applied on ten varieties. Highest influence of nitrogen was recorded with high doses of N application for all the traits studied. Among the varieties, the variety CH-812 recorded highest green pods per plot, number of pods per plant, pod diameter, number of green seeds per pod and green pod yield per plant in addition to earliest in flowering. It was observed that varieties early in flowering recorded higher green pod yield under all three N application regimes. Variety VL-65 recorded the highest number of branches per plant and pod length. Low number of branches per plant, number of pods per plant, pod diameter, pod length, number of green seeds per pod, 10 pod weight were responsible for lower green pod yield with low nitrogen application (80 kg/ha). Variety Pant Anupam and IVRFB-3 showed highest response for days to flowering and green pods per plot respectively, with higher dose of nitrogen application. Variety CH-812 was found most suitable for cultivation with high Nitrogen application (180 kg/ha) for higher green pod yield in hilly areas of J&K.
Predominant melliferous plants of the western Sudano Guinean zone of Cameroon

Between September 2003 and March 2005, melissopalynological methods were used to access the predominant melliferous plants (PMP) in 104 honey samples collected from the Soudano Guinean highlands zone of west Cameroon. A total of 19 PMP from 11 families were identified, Asteraceae is the most represented. Trees and herbs were frequently exploited. Spontaneous PMP were more represented. Perennial PMP were highly visited by Apis mellifera adansonii . PMP with white colour flower are the most utilized by bees compared to other colours. When seasonal exploitation was considered, the proportion of PMP exploited in the rainy season was higher. Eucalyptus saligna , Terminalia mantaly and Pterocarpus soyauxii were frequently exploited. Key words: Apis mellifera adansonii , melliferous plant, predominant, harvested.
Expression of α-Amylase by Aspergillus flavus in Medium: Effect of Nitrogen Source of Growth

Aspergillus flavus is contaminant of storage products in the tropics. A defined medium with starch as carbon source and varied nitrogen sources was inoculated with spore suspensions of approximately 5x10 5 spores per ml of Aspergillus flavus. The nitrogen sources were ammonium chloride, urea, potassium nitrate, ammonium sulphate, glycine, sodium nitrate, tryptone and peptone. Extracellular α-amylase was produced by the fungus within a period of ten days in the inoculated defined medium. Peptone was able to induce highest α-amylase activity, expressed as 546 units/mg protein on the ninth day of inoculation of medium. Least activity were with tryptone and ammonium sulphate with optimum activities expressed as 5 units/mg protein on the eighth, ninth and tenth days for tryptone and nil α-amylase activity on the tenth day when ammonium sulphate was nitrogen source.
Physiological Parameters, Isoenzymes and Hormonal Profiling In Different Varieties of Dates Palm in United Arab Emirates

The present investigation was carried out to explore the physiological changes in early, mid and late varieties of date palms in United Arab Emirates. The concentrations of biochemicals and antioxidant compounds, activities of antioxidant enzymes with their isoenzyme profiles, endogenous phytohormone contents were studied from preflowering, flowering, and post-flowering stages. Two varieties each from early (Shaham, Khanezi), mid (Barhee, Nabthasaif) and late (Khasab, Fardh) flowering types were used in the study. The protein content was higher in early varieties in preflowering stage, but lower in other two varieties. The phenol showed an opposite trend to protein. Ascorbic acid, reduced glutathione and tocopherol showed significant variation in different varieties. Similarly, the antioxidant enzyme ascorbate peroxidase was higher in preflowering stage in all varieties. Superoxide dismutase, polyphenol oxidase and catalase activities were highest in Bharhee for all the stages. Peroxidase activity (POX) was highest in Fardh variety of date palm whereas Khanezi exhibited the lowest. Several isoperoxidases bands were observed in gel electrophoresis at the time of flowering. The phytohormones varied within varieties. The levels of gibberellic acid, indole acetic acid, zeatin, and abscisic acid contents were positively influenced in pre-flowering and flowering stages due to the flower development process. The hormonal contents showed a transient rise in the preflowering stage and decreased during the flowering time and elevated in the postflowering stage. This study provided an insight into the possible roles of biochemicals, antioxidants with isoenzymes and endogenous hormones and their interactions in the regulation of flower development in different date palm varieties.
DNA FINGERPRINTING OF MERCURY-RESISTANT BACILLUS ISOLATED FROM THE INDUSTRIAL AREAS IN CAIRO, EGYPT -

Five mercury-resistant bacteria were successfully isolated from eighteen soil samples, collected from two of the Nile river bank districts, north and south Cairo where mercury is dumping from the surrounding industrial regions. Isolates were able to grow on basal medium supplemented with 100 ppm HgCl2.The acridine orange treatment revealed that the mercury-resistant gene is not plasmid-borne. The biochemical analysis affiliated the isolates to genus Bacillus. Pulsed-field gel electrophoresis of their DNA digested with AluI produced a characteristic genomic fingerprinting pattern with common conserved regions among them.