Miracle-dz/UniFAR-FTUs huggingface dataset:
Insulin-like Growth Factor Binding Protein 3 Mediates Retinoic Acid- and Transforming Growth Factor β2-induced Growth Inhibition in Human Breast Cancer Cells

Retinoic acid (RA) is a potent in vitro inhibitor of cell proliferation in various malignant cell lines. The exact mechanisms of its actions, however, are not fully understood. To further elucidate the nature of this inhibition, we investigated the effects of RA in an estrogen receptor-negative human breast cancer cell line, MDA-MB-231. RA (0.01-5 µm) significantly inhibited MDA-MB-231 cell growth by 35-40% as compared with untreated controls. Similar growth inhibitory actions were observed when cells were treated with transforming growth factor β2 (TGF-β2), another factor with antiproliferative actions in breast cancer cells. Both RA and TGF-β2 increased the levels of insulin-like growth factor binding protein (IGFBP) 3 (2-3-fold) and mRNA (1.5-2-fold), whereas IGFBP-4 levels remained essentially unchanged. The direct involvement of IGFBP-3 in cell growth inhibition was further confirmed by its action on cell growth: exogenous IGFBP-3 directly and significantly inhibited MDA-MB-231 cell number by 40%. These results provided circumstantial evidence that IGFBP-3 may mediate RA and TGF-β2 growth inhibitory actions in human breast cancer cells. To test this hypothesis, we used an antisense IGFBP-3 oligodeoxynucleotide (ODN) which specifically inhibits IGFBP-3 expression. The antisense IGFBP-3 ODN dramatically blocked both RA- and TGF-β2-induced increases in IGFBP-3 protein (90%) and mRNA levels (90%). This effect was not observed when RA- or TGF-β2-exposed cells were treated with sense IGFBP-3 ODN. Moreover, antisense ODN did not significantly affect IGFBP-4 protein or mRNA levels, strongly supporting the specificity of the antisense IGFBP-3 ODN effect on IGFBP-3 mRNA. This specific effect of antisense IGFBP-3 ODN on IGFBP-3 protein and mRNA levels was accompanied by significant attenuation of the inhibition of cell proliferation attained with RA or TGF-β2 (approximately 40% of either RA- or TGF-β2-induced inhibition). The control sense IGFBP-3 ODN did not reduce the growth inhibition observed with either RA or TGF-β2. These results indicate that IGFBP-3 is an important mediator of RA-and TGF-β2-induced cell growth inhibition in human breast cancer cells.
Winter migration and diving behaviour of porbeagle shark, Lamna nasus, in the Northeast Atlantic

Saunders, R. A. , Royer, F. , and Clarke, M. W. 2011. Winter migration and diving behaviour of porbeagle shark, Lamna nasus, in the Northeast Atlantic. – ICES Journal of Marine Science, 68: 166–174.The porbeagle is one of the top marine predators in the North Atlantic. However, little is known about its biology, abundance, or spatial ecology there. Results are presented on the migration and behaviour of three porbeagles tagged with archival pop-up tags off Ireland between September 2008 and January 2009. One shark migrated >2400 km to the northwest of Morocco, residing around the Bay of Biscay for approximately 30 days. The other two remained more localized in off-shelf regions around the Celtic Sea/Bay of Biscay and off western Ireland. The sharks occupied a broad vertical depth range (0–700 m) and a relatively limited temperature range (∼9–17°C), with notable variations in diving behaviour between individual sharks. There were distinct day–night differences in depth distribution, each shark being positioned higher in the water column by night than by day. Night-time depth distribution also appeared to be driven by the lunar cycle during broad-scale migration through oceanic waters. Our results show that porbeagles occupy and traverse regions of high fishing activity where they are potentially vulnerable to population depletion. Such large-scale movement outside the ICES Area underlines the need for international coordination in their assessment and management.
First detection of strains of Varroa destructor resistant to coumaphos. Results of laboratory tests and field trials

The susceptibility of four populations of Varroa destructorto the organophosphorous aca- ricide coumaphos was studied. The mites were taken from apiaries kept in Lombardy (northern Italy) and tested with a laboratory assay on paraffin wax with known concentrations of coumaphos. The sus- ceptibility of two populations to coumaphos was close to that of susceptible populations, indicated in the literature (LC 50 at 24 hours: 12.6 μg/g); a third population showed a significant, but slight increase in tolerance (LC 50 at 24 hours: 29 μg/g) while the fourth population had a much higher LC 50 (>200 μg/g at 24 hours). In subsequent field trials carried out in the apiary in which the latter population had been sampled, the total average efficacy of two treatments with Perizin ® (the com- mercial formulation of coumaphos) in colonies without capped brood was 46% (28-88%). coumaphos / Varroa destructor / resistance / bioassay / field trial
Ecology and Distribution of the Introduced Moss Campylopus introflexus (Dicranaceae) In Western North America

Abstract Campylopus introflexus (Hedw.) Brid. is a moss native to the southern hemisphere and well documented as an invasive species throughout Europe. The species was first collected in North America in 1967 in Del Norte Co., California, and now occurs primarily in coastal areas from Santa Barbara Co. to southern British Columbia. Herbarium specimens were assembled and verified to document the distribution of the species in western North America. Collection dates of specimens indicate a rapid invasion along the coast north and south from the first record, with a slower establishment of inland populations. The species is most prevalent in coastal, foggy areas. Many of the populations are associated with anthropogenic environments, but several populations appear to be invading relatively undisturbed sites. These are mostly characterized by poor soils along the coast, with the largest populations associated with Bishop Pine forests and stabilized sand dunes. A brief summary of ecological literature documenting the European invasion of C. introflexus suggests that the species, especially in the presence of disturbance, has the potential to negatively impact native bryophyte, lichen, and vascular plant species.
Accumulation and recycling of PCBs and PAHs in artificially eutrophied Lake 227

The influence of lake trophic status on the cycling and burial of polychlorinated biphenyls (PCB's) and polycyclic aromatic hydrocarbons (PAH's) was examined in Lake 227 (L227), an artificially eutrophied lake in the Experimental Lakes Area, northwestern Ontario, Canada. Sedimentary accumulation of PCB's, PAH's, and organic carbon (OC) was determined pre- and post-eutrophication in L227 and compared with accumulation in other regional lakes. Mass and OC accumulation increased an average of 1.4 and 2.0 times, respectively, since nutrient addition began in June 1969. ΣPCB and ΣPAH sediment accumulation rates and profiles in L227 were similar to those in Lake Superior and other proximate and midlatitude lakes unimpacted by point sources. Eutrophication did not increase contaminant accumulation. In general, individual PAH accumulation rates declined following eutrophication, which coincided with similar signals elsewhere. Perylene declined markedly (4 times) since eutrophication as a result of decreased in si.
The influence of defoliation height on dry‐matter partitioning and CO2 exchange of perennial ryegrass miniature swards

This study investigated the effects of defoliation intensity on the above- and below-ground plant mass, rates of CO2 exchange and leaf appearance rate of ryegrass miniature swards maintained at constant cutting height ranging from 20 mm to 160 mm for 5 months. Total plant mass, above-ground herbage mass and root mass increased as cutting height increased from 20 to 120 mm. Further increase in cutting height did not increase total plant mass or its components. Leaf appearance rate and photosynthesis per unit of leaf dry matter (DM) decreased as defoliation height increased from 20 to 160 mm. Gross and net CO2 uptake per unit soil surface area increased with cutting height to 120 mm. Further increase in cutting height to 160 mm decreased gross and net CO2 uptake and herbage harvested. A multivariate canonical discriminant analysis indicated different responses of root and shoot mass to cutting height and a reduction in CO2 uptake rate at the 160 mm cutting height. The implications of those responses to defoliation management of forage plants are discussed.
SPORANGIAL STRUCTURE AND ZOOSPOROGENESIS IN CHORDA TOMENTOSA (LAMINARIALES) 1, 2, 3

Members of the genus Chorda represent the simplest form of sporophyte in the order Laminariales. The present study deals with reproduction in Chorda tomentosa, involving the initiation, growth, and structure of the sporangium and the process of zoosporogenesis. The simple tube‐like sporophyte of Chorda tomentosa grows in diameter by means of repeated anticlinal divisions in a superficial meristematic layer known as the meristoderm. The onset of reproduction is marked by the conversion of the meristoderm from contributing cells to the vegetative plant body to producing 2 new cell types: paraphyses and sporangial mother cells. At the time of initiation, sporangial mother cells are crescent shaped and possess a densely staining cytoplasm. Sporangial mother cells increase in size, become ellipsoid, decrease in staining density, and undergo meiosis. After meiosis, sporangia increase in size while their nuclei undergo successive cycles of synchronous mitotic divisions. Sporangia increase to a maximum length of 120 μ;m at which time they possess the characteristic “cap” found in all members of the order studied thus far. At this stage the protoplast of the sporangium is organized into a peripheral layer of nucleus‐chloroplast pairs and a central region of vacuoles. Cleavage furrows begin to form at the cell membrane and are met by furrows developing in the interior of the cytoplasm resulting in the division of the entire protoplast into separate units. Each unit is an individual zoospore. The biflagellate zoospores contain a nucleus, one chloroplast with eyespot, perinuclear Golgi, and several bodies of presumed storage carbohydrate. The occurrence of a small population of early developing sporangia is described. In essential details, the origin, development, and structure of sporangia in Chorda tomentosa are identical to all earlier observations in the Laminariales.
Estimating Midday Leaf and Stem Water Potentials of Mature Pecan Trees from Soil Water Content and Climatic Parameters

Diurnal and temporal patterns of stem water potential (cstem )a nd leaf water potential (cleaf) were determined during June to Sept. 2010 and 2011 at lower (2.5 m tree height), mid- (4.6 m), and upper (7.6 m) canopy positions for two flood-irrigated, mature pecan (Carya illinoinensis (Wangenh.) K. Koch) orchards near Las Cruces, NM. Diurnal measurements of cstem and cleaf at three canopy heights were correlated under both dry and wet soil conditions. However, although soil water contents at Site 2 (silty clay loam texture) remained higher compared with Site 1 (sandy loam), cstem and cleaf values, particularlyunderdrysoilconditionsatSite2,wereconsistentlylower,showingtheeffectof clayey soil texture on pecan water stress. Diurnal patterns of cstem and cleaf indicated that measurements of cstemand cleaf should be made close to early afternoon (between 1400 and 1500 HR Mountain Standard Time) to evaluate mature pecan water stress, which also corresponded to maximum climatic stress conditions. Midday cstem and cleaf measured at three canopy heights over several irrigation cycles during the 2010 season were correlated with one another, midday soil water content at different depths, and atmospheric vapor pressure deficit (VPD). Multiple regression analysis (between midday cstem or cleaf and midday uavg (soil water content at 0 to 40 cm),air temperature (Tmd), and relative humidity (RHmd)) during the 2010 season revealed that two-parameter regression models (cstem or cleaf = f (midday uavg and Tmd)) were the most significant for the interpretation of midday cstem or cleaf at both sites. Using the two-parameter model, predictions of cstem and cleaf measured on the both shaded and sunlit sides of trees at three canopy heights for 2011 showed good agreement between measured and predicted cstem and cleaf (R 2 ranged from 0.70 to 0.98). Two-parameter models derived in an earlier study generally underpredicted cstem both in 2010 and 2011, which further supported the importance of the time of midday cstem and cleaf measurements suggested in this study.
Wetland Food Resources for Spring-Migrating Ducks in the Upper Mississippi River and Great Lakes Region

Wetlands in the Upper Mississippi River and Great Lakes Region (UMRGLR) must annually sustain populations of migrating waterfowl from the mid-continent of North America. We used multi-stage sampling to estimate plant and invertebrate food biomasses (kg/ha) for ducks in 3 wetland habitat types at 6 stop-over locations in the UMRGLR during 2006 and 2007. Total biomass was greatest in palustrine emergent (PEM; x ¼ 208 kg/ha, SE ¼ 23, median ¼ 120), followed by palustrine forested (PF; x ¼ 87 kg/ha, SE ¼ 7; median ¼ 43), and lacustrine-riverine (LR; x ¼ 52 kg/ha, SE ¼ 7; median ¼ 27) wetlands. Ducks that foraged in forested and LR wetlands encountered the least food abundance during spring in the UMRGLR. Our estimates of food abundance were the lowest reported among other landscape scale surveys from mid-continent North America. About 1 in every 5 PEM wetlands and over half of our PF and LR wetlands that we sampled contained <50 kg/ha of food, suggesting many had little or no forage value to ducks during spring. Biomass of plant foods generally exceeded invertebrate biomass in all habitat types, although invertebrate biomass estimates exceeded plant biomass in 8 of 29 sites when considered by wetland type and year. Total food biomass estimates varied widely (x ¼ 6-425 kg/ha) between years and among habitats; thus, using global arithmetic means to estimate food abundance for conservation planning obscures fine scale temporal and spatial variation that may be necessary for management on local and sub-regional levels. Distributions of food biomass estimates were right-skewed, causing us to question whether arithmetic means realistically represent levels of food abundance that all ducks encounter during spring migration. Alternative measures of central tendency (e.g., median) may be more biologically realistic, particularly if spring-migrating ducks are not distributed in an ideal-free manner with respect to food abundance. Future research should determine how ducks distribute themselves in relation to variation in food abundance in space and time during spring migration to strengthen the biological approach to conservation planning in non- breeding Joint Venture areas of the North American Waterfowl Management Plan. 2011 The Wildlife Society.
Determination of diagnostic species with statistical fidelity measures

Abstract Statistical measures of fidelity, i.e. the concentration of species occurrences in vegetation units, are reviewed and compared. The focus is on measures suitable for categorical data which are based on observed species frequencies within a vegetation unit compared with the frequencies expected under random distribution. Particular attention is paid to Bruelheide's u value. It is shown that its original form, based on binomial distribution, is an asymmetric measure of fidelity of a species to a vegetation unit which tends to assign comparatively high fidelity values to rare species. Here, a hypergeometric form of u is introduced which is a symmetric measure of the joint fidelity of species to a vegetation unit and vice versa. It is also shown that another form of the binomial u value may be defined which measures the asymmetric fidelity of a vegetation unit to a species. These u values are compared with phi coefficient, chi‐square, G statistic and Fisher's exact test. Contrary to the other measures, phi coefficient is independent of the number of relevés in the data set, and like the hypergeometric form of u and the chi‐square it is little affected by the relative size of the vegetation unit. It is therefore particularly useful when comparing species fidelity values among differently sized data sets and vegetation units. However, unlike the other measures it does not measure any statistical significance and may produce unreliable results for small vegetation units and small data sets. The above measures, all based on the comparison of observed/expected frequencies, are compared with the categorical form of the Dufrêne‐Legendre Indicator Value Index, an index strongly underweighting the fidelity of rare species. These fidelity measures are applied to a data set of 15 989 relevés of Czech herbaceous vegetation. In a small subset of this data set which simulates a phytosociological table, we demonstrate that traditional table analysis fails to determine diagnostic species of general validity in different habitats and large areas. On the other hand, we show that fidelity calculations used in conjunction with large data sets can replace expert knowledge in the determination of generally valid diagnostic species. Averaging positive fidelity values for all species within a vegetation unit is a useful approach to measure quality of delimination of the vegetation unit. We propose a new way of ordering species in synoptic species‐by‐relevé tables, using fidelity calculations. Nomenclature:Ehrendorfer (1973).
Purification and partial characterisation of a novel trypsin-like cysteine protease from Metarhizium anisopliae

Trypsin-like enzymes from the entomopathogenic fungus Metarhizium anisopliae have been characterised. Two proteases with tryptic activity were purified by narrow range isoelectric focussing and affinity chromatography. One of these proteases, with an isoelectric point of 5.4 and a molecular mass of 28.8 kDa is a ‘classical’ trypsin belonging to the serine protease class. The other protease, with an isoelectric point of 4.6 and a molecular mass of 26.7 kDa, demonstrates trypsin-like specificity but, on the basis of inhibition and activation studies, belongs to the cysteine protease family and as such is the first fungal protease to be found of this type. The amino acid composition, kinetic constants and activity against proteinaceous substrates, including locust cuticle have been determined.
An efficient hairy root culture system for Withania somnifera (L.) Dunal

Withania somnifera is an important aromatic medicinal plant and possesses wide array of pharmacological properties. In the present investigation, an improved version of hairy root culture system was developed by optimizing various transformation parameters such as type of explant, concentration of acetosyringone, Agrobacterium types and co-cultivation period. Between the leaf and cotyledon explants and two Agrobacterium rhizgenes strains (R1000 and A4) tested, leaf explants infected with R1000 and cocultured for five days on MS basal half strength medium in the presence of acetosyringone (100 µM) attained a higher frequency (88%) of hairy root induction. By adopting this protocol, we could utilize the hairy root culture for industrial scale production of withanolides. Keywords: Leaf explant, Agrobacterium rhizogenes , Withania somnifera, co-cultivation period, acetosyringone. African Journal of Biotechnology , Vol 13(43) 4141-4147
EXAMINATION OF FLORAL NECTAR OF CITRUS, COTTON, AND ARIZONA DESERT PLANTS FOR MICROBES

On a recherche la presence de bacteries, de levures et de moisissures dans le nectar floral de 3 varietes de coton cultivees en champ, de 9 varietes cultivees sous serre, de 5 varietes d'agrumes, du cactus geant (Cereus giganteus) et du figuier de Barbarie. Les resultats sont discutes par rapport a d'eventuelles substances antimicrobiennes presentes dans le nectar et a l'origine de la microflore des abeilles. Le nectar ne semble jouer qu'un role mineur dans le processus de contamination microbienne
A systems approach to cellular signal transduction

Vital cellular processes such as growth, gene expression, and homeostasis depend on the correct transmission of molecular signals within and between cells. The vast complexity of these molecular signaling networks has necessitated the use of mathematical methods to model, characterize, and predict cellular responses. The work presented in this dissertation shows how computational methods were used to elucidate two clinicallyrelevant cellular signaling responses: (i) phosphotyrosine signaling through the epidermal growth factor receptor (EGFR), a receptor tyrosine kinase that is commonly overexpressed or structurally altered in human cancers; and (ii) phosphoinositide and calcium signaling in human platelets---the key cellular mediators of hemostasis and pathological thrombus formation. The kinetic model of EGFR-mediated signaling in wildtype and mutant cells showed how mutant forms of the receptor use an irregular pattern of tyrosine phosphorylation that preferentially activates the survival oncoprotein, Akt. By quantifying the amount of signal flow through diverging pathways downstream of the receptor, our calculations provided a mechanistic explanation for the clinical observation that therapeutic tyrosine kinase inhibitors can control tumor growth in cells bearing certain EGFR mutations. In the second major study, a kinetic model of ADP-stimulated calcium release in human platelets was used to make precise, quantitative predictions about the molecular makeup and structural properties of the platelet. Specifically, we found that the resting structure of platelets places strong restrictions on several biophysical quantities, such as the resting concentration of free inositol 1,4,5-trisphosphate, the ratio of calcium ATPase pumps to release channels, and the size of the calcium storage compartment. Notably, the model also demonstrated that the irregular calcium spiking behavior observed in single ADP-stimulated platelets is due to the extremely small cellular volume. A novel method for constructing kinetic signaling networks, based on restricting the steady-state properties of the model, is also presented. Future applications and extensions of the systems approach to signal transduction modeling are discussed in the final chapter. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Genomics & Computational Biology First Advisor Scott Diamond Second Advisor Ravi Radhakrishnan This dissertation is available at ScholarlyCommons: http://repository.upenn. edu/edissertations/8
On the morphological significance of certain cranio‐vertebral variations

Among the anatomical problems having received additional elucidation of late must be noted that of cranio-vertebralvariation. The road pursued in connection with it is fairly similar for all such phenomena: it led over topographic description and speculative conjecturing to the study of ontogenetic conditions and biological argumentation. Considerable literature has been accumulated on the above subject, while only a limited number of contributions have approached its causal nature from the comparative and ontogenetic points of view. A brief historical review pointing out the principal stations may precede a few personal observations which in the light of recent investigation have acquired more decided significance.