bluuebunny/crossref_metadata_2025_split huggingface dataset:
HBV genotypes in India: do they influence disease severity?
Authors: Madan Kaushal , Batra Yogesh , Sreenivas Vishnubhatla , Mizokami Masashi , Tanaka Yasuhito , Chalamalasetty Sreenivasa Baba , Panda Subrat K. , Acharya Subrat K. 
Published: January 2009

Aims:  Association of HBV genotypes (especially A and D) with severity of liver disease is controversial. We studied the influence of HBV genotypes on liver disease severity among Indian patients.Methods:  We selected 247 HBV infected patients (42 acute hepatitis, 87 carriers, 44 chronic hepatitis B [CHB], 35 liver cirrhosis [LC] and 40 hepatocellular carcinoma [HCC]). Genotyping of stored sera was performed using genotype‐specific enzyme‐linked immunosorbent assay (ELISA) and restriction fragment length polymorphism (RFLP). The distribution of genotypes in disease states of differing clinical, histological and biochemical severity were compared.Results:  The most common genotype was D (162/237, 68.3%), followed by A (61, 25.7%) and C (14, 5.9%). The distribution of HBV genotypes between patients with acute hepatitis and CHB (carriers + CHB + LC + HCC), or between carriers and disease states (CHB + LC + HCC), or between mild chronic infection (carriers + CHB) and complications of chronic HBV infection (LC + HCC) was similar. Eighty‐seven patients had liver biopsy; the median histological activity index (HAI) and fibrosis stage at baseline were similar between genotype groups (four [1–9] genotype A [n = 28]), three (2–4) genotype C (n = 4) and four (1–10) genotype D (n = 55); P = 0.33 for HAI score; (0.5 [0–6] genotype A, 0.5 [0–4] genotype C and 1 [0–6] genotype D; P = 0.92 for fibrosis stage). The response to therapy was similar between the genotypes.Conclusion:  Clinical, histological severity and therapeutic responses are similar among patients with HBV genotypes A and D.
Learning the Dynamic Processes of Color and Light in Interior Design
Authors: Poldma Tiiu 
Published: January 2009

Interior environments and their design are profoundly influenced by how designers integrate color and light with form and space. In our increasingly global world, new lighting technologies are changing our perception of color and light and subsequently our interrelationships with one another and with interior space. This alters the choices that we have as designers when we make both color and light decisions. Traditional light and color theories are being challenged with new lighting approaches that are complex, dynamic, and that are changing people's immediate experiences within spaces. Currently, new light technologies alter our perceptual relationships with people and forms, as light, its spectral color, and the forms its affects are more interactive and modulated in real time. Usually, in interior design coursework, students learn about color and light as static theories that they are then asked to apply within the interior design of spaces in subsequent design studios. Through a presentation and examination of the course “Color and Light in Interior Design,” this paper proposes considering integrating color and light theories with new contexts of dynamic, integrated human experiences of color and light in interior space. Students acquire learning experiences that integrate theory and practice by understanding the complex interrelationships of light, color, and objects in interior spaces as interactive, and by exploring design concepts in actual environments as a laboratory where they can test theories and their own ideas. The course structure is described and the theories underlying the course goals are explored. Color and light theories are considered in the context of emerging technologies and how phenomenological approaches affect our perceptions and experiences in spaces. Student examples of two of the four course projects are presented as these put theories into practice. The discussion shows that light and color theory, when explored in this way, stimulates both comprehensive and creative responses that integrate new technology with aesthetic theory and functional aspects of well–designed light/color solutions. The integrating of practice into theory stimulates reflective thinking and an understanding of situated contexts in interior design problem solving. The course develops emerging necessities of understanding dynamic color/light concepts that contribute to broadening interior design applied knowledge.
Field variable-head test in low-permeability materials: Assessing the effects of trapped gas pocket and cavity expansion
Authors: Chapuis Robert P. 
Published: January 2009

Trapped gas and cavity expansion may affect the data of a variable-head test in a monitoring well. In a low-permeability material, some gas may be trapped in the top of the filter pack. Presence of a gas pocket may be alleged when the initial change in water level in the pipe is less than the theoretical value due to the slug volume. A variable-head test with trapped gas is described by three equations to be solved simultaneously. The gas pocket contraction leads to an underestimation of the hydraulic conductivity, k, especially for small pipes used to test natural or compacted clay. It must be considered, however, that the difference between the theoretical and measured changes in initial water level is due to the sum of trapped gas contraction plus cavity expansion (falling-head) or trapped gas expansion plus cavity contraction (rising head). This difference cannot be used to assess the volume of trapped gas unless an independent mechanical test has established the material deformability. For example, pressuremeter tests can be done in cavities that are prepared with the same care as those used for the installation of piezometers. A simple test that consists of adding or removing known volumes of water in the pipe of the piezometer is described. Field data are provided along with the method to handle them and extract the correct k value. To avoid gas entrapment in the filter pack, a small diameter plastic tube can be installed and used as a gas vent.
Tree species distribution and its impact on soil properties, and nitrogen and phosphorus mineralization in a humid subtropical forest ecosystem of northeastern India
Authors: Kamei Jenpuiru , Pandey H. N. , Barik S. K. 
Published: January 2009

The impact of tree species on net N and P mineralization, and soil properties beneath their canopy were studied in a subtropical evergreen broad-leaved forest of northeastern India. Four types of experimental plots were identified based on tree species dominance. The first plot was dominated by Myrica esculenta Buch.-Ham. ex D. Don., the second by Rhododendron arboreum Sm., the third by Neolitsea cassia Koster., and the fourth was a mixed-species plot. Organic carbon content (3.11%) and NH4+-N concentration (11.40 μg·g–1) in the Rhododendron plot, pH (4.64) and total N content (0.89%) in the mixed plot, available P (5.16 μg·g–1) and NO3–-N (8.63 μg·g–1) concentrations in the Neolitsea plot were significantly higher (p < 0.001) than the other plots. All these soil parameters were lowest in the Myrica plot. The net N and P mineralization rates in an annual cycle across different plots ranged between 18.83 and 22.14 μg·g–1·month–1and between 4.54 and 5.87 μg·g–1·month–1, respectively. The flux varied significantly (p < 0.001) among the plots, the lowest and highest being in the Myrica plot and mixed plots, respectively. The differences in soil properties and in net N and P mineralization among different species plots were related to litter quality and yield of the respective species as well as soil microenvironment.
Growth and photosynthetic responses of two coniferous species to experimental warming and nitrogen fertilization
Authors: Zhao Chunzhang , Liu Qing 
Published: January 2009

The paper studied the short-term effects of experimental warming, nitrogen fertilization, and their combination on growth and photosynthetic performances of Picea asperata Mast. and Pinus tabulaeformis Carr. seedlings. These seedlings were subjected to two levels of temperature (ambient temperature and infrared heater warming) and two nitrogen levels (0 and 25 g N·m–2·year–1) for 6 months. Warming alone and fertilization alone significantly increased biomass accumulation and photosynthetic performances of both two species. The combination of warming and fertilization stimulated greater accumulation of stem, root, and total biomass and further increased chlorophyll content and net photosynthesis rate (A) in Pinus tabulaeformis seedlings. However, for Picea asperata seedlings, the interaction induced less increment in plant height, total biomass, chlorophyll contents, A, and the efficiency of photosystem than nitrogen treatment alone. These results implied that both climate warming and nitrogen addition were favorable for the early growth of both coniferous species; the interaction of these two factors caused adding or multiplying single-factor effects in the case of Pinus tabulaeformis seedlings but dampening them in the case of Picea asperata seedlings, at least in short time.
The effect of nursery substrate and fertilization on the growth and ectomycorrhizal status of containerized and outplanted seedlings of Picea abies
Authors: Vaario Lu-Min , Tervonen Arja , Haukioja Kati , Haukioja Markku , Pennanen Taina , Timonen Sari 
Published: January 2009

Over a 5 year period, we examined the influence of substrate and fertilization on nursery growth and outplanting performance of Norway spruce (Picea abies (L.) Karst.). We focused on the relative growth and development of roots and shoots and the colonization intensity and diversity of ectomycorrhizal (ECM) fungi. In the nursery, a conventional substrate (low-humified Sphagnum peat) supplemented with woody material (wood fibre and pine bark) and either mineral or organic fertilizers yielded shorter seedlings than those grown on the unmodified substrate. However, after outplanting, the growth rate of seedlings cultivated on modified substrates was higher than that of seedlings grown on the unmodified substrate. Seedlings cultivated in modified substrates had significantly higher root/shoot ratios and ECM diversity; the latter remained significant after ≥3 years of outplanting. Seedlings grown on a substrate containing 50% woody material and supplemented with organic fertilizer had the highest growth rate among all seedlings during the 3 year period of outplanting. Colonization intensity of ECM fungi was high in all seedlings except for those grown in heavily fertilized substrate. This study suggests that nursery techniques that produce seedlings with higher root/shoot ratios and ECM diversities could improve plantation success and growth rate for at least the first 3 years of outplanting.
Spatial distribution of forest landscape change in western New York from presettlement to the present
Authors: Wang Yi-Chen , Kronenfeld Barry J. , Larsen Chris P.S. 
Published: January 2009

Changes in tree taxon composition and distribution in western New York over a 200 year time period ca. 1797–1993 were examined by comparing the presettlement land survey with the US Forest Inventory and Analysis (FIA) survey. To ensure data quality, biases in presettlement bearing tree selection and FIA plot location were assessed. A 6 mile × 6 mile grid of taxa abundance was then estimated using geostatistics. Overall, significant changes in taxon composition occurred, with the taxa most abundant in the presettlement land survey — beech (37.0%), sugar maple (21.0%), and eastern hemlock (8.3%) — being replaced by sugar maple (19.2%), ash (11.7%), and red maple (11.4%) in the FIA survey. Spatially resolved comparisons showed that the landscape changed from fairly spatially homogeneous to more heterogeneous; in the presettlement survey, the most abundant taxon in most of the 6 mile × 6 mile grid cells was beech, while in the present survey, the most abundant taxon in most of the cells was one of several early successional taxa that each displayed a distinctly clustered geographic pattern of dominance. The clusters of dominance of the different early successional taxa may correspond to environmental factors. This study demonstrates the insights available through spatially resolved analyses of changes in the forest landscape between presettlement and present.
Age-class differences in shoot photosynthesis and water relations of Fraser fir (Abies fraseri), southern Appalachian Mountains, USA
Authors: Reinhardt Keith , Johnson Daniel M. , Smith William K. 
Published: January 2009

Fraser fir ( Abies fraseri (Pursh) Poir.) is an endemic tree species found only in refugial mountain-top forests in the southern Appalachian Mountains, USA. Very few studies have investigated the ecophysiology of this species in its natural environment. We measured and compared photosynthetic gas exchange and water relations of understory germinant seedlings (<3 cm height), older seedlings (>3 years old and ~0.15–1 m tall), and saplings (>10 years old and ~1–2 m tall) on a leaf-level basis. No significant differences in gas exchange were found among the age classes, although midday xylem water potentials were significantly different among the age classes. Differences in maximum photosynthesis (Amax) were <13%, ranging between 2.4 and 2.7 μmol·m–2·s–1 (P = 0.26). Maximum leaf conductances (gmax) were between 0.16 and 0.18 mol·m–2·s–1, varying less than 13% (P = 0.15). Midday xylem water potentials were similar between SE and SA (–1.2 to –1.4 MPa), but GS values were significantly less negative (–0.2 to –0.5 MPa). Thus, gas exchange and water relations in these understory age classes appeared similar, indicating no particular limitation to advanced regeneration between age classes.
A bioeconomic approach to assess the impact of an alien invasive insect on timber supply and harvesting: a case study with Sirex noctilio in eastern Canada
Authors: Yemshanov Denys , McKenney Daniel W. , de Groot Peter , Haugen Dennis , Sidders Derek , Joss Brent 
Published: January 2009

This study presents a model that assesses the potential impact of a new alien insect species, Sirex noctilio Fabricius, on pine timber supply and harvest activities in eastern Canada. We integrate the spread of S. noctilio with a broad-scale growth and harvest allocation model. Projections of pine mortality range between 25 × 106 and 115 × 106 m3 over 20 years depending on S. noctilio spread and impact assumptions. Our model suggests Ontario could experience the highest, most immediate losses (78% of the potential losses across eastern Canada), with Quebec sustaining most of the rest of the losses over the next 20 years. Potential losses of $86 to $254 million per year are simulated after 20 years. The net present value of total harvest losses after 28 years of outbreak ranges between $0.7 to $2.1 billion. Adaptation policies decrease short-term losses by 46%–55% and delay larger harvest failures by 9–11 years. Without harvest adaptation, failures to maintain annual allowable cut levels may occur once the total area infested exceeds 15 × 106 ha. While better understanding and representing S. noctilio behaviour will involve a significant effort, there is a strong demand by policy makers for this kind of information.
Compatible diameter and height increment models for lodgepole pine, trembling aspen, and white spruce
Authors: Nunifu Thompson K. 
Published: January 2009

In this study, compatible height and diameter increment models were fitted for lodgepole pine ( Pinus contorta Dougl. ex Loud. var. latifolia Engelm.), trembling aspen ( Populus tremuloides Michx.), and white spruce ( Picea glauca (Moench) Voss), using the relationship between diameter and height growth. It was assumed that tree diameter increment is directly proportional to height increment, and the proportionality constant is a function of competition and site productivity. The results showed that the fit statistics are comparable with results of other studies, with adjusted R2ranging from 30% to 50%. A validation test of the models, using independent permanent sample plots data, showed that the short-term predictions of the models for both pure and mixedwood stands are fairly unbiased. The models also gave reasonable average height growth and diameter growth trajectories for pure stands of the three species and also projected long-term mixedwood (aspen – white spruce mixture) volume growth dynamics reasonably well. The models also projected reasonably well (i) the effect of increasing initial stem density on average diameter and height, and (ii) the stand volume compared with an older version the Mixedwood Growth Model (ver. 2000A). It was concluded that explicitly linking tree height and diameter increment models does not only have a solid ecological basis, but it also results in a compatible prediction of tree growth and stand dynamics.
Antitumor Effects of a Combined 5-Aza-2′Deoxycytidine and Valproic Acid Treatment on Rhabdomyosarcoma and Medulloblastoma in Ptch Mutant Mice
Authors: Ecke Ines , Petry Frauke , Rosenberger Albert , Tauber Svantje , Mönkemeyer Sven , Hess Ina , Dullin Christian , Kimmina Sarah , Pirngruber Judith , Johnsen Steven A. , Uhmann Anja , Nitzki Frauke , Wojnowski Leszek , Schulz-Schaeffer Walter , Witt Olaf , Hahn Heidi 
Published: January 2009

Abstract
Patched (Ptch) heterozygous mice develop medulloblastoma (MB) and rhabdomyosarcoma (RMS) resembling the corresponding human tumors. We have previously shown that epigenetic silencing of the intact Ptch allele contributes to tumor formation in this model. Here, we investigated whether targeting of epigenetic silencing mechanisms could be useful in the treatment of Ptch-associated cancers. A reduction of endogenous DNA methyltransferase1 (Dnmt1) activity significantly reduced tumor incidence in heterozygous Ptch knockout mice. A combined treatment with the Dnmt inhibitor 5-aza-2′deoxycytidine (5-aza-dC) and the histone deacetlyase (HDAC) inhibitor valproic acid (VPA) efficiently prevented MB and RMS formation, whereas monotherapies with either drug were less effective. Wild-type Ptch expression was efficiently reactivated in tumors by 5-aza-dC/VPA combination therapy. This was associated with reduced methylation of the Ptch promoter and induction of histone hyperacetylation suggesting inhibition of HDACs in vivo. However, the treatment was not effective in clinically overt, advanced stage tumors. This is a first in vivo demonstration that targeting of Dnmt and HDAC activities is highly effective in preventing formation of Ptch-associated tumors. The results suggest a novel clinical strategy for consolidation therapy of corresponding tumors in humans after completion of conventional treatment. Our data also suggest that epigenetic therapy may be less effective in treating advanced stages of tumors, at least in this tumor model. [Cancer Res 2009;69(3):887–95]
Smad Ubiquitination Regulatory Factor 2 Promotes Metastasis of Breast Cancer Cells by Enhancing Migration and Invasiveness
Authors: Jin Chaoyang , Yang Yu-an , Anver Miriam R. , Morris Nicole , Wang Xiangchun , Zhang Ying E. 
Published: January 2009

Abstract
Controlled protein degradation mediated by ubiquitin/proteasome system (UPS) plays a crucial role in modulating a broad range of cellular responses. Dysregulation of the UPS often accompanies tumorigenesis and progression. Here, we report that Smad ubiquitination regulatory factor 2 (Smurf2), a HECT-domain containing E3 ubiquitin ligase, is up-regulated in certain breast cancer tissues and cells. We show that reduction of Smurf2 expression with specific short interfering RNA in metastatic breast cancer cells induces cell rounding and reorganization of the actin cytoskeleton, which are associated with a less motile and invasive phenotype. Overexpression of Smurf2 promotes metastasis in a nude mouse model and increases migration and invasion of breast cancer cells. Moreover, expression of Smurf2CG, an E3 ligase–defective mutant of Smurf2, suppresses the above metastatic behaviors. These results establish an important role for Smurf2 in breast cancer progression and indicate that Smurf2 is a novel regulator of breast cancer cell migration and invasion. [Cancer Res 2009;69(3):735–40]
Membrane Microvesicles as Actors in the Establishment of a Favorable Prostatic Tumoral Niche: A Role for Activated Fibroblasts and CX3CL1-CX3CR1 Axis
Authors: Castellana Donatello , Zobairi Fatiha , Martinez Maria Carmen , Panaro Maria Antonietta , Mitolo Vincenzo , Freyssinet Jean-Marie , Kunzelmann Corinne 
Published: January 2009

AbstractTumor microenvironment is enriched in plasma membrane microvesicles (MV) shed from all cell types that constitute the tumor mass, reflecting the antigenic profile of the cells they originate from. Fibroblasts and tumor cells mutually communicate within tumor microenvironment. Recent evidences suggest that tumor-derived MVs (TMV) exert a broad array of biological functions in cell-to-cell communication. To elucidate their role in cancer-to-fibroblast cell communication, TMV obtained from two prostate carcinoma cell lines with high and weak metastatic potential (PC3 and LnCaP, respectively) have been characterized. TMV exhibit matrix metalloproteinases (MMP) and extracellular MMP inducer at their surface, suggesting a role in extracellular matrix degradation. Moreover, TMV not only induce the activation of fibroblasts assessed through extracellular signal-regulated kinase 1/2 phosphorylation and MMP-9 up-regulation, increase motility and resistance to apoptosis but also promote MV shedding from activated fibroblasts able in turn to increase migration and invasion of highly metastatic PC3 cells but not LnCaP cells. PC3 cell chemotaxis seems, at least partially, dependent on membrane-bound CX3CL1/fractalkine ligand for chemokine receptor CX3CR1. The present results highlight a mechanism of mutual communication attributable not only to soluble factors but also to determinants harbored by MV, possibly contributing to the constitution of a favorable niche for cancer development. [Cancer Res 2009;69(3):785–93]
ADP-Ribosylation Factor 6 Regulates Glioma Cell Invasion through the IQ-Domain GTPase-Activating Protein 1-Rac1–Mediated Pathway
Authors: Hu Bo , Shi Binhai , Jarzynka Michael J. , Yiin Jia-Jean , D'Souza-Schorey Crislyn , Cheng Shi-Yuan 
Published: January 2009

Abstract
A common pathobiological feature of malignant gliomas is the insidious infiltration of single tumor cells into the brain parenchyma, rendering these deadly tumors virtually incurable with available therapies. In this study, we report that ADP-ribosylation factor 6 (ARF6), a Ras superfamily small GTPase, is abundantly expressed in invasive human glioma cells. Cellular depletion of ARF6 by small interfering RNA decreased Rac1 activation, impaired HGF-stimulated and serum-stimulated glioma cell migration in vitro, and markedly decreased the invasive capacity of invasive glioma in the brain. Furthermore, ectopic expression of ARF6 in glioma cells promoted cell migration via the activation of Rac1. Upon stimulation of glioma cells with HGF, we show that IQ-domain GTPase-activating protein 1 (IQGAP1) is recruited and overlaps with ARF6 at the leading edge of migrating cells. However, cellular depletion of ARF6 abrogated this recruitment of IQGAP1 and attenuated the formation of surface protrusions. ARF6 forms complexes with Rac1 and IQGAP1 in glioma cells upon HGF stimulation, and knockdown of IQGAP1 significantly inhibits ARF6-induced Rac1 activation and cell migration. Taken together, these data suggest that ARF6-mediated Rac1 activation is essential for glioma cell invasion via a signaling pathway that requires IQGAP1. [Cancer Res 2009;69(3):794–801]