bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional convergence of developmentally and adult‐generated granule cells in dentate gyrus circuits supporting hippocampus‐dependent memory
Authors: Stone Scellig S.D. , Teixeira Cátia M. , Zaslavsky Kirill , Wheeler Anne L. , Martinez‐Canabal Alonso , Wang Afra H. , Sakaguchi Masanori , Lozano Andres M. , Frankland Paul W. 
Published: September 2010

AbstractIn the hippocampus, the production of dentate granule cells (DGCs) persists into adulthood. As adult‐generated neurons are thought to contribute to hippocampal memory processing, promoting adult neurogenesis therefore offers the potential for restoring mnemonic function in the aged or diseased brain. Within this regenerative context, one key issue is whether developmentally generated and adult‐generated DGCs represent functionally equivalent or distinct neuronal populations. To address this, we labeled separate cohorts of developmentally generated and adult‐generated DGCs and used immunohistochemical approaches to compare their integration into circuits supporting hippocampus‐dependent memory in intact mice. First, in the water maze task, rates of integration of adult‐generated DGCs were regulated by maturation, with maximal integration not occurring until DGCs were five or more weeks in age. Second, these rates of integration were equivalent for embryonically, postnatally, and adult‐generated DGCs. Third, these findings generalized to another hippocampus‐dependent task, contextual fear conditioning. Together, these experiments indicate that developmentally generated and adult‐generated DGCs are integrated into hippocampal memory networks at similar rates, and suggest a functional equivalence between DGCs generated at different developmental stages. © 2010 Wiley Periodicals, Inc.
Delineation of hydrologically similar units in a watershed based on fuzzy classification of soil hydraulic properties
Authors: Santra Priyabrata , Das Bhabani Sankar , Chakravarty Debashish 
Published: September 2010

AbstractEvaluation of flow and transport processes in a watershed‐scale requires that the watershed be divided into homogenous spatial units referred to as hydrologically similar units (HSUs). Although a few discretization schemes are already in use, a universally acceptable method of obtaining HSUs is yet to emerge. In this study, we developed a fuzzy inference system (FIS) to classify the saturated hydraulic conductivity (Ks) and two water‐retention parameters α and n into fuzzy logic‐based soil hydrologic classes (FSHCs). Analysis of these classes showed that soil properties within an FSHC have less variability and those between two FSHCs have large variability. This result suggested that soils belonging to a specific FSHC may be more similar than those across different FSHCs and may be grouped together to represent an HSU. Soils within a specific hydrologic class were aggregated to delineate HSUs within the watershed. For the Dengei Pahad micro‐watershed (DPW), this approach showed five distinct regions representing a discretized zone having similar soil hydraulic properties. Application of this approach on a larger international database of soil hydraulic properties revealed that the developed hydrologic classes are quite comparable across different databases. The delineated HSUs based on these FSHCs were also better than the soil series map of the watershed in maintaining the soil heterogeneity of the watershed. Moreover, this new discretization scheme using the SWAT modelling environment showed better performance than the soil series‐based discretization approach. Copyright © 2010 John Wiley & Sons, Ltd.
Hydrological response of a Brazilian semi‐arid catchment to different land use and climate change scenarios: a modelling study
Authors: Montenegro A. , Ragab R. 
Published: September 2010

AbstractBrazilian semi‐arid regions are characterized by water scarcity, vulnerability to desertification, and climate variability. The investigation of hydrological processes in this region is of major interest not only for water planning strategies but also to address the possible impact of future climate and land‐use changes on water resources. A hydrological distributed catchment‐scale model (DiCaSM) has been applied to simulate hydrological processes in a small representative catchment of the Brazilian northeast semi‐arid region, and also to investigate the impact of climate and land‐use changes, as well as changes associated with biofuel/energy crops production. The catchment is part of the Brazilian network for semi‐arid hydrology, established by the Brazilian Federal Government. Estimating and modelling streamflow (STF) and recharge in semi‐arid areas is a challenging task, mainly because of limitation in in situ measurements, and also due to the local nature of some processes. Direct recharge measurements are very difficult in semi‐arid catchments and contain a high level of uncertainty. The latter is usually addressed by short‐ and long‐time‐scale calibration and validation at catchment scale, as well as by examining the model sensitivity to the physical parameters responsible for the recharge. The DiCaSM model was run from 2000 to 2008, and streamflow was successfully simulated, with a Nash–Sutcliffe (NS) efficiency coefficient of 0·73, and R2 of 0·79. On the basis of a range of climate change scenarios for the region, the DiCaSM model forecasted a reduction by 35%, 68%, and 77%, in groundwater recharge (GWR), and by 34%, 65%, and 72%, in streamflow, for the time spans 2010–2039, 2040–2069, and 2070–2099, respectively, could take place for a dry future climate scenario. These reductions would produce severe impact on water availability in the region. Introducing castor beans to the catchment would increase the GWR and streamflow, mainly if the caatinga areas would be converted into castor beans production. Changing an area of 1000 ha from caatinga to castor beans would increase the GWR by 46% and streamflow by 3%. If the same area of pasture is converted into castor beans, there would be an increase in GWR and streamflow by 24% and 5%, respectively. Such results are expected to contribute towards environmental policies for north‐east Brazil (NEB), and to biofuel production perspectives in the region. Copyright © 2010 John Wiley & Sons, Ltd.
Suspended solid yield from forest harvesting on upland blanket peat
Authors: Rodgers Michael , O'Connor Mark , Robinson Mark , Muller Markus , Poole Russell , Xiao Liwen 
Published: September 2010

AbstractForest harvesting activities, if not carefully carried out, can disturb the forest soils and can cause significant suspended solid concentration increases in receiving water. This study examined how harvesting, following forestry guidelines, influenced suspended solid concentrations and loads in the receiving water of a blanket peat salmonid catchment. The study site comprised of two forest coupes of 34‐year‐old conifers drained by a first‐order stream. The upper coupe was not felled and acted as a baseline ‘control’ catchment; the downstream coupe was completely harvested in summer 2005 and served as the ‘experimental’ catchment. Good management practices such as the proper use of brash mats and harvesting only in dry weather were implemented to minimize soil surface disturbance and streambank erosion. Stream flow and suspended solid measurements at an upstream station (US) and a downstream station (DS) in the study stream commenced over a year before felling took place. The suspended solid concentrations, yields and release patterns at US and DS were compared before and after harvesting. These showed that post‐guideline harvesting of upland blanket peat forest did not significantly increase the suspended solid concentrations in the receiving water and the aquatic zone need not be adversely affected by soil releases from sites without a buffer strip. Copyright © 2010 John Wiley & Sons, Ltd.
Understanding and modelling spatial drain–aquifer interactions in a low‐lying coastal aquifer—the Thurne catchment, Norfolk, UK
Authors: Simpson Trevor B. , Holman Ian P. , Rushton Ken R. 
Published: September 2010

AbstractSeawater intrusion into fresh groundwater formations generally results inadvertently from human activities, such as over‐abstraction from coastal aquifers. This article describes the data analysis to quantify drain–aquifer interactions in a low‐lying pump‐drained coastal aquifer, which is subject to saline intrusion due to widespread land drainage, and the resulting development and application of a numerical groundwater model to understand the spatial groundwater system behaviour (including groundwater salinity fluxes). Without measured flow data in this pump‐drained catchment, a novel groundwater head‐dependent approach to hydrograph separation is described. Time‐variant and time‐invariant MODFLOW analyses are utilised to examine the flow processes. A new approach to calculate drain coefficients, which represent the extensive network of drainage ditches in the regional model, using field information, is described; the sum of the drainage coefficients are close to the values independently estimated from the head‐dependent hydrograph separation. Results show that (1) the groundwater flows into the drainage systems are well reproduced using the new drain coefficients, (2) particle tracking of fresh and saline water can explain observed spatial salinity distribution within drainage networks and (3) the modelled flow of seawater across the coast is approximately 25% greater than that discharged by the pumps, demonstrating the need for drainage management to be aware of the slow response of groundwater systems to past drainage system changes. The article demonstrates that numerical groundwater modelling can produce the improved understanding needed to inform management decisions in such complex environments. Copyright © 2010 John Wiley & Sons, Ltd.
Environmental controls of wood entrapment in upper Midwestern streams
Authors: Merten Eric Christopher , Finlay Jacques , Johnson Lucinda , Newman Raymond , Stefan Heinz , Vondracek Bruce 
Published: September 2010

AbstractWood deposited in streams provides a wide variety of ecosystem functions, including enhancing habitat for key species in stream food webs, increasing geomorphic and hydraulic heterogeneity and retaining organic matter. Given the strong role that wood plays in streams, factors that influence wood inputs, retention and transport are critical to stream ecology. Wood entrapment, the process of wood coming to rest after being swept downstream at least 10 m, is poorly understood, yet important for predicting stream function and success of restoration efforts. Data on entrapment were collected for a wide range of natural wood pieces (n= 344), stream geomorphology and hydraulic conditions in nine streams along the north shore of Lake Superior in Minnesota. Locations of pieces were determined in summer 2007 and again following an overbank stormflow event in fall 2007. The ratio of piece length to effective stream width (length ratio) and the weight of the piece were important in a multiple logistic regression model that explained 25% of the variance in wood entrapment. Entrapment remains difficult to predict in natural streams, and often may simply occur wherever wood pieces are located when high water recedes. However, this study can inform stream modifications to discourage entrapment at road crossings or other infrastructure by applying the model formula to estimate the effective width required to pass particular wood pieces. Conversely, these results could also be used to determine conditions (e.g. pre‐existing large, stable pieces) that encourage entrapment where wood is valued for ecological functions. Copyright © 2010 John Wiley & Sons, Ltd.
EGFR and HER3 mRNA expression levels predict distant metastases in locally advanced rectal cancer
Authors: Ho‐Pun‐Cheung Alexandre , Assenat Eric , Bascoul‐Mollevi Caroline , Bibeau Frédéric , Boissière‐Michot Florence , Cellier Dominic , Azria David , Rouanet Philippe , Senesse Pierre , Ychou Marc , Lopez‐Crapez Evelyne 
Published: September 2010

AbstractAberrant activation of the HER signaling pathways plays a critical role in the invasive and metastatic potential of tumors. The aim of this study was to address whether, in rectal cancer, alterations of these pathways could have a value as prognostic factors to be used to identify patients who are at risk of distant metastases. Therefore, the mRNA expression of the four members of the HER family as well as the frequency of PTEN allelic loss and KRAS/BRAF mutations were determined in pretreatment biopsies from a series of 100 locally advanced rectal cancers and then their ability to predict distant metastases was evaluated. Over‐expression of EGFR (p = 0.021), HER2 (p = 0.011) and HER3 (p = 0.020) was significantly associated with worse metastasis‐free survival in univariate analysis. In multivariate analysis, both over‐expression of EGFR (p = 0.028) and HER3 (p = 0.011) remained independent prognostic factors for distant metastasis. In conclusion, quantification of EGFR and HER3 mRNA expression in pretreatment biopsies may be useful to identify patients who are at risk of developing metastases.
Tumor‐reactive CD4+CD8αβ+ CD103+ αβT cells: A prevalent tumor‐reactive T‐cell subset in metastatic colorectal cancers
Authors: Sarrabayrouse Guillaume , Corvaisier Murielle , Ouisse Laure‐Hélène , Bossard Céline , Mével Bernard Le , Potiron Lucien , Meurette Guillaume , Gervois Nadine , Jotereau Francine 
Published: September 2010

AbstractHigh level of T‐cell infiltration in colorectal carcinomas (CRCs) is a good prognostic indicator, but the tumor reactivity of this infiltrate (tumor infiltrating lymphocytes [TIL]) is poorly documented. This study examined the presence, phenotype and functional features of tumor‐reactive lymphocytes in human CRC. Freshly dissociated TIL and T cell lines were isolated from CRC samples and from some paired normal colonic mucosa. Four tumor cell lines were obtained. Autologous tumor reactivity of CRC TIL and tumor‐reactive cell features were analyzed. We demonstrate the presence among CRC TIL of variable fractions (up to 18%) of double positive CD4+CD8αβ+ (DP) αβ T cells. Interestingly, a high proportion (16–20%) of this TIL subset displayed tumor reactivity, whilst this was the case for no or few single positive TIL. Low levels of DP TIL were found in most CRC samples and in normal colonic mucosa, but these cells were higher in metastatic CRC. Furthermore, we showed that DP TIL were polyclonal, restricted by HLA class‐I, proliferated poorly and secreted higher amounts of IL‐4 and IL‐13 than single positive T cells, on cognate or CD3 stimulation. DP CRC TIL also expressed CD103, confirming their mucosal origin. Increased frequencies of tumor‐reactive DP TIL in metastatic CRC suggest that these cells play a role in the metastatic process of this cancer. Based on their high secretion of IL‐4 and IL‐13 and on previously described roles of these cytokines in cancers, we postulate that DP TIL could favor CRC growth or metastasis and/or downmodulate immune responses to these tumors.
Identification of frequently mutated genes with relevance to nonsense mediated mRNA decay in the high microsatellite instability cancers
Authors: Shin Nara , You Kwon Tae , Lee Hanna , Kim Won Kyu , Song Meiying , Choi Hee‐Jung , Rhee Hwanseok , Nam Suk Woo , Kim Hoguen 
Published: September 2010

AbstractFrameshift mutations at coding mononucleotide repeats (cMNR) are frequent in high‐microsatellite instability (MSI‐H) cancers. Frameshift mutations in cMNR result in the formation of a premature termination codon (PTC) in the transcribed mRNA, and these abnormal mRNAs are generally degraded by nonsense mediated mRNA decay (NMD). We have identified novel genes that are frequently mutated at their cMNR by blocking NMD in two MSI‐H cancer cell lines. After blocking NMD, we screened for differentially expressed genes using DNA microarrays, and then used database analysis to select 28 candidate genes containing cMNR with more than 9 nucleotide repeats. cMNR mutations have not been previously reported in MSI‐H cancers for 15 of the 28 genes. We analyzed the cMNR mutation of each of the 15 genes in 10 MSI‐H cell lines and 21 MSI‐H cancers, and found frequent mutations of 12 genes in MSI‐H cell lines and cancers, but not in microsatellite stable (MSS) cancers. Among these genes, the most frequently mutated in MSI‐H cell lines were MLL3 (70%), PHACTR4 (70%), RUFY2 (50%) and TBC1D23 (50%). MLL3, which has already been implicated in cancer, had the highest mutation frequency in MSI‐H cancers (48%). Our combined approach of NMD block, database search, and mutation analysis has identified a large number of genes mutated in their cMNR in MSI‐H cancers. The identified mutations are expected to contribute to MSI‐H tumorigenesis by causing an absence of gene expression or low gene dosage effects.
Enhancement of a multianalyte serum biomarker panel to identify lymph node metastases in non‐small cell lung cancer with circulating autoantibody biomarkers
Authors: Patel Kalpa , Farlow Erin C. , Kim Anthony W. , Lee Bao‐Shiang , Basu Sanjib , Coon John S. , DeCresce David , Thimothy Lida , Walters Kelly A. , Fhied Cristina , Chang Christopher , Chen Ssu‐Hsien , Faber L. Penfield , Bonomi Philip , Liptay Michael J. , Borgia Jeffrey A. 
Published: September 2010

AbstractWe recently reported the development of a multianalyte serum algorithm to identify nodal status in non‐small cell lung cancer (NSCLC) patients facing an anatomic resection with curative intent. This study aims to enhance the overall performance characteristics of this test by adding autoantibody biomarkers identified through immunoproteomic discovery. More specifically, we used sera from 20 NSCLC patients to probe 2‐D immunoblots of HCC827 lysates for tumor‐associated autoantigens. Relevant differences in immunoreactivity associated with pathological nodal status were then identified via tandem mass spectrometry. Identified autoantigens were then developed into Luminex immunobead assays alongside a series of autoantigen targets relevant to early‐disease detection. These assays were then used to measure circulating autoantibody levels in the identical cohort of NSCLC patients used in our original study. This strategy identified 11 autoantigens found primarily in patients with disease progression to the locoregional lymph nodes. Custom Luminex‐based “direct‐capture” assays (25 total; including autoantibody targets relevant to early‐disease detection) were assembled to measure autoantibody levels in sera from 107 NSCLC patients. Multivariate classification algorithms were then used to identify the optimal combination of biomarkers when considered collectively with our original 6‐analyte serum panel. The new algorithm resulting from this analysis consists of TNF‐α, TNF‐RI, MIP‐1α and autoantibodies against Ubiquilin‐1, hydroxysteroid‐(17‐β)‐dehydrogenase, and triosephosphate isomerase. The inclusion of autoantibody biomarkers provided a dramatic improvement in the overall test performance characteristics, relative to the original test panel, including an 11% improvement in the classification efficiency.
Affinity‐matured anti‐glycoprotein NMB recombinant immunotoxins targeting malignant gliomas and melanomas
Authors: Kuan Chien‐Tsun , Wakiya Kenji , Keir Stephen T. , Li Jianjun , Herndon James E. , Pastan Ira , Bigner Darell D. 
Published: September 2010

AbstractGlycoprotein NMB (GPNMB), a transmembrane glycoprotein highly expressed in high‐grade gliomas (HGGs), is an attractive target in cancer immunotherapy. We isolated a GPNMB‐specific scFv clone, G49, from a human synthetic phage‐display library. To obtain mutant single‐chain variable‐fragment antibodies (scFvs) with improved affinity and immunotoxins with increased activity, we subjected G49 to in vitro affinity maturation by a complementarity‐determining‐region (CDR) random‐mutagenesis technique. Using light‐chain CDR3 mutagenesis, cell‐based panning by phage display, subsequent heavy‐chain CDR1 mutagenesis, and flow‐cytometric selection by yeast‐surface display, we generated the mutant scFv clone 902V, with an overall 11‐fold increase in affinity for GPNMB. Clone 902V was further randomized throughout the whole scFv by error‐prone PCR, and one mutant, F6V, was selected by yeast‐surface display. F6V scFv, differing from 902V by one amino‐acid change in the light‐chain CDR2, exhibited an affinity for GPNMB of 0.30 nM. The F6V mutant scFv clone was fused with a truncated form of Pseudomonas exotoxin A to form the immunotoxin F6V‐PE38. F6V‐PE38 demonstrated significant protein‐synthesis‐inhibition activity on GPNMB‐expressing glioma and malignant melanoma cells (IC50 = 0.5 ng/ml [8 pM]), a 60‐fold improvement over G49 activity, but no cytotoxicity on GPNMB‐negative cells. Furthermore, F6V‐PE38 exhibited significant antitumor activity against subcutaneous malignant glioma xenografts in two nude‐mouse models and a melanoma neoplastic meningitis model in athymic rats. These GPNMB‐specific scFv antibodies and immunotoxins hold promise as reagents in targeted therapy for HGGs and other GPNMB‐expressing malignancies.
Recent trends in colorectal cancer mortality in Europe
Authors: Bosetti Cristina , Levi Fabio , Rosato Valentina , Bertuccio Paola , Lucchini Franca , Negri Eva , La Vecchia Carlo 
Published: September 2010

AbstractColorectal cancer mortality has been declining over the last two decades in Europe, particularly in women, the trends being, however, different across countries and age groups. We updated to 2007 colorectal cancer mortality trends in Europe using data from the World Health Organization (WHO). Rates were analyzed for the overall population and separately in young, middle‐age and elderly populations. In the European Union (EU), between 1997 and 2007 mortality from colorectal cancer declined by around 2% per year, from 19.7 to 17.4/100,000 men (world standardized rates) and from 12.5 to 10.5/100,000 women. Persisting favorable trends were observed in countries of western and northern Europe, while there were more recent declines in several countries of eastern Europe, including the Czech Republic, Hungary and Slovakia particularly in women (but not Romania and the Russian Federation). In 2007, a substantial excess in colorectal cancer mortality was still observed in Slovakia, Hungary, Croatia, the Czech Republic and Slovenia in men (rates over 25/100,000), and in Hungary, Norway, Denmark and Slovakia in women (rates over 14/100,000). Colorectal mortality trends were more favorable in the young (30–49 years) from most European countries, with a decline of ∼2% per year since the early 1990s in both men and women from the EU. The recent decreases in colorectal mortality rates in several European countries are likely due to improvements in (early) diagnosis and treatment, with a consequent higher survival from the disease. Interventions to further reduce colorectal cancer burden are, however, still warranted, particularly in eastern European countries.