bluuebunny/crossref_metadata_2025_split huggingface dataset:
Utility of the Neuropsychological Assessment Battery in detecting cognitive impairment after unilateral stroke
Authors: STRICKER NIKKI H. , TYBUR JOSHUA M. , SADEK JOSEPH R. , HAALAND KATHLEEN Y. 
Published: July 2010

AbstractThis study evaluated the clinical utility of the Neuropsychological Assessment Battery (NAB) in a stroke sample by examining the NAB’s ability to differentiate a chronic stroke group with radiologically confirmed unilateral damage (n = 42) and a demographically matched healthy control (HC) group (n = 36). The stroke group performed more poorly than the control group across NAB Total score and all five Domain scores. Receiver operator curves (ROC) were derived and area under the curve (AUC) showed moderate diagnostic effectiveness (AUC .70 to .90) for NAB Total score, all five Domain scores, a motor composite, and a Global Deficit Score (GDS) that has been shown to closely approximate clinical ratings of neuropsychological impairment. The NAB Total, GDS, and motor composite had comparable clinical utility, whereas the Attention and Executive domain scores demonstrated better classification utility compared with the Memory domain. Because 90.5% of our stroke sample had middle cerebral artery territory strokes, the comparison of motor and cognitive classification utility may be biased. However, follow-up analyses showed that the NAB accounted for additional variance even when motor composite was included in the model. Sensitivity, specificity, and odds ratios at various clinical cutoffs are provided. These results suggest that the NAB is a useful clinical tool for detection of cognitive deficits in individuals with chronic unilateral stroke, although lenient clinical cutoffs appear warranted to maximize sensitivity. (JINS, 2010, 16, 813–821.)
Genome informatics of influenza A: from data sharing to shared analytical capabilities
Authors: Janies Daniel A. , Voronkin Igor O. , Das Manirupa , Hardman Jori , Treseder Travis W. , Studer Jonathon 
Published: July 2010

AbstractEmerging infectious diseases are critical issues of public health and the economic and social stability of nations. As demonstrated by the international response to the severe acute respiratory syndrome (SARS) and influenza A, rapid genomic sequencing is a crucial tool to understand diseases that occur at the interface of human and animal populations. However, our ability to make sense of sequence data lags behind our ability to acquire the data. The potential of sequence data on pathogens is not fully realized until raw data are translated into public health intelligence. Sequencing technologies have become highly mechanized. If the political will for data sharing remains strong, the frontier for progress in emerging infectious diseases will be in analysis of sequence data and translation of results into better public health science and policy. For example, applying analytical tools such as Supramap (http://supramap.osu.edu) to genomic data for pathogens, public health scientists can track specific mutations in pathogens that confer the ability to infect humans or resist drugs. The results produced by the Supramap application are compelling visualizations of pathogen lineages and features mapped into geographic information systems that can be used to test hypotheses and to follow the spread of diseases across geography and hosts and communicate the results to a wide audience.
Der kleine Unterschied – Wie der Mensch zur Sprache kam
Authors: Rütsche Bruno , Meyer Martin 
Published: July 2010

Die Frage, wie der Mensch zur Sprache kam, findet seit jeher das Interesse interdisziplinärer Forschung. Die vorliegende Arbeit liefert einen zusammenfassenden Überblick über jüngste Entwicklungen aus verschiedenen wissenschaftlichen Feldern (z. B. biologische Anthropologie, Paläogenetik, kognitive Neurowissenschaft, funktionelle Neuroanatomie), in denen in den letzten Jahren entscheidende Einsichten hinsichtlich des Ursprungs der menschlichen Sprache gelungen sind. Dieser Beitrag diskutiert eine Reihe von Aspekten, die mutmasslich einen entscheidenden Einfluss auf die Evolution der Sprache hatten. Insbesondere weist unser Überblick auf die Bedeutung neuroanatomischer Veränderungen im Laufe der Entwicklungsgeschichte der Homininen hin, wobei primär auf die Relevanz von strukturellen Hemisphärenasymmetrien sowie der kortiko-kortikalen Konnektivität eingegangen wird. Im Zusammenhang mit der Frage nach der ursprünglichen Modalität der menschlichen Sprache beziehungsweise dem funktionellen Äquivalent bei nichtmenschlichen Primaten, betont unsere zusammenfassende Betrachtung der sprachevolutionären Forschung die Perspektive eines gestischen anstatt eines vokalen Ursprungs. Insbesondere das Konzept der „Spiegelneurone“ als zerebrale Grundlage von Imitation und Lernen gilt mittlerweile als ein wichtiger Bestandteil eines akzeptablen und plausiblen Modells, welches diverse ältere Erklärungsansätze integriert.
Land Use and Climate Variability Amplify Contaminant Pulses
Authors: Kaushal Sujay S. , Pace Michael L. , Groffman Peter M. , Band Lawrence E. , Belt Kenneth T. , Meyer Paul M. , Welty Claire 
Published: June 2010

In 2002, the mid‐ Atlantic region experienced record drought levels. In September 2003, Tropical Storm Isabel produced large amounts of rainfall in the Chesapeake Bay region, and freshwater flow into the Chesapeake Bay was 400% above the long‐ term monthly average (http://chesapeake.usgs.gov/isabelinfo.html). Record drought conditions followed by a very wet year coincided with pulsed watershed nitrogen exports and one of the most severe zones of hypoxia, or “dead zones,” reported in the Chesapeake Bay.Large pulses of contaminants such as this event may occur more often given evidence of increased variability of precipitation and hydrologic extremes occurring with climate change [Intergovernmental Panel on Climate Change (IPCC), 2007]. Conversion of land to human‐ dominated uses has increased contaminant loads in streams and rivers and further transformed hydrologic cycles [Vitousek et al., 1997]. Together, land use and climate change may interact in unexpected ways to alter the amplitude, frequency, and duration of contaminant pulses in streams and rivers (i.e., large contaminant loads that are transported over relatively short time scales).
Bimolecular fluorescence complementation analysis of eukaryotic fusion products
Authors: Lin Ho‐Pi , Vincenz Claudius , Eliceiri Kevin W. , Kerppola Tom K. , Ogle Brenda M. 
Published: July 2010

Background information. Cell fusion is known to underlie key developmental processes in humans and is postulated to contribute to tissue maintenance and even carcinogenesis. The mechanistic details of cell fusion, especially between different cell types, have been difficult to characterize because of the dynamic nature of the process and inadequate means to track fusion products over time. Here we introduce an inducible system for detecting and tracking live cell fusion products in vitro and potentially in vivo. This system is based on BiFC (bimolecular fluorescence complementation) analysis. In this approach, two proteins that can interact with each other are joined to fragments of a fluorescent protein and are expressed in separate cells. The interaction of said proteins after cell fusion produces a fluorescent signal, enabling the identification and tracking of fusion products over time.Results. Long‐term tracking of fused p53‐deficient cells revealed that hybrid cells were capable of proliferation. In some cases, proliferation was preceded by nuclear fusion and division was asymmetric (69%±2% of proliferating hybrids), suggesting chromosomal instability. In addition, asymmetric division following proliferation could give rise to progeny indistinguishable from unfused counterparts.Conclusions. These results support the possibility that the chromosomal instability characteristic of tumour cells may be incurred as a consequence of cell fusion and suggest that the role of cell fusion in carcinogenesis may have been masked to this point for lack of an inducible method to track cell fusion. In sum, the BiFC‐based approach described here allows for comprehensive studies of the mechanism and biological impact of cell fusion in nature.
How individuals with self‐reported anxiety and depression experienced a combination of individual counselling with an adventurous outdoor experience: A qualitative evaluation
Authors: Kyriakopoulos Alex 
Published: July 2010

AbstractBackground: Adventure therapy is a short‐term experiential psychotherapeutic approach that utilises adventurous activities and being in natural environments in order to facilitate therapeutic change in clients. The present paper examines how students with self‐reported anxiety and depression experienced participating in an innovative intervention that combined individual therapy with an adventurous outdoor experience. Clients participating in the Adventure Therapy Project received between 10–15 one‐to‐one counselling sessions prior to the outdoor experience, as well as ongoing counselling following it. Method: Interpretative Phenomenological Analysis was used in order to record and analyse the experiences of three male and three female students who presented at a major UK university student counselling service with self‐reported depression and anxiety. Findings: Twelve themes emerged which were categorised into four major domains: enhancing intrapersonal relationships; improving interpersonal relationships; providing an experiential outdoor venue for achieving therapeutic change; offering a secure, personal place for achieving inner healing. The intervention was perceived to improve the ways in which interviewees related towards themselves and other people. Interviewees perceived the counselling sessions as offering a safe therapeutic space within which they could unveil their anxieties and achieve inner healing. Conclusions: Outdoor experiences offer an experiential venue for achieving personal change and, it appears enhance the therapeutic process. Prior and subsequent individual therapy increases the benefits of such experiences.
Integration of pathway knowledge into a reweighted recursive feature elimination approach for risk stratification of cancer patients
Authors: Johannes Marc , Brase Jan C. , Fröhlich Holger , Gade Stephan , Gehrmann Mathias , Fälth Maria , Sültmann Holger , Beißbarth Tim 
Published: July 2010

AbstractMotivation: One of the main goals of high-throughput gene-expression studies in cancer research is to identify prognostic gene signatures, which have the potential to predict the clinical outcome. It is common practice to investigate these questions using classification methods. However, standard methods merely rely on gene-expression data and assume the genes to be independent. Including pathway knowledge a priori into the classification process has recently been indicated as a promising way to increase classification accuracy as well as the interpretability and reproducibility of prognostic gene signatures.Results: We propose a new method called Reweighted Recursive Feature Elimination. It is based on the hypothesis that a gene with a low fold-change should have an increased influence on the classifier if it is connected to differentially expressed genes. We used a modified version of Google's PageRank algorithm to alter the ranking criterion of the SVM-RFE algorithm. Evaluations of our method on an integrated breast cancer dataset comprising 788 samples showed an improvement of the area under the receiver operator characteristic curve as well as in the reproducibility and interpretability of selected genes.Availability: The R code of the proposed algorithm is given in Supplementary Material.Contact: m.johannes@DKFZ-heidelberg.de; tim.beissbarth@ams.med.uni-goettingen.deSupplementary information: Supplementary data are available at Bioinformatics online.
Do we have enough information to apply the ecosystem approach to management of deep-sea fisheries? An example from the West of Scotland
Authors: Heymans Johanna J. , Howell Kerry L. , Ayers Morag , Burrows Michael T. , Gordon John D. M. , Jones Emma G. , Neat Francis 
Published: July 2010

Abstract
Heymans, J. J., Howell, K. L., Ayers, M., Burrows, M. T., Gordon, J. D. M., Jones, E. G., and Neat, F. 2011. Do we have enough information to apply the ecosystem approach to management of deep-sea fisheries? An example from the West of Scotland. – ICES Journal of Marine Science, 68: 265–280. There is currently a global call for more use of an ecosystem approach to fisheries management (EAFM), and ecosystem models such as Ecopath with Ecosim (EwE) are being used to provide a holistic view of ecosystem–fisheries interactions. Although these can be useful for an EAFM, the relative paucity of data available for deep-sea ecosystems raises concerns whether we can effectively apply an EAFM to the deep sea. The deep-sea ecosystem off the west coast of Scotland has been studied for longer and in more detail than most. This study assimilates the significant published and unpublished information available on this ecosystem into an EwE model. The results suggest that there are sufficient data available to construct an ecosystem model, but the quality of the data varies and serious potential sources of error are present in biomass and discard estimates. The assumptions needed to produce a model are varied and must be considered when interpreting the outputs of the model. Ecosystem modelling provides a unique view of the deep-water ecosystem and facilitates hypothesis development concerning predator–prey and inter-fishery interactions. Sharks are used to illustrate the benefits of using an ecosystem model to describe changes in their biomass and their prey species. The results show that both fishing for sharks and fishing for their prey affect the biomass of sharks.
Changes in diet and trophic position of a top predator 10 years after a mass mortality of a key prey
Authors: Chiaradia André , Forero Manuela G. , Hobson Keith A. , Cullen J. Mike 
Published: June 2010

Abstract
Chiaradia, A., Forero, M. G., Hobson, K. A., and Cullen, J. M. 2010. Changes in diet and trophic position of a top predator 10 years after a mass mortality of a key prey. – ICES Journal of Marine Science, 67: 1710–1720. After the disappearance of primary prey, seabirds exhibit gradually decreased breeding performance, and eventually the population size drops. Results are presented of an investigation into the diet of little penguins (Eudyptula minor) at Phillip Island, Australia, during a period when their key prey, pilchard (Sardinops sagax), declined dramatically. Data from stomach flushing (1982–2006) were used, supported by stable isotope (δ15N, δ13C) analyses of blood samples (2003, 2004, and 2006). The effect of the pilchard mortality on penguin diet was immediate, the birds shifting to a diet almost devoid of pilchard, and this was followed by 2 years of low breeding success, with considerably fewer penguins coming ashore. During periods when pilchard was not part of the diet, penguins consumed prey of a higher trophic level, e.g. higher values of δ15N. Variability in penguin blood δ15N coincided with years of low prey diversity. The disappearance of pilchard resulted in a decrease in prey diversity and led penguins to “fish up” the foodweb, possibly because of the simplified trophic structure. After 1998, however, breeding success re-attained average levels and the numbers of penguins coming ashore increased, probably because of increased abundance of prey other than pilchard after a 3-year period of food scarcity. Although little penguins apparently compensated over time, a less-flexible diet could make them ultimately vulnerable to further changes in their foodweb.
Bowel Habits in the First 24 Months of Life: Preterm‐ Versus Term‐born Infants
Authors: Bekkali N , Moesker FM , Van Toledo L , Reitsma JB , Hamers SL , Valerio PG , Benninga MA 
Published: July 2010

ABSTRACTBackground and Aim:New prospective studies concerning feeding and bowel habits of term and preterm infants from birth to 24 months of life are needed. The aim of the present study was to describe and compare feeding and bowel habits between term‐ and preterm‐born infants starting from birth up to the age of 24 months.Patients and Methods:Between August and November 2006 all of the infants admitted to an academic and nonacademic neonatal care unit with gestational age 25 to 42 weeks participated in the study. Bowel diaries were recorded 1 and 2 weeks, and 3, 6, 12, and 24 months after birth. Infants with gastrointestinal surgery, neurological diseases, metabolic diseases, or congenital abnormalities were excluded.Results:A total of 199 (126 preterm) infants were eligible; 153 gave consent for participation. Although feeding frequency was higher in the first 3 months in the preterm born, overall feeding frequency decreased between the first 3 follow‐up periods (P < 0.001) in both groups. In the first and second week, breast‐fed infants had 2.41 more episodes of defecation per week compared with the formula‐fed infants (P = 0.017 and P = 0.021, respectively). Higher median (10th percentile–90th percentile) defecation frequency was only found in week 1 in the term compared with the preterm group (24 [9.4–31.6] versus 16 [6.5–31]; P = 0.002). The overall median defecation frequency was 16 (7–30) per week from birth up to the age of 24 months over the total group of participating infants.Conclusions:Term and preterm infants have a comparable defecation frequency from the second week of life up to the age of 24 months.
Complications of Congenital Portosystemic Shunts in Children: Therapeutic Options and Outcomes
Authors: Franchi‐Abella Stéphanie , Branchereau Sophie , Lambert Virginie , Fabre Monique , Steimberg Clarisa , Losay Jean , Riou Jean‐Yves , Pariente Danièle , Gauthier Frédéric , Jacquemin Emmanuel , Bernard Olivier 
Published: July 2010

ABSTRACTBackground and Objective:Congenital portosystemic shunts are rare vascular malformations that lead to severe complications. Their management is controversial. The aim of this study was to propose a clear definition of the risks and management of congenital portosystemic shunts in children according to our experience and a review of the literature.Patients and Methods:Twenty‐two children with a complicated congenital portosystemic shunt were studied in our institution. When necessary, management included portal pressure measurement and portal vein angiography during an occlusion test and closure of the shunt by surgical and/or endovascular methods.Results:Five neonates with intrahepatic shunts presented with cholestasis that resolved spontaneously, and 17 older children presented with liver tumors (13) and/or hepatopulmonary syndrome (2), pulmonary artery hypertension (3), portosystemic encephalopathy (3), heart failure (1), and glomerulonephritis (1). The portosystemic shunt was extrahepatic (11) or intrahepatic (6). Portosystemic shunts were closed by endovascular methods in 5 children and surgically in 10, 4 of whom had portal pressure during occlusion above 35 mmHg and extremely hypoplastic or undetectable portal veins requiring banding of the fistula before closure. Shunt closure resulted in restoration of intrahepatic portal flow in all, with complete or partial regression of benign liver masses, and regression or stabilization of pulmonary, cardiac, neurological, and renal complications.Conclusions:Congenital portosystemic shunt carries risks of severe complications in children. Closure of a shunt persisting after age 2 years should be considered preventively. Intrahepatic portal flux restoration can be expected, even when intrahepatic portal veins are extremely hypoplastic or undetectable.
Preparation of Pseudotyped Lentiviral Vectors Resistant to Inactivation by Serum Complement
Authors: Guibinga Ghiabe H. , Friedmann Theodore 
Published: July 2010

INTRODUCTIONA major obstacle to in vivo delivery of lentivirus or other retroviral vectors is their lability in the presence of serum. In vivo, these viral particles are rapidly destroyed by nonspecific complement-mediated degradation mechanisms. The eventual effective use of retroviral vectors for in vivo gene delivery would be greatly facilitated by the development of methods to protect the viral particles from such degradation. This protocol describes methods for the production of complement-stabilized lentiviral vectors either by pseudotyping the viral particles with a fusion envelope protein containing the complement-regulatory protein CD55 (decay accelerating factor, DAF) or by coassembly with the native DAF protein. An in vitro serum inactivation assay is also described.
Purification of Epitope-Tagged Transcription Factor IID
Authors: Carey Michael F. , Peterson Craig L. , Smale Stephen T. 
Published: July 2010

INTRODUCTIONTranscription factor IID (TFIID) is one of the most critical factors in transcription complex assembly because it recognizes a core promoter and interacts with chromatin and activator proteins. This protocol uses immunoaffinity chromatography in a simple two-step procedure to purify modified TFIID to homogeneity with limited loss of activity. In brief, a short peptide containing the influenza virus hemagglutinin (HA) tag is fused onto the amino terminus of TATA-binding protein (TBP), and a retroviral transfer system is used to generate a HeLa cell line stably expressing the HA-tagged TBP. Extracts from this cell line contain TFIID, which stably incorporates the epitope-tagged TBP. The TFIID is partially purified from these extracts using phosphocellulose chromatography and then immunopurified using a resin containing protein A-Sepharose beads cross-linked to a monoclonal antibody against the influenza epitope. The TFIID is then eluted from the immunoaffinity resin in pure form using an HA peptide. The resulting TFIID contains a complete complement of TBP-associated factors (TAFs) and can be used in transcription, electrophoretic mobility shift assays (EMSA), and footprinting assays; its purity is well suited for many other studies.
Homogenization of Mammalian Tissue
Authors: Simpson Richard J. 
Published: July 2010

INTRODUCTIONTo purify or characterize an intracellular protein, it is important to choose an efficient method for disrupting the cell or tissue that rapidly releases the protein from its intracellular compartment into a buffer that is not harmful to the biological activity of the protein of interest. One of the most widely used methods for disrupting soft tissues is homogenization. This protocol describes three processes for homogenization of animal tissues using mechanical shear: a Potter-Elvehjem glass-Teflon homogenizer, a Dounce hand homogenizer, or a handheld Waring Blendor. These methods are rapid and pose little risk to proteins other than the release of proteases from other cellular compartments. Proteolytic degradation can be minimized by the inclusion of protease inhibitors in the homogenization buffers. An optional procedure to remove mucin from tissue homogenates is also presented.
Transfection of Cells with DNA Encoding a Visible Fluorescent Protein-Tagged Lipid-Binding Domain
Authors: Schultz Carsten , Neef Anne B. , Gadella Theodorus W. , Goedhart Joachim 
Published: July 2010

INTRODUCTIONVisualization of a certain lipid species can be achieved by producing a fusion protein between a lipid-binding domain and a visible fluorescent protein (VFP). After a DNA construct for a VFP-tagged lipid-binding domain has been prepared, the desired cell line is transfected with the DNA and visualized using fluorescence microscopy, as described here. The DNA encoding a VFP-tagged lipid-binding domain is isolated from Escherichia coli, and the cells to be transfected are grown on glass-bottom dishes or on coverslips. We routinely perform transfection with commercially available reagents, although, depending on the cell line, the calcium phosphate precipitation method may provide an economic alternative.