bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nondestructive measurement and high-precision evaluation of the electrical conductivity of doped GaAs wafers using microwaves
Authors: Liu Linsheng , Ju Yang 
Published: December 2010

A nondestructive method for measuring the electrical conductivity of doped GaAs wafers using a compact microwave instrument is presented. Based on the characteristics of the microwave detector and the fact that the microwave measurement is independent of the thickness of the wafer, the analytical and explicit expressions to evaluate the electrical conductivity of the wafer are derived. Using this method, only the voltages of the reflected signals for two wafer samples whose conductivities are known are required to calibrate the two undetermined constants in the equation. Then, the conductivity of any other wafer can be evaluated by substituting the measured voltage of the reflected signal into the explicit expressions. Seven different doped GaAs wafers with thickness larger than 350 μm and conductivities in the range of 1.3 × 104 S/m to 7.6 × 104 S/m are measured in the experiment, two of which are used for calibration. The evaluated results agree well with those obtained by the conventional Hall effect measurement method, with an evaluation error less than ±4.5%. The proposed method is potentially useful for the contactless and nondestructive evaluation of the electrical conductivity of any kind of semiconductor wafer.
Synchronous environmental and cultural change in the prehistory of the northeastern United States
Authors: Munoz Samuel E. , Gajewski Konrad , Peros Matthew C. 
Published: December 2010

Climatic changes during the late Quaternary have resulted in substantial, often abrupt, rearrangements of terrestrial ecosystems, but the relationship between these environmental changes and prehistoric human culture and population size remains unclear. Using a database of archaeological radiocarbon dates alongside a network of paleoecological records (sedimentary pollen and charcoal) and paleoclimatic reconstructions, we show that periods of cultural and demographic change in the northeastern United States occurred at the same times as the major environmental-climatic transitions of that region. At 11.6, 8.2, 5.4, and 3.0 kyr BP (10
3
calendar years before present), changes in forest composition altered the distribution, availability, and predictability of food resources which triggered technological adjustments manifested in the archaeological record. Human population level has varied in response to these external changes in ecosystems, but the adoption of maize agriculture during the late Holocene also resulted in a substantial population increase. This study demonstrates the long-term interconnectedness of prehistoric human cultures and the ecosystems they inhabited, and provides a consolidated environmental-cultural framework from which more interdisciplinary research and discussion can develop. Moreover, it emphasizes the complex nature of human responses to environmental change in a temperate region.
RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries
Authors: Habegger Lukas , Sboner Andrea , Gianoulis Tara A. , Rozowsky Joel , Agarwal Ashish , Snyder Michael , Gerstein Mark 
Published: December 2010

Abstract
Summary: The advent of next-generation sequencing for functional genomics has given rise to quantities of sequence information that are often so large that they are difficult to handle. Moreover, sequence reads from a specific individual can contain sufficient information to potentially identify and genetically characterize that person, raising privacy concerns. In order to address these issues, we have developed the Mapped Read Format (MRF), a compact data summary format for both short and long read alignments that enables the anonymization of confidential sequence information, while allowing one to still carry out many functional genomics studies. We have developed a suite of tools (RSEQtools) that use this format for the analysis of RNA-Seq experiments. These tools consist of a set of modules that perform common tasks such as calculating gene expression values, generating signal tracks of mapped reads and segmenting that signal into actively transcribed regions. Moreover, the tools can readily be used to build customizable RNA-Seq workflows. In addition to the anonymization afforded by MRF, this format also facilitates the decoupling of the alignment of reads from downstream analyses.
Availability and implementation: RSEQtools is implemented in C and the source code is available at http://rseqtools.gersteinlab.org/.
Contact: lukas.habegger@yale.edu; mark.gerstein@yale.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
MSPocket: an orientation-independent algorithm for the detection of ligand binding pockets
Authors: Zhu Hongbo , Pisabarro M. Teresa 
Published: December 2010

Abstract
Motivation: Identification of ligand binding pockets on proteins is crucial for the characterization of protein functions. It provides valuable information for protein–ligand docking and rational engineering of small molecules that regulate protein functions. A major number of current prediction algorithms of ligand binding pockets are based on cubic grid representation of proteins and, thus, the results are often protein orientation dependent.
Results: We present the MSPocket program for detecting pockets on the solvent excluded surface of proteins. The core algorithm of the MSPocket approach does not use any cubic grid system to represent proteins and is therefore independent of protein orientations. We demonstrate that MSPocket is able to achieve an accuracy of 75% in predicting ligand binding pockets on a test dataset used for evaluating several existing methods. The accuracy is 92% if the top three predictions are considered. Comparison to one of the recently published best performing methods shows that MSPocket reaches similar performance with the additional feature of being protein orientation independent. Interestingly, some of the predictions are different, meaning that the two methods can be considered complementary and combined to achieve better prediction accuracy. MSPocket also provides a graphical user interface for interactive investigation of the predicted ligand binding pockets. In addition, we show that overlap criterion is a better strategy for the evaluation of predicted ligand binding pockets than the single point distance criterion.
Availability: The MSPocket source code can be downloaded from http://appserver.biotec.tu-dresden.de/MSPocket/. MSPocket is also available as a PyMOL plugin with a graphical user interface.
Contact: hongboz@biotec.tu-dresden.de; mayte@biotec.tu-dresden.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Protective Effect of Pioglitazone Against Endotoxin‐Induced Liver Injury through Prevention of Kupffer Cell Sensitization
Authors: Enomoto Nobuyuki , Takei Yoshiyuki , Yamashima Shunhei , Ikejima Kenichi , Kitamura Tsuneo , Sato Nobuhiro 
Published: December 2010

Abstract: Background: Activation of Kupffer cells by lipopolysaccharide (LPS) plays a pivotal role in the onset of pathophysiological events that occur during endotoxemia and intracellular calcium ([Ca2+]i) is involved in LPS‐stimulated cytokine production. TNF‐α is produced exclusively by the monocyte‐macrophage lineage, including Kupffer cells, and pioglitazone has been shown to reduce TNF‐α production from macrophages. On the other hand, there is increasing evidence that TNF‐α plays a major role in the initiation and/or progression of multiple organ failure syndrome. Therefore, the purpose of this work was to determine whether pioglitazone could prevent LPS‐induced liver injuryMethods: Rats were given a single oral dose of pioglitazone (500 μg/kg). To assess the sensitization of Kupffer cells, LPS (5 mg/kg) was administered IV and transaminases were evaluated 24 hr later. Kupffer cells were isolated 2 hr after pioglitazone treatment. After addition of LPS, [Ca2+]i was measured using a microspectrofluorometer with the fluorescent indicator, fura‐2, and TNF‐α was measured by ELISAResults: LPS increased transaminases dramatically and elevation of serum transaminases were diminished markedly by pioglitazone. In isolated Kupffer cells, the LPS‐induced increase in [Ca2+]i and TNF‐α production were suppressed by treated with pioglitazoneConclusions: Therefore, it is concluded that pioglitazone prevents LPS induced liver injury via a mechanism dependent on suppression of TNF‐α production from Kupffer cells.
Neural correlates of verbal learning in adolescent alcohol and marijuana users
Authors: Schweinsburg Alecia Dager , Schweinsburg Brian C. , Nagel Bonnie J. , Eyler Lisa T. , Tapert Susan F. 
Published: December 2010

ABSTRACTAims  Alcohol and marijuana are the most widely used intoxicants among adolescents, yet their potential unique and interactive influences on the developing brain are not well established. Brain regions subserving learning and memory undergo continued maturation during adolescence, and may be particularly susceptible to substance‐related neurotoxic damage. In this study, we characterize brain response during verbal learning among adolescent users of alcohol and marijuana.Design  Participants performed a verbal paired associates encoding task during functional magnetic resonance imaging (fMRI) scanning.Setting  Adolescent subjects were recruited from local public schools and imaged at a university‐based fMRI center.Participants  Participants were 74 16–18‐year‐olds, divided into four groups: (i) 22 controls with limited alcohol and marijuana experience, (ii) 16 binge drinkers, (iii) eight marijuana users and (iv) 28 binge drinking marijuana users.Measurements  Diagnostic interview ensured that all teens were free from neurological or psychiatric disorders; urine toxicology and breathalyzer verified abstinence for 22–28 days before scanning; a verbal paired associates task was administered during fMRI.Findings  Groups demonstrated no differences in performance on the verbal encoding task, yet exhibited different brain response patterns. A main effect of drinking pointed to decreased inferior frontal but increased dorsal frontal and parietal fMRI response among binge drinkers (corrected P < 0.05). There was no main effect of marijuana use. Binge drinking × marijuana interactions were found in bilateral frontal regions (corrected P < 0.05), where users of either alcohol or marijuana showed greater response than non‐users, but users of both substances resembled non‐users.Conclusions  Adolescent substance users demonstrated altered fMRI response relative to non‐using controls, yet binge drinking appeared to be associated with more differences in activation than marijuana use. Alcohol and marijuana may have interactive effects that alter these differences, particularly in prefrontal brain regions.
Organ identity and environmental conditions determine the effectiveness of nonhost resistance in the interaction between Arabidopsis thaliana and Magnaporthe oryzae
Authors: SCHREIBER CHRISTINE , SLUSARENKO ALAN J. , SCHAFFRATH ULRICH 
Published: December 2010

SUMMARYMechanisms leading to nonhost resistance of plants against nonadapted pathogens are thought to have great potential for the future management of agriculturally important diseases. In this article, we report an investigation of nonhost resistance motivated by the advantages of studying an interaction between two model organisms, namely Arabidopsis thaliana and Magnaporthe oryzae. During the course of our studies, however, we discovered an unexpected plasticity in the responses of Arabidopsis against this ostensibly nonhost pathogen. Thus, we elucidated that certain experimental conditions, such as the growth of plants under long days at constantly high humidity and the use of high inoculum concentrations of M. oryzae conidia, forced the interaction in leaves of some Arabidopsis ecotypes towards increased compatibility. However, sporulation was never observed. Furthermore, we observed that roots were generally susceptible to M. oryzae, whereas leaves, stems and hypocotyls were not infected. It must be concluded, therefore, that Arabidopsis roots lack an effective defence repertoire against M. oryzae, whereas its leaves possess such nonhost defence mechanisms. In summary, our findings point to organ‐specific determinants and environmental conditions influencing the effectiveness of nonhost resistance in plants.
Underwater‐seal nasogastric tube drainage to relieve gastric distension caused by air swallowing
Authors: Solomon A. W. , Bramall J. C. , Ball J. 
Published: December 2010

SummaryAir swallowing can occur as a psychogenic phenomenon, because of abnormal anatomy, or during non‐invasive positive pressure ventilation. Gross distension of the stomach with air can have severe consequences for the respiratory and gastrointestinal systems. We report the case of a 62‐year‐old man with severe dynamic hyperinflation due to chronic obstructive pulmonary disease, who developed respiratory failure requiring intubation a few hours after radical prostatectomy. Following a percutaneous tracheostomy and weaning of sedation on day six, his abdomen began to enlarge progressively. X‐rays revealed massive gastric distension due to air swallowing, which continued despite all efforts to optimise therapy. The use of an underwater seal drainage system on a nasogastric tube improved ventilation and ultimately aided weaning from mechanical support.
Allogeneic haematopoietic stem cell transplantation for myelofibrosis: a report of the Société Française de Greffe de Moelle et de Thérapie Cellulaire (SFGM‐TC)
Authors: Robin Marie , Tabrizi Reza , Mohty Mohamad , Furst Sabine , Michallet Mauricette , Bay Jacques‐Olivier , Cahn Jean‐Yves , De Coninck Eric , Dhedin Nathalie , Bernard Marc , Rio Bernard , Buzyn Agnès , Huynh Anne , Bilger Karin , Bordigoni Pierre , Contentin Nathalie , Porcher Raphaël , Socié Gérard , Milpied Noel 
Published: December 2010

SummaryAllogeneic haematopoietic stem‐cell transplantation (HSCT) is the only curative treatment for myelofibrosis. We report an analysis of the Société Française de Greffe de Moelle et de Thérapie Cellulaire (SFGM‐TC) registry including patients with myelofibrosis transplanted between 1997 and 2008. Potential risk factors affecting engraftment, non‐relapse mortality (NRM), overall survival (OS) and progression‐free survival (PFS) were analysed. One hundred and forty‐seven patients, aged 20–68 (median 53) years, diagnosed with primary (53%) or secondary myelofibrosis underwent HSCT; 59% of patients were transplanted from a matched sibling donor. The conditioning regimen was myeloablative in 31% of patients. Ninety percent of the patients engrafted. Factors affecting favourably engraftment were splenectomy before HSCT, human leucocyte antigen (HLA) matched sibling donor, peripheral stem cell use as source of stem cells and absence of pre‐transplant thrombocytopenia. Four‐year OS, PFS and NRM survival were 39% (95%confidence interval [CI]: 31–50), 32% (95%CI: 24–43) and 39% (95%CI 30–48), respectively. Multivariate analysis indicated that HLA‐identical sibling donor, chronic phase disease and splenectomy in men had favourable impact on OS.
Epistemic activities and collaborative learning: towards an analytical model for studying knowledge construction in networked learning settings
Authors: Zenios Maria 
Published: December 2010

AbstractThe aim of this paper is to provide an analytical model for studying knowledge creation among geographically dispersed students in an online postgraduate programme by using the concept of epistemic activity. Rooted in qualitative methodologies, it takes a case study approach which strengthens the grounding of theory on social learning by using triangulation of evidence from online discussions and seven semi‐structured interviews. The analytical model that emerges, distinguishes a set of moves that serve understanding negotiation of meaning and co‐construction of knowledge in online discussion. The findings of the study suggest that knowledge advancement processes can be understood as part of identifying key strategies in the form of online epistemic activities for postgraduate learners in a networked learning context. The paper offers a conceptual account for researching knowledge construction in higher education.
Clinical findings in patients with GLI2 mutations – phenotypic variability
Authors: Bertolacini CDP , Ribeiro‐Bicudo LA , Petrin A , Richieri‐Costa A , Murray JC 
Published: December 2010

Bertolacini CDP, Ribeiro‐Bicudo LA, Petrin A, Richieri‐Costa A, Murray JC. Clinical findings in patients with GLI2 mutations – phenotypic variability.Mutations in the human GLI2 gene were first reported in association with defective anterior pituitary formation, panhypopituitarism, and forebrain anomalies represented by typical holoprosencephaly (HPE) and holoprosencephaly‐like (HPE‐L) phenotypes and postaxial polydactyly. Subsequently, anophthalmia plus orbital anomalies, heminasal aplasia, branchial arch anomalies and polydactyly have also been incorporated into the general phenotype. Here we described six Brazilian patients with phenotypic manifestations that range from isolated cleft lip/palate with polydactyly, branchial arch anomalies to semi‐lobar holoprosencephaly. Novel sequence variants were found in the GLI2 gene in patients with marked involvement of the temporomandibular joint (TMJ), a new clinical finding observed with mutations of this gene. Clinical, molecular and genetic aspects are discussed.
THE WHAT, HOW AND WHO OF HUMANITY BEFORE GOD: THEOLOGICAL ANTHROPOLOGY AND THE BIBLE IN THE TWENTY‐FIRST CENTURY
Authors: FORD DAVID F. 
Published: December 2010

AbstractDavid Kelsey's Eccentric Existence. A Theological Anthropology is read in the context of the traditions of Christian theology, especially in Europe and North America, and of Kelsey's Yale colleagues. Its theocentric, scriptural and thoughtfully experimental contribution to theological anthropology from the perspectives of creation, consummation and reconciliation is analysed, appreciated and assessed. Implications of Kelsey's identification of three distinct plotlines in the Bible are explored. Questions are raised about the range of his Christian conversations, the limitations of his reliance on narrative, his neglect of significant parts of the Bible and Christian tradition, and his focus on the interaction with secular rather than religious dimensions of the contemporary world.
Exploring the experiences of people with intellectual disabilities when service users die
Authors: Ryan Karen , Guerin Suzanne , Dodd Philip , McEvoy John 
Published: December 2010

Accessible summary
People with intellectual disabilities are living for longer than ever before and are experiencing the deaths of their friends and other service users.
This study describes the experiences of people with intellectual disabilities who have lived through the death of a friend or service user from the point of view of staff from intellectual disability and palliative care services.
It is important to understand the experiences of people with intellectual disabilities to try and help people cope with the deaths of their friends.
The study shows that it helps to include people with intellectual disabilities when their friends become unwell and to talk openly with them about what is happening.
SummaryResearch is lacking on the effect of the deaths of fellow service users on people with intellectual disabilities. This qualitative study formed part of a project which aimed to describe the provision of palliative care to people with intellectual disabilities in Ireland and to assess the population’s palliative care needs. We report on findings from 16 focus groups held with staff in which participants described their perception of the experiences of people with intellectual disabilities when other service users die. Interviews were analysed using Framework Analysis. The findings highlight the emotional impact of the death of a friend on people with intellectual disabilities. Situations where staff facilitated the involvement of services users are described, and the study points to the benefits of this approach. Possible barriers to involvement are highlighted. The findings affirm the importance of ensuring that people with intellectual disabilities have a good understanding of the concept of death to alleviate the bereavement experience.
Heat perception and signalling in plants: a tortuous path to thermotolerance
Authors: Saidi Younousse , Finka Andrija , Goloubinoff Pierre 
Published: December 2010

SummaryAn accurate assessment of the rising ambient temperature by plant cells is crucial for the timely activation of various molecular defences before the appearance of heat damage. Recent findings have allowed a better understanding of the early cellular events that take place at the beginning of mild temperature rise, to timely express heat‐shock proteins (HSPs), which will, in turn, confer thermotolerance to the plant. Here, we discuss the key components of the heat signalling pathway and suggest a model in which a primary sensory role is carried out by the plasma membrane and various secondary messengers, such as Ca2+ ions, nitric oxide (NO) and hydrogen peroxide (H2O2). We also describe the role of downstream components, such as calmodulins, mitogen‐activated protein kinases and Hsp90, in the activation of heat‐shock transcription factors (HSFs). The data gathered for land plants suggest that, following temperature elevation, the heat signal is probably transduced by several pathways that will, however, coalesce into the final activation of HSFs, the expression of HSPs and the onset of cellular thermotolerance.
The flavonoid baicalein promotes NMDA receptor‐dependent long‐term potentiation and enhances memory
Authors: Wang Wei , Wang Fang , Yang Yuan‐Jian , Hu Zhuang‐Li , Long Li‐Hong , Fu Hui , Xie Na , Chen Jian‐Guo 
Published: December 2010

BACKGROUND AND PURPOSE There is growing interest in the physiological functions of flavonoids, especially in their effects on cognitive function and on neurodegenerative diseases. The aim of the current investigation was to evaluate the role of the flavonoid baicalein in long‐term potentiation (LTP) in the hippocampal CA1 region and cognitive behavioural performance.EXPERIMENTAL APPROACH Effects of baicalein on LTP in rat hippocampal slices were investigated by electrophysiological methods. Phosphorylation of Akt (at Ser473), the extracellular signal‐regulated kinase (ERK1/2) and the transcription factor cAMP response element‐binding protein (CREB) (at Ser133) were analysed by Western blot. Fear conditioning was used to determine whether baicalein could improve learning and memory in rats.KEY RESULTS Baicalein enhanced the N‐methyl‐d‐aspartate glutamate receptor‐dependent LTP in a bell‐shaped concentration‐dependent manner. Addition of the lipoxygenase metabolites 12(S)‐HETE and 12(S)‐HPETE did not reverse these effects of baicalein. Baicalein treatment enhanced phosphorylation of Akt during induction of LTP with the same bell‐shaped dose–response curve. LTP potentiation induced by baicalein was blocked by inhibitors of phosphoinositide 3‐kinase. CREB phosphorylation was also increased in the CA1 region of baicalein‐treated slices. Baicalein‐treated rats performed significantly better than controls in a hippocampus‐dependent contextual fear conditioning task. Furthermore, baicalein treatment selectively increased the phosphorylation of Akt and CREB in the CA1 region of hippocampus, but not in the prefrontal cortex, after fear conditioning training.CONCLUSIONS AND IMPLICATIONS Our results demonstrate that the flavonoid baicalein can facilitate memory, and therefore it might be useful in the treatment of patients with memory disorders.