bluuebunny/crossref_metadata_2025_split huggingface dataset:
Temporal Annotation and Representation
Authors: Verhagen Marc , Moszkowicz Jessica L. 
Published: March 2009

AbstractThe goal of temporal annotation is to mark up all elements of a text that are relevant to the temporal interpretation of that text. As such, temporal annotation reveals part of the semantics of a text. We describe recent approaches to temporal annotation, focusing on the recently developed annotation language TimeML. In addition, we describe a couple of systems aimed at temporally parsing texts. We motivate the use of temporal annotation from a question answering viewpoint and describe some earlier insights from theoretical linguistics on what the temporal properties of language constructs are.
Isolation and characterization of microsatellites in the bird‐pollinated, autohexaploid, Eremophila glabra ssp. glabra (R.Br. (Ostenf.)) (Myoporaceae), an Australian endemic plant
Authors: ELLIOTT C. P. 
Published: March 2009

AbstractThirty‐eight microsatellite loci were developed for the bird pollinated, autohexaploid, Eremophila glabra ssp. glabra. A genomic library was screened with dinucleotide and trinucleotide sequence repeats. Polymorphism ranged from one to 21 alleles per locus. Twenty‐four loci exhibited null alleles, based on patterns of inheritance between maternal and progeny phenotypes. Cross‐species amplification of nine Eremophila species was successful for most primers, indicating wide applicability across the genus. These microsatellites will be used to study the gene flow patterns of fragmented populations of E. glabra ssp. glabra.
Establishing the Sri Lanka Clinical Trials Registry
Authors: Ranawaka Udaya K , Goonaratna Colvin 
Published: March 2009

AbstractRecognizing the need for a national body for trial registration, the Sri Lanka Medical Association took up the challenge of setting up the Sri Lanka Clinical Trials Registry. The registry was established in November 2006, the first functioning trial registry in South Asia. The Sri Lanka Clinical Trials Registry is now a primary registry affiliated to the Registry Network of the International Clinical Trials Registry Platform of the World Health Organization. The Sri Lanka Clinical Trials Registry has not been a mere repository for trial data but has also had a positive influence on the research community in Sri Lanka.
Meta‐analysis of randomized trials for health care interventions: one for all?
Authors: Sun Xin , Guyatt Gordon 
Published: March 2009

AbstractMeta‐analysis of randomized trials stands at the top of the epidemiological designs to test the effect of health care interventions. Ideally, it systematically and comprehensively collects the relevant randomized trials, and pools the trials to generate a single estimate of effects. However, the rationale for meta‐analysis may not always be thoughtfully considered, and overlooking underlying principles may cause illusions. This article revisits the rationale for meta‐analysis, discusses how meta‐analysis can be misleading, and summarizes approaches to critically and judiciously interpret and use the results of meta‐analysis.
Background, introduction and activity of the Japan Primary Registries Network
Authors: Shiokawa Tomonori 
Published: March 2009

AbstractRegarding registration and publication of clinical trials, there are now three registry organizations in Japan; the University Hospital Medical Information Network (UMIN), the Japan Pharmaceutical Information Center (JAPIC) and the Japan Medical Association – Center for Clinical Trials (JMACCT). In addition, a portal site which supports searching for information on clinical trials in all three registries has been operated by the National Institute of Public Health (NIPH). After we established a cooperative system, we became a WHO Primary Registry on October 16, 2008 and announced this in Japan on the next day. This cooperation system is called the Japan Primary Registries Network (JPRN).In order to show that this type of network works well as a Primary Registry, we are cooperating with global activities of World Health Organization's International Clinical Trial Registry Platform (WHO ICTRP) to promote clinical trials and propose appropriate idea to the world.
NF-κB p50 Plays Distinct Roles in the Establishment and Control of Murine Gammaherpesvirus 68 Latency
Authors: Krug Laurie T. , Collins Christopher M. , Gargano Lisa M. , Speck Samuel H. 
Published: March 2009

ABSTRACTNF-κB signaling is critical to the survival and transformation of cells infected by the human gammaherpesviruses Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus. Here we have examined how elimination of the NF-κB transcription factor p50 from mice affects the life cycle of murine gammaherpesvirus 68 (MHV68). Notably, mice lacking p50 in every cell type were unable to establish a sufficiently robust immune response to control MHV68 infection, leading to high levels of latently infected B cells detected in the spleen and persistent virus replication in the lungs. The latter correlated with very low levels of virus-specific immunoglobulin G (IgG) in the infected p50−/−mice at day 48 postinfection. Because the confounding impact of the loss of p50 on the host response to MHV68 infection prevented a direct analysis of the role of this NF-κB family member on MHV68 latency in B cells, we generated and infected mixed p50+/+/p50−/−bone marrow chimeric mice. We show that the chimeric mice were able to control acute virus replication and exhibited normal levels of virus-specific IgG at 3 months postinfection, indicating the induction of a normal host immune response to MHV68 infection. However, in p50+/+/p50−/−chimeric mice the p50−/−B cells exhibited a significant defect compared to p50+/+B cells in supporting MHV68 latency. In addition to identifying a role for p50 in the establishment of latency, we determined that the absence of p50 in a subset of the hematopoietic compartment led to persistent virus replication in the lungs of the chimeric mice, providing evidence that p50 is required for controlling virus reactivation. Taken together, these data demonstrate that p50 is required for immune control by the host and has distinct tissue-dependent roles in the regulation of murine gammaherpesvirus latency during chronic infection.
Unraveling Viral Interleukin-6 Binding to gp130 and Activation of STAT-Signaling Pathways Independently of the Interleukin-6 Receptor
Authors: Adam Nina , Rabe Björn , Suthaus Jan , Grötzinger Joachim , Rose-John Stefan , Scheller Jürgen 
Published: March 2009

ABSTRACTHuman herpesvirus 8 encodes a viral version of interleukin-6 (vIL-6) which shows 25% sequence homology with human IL-6. In contrast to human IL-6, which first binds to the IL-6 receptor (IL-6R) and only subsequently associates with the signal transducing receptor subunit gp130, vIL-6 has been shown to directly bind to gp130 without the need of IL-6R. As a functional consequence, vIL-6 can activate far more target cells in the body since all cells express gp130, but only cells such as hepatocytes and some leukocytes express IL-6R. We sought to understand which amino acid sequences within the vIL-6 protein were responsible for its ability to bind and activate gp130 independent of IL-6R. As a first approach, we constructed chimeric IL-6 proteins in which all known gp130 interacting sites (sites II and III) were sequentially transferred from vIL-6 into the human IL-6 protein. To our surprise, human IL-6 carrying all gp130 interacting sites from vIL-6 did not show IL-6R-independent gp130 activation. Even more surprisingly, the loop between helix B and C of vIL-6, clearly shown in the crystal structure not to be in contact with gp130, is indispensable for direct binding to and activation of gp130. This points to an IL-6R induced change of site III conformation in human IL-6, which is already preformed in vIL-6. These data indicate a novel activation mechanism of human IL-6 by the IL-6R that will be important for the construction of novel hyperactive cytokine variants.
A Yeast Glycoprotein Shows High-Affinity Binding to the Broadly Neutralizing Human Immunodeficiency Virus Antibody 2G12 and Inhibits gp120 Interactions with 2G12 and DC-SIGN
Authors: Luallen Robert J. , Fu Hu , Agrawal-Gamse Caroline , Mboudjeka Innocent , Huang Wei , Lee Fang-Hua , Wang Lai-Xi , Doms Robert W. , Geng Yu 
Published: March 2009

ABSTRACT

The human immunodeficiency virus type 1 (HIV-1) envelope (Env) protein contains numerous N-linked carbohydrates that shield conserved peptide epitopes and promote
trans
infection by dendritic cells via binding to cell surface lectins. The potent and broadly neutralizing monoclonal antibody 2G12 binds a cluster of high-mannose-type oligosaccharides on the gp120 subunit of Env, revealing a conserved and highly exposed epitope on the glycan shield. To find an effective antigen for eliciting 2G12-like antibodies, we searched for endogenous yeast proteins that could bind to 2G12 in a panel of
Saccharomyces cerevisiae
glycosylation knockouts and discovered one protein that bound weakly in a Δ
pmr1
strain deficient in hyperglycosylation. 2G12 binding to this protein, identified as Pst1, was enhanced by adding the Δ
mnn1
deletion to the Δ
pmr1
background, ensuring the exposure of terminal α1,2-linked mannose residues on the D1 and D3 arms of high-mannose glycans. However, optimum 2G12 antigenicity was found when Pst1, a heavily N-glycosylated protein, was expressed with homogenous Man
8
GlcNAc
2
structures in Δ
och1
Δ
mnn1
Δ
mnn4
yeast. Surface plasmon resonance analysis of this form of Pst1 showed high affinity for 2G12, which translated into Pst1 efficiently inhibiting gp120 interactions with 2G12 and DC-SIGN and blocking 2G12-mediated neutralization of HIV-1 pseudoviruses. The high affinity of the yeast glycoprotein Pst1 for 2G12 highlights its potential as a novel antigen to induce 2G12-like antibodies.
Herpes Simplex Virus Type 1 Regulatory Protein ICP0 Aids Infection in Cells with a Preinduced Interferon Response but Does Not Impede Interferon-Induced Gene Induction
Authors: Everett Roger D. , Orr Anne 
Published: March 2009

ABSTRACT
Several independent lines of evidence indicate that interferon-mediated innate responses are involved in controlling herpes simplex virus type 1 (HSV-1) infection and that the viral immediate-early regulatory protein ICP0 augments HSV-1 replication in interferon-treated cells. However, this is a complex situation in which the experimental outcome is determined by the choice of multiplicity of infection and cell type and by whether cultured cells or animal models are used. It is now known that neither STAT1 nor interferon regulatory factor 3 (IRF-3) play essential roles in the replication defect of ICP0-null mutant HSV-1 in cultured cells. This study set out to investigate the specific role of ICP0 in HSV-1 resistance to the interferon defense. We have used a cell line in which ICP0 expression can be induced at levels similar to those during the early stages of a normal infection to determine whether ICP0 by itself can interfere with interferon or IRF-3-dependent signaling and whether ICP0 enables the virus to circumvent the effects of interferon-stimulated genes (ISGs). We found that the presence of ICP0 was unable to compromise ISG induction by either interferon or double-stranded RNA. On the other hand, ICP0 preexpression reduced but did not eliminate the inhibitory effects of ISGs on HSV-1 infection, with the extent of the relief being highly dependent on multiplicity of infection. The results are discussed in terms of the relationships between ICP0 and intrinsic and innate antiviral resistance mechanisms.
Shared Mapping of Own and Others' Bodies in Visuotactile Bimodal Area of Monkey Parietal Cortex
Authors: Ishida Hiroaki , Nakajima Katsumi , Inase Masahiko , Murata Akira 
Published: March 2009

Abstract
Parietal cortex contributes to body representations by integrating visual and somatosensory inputs. Because mirror neurons in ventral premotor and parietal cortices represent visual images of others' actions on the intrinsic motor representation of the self, this matching system may play important roles in recognizing actions performed by others. However, where and how the brain represents others' bodies and correlates self and other body representations remain unclear. We expected that a population of visuotactile neurons in simian parietal cortex would represent not only own but others' body parts. We first searched for parietal visuotactile bimodal neurons in the ventral intraparietal area and area 7b of monkeys, and then examined the activity of these neurons while monkeys were observing visual or tactile stimuli placed on the experimenter's body parts. Some bimodal neurons with receptive fields (RFs) anchored on the monkey's body exhibited visual responses matched to corresponding body parts of the experimenter, and visual RFs near that body part existed in the peripersonal space within approximately 30 cm from the body surface. These findings suggest that the brain could use self representation as a reference for perception of others' body parts in parietal cortex. These neurons may contribute to spatial matching between the bodies of the self and others in both action recognition and imitation.
Eight Problems for the Mirror Neuron Theory of Action Understanding in Monkeys and Humans
Authors: Hickok Gregory 
Published: March 2009

AbstractThe discovery of mirror neurons in macaque frontal cortex has sparked a resurgence of interest in motor/embodied theories of cognition. This critical review examines the evidence in support of one of these theories, namely, that mirror neurons provide the basis of action understanding. It is argued that there is no evidence from monkey data that directly tests this theory, and evidence from humans makes a strong case against the position.
Fast Forward: Supramarginal Gyrus Stimulation Alters Time Measurement
Authors: Wiener Martin , Hamilton Roy , Turkeltaub Peter , Matell Matthew S. , Coslett H. B. 
Published: March 2009

AbstractThe neural basis of temporal processing is unclear. We addressed this important issue by performing two experiments in which repetitive transcranial magnetic stimulation (rTMS) was administered in different sessions to the left or right supramarginal gyrus (SMG) or vertex; in both tasks, two visual stimuli were presented serially and subjects were asked to judge if the second stimulus was longer than the first (standard) stimulus. rTMS was presented on 50% of trials. Consistent with a previous literature demonstrating the effect of auditory clicks on temporal judgment, rTMS was associated with a tendency to perceive the paired visual stimulus as longer in all conditions. Crucially, rTMS to the right SMG was associated with a significantly greater subjective prolongation of the associated visual stimulus in both experiments. These findings demonstrate that the right SMG is an important element of the neural system underlying temporal processing and, as discussed, have implications for neural and cognitive models of temporal perception and attention.
Discrete Object Representation, Attention Switching, and Task Difficulty in the Parietal Lobe
Authors: Cusack Rhodri , Mitchell Daniel J. , Duncan John 
Published: March 2009

AbstractAn important component of perception, attention, and memory is the structuring of information into subsets (“objects”), which allows some parts to be considered together but kept separate from others. Portions of the posterior parietal lobe respond proportionally to the number of objects in the scope of attention and short-term memory, up to a capacity limit of around four, suggesting they have a role in this important process. This study investigates the relationship of discrete object representation to other parietal functions. Two experiments and two supplementary analyses were conducted to evaluate responsivity in parietal regions to the number of objects, the number of spatial locations, attention switching, and general task difficulty. Using transparent motion, it was found that a posterior and inferior parietal response to multiple objects persists even in the absence of a change in visual extent or the number of spatial locations. In a monitoring task, it was found that attention switching (or task difficulty) and object representation have distinct neural signatures, with the former showing greater recruitment of an anterior and lateral intraparietal sulcus (IPS) region, but the latter in a posterior and lateral region. A dissociation was also seen between selectivity for object load across tasks in the inferior IPS and feature or object-related memory load in the superior IPS.
Attitudes toward Animals: The Effect of Priming Thoughts of Human-Animal Similarities and Mortality Salience on the Evaluation of Companion Animals
Authors: Loughnan Stephen , Halloran Michael , Beatson Ruth 
Published: March 2009

AbstractHuman attitudes toward nonhuman animals are complex and quite contradictory. They can range between extremely negative (animal cruelty) to positive (treating companion animals like human surrogates). Attitudes toward animals are especially negative when people think about human creatureliness and personal mortality. This paper investigates people's attitudes toward highly valued animals (companion animals). The research presented here tested whether companion-animal caregivers would respond to reminders of human creatureliness and mortality salience (MS) with more negative attitudes toward pets. Participants completed an online survey in which MS and human-creatureliness conditions were manipulated. Results showed that, under MS, even pet owners responded to reminders of human creatureliness with less positive attitudes toward the average pet. Thus, the effects observed in previous research extend to more popular animals, even among people with presumably positive attitudes toward animals.
A Crime that Offends the Conscience of Humanity: A Proposal to Reclassify Trafficking in Women as an International Crime
Authors: Tavakoli Nina 
Published: March 2009

AbstractThe current international legal framework for the prosecution of trafficking of women needs to be revisited if trafficking is to be combated more effectively. The treatment of trafficking as a transnational, rather than an international crime denies its essence as a crime that offends the conscience of humankind and which strikes at the heart of international order. This failure is symptomatic of an international legal order that prioritises and affords greater protection to abuses of men's as opposed to women's human rights.
The Difficulties of Exercising Extraterritorial Criminal Jurisdiction: The Acquittal of a Dutch Businessman for Crimes Committed in Liberia
Authors: van den Herik Larissa 
Published: March 2009

AbstractReports of the NGO Global Witness in which the implication of the Dutchman Kouwenhoven in the civil war in Liberia was exposed served as the lead for the Dutch Prosecution Office to start a criminal case against this national. In June 2006, the Dutch businessman Guus Kouwenhoven was convicted in first instance for the violation of an arms embargo, but acquitted of the count on war crimes. On appeal, Kouwenhoven was fully acquitted of all charges. In its judgment quashing the prior conviction, the Dutch Court of Appeal heavily criticized the Public Prosecutor and observed that the case against Kouwenhoven was built on quicksand. Even though not based on universal jurisdiction, the case does illustrate the inherent complexities of exercising extraterritorial criminal jurisdiction. A remarkable aspect of the case is that the Court of Appeal evaluated the evidence presented in a fundamentally different way than the Court of First Instance had done. This might be related to the inherent difficulties of assessing “foreign evidence”. In this note, it is argued that when adjudicating such foreign cases, national judges being unfamiliar with the historical and cultural setting in which the alleged crimes took place, should call upon experts on the region to assist in the evaluation of the evidence. In terms of substance, the case leads to interesting questions as to how charges of illegal arms trade do and should relate to charges of complicity in war crimes.
Mitochondrial pseudogenes in the nuclear genome of Aedes aegypti mosquitoes: implications for past and future population genetic studies
Authors: Hlaing Thaung , Tun-Lin Willoughby , Somboon Pradya , Socheat Duong , Setha To , Min Sein , Chang Moh Seng , Walton Catherine 
Published: March 2009

AbstractBackgroundMitochondrial DNA (mtDNA) is widely used in population genetic and phylogenetic studies in animals. However, such studies can generate misleading results if the species concerned contain nuclear copies of mtDNA (Numts) as these may amplify in addition to, or even instead of, the authentic target mtDNA. The aim of this study was to determine if Numts are present inAedes aegyptimosquitoes, to characterise any Numts detected, and to assess the utility of using mtDNA for population genetics studies in this species.ResultsBLAST searches revealed large numbers of Numts in theAe. aegyptinuclear genome on 146 supercontigs. Although the majority are short (80% < 300 bp), some Numts are almost full length mtDNA copies. These long Numts are not due to misassembly of the nuclear genome sequence as the Numt-nuclear genome junctions could be recovered by amplification and sequencing. Numt evolution appears to be a complex process inAe. aegyptiwith ongoing genomic integration, fragmentation and mutation and the secondary movement of Numts within the nuclear genome.The PCR amplification of the putative mtDNA nicotinamide adenine dinucleotide dehydrogenase subunit 4 (ND4) gene from 166 Southeast AsianAe. aegyptimosquitoes generated a network with two highly divergent lineages (clade 1 and clade 2). Approximately 15% of theND4sequences were a composite of those from each clade indicating Numt amplification in addition to, or instead of, mtDNA. Clade 1 was shown to be composed at least partially of Numts by the removal of clade 1-specific bases from composite sequences following enrichment of the mtDNA. It is possible that all the clade 1 sequences in the network were Numts since the clade 2 sequences correspond to the known mitochondrial genome sequence and since all the individuals that produced clade 1 sequences were also found to contain clade 2 mtDNA-like sequences using clade 2-specific primers. However, either or both sets of clade sequences could have Numts since the BLAST searches revealed two long Numts that match clade 2 and one long Numt that matches clade 1. The substantial numbers of mutations in clonedND4PCR products also suggest there are both recently-derived clade 1 and clade 2 Numt sequences.ConclusionWe conclude that Numts are prevalent inAe. aegyptiand that it is difficult to distinguish mtDNA sequences due to the presence of recently formed Numts. Given this, future population genetic or phylogenetic studies inAe. aegyptishould use nuclear, rather than mtDNA, markers.