bluuebunny/crossref_metadata_2025_split huggingface dataset:
From Mexico to Mali: four years in the history of clinical trial registration
Authors: Ghersi Davina , Pang Tikki 
Published: March 2009

AbstractIn the 4 years between the Ministerial Forums on research and health held in Mexico in 2004 and Mali in 2008, the landscape of clinical trial registration changed significantly. When the ICMJE announced that they would no longer consider publishing the findings of clinical trials unless the research had been prospectively registered, they were key to shifting the way the clinical trials community thinks about research transparency. The argument in favour of greater transparency had been building for more than 20 years. By 2004 there was consistent and convincing evidence of the existence of publication bias and the damage this does to people's ability to make well informed decisions about health care. There is now increasing acceptance that the registration of clinical trials in a publicly accessible registry is a scientific, ethical and moral responsibility. In 2004, less than 3000 clinical trials were registered on databases meeting ICMJE criteria. There are now more than 19000 and, in some countries, prospective registration in a publicly accessible registry is now a legal requirement. Further, since October 2008, prospective registration is required if researchers wish to comply with the Declaration of Helsinki. However, despite these advances and incentives, trial registration in many countries remains far from comprehensive and stronger enforcement mechanisms may be needed in those countries.
Prospective Registration of Clinical Trials in India: Strategies, Achievements & Challenges
Authors: Tharyan Prathap 
Published: March 2009

Abstract Objective This paper traces the development of the Clinical Trial Registry‐India (CTRI) against the backdrop of the inequities in healthcare and the limitations in the design, conduct, regulation, oversight and reporting of clinical trials in India. It describes the scope and goals of the CTRI, the data elements it seeks and the process of registering clinical trials. It reports progress in trial registration in India and discusses the challenges in ensuring that healthcare decisions are informed by all the evidence. Methods A descriptive survey of developments in clinical trial registration in India from publications in the Indian medical literature supplemented by firsthand knowledge of these developments and an evaluation of how well clinical trials registered in the CTRI up to 10 January, 2009 comply with the requirements of the CTRI and the World Health Organization's International Clinical Trial Registry (WHO ICTRP). Results Considerable inequities exist within the Indian health system. Deficiencies in healthcare provision and uneven regulation of, and access to, affordable healthcare co‐exists with a large private health system of uneven quality. India is now a preferred destination for outsourced clinical trials but is plagued by poor ethical oversight of the many trial sites and scant information of their existence. The CTRI's vision of conforming to international requirements for transparency and accountability but also using trial registration as a means of improving trial design, conduct and reporting led to the selection of registry‐specific dataset items in addition to those endorsed by the WHO ICTRP. Compliance with these requirements is good for the trials currently registered but these trials represent only a fraction of the trials in progress in India. Conclusion Prospective trial registration is a reality in India. The challenges facing the CTRI include better engagement with key stakeholders to ensure increased prospective registration of clinical trials and utilization of existing legislative opportunities to complement these efforts.
Induction of Escherichia coli O157:H7 into the viable but non‐culturable state by chloraminated water and river water, and subsequent resuscitation
Authors: Liu Yanming , Wang Chuan , Tyrrell Gregory , Hrudey Steve E. , Li Xing‐Fang 
Published: March 2009

SummaryInduction of culturable Escherichia coli O157:H7 cells into a viable but non‐culturable (VBNC) state by chloraminated tap water was carefully investigated; as many as 90% of initial cells entered into a VBNC state within 15 min, compared with 14% in river water within 14 weeks. To understand what specific stresses may induce E. coli O157:H7 into a VBNC state, chloraminated tap water, autoclaved river water, and media with known ingredients (PBS buffer and deionized water) at 4°C or 25°C were used to examine induction efficiency. Chloramination alone, or the combination of starvation with either low temperature or osmotic pressure, induced E. coli O157:H7 into a VBNC state, while starvation alone did not induce the bacteria into a VBNC state within 1.5 years. The mRNA of the rfbE and fliC genes was detected in the 10‐month‐old VBNC cells induced by river water, confirming the viability of E. coli O157:H7 VBNC cells. The VBNC cells induced by chloraminated water and the 10‐month‐old VBNC cells induced by river water were first resuscitated using autoinducers produced by E. coli O157:H7 itself in a serum‐based medium; the VBNC cells of bovine isolates recovered more efficiently compared with those of clinical isolates. These results demonstrate a potential health risk of VBNC E. coli O157:H7 in environmental water and the utility of monitoring viable E. coli O157:H7 including VBNC cells based on the mRNA of the rfbE and fliC genes.
Microbial growth in Arctic tundra soil at −2°C
Authors: McMahon Shawna K. , Wallenstein Matthew D. , Schimel Joshua P. 
Published: March 2009

SummaryThere is some evidence that microbes inhabiting permanently frozen environments are capable of cell maintenance and growth under in situ conditions. In contrast, Arctic tundra surface soils that are only frozen during the winter have exhibited CO2 respiration under frozen conditions. This could result from maintenance metabolism fuelled by recycling cell material, but does necessarily indicate growth, which requires the synthesis of new cell material. We used 13C‐glucose to trace C into membrane lipids and 5‐bromo‐3‐deoxyuridine to monitor DNA synthesis in a laboratory microcosm study on Arctic tundra soils. Organisms were not equally active: fungi incorporated more C than any other group. Although some bacteria were growing, Gram(+) bacteria were almost completely inactive. Shrub tundra microbes were more active in early winter than tussock microbes, incorporating more C and synthesizing more DNA. In late winter, the C incorporation pattern reversed, although DNA production was similar. We demonstrated for the first time that microbes in frozen tundra soils synthesized new cell membranes and DNA, processes fundamentally associated with growth. That microbes can grow during Arctic winters may have important implications for C cycle modelling under a changing climate.
Selection of H5N1 Influenza Virus PB2 during Replication in Humans
Authors: Le Quynh Mai , Sakai-Tagawa Yuko , Ozawa Makoto , Ito Mustumi , Kawaoka Yoshihiro 
Published: March 2009

ABSTRACT
Highly pathogenic H5N1 influenza viruses continue to cause concern, even though currently circulating strains are not efficiently transmitted among humans. For efficient transmission, amino acid changes in viral proteins may be required. Here, we examined the amino acids at positions 627 and 701 of the PB2 protein. A direct analysis of the viral RNAs of H5N1 viruses in patients revealed that these amino acids contribute to efficient virus propagation in the human upper respiratory tract. Viruses grown in culture or eggs did not always reflect those in patients. These results emphasize the importance of the direct analysis of original specimens.
Simulating Henipavirus Multicycle Replication in a Screening Assay Leads to Identification of a Promising Candidate for Therapy
Authors: Porotto Matteo , Orefice Gianmarco , Yokoyama Christine C. , Mungall Bruce A. , Realubit Ronald , Sganga Michael L. , Aljofan Mohamad , Whitt Michael , Glickman Fraser , Moscona Anne 
Published: March 2009

ABSTRACT
Nipah (NiV) and Hendra (HeV) viruses are emerging zoonotic paramyxoviruses that cause encephalitis in humans, with fatality rates of up to 75%. We designed a new high-throughput screening (HTS) assay for inhibitors of infection based on envelope glycoprotein pseudotypes. The assay simulates multicycle replication and thus identifies inhibitors that target several stages of the viral life cycle, but it still can be carried out under biosafety level 2 (BSL-2) conditions. These features permit a screen for antivirals for emerging viruses and select agents that otherwise would require BSL-4 HTS facilities. The screening of a small compound library identified several effective molecules, including the well-known compound chloroquine, as highly active inhibitors of pseudotyped virus infection. Chloroquine inhibited infection with live HeV and NiV at a concentration of 1 μM in vitro (50% inhibitory concentration, 2 μM), which is less than the plasma concentrations present in humans receiving chloroquine treatment for malaria. The mechanism for chloroquine's antiviral action likely is the inhibition of cathepsin L, a cellular enzyme that is essential for the processing of the viral fusion glycoprotein and the maturation of newly budding virions. Without this processing step, virions are not infectious. The identification of a compound that inhibits a known cellular target that is important for viral maturation but that had not previously been shown to have antiviral activity for henipaviruses highlights the validity of this new screening assay. Given the established safety profile and broad experience with chloroquine in humans, the results described here provide an option for treating individuals infected by these deadly viruses.
The Epstein-Barr Virus Alkaline Exonuclease BGLF5 Serves Pleiotropic Functions in Virus Replication
Authors: Feederle R. , Bannert H. , Lips H. , Müller-Lantzsch N. , Delecluse H.-J. 
Published: March 2009

ABSTRACT
The Epstein-Barr virus (EBV) alkaline exonuclease BGLF5 has previously been recognized to contribute to immune evasion by downregulating production of HLA molecules during virus replication. We have constructed a BGLF5-null virus mutant to determine BGLF5's functions during EBV viral replication. Quantification of virus production in permissive 293 cells carrying a ΔBGLF5 genome identified a 17- to 21-fold reduction relative to complemented or wild-type controls. Detailed monitoring of ΔBGLF5 replication evidenced an impaired virus nucleocapsid maturation, a reduced primary egress and a 1.4-fold reduction in total viral DNA synthesis. ΔBGLF5 single-unit-length viral genomes were not only less abundant but also migrated faster than expected in gel electrophoresis. We concluded that BGLF5 pertained both to the generation and to the processing of viral linear genomes. ΔBGLF5 phenotypic traits were reminiscent of those previously identified in a mutant devoid of UL12, BGLF5's homolog in herpes simplex virus type 1, and indeed UL12 was found to partially complement the ΔBGLF5 phenotype. However, BGLF5-specific functions could also be identified; the nuclear membrane of replicating cells displayed images of reduplication and complex folding that could be completely corrected by BGLF5 but not UL12. Similar nuclear abnormalities were previously observed in cells transfected with BFLF2 and BFRF1, two viral proteins crucial for EBV nuclear egress. Interestingly, ΔBGLF5 cells produced more BFLF2 than wild-type or complemented counterparts. The present study provides an overview of BGLF5's functions that will guide future molecular studies. We anticipate that the 293/ΔBGLF5 cell line will be instrumental in such developments.
The Human Immunodeficiency Virus Type 2 Vpx Protein Usurps the CUL4A-DDB1
DCAF1
Ubiquitin Ligase To Overcome a Postentry Block in Macrophage Infection
Authors: Bergamaschi Anna , Ayinde Diana , David Annie , Le Rouzic Erwann , Morel Marina , Collin Gilles , Descamps Diane , Damond Florence , Brun-Vezinet Françoise , Nisole Sebastien , Margottin-Goguet Florence , Pancino Gianfranco , Transy Catherine 
Published: March 2009

ABSTRACT

The human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) genomes encode several auxiliary proteins that have increasingly shown their importance in the virus-host relationship. One of these proteins, Vpx, is unique to the HIV-2/SIVsm lineage and is critical for viral replication in macrophages. The functional basis for this requirement, as well as the Vpx mode of action, has remained unexplained, and it is all the more enigmatic that HIV type 1 (HIV-1), which has no Vpx counterpart, can infect macrophages. Here, we underscore DCAF1 as a critical host effector of Vpx in its ability to mediate infection and long-term replication of HIV-2 in human macrophages. Vpx assembles with the CUL4A-DDB1 ubiquitin ligase through DCAF1 recruitment. Precluding Vpx present in the incoming virions from recruiting DCAF1 in target macrophages leads to a postentry block characterized by defective accumulation of HIV-2 reverse transcripts. In addition, Vpx from SIVsm functionally complements Vpx-defective HIV-2 in a DCAF1-binding-dependent manner. Altogether, our data point to a mechanism in which Vpx diverts the Cul4A-DDB1
DCAF1
ligase to inactivate an evolutionarily conserved factor, which restricts macrophage infection by HIV-2 and closely related simian viruses.
Virus-Specific Cytolytic Antibodies to Nonstructural Protein 1 of Japanese Encephalitis Virus Effect Reduction of Virus Output from Infected Cells
Authors: Krishna Venkatramana D. , Rangappa Manjuladevi , Satchidanandam Vijaya 
Published: March 2009

ABSTRACTWe demonstrate the presence of nonstructural protein 1 (NS1)-specific antibodies in a significant proportion of convalescent-phase human serum samples obtained from a cohort in an area where Japanese encephalitis virus (JEV) is endemic. Sera containing antibodies to NS1 but not those with antibodies to other JEV proteins, such as envelope, brought about complement-mediated lysis of JEV-infected BHK-21 cells. Target cells infected with a recombinant poxvirus expressing JEV NS1 on the cell surface confirmed the NS1 specificity of cytolytic antibodies. Mouse anti-NS1 cytolytic sera caused a complement-dependent reduction in virus output from infected human cells, demonstrating their important role in viral control. Antibodies elicited by JEV NS1 did not cross lyse West Nile virus- or dengue virus-infected cells despite immunoprecipitating the NS1 proteins of these related flaviviruses. Additionally, JEV NS1 failed to bind complement factor H, in contrast to NS1 of West Nile virus, suggesting that the NS1 proteins of different flaviviruses have distinctly different mechanisms for interacting with the host. Our results also point to an important role for JEV NS1-specific human immune responses in protection against JE and provide a strong case for inclusion of the NS1 protein in next generation of JEV vaccines.
Mixtures of Complete andpif1- andpif2-Deficient Genotypes Are Required for Increased Potency of an Insect Nucleopolyhedrovirus
Authors: Clavijo Gabriel , Williams Trevor , Simón Oihane , Muñoz Delia , Cerutti Martine , López-Ferber Miguel , Caballero Primitivo 
Published: March 2009

ABSTRACTThe insecticidal potency of a nucleopolyhedrovirus population (SfNIC) that infectsSpodoptera frugiperda(Lepidoptera) is greater than the potency of any of the component genotypes alone. Occlusion bodies (OBs) produced in mixed infections comprising the complete genotype and a deletion genotype are as pathogenic as the natural population of genotypes from the field. To test whether this increased potency was due to the deletion or to some other characteristic of the deletion variant genome, we used the SfNIC-B genome to construct a recombinant virus (SfNIC-BΔ16K) with the same 16.4-kb deletion as that observed in SfNIC-C and another recombinant (SfNIC-BΔpifs) with a deletion encompassing two adjacent genes (pif1andpif2) that are essential for transmission per os. Mixtures comprising SfNIC-B and SfNIC-BΔ16K in OB ratios that varied between 10:90 and 90:10 were injected into insects, and the progeny OBs were fed to larvae in an insecticidal potency assay. A densitometric analysis of PCR products indicated that SfNIC-B was generally more abundant than expected in mixtures based on the proportions of OBs used to produce the inocula. Mixtures derived from OB ratios of 10, 25, or 50% of SfNIC-BΔ16K and the corresponding SfNIC-B proportions showed a significant increase in potency compared to SfNIC-B alone. The results of potency assays with mixtures comprising various proportions of SfNIC-B plus SfNIC-BΔpifswere almost identical to the results observed with SfNIC-BΔ16K, indicating that deletion of thepifgene region was responsible for the increased potency observed in mixtures of SfNIC-B and each deletion recombinant virus. Subsequently, mixtures produced from OB ratios involving 10 or 90% of SfNIC-BΔ16K with the corresponding proportions of SfNIC-B were subjected to four rounds of per os transmission in larvae. The composition of each experimental mixture rapidly converged to a common equilibrium with a genotypic composition of ∼85% SfNIC-B plus ∼15% SfNIC-BΔ16K. Nearly identical results were observed in peroral-passage experiments involving mixtures of SfNIC-B plus SfNIC-BΔpifs. We conclude that (i) the deletion of thepif1andpif2region is necessary and sufficient to explain the increased potency observed in mixtures of complete and deletion genotypes and (ii) viral populations with decreased ratios ofpif1- andpif2-deficient genotypes in the virus population increase the potency of genotypic mixtures and are likely to positively influence the transmission of this pathogen.
Characterization of Respiratory Syncytial Virus M- and M2-Specific CD4 T Cells in a Murine Model
Authors: Liu Jie , Ruckwardt Tracy J. , Chen Man , Johnson Teresa R. , Graham Barney S. 
Published: March 2009

ABSTRACTCD4 T cells have been shown to play an important role in the immunity and immunopathogenesis of respiratory syncytial virus (RSV) infection. We identified two novel CD4 T-cell epitopes in the RSV M and M2 proteins with core sequences M213-223(FKYIKPQSQFI) and M227-37(YFEWPPHALLV). Peptides containing the epitopes stimulated RSV-specific CD4 T cells to produce gamma interferon (IFN-γ), interleukin 2 (IL-2), and other Th1- and Th2-type cytokines in an I-Ab-restricted pattern. Construction of fluorochrome-conjugated peptide-I-Abclass II tetramers revealed RSV M- and M2-specific CD4 T-cell responses in RSV-infected mice in a hierarchical pattern. Peptide-activated CD4 T cells from lungs were more activated and differentiated, and had greater IFN-γ expression, than CD4 T cells from the spleen, which, in contrast, produced greater levels of IL-2. In addition, M209-223peptide-activated CD4 T cells reduced IFN-γ and IL-2 production in M- and M2-specific CD8 T-cell responses to Db-M187-195and Kd-M282-90peptides more than M225-39peptide-stimulated CD4 T cells. This correlated with the fact that I-Ab-M209-223tetramer-positive cells responding to primary RSV infection had a much higher frequency of FoxP3 expression than I-Ab-M226-39tetramer-positive CD4 T cells, suggesting that the M-specific CD4 T-cell response has greater regulatory function. Characterization of epitope-specific CD4 T cells by novel fluorochrome-conjugated peptide-I-Abtetramers allows detailed analysis of their roles in RSV pathogenesis and immunity.
Involvement of Creatine Kinase B in Hepatitis C Virus Genome Replication through Interaction with the Viral NS4A Protein
Authors: Hara Hiromichi , Aizaki Hideki , Matsuda Mami , Shinkai-Ouchi Fumiko , Inoue Yasushi , Murakami Kyoko , Shoji Ikuo , Kawakami Hayato , Matsuura Yoshiharu , Lai Michael M. C. , Miyamura Tatsuo , Wakita Takaji , Suzuki Tetsuro 
Published: March 2009

ABSTRACTPersistent infection with hepatitis C virus (HCV) is a major cause of chronic liver diseases. The aim of this study was to identify host cell factor(s) participating in the HCV replication complex (RC) and to clarify the regulatory mechanisms of viral genome replication dependent on the host-derived factor(s) identified. By comparative proteome analysis of RC-rich membrane fractions and subsequent gene silencing mediated by RNA interference, we identified several candidates for RC components involved in HCV replication. We found that one of these candidates, creatine kinase B (CKB), a key ATP-generating enzyme that regulates ATP in subcellular compartments of nonmuscle cells, is important for efficient replication of the HCV genome and propagation of infectious virus. CKB interacts with HCV NS4A protein and forms a complex with NS3-4A, which possesses multiple enzyme activities. CKB upregulates both NS3-4A-mediated unwinding of RNA and DNA in vitro and replicase activity in permeabilized HCV replicating cells. Our results support a model in which recruitment of CKB to the HCV RC compartment, which has high and fluctuating energy demands, through its interaction with NS4A is important for efficient replication of the viral genome. The CKB-NS4A association is a potential target for the development of a new type of antiviral therapeutic strategy.
Suppression of Host Gene Expression by nsp1 Proteins of Group 2 Bat Coronaviruses
Authors: Tohya Yukinobu , Narayanan Krishna , Kamitani Wataru , Huang Cheng , Lokugamage Kumari , Makino Shinji 
Published: March 2009

ABSTRACTnsp1 protein of severe acute respiratory syndrome coronavirus (SARS-CoV), a group 2b CoV, suppresses host gene expression by promoting host mRNA degradation and translation inhibition. The present study analyzed the activities of nsp1 proteins from the group 2 bat CoV strains Rm1, 133, and HKU9-1, belonging to groups 2b, 2c, and 2d, respectively. The host mRNA degradation and translational suppression activities of nsp1 of SARS-CoV and Rm1 nsp1 were similar and stronger than the activities of the nsp1 proteins of 133 and HKU9-1. Rm1 nsp1 expression intransstrongly inhibited the induction of type I interferon (IFN-I) and IFN-stimulated genes in cells infected with an IFN-inducing SARS-CoV mutant, while 133 and HKU9-1 nsp1 proteins had relatively moderate IFN-inhibitory activities. The results of our studies suggested a conserved function among nsp1 proteins of SARS-CoV and group 2 bat CoVs.