bluuebunny/crossref_metadata_2025 huggingface dataset:
Temporal Parts
Authors: McGrath Matthew
Published: August 2007

This article discusses recent work in metaphysics on temporal parts. After a short introduction introducing the notion of a temporal part, we examine several well‐known arguments for the view that ordinary material objects such as tables, trees, and persons have temporal parts: (1) positing temporal parts makes it possible to solve puzzles of coincidence (e.g., the statue/lump puzzle); (2) positing temporal parts makes it possible to solve the problem of intrinsic change over time; and (3) the existence of temporal parts can be demonstrated based on considerations about vagueness in composition. We conclude by examining briefly a recent argument that the dispute over whether there are temporal parts is merely verbal.
Hume's Distinction between Philosophical Anatomy and Painting
Authors: Abramson Kate
Published: August 2007

Although the implications of Hume's distinction between philosophical ‘anatomy’ and ‘painting’ have been the subject of lively scholarly debates, it is a puzzling fact that the details of the distinction itself have largely been a matter of interpretive presumption rather than debate. This would be unproblematic if Hume's views about these ‘two species of philosophy’ were obvious, or if there were a rich standard interpretation of the distinction that we had little reason to doubt. But a careful review of the literature shows neither to be the case. We are far from scholarly consensus about Hume's vision of philosophical anatomy and painting, and what unity there is rests on extremely unsteady ground and leaves important questions unanswered. In this article, my aim is three‐fold: first, to show that the appearance of well‐grounded scholarly unity about Hume's distinction is illusory; second, to dispose of those misinterpretations of Hume's distinction that are sufficiently at odds with the text that they can be demonstrated to be false in this context; and third, to explore in sufficient detail the numerous questions one might raise about the content of Hume's distinction so that the stage might at last be properly set for a truly full account of Hume's distinction between philosophical anatomy and painting.
Comment on "Deep Mixing of
3
He: Reconciling Big Bang and Stellar Nucleosynthesis"
Authors: Balser Dana S. , Rood Robert T. , Bania T. M.
Published: August 2007

Eggleton
et al
. (Reports, 8 December 2006, p. 1580) reported on a deep-mixing mechanism in low-mass stars caused by a Rayleigh-Taylor instability that destroys all of the helium isotope
3
He produced during the star's lifetime. Observations of
3
He in planetary nebulae, however, indicate that some stars produce prodigious amounts of
3
He. This is inconsistent with the claim that all low-mass stars should destroy
3
He.
The U.S. in the Rebuilding of European Science
Authors: Gaudillière Jean-Paul
Published: August 2007

American Hegemony and the Postwar Reconstruction of Science in Europe
.
By John Krige
. MIT Press, Cambridge, MA, 2006. 388 pp. $40, £25.95. ISBN 9780262112970. Transformations: Studies in the History of Science and Technology.

Krige discusses the intersection of postwar foreign policy and science in Europe and the interactions of Americans and Europeans in the rebuilding of Europe's scientific infrastructure
Alfvén Waves in the Solar Corona
Authors: Tomczyk S. , McIntosh S. W. , Keil S. L. , Judge P. G. , Schad T. , Seeley D. H. , Edmondson J.
Published: August 2007

Alfvén waves, transverse incompressible magnetic oscillations, have been proposed as a possible mechanism to heat the Sun's corona to millions of degrees by transporting convective energy from the photosphere into the diffuse corona. We report the detection of Alfvén waves in intensity, line-of-sight velocity, and linear polarization images of the solar corona taken using the FeXIII 1074.7-nanometer coronal emission line with the Coronal Multi-Channel Polarimeter (CoMP) instrument at the National Solar Observatory, New Mexico. Ubiquitous upward propagating waves were seen, with phase speeds of 1 to 4 megameters per second and trajectories consistent with the direction of the magnetic field inferred from the linear polarization measurements. An estimate of the energy carried by the waves that we spatially resolved indicates that they are too weak to heat the solar corona; however, unresolved Alfvén waves may carry sufficient energy.
Structural Basis of DNA Replication Origin Recognition by an ORC Protein
Authors: Gaudier Martin , Schuwirth Barbara S. , Westcott Sarah L. , Wigley Dale B.
Published: August 2007

DNA replication in archaea and in eukaryotes share many similarities. We report the structure of an archaeal origin recognition complex protein, ORC1, bound to an origin recognition box, a DNA sequence that is found in multiple copies at replication origins. DNA binding is mediated principally by a C-terminal winged helix domain that inserts deeply into the major and minor grooves, widening them both. However, additionalDNA contacts are made with the N-terminalAAA
+
domain, which inserts into the minor groove at a characteristic G-rich sequence, inducing a 35° bend in the duplex and providing directionality to the binding site. Both contact regions also induce substantial unwinding of the DNA. The structure provides insight into the initial step in assembly of a replication origin and recruitment of minichromosome maintenance (MCM) helicase to that origin.
Cap-Independent Translation Is Required for Starvation-Induced Differentiation in Yeast
Authors: Gilbert Wendy V. , Zhou Kaihong , Butler Tamira K. , Doudna Jennifer A.
Published: August 2007

Cellular internal ribosome entry sites (IRESs) are untranslated segments of mRNA transcripts thought to initiate protein synthesis in response to environmental stresses that prevent canonical 5′ cap–dependent translation. Although numerous cellular mRNAs are proposed to have IRESs, none has a demonstrated physiological function or molecular mechanism. Here we show that seven yeast genes required for invasive growth, a developmental pathway induced by nutrient limitation, contain potent IRESs that require the initiation factor eIF4G for cap-independent translation. In contrast to the RNA structure-based activity of viral IRESs, we show that an unstructured A-rich element mediates internal initiation via recruitment of the poly(A) binding protein (Pab1) to the 5′ untranslated region (UTR) of invasive growth messages. A 5′UTR mutation that impairs IRES activity compromises invasive growth, which indicates that cap-independent translation is required for physiological adaptation to stress.
Postgenomic Musings
Authors: Pigliucci Massimo
Published: August 2007

The Origins of Genome Architecture
.
By Michael Lynch
. Sinauer Associates, Sunderland, MA, 2007. 510 pp. $59.95. ISBN 9780878934843.

In this consideration of the origins of architectural diversity within and among prokaryotic and eukaryotic genomes, Lynch argues for the importance of mechanisms besides natural selection.
Serodiagnosis of Anthroponotic Cutaneous Leishmaniasis (ACL) Caused byLeishmania tropicain Sanliurfa Province, Turkey, Where ACL Is Highly Endemic
Authors: Zeyrek Fadile Yildiz , Korkmaz Metin , Özbel Yusuf
Published: August 2007

In this study, we aimed to evaluate the validity of the conventional enzyme-linked immunosorbent assay (ELISA) and the Western blotting test for the diagnosis of anthroponotic cutaneous leishmaniasis (ACL) using serum samples obtained from 51 patients with parasitologically proven nontreated CL (NonT-CL patients) and 62 patients under treatment for CL (UT-CL patients). Additionally, 29 serum samples obtained from patients with parasitologically and serologically proven visceral leishmaniasis (VL) were also used as positive controls, and serum samples from 43 blood donors were used as negative controls. All sera were diluted to the same dilution (1/100).Leishmania infantumMON-1 was used as the antigen in the conventional ELISA. The sera of 27 (93.1%) of 29 VL patients were seropositive by ELISA, while the sera of 40 (78.4%) of 51 NonT-CL patients and 43 (69.3%) of 62 UT-CL patients were seropositive by the conventional ELISA. The absorbance values of the CL patients' sera were significantly lower than the absorbance values of the VL patients' sera. Bands between 15 and 118 kDa were detected in two groups of CL patients. Among all bands, the 63-kDa band was found to be more sensitive (88.5%). When we evaluated the Western blotting results for the presence of at least one of the diagnostic antigenic bands, the sensitivity was calculated to be 99.1%. By using serological tests, a measurable antibody response was detected in most of the CL patients in Sanliurfa, Turkey. It is also noted that this response can be changed according to the sizes, types, and numbers of lesions that the patient has. The Western blot test was found to be more sensitive and valid than the conventional ELISA for the serodiagnosis of ACL. In some instances, when it is very difficult to demonstrate the presence of parasites in the smears, immunodiagnosis can be a valuable alternative for the diagnosis of ACL.
Evaluation of a Single-Platform Technology for Lymphocyte Immunophenotyping
Authors: Higgins Jeanette , Hill Valerie , Lau Karen , Simpson Virginia , Roayaei Jean , Klabansky Rick , Stevens Randy A. , Metcalf Julia A. , Baseler Michael
Published: August 2007

An accurate and reproducible CD4 count is a fundamental clinical tool for monitoring and treating human immunodeficiency virus infection and its complications. Two methods exist for calculating absolute CD4 counts: dual-platform technology (DPT) and single-platform technology (SPT). Numerous studies have documented the unacceptably wide range of variation in absolute CD4 counts between laboratories. SPT was introduced in 1996 to reduce the interlaboratory variation in absolute CD4 counts. The aim of this study was to compare DPT with the BD Biosciences Trucount method (an SPT method). Both the percentages of CD4 (
r
= 0.986;
P
= 0.0541) and the absolute CD4 counts (
r
= 0.960;
P
= 0.0001) had very good correlation between the two methods. However, poor correlation was observed for the CD8
+
RO
−
(
r
= 0.314;
P
= 0.0002), CD8
+
DR
+
(
r
= 0.666;
P
= 0.0138), CD3
+
CD38
+
(
r
= 0.8000;
P
= 0.0004), CD3
+
CD25
+
(
r
= 0.464;
P
= 0.0082), and CD4
+
CD38
+
(
r
= 0.357;
P
= 0.0127) measurements.
High Prevalence and Increased Severity of Pathology of Bovine Tuberculosis in Holsteins Compared to Zebu Breeds under Field Cattle Husbandry in Central Ethiopia
Authors: Ameni Gobena , Aseffa Abraham , Engers Howard , Young Douglas , Gordon Stephen , Hewinson Glyn , Vordermeier Martin
Published: August 2007

A comparative study on the prevalence and pathology of bovine tuberculosis (TB) was conducted on 5,424 cattle (2,578 zebus, 1,921 crosses, and 925 Holsteins), which were kept on pasture in the central highlands of Ethiopia, using a comparative intradermal tuberculin test, postmortem examination, and bacteriology. The overall prevalence of bovine TB was 13.5%; prevalence was higher in Holsteins than either zebus (22.2% versus 11.6%, χ2= 61.8;P< 0.001) or crosses (22.2% versus 11.9%, χ2= 50.7;P< 0.001). Moreover, the severity of pathology in Holsteins (mean ± standard error of the mean [SEM], 6.84 ± 0.79) was significantly higher (P= 0.018) than the severity of pathology in zebus (5.21 ± 0.30). In addition, the risk of TB in Holsteins was more than twice (odds ratio [OR] = 2.32; 95% confidence interval [CI] = 1.89, 2.85) that in zebus. Animals between 5 and 9 years of age were at higher (OR = 2.37; 95% CI = 1.80, 3.12) risk of bovine TB than those 2 years of age or below. A significant difference (χ2= 351;P< 0.001) in the occurrence of TB lesions in lymph nodes was recorded; the mesenteric lymph node (mean pathology score ± SEM, 1.95 ± 0.08) was most severely affected, followed by the retropharyngeal (0.80 ± 0.05) and caudal mediastinal (0.8 ± 0.06) lymph nodes. Fifty-six percent (n= 145) of the animals with gross TB lesions were culture positive; the lowest culture positivity was recorded in the skin lesions (27.3%) and the lesions of the mesenteric lymph node (31.5%). Both the skin test response and the postmortem findings suggested a higher susceptibility to bovine TB in Holsteins than zebus under identical field husbandry conditions (on pasture). In the light of increased numbers of Holstein cattle introduced into this area to raise milk production to satisfy the needs of Addis Ababa's growing population, these findings highlight the need for a control program in these herds.
Comparison between O Serotyping Method and Multiplex Real-Time PCR To Identify DiarrheagenicEscherichia coliin Taiwan
Authors: Yang Ji-Rong , Wu Fang-Tzy , Tsai Jin-Lai , Mu Jung-Jung , Lin Ling-Fen , Chen Kuang-Lo , Kuo Steve Hsu-Sung , Chiang Chuen-Sheue , Wu Ho-Sheng
Published: August 2007

To compare the diarrheagenicEscherichia coli(DEC) identifications obtained between traditional O serotyping and modern virulence gene detection assays, we developed a multiplex real-time PCR assay by detecting six specific virulence genes for enteropathogenicE. coli(EPEC), enterohemorrhagicE. coli(EHEC), enterotoxigenicE. coli(ETEC), and enteroinvasiveE. coli(EIEC). Among 261 clinical diarrheal stool samples, a total of 137 suspected DEC (sDEC) isolates were identified by the use of commercially available antisera. The most prevalent serogroups were O1 (12/137; 8.7%), O25 (9/137; 6.5%), and O44 (9/137; 6.5%). The specific virulence genes for the 137 sDEC isolates were analyzed by the multiplex real-time PCR assay. Fifteen (10.9%) of 137 isolates were confirmed to be true DEC strains, indicating that the serotypic markers did not correlate with the specific virulence genes. ETEC (66.7%) was the most prevalent, followed by EIEC (20%) and EPEC (13.3%). No EHEC strains were identified in the specimens. Four novel serotypes were found in the study: two in EPEC strains (O111:H9 and O63:H6) and two in EIEC strains (O63:H9 and O169:H9). In conclusion, the real-time PCR assay considerably reduces the high false-positive rate from the use of serotyping alone, and thus, it is suggested that serogrouping-based methods are inadequate for the identification of DEC isolates, although they are useful for the identification of a limited number of serogroups. In addition, ETEC, EPEC, and EIEC strains were present in 5.7% (15/261) of the diarrheal patients in northern Taiwan in 2006.
Single-Nucleotide-Polymorphism Typing and Genetic Relationships of
Salmonella enterica
Serovar Typhi Isolates
Authors: Octavia Sophie , Lan Ruiting
Published: August 2007

Salmonella enterica
serovar Typhi is a clone with a low level of variation. We developed a molecular typing method for serovar Typhi using 38 genome-wide single-nucleotide polymorphisms (SNPs) as markers detected by PCR-restriction enzyme digestion. The 73 worldwide serovar Typhi isolates studied were separated into 23 SNP profiles and four distinct genetic groups. Serovar Typhi isolates expressing the unique flagellar antigen z66 were found to cluster together and branch off from the ancestral group, suggesting that serovar Typhi was initially monophasic with only an H1 antigen and subsequently gained the z66 antigen. Typing using the 38 SNPs gave a discriminatory power of 0.87, and a minimum of 16 SNPs may be used to achieve the same level of differentiation. The SNP typing method we developed will be a valuable tool for global epidemiology studies of serovar Typhi.
Clonal Expansion and Microevolution of Quinolone-Resistant
Salmonella enterica
Serotype Typhi in Vietnam from 1996 to 2004
Authors: Le Thi Anh Hong , Fabre Laëtitia , Roumagnac Philippe , Grimont Patrick A. D. , Scavizzi Maurice R. , Weill François-Xavier
Published: August 2007

Salmonella enterica
serotype Typhi clinical isolates (
n
= 91) resistant to nalidixic acid (Nal
r
) were collected from sporadic cases and minor outbreaks throughout Vietnam between 1996 and 2004. These isolates were typed and compared by four methods: Vi phage typing, PstI ribotyping, XbaI and SpeI pulsed-field gel electrophoresis (PFGE), and single-nucleotide polymorphism (SNP) analysis. The results indicated that 65% of the isolates were not typeable by Vi phage typing. In contrast, the ribotyping and, with more accuracy, the SNP analysis methods indicated that all Nal
r
isolates belonged to a single clone (ribotype 3a, haplotype H58) that was found previously and that largely consisted of plasmid-encoded multidrug-resistant serotype Typhi isolates. PFGE demonstrated the occurrence of microevolution within this clone. We identified two major combined PFGE profiles: X1-S1 and X3-S6. X3-S6 predominated between 1996 and 2002 but was replaced by X1-S1 after 2002. Nevertheless, PFGE, with a Simpson's index of 0.78, was not considered an optimal discriminatory method for investigating typhoid fever outbreaks in Vietnam. The rate of quinolone resistance increased and the rate of multidrug resistance decreased during the study period. From 2002 to 2004, 80.6% of the isolates from South Vietnam were resistant only to Nal. The mechanism of Nal resistance in most of the isolates (94%) was a mutation in the quinolone resistance-determining chromosomal region of
gyrA
that led to the amino acid substitution Ser83Phe. No plasmid-located
qnrA
,
qnrB
, or
qnrS
was detected.
Narrow-Spectrum Cephalosporin Susceptibility Testing of
Escherichia coli
with the BD Phoenix Automated System: Questionable Utility of Cephalothin as a Predictor of Cephalexin Susceptibility
Authors: Zhang Sean X. , Parisian Fern , Yau Yvonne , Fuller Jeffrey D. , Poutanen Susan M. , Richardson Susan E.
Published: August 2007

The resistance of
Escherichia coli
to cephalothin was found to be overestimated when the Phoenix automated susceptibility system was used to determine resistance compared to reference broth microdilution, a finding that jeopardized the use of cephalexin for first-line treatment of urinary tract infections in children. In addition, using broth microdilution, we studied the accuracy of either cephalothin or cefazolin in predicting cephalexin susceptibility. In contrast to the recommendation of the Clinical Laboratory Standards Institute (CLSI), we found that cephalothin is not a reliable predictor of cephalexin susceptibility. Cefazolin performs no better in this role. We suggest that laboratories should consider testing and reporting cefazolin and cephalexin independently, according to clinical need.
Performance of a Pneumolysin Enzyme-Linked Immunosorbent Assay for Diagnosis of Pneumococcal Infections
Authors: del Mar García-Suárez María , Cima-Cabal María Dolores , Villaverde Roberto , Espinosa Emma , Falguera Miquel , de Los Toyos Juan R. , Vázquez Fernando , Méndez Francisco J.
Published: August 2007

A pneumolysin-specific enzyme-linked immunosorbent assay (PLY-ELISA) for the detection of pneumolysin in urine was developed and evaluated in comparison with the commercially available Binax Now
Streptococcus pneumoniae
test (Binax, Portland, ME) for the diagnosis of pneumococcal infections. Assay sensitivity was evaluated using urine from 108 patients with culture-confirmed pneumococcal infections. In adults, the sensitivity and specificity of the PLY-ELISA were 56.6% and 92.2%, respectively. In children with nasopharyngeal pneumococcal carriage, PLY-ELISA and Binax Now
S. pneumoniae
test sensitivities were 62.5% and 87.5%, respectively, while specificities were 94.4% and 27.8%, respectively. In children with nonnasopharyngeal pneumococcal carriage, PLY-ELISA and Binax Now
S. pneumoniae
test sensitivities were 68.7% and 93.7%, respectively, and test specificities were 94.1% and 41.2%, respectively. The persistence of pneumolysin in urine of pneumococcal pneumonia patients decreased significantly after 4 to 6 days of treatment. Our data suggest that combining the high specificity of the PLY-ELISA with the high sensitivity of the Binax Now
S. pneumoniae
test would enable pneumococcal infections to be accurately diagnosed in children.
First Detection of G12 Rotaviruses in Newborns with Neonatal Rotavirus Infection at All India Institute of Medical Sciences, New Delhi, India
Authors: Ray Pratima , Sharma S. , Agarwal R. K. , Longmei K. , Gentsch J. R. , Paul V. K. , Glass R. I. , Bhan M. K.
Published: August 2007

Rotavirus genotype G12 strains were detected for the first time among newborns with asymptomatic rotavirus infection (74% of 39 rotavirus strains isolated from the infected infants were genotype G12) in the nursery of the All India Institute of Medical Sciences during a period from 2005 to 2006. Sequence analysis of the VP7 genes from these neonatal strains indicated a high level of homology to other G12 strains reported worldwide, suggesting the recent emergence of these strains in humans. Such nosocomial infections of newborns represent a potential source of introduction of novel rotavirus serotypes into the community.
Inhibition of Foot-and-Mouth Disease Virus Infections in Cell Cultures with Antisense Morpholino Oligomers
Authors: Vagnozzi Ariel , Stein David A. , Iversen Patrick L. , Rieder Elizabeth
Published: August 2007

Foot-and-mouth disease (FMD) is a highly contagious viral disease of cloven-hoofed ungulates that can lead to severe losses in the livestock production and export industries. Although vaccines have been extensively used to control FMD, there is no antiviral therapy available to treat ongoing infections with FMD virus (FMDV). Six peptide-conjugated morpholino oligomers (PPMOs) with sequences complementary to various 21-nucleotide segments of the 5′ and 3′ untranslated regions (UTRs) of the FMDV genome (strain A
24
Cruzeiro/Brazil/1955 [A
24
Cru]) were evaluated in cell cultures. Three of the PPMOs, targeting domain 5 of the internal ribosome entry site (5D PPMO), and the two translation start codon regions (AUG1 and AUG2 PPMOs), showed high levels of anti-FMDV activity. A dose-dependent and sequence-specific reduction in viral titers of greater than 5 log
10
, with a concomitant reduction of viral protein and RNA expression, was achieved at low micromolar concentrations. Under identical conditions, three other PPMOs targeting the 5′-terminal region of the genome, the
cis
-acting replication element in the 5′ UTR, and the 3′ “ab” stem-loop showed less dramatic titer reductions of 1.5 log
10
to 2 log
10
. Treatment with 5D PPMO reduced the titers of FMDV strains representing five different serotypes by 2 log
10
to 4 log
10
compared to those of the controls. A
24
Cru-infected BHK-21 cells treated repeatedly with 5D or AUG2 PPMO generated resistant viruses for which phenotypic and genotypic properties were defined. Notably, three passages with low concentrations of the AUG1 PPMO extinguished all traces of detectable virus. The results indicate that PPMOs have potential for treating FMDV infections and that they also represent useful tools for studying picornaviral translation and evolution.
Identification of an Arsenic-Sensitive Block to Primate Lentiviral Infection of Human Dendritic Cells
Authors: Pion Marjorie , Stalder Romaine , Correa Rafael , Mangeat Bastien , Towers Greg J. , Piguet Vincent
Published: August 2007

Dendritic cells are central to the early events of human immunodeficiency virus type 1 (HIV-1) transmission, but HIV-1 infects dendritic cells inefficiently in vitro compared to activated CD4
+
T cells. There is a strong postentry restriction of HIV-1 infection in dendritic cells, partly mediated by the cellular restriction factor APOBEC3G. Here, we reveal that arsenic trioxide markedly increases HIV infection of immature and mature dendritic cells as well as blood-derived myeloid dendritic cells in an APOBEC3G- and TRIM5α-independent way. Our data suggest the presence of powerful, arsenic-sensitive antiviral activities in primary human immune cells of the dendritic cell lineage.
Characterization of Hepatitis C Virus Deletion Mutants Circulating in Chronically Infected Patients
Authors: Noppornpanth Suwanna , Smits Saskia L. , Lien Truong Xuan , Poovorawan Yong , Osterhaus Albert D. M. E. , Haagmans Bart L.
Published: August 2007

Hepatitis C virus (HCV) has a linear positive-stranded RNA genome of ∼9,600 nucleotides in length and displays a high level of sequence diversity caused by high mutation rates and recombination. However, when we performed long distance reverse transcription-PCRs on HCV RNA isolated from serum of chronic HCV patients, not only full-length HCV genomes but also HCV RNAs which varied in size from 7,600 to 8,346 nucleotides and contained large in-frame deletions between E1 and NS2 were amplified. Carefully designed control experiments indicated that these deletion mutants are a bona fide natural RNA species, most likely packaged in virions. Moreover, deletion mutants were detected in sera of patients infected with different HCV genotypes. We observed that 7/37 (18.9%) of genotype 1, 5/43 (11.6%) of genotype 3, and 4/13 (30.7%) of genotype 6 samples contained HCV deletion mutant genomes. These observations further exemplify HCV's huge genetic diversity and warrant studies to explore their biological relevance.
Recovery of
Nicotiana benthamiana
Plants from a Necrotic Response Induced by a Nepovirus Is Associated with RNA Silencing but Not with Reduced Virus Titer
Authors: Jovel Juan , Walker Melanie , Sanfaçon Hélène
Published: August 2007

Recovery of plants from virus-induced symptoms is often described as a consequence of RNA silencing, an antiviral defense mechanism. For example, recovery of
Nicotiana clevelandii
from a nepovirus (tomato black ring virus) is associated with a decreased viral RNA concentration and sequence-specific resistance to further virus infection. In this study, we have characterized the interaction of another nepovirus, tomato ringspot virus (ToRSV), with host defense responses during symptom induction and subsequent recovery. Early in infection, ToRSV induced a necrotic phenotype in
Nicotiana benthamiana
that showed characteristics typical of a hypersensitive response. RNA silencing was also activated during ToRSV infection, as evidenced by the presence of ToRSV-derived small interfering RNAs (siRNAs) that could direct degradation of ToRSV sequences introduced into sensor constructs. Surprisingly, disappearance of symptoms was not accompanied by a commensurate reduction in viral RNA levels. The stability of ToRSV RNA after recovery was also observed in
N. clevelandii
and
Cucumis sativus
and in
N. benthamiana
plants carrying a functional RNA-dependent RNA polymerase 1 ortholog from
Medicago truncatula
. In experiments with a reporter transgene (green fluorescent protein), ToRSV did not suppress the initiation or maintenance of transgene silencing, although the movement of the silencing signal was partially hindered. Our results demonstrate that although RNA silencing is active during recovery, reduction of virus titer is not required for the initiation of this phenotype. This scenario adds an unforeseen layer of complexity to the interaction of nepoviruses with the host RNA silencing machinery. The possibility that viral proteins, viral RNAs, and/or virus-derived siRNAs inactivate host defense responses is discussed.
Human Immunodeficiency Virus Type 1 Controllers but Not Noncontrollers Maintain CD4 T Cells Coexpressing Three Cytokines
Authors: Kannanganat Sunil , Kapogiannis Bill G. , Ibegbu Chris , Chennareddi Lakshmi , Goepfert Paul , Robinson Harriet L. , Lennox Jeffrey , Amara Rama Rao
Published: August 2007

Here, we evaluate the cytokine coexpression profiles of human immunodeficiency virus (HIV)-specific CD4 T cells for the expression of the cytokines gamma interferon (IFN-γ), interleukin-2, and tumor necrosis factor alpha. In controllers, CD4 T cells producing three or two cytokines (triple producers and double producers, respectively) represented >50% of the total response. In contrast, in noncontrollers ∼75% of responding cells produced only one cytokine (single producers), mostly IFN-γ. Cells producing three cytokines were functionally superior to those producing single cytokines and showed an inverse correlation (P< 0.001) with viral load. These results demonstrate a strong association between the maintenance of highly functional CD4 T cells producing three cytokines and control of HIV-1.
Structure of Adeno-Associated Virus Serotype 8, a Gene Therapy Vector
Authors: Nam Hyun-Joo , Lane Michael Douglas , Padron Eric , Gurda Brittney , McKenna Robert , Kohlbrenner Erik , Aslanidi George , Byrne Barry , Muzyczka Nicholas , Zolotukhin Sergei , Agbandje-McKenna Mavis
Published: August 2007

Adeno-associated viruses (AAVs) are being developed as gene therapy vectors, and their efficacy could be improved by a detailed understanding of their viral capsid structures. AAV serotype 8 (AAV8) shows a significantly greater liver transduction efficiency than those of other serotypes, which has resulted in efforts to develop this virus as a gene therapy vector for hemophilia A and familial hypercholesterolemia. Pseudotyping studies show that the differential tissue tropism and transduction efficiencies exhibited by the AAVs result from differences in their capsid viral protein (VP) amino acids. Towards identifying the structural features underpinning these disparities, we report the crystal structure of the AAV8 viral capsid determined to 2.6-Å resolution. The overall topology of its common overlapping VP is similar to that previously reported for the crystal structures of AAV2 and AAV4, with an eight-stranded β-barrel and long loops between the β-strands. The most significant structural differences between AAV8 and AAV2 (the best-characterized serotype) are located on the capsid surface at protrusions surrounding the two-, three-, and fivefold axes at residues reported to control transduction efficiency and antibody recognition for AAV2. In addition, a comparison of the AAV8 and AAV2 capsid surface amino acids showed a reduced distribution of basic charge for AAV8 at the mapped AAV2 heparin sulfate receptor binding region, consistent with an observed non-heparin-binding phenotype for AAV8. Thus, this AAV8 structure provides an additional platform for mutagenesis efforts to characterize AAV capsid regions responsible for differential cellular tropism, transduction, and antigenicity for these promising gene therapy vectors.
The Level of Friend Retrovirus Replication Determines the Cytolytic Pathway of CD8+T-Cell-Mediated Pathogen Control
Authors: Zelinskyy Gennadiy , Balkow Sandra , Schimmer Simone , Werner Tanja , Simon Markus M. , Dittmer Ulf
Published: August 2007

Cytotoxic T cells (CTL) play a central role in the control of viral infections. Their antiviral activity can be mediated by at least two cytotoxic pathways, namely, the granule exocytosis pathway, involving perforin and granzymes, and the Fas-FasL pathway. However, the viral factor(s) that influences the selection of one or the other pathway for pathogen control is elusive. Here we investigate the role of viral replication levels in the induction and activation of CTL, including their effector potential, during acute Friend murine leukemia virus (F-MuLV) infection. F-MuLV inoculation results in a low-level infection of adult C57BL/6 mice that is enhanced about 500-fold upon coinfection with the spleen focus-forming virus (SFFV). Both the low- and high-level F-MuLV infections generated CD8+effector T cells that were essential for the control of viral replication. However, the low-level infection induced CD8+T cells expressing solely FasL but not the cytotoxic molecules granzymes A and B, whereas the high-level infection resulted in induction of CD8+effector T cells secreting molecules of the granule exocytosis pathway. By using knockout mouse strains deficient in one or the other cytotoxic pathway, we found that low-level viral replication was controlled by CTL that expressed FasL but control of high-level viral replication required perforin and granzymes. Additional studies, in which F-MuLV replication was enhanced experimentally in the absence of SFFV coinfection, supported the notion that only the replication level of F-MuLV was the critical factor that determined the differential expression of cytotoxic molecules by CD8+T cells and the pathway of CTL cytotoxicity.
Rapid identification ofCandidaspecies in oral rinse solutions by PCR
Authors: Liguori Giorgio , Lucariello Angela , Colella Giuseppe , De Luca Antonio , Marinelli Paolo
Published: August 2007

Aims:To determine the sensitivity and specificity of a multiplex PCR assay for the contemporary identification of major species involved in oral candidiasis, without extraction and purification of DNA from the samples under investigation; and evaluation of this method in comparison with routine phenotypic culture identification.

Methods:78 oral rinse solutions were collected. The concentrated oral rinse technique was used for a quantitative and qualitative study. Research and identification ofCandidaspp, with routine phenotypic culture identification (germ-tube test in serum at 37°C for 3 hours and sugar assimilation strip analysis), were performed. Each sample was analysed with multiplex PCR directly on oral rinse solution. Samples giving discrepant results between routine phenotypic and PCR identification methods were resubcultured on CHROMagar Candida plates. The fungus-specific primers ITS1, ITS2, CA3, and CA4 were used. For the identification of other species (C kefyr,C famataandC dubliniensis), ITS1F, ITS1K, and ITS2D primers were designed.

Results:Multiplex PCR correctly identified all samples, including those with single species, or with mixed species, negative samples and positive samples which appeared to be negative from routine phenotypic methods.

Conclusion:This multiplex PCR assay provides a rapid alternative to the conventional culture based technique for the identification and speciation of the most frequently isolatedCandidaspecies. The absence of an extraction method made identification of 10 species possible in a few hours.
Implications of method specific creatinine adjustments on General Medical Services chronic kidney disease classification
Authors: Reynolds Timothy M , Twomey Patrick J
Published: August 2007

Aims:To evaluate the impact of different equations for calculation of estimated glomerular filtration rate (eGFR) on general practitioner (GP) workload.

Methods:Retrospective evaluation of routine workload data from a district general hospital chemical pathology laboratory serving a GP patient population of approximately 250 000. The most recent serum creatinine result from 80 583 patients was identified and used for the evaluation. eGFR was calculated using one of three different variants of the four-parameter Modification of Diet in Renal Disease (MDRD) equation.

Results:The original MDRD equation (eGFR186) and the modified equation with assay-specific data (eGFR175corrected) both identified similar numbers of patients with stage 4 and stage 5 chronic kidney disease (ChKD), but the modified equation without assay specific data (eGFR175) resulted in a significant increase in stage 4 ChKD. For stage 3 ChKD the eGFR175identified 28.69% of the population, the eGFR186identified 21.35% of the population and the eGFR175correctedidentified 13.6% of the population.

Conclusions:Depending on the choice of equation there can be very large changes in the proportions of patients identified with the different stages of ChKD. Given that according to the General Medical Services Quality Framework, all patients with ChKD stages 3–5 should be included on a practice renal registry, and receive relevant drug therapy, this could have significant impacts on practice workload and drug budgets. It is essential that practices work with their local laboratories.
Attitudes of research ethics board chairs towards disclosure of research results to participants: results of a national survey
Authors: MacNeil S Danielle , Fernandez Conrad V
Published: August 2007

Background:The offer of aggregate study results to research participants following study completion is increasingly accepted as a means of demonstrating greater respect for participants. The attitudes of research ethics board (REB) chairs towards this practice, although integral to policy development, are unknown.

Objectives:To determine the attitudes of REB chairs and the practices of REBs with respect to disclosure of results to research participants.

Design:A postal questionnaire was distributed to the chairs of English-language university-based REBs in Canada. In total, 88 REB chairs were eligible. The questionnaire examined respondents’ attitudes towards offering participants completed study results, methods for delivering this information, and barriers to disclosing results.

Findings:The response rate was 89.8%. Chairs were highly supportive (94.8%) of offering results to research participants. Only 19.5% of chairs responded that a policy or guideline that governed the return of research results to participants existed at their institution. Most chairs (72.0%) supported the idea of their REB instituting a set of guidelines recommending that researchers offer results to participants in a lay format. Chairs identified the major impediments to the implementation of programmes offering to return results to participants as being financial cost (57.5%) and retaining contact with research participants (78.1%).

Conclusions:University-based REB chairs overwhelmingly support the offer of research results to participants. This is incongruent with the frequent lack of existing REB guidelines recommending this practice. REBs should support guidelines that diminish identified barriers and promote consistency in offering to return results.
Views of patients with heart failure about their role in the decision to start implantable cardioverter–defibrillator treatment: prescription rather than participation
Authors: Ågård Anders , Löfmark Rurik , Edvardsson Nils , Ekman Inger
Published: August 2007

Background:There is a shortage of reports on what potential recipients of implantable cardioverter–defibrillators (ICDs) need to be informed about and what role they can and want to play in the decision-making process when it comes to whether or not to implant an ICD.

Aims:To explore how patients with heart failure and previous episodes of malignant arrhythmia experience and view their role in the decision to initiate ICD treatment.

Patients and methods:A qualitative content analysis of semistructured interviews was used. The study population consisted of 31 outpatients with moderate heart failure at the time of their first ICD implantation.

Setting:The study was performed at Sahlgrenska University Hospital, Göteborg, Sweden.

Results:None of the respondents had discussed the alternative option of receiving treatment with anti-arrhythmic drugs, the estimated risk of a fatal arrhythmia, or the expected time of survival from heart failure in itself. Even so, very little criticism was directed at the lack of information or the lack of participation in the decision-making process. The respondents felt that they had to rely on the doctors’ recommendation when it comes to such a complex and important decision. None of them regretted implantation of the ICD.

Conclusions:The respondents were confronted by a matter of fact. They needed an ICD and were given an offer they could not refuse, simply because life was precious to them. Being able to give well-informed consent seemed to be a matter of less importance for them.
Am I my brother’s gatekeeper? Professional ethics and the prioritisation of healthcare
Authors: Hunter David
Published: August 2007

At the 5th International Conference on Priorities in Health Care in Wellington, New Zealand, 2004, one resonating theme was that for priority setting to be effective, it has to include clinicians in both decision making and the enforcement of those decisions. There was, however, a disturbing undertone to this theme, namely that doctors, in particular, were unjustifiably thwarting good systems of prioritising scarce healthcare resources. This undertone seems unfair precisely because doctors may, and in some cases do, feel obligated by their professional ethics to remain uninvolved either in deciding priorities and in some cases in enforcing them. I will argue that the professional role of a doctor ought not be considered inconsistent with the role of a priority setter or enforcer, as long as one crucial element is in place, a rationally coherent and broadly justifiable regime for prioritising healthcare. Given this I conclude both that prioritisation and doctoring are not incompatible under certain conditions, and that the education of healthcare professionals ought to include material on distributive justice in healthcare.
The three official language versions of the Declaration of Helsinki: what’s lost in translation?
Authors: Carlson Robert V , van Ginneken Nadja H , Pettigrew Luisa M , Davies Alan , Boyd Kenneth M , Webb David J
Published: August 2007

Background:The Declaration of Helsinki, the World Medical Association’s (WMA’s) statement of ethical guidelines regarding medical research, is published in the three official languages of the WMA: English, French and Spanish.

Methods:A detailed comparison of the three official language versions was carried out to determine ways in which they differed and ways in which the wording of the three versions might illuminate the interpretation of the document.

Results:There were many minor linguistic differences between the three versions. However, in paragraphs 1, 6, 29, 30 and in the note of clarification to paragraph 29, there were differences that could be considered potentially significant in their ethical relevance.

Interpretation:Given the global status of the Declaration of Helsinki and the fact that it is translated from its official versions into many other languages for application to the ethical conduct of research, the differences identified are of concern. It would be best if such differences could be eliminated but, at the very least, a commentary to explain any differences that are unavoidable on the basis of language or culture should accompany the Declaration of Helsinki. This evidence further strengthens the case for international surveillance of medical research ethics as has been proposed by the WMA.
Autonomy or protection from harm? Judgements of German courts on care for the elderly in nursing homes
Authors: Sammet Kai
Published: August 2007

The increase in life expectancy in developed countries has lead to an increase in the number of elderly people cared for in nursing homes. Given the physical frailty and deterioration of mental capacities in many of these residents, questions arise as to their autonomy and to their protection from harm. In 2005, one of the highest German courts, the Bundesgerichtshof (BGH) issued a seminal judgement that dealt with the obligations of nursing homes and with the preserving of autonomy and privacy in nursing home residents. An elderly woman had sustained a fracture of the neck of the femur during a fall. The health insurance company held that the nursing home had breached its obligations to protect her from falling and sued the home for the hospital costs of her treatment. However, the BGH maintained that the case of the health insurance was not justified. It held that obligations of nursing homes have to be limited to normal arrangements within reasonable financial and personal effort, and that the autonomy of residents had to be protected from unnecessary interference. Permanent control or even restraining measures to reduce each risk would deprive the patient fully of her autonomy, and must therefore be hindered. Other judgments of other courts have emphasised the “protectionist” approach. The article deals with these different approaches and comments on both rationales. It will be shown that both approaches must be differentiated to establish fully autonomy and protection for nursing home residents.
Low medically certified sickness absence among employees with poor health status predicts future health improvement: the Whitehall II study: Table 1
Authors: Kivimäki M , Ferrie J E , Shipley M J , Vahtera J , Singh-Manoux A , Marmot M G , Head J
Published: August 2007

Background:

High sickness absence is associated with poor health status, but it is not known whether low levels of sickness absence among people with poor health predict future health improvement.

Objective:

To examine the association between medically certified sickness absence and subsequent change in health among initially unhealthy employees.

Methods:

5210 employees (3762 men, 1448 women) whose self-rated health status remained stable (either good or poor) between data phases 1 and 2 were divided into three groups according to their rate of medically certified absences during this period (0 vs >0–5 vs >5 absence spells longer than 7 days per 10 person-years). Subsequent change in health status was determined by self-rated health at follow-up (phase 3).

Results:

After adjustment for age and sex, there was a strong contemporaneous association between lower sickness absence and better health status. Among participants reporting poor health, low absence was associated with subsequent improvement in health status (odds ratio 2.66, 95% CI 1.78 to 4.02 for no absence vs >5 certified spells per 10 years). This association was only partially explained by known existing morbidity, socioeconomic position and risk factors.

Conclusions:

Low levels of medically certified sickness absence seem to be associated with positive change in health status among employees in poor health. Further research is needed to examine whether lower sickness absence also marks a more favourable prognosis for specific diseases.
Thermal and microwave assisted synthesis of N-aroylamino acridinediones
Authors: Josephrajan T , Ramakrishnan V T
Published: August 2007

A series of N-aroylamino acridinediones (3a–3d and6a–6e) have been synthesized from tetraketones (1 and 4) and benzoic hydrazides (2a–2d and 5a–5e) under thermal and microwave irradiation conditions with solid supports.Key words: acridine, hydrazide, microwave irradiation.
Comparative studies of univariate and multivariate optimizations for manganese determination in antihypertensive drugs by electrothermal atomic absorption spectrometry
Authors: Silveira Josianne Nicácio , Lara Paulo Celso Pereira , Dias Michelle Batista , Nascentes Clésia Cristina , Demicheli Cynthia , Borba da Silva José Bento
Published: August 2007

Comparative studies using the univariate and multivariate optimizations (factorial design) were undertaken to determine manganese in antihypertensive drugs by electrothermal atomic absorption spectrometry (ET AAS). For the univariate method, the optimum pyrolysis and atomization temperatures were 500 and 2200 °C, and for multivariate analysis, the temperatures were 500 and 2400 °C, respectively. No differences were observed between the methods with respect to the slopes of the calibration curves, recoveries, results for certified urine samples for the two levels, and the averages of the intra- and inter-assay coefficients of variation (CV) using Student t and F tests as a statistical tool (P < 0.05). Calibration was performed by matrix matching. All other studies were made using the optimized multivariate conditions. The characteristic mass was of 0.68 ± 0.17 pg (the recommended mass is 0.60 pg). The limits of detection and quantification were 0.23 and 0.77 µg L-1, respectively. Intra- and inter-assay studies on the drug spiked with 0.5, 1.0, and 1.5 µg L-1 of Mn yielded mean results of 3.6 ± 1.9% and 9.6 ± 2.2%, respectively. For the intra-assay evaluation, seven samples of each concentration were evaluated for Mn on the same day, whereas, for the inter-assay study, these solutions were analyzed in three replicates during three consecutive days. Recovery studies on the drug spiked with three levels of Mn (n  =  7 for each level) furnished results between 101.4 ± 17.2% and 106.6 ± 7.5%. The results of a certified urine sample analysis (two levels of Mn) agreed at a 95% level of confidence. Forty eight antihy pertensive drug samples were analyzed, and the drug contents varied between 2.9 ng and 1.9 µg capsule-1.Key words: manganese, antihypertensive drugs, electrothermal atomic absorption spectrometry, multivariate optimization.