bluuebunny/crossref_metadata_2025_split huggingface dataset:
Persistence of
Escherichia coli
Clones and Phenotypic and Genotypic Antibiotic Resistance in Recurrent Urinary Tract Infections in Childhood
Authors: Kõljalg Siiri , Truusalu Kai , Vainumäe Inga , Stsepetova Jelena , Sepp Epp , Mikelsaar Marika 
Published: October 2008

ABSTRACT

We assessed the clonality of consecutive
Escherichia coli
isolates during the course of recurrent urinary tract infections (RUTI) in childhood in order to compare clonality with phenotypic antibiotic resistance patterns, the presence of integrons, and the presence of the
sul1
,
sul2
, and
sul3
genes. Altogether, 78 urinary
E. coli
isolates from 27 children, who experienced recurrences during a 1-year follow-up after the first attack of acute pyelonephritis, were investigated. The MICs of sulfamethoxazole, trimethoprim-sulfamethoxazole (SXT), ampicillin, cefuroxime, cefotaxime, and gentamicin and the presence or absence of the
intI
gene for class 1 integrons and the sulfamethoxazole resistance-encoding genes
sul1
,
sul2
, and
sul3
were determined. All
E. coli
strains were genotyped by pulsed-field gel electrophoresis. There were no significant differences in the prevalences of resistance to beta-lactams and SXT between initial and consecutive
E. coli
isolates (41 versus 45% and 41 versus 29%, respectively). However, the
E. coli
strains obtained after SXT administration more frequently carried two or more
sul
genes than the nonexposed strains (9/21 [43%] versus 11/57 [19%], respectively;
P
= 0.044). In 78% of the patients, the recurrence of unique clonal
E. coli
strains alone or combined with individual strains was detected. Phenotypic resistance and the occurrence of
sul
genes were more stable in clonal strains than in individual strains (odds ratios, 8.7 [95% confidence interval {95% CI}, 1.8 to 40.8] and 4.4 [95% CI, 1.1 to 17.7], respectively). Thus, in children with RUTIs, the majority of
E. coli
strains from consecutive episodes are unique persisting clones, with rare increases in the initially high antimicrobial resistance, the presence of
sul
genes, and the presence of integrons.
Physiological and Molecular Characterization of Atypical Isolates of
Malassezia furfur
Authors: González A. , Sierra R. , Cárdenas M. E. , Grajales A. , Restrepo S. , Cepero de García M. C. , Celis A. 
Published: October 2008

ABSTRACT

The species constituting the genus
Malassezia
are considered to be emergent opportunistic yeasts of great importance. Characterized as lipophilic yeasts, they are found in normal human skin flora and sometimes are associated with different dermatological pathologies. We have isolated seven
Malassezia
species strains that have a different Tween assimilation pattern from the one typically used to differentiate
M. furfur
,
M. sympodialis
, and
M. slooffiae
from other
Malassezia
species. In order to characterize these isolates of
Malassezia
spp., we studied their physiological features and conducted morphological and molecular characterization by PCR-restriction fragment length polymorphism and sequencing of the 26S and 5.8S ribosomal DNA-internal transcribed spacer 2 regions in three strains from healthy individuals, four clinical strains, and eight reference strains. The sequence analysis of the ribosomal region was based on the Blastn algorithm and revealed that the sequences of our isolates were homologous to
M. furfur
sequences. To support these findings, we carried out phylogenetic analyses to establish the relationship of the isolates to
M. furfur
and other reported species. All of our results confirm that all seven strains are
M. furfur
; the atypical assimilation of Tween 80 was found to be a new physiological pattern characteristic of some strains isolated in Colombia.
Evidence for Clonal Dissemination of the Serotype K1
Klebsiella pneumoniae
Strain Causing Invasive Liver Abscesses in Korea
Authors: Chung Doo Ryeon , Lee Ha Rim , Lee Seung Soon , Kim Shin Woo , Chang Hyun-Ha , Jung Sook-In , Oh Myoung-don , Ko Kwan Soo , Kang Cheol-In , Peck Kyong Ran , Song Jae-Hoon 
Published: October 2008

ABSTRACT

Seventy-three liver abscess isolates of serotype K1
Klebsiella pneumoniae
from a nationwide collection in Korea were genotypically characterized using pulsed-field gel electrophoresis and multilocus sequence typing. We found that serotype K1
K. pneumoniae
strains that caused liver abscesses in Korea were genotypically related and that most were sequence type 23.
Survival of Nosocomial Bacteria and Spores on Surfaces and Inactivation by Hydrogen Peroxide Vapor
Authors: Otter Jonathan A. , French Gary L. 
Published: October 2008

ABSTRACTWith inocula of 6 to 7 log10CFU, most vegetative bacteria and spores tested survived on surfaces for more than 5 weeks, but all were inactivated within 90 min of exposure to hydrogen peroxide vapor in a 100-m3test room even in the presence of 0.3% bovine serum albumin to simulate biological soiling.
Differing Roles of Inner Tegument Proteins pUL36 and pUL37 during Entry of Herpes Simplex Virus Type 1
Authors: Roberts Ashley P. E. , Abaitua Fernando , O'Hare Peter , McNab David , Rixon Frazer J. , Pasdeloup David 
Published: October 2008

ABSTRACT

Studies with herpes simplex virus type 1 (HSV-1) have shown that secondary envelopment and virus release are blocked in mutants deleted for the tegument protein gene UL36 or UL37, leading to the accumulation of DNA-containing capsids in the cytoplasm of infected cells. The failure to assemble infectious virions has meant that the roles of these genes in the initial stages of infection could not be investigated. To circumvent this, cells infected at a low multiplicity were fused to form syncytia, thereby allowing capsids released from infected nuclei access to uninfected nuclei without having to cross a plasma membrane. Visualization of virus DNA replication showed that a UL37-minus mutant was capable of transmitting infection to all the nuclei within a syncytium as efficiently as the wild-type HSV-1 strain 17
+
did, whereas infection by UL36-minus mutants failed to spread. Thus, these inner tegument proteins have differing functions, with pUL36 being essential during both the assembly and uptake stages of infection, while pUL37 is needed for the formation of virions but is not required during the initial stages of infection. Analysis of noninfectious enveloped particles (L-particles) further showed that pUL36 and pUL37 are dependent on each other for incorporation into tegument.
Genetic History of Hepatitis C Virus in East Asia
Authors: Pybus Oliver G. , Barnes Eleanor , Taggart Rachel , Lemey Philippe , Markov Peter V. , Rasachak Bouachan , Syhavong Bounkong , Phetsouvanah Rattanaphone , Sheridan Isabelle , Humphreys Isla S. , Lu Ling , Newton Paul N. , Klenerman Paul 
Published: October 2008

ABSTRACTThe hepatitis C virus (HCV), which currently infects an estimated 3% of people worldwide, has been present in some human populations for several centuries, notably HCV genotypes 1 and 2 in West Africa and genotype 6 in Southeast Asia. Here we use newly developed methods of sequence analysis to conduct the first comprehensive investigation of the epidemic and evolutionary history of HCV in Asia. Our analysis includes new HCV core (n= 16) and NS5B (n= 14) gene sequences, obtained from serum samples of jaundiced patients from Laos. These exceptionally diverse isolates were analyzed in conjunction with all available reference strains using phylogenetic and Bayesian coalescent methods. We performed statistical tests of phylogeographic structure and applied a recently developed “relaxed molecular clock” approach to HCV for the first time, which indicated an unexpectedly high degree of rate variation. Our results reveal a >1,000-year-long development of genotype 6 in Asia, characterized by substantial phylogeographic structure and two distinct phases of epidemic history, before and during the 20th century. We conclude that HCV lineages representing preexisting and spatially restricted strains were involved in multiple, independent local epidemics during the 20th century. Our analysis explains the generation and maintenance of HCV diversity in Asia and could provide a template for further investigations of HCV spread in other regions.
Trafficking through the Rev/RRE Pathway Is Essential for Efficient Inhibition of Human Immunodeficiency Virus Type 1 by an Antisense RNA Derived from the Envelope Gene
Authors: Ward Alex M. , Rekosh David , Hammarskjold Marie-Louise 
Published: October 2008

ABSTRACT
A human immunodeficiency virus type 1 (HIV-1)-based vector expressing an antisense RNA directed against HIV-1 is currently in clinical trials. This vector has shown a remarkable ability to inhibit HIV-1 replication, in spite of the fact that therapeutic use of unmodified antisense RNAs has generally been disappointing. To further analyze the basis for this, we examined the effects of different plasmid-based HIV-1 long-terminal-repeat-driven constructs expressing antisense RNA to the same target region in HIV-1 but containing different export elements. Two of these vectors were designed to express antisense RNA containing either a Rev response element (RRE) or a Mason-Pfizer monkey virus (MPMV) constitutive transport element (CTE). In the third vector, no specific transport element was provided. Efficient inhibition of HIV-1 virus production was obtained with the RRE-driven antisense RNA. This construct also efficiently inhibited p24 production from a pNL4-3 provirus that used the MPMV CTE for RNA export. In contrast, little inhibition was observed with the constructs lacking an RRE. Furthermore, when the RRE-driven antisense RNA was redirected to the Tap/Nxf1 pathway, utilized by the MPMV CTE, through the expression of a RevM10-Tap fusion protein, the efficiency of antisense inhibition was greatly reduced. These results indicate that efficient inhibition requires trafficking of the antisense RNA through the Rev/RRE pathway. Mechanistic studies indicated that the Rev/RRE-mediated inhibition did not involve either nuclear retention or degradation of target mRNA, since target RNA was found to export and associate normally with polyribosomes. However, protein levels were significantly reduced. Taken together, our results suggest a new mechanism for antisense inhibition of HIV mediated by Rev/RRE.
Randomization and In Vivo Selection Reveal a GGRG Motif Essential for Packaging Human Immunodeficiency Virus Type 2 RNA
Authors: Baig Tayyba T. , Lanchy Jean-Marc , Lodmell J. Stephen 
Published: October 2008

ABSTRACT
The packaging signal (ψ) of human immunodeficiency virus type 2 (HIV-2) is present in the 5′ noncoding region of RNA and contains a 10-nucleotide palindrome (pal; 5′-392-GGAGUGCUCC) located upstream of the dimerization signal stem-loop 1 (SL1). pal has been shown to be functionally important in vitro and in vivo. We previously showed that the 3′ side of pal (GCUCC-3′) is involved in base-pairing interactions with a sequence downstream of SL1 to make an extended SL1, which is important for replication in vivo and the regulation of dimerization in vitro. However, the role of the 5′ side of pal (5′-GGAGU) was less clear. Here, we characterized this role using an in vivo SELEX approach. We produced a population of HIV-2 DNA genomes with random sequences within the 5′ side of pal and transfected these into COS-7 cells. Viruses from COS-7 cells were used to infect C8166 permissive cells. After several weeks of serial passage in C8166 cells, surviving viruses were sequenced. On the 5′ side of pal there was a striking convergence toward a GGRGN consensus sequence. Individual clones with consensus and nonconsensus sequences were tested in infectivity and packaging assays. Analysis of individuals that diverged from the consensus sequence showed normal viral RNA and protein synthesis but had replication defects and impaired RNA packaging. These findings clearly indicate that the GGRG motif is essential for viral replication and genomic RNA packaging.
Correlation of Vaccine-Elicited Systemic and Mucosal Nonneutralizing Antibody Activities with Reduced Acute Viremia following Intrarectal Simian Immunodeficiency Virus SIV
mac251
Challenge of Rhesus Macaques
Authors: Hidajat Rachmat , Xiao Peng , Zhou Qifeng , Venzon David , Summers L. Ebonita , Kalyanaraman Vaniambadi S. , Montefiori David C. , Robert-Guroff Marjorie 
Published: October 2008

ABSTRACT

Cell-mediated immunity and neutralizing antibodies contribute to control of human immunodeficiency virus/simian immunodeficiency virus (HIV/SIV) infection, but the role of nonneutralizing antibodies is not defined. Previously, we reported that sequential oral/oral or intranasal/oral (I/O) priming with replication-competent adenovirus type 5 host range mutant (Ad5hr)-SIV recombinants, followed by intramuscular envelope protein boosting, elicited systemic and mucosal cellular immunity and exhibited equivalent, significant reductions of chronic viremia after rectal SIV
mac251
challenge. However, I/O priming gave significantly better control of acute viremia. Here, systemic and mucosal humoral immunity were investigated for potential correlates with the acute challenge outcome. Strong serum binding but nonneutralizing antibody responses against SIV
mac251
were induced in both groups. Antibody responses appeared earlier and overall were higher in the I/O group. Reduced acute viremia was significantly correlated with higher serum binding titer, stronger antibody-dependent cellular cytotoxicity activity, and peak prechallenge and 2-week-postchallenge antibody-dependent cell-mediated viral inhibition (ADCVI). The I/O group consistently displayed greater anti-envelope immunoglobulin A (IgA) antibody responses in bronchoalveolar lavage and a stronger rectal anti-envelope IgA anamnestic response 2 weeks postchallenge. Pre- and postchallenge rectal secretions inhibited SIV transcytosis across epithelial cells. The inhibition was significantly higher in the I/O group, although a significant correlation with reduced acute viremia was not reached. Overall, the replicating Ad5hr-SIV priming/envelope boosting approach elicited strong systemic and mucosal antibodies with multiple functional activities. The pattern of elevated immune responses in the I/O group is consistent with its better control of acute viremia mediated, at least in part, by ADCVI activity and transcytosis inhibition.
Prion Strain Targeting Independent of Strain-Specific Neuronal Tropism
Authors: Ayers Jacob I. , Kincaid Anthony E. , Bartz Jason C. 
Published: October 2008

ABSTRACT

While neuropathological features that define prion strains include spongiform degeneration and deposition patterns of PrP
Sc
, the underlying mechanism for the strain-specific differences in PrP
Sc
targeting is not known. To investigate prion strain targeting, we inoculated hamsters in the sciatic nerve with either the hyper (HY) or drowsy (DY) strain of the transmissible mink encephalopathy (TME) agent. Both TME strains were initially retrogradely transported in the central nervous system (CNS) exclusively by four descending motor tracts. The locations of HY and DY PrP
Sc
deposition were identical throughout the majority of the incubation period. However, differences in PrP
Sc
deposition between these strains were observed upon development of clinical disease. The differences observed were unlikely to be due to strain-specific neuronal tropism, since comparison of PrP
Sc
deposition patterns by different routes of infection indicated that all brain areas were susceptible to prion infection by both TME strains. These findings suggest that prion transport and differential susceptibility to prion infection are not solely responsible for prion strain targeting. The data suggest that differences in PrP
Sc
distribution between strains during clinical disease are due to differences in the length of time that PrP
Sc
has to spread in the CNS before the host succumbs to disease.
Health-related quality of life and visual and cognitive impairment among nursing-home residents
Authors: Elliott A F , McGwin G , Owsley C 
Published: October 2008

Aim:To examine whether the relationship between vision impairment and health-related quality of life (HRQoL) in nursing-home residents is impacted by coexisting cognitive impairment.Methods:This cross-sectional study involved a total of 382 English-speaking older adults (>55 years of age) with ⩾13 on the Mini Mental State Exam (MMSE) from seventeen nursing homes in Birmingham, Alabama. Assessments were taken of visual acuity (Lighthouse Near Visual Acuity Test), cognition (MMSE) and health-related quality of life (Nursing Home Vision-Targeted Health-Related Quality of Life Questionnaire, VF-14, and the SF-36).Results:A greater portion of participants had both vision and cognitive impairments (38.5%) as compared with those with neither impairment (21.5%), vision impairment alone (13.4%), and cognitive impairment alone (26.7%). Cognitive impairment did not modify the impact of vision impairment on HRQoL. The reduction in HRQoL associated with vision impairment was similar for those with and without cognitive impairment.Conclusion:The deleterious impact of vision impairment on HRQoL in nursing-home residents was not exacerbated by the co-occurrence of cognitive impairment. Ageing-related visual impairment in nursing-home residents is often reversible through treatment leading to improved HRQoL, and thus it is clinically important to know that cognitive impairment is unlikely to interfere with this benefit.
“If you cannot tolerate that risk, you should never become a physician”: a qualitative study about existential experiences among physicians
Authors: Aase M , Nordrehaug J E , Malterud K 
Published: October 2008

Background and objectives:Physicians are exposed to matters of existential character at work, but little is known about the personal impact of such issues.Methods:To explore how physicians experience and cope with existential aspects of their clinical work and how such experiences affect their professional identities, a qualitative study using individual semistructured interviews has analysed accounts of their experiences related to coping with such challenges. Analysis was by systematic text condensation. The purposeful sample comprised 10 physicians (including three women), aged 33–66 years, residents or specialists in cardiology or cardiothoracic surgery, working in a university hospital with 24-hour emergency service and one general practitioner.Results:Participants described a process by which they were able to develop a capacity for coping with the existential challenges at work. After episodes perceived as shocking or horrible earlier in their career, they at present said that they could deal with death and mostly keep it at a distance. Vulnerability was closely linked to professional responsibility and identity, perceived as a burden to be handled. These demands were balanced by an experience of meaning related to their job, connected to making a difference in their patients’ lives. Belonging to a community of their fellows was a presupposition for coping with the loneliness and powerlessness related to their vulnerable professional position.Conclusions:Physicians’ vulnerability facing life and death has been underestimated. Belonging to caring communities may assist growth and coping on exposure to existential aspects of clinical work and developing a professional identity.
Information and participation in decision-making about treatment: a qualitative study of the perceptions and preferences of patients with rheumatoid arthritis
Authors: Schildmann J , Grunke M , Kalden J R , Vollmann J 
Published: October 2008

Objectives:To elicit the perceptions and preferences of patients with rheumatoid arthritis regarding information and participation in treatment decision-making. To analyse the patients’ narratives on the background of the ethical discourse on various approaches to treatment decision-making.Design:In-depth interviews with themes identified using principles of grounded theory.Participants:22 patients with long-standing rheumatoid arthritis.Main outcome measures:Qualitative data on patients’ perceptions and preferences regarding information and participation in decision-making about treatment.Results:Decision-making about treatment has been described by the patients as a process consisting of different stages with shifting loci of control and responsibility. Patients initially received one treatment recommendation and were not aware of alternative treatment options. Those participants in this study who wanted information about negative effects of a treatment cited “interest in one’s own health” and the potential “use of information” as reasons for their preference. The physicians’ expert knowledge and clinical experience regarding the effects of medication were cited as arguments by patients for a treatment recommendation.Conclusions:The patients’ accounts of decision-making about treatment differ from models of physician–patient relationship that have been put forward in ethical discourse. These differences may be relevant with respect to the starting point of an ethical analysis of treatment decision-making. Patients’ accounts with respect to a lack of information on treatment alternatives point to ethically relevant challenges regarding treatment decision-making in clinical practice.
Suicide assisted by two Swiss right-to-die organisations
Authors: Fischer S , Huber C A , Imhof L , Mahrer Imhof R , Furter M , Ziegler S J , Bosshard G 
Published: October 2008

Background:In Switzerland, non-medical right-to-die organisations such as Exit Deutsche Schweiz and Dignitas offer suicide assistance to members suffering from incurable diseases.Objectives:First, to determine whether differences exist between the members who received assistance in suicide from Exit Deutsche Schweiz and Dignitas. Second, to investigate whether the practices of Exit Deutsche Schweiz have changed since the 1990s.Methods:This study analysed all cases of assisted suicide facilitated by Exit Deutsche Schweiz (E) and Dignitas (D) between 2001 and 2004 and investigated by the University of Zurich’s Institute of Legal Medicine (E: n = 147; D: n = 274, total: 421). Furthermore, data from the Exit Deutsche Schweiz study which investigated all cases of assisted suicide during the period 1990–2000 (n = 149) were compared with the data of the present study.Results:More women than men were assisted in both organisations (D: 64%; E: 65%). Dignitas provided more assistance to non-residents (D: 91%; E: 3%; p = 0.000), younger persons (mean age in years (SD): D: 64.5 (14.1); E: 76.6 (13.3); p = 0.001), and people suffering from fatal diseases such as multiple sclerosis and amyotrophic lateral sclerosis (D: 79%; E: 67%; p = 0.013). Lethal medications were more often taken orally in cases assisted by Dignitas (D: 91%; E: 76%; p = 0.000). The number of women and the proportion of older people suffering from non-fatal diseases among suicides assisted by Exit Deutsche Schweiz has increased since the 1990s (women: 52% to 65%, p = 0.031; mean age in years (SD): 69.3 (17.0) to 76.9 (13.3), p = 0.000), non-fatal diseases: 22% to 34%, p = 0.026).Conclusions:Weariness of life rather than a fatal or hopeless medical condition may be a more common reason for older members of Exit Deutsche Schweiz to commit suicide. The strong over-representation of women in both Exit Deutsche Schweiz and Dignitas suicides is an important phenomenon so far largely overlooked and in need of further study.