bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biofilm Production by
Candida
Species and Inadequate Antifungal Therapy as Predictors of Mortality for Patients with Candidemia
Authors: Tumbarello Mario , Posteraro Brunella , Trecarichi Enrico Maria , Fiori Barbara , Rossi Marianna , Porta Rosaria , de Gaetano Donati Katleen , La Sorda Marilena , Spanu Teresa , Fadda Giovanni , Cauda Roberto , Sanguinetti Maurizio 
Published: April 2007

ABSTRACT

Nosocomial
Candida
bloodstream infections rank among infections with highest mortality rates. A retrospective cohort analysis was conducted at Catholic University Hospital to estimate the risk factors for mortality of patients with candidemia. We reviewed records for patients with a
Candida
bloodstream infection over a 5-year period (January 2000 through December 2004). Two hundred ninety-four patients (42.1% male; mean age ± standard deviation, 65 ± 12 years) were studied. Patients most commonly were admitted with a surgical diagnosis (162 patients [55.1%]), had a central venous catheter (213 [72.4%]), cancer (118 [40.1%]), or diabetes (58 [19.7%]). One hundred fifty-four (52.3%) patients died within 30 days. Of 294 patients, 168 (57.1%) were infected by
Candida albicans
, 64 (21.7%) by
Candida parapsilosis
, 28 (9.5%) by
Candida tropicalis
, and 26 (8.8%) by
Candida glabrata
. When fungal isolates were tested for biofilm formation capacity, biofilm production was most commonly observed for isolates of
C. tropicalis
(20 of 28 patients [71.4%]), followed by
C. glabrata
(6 of 26 [23.1%]),
C. albicans
(38 of 168 [22.6%]), and
C. parapsilosis
(14 of 64 [21.8%]). Multivariable analysis identified inadequate antifungal therapy (odds ratio [OR], 2.35; 95% confidence interval [95% CI], 1.09 to 5.10;
P
= 0.03), infection with overall biofilm-forming
Candida
species (OR, 2.33; 95% CI, 1.26 to 4.30;
P
= 0.007), and Acute Physiology and Chronic Health Evaluation III scores (OR, 1.03; 95% CI, 1.01 to 1.15;
P
< 0.001) as independent predictors of mortality. Notably, if mortality was analyzed according to the different biofilm-forming
Candida
species studied, only infections caused by
C. albicans
(
P
< 0.001) and
C. parapsilosis
(
P
= 0.003) correlated with increased mortality. Together with well-established factors,
Candida
biofilm production was therefore shown to be associated with greater mortality of patients with candidemia, probably by preventing complete organism eradication from the blood.
Three-Year Longitudinal Study of Genotypes of
Mycobacterium tuberculosis
Isolates in Tuscany, Italy
Authors: Lari Nicoletta , Rindi Laura , Bonanni Daniela , Rastogi Nalin , Sola Christophe , Tortoli Enrico , Garzelli Carlo 
Published: April 2007

ABSTRACT

The genetic diversity of 829 strains of
Mycobacterium tuberculosis
isolated during a 3-year period in Tuscany, Italy, a country with a low prevalence of tuberculosis, from 480 Italian-born and 349 foreign-born patients was determined by spoligotyping. The predominant spoligotype families were T (30.2% of isolates), Haarlem (19.9%), and the Latino-American and Mediterranean family (LAM) (11.2%); the remaining isolates were distributed among the Beijing (6.5%), S (4.2%), East Africa-India (EAI) (3.0%), Bovis (2.3%), Central Asia (CAS) (2.1%), Africanum (1.3%), and X (1.2%) families or were undefined (2.7%) or orphan (14.1%) isolates. Isolates of the families T, Haarlem, Bovis, and X were distributed among Italian- and foreign-born patients almost proportionally to the patients' numbers. Isolates of the LAM family were prevalent in foreign-born people (13.5%, versus 9.6% in Italian-born patients). Isolates of the S family were found almost exclusively in Italian-born patients, while strains of families EAI and CAS were isolated almost exclusively from foreign-born patients; Africanum isolates were all from African-born patients. The isolates of the Beijing family showed a trend to a steady increase during the survey. The prevalence of Beijing strains was 11.7% among foreign-born people and 2.7% among Italian-born patients. The Beijing strains were typed by the standardized IS
6110
restriction fragment length polymorphism assay, which yielded a total of 38 distinct IS
6110
patterns; 21 isolates (39.6%) occurred in six distinct clusters; of these, three contained two isolates and the other three contained four, five and six isolates, thus demonstrating that Beijing strains caused several tuberculosis outbreaks in the region. These findings indicate that transmission of Beijing strains between immigrants and the autochthonous population has occurred frequently and suggests an ongoing active transmission of the Beijing genotype in the region.
Inhibition of the Alpha/Beta Interferon Response by Mouse Hepatitis Virus at Multiple Levels
Authors: Roth-Cross Jessica K. , Martínez-Sobrido Luis , Scott Erin P. , García-Sastre Adolfo , Weiss Susan R. 
Published: April 2007

ABSTRACTMouse hepatitis virus (MHV) was used as a model to study the interaction of coronaviruses with the alpha/beta interferon (IFN-α/β) response. While MHV strain A59 appeared to induce IFN-β gene transcription and low levels of nuclear translocation of the IFN-β transcription factor interferon regulatory factor 3 (IRF-3), MHV did not induce IFN-β protein production during the course of infection in L2 mouse fibroblast cells. In addition, MHV was able to significantly decrease the level of IFN-β protein induced by both Newcastle disease virus (NDV) and Sendai virus infections, without targeting it for proteasomal degradation and without altering the nuclear translocation of IRF-3 or IFN-β mRNA production or stability. These results indicate that MHV infection causes an inhibition of IFN-β production at a posttranscriptional level, without altering RNA or protein stability. In contrast, MHV induced IFN-β mRNA and protein production in the brains of infected animals, suggesting that the inhibitory mechanisms observed in vitro are not enough to prevent IFN-α/β production in vivo. Furthermore, MHV replication is highly resistant to IFN-α/β action, as indicated by unimpaired MHV replication in L2 cells pretreated with IFN-β. However, when L2 cells were coinfected with MHV and NDV in the presence of IFN-β, NDV, but not MHV, replication was inhibited. Thus, rather than disarming the antiviral activity induced by IFN-β pretreatment completely, MHV may be inherently resistant to some aspects of the antiviral state induced by IFN-β. These findings show that MHV employs unique strategies to circumvent the IFN-α/β response at multiple steps.
Human Cytomegalovirus UL84 Interacts with an RNA Stem-Loop Sequence Found within the RNA/DNA Hybrid Region of
ori
Lyt
Authors: Colletti Kelly S. , Smallenburg Kate E. , Xu Yiyang , Pari Gregory S. 
Published: April 2007

ABSTRACT

Human cytomegalovirus (HCMV) lytic DNA replication is initiated at the complex
cis
-acting
ori
Lyt region, which spans nearly 3 kb. DNA synthesis requires six core proteins together with UL84 and IE2. Previously, two essential regions were identified within
ori
Lyt. Essential region I (nucleotides [nt] 92209 to 92573) can be replaced with the constitutively active simian virus 40 promoter, which in turn eliminates the requirement for IE2 in the origin-dependent transient-replication assay. Essential region II (nt 92979 to 93513) contains two elements of interest: an RNA/DNA hybrid domain and an inverted repeat sequence capable of forming a stem-loop structure. Our studies now reveal for the first time that UL84 interacts with a stem-loop RNA oligonucleotide in vitro, and although UL84 interacted with other nucleic acid substrates, a specific interaction occurred only with the RNA stem-loop. Increasing concentrations of purified UL84 produced a remarkable downward-staircase pattern, which is not due to a nuclease activity but is dependent upon the presence of secondary structures, suggesting that UL84 modifies the conformation of the RNA substrate. Cross-linking experiments show that UL84 possibly changes the conformation of the RNA substrate. The addition of purified IE2 to the in vitro binding reaction did not affect binding to the stem-loop structure. Chromatin immunoprecipitation assays performed using infected cells and purified virus show that UL84 is bound to
ori
Lyt in a region adjacent to the RNA/DNA hybrid and the stem-loop structure. These results solidify UL84 as the potential initiator of HCMV DNA replication through a unique interaction with a conserved RNA stem-loop structure within
ori
Lyt.
Viral Alteration of Cellular Translational Machinery Increases Defective Ribosomal Products
Authors: Berglund Peter , Finzi Diana , Bennink Jack R. , Yewdell Jonathan W. 
Published: April 2007

ABSTRACTHere we show that cells expressing genes inserted into Semliki Forest virus (SFV) vectors generate a large fraction of defective ribosomal products (DRiPs) due to frequent initiation on downstream Met residues. In monopolizing the host cell translational machinery, SFV reduces levels of translation eukaryotic initiation factor 4E (eIF4E), diminishes phosphorylation of ribosome subunit S6, and phosphorylates translation initiation factor eIF2α. We show that the last event is required for SFV mistranslation of inserted genes. Downstream initiation is suppressed by fusing inserted genes with the open reading frame encoding the SFV capsid, demonstrating that one function of the capsid element is to enable ribosomes to initiate translation in the proper location. These results show that in modifying translation, viral vectors can unpredictably increase the generation of truncated polypeptides and thereby the DRiP fraction of inserted gene products, which can potentially affect their yield, therapeutic efficacy, and immunogenicity.
Diverse Herpes Simplex Virus Type 1 Thymidine Kinase Mutants in Individual Human Neurons and Ganglia
Authors: Wang Kening , Mahalingam Gowtham , Hoover Susan E. , Mont Erik K. , Holland Steven M. , Cohen Jeffrey I. , Straus Stephen E. 
Published: April 2007

ABSTRACTMutations in the thymidine kinase gene (tk) of herpes simplex virus type 1 (HSV-1) explain most cases of virus resistance to acyclovir (ACV) treatment. Mucocutaneous lesions of patients with ACV resistance contain mixed populations oftkmutant and wild-type virus. However, it is unknown whether human ganglia also contain mixed populations since the replication of HSVtkmutants in animal neurons is impaired. Here we report the detection of mutated HSVtksequences in human ganglia. Trigeminal and dorsal root ganglia were obtained at autopsy from an immunocompromised woman with chronic mucocutaneous infection with ACV-resistant HSV-1. The HSV-1tkopen reading frames from ganglia were amplified by PCR, cloned, and sequenced.tkmutations were detected in a seven-G homopolymer region in 11 of 12 ganglia tested, with clonal frequencies ranging from 4.2 to 76% HSV-1tkmutants per ganglion. In 8 of 11 ganglia, the mutations were heterogeneous, varying from a deletion of one G to an insertion of one to three G residues, with the two-G insertion being the most common. Each ganglion had its own pattern of mutant populations. When individual neurons from one ganglion were analyzed by laser capture microdissection and PCR, 6 of 14 HSV-1-positive neurons were coinfected with HSVtkmutants and wild-type virus, 4 of 14 were infected with wild-type virus alone, and 4 of 14 were infected withtkmutant virus alone. These data suggest that diversetkmutants arise independently under drug selection and establish latency in human sensory ganglia alone or together with wild-type virus.
Interaction of the C-Terminal Domains of Sendai Virus N and P Proteins: Comparison of Polymerase-Nucleocapsid Interactions within the Paramyxovirus Family
Authors: Houben Klaartje , Marion Dominique , Tarbouriech Nicolas , Ruigrok Rob W. H. , Blanchard Laurence 
Published: April 2007

ABSTRACT

Interaction of the C-terminal domains of Sendai virus (SeV) P and N proteins is crucial for RNA synthesis by correctly positioning the polymerase complex (L+P) onto the nucleocapsid (N/RNA). To better understand this mechanism within the paramyxovirus family, we have studied the complex formed by the SeV C-terminal domains of P (PX) and N (N
TAIL
) proteins by solution nuclear magnetic resonance spectroscopy. We have characterized SeV N
TAIL
, which belongs to the class of intrinsically disordered proteins, and precisely defined the binding regions within this latter domain and within PX. SeV N
TAIL
binds with residues 472 to 493, which have a helical propensity (residues 477 to 491) to the surface created by helices α2 and α3 of PX with a 1:1 stoichiometry, as was also found for measles virus (MV). The binding interface is dominated by charged residues, and the dissociation constant was determined to be 57 ± 18 μM under conditions of the experiment (i.e., in 0.5 M NaCl). We have also shown that the extreme C terminus of SeV N
TAIL
does not interact with PX, which is in contrast to MV, where a second binding site was identified. In addition, the interaction surfaces of the MV proteins are hydrophobic and a stronger binding constant was found. This gives a good illustration of how selection pressure allowed the C-terminal domains of N and P proteins to evolve concomitantly within this family of viruses in order to lead to protein complexes having the same three-dimensional fold, and thus the same function, but with completely different binding interfaces.
Predictable αβ T-Cell Receptor Selection toward an HLA-B*3501-Restricted Human Cytomegalovirus Epitope
Authors: Brennan Rebekah M. , Miles John J. , Silins Sharon L. , Bell Melissa J. , Burrows Jacqueline M. , Burrows Scott R. 
Published: April 2007

ABSTRACTHuman cytomegalovirus (HCMV) elicits a very large burden on the immune system, with approximately one in ten T cells being reserved solely to manage this infection. However, information on the clonotypic composition of these vast T-cell populations is limited. In this study, we sequenced 116 T-cell receptor (TcR) α/β-chains specific for the highly immunogenic HLA-B*3501-resticted epitope IPSINVHHY from the pp65 antigen. Interestingly, T cells recovered from all donors bore an identical or near-identical TRBV28/TRBJ1-4/TRAV17/TRAJ33 TcR. The ability to predict the responding αβ TcR repertoire before viral infection should prove a powerful tool for basic and clinical immunology.
DNA Immunization with Plasmids Encoding Fusion and Nucleocapsid Proteins of Bovine Respiratory Syncytial Virus Induces a Strong Cell-Mediated Immunity and Protects Calves against Challenge
Authors: Boxus Mathieu , Tignon Marylène , Roels Stefan , Toussaint Jean-François , Walravens Karl , Benoit Marie-Ange , Coppe Philippe , Letesson Jean-Jacques , Letellier Carine , Kerkhofs Pierre 
Published: April 2007

ABSTRACT
Respiratory syncytial viruses (RSV) are one of the most important respiratory pathogens of humans and cattle, and there is currently no safe and effective vaccine prophylaxis. In this study, we designed two codon-optimized plasmids encoding the bovine RSV fusion (F) and nucleocapsid (N) proteins and assessed their immunogenicity in young calves. Two administrations of both plasmids elicited low antibody levels but primed a strong cell-mediated immunity characterized by lymphoproliferative response and gamma interferon production in vitro and in vivo. Interestingly, this strong cellular response drastically reduced viral replication, clinical signs, and pulmonary lesions after a highly virulent challenge. Moreover, calves that were further vaccinated with a killed-virus vaccine developed high levels of neutralizing antibody and were fully protected following challenge. These results indicate that DNA vaccination could be a promising alternative to the classical vaccines against RSV in cattle and could therefore open perspectives for vaccinating young infants.
Binding-Site Identification and Genotypic Profiling of Hepatitis C Virus Polymerase Inhibitors
Authors: Pauwels Frederik , Mostmans Wendy , Quirynen Ludo M. M. , van der Helm Liesbet , Boutton Carlo W. , Rueff Anne-Stéphanie , Cleiren Erna , Raboisson Pierre , Surleraux Dominique , Nyanguile Origène , Simmen Kenneth A. 
Published: April 2007

ABSTRACTThe search for hepatitis C virus polymerase inhibitors has resulted in the identification of several nonnucleoside binding pockets. The shape and nature of these binding sites differ across and even within diverse hepatitis C virus genotypes. These differences confront antiviral drug discovery with the challenge of finding compounds that are capable of inhibition in variable binding pockets. To address this, we have established a hepatitis C virus mutant and genotypic recombinant polymerase panel as a means of guiding medicinal chemistry through the elucidation of the site of action of novel inhibitors and profiling against genotypes. Using a genotype 1b backbone, we demonstrate that the recombinant P495L, M423T, M414T, and S282T mutant enzymes can be used to identify the binding site of an acyl pyrrolidine analog. We assess the inhibitory activity of this analog and other nonnucleoside inhibitors with our panel of enzyme isolates generated from clinical sera representing genotypes 1a, 1b, 2a, 2b, 3a, 4a, 5a, and 6a.
Enhanced Antiviral Activity against Foot-and-Mouth Disease Virus by a Combination of Type I and II Porcine Interferons
Authors: Moraes Mauro Pires , de los Santos Teresa , Koster Marla , Turecek Traci , Wang He , Andreyev Vladimir G. , Grubman Marvin J. 
Published: April 2007

ABSTRACTPreviously, we showed that type I interferon (alpha/beta interferon [IFN-α/β]) can inhibit foot-and-mouth disease virus (FMDV) replication in cell culture, and swine inoculated with 109PFU of human adenovirus type 5 expressing porcine IFN-α (Ad5-pIFN-α) were protected when challenged 1 day later. In this study, we found that type II pIFN (pIFN-γ) also has antiviral activity against FMDV in cell culture and that, in combination with pIFN-α, it has a synergistic antiviral effect. We also observed that while each IFN alone induced a number of IFN-stimulated genes (ISGs), the combination resulted in a synergistic induction of some ISGs. To extend these studies to susceptible animals, we inoculated groups of swine with a control Ad5, 108PFU of Ad5-pIFN-α, low- or high-dose Ad5-pIFN-γ, or a combination of Ad5-pIFN-α and low- or high-dose Ad5-pIFN-γ and challenged all groups with FMDV 1 day later. The control group and the groups inoculated with either Ad5-pIFN-α or a low dose of Ad5-pIFN-γ developed clinical disease and viremia. However, the group that received the combination of both Ad5-IFNs with the low dose of Ad5-pIFN-γ was completely protected from challenge and had no viremia. Similarly the groups inoculated with the combination of Ad5s with the higher dose of Ad5-pIFN-γ or with only high-dose Ad5-pIFN-γ were protected. The protected animals did not develop antibodies against viral nonstructural (NS) proteins, while all infected animals were NS protein seropositive. No antiviral activity or significant levels of IFNs were detected in the protected groups, but there was an induction of some ISGs. The results indicate that the combination of type I and II IFNs act synergistically to inhibit FMDV replication in vitro and in vivo.
Highly Conserved Configuration of Catalytic Amino Acid Residues among Calicivirus-Encoded Proteases
Authors: Oka Tomoichiro , Yamamoto Mami , Yokoyama Masaru , Ogawa Satoko , Hansman Grant S. , Katayama Kazuhiko , Miyashita Kana , Takagi Hirotaka , Tohya Yukinobu , Sato Hironori , Takeda Naokazu 
Published: April 2007

ABSTRACT

A common feature of caliciviruses is the proteolytic processing of the viral polyprotein catalyzed by the viral 3C-like protease encoded in open reading frame 1 (ORF1). Here we report the identification and structural characterization of the protease domains and amino acid residues in sapovirus (SaV) and feline calicivirus (FCV). The in vitro expression and processing of a panel of truncated ORF1 polyproteins and corresponding mutant forms showed that the functional protease domain is 146 amino acids (aa) in SaV and 154 aa in FCV. Site-directed mutagenesis of the protease domains identified four amino acid residues essential to protease activities: H
31
, E
52
, C
116
, and H
131
in SaV and H
39
, E
60
, C
122
, and H
137
in FCV. A computer-assisted structural analysis showed that despite high levels of diversity in the primary structures of the protease domains in the family
Caliciviridae
, the configurations of the H, E, C, and H residues are highly conserved, with these residues positioned closely along the inner surface of the potential binding cleft for the substrate. These results strongly suggest that the H, E, C, and H residues are involved in the formation of a conserved catalytic surface of the SaV and FCV 3C-like proteases.
Polynomial‐time computability of the edge‐reliability of graphs using Gilbert′s formula
Authors: Marlowe Thomas J. , Schoppmann Laura 
Published: April 2007

Reliability is an important consideration in analyzing computer and other communication networks, but current techniques are extremely limited in the classes of graphs which can be analyzed efficiently. While Gilbert′s formula establishes a theoretically elegant recursive relationship between the edge reliability of a graph and the reliability of its subgraphs, naive evaluation requires consideration of all sequences of deletions of individual vertices, and for many graphs has time complexity essentially
Θ
(N!). We discuss a general approach which significantly reduces complexity, encoding subgraph isomorphism in a finer partition by invariants, and recursing through the set of invariants.We illustrate this approach using threshhold graphs, and show that any computation of reliability using Gilbert′s formula will be polynomial‐time if and only if the number of invariants considered is polynomial; we then show families of graphs with polynomial‐time, and non‐polynomial reliability computation, and show that these encompass most previously known results.We then codify our approach to indicate how it can be used for other classes of graphs, and suggest several classes to which the technique can be applied.
Pattern of Local Recurrence After Conservative Surgery and Radiotherapy for Soft Tissue Sarcoma
Authors: Cleator Susan J. , Cottrill Chris , Harmer Clive 
Published: April 2007

Purpose: Over the past three decades our centre has adopted a policy of conservative surgery followed by adjuvant radicaldose
radiotherapy for medium‐and high‐grade soft tissue sarcomas. For all cases of local recurrence following this treatment
we aimed to define the spatial relationship between sites of recurrence and the positions of the phase 1 and 2 radiotherapy
volumes.Patients: We identified 25 cases of local recurrence recorded on our soft tissue sarcoma database between 1986 and 1999
inclusive. We excluded patients with macroscopic residual disease following surgery. Most patients were treated with a phase
I volume corresponding to the entire muscle compartment (50 Gy in 25 fractions over 5 weeks) and a phase II volume corresponding
to the tumour bed (10 Gy in five fractions). Six of the patients were treated according to a hyperfractionated
regimen.Methods: For each case we reviewed the diagnostic imaging, planning radiographs and prescription sheets. We audited
whether treatment had been given according to protocol and defined whether recurrence had arisen in the phase 1 volume,
phase 2 volume or ‘out of field’.Results: Four (16%) patients recurred within the phase I volume, 17 (68%) recurred within the phase II volume and four
(16%) outside the irradiated volume including one marginal recurrence. In six patients there had been deviation from our
radiotherapy protocol (usually unavoidable) including all three true out of field recurrences.Discussion: The majority of recurrences occur in the phase 2 volume. Prospective multi‐centre data collection and, ideally,
a prospective randomised trial are required to formulate an improved treatment policy with respect to radiotherapy margins
and dose.