bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiplexed Luminex xMAP Assay for Detection and Identification of Five Adenovirus Serotypes Associated with Epidemics of Respiratory Disease in Adults
Authors: Washington Cicely , Metzgar David , Hazbón Manzour Hernando , Binn Leonard , Lyons Arthur , Coward Carl , Kuschner Robert 
Published: April 2010

ABSTRACTSeveral serotypes of human adenovirus (HAdV) cause acute respiratory disease (ARD) among healthy adults, sometimes generating broad outbreaks with high attack rates and occasional fatalities. Timely serotype identification provides valuable epidemiological information and significantly contributes to prevention (vaccination) strategies. The prevalence of specific serotypes causing ARD varies geographically. HAdV-3, HAdV-4, HAdV-7, HAdV-14, and HAdV-21 are the serotypes most commonly found in adult populations in the Western Hemisphere. Unfortunately, conventional serotype identification is a tedious process which can take a week or longer. For this reason, new molecular methods for serotype identification are needed. Commercially available rapid antigen and PCR assays for the detection of HAdV are universal but do not distinguish between the different serotypes. We describe the development of a sensitive and specific multiplex assay capable of identifying serotypes 3, 4, 7, 14, and 21. Two sets of primers were used for nonspecific (universal) PCR amplification, and serotype-specific probes coupled to Luminex tags were used for target-specific extension (TSE). PCR and TSE primers were designed using known hexon gene sequences of HAdV. The TSE products of HAdV-3, HAdV-4, HAdV-7, HAdV-14, and HAdV-21 were correctly identified using the Luminex xMAP fluid microsphere-based array system. No cross-reactivity with other respiratory pathogens or other HAdV serotypes was observed. This multiplexed assay can be expanded to include more serotypes and will allow broad and rapid detection and identification of adenoviral serotypes in a high-throughput environment.
Detection ofCampylobacter jejuniby Culture and Real-Time PCR in a French Cohort of Patients with Guillain-Barré Syndrome
Authors: Sivadon-Tardy Valérie , Orlikowski David , Porcher Raphael , Ronco Esthel , Caudie Christiane , Roussi Jacqueline , Fauchère Jean-Louis , Mégraud Francis , Tabor Helen , Sharshar Tarek , Annane Djillali , Raphaël Jean-Claude , Gaillard Jean-Louis 
Published: April 2010

ABSTRACTBacteriological culture and real-time PCR (RT-PCR) were used to detectCampylobacter jejuniin fecal samples from a French cohort of 237 patients with Guillain-Barré syndrome (GBS). We provide evidence that diverse serotypes and genotypes ofC. jejuniare a major trigger of GBS in France.
Response of Subgingival Bacteria to Smoking Cessation
Authors: Delima Suzanne L. , McBride Robert K. , Preshaw Philip M. , Heasman Peter A. , Kumar Purnima S. 
Published: April 2010

ABSTRACT

It has been demonstrated that smoking cessation alters the subgingival microbial profile; however, the response of individual bacteria within this ecosystem has not been well studied. The aim of this investigation, therefore, was to longitudinally examine the effect of smoking cessation on the prevalence and levels of selected subgingival bacteria using molecular approaches for bacterial identification and enumeration. Subgingival plaque was collected from 22 smokers at the baseline and 12 months following periodontal nonsurgical management and smoking cessation counseling. The prevalence and abundance of selected organisms were examined using nested PCR and multiplexed bead-based flow cytometry. Eleven subjects successfully quit smoking over 12 months (quitters), while 11 continued to smoke throughout (smokers). Smoking cessation led to a decrease in the prevalence of
Porphyromonas endodontalis
and
Dialister pneumosintes
at 12 months and in the levels of
Parvimonas micra
,
Filifactor alocis
, and
Treponema denticola
. Smoking cessation also led to an increase in the levels of
Veillonella parvula
. Following nonsurgical periodontal therapy and smoking cessation, the subgingival microbiome is recolonized by a greater number of health-associated species and there are a significantly lower prevalence and abundance of putative periodontal pathogens. The results indicate a critical role for smoking cessation counseling in periodontal therapy for smokers in order to effectively alter the subgingival microbiome.
Spectrum and Prevalence of Fungi Infecting Deep Tissues of Lower-Limb Wounds in Patients with Type 2 Diabetes
Authors: Chellan Gopi , Shivaprakash Shashikala , Karimassery Ramaiyar Sundaram , Varma Ajit Kumar , Varma Narendra , Thekkeparambil Sukumaran Mangalanandan , Rohinivilasam Vasukutty Jayakumar , Bal Arun , Kumar Harish 
Published: April 2010

ABSTRACTThe prevalence rate and spectrum of fungi infecting deep tissues of diabetic lower-limb wounds (DLWs) have not been previously studied. Five hundred eighteen (382 male and 136 female) consecutive patients with type 2 diabetes hospitalized due to infected lower-limb wounds were enlisted in this study. Deep tissue (approximately 0.5- × 0.5-cm size) taken perioperatively from the wound bed was cultured for fungi. Fungi was found in 27.2% (141/518) of the study population.Candida parapsilosis(25.5%),Candida tropicalis(22.7%),Trichosporon asahii(12.8%),Candida albicans(10.6%), andAspergillusspecies (5.0%) were the most predominant fungal isolates. Of the fungal isolates, 17.7% were resistant to itraconazole, 6.9% were resistant to amphotericin B, 6.9% were resistant to voriconazole, 3.9% were resistant to fluconazole, and 1.5% were resistant to flucytosine. Of the population, 79.7% (413/518) had bacterial infection in deep tissue. The predominant isolates wereEnterococcus faecalis(14.1%),Staphylococcus aureus(12.2%), andPseudomonas aeruginosa(10.8%). Mixed fungal and bacterial infections were seen in 21.4% of patients, while 5.8% had only fungal infection and 58.3% had only bacterial infections. Another 14.5% had neither bacteria nor fungi in the deep tissue. Patients with higher glycosylated hemoglobin levels had significantly more fungal infections. Our study reveals that deep-seated fungal infections are high in DLWs. In the context of delayed wound healing and amputation rates due to DLWs, it is important to study the pathogenicity of fungi in deep tissues of DLWs and their possible contribution to delayed wound healing. The role of antifungal agents in wound management needs to be evaluated further.
The Crystal Structure of Porcine Reproductive and Respiratory Syndrome Virus Nonstructural Protein Nsp1β Reveals a Novel Metal-Dependent Nuclease
Authors: Xue Fei , Sun Yuna , Yan Liming , Zhao Cong , Chen Ji , Bartlam Mark , Li Xuemei , Lou Zhiyong , Rao Zihe 
Published: April 2010

ABSTRACT

Porcine reproductive and respiratory syndrome virus (PRRSV), a member of the
Arteriviridae
family of
Nidovirales
, is the causative agent of porcine reproductive and respiratory syndrome, which results in enormous economic losses in the swine industry. As the second protein encoded by the PRRSV genome, nsp1β cleaves itself from the downstream nsp2 protein via a C-terminal papain-like cysteine protease (PCP) domain. Although nsp1β is known to be involved in virulence, its precise role in the process of viral infection remains unclear. In this work, we describe the homodimeric crystal structure of PRRSV nsp1β in its natural, self-processed form. We show that the architecture of its N-terminal domain (NTD) adopts a fold closely resembling that of several known nucleases and has intrinsic nuclease activity that is strongly activated by manganese ions
in vitro
. Key features, however, distinguish nsp1β from characterized nucleases, including the C-terminal PCP domain (which is responsible for the self-release of nsp1β from nsp2), a linker domain (LKD) that connects the NTD and the PCP domain, and a C-terminal extension (CTE) that binds to and is stabilized by the putative substrate binding site of the PCPβ domain. Combined with the reported nuclear localization of this protein, these results shed light on the self-processing mode and precise biological function of nsp1β and thus offer a multitarget template for future drug discovery.
HIV-1 Resistance to CCR5 Antagonists Associated with Highly Efficient Use of CCR5 and Altered Tropism on Primary CD4
+
T Cells
Authors: Pfaff Jennifer M. , Wilen Craig B. , Harrison Jessamina E. , Demarest James F. , Lee Benhur , Doms Robert W. , Tilton John C. 
Published: April 2010

ABSTRACT

We previously reported on a panel of HIV-1 clade B envelope (Env) proteins isolated from a patient treated with the CCR5 antagonist aplaviroc (APL) that were drug resistant. These Envs used the APL-bound conformation of CCR5, were cross resistant to other small-molecule CCR5 antagonists, and were isolated from the patient's pretreatment viral quasispecies as well as after therapy. We analyzed viral and host determinants of resistance and their effects on viral tropism on primary CD4
+
T cells. The V3 loop contained residues essential for viral resistance to APL, while additional mutations in gp120 and gp41 modulated the magnitude of drug resistance. However, these mutations were context dependent, being unable to confer resistance when introduced into a heterologous virus. The resistant virus displayed altered binding between gp120 and CCR5 such that the virus became critically dependent on the N′ terminus of CCR5 in the presence of APL. In addition, the drug-resistant Envs studied here utilized CCR5 very efficiently: robust virus infection occurred even when very low levels of CCR5 were expressed. However, recognition of drug-bound CCR5 was less efficient, resulting in a tropism shift toward effector memory cells upon infection of primary CD4
+
T cells in the presence of APL, with relative sparing of the central memory CD4
+
T cell subset. If such a tropism shift proves to be a common feature of CCR5-antagonist-resistant viruses, then continued use of CCR5 antagonists even in the face of virologic failure could provide a relative degree of protection to the T
CM
subset of CD4
+
T cells and result in improved T cell homeostasis and immune function.
Neuraminidase Receptor Binding Variants of Human Influenza A(H3N2) Viruses Resulting from Substitution of Aspartic Acid 151 in the Catalytic Site: a Role in Virus Attachment?
Authors: Lin Yi Pu , Gregory Victoria , Collins Patrick , Kloess Johannes , Wharton Stephen , Cattle Nicholas , Lackenby Angie , Daniels Rodney , Hay Alan 
Published: April 2010

ABSTRACT
Changes in the receptor binding characteristics of human H3N2 viruses have been evident from changes in the agglutination of different red blood cells (RBCs) and the reduced growth capacity of recently isolated viruses, particularly in embryonated eggs. An additional peculiarity of viruses circulating in 2005 to 2009 has been the poor inhibition of hemagglutination by postinfection ferret antisera for many viruses isolated in MDCK cells, including homologous reference viruses. This was shown not to be due to an antigenic change in hemagglutinin (HA) but was shown to be the result of a mutation in aspartic acid 151 of neuraminidase (NA) to glycine, asparagine, or alanine, which caused an oseltamivir-sensitive agglutination of RBCs. The D151G substitution was shown to cause a change in the specificity of NA such that it acquired the capacity to bind receptors, which were refractory to enzymatic cleavage, without altering its ability to remove receptors for HA. Thus, the inhibition of NA-dependent agglutination by the inclusion of oseltamivir carboxylate in the assay was effective in restoring the anti-HA specificity of the hemagglutination inhibition (HI) assay for monitoring antigenic changes in HA. Since the NA-dependent binding activity did not affect virus neutralization, and virus populations in clinical specimens possessed, at most, low levels of the “151 mutant,” the biological significance of this feature of NA in, for example, immune evasion is unclear. It is apparent, however, that an important role of aspartic acid 151 in the activity of NA may be to restrict the specificity of the NA interaction and its receptor-destroying activity to complement that of HA receptor binding.
Intracellular Sorting Signals for Sequential Trafficking of Human Cytomegalovirus UL37 Proteins to the Endoplasmic Reticulum and Mitochondria
Authors: Williamson Chad D. , Colberg-Poley Anamaris M. 
Published: April 2010

ABSTRACT
Human cytomegalovirus UL37 antiapoptotic proteins, including the predominant UL37 exon 1 protein (pUL37x1), traffic sequentially from the endoplasmic reticulum (ER) through the mitochondrion-associated membrane compartment to the mitochondrial outer membrane (OMM), where they inactivate the proapoptotic activity of Bax. We found that widespread mitochondrial distribution occurs within 1 h of pUL37x1 synthesis. The pUL37x1 mitochondrial targeting signal (MTS) spans its first antiapoptotic domain (residues 5 to 34) and consists of a weak hydrophobicity leader (MTSα) and proximal downstream residues (MTSβ). This MTS arrangement of a hydrophobic leader and downstream proximal basic residues is similar to that of the translocase of the OMM 20, Tom20. We examined whether the UL37 MTS functions analogously to Tom20 leader. Surprisingly, lowered hydropathy of the UL37x1 MTSα, predicted to block ER translocation, still allowed dual targeting of mutant to the ER and OMM. However, increased hydropathy of the MTS leader caused exclusion of the UL37x1 high-hydropathy mutant from mitochondrial import. Conversely, UL37 MTSα replacement with the Tom20 leader did not retarget pUL37x1 exclusively to the OMM; rather, the UL37x1-Tom20 chimera retained dual trafficking. Moreover, replacement of the UL37 MTSβ basic residues did not reduce OMM import. Ablation of the MTSα posttranslational modification site or of the downstream MTS proline-rich domain (PRD) increased mitochondrial import. Our results suggest that pUL37x1 sequential ER to mitochondrial trafficking requires a weakly hydrophobic leader and is regulated by MTSβ sequences. Thus, HCMV pUL37x1 uses a mitochondrial importation pathway that is genetically distinguishable from that of known OMM proteins.
Establishment of HIV Latency in Primary CD4+Cells Is due to Epigenetic Transcriptional Silencing and P-TEFb Restriction
Authors: Tyagi Mudit , Pearson Richard John , Karn Jonathan 
Published: April 2010

ABSTRACTThe development of suitable experimental systems for studying HIV latency in primary cells that permit detailed biochemical analyses and the screening of drugs is a critical step in the effort to develop viral eradication strategies. Primary CD4+T cells were isolated from peripheral blood and amplified by antibodies to the T-cell receptor (TCR). The cells were then infected by lentiviral vectors carrying fluorescent reporters and either the wild-type Tat gene or the attenuated H13L Tat gene. After sorting for the positive cells and reamplification, the infected cells were allowed to spontaneously enter latency by long-term cultivation on the H80 feeder cell line in the absence of TCR stimulation. By 6 weeks almost all of the cells lost fluorescent protein marker expression; however, more than 95% of these latently infected cells could be reactivated after stimulation of the TCR by α-CD3/CD28 antibodies. Chromatin immunoprecipitation assays showed that, analogously to Jurkat T cells, latent proviruses in primary CD4+T cells are enriched in heterochromatic markers, including high levels of CBF-1, histone deacetylases, and methylated histones. Upon TCR activation, there was recruitment of NF-κB to the promoter and conversion of heterochromatin structures present on the latent provirus to active euchromatin structures containing acetylated histones. Surprisingly, latently infected primary cells cannot be induced by tumor necrosis factor alpha because of a restriction in P-TEFb levels, which can be overcome by activation of the TCR. Thus, a combination of restrictive chromatin structures at the HIV long terminal repeat and limiting P-TEFb levels contribute to transcriptional silencing leading to latency in primary CD4+T cells.
Delineation of the Preferences and Requirements of the Human Immunodeficiency Virus Type 1 Dimerization Initiation Signal by Using an
I
n Vivo
Cell-Based Selection Approach
Authors: Hussein Islam T. M. , Ni Na , Galli Andrea , Chen Jianbo , Moore Michael D. , Hu Wei-Shau 
Published: April 2010

ABSTRACT
HIV-1 packages two copies of RNA into one particle, and the dimerization initiation signal (DIS) in the viral RNA plays an important role in selecting the copackaged RNA partner. We analyzed the DIS sequences of the circulating HIV-1 isolates in the GenBank database and observed that, in addition to the prevalent GCGCGC, GTGCAC, and GTGCGC sequences, there are many other minor variants. To better understand the requirements for the DIS to carry out its function, we generated a plasmid library containing a subtype B HIV-1 genome with a randomized DIS, infected cells with viruses derived from the library, and monitored the emergence of variants at different time points until 100 days postinfection. We observed rapid loss of viral diversity and found that the selected variants contained palindromes in the DIS. The “wild-type” GCGCGC-containing virus was a major variant, whereas GTGCAC- and GTGCGC-containing viruses were present at low frequencies. Additionally, other 6-nucleotide (nt) palindromic sequences were selected; a major category of the selected variants contained two GC dyads in the center of the palindrome, flanked by a non-GC dyad. Surprisingly, variants with GC-rich 4-nt palindromes were sustained throughout the selection period at significant frequencies (∼12 to 38%); of these, variants containing the CGCGC sequence were observed frequently, suggesting that this sequence has a selection advantage. These results revealed that multiple sequences can fulfill the function of the HIV-1 DIS. A common feature of the selected DIS sequence is a 4- or 6-nt GC-rich palindrome, although not all sequences with these characteristics were selected, suggesting the presence of other unidentified interactions.
Wingspan experience at Beijing Tiantan Hospital: new insights into the mechanisms of procedural complication from viewing intraoperative transient ischemic attacks during awake stenting for vertebrobasilar stenosis
Authors: Jiang W-J , Yu W , Du B , Wong E H C , Gao F 
Published: April 2010

Background and aimIntracranial vertebrobasilar artery (VBA) stenosis portends a stroke and death rate of 8.5–22.8% annually despite medical therapy. Stenting has emerged as a treatment option but also carries substantial risk. Awake stenting under local anesthesia to minimize major procedural complication was investigated.MethodsBetween January 2007 and December 2008, 43 of 46 consecutive patients with severe symptomatic intracranial VBA stenosis underwent elective angioplasty assisted with self-expanding Wingspan stent under local anesthesia at our institute. All data were collected prospectively.ResultsAll 43 patients tolerated the stenting procedure under local anesthesia well. Forty-two patients (97.7%) were stented successfully. Within 30 days, there were three periprocedural strokes, including thromboembolic infarct, pontine perforator infarct and intracranial hemorrhage, without fatality. In addition, five patients had intraoperative brainstem transient ischemic attacks (TIAs) seconds after the deployment of the stent delivery system across the tortuous VBA. The symptoms and signs included impaired consciousness (n=5), dysarthria (n=3), convulsion (n=2), conjugate horizontal gaze palsy (n=2), nystagmus (n=2) and pinpoint pupils (n=1). There was angiographic evidence of VBA straightening without thromboembolism. The TIAs resolved within minutes of prompt removal of the delivery catheter.ConclusionsVBA stenting under local anesthesia is feasible with a 7% periprocedural stroke risk. Awake stenting allows timely detection of intraoperative TIAs. The mechanism of intraoperative TIA appears to be stent delivery system induced VBA straightening and distortion of its vascular tree. A devastating stroke may ensue if the TIA is not detected and distortion of VBA perforators is not reversed promptly.
PREPARATION OF FUNCTIONALIZED MWCNTs COATING WITH MgO VIA SIMPLE PRECIPITATION METHOD
Authors: ZAVAREH S. , MAJEDI F. , SHARIF M. A. Sh. , GOLESTANIFARD F. , ESMAILIAN M. 
Published: April 2010

Multiwalled carbon nanotubes (MWCNTs) were coated with MgO nanoparticles using simple precipitation method. The nanometer-sized Mg(OH)2 particles were precipitated on the surface of functionalized MWCNTs by reaction between MgSO4 solution and NH4OH as an alkaline agent. The growth of Mg(OH)2 particles was controlled by adjusting the alkaline concentration, salt concentration and feed rate in simple precipitation method. The samples have been characterized by scanning electron microscopy (SEM), energy dispersive X-ray spectrometry (EDS), X-ray diffraction (XRD) and thermal gravimetric analysis (TG). The results showed a nominally complete coating over the entire outer surface of MWCNTs and the oxidation resistance of MWCNTs was improved by the MgO coating significantly.
Statin Use and Colorectal Adenoma Risk: Results from the Adenoma Prevention with Celecoxib Trial
Authors: Bertagnolli Monica M. , Hsu Meier , Hawk Ernest T. , Eagle Craig J. , Zauber Ann G. 
Published: April 2010

Abstract
Statins are widely prescribed for cardiovascular disease prevention and also commonly used in patients at high risk for colorectal cancer. We report the results of a planned secondary analysis of the relationship between statin use and colorectal adenoma risk in a large chemoprevention trial. The Adenoma Prevention with Celecoxib (APC) trial randomized 2,035 adenoma patients to receive placebo (679 patients), 200 mg celecoxib twice daily (bid; 685 patients), or 400 mg celecoxib bid (671 patients). The study collected complete medical history and medication use data and performed colonoscopic surveillance to 5 years after study enrollment. The effects of statin use on newly detected adenomas and cardiovascular adverse events were analyzed as time-dependent variables by multivariable Cox regression. Statins were used by 36% (n = 730) of APC trial participants. When adjusted for covariates including cardioprotective aspirin use, age, and sex, participants on the placebo arm who used statins at any time had no benefit over 5 years compared with never users (risk ratio, 1.24; 95% confidence interval, 0.99-1.56; P = 0.065). Statin use for &gt;3 years increased adenoma risk over 5 years (risk ratio, 1.39; 95% confidence interval, 1.04-1.86; P = 0.024). For all comparisons of patients treated with celecoxib, adenoma detection rates for statin users and nonusers were equivalent. Consistent with their use in patients at high risk, cardiovascular serious adverse events were more common among statin users. For patients at high risk of colorectal cancer, statins do not protect against colorectal neoplasms and may even increase the risk of developing colorectal adenomas. Cancer Prev Res; 3(5); 588–96. ©2010 AACR.
Statins and the Colorectum: Hope for Chemoprevention?
Authors: Baron John A. 
Published: April 2010

Abstract
This perspective on Bertagnolli et al. (beginning on p. 588 in this issue of the journal) and Lipkin et al. (beginning on p. 597) considers the likelihood that statins have chemopreventive efficacy in the large bowel. An observational analysis within a clinical trial of celecoxib found no benefit of statin use on the risk of colorectal adenomas (and some suggestions of an adverse effect). On the other hand, variation in the 3-hydroxy-3-methylglutaryl coenzyme A reductase gene modified the association of statins with risk of colorectal cancer. The perspective discusses the implications of these data and how they fit into the context of previous investigations. Cancer Prev Res; 3(5); 573–5. ©2010 AACR.