bluuebunny/crossref_metadata_2025 huggingface dataset:
Antimicrobial Photodynamic Therapy on Drug‐resistant Pseudomonas aeruginosa‐induced Infection. An In Vivo Study†
Authors: Hashimoto Maria C. E. , Prates Renato A. , Kato Ilka T. , Núñez Silvia C. , Courrol Lília C. , Ribeiro Martha S.
Published: March 2012

Pseudomonas aeruginosa is considered one of the most important pathogens that represent life‐threatening risk in nosocomial environments, mainly in patients with severe burns. Antimicrobial photodynamic therapy (aPDT) has been effective to kill bacteria. The purpose of this study was to develop a burn wound and bloodstream infection model and verify aPDT effects on it. In vitro, we tested two wavelengths (blue and red LEDs) on a clinical isolate of P. aeruginosa strain with resistance to multiple antibiotics using HB:La+3 as photosensitizer. Verapamil® associated to aPDT was also studied. In vivo, P. aeruginosa‐infected burned mice were submitted to aPDT. Bacterial counting was performed on local infection and bloodstream. Survival time of animals was also monitored. In this study, aPDT was effective to reduce P. aeruginosa in vitro. In addition, Verapamil® assay showed that HB:La+3 is not recognized by ATP‐binding cassete (ABC) efflux pump mechanism. In the in vivo study, aPDT was able to reduce bacterial load in burn wounds, delay bacteremia and keep the bacterial levels in blood 2–3 logs lower compared with an untreated group. Mice survival was increased on 24 h. Thus, this result suggests that aPDT may also be a novel prophylactic treatment in the care of burned patients.
Evaluation of two new automated chemiluminescent assays (HemosIL®AcuStar HIT‐IgG and HemosIL®AcuStar HIT‐Ab) for the detection of heparin‐induced antibodies in the diagnosis of heparin‐induced thrombocytopenia
Authors: VAN HOECKE F. , DEVREESE K.
Published: March 2012

Introduction:  Recently, two new, fully automated quantitative chemiluminescent immunoassays, the HemosIL® AcuStar HIT‐IgG (PF4‐H), specific for IgG anti‐PF4/H antibodies, and the HemosIL® AcuStar HIT‐Ab(PF4‐H), detecting IgG, IgM and IgA anti‐PF4/H antibodies, were introduced into the market. In this study, their performance was compared mutually and with the Zymutest HIA IgG and HIA IgGAM ELISA.

Methods:  Citrated plasmas from 87 patients with clinical suspicion of heparin‐induced thrombocytopenia (HIT) were analyzed with all four assays and with a functional confirmation assay. Apart from the manufacturer’s cutoffs, optimalized cutoffs were evaluated as well.

Results:  Sensitivities of all assays were 100%. The Acustar HIT‐IgG assay showed a higher specificity compared with the HIT‐Ab assay (85%vs. 73%), using the manufacturer’s cutoffs. Specificities of all assays, except for the AcuStar HIT‐IgG, could be significantly improved when altering the cutoff. Titers were significantly higher for the HIT‐Ab assay compared with the HIT‐IgG assay (P = 0.0001). This was also the case for the patients with confirmed HIT (P = 0.0495), indicating that the one cutoff (1.0 OD) for both Acustar assays, as proposed by the manufacturer, can be adapted for the AcuStar Hit‐Ab assay resulting in an increased specificity.

Conclusion:  Performance characteristics of the Acustar HIT‐IgG and HIT‐Ab assay are comparable to the Zymutest HIA IgG and HIA IgGAM.
Experience of child and adolescent mental health clinicians working within an at‐risk mental state for psychosis service: a qualitative study
Authors: Welsh Patrick , Tiffin Paul A.
Published: March 2012

Aim: To qualitatively examine the common experiences of child and adolescent mental health clinicians working with adolescents suspected of having an ‘at‐risk mental state’ (ARMS) for psychosis.

Methods: A semistructured interview was conducted with six experienced child and adolescent mental health clinicians working in North East England.

Results: A thematic analysis of clinicians' experiences indicated that the identification and management of an ARMS within this patient group is particularly complex. In terms of treatment options, approaches that promoted social inclusion were favoured, but the use of antipsychotic medication was perceived as a ‘last resort’, requiring serious consideration. Clear guidelines and an overall consensus were judged to be lacking in terms of coordinating care and multi‐agency working practices.

Conclusions: Establishing a formalized care pathway that also incorporates regular training and supervision may be required by this and other clinical services working with adolescents suspected of having an ARMS. Improved identification, a firmer evidence base regarding treatment practices and clear guidelines are required for this age group. This need will become more urgent should a psychosis risk syndrome be included as a diagnostic category in the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM‐V).
Genetic structure of a giant honey bee (Apis dorsata) population in northern Thailand: implications for conservation
Authors: RATTANAWANNEE ATSALEK , CHANCHAO CHANPEN , LIM JULIANNE , WONGSIRI SIRIWAT , OLDROYD BENJAMIN P.
Published: March 2012

Abstract.  1. The giant honey bee, Apis dorsata, is a keystone pollinator. The species is heavily hunted throughout Thailand. Furthermore, forest clearing, widespread use of pesticides and proliferation of street lighting (which attracts bees, often resulting in their death) are likely to have significant impacts on population viability.

2. We examined the relatedness and genetic variation within and between aggregations of A. dorsata nests. Microsatellite analysis of 54 nests in three aggregations showed that no colonies were related as mother–daughter. Thus, if reproduction occurred at our study sites, daughter colonies dispersed. This suggests that rapid increases in A. dorsata colony numbers during general flowering events most likely occur by swarms arriving from other areas rather than by in situ reproduction.

3. The population has high levels of heterozygosity. Fst values between aggregations were not significantly different from zero (P > 0.05). This suggests that despite the formidable anthropogenic pressures that the A. dorsata population endures in northern Thailand, the species continues to enjoy a large effective population size and has high connectedness.

4. We conclude that A. dorsata is currently able to tolerate habitat fragmentation and annual harvesting. We speculate that the population is sustained by immigration from forested regions to the northwest of our study sites in Burma.
The value of positron emission tomography in early detection of lung cancer in high‐risk population: a systematic review
Authors: Chang Cheng‐Yu , Chang Shu‐Ju , Chang Shih‐Chieh , Yuan Mei‐Kang
Published: March 2012

Background:  Early detection trials with chest radiography and sputum cytology were ineffective in decreasing lung cancer mortality. The advent of low‐dose spiral chest computed tomography (LDCT) provided clinicians with a new tool that could be with early diagnosis; however, this also raised significant concerns regarding the systematic use of LDCT with its high false‐positive rate for benign nodules. At this time, there is limited information about the true role of PET (positron emission tomography) for early detection of lung cancer.

Methods:  We used systematic methods, including Preferred Reporting Items for Systematic reviews and Meta‐Analyses statement, to identify relevant studies, assess study eligibility, evaluate study methodological quality, and summarize findings regarding diagnostic accuracy and outcome.

Results:  In total, only seven eligible studies were selected from 82 potentially relevant studies. The sensitivity of 18F‐FDG‐PET for the detection of T1 lung cancers ranged between 68% and 95%. The rate of detection tended to be lower for carcinoid tumors, adenocarcinoma and bronchoalveolar cell carcinomas. FDG‐PET using SUV (standardized uptake value) level can predict the outcome of the screening detected lung cancer. A combination of FDG‐PET and LDCT may improve screening for lung cancer in high‐risk patients.

Conclusions:  PET or PET/CT may be used as a useful tool for early detection of lung cancer in high‐risk population based on the existing information. However, there is still limited information with regards to evidence of survival benefits from PET screening in high‐risk patients.

Please cite this paper as: Chang C‐Y, Chang S‐J, Chang S‐C and Yuan M‐K. The value of positron emission tomography in early detection of lung cancer in high‐risk population: a systematic review. Clin Respir J 2013; 7: 1–6.
Prevention of hepatitis B virus reactivation in patients receiving immunosuppressive therapy or chemotherapy
Authors: Oketani Makoto , Ido Akio , Uto Hirofumi , Tsubouchi Hirohito
Published: March 2012

With the increasing use of potent immunosuppressive therapy, reactivation of hepatitis B virus (HBV) in endemic regions is becoming a clinical problem requiring special attention. A recent annual nationwide survey clarified that HBV reactivation related to immunosuppressive therapy has been increasing in patients with malignant lymphoma, other hematological malignancies, oncological or rheumatological disease. In the survey, rituximab plus steroid‐containing chemotherapy was identified as a risk factor for HBV reactivation in hepatitis B surface antigen (HBsAg) negative patients with malignant lymphoma. In this setting, HBV reactivation resulted in fatal fulminant hepatitis regardless of the treatment of nucleoside analog. The Intractable Hepatobiliary Disease Study Group and the Study Group for the Standardization of Treatment of Viral Hepatitis Including Cirrhosis jointly developed guidelines for preventing HBV reactivation. The essential features of the guideline are as follows. All patients should be screened for HBsAg by a sensitive method before the start of immunosuppressive therapy. Second, hepatitis B core antigen (HBcAb) and hepatitis B surface antibody (HBsAb) testing should be performed in HBsAg negative patients, especially those receiving intensive immunosuppressive therapy. Prophylaxis with nucleoside analogs is essential for preventing HBV reactivation in HBsAg positive patients. In contrast, HBsAg negative with HBcAb and/or HBsAb positive patients should be monitored monthly for an increase in serum HBV DNA during and 12 months after completion of chemotherapy. Nucleoside analogs should be administrated immediately when HBV DNA becomes positive during this period. This strategy facilitates commencement of nucleoside analogs at an early stage of HBV reactivation and results in prevention of severe hepatitis.
Cistanche deserticola extract increases bone formation in osteoblasts
Authors: Li Te-Mao , Huang Hsin-Chih , Su Chen-Ming , Ho Tin-Yun , Wu Chi-Ming , Chen Wen-Chi , Fong Yi-Chin , Tang Chih-Hsin
Published: March 2012

Objectives

We investigated the effect of Cistanche deserticola Ma. (CD) on bone formation by cultured osteoblasts.

Methods

The mineralized nodule formation assay was used to examine the in-vitro effects of CD on bone formation. Alkaline phosphatase (ALP), bone morphogenetic proteins (BMP)-2 and osteopontin (OPN) mRNA expression was analysed by quantitative real-time polymerase chain reaction. The mechanism of action of CD extract was investigated using Western blotting. The in-vivo anti-osteoporotic effect of CD extract was assessed in ovariectomized mice.

Key findings

CD extract had no effect on the proliferation, migration or wound healing of cultured osteoblasts, but increased ALP, BMP-2 and OPN mRNA and bone mineralization. Mitogen-activated protein kinase (MAPK) or nuclear factor (NF)-κB inhibitors reduced CD extract-induced bone formation and ALP, BMP-2 and OPN expression. However, CD extract did not affect osteoclastogenesis. In addition, CD extract prevented the bone loss induced by ovariectomy in vivo.

Conclusions

CD may be a novel bone formation agent for the treatment of osteoporosis.
A review of the medication pathway in rural Queensland, Australia
Authors: Tan Amy Chen Wee , Emmerton Lynne , Hattingh Hendrika Laetitia
Published: March 2012

Objectives

It is well established that rural areas have compromised access to health services, including medication services. This paper reviews the practice developments for rural health professionals in relation to medication processes, with a focus on regulatory provisions in Queensland, Australia, and a view to identifying opportunities for enhanced pharmacy involvement.

Methods

Literature referring to ‘medication/medicine’, ‘rural/remote’, ‘Australia’ and ‘pharmacy/pharmacist/pharmaceutical’ was identified via EBSCOhost, Ovid, Informit, Pubmed, Embase and The Cochrane Library. Australian Government reports and conference proceedings were sourced from relevant websites. Legislative and policy documents reviewed include drugs and poisons legislation, the National Medicines Policy and the Australian Pharmaceutical Advisory Council guidelines.

Key findings

The following developments enhance access to medication services in rural Queensland: (1) endorsement of various non-medical prescribers, (2) authorisation of registered nurses, midwives, paramedics and Indigenous health workers to supply medications in sites without pharmacists, (3) skill-mixing of nursing staff in rural areas to ease medication administration tasks, (4) establishment of pharmacist-mediated medication review services, (5) electronic transfer of medical orders or prescriptions and (6) enhanced transfer of medication information between metropolitan and rural, and public and private facilities.

Conclusions

This review identified a divide between medication access and medication management services. Initiatives aiming to improve supply of (access to) medications focus on scopes of practice and endorsements for non-pharmacist rural healthcare providers. Medication management remains the domain of pharmacists, and is less well addressed by current initiatives. Pharmacists' involvement in rural communities could be enhanced through tele-pharmacy, outreach support and sessional support.
Respiratory motion sampling in 4DCT reconstruction for radiotherapy
Authors: Chi Yuwei , Liang Jian , Qin Xu , Yan Di
Published: March 2012

Purpose:

Phase‐based and amplitude‐based sorting techniques are commonly used in four‐dimensional CT (4DCT) reconstruction. However, effect of these sorting techniques on 4D dose calculation has not been explored. In this study, the authors investigated a candidate 4DCT sorting technique by comparing its 4D dose calculation accuracy with that for phase‐based and amplitude‐based sorting techniques.

Method:

An optimization model was formed using organ motion probability density function (PDF) in the 4D dose convolution. The objective function for optimization was defined as the maximum difference between the expected 4D dose in organ of interest and the 4D dose calculated using a 4DCT sorted by a candidate sampling method. Sorting samples, as optimization variables, were selected on the respiratory motion PDF assessed during the CT scanning. Breathing curves obtained from patients' 4DCT scanning, as well as 3D dose distribution from treatment planning, were used in the study. Given the objective function, a residual error analysis was performed, and k‐means clustering was found to be an effective sampling scheme to improve the 4D dose calculation accuracy and independent with the patient‐specific dose distribution.

Results:

Patient data analysis demonstrated that the k‐means sampling was superior to the conventional phase‐based and amplitude‐based sorting and comparable to the optimal sampling results. For phase‐based sorting, the residual error in 4D dose calculations may not be further reduced to an acceptable accuracy after a certain number of phases, while for amplitude‐based sorting, k‐means sampling, and the optimal sampling, the residual error in 4D dose calculations decreased rapidly as the number of 4DCT phases increased to 6.

Conclusion:

An innovative phase sorting method (k‐means method) is presented in this study. The method is dependent only on tumor motion PDF. It could provide a way to refine the phase sorting in 4DCT reconstruction and is effective for 4D dose accumulation. Optimized sorting techniques could achieve acceptable residuals (less than 0.5% of the prescription dose) using 6 sorting samples, which is much better than amplitude‐based or phase‐based sorting. Further increase in sorting phase number exceeding 6 or more may not be necessary when using the k‐means sampling or optimal sampling points.
Nuclear Fuel in a Reactor Accident
Authors: Burns Peter C. , Ewing Rodney C. , Navrotsky Alexandra
Published: March 2012

Mechanics of a Meltdown

For all the potential hazards presented by nuclear power plants, there have been very few incidents that have caused human or environmental harm. However, those that have happened have often had disastrous consequences, for example, the accidents at Chernobyl in Ukraine and, just last year, at Fukushima Daiichi in Japan.

Burns
et al.

(p.
1184
; see the cover) review the state of knowledge on the chemical and physical processes following the nuclear reactor accident and how these results may inform decision-making during future events. Because a large portion of prior research has focused on radionuclide transport following leaks from nuclear waste repositories, and not active reactors, experiments at the more extreme conditions experienced in major nuclear core-melt accidents may have more predictive value.
Atomic View of a Toxic Amyloid Small Oligomer
Authors: Laganowsky Arthur , Liu Cong , Sawaya Michael R. , Whitelegge Julian P. , Park Jiyong , Zhao Minglei , Pensalfini Anna , Soriaga Angela B. , Landau Meytal , Teng Poh K. , Cascio Duilio , Glabe Charles , Eisenberg David
Published: March 2012

A Toxic Barrel

Many studies have suggested that oligomers are an important toxic species in amyloid diseases such as Alzheimer's disease. In an effort to better define these oligomers,

Laganowsky
et al.

(p.
1228
) identified a segment of the fibril-forming protein αB crystalline (ABC) that forms both amyloid fibrils and a relatively stable oligomer. ABC oligomers were toxic in a cell viability assay and were recognized by an amyloid-oligomer–specific antibody. A crystal structure of the oligomers showed that six peptides formed an antiparallel barrel termed a cylindrin. Amyloid oligomers are likely to be structurally polymorphic, but cylindrin-like assemblies offer a model for these elusive structures.
Natural SIV Hosts: Showing AIDS the Door
Authors: Chahroudi Ann , Bosinger Steven E. , Vanderford Thomas H. , Paiardini Mirko , Silvestri Guido
Published: March 2012

Lessons from SIV

HIV infection in humans is a chronic infection and, if left untreated, the majority of infected individuals will succumb to AIDS. Many species of African nonhuman primates are chronically infected with simian immunodeficiency virus (SIV); however, in the majority of these species, the animals remain healthy despite the presence of high viral loads.

Chahroudi
et al.

(p.
1188
) review the underlying immune mechanisms that help protect natural hosts from progressing to AIDS and how these responses differ from what is observed in HIV-infected humans and SIV-infected nonhuman primate species that develop AIDS.
Nucleosomes Suppress Spontaneous Mutations Base-Specifically in Eukaryotes
Authors: Chen Xiaoshu , Chen Zhidong , Chen Han , Su Zhijian , Yang Jianfeng , Lin Fangqin , Shi Suhua , He Xionglei
Published: March 2012

Nucleosome Maps and Mutation

Understanding the processes governing the accumulation of mutations impacts many facets of evolutionary biology. Combining data from a mutation accumulation experiment in a DNA repair-deficient yeast strain with genome-wide substitution,

Chen
et al.

(p.
1235
) demonstrate that C/G to T/A changes are more likely to affect regions that are nucleosome-free. Furthermore, a similar pattern was seen when comparative analyses were performed among yeast species and in lines of Medaka fish and nematodes. The results are consistent with a model in which DNA bound by nucleosomes is protected against mutations caused by DNA damage.
Comment on “Fossilized Nuclei and Germination Structures Identify Ediacaran ‘Animal Embryos’ as Encysting Protists”
Authors: Xiao Shuhai , Knoll Andrew H. , Schiffbauer James D. , Zhou Chuanming , Yuan Xunlai
Published: March 2012

On the basis of putative nuclei and endospores, Huldtgren
et al
. (Reports, 23 December 2011, p. 1696) propose that embryo-like Doushantuo microfossils are nonmetazoan holozoans akin to mesomycetozoeans. However, both size and preservation preclude interpretation of internal structures as nuclei. Moreover, the authors may have conflated two different populations; some specimens display a pseudoparenchymatous organization incompatible with a mesomycetozoean comparison.
Swell Approaches for Changing Polymer Shapes
Authors: Sharon Eran
Published: March 2012

Patterning of cross-linked regions in polymer gel sheets with ultraviolet light creates unequal stresses and drives their buckling into complex three-dimensional shapes.
Response to Comment on “Fossilized Nuclei and Germination Structures Identify Ediacaran ‘Animal Embryos’ as Encysting Protists”
Authors: Huldtgren Therese , Cunningham John A. , Yin Chongyu , Stampanoni Marco , Marone Federica , Donoghue Philip C. J. , Bengtson Stefan
Published: March 2012

The objections of Xiao
et al
. to our reinterpretation are based on incorrect assumptions. The lack of nanocrystals lining the nuclear membrane is consistent with membrane fossilization, and nucleus volume through development is correlated to cytoplasm volume and fully consistent with sizes of eukaryote nuclei. Identical envelope structure unites the developmental stages of the fossils, and 2

n

cleavage and Y-shaped junctions are holozoan symplesiomorphies.
Youth Culture in the Adult Brain
Authors: Kempermann Gerd
Published: March 2012

Differences in information processing between older and newly born neurons are observed in the mammalian hippocampus.
Roy J. Britten (1919–2012)
Authors: Davidson Eric H.
Published: March 2012

A molecular biologist founded fundamental concepts in DNA sequence organization and gene expression that underlie modern genomics and genome evolution.
Last Hurrah: Final Tevatron Data Show Hints of Higgs Boson
Authors: Cho Adrian
Published: March 2012

This week, scientists working with an atom smasher called the Tevatron, which shut down in September 2011, reported that, having analyzed all the data they'll ever get, they see hints of the Higgs boson.
Extraordinary Eyes
Authors: Pennisi Elizabeth
Published: March 2012

The mantis shrimp's compound eyes, which are on stalks, are part of a complex visual system. They constantly scan back and forth, taking in the scene and building up an image line by line.
Radioactive Limbo
Authors: Normile Dennis
Published: March 2012

While the tsunami-ravaged Tohoku region plans its recovery (
see main text
), contaminated areas around the Fukushima Daiichi power plant are a no-man's land that may remain deserted for decades.
Nuclear Ambivalence No More?
Authors: Normile Dennis
Published: March 2012

The crisis at Fukushima Daiichi nuclear power plant that riveted the world last spring has had a potent effect on the industry's future.
Risk of Invasive Haemophilus influenzae Type b (Hib) Disease in Adults with Secondary Immunodeficiency in the Post-Hib Vaccine Era
Authors: Nix Eli B. , Hawdon Nicole , Gravelle Sean , Biman Birubi , Brigden Malcolm , Malik Saleem , McCready William , Ferroni Garry , Ulanova Marina
Published: March 2012

Prior to the introduction ofHaemophilus influenzaetype b (Hib) conjugate vaccines, invasive Hib disease affected almost exclusively children. According to some recent studies, in the postvaccine era, adults, the elderly, and immunocompromised persons can be affected more often than children. As the production of type-specific anti-capsular polysaccharide antibodies is the major defense mechanism against Hib, individuals with defects in humoral immune responses have high susceptibility to infections caused by Hib. We hypothesized that nonvaccinated adults with chronic conditions causing immunosuppression may lack protective antibody to Hib. We assessed serum anti-Hib IgG levels and bactericidal activity in 59 patients with chronic renal failure, 30 patients with type 2 diabetes mellitus, 28 patients with chronic obstructive pulmonary disease (COPD), and 20 patients with multiple myeloma compared to 32 healthy controls of similar age. Considering antibody at >0.15 μg/ml as the protective correlate in unvaccinated individuals, we detected subprotective Hib antibody levels in 29% of chronic renal failure, 20% of diabetes, 14% of COPD, and 55% of myeloma patients compared to 3% of healthy controls. Additionally, 70% of myeloma and 58% of chronic renal failure patients did not have detectable serum bactericidal activity against Hib. Among individuals with severe diseases causing secondary immunodeficiency, patients with multiple myeloma and chronic renal failure are at an increased risk of invasive Hib disease. Considering that Hib continues to circulate in the population, this study provides a rationale for the immunization of some adult patients with secondary immunodeficiency with the pediatric Hib vaccine to achieve protective immunity.
Fecal Carriage of Carbapenemase-Producing Enterobacteriaceae: a Hidden Reservoir in Hospitalized and Nonhospitalized Patients
Authors: Gijón Desirèe , Curiao Tânia , Baquero Fernando , Coque Teresa M. , Cantón Rafael
Published: March 2012

Fecal carriage of carbapenemase-producing
Enterobacteriaceae
(CPE) has not been extensively investigated, except in the cases of selected patients at risk, mostly during outbreaks. A total of 1,100 fecal samples randomly collected in our institution in two different periods in 2006 (
n
= 600) and 2009–2010 (
n
= 500) from hospitalized (26.8%) and nonhospitalized (73.2%) patients were screened for CPE. The first period coincided with an outbreak of VIM-1-producing
Enterobacteriaceae
, and the second one coincided with the emergence of KPC enzymes in our hospital. Diluted samples in saline were cultured in Luria-Bertani broth with 1 μg/ml imipenem and subcultured in MacConkey agar plates with 4 μg/ml ceftazidime. Growing colonies were screened for CPE (modified Hodge test and EDTA and boronic acid synergy tests). Carbapenemase genes, plasmids in which they are located, and clonal relatedness were determined. Individuals who exhibited fecal carriage of CPE (11/1,043, 1.1%; 95% confidence interval [CI], 0.53 to 1.88) included 8 hospitalized (carriage rate, 2.9%; 95% CI, 1.24 to 5.55) and 3 nonhospitalized patients (carriage rate, 0.4%; 95% CI, 0.08 to 1.14), the latter being identified in 2009. Eighty-two percent of colonized patients were not infected with CPE. Isolates harboring
bla
VIM-1
with or without
bla
SHV-12
were identified as
Klebsiella pneumoniae
(
n
= 8; ST39, ST688, ST253, and ST163),
Enterobacter cloacae
(
n
= 3; two pulsed-field gel electrophoresis [PFGE] types),
Escherichia coli
(
n
= 2; ST155 and ST2441), and
Citrobacter freundii
(
n
= 1). Some of these lineages had previously been detected in our institution. The
bla
VIM-1
gene was a member of the class 1 integrons In110 (
bla
VIM-1
-
aacA4-aadA1
) and In113 (
bla
VIM-1
-
aacA4-dhfrII
) located on plasmids IncN (
n
= 11; 30 to 50 kb) and IncHI2 (
n
= 3; 300 kb), respectively. Dissemination of
bla
VIM-1
class-1 integrons within highly transferable plasmids in a polyclonal population has potentially contributed to the maintenance and spread of CPE.
Evaluation of the GenBank, EzTaxon, and BIBI Services for Molecular Identification of Clinical Blood Culture Isolates That Were Unidentifiable or Misidentified by Conventional Methods
Authors: Park Kyung Sun , Ki Chang-Seok , Kang Cheol-In , Kim Yae-Jean , Chung Doo Ryeon , Peck Kyong Ran , Song Jae-Hoon , Lee Nam Yong
Published: March 2012

We compared the 16S rRNA gene sequencing results analyzed with the GenBank, EzTaxon, and BIBI databases for blood culture specimens for which identifications were incomplete, conflicting, or unidentifiable using conventional methods. Analyses performed using GenBank combined with EzTaxon (kappa = 0.79) were more discriminative than those using other databases alone or in combination with a second database.
Multicytokine Detection Improves Latent Tuberculosis Diagnosis in Health Care Workers
Authors: Rubbo Pierre-Alain , Nagot Nicolas , Le Moing Vincent , Brabet Marylène , Bourdin Arnaud , Nogué Erika , Bolloré Karine , Vendrell Jean-Pierre , Van De Perre Philippe , Tuaillon Edouard
Published: March 2012

In a low-incidence setting, health care workers (HCW) are at a higher risk of tuberculosis than the general population. The suboptimal sensitivity of the QuantiFERON-TB Gold In-Tube (QFT) test remains a critical issue when identifying occupational latent tuberculosis infection (LTBI) in HCW. The aim of this study was to identify additional biomarkers in order to overcome the limits of gamma interferon (IFN-γ) release assays (IGRAs) and improve the performance of LTBI diagnosis within this population. Seventy Bacille Calmette-Guérin-vaccinated HCW regularly exposed toMycobacterium tuberculosiswere grouped according to QFT results into an LTBI-positive group (positive QFT,n= 8), an LTBI-negative group (normal QFT and negative tuberculin skin test [TST],n= 21), and an undetermined group (subpositive QFT and/or positive TST,n= 41). The secretion of 22 cytokines in response to QFT-specific stimulation was quantified using a multiparameter-based immunoassay. As a result, thresholds discriminating LTBI-positive from LTBI-negative HCW were established by comparing areas under the receiver operating characteristic curves for interleukin-2 (IL-2), IL-15, IFN-γ-induced protein 10 (IP-10), and the monokine induced by IFN-γ (MIG), which are biomarkers differentially secreted by the two groups. The combination of IL-15 and MIG provided a sensitivity of 100% and a specificity of 94.1% in distinguishing LTBI-positive from LTBI-negative HCW. When using IL-15 and MIG among the undetermined group, 6/45 HCW could be classified in the LTBI-positive group. The use of additional biomarkers after IGRA screening could improve the diagnosis of LTBI. The performance of these biomarkers and their use in combination with TST and/or QFT, as well as the cost-effectiveness of such a diagnostic strategy, should be evaluated in further larger clinical trials.
Simultaneously High Prevalences of Hepatitis B and C Virus Infections in a Population in Putian County, China
Authors: Lu Wen-Ping , Lin Guo-Xian , Shi Shuang , Dong Jia-Hong
Published: March 2012

This study investigated a rare area of endemicity with a high prevalence of both hepatitis B virus (HBV) and hepatitis C virus (HCV) infections, in Putian County, China. Among 1,050 subjects, the overall prevalence of HBsAg seropositivity was 15.8%, and that of anti-HCV seropositivity was 28.9%. Intrafamilial viral transmission might be the major cause of the high prevalence of HBV infection in this region. However, HCV infection was shown to be associated with the use of inadequately sterilized medical equipment.
Real-Time PCR Assay for Identification of Blastomyces dermatitidis in Culture and in Tissue
Authors: Sidamonidze Ketevan , Peck Marcia K. , Perez Michael , Baumgardner Dennis , Smith Gerald , Chaturvedi Vishnu , Chaturvedi Sudha
Published: March 2012

The TaqMan real-time PCR assay was developed from theBlastomyces dermatitidis BAD1gene promoter. The assay identified all haplotypes ofB. dermatitidisand five of six positive paraffin-embedded tissues. The assay sensitivity threshold was 1 pg genomic DNA of the mold form and 2 CFU of the yeast form ofB. dermatitidis. No cross-reactivity was observed against other fungal DNA. The assay allowed rapid (5-h) identification ofB. dermatitidisfrom culture and from clinical specimens.
Analysis of Transmitted Resistance to Raltegravir and Selective Pressure among HIV-1-Infected Patients on a Failing HAART in São Paulo, Brazil
Authors: Mantovani N. P. , Azevedo R. G. , Rabelato J. T. , Sanabani S. , Diaz R. S. , Komninakis S. V.
Published: March 2012

We studied the presence of primary resistance to raltegravir (RAL), natural polymorphisms, and selection pressure on HIV-1 integrase. We found a high frequency of integrase polymorphisms related to the resistance to RAL and sequence stability. Further studies are needed to determine the importance of these polymorphisms to RAL resistance.
Incidence of Recent Human Immunodeficiency Virus Infection at Two Voluntary Counseling Testing Centers in Pernambuco, Brazil, from 2006 to 2009
Authors: de Lima Kledoaldo Oliveira , Salustiano Daniela Medeiros , Coêlho Maria Rosângela Cunha Duarte , Cavalcanti Ana Maria Salustiano , Diaz Ricardo Sobhie , Lacerda Heloísa Ramos
Published: March 2012

This study shows HIV-1 incidence in the northeastern region of Brazil, where the HIV epidemic has spread recently. Incidence was higher among men (1.34%; 95% confidence interval [CI], 1.00% to 1.69%) than among women (0.55%; 95% CI, 0.43% to 0.68%) (
P
< 0.0001), and there was an association between younger age and recent HIV infection (
P
< 0.004).
Performance of the Novel QiagenartusQS-RGQ Viral Load Assays Compared to That of the Abbott RealTime System with Genetically Diversified HIV and Hepatitis C Virus Plasma Specimens
Authors: Drexler Jan Felix , Reber Ulrike , Wuttkopf Andrea , Eis-Hübinger Anna Maria , Drosten Christian
Published: March 2012

We compared two novel Qiagen QS-RGQ viral load assays with the established Abbott RealTime assays on a highly diversified panel of 121 human immunodeficiency virus (HIV) and 107 hepatitis C virus (HCV) specimens. The quantifications correlated well for all HIV and HCV types, but Qiagen yielded higher HCV concentrations than Abbott, predominantly in genotypes 4 and 5.
A Novel δ-Hemolysis Screening Method for Detecting Heteroresistant Vancomycin-Intermediate Staphylococcus aureus and Vancomycin-Intermediate S. aureus
Authors: Cafiso V. , Bertuccio T. , Spina D. , Purrello S. , Blandino G. , Stefani Stefania
Published: March 2012

We assessed a new screening method, based on δ-hemolysin production in the presence of 6 mg/liter vancomycin, to distinguish heteroresistant vancomycin-intermediate
Staphylococcus aureus
(hVISA) and vancomycin-intermediate
S. aureus
(VISA) from vancomycin-susceptible
S. aureus
(VSSA). On 37 clinical methicillin-resistant
S. aureus
(MRSA) isolates, hVISA and VISA displayed no δ-hemolysis whereas VSSA displayed strong δ-hemolysis, showing 91.6% sensitivity. These data, supported by real-time reverse transcription PCR (real-time RT-PCR) highlighting an
hld
downregulation, i.e., VSSA>hVISA>VISA, define this new assay as a valid screening method.
Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry Analysis of Gram-Positive, Catalase-Negative Cocci Not Belonging to the Streptococcus or Enterococcus Genus and Benefits of Database Extension
Authors: Christensen Jens Jørgen , Dargis Rimtas , Hammer Monja , Justesen Ulrik Stenz , Nielsen Xiaohui C. , Kemp Michael ,   The Danish MALDI-TOF MS Study Group
Published: March 2012

Matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry with a Bruker Daltonics microflex LT system was applied to 90 well-characterized catalase-negative, Gram-positive cocci not belonging to the streptococci or enterococci. Biotyper version 2.0.43.1 software was used singly or in combination with a database extension generated in this study with 51 collection strains from 16 genera. Most strains were identified by using both databases individually, and some were identified only by applying the combined database. Thus, the methodology is very useful and the generated database extension was helpful.
Automating HIV Drug Resistance Genotyping with RECall, a Freely Accessible Sequence Analysis Tool
Authors: Woods Conan K. , Brumme Chanson J. , Liu Tommy F. , Chui Celia K. S. , Chu Anna L. , Wynhoven Brian , Hall Tom A. , Trevino Christina , Shafer Robert W. , Harrigan P. Richard
Published: March 2012

Genotypic HIV drug resistance testing is routinely used to guide clinical decisions. While genotyping methods can be standardized, a slow, labor-intensive, and subjective manual sequence interpretation step is required. We therefore performed external validation of our custom software RECall, a fully automated sequence analysis pipeline. HIV-1 drug resistance genotyping was performed on 981 clinical samples at the Stanford Diagnostic Virology Laboratory. Sequencing trace files were first interpreted manually by a laboratory technician and subsequently reanalyzed by RECall, without intervention. The relative performances of the two methods were assessed by determination of the concordance of nucleotide base calls, identification of key resistance-associated substitutions, and HIV drug resistance susceptibility scoring by the Stanford Sierra algorithm. RECall is freely available athttp://pssm.cfenet.ubc.ca. In total, 875 of 981 sequences were analyzed by both human and RECall interpretation. RECall analysis required minimal hands-on time and resulted in a 25-fold improvement in processing speed (∼150 technician-hours versus ∼6 computation-hours). Excellent concordance was obtained between human and automated RECall interpretation (99.7% agreement for >1,000,000 bases compared). Nearly all discordances (99.4%) were due to nucleotide mixtures being called by one method but not the other. Similarly, 98.6% of key antiretroviral resistance-associated mutations observed were identified by both methods, resulting in 98.5% concordance of resistance susceptibility interpretations. This automated sequence analysis tool provides both standardization of analysis and a significant improvement in data workflow. The time-consuming, error-prone, and dreadfully boring manual sequence analysis step is replaced with a fully automated system without compromising the accuracy of reported HIV drug resistance data.
Complete Genome Sequence of Porcine Reproductive and Respiratory Syndrome Virus Isolated from Piglet Stool Samples
Authors: Song Tao , Fang Liurong , Zeng Songlin , Li Bin , Chen Huanchun , Xiao Shaobo
Published: March 2012

WUH4 is a highly pathogenic North American porcine reproductive and respiratory syndrome virus (PRRSV). Unlike previous PRRSV isolates, which were mainly recovered from sera or tissues, WUH4 was isolated from a piglet stool sample. Here we announce its complete genome sequence.
SUMO Binding by the Epstein-Barr Virus Protein Kinase BGLF4 Is Crucial for BGLF4 Function
Authors: Li Renfeng , Wang Leyao , Liao Gangling , Guzzo Catherine M. , Matunis Michael J. , Zhu Heng , Hayward S. Diane
Published: March 2012

An Epstein-Barr virus (EBV) protein microarray was used to screen for proteins binding noncovalently to the small ubiquitin-like modifier SUMO2. Among the 11 SUMO binding proteins identified was the conserved protein kinase BGLF4. The mutation of potential SUMO interaction motifs (SIMs) in BGLF4 identified N- and C-terminal SIMs. The mutation of both SIMs changed the intracellular localization of BGLF4 from nuclear to cytoplasmic, while BGLF4 mutated in the N-terminal SIM remained predominantly nuclear. The mutation of the C-terminal SIM yielded an intermediate phenotype with nuclear and cytoplasmic staining. The transfer of BGLF4 amino acids 342 to 359 to a nuclear green fluorescent protein (GFP)-tagged reporter protein led to the relocalization of the reporter to the cytoplasm. Thus, the C-terminal SIM lies adjacent to a nuclear export signal, and coordinated SUMO binding by the N- and C-terminal SIMs blocks export and allows the nuclear accumulation of BGLF4. The mutation of either SIM prevented SUMO bindingin vitro. The ability of BGLF4 to abolish the SUMOylation of the EBV lytic cycle transactivator ZTA was dependent on both BGLF4 SUMO binding and BGLF4 kinase activity. The global profile of SUMOylated cell proteins was also suppressed by BGLF4 but not by the SIM or kinase-dead BGLF4 mutant. The effective BGLF4-mediated dispersion of promyelocytic leukemia (PML) bodies was dependent on SUMO binding. The SUMO binding function of BGLF4 was also required to induce the cellular DNA damage response and to enhance the production of extracellular virus during EBV lytic replication. Thus, SUMO binding by BGLF4 modulates BGLF4 function and affects the efficiency of lytic EBV replication.
Anti-Tetherin Activities of HIV-1 Vpu and Ebola Virus Glycoprotein Do Not Involve Removal of Tetherin from Lipid Rafts
Authors: Lopez Lisa A. , Yang Su Jung , Exline Colin M. , Rengarajan Srinivas , Haworth Kevin G. , Cannon Paula M.
Published: March 2012

BST-2/tetherin is an interferon-inducible host restriction factor that blocks the release of newly formed enveloped viruses. It is enriched in lipid raft membrane microdomains, which are also the sites of assembly of several enveloped viruses. Viral anti-tetherin factors, such as the HIV-1 Vpu protein, typically act by removing tetherin from the cell surface. In contrast, the Ebola virus glycoprotein (GP) is unusual in that it blocks tetherin restriction without apparently altering its cell surface localization. We explored the possibility that GP acts to exclude tetherin from the specific sites of virus assembly without overtly removing it from the cell surface and that lipid raft exclusion is the mechanism involved. However, we found that neither GP nor Vpu had any effect on tetherin's distribution within lipid raft domains. Furthermore, GP did not prevent the colocalization of tetherin and budding viral particles. Contrary to previous reports, we also found no evidence that GP is itself a raft protein. Together, our data indicate that the exclusion of tetherin from lipid rafts is not the mechanism used by either HIV-1 Vpu or Ebola virus GP to counteract tetherin restriction.
Generation of an HIV-1-Resistant Immune System with CD34
+
Hematopoietic Stem Cells Transduced with a Triple-Combination Anti-HIV Lentiviral Vector
Authors: Walker Jon E. , Chen Rachel X. , McGee Jeannine , Nacey Catherine , Pollard Richard B. , Abedi Mehrdad , Bauer Gerhard , Nolta Jan A. , Anderson Joseph S.
Published: March 2012

HIV gene therapy has the potential to offer an alternative to the use of current small-molecule antiretroviral drugs as a treatment strategy for HIV-infected individuals. Therapies designed to administer HIV-resistant stem cells to an infected patient may also provide a functional cure, as observed in a bone marrow transplant performed with hematopoietic stem cells (HSCs) homozygous for the CCR5-Δ32-bp allele. In our current studies, preclinical evaluation of a combination anti-HIV lentiviral vector was performed,
in vivo
, in humanized NOD-RAG1
−/−
IL2rγ
−/−
knockout mice. This combination vector, which displays strong preintegration inhibition of HIV-1 infection
in vitro
, contains a human/rhesus macaque TRIM5α isoform, a CCR5 short hairpin RNA (shRNA), and a TAR decoy. Multilineage hematopoiesis from anti-HIV lentiviral vector-transduced human CD34
+
HSCs was observed in the peripheral blood and in various lymphoid organs, including the thymus, spleen, and bone marrow, of engrafted mice. Anti-HIV vector-transduced CD34
+
cells displayed normal development of immune cells, including T cells, B cells, and macrophages. The anti-HIV vector-transduced cells also displayed knockdown of cell surface CCR5 due to the expression of the CCR5 shRNA. After
in vivo
challenge with either an R5-tropic BaL-1 or X4-tropic NL4-3 strain of HIV-1, maintenance of human CD4
+
cell levels and a selective survival advantage of anti-HIV gene-modified cells were observed in engrafted mice. The data provided from our study confirm the safety and efficacy of this combination anti-HIV lentiviral vector in a hematopoietic stem cell gene therapy setting for HIV and validates its potential application in future clinical trials.
Recombinant Influenza A Viruses with Enhanced Levels of PB1 and PA Viral Protein Expression
Authors: Belicha-Villanueva Alan , Rodriguez-Madoz Juan R. , Maamary Jad , Baum Alina , Bernal-Rubio Dabeiba , Minguito de la Escalera Maria , Fernandez-Sesma Ana , García-Sastre Adolfo
Published: March 2012

Influenza A viruses containing the promoter mutations G3A/C8U in a given segment express increased levels of the corresponding viral protein during infection due to increased levels of mRNA or cRNA species. The replication of these recombinant viruses is attenuated, and they have an enhanced shedding of noninfectious particles and are incapable of antagonizing interferon (IFN) effectively. Our findings highlight the possibility of increasing influenza virus protein expression and the need for a delicate balance between influenza viral replication, protein expression, and assembly.
The Myristate Moiety and Amino Terminus of Vaccinia Virus L1 Constitute a Bipartite Functional Region Needed for Entry
Authors: Foo Chwan Hong , Whitbeck J. Charles , Ponce-de-León Manuel , Saw Wan Ting , Cohen Gary H. , Eisenberg Roselyn J.
Published: March 2012

Vaccinia virus (VACV) L1 is a myristoylated envelope protein which is required for cell entry and the fusion of infected cells. L1 associates with members of the entry-fusion complex (EFC), but its specific role in entry has not been delineated. We recently demonstrated (Foo CH, et al., Virology 385:368–382, 2009) that soluble L1 binds to cells and blocks entry, suggesting that L1 serves as the receptor-binding protein for entry. Our goal is to identify the structural domains of L1 which are essential for its functions in VACV entry. We hypothesized that the myristate and the conserved residues at the N terminus of L1 are critical for entry. To test our hypothesis, we generated mutants in the N terminus of L1 and used a complementation assay to evaluate their ability to rescue infectivity. We also assessed the myristoylation efficiency of the mutants and their ability to interact with the EFC. We found that the N terminus of L1 constitutes a region that is critical for the infectivity of VACV and for myristoylation. At the same time, the nonmyristoylated mutants were incorporated into mature virions, suggesting that the myristate is not required for the association of L1 with the viral membrane. Although some of the mutants exhibited altered structural conformations, two mutants with impaired infectivity were similar in conformation to wild-type L1. Importantly, these two mutants, with changes at A4 and A5, undergo myristoylation. Overall, our results imply dual differential roles for myristate and the amino acids at the N terminus of L1. We propose a myristoyl switch model to describe how L1 functions.