bluuebunny/crossref_metadata_2025_split huggingface dataset:
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.
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

ABSTRACTPrior 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

ABSTRACT

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

ABSTRACT
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

ABSTRACTIn 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

ABSTRACT
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

ABSTRACTThe 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

ABSTRACTWe 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

ABSTRACT

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

ABSTRACTWe 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

ABSTRACT

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

ABSTRACT
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

ABSTRACTGenotypic 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

ABSTRACT
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

ABSTRACTAn 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

ABSTRACT
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

ABSTRACT

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

ABSTRACT
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.