bluuebunny/crossref_metadata_2025_split huggingface dataset:
Toward truly combined PET/CT imaging using PET detectors and photon counting CT with iterative reconstruction implementing physical detector response
Authors: Thibaudeau Christian , Bérard Philippe , Tétrault Marc‐André , Leroux Jean‐Daniel , Bergeron Mélanie , Fontaine Réjean , Lecomte Roger 
Published: August 2012

Purpose:This paper intends to demonstrate the feasibility of truly combined PET/CT imaging and addresses some of the major challenges raised by this dual modality approach. A method is proposed to retrieve maximum accuracy out of limited resolution computed tomography (CT) scans acquired with positron emission tomography (PET) detectors.Methods:A PET/CT simulator was built using the LabPET™ detectors and front‐end electronics. Acquisitions of energy‐binned data sets were made using this low spatial resolution CT system in photon counting mode. To overcome the limitations of the filtered back‐projection technique, an iterative reconstruction library was developed and tested for the counting mode CT. Construction of the system matrix is based on a preregistered raster scan from which the experimental detector response is obtained. PET data were obtained sequentially with CT in a conventional manner.Results:A meticulous description of the system geometry and misalignment corrections is imperative and was incorporated into the matrix definition to achieve good image quality. Using this method, no sinogram precorrection or interpolation is necessary and measured projections can be used as raw input data for the iterative reconstruction algorithm. Genuine dual modality PET/CT images of phantoms and animals were obtained for the first time using the same detection platform.Conclusions:CT and fused PET/CT images show that LabPET™ detectors can be successfully used as individual X‐ray photon counting devices for low‐dose CT imaging of the anatomy in a molecular PET imaging context.
Ultrasound GLCM texture analysis of radiation‐induced parotid‐gland injury in head‐and‐neck cancer radiotherapy: An in vivo study of late toxicity
Authors: Yang Xiaofeng , Tridandapani Srini , Beitler Jonathan J. , Yu David S. , Yoshida Emi J. , Curran Walter J. , Liu Tian 
Published: August 2012

Purpose:Xerostomia (dry mouth), secondary to irradiation of the parotid glands, is one of the most common side effects of head‐and‐neck cancer radiotherapy. Diagnostic tools able to accurately and efficiently measure parotid gland injury have yet to be introduced into the clinic. This study's purpose is to investigate sonographic textural features as potential imaging signatures for quantitative assessment of parotid‐gland injury after head‐and‐neck radiotherapy.Methods:The authors have investigated a series of sonographic features obtained from the gray level co‐occurrence matrix (GLCM) – a second order statistical method of texture analysis. These GLCM textural features were selected based on empirical observations that the normal parotid gland exhibits homogeneous echotexture, whereas the postradiotherapy parotid gland often exhibits heterogeneous echotexture. We employed eight sonographic features: (1) angular second moment (ASM), (2) inverse differential moment (IDM), (3) contrast, (4) variance, (5) correlation, (6) entropy, (7) cluster shade, and (8) cluster prominence. Altogether, sonographic properties of the parotid glands were quantified by their degrees of homogeneity (ASM and IDM), heterogeneity (contrast and variance), smoothness (correlation), randomness (entropy), and symmetry (cluster shade and prominence). The sonographic features were tested in a pilot study of 12 postradiotherapy patients and 7 healthy volunteers. The mean follow‐up time for the postradiotherapy patients was 17.2 months (range: 12.1–23.9 months) and the mean radiation dose to the parotid glands was 32.3 Gy (range: 11.0–63.4 Gy). Each participant underwent one ultrasound study in which longitudinal (vertical) ultrasound scans were performed on the bilateral parotids – a total of 24 postirradiation and 14 normal parotid glands were examined. The 14 normal parotid glands served as the control group. A radiologist contoured the parotid glands on the B‐mode images and the sonographic features were computed from the contoured region‐of‐interest.Results:The authors observed significant differences (p < 0.05) in all sonographic features between the normal and postradiotherapy parotid glands. The sonographic findings were consistent with the clinical observations of the ultrasound images: normal parotid glands exhibited homogeneous texture, while the postradiotherapy parotid glands exhibited heterogeneous echotexture (e.g., hyperechoic lines and spots), which likely represents fibrosis.Conclusions:The authors have demonstrated the feasibility of ultrasonic texture evaluation of parotid glands; and the sonographic features may serve as imaging signatures to assess radiation‐induced parotid injury.
Acquisition of Maternal Antibodies both from the Placenta and by Lactation Protects Mouse Offspring from Yersinia pestis Challenge
Authors: Qi Zhizhen , Zhao Haihong , Zhang Qingwen , Bi Yujing , Ren Lingling , Zhang Xuecan , Yang Hanqing , Yang Xiaoyan , Wang Qiong , Li Cunxiang , Zhou Jiyuan , Xin Youquan , Yang Yonghai , Yang Huiying , Du Zongmin , Tan Yafang , Han Yanping , Song Yajun , Zhou Lei , Zhang Pingping , Cui Yujun , Yan Yanfeng , Zhou Dongsheng , Yang Ruifu , Wang Xiaoyi 
Published: August 2012

ABSTRACTArtificially passive immunization has been demonstrated to be effective againstYersinia pestisinfection in animals. However, maternal antibodies' protective efficacy against plague has not yet been demonstrated. Here, we evaluated the kinetics, protective efficacy, and transmission modes of maternal antibodies, using mice immunized with plague subunit vaccine SV1 (20 μg of F1 and 10 μg of rV270). The results showed that the rV270- and F1-specific antibodies could be detected in the sera of newborn mice (NM) until 10 and 14 weeks of age, respectively. There was no antibody titer difference between the parturient mice immunized with SV1 (PM-S) and the caesarean-section newborns (CSN) from the PM-S or between the lactating mice immunized by SV1 (LM-S) and the cross-fostered mice (CFM) during 3 weeks of lactation. The NM had a 72% protection against 4,800 CFUY. pestisstrain 141 challenge at 6 weeks of age, whereas at 14 weeks of age, NM all succumbed to 5,700 CFU ofY. pestischallenge. After 7 weeks of age, CFM had an 84% protection against 5,000 CFU ofY. pestischallenge. These results indicated that maternal antibodies induced by the plague subunit vaccine in mother mice can be transferred to NM by both placenta and lactation. Passive antibodies from the immunized mothers could persist for 3 months and provide early protection for NM. The degree of early protection is dependent on levels of the passively acquired antibody. The results indicate that passive immunization should be an effective countermeasure against plague during its epidemics.
Microbiological Analysis of Nontyphoidal Salmonella Strains Causing Distinct Syndromes of Bacteremia or Enteritis in HIV/AIDS Patients in San Diego, California
Authors: Preziosi Michael J. , Kandel Sean M. , Guiney Donald G. , Browne Sara H. 
Published: August 2012

ABSTRACT

Recurrent invasive nontyphoidal
Salmonella
(NTS) infection is an AIDS-defining illness that has become less common in the developed world in the era of highly active antiretroviral therapy (HAART), while it has emerged as a major public health problem in developing countries, particularly sub-Saharan Africa. We retrospectively analyzed
Salmonella
(NTS) infection in HIV/AIDS patients from June 2003 until December 2009 at the University of California, San Diego (UCSD), Medical Center. Bacterial isolates from all patients were tested for selected microbiological properties, including major
Salmonella
(NTS) virulence loci
rpoS
,
sodCI
,
spvB
, and
sseI
. Fourteen percent of all
Salmonella
(NTS) cases recorded at the UCSD Medical Center during this period occurred in known HIV/AIDS patients. The clinical presentations in HIV patients fell into two distinct groups, bacteremia and enteritis. There was little clinical overlap between these two syndromes. All strains were positive for the presence of the
rpoS and sodCI
virulence loci, and 75% of strains were positive for the presence of the
spvB
and
sseI
loci. Antibiotic susceptibility assay showed that all strains were susceptible to trimethoprim-sulfamethoxazole and ciprofloxacin. The clinical presentation did not have a clear relationship to the CD4
+
cell count. Of the bacteremic isolates, all but one isolate, drawn from a patient with substantial enteric comorbidities, had all of the virulence genes tested, but 66% of nonbacteremic, enteritis strains also contained all the tested virulence loci. In conclusion, neither patients' CD4
+
cell count nor bacterial strain properties necessarily predicted the clinical presentation of HIV/AIDS patients with
Salmonella
(NTS) infection, and AIDS patients can have episodes of
Salmonella
enteritis without dissemination.
Cryopreservation of Mycobacterium tuberculosis Complex Cells
Authors: Shu Zhiquan , Weigel Kris M. , Soelberg Scott D. , Lakey Annie , Cangelosi Gerard A. , Lee Kyong-Hoon , Chung Jae-Hyun , Gao Dayong 
Published: August 2012

ABSTRACT

Successful long-term preservation of
Mycobacterium tuberculosis
cells is important for sample transport, research, biobanking, and the development of new drugs, vaccines, biomarkers, and diagnostics. In this report,
Mycobacterium
bovis
bacillus Calmette-Guérin and
M. tuberculosis
H37Ra were used as models of
M. tuberculosis
complex strains to study cryopreservation of
M. tuberculosis
complex cells in diverse sample matrices at different cooling rates. Cells were cryopreserved in diverse sample matrices, namely, phosphate-buffered saline (PBS), Middlebrook 7H9 medium with or without added glycerol, and human sputum. The efficacy of cryopreservation was quantified by microbiological culture and microscopy with BacLight LIVE/DEAD staining. In all sample matrices examined, the microbiological culture results showed that the cooling rate was the most critical factor influencing cell viability. Slow cooling (a few degrees Celsius per minute) resulted in much higher
M. tuberculosis
complex recovery rates than rapid cooling (direct immersion in liquid nitrogen) (
P
< 0.05). Among the three defined cryopreservation media (PBS, 7H9, and 7H9 plus glycerol), there was no significant differential effect on viability (
P
= 0.06 to 0.87). Preincubation of thawed
M. tuberculosis
complex cells in 7H9 broth for 20 h before culture on solid Middlebrook 7H10 plates did not help the recovery of the cells from cryoinjury (
P
= 0.14 to 0.71). The BacLight LIVE/DEAD staining kit, based on Syto 9 and propidium iodide (PI), was also applied to assess cell envelope integrity after cryopreservation. Using the kit, similar percentages of “live” cells with intact envelopes were observed for samples cryopreserved under different conditions, which was inconsistent with the microbiological culture results. This implies that suboptimal cryopreservation might not cause severe damage to the cell wall and/or membrane but instead cause intracellular injury, which leads to the loss of cell viability.
Rapid Detection of the Mycobacterium tuberculosis Complex by Use of Quenching Probe PCR (geneCube)
Authors: Hida Yukio , Hisada Kyoko , Shimada Akihiro , Yamashita Masanori , Kimura Hideki , Yoshida Haruyoshi , Iwasaki Hiromichi , Iwano Masayuki 
Published: August 2012

ABSTRACT

Early detection of tuberculosis (TB) is essential for infection control. The geneCube (Toyobo) is a novel fully automated gene analyzer that can amplify target DNAs within 60 min. In this study, we evaluated the ability of the geneCube to directly detect
Mycobacterium tuberculosis
complex (MTBC) and
Mycobacterium avium
complex (MAC) in clinical specimens. The results were then compared with those obtained using conventional culture, microscopy, and the Cobas Amplicor assay (Roche). We examined a total of 516 frozen samples from 69 patients who showed culture-positive infection (73 samples; 39 MTBC, 32 MAC, and 2 mixed infections) and from 354 patients who were culture negative (443 samples). Assays using the geneCube had a sensitivity of 85.4% and a specificity of 99.8% for detection of MTBC and a sensitivity of 85.3% and a specificity of 99.8% for detection of MAC. These results are similar to those obtained using the Amplicor system but were obtained much more rapidly (1 h with the geneCube versus 5.5 h with the Amplicor system). The geneCube thus enables a significant shortening of the assay time with no loss of sensitivity or specificity.
Genetic Characterization of a Vancomycin-Resistant Staphylococcus aureus Isolate from the Respiratory Tract of a Patient in a University Hospital in Northeastern Iran
Authors: Azimian Amir , Havaei Seyed Asghar , Fazeli Hosein , Naderi Mahmood , Ghazvini Kiarash , Samiee Siamak Mirab , Soleimani Masoud , Peerayeh Shahin Najar 
Published: August 2012

ABSTRACT

Emergence of vancomycin-intermediate
Staphylococcus aureus
(VISA) and vancomycin-resistant
S. aureus
(VRSA) strains has led to global concerns about treatments for staphylococcal infections. These strains are currently rare even though there is an upward trend in their reported incidence. Therefore, appropriate screening and epidemiological evaluation of VRSA strains can affect future global health care policies. Isolates of
Staphylococcus aureus
were obtained from various clinical samples and were then evaluated with agar screening, disk diffusion, and MIC methods to determine resistance to vancomycin and methicillin. After confirmation of the isolated VRSA strain, genetic analysis was performed by evaluating
mecA
and
vanA
gene presence, SCC
mec
,
agr
, and
spa
types, and toxin profiles. Multilocus sequence typing (MLST) and plasmid analysis were also performed. The VRSA strain was resistant to oxacillin (MIC of 128 μg/ml) and vancomycin (MIC of 512 μg/ml). Disk diffusion antimicrobial susceptibility tests showed resistance to oxacillin, vancomycin, levofloxacin, ciprofloxacin, trimethoprim-sulfamethoxazole, clindamycin, rifampin, and tetracycline. The isolate was susceptible to minocycline and gentamicin. PCRs were positive for the
mecA
and
vanA
genes. Other genetic characteristics include SCC
mec
type III,
agr
I,
spa
type t037, and sequence type (ST) 1283. The plasmid profile shows five plasmids with a size of ∼1.7 kb to >10 kb. The isolated VRSA strain was obtained from a critically ill hospitalized patient. Genetic analysis of this strain suggested that the strain was a methicillin-resistant
S. aureus
(MRSA) clone endemic in Asia that underwent some genetic changes, such as mutation in the
gmk
gene and acquisition of the
vanA
gene.
Russian “Successful” Clone B0/W148 of Mycobacterium tuberculosis Beijing Genotype: a Multiplex PCR Assay for Rapid Detection and Global Screening
Authors: Mokrousov Igor , Narvskaya Olga , Vyazovaya Anna , Otten Tatiana , Jiao Wei-Wei , Gomes Lia Lima , Suffys Philip N. , Shen A-Dong , Vishnevsky Boris 
Published: August 2012

ABSTRACT

We describe a multiplex PCR assay to detect the
Mycobacterium tuberculosis
Beijing genotype variant B0/W148, which is considered a “successful” clone of
M. tuberculosis
, widespread in Russia. Specificity and sensitivity of the assay were 100% based on the analysis of a collection of 516
M. tuberculosis
isolates of different genotypes and origins. This assay may be used for accurate and simple detection and surveillance of this clinically and epidemiologically important variant of
M. tuberculosis
.
Reconstituting the Epidemic History of HIV Strain CRF01_AE among Men Who Have Sex with Men (MSM) in Liaoning, Northeastern China: Implications for the Expanding Epidemic among MSM in China
Authors: An Minghui , Han Xiaoxu , Xu Junjie , Chu Zhenxing , Jia Manhong , Wu Hao , Lu Lin , Takebe Yutaka , Shang Hong 
Published: August 2012

ABSTRACT
HIV CRF01_AE accounted for 84% of the recent infections among men who have sex with men (MSM) in Liaoning Province of northeastern China. CRF01_AE strains were grouped into two distinct clusters (designated clusters 1 and 2) that were also detected in other regions in China. Phylodynamics study revealed that these two CRF01_AE strains were independently introduced into the population of MSM in China in the early and mid-1990s. Our study elucidated unique features of dynamics and interrelationships of MSM epidemics in China.
Identification of RNA-Protein Interaction Networks Involved in the Norovirus Life Cycle
Authors: Vashist Surender , Urena Luis , Chaudhry Yasmin , Goodfellow Ian 
Published: August 2012

ABSTRACT

Human noroviruses are one of the major causes of acute gastroenteritis in the developed world, yet our understanding of their molecular mechanisms of genome translation and replication lags behind that for many RNA viruses. Due to the nonculturable nature of human noroviruses, many related members of the
Caliciviridae
family of small RNA viruses are often used as model systems to dissect the finer details of the norovirus life cycle. Murine norovirus (MNV) has provided one such system with which to study the basic mechanisms of norovirus translation and replication in cell culture. In this report we describe the use of riboproteomics to identify host factors that interact with the extremities of the MNV genome. This network of RNA-protein interactions contains many well-characterized host factors, including PTB, La, and DDX3, which have been shown to play a role in the life cycle of other RNA viruses. By using RNA coimmunoprecipitation, we confirmed that a number of the factors identified using riboproteomics are associated with the viral RNA during virus replication in cell culture. We further demonstrated that RNA inhibition-mediated knockdown of the intracellular levels of a number of these factors inhibits or slows norovirus replication in cell culture, allowing identification of new intracellular targets for this important group of pathogens.
Temporal Association of HLA-B*81:01- and HLA-B*39:10-Mediated HIV-1 p24 Sequence Evolution with Disease Progression
Authors: Ntale R. S. , Chopera D. R. , Ngandu N. K. , Assis de Rosa D. , Zembe L. , Gamieldien H. , Mlotshwa M. , Werner L. , Woodman Z. , Mlisana K. , Abdool Karim S. , Gray C. M. , Williamson C. ,   the CAPRISA 002 Study Team
Published: August 2012

ABSTRACT

HLA-B*81:01 and HLA-B*39:10 alleles have been associated with viremic control in HIV-1 subtype C infection. Both alleles restrict the TL9 epitope in p24 Gag, and cytotoxic-T-lymphocyte (CTL)-mediated escape mutations in this epitope have been associated with an
in vitro
fitness cost to the virus. We investigated the timing and impact of mutations in the TL9 epitope on disease progression in five B*81:01- and two B*39:10-positive subtype C-infected individuals. Whereas both B*39:10 participants sampled at 2 months postinfection had viruses with mutations in the TL9 epitope, in three of the five (3/5) B*81:01 participants, TL9 escape mutations were only detected 10 months after infection, taking an additional 10 to 15 months to reach fixation. In the two remaining B*81:01 individuals, one carried a TL9 escape variant at 2 weeks postinfection, whereas no escape mutations were detected in the virus from the other participant for up to 33 months postinfection, despite CTL targeting of the epitope. In all participants, escape mutations in TL9 were linked to coevolving residues in the region of Gag known to be associated with host tropism. Late escape in TL9, together with coevolution of putative compensatory mutations, coincided with a spontaneous increase in viral loads in two individuals who were otherwise controlling the infection. These results provide
in vivo
evidence of the detrimental impact of B*81:01-mediated viral evolution, in a single Gag p24 epitope, on the control of viremia.
Discovery of Severe Fever with Thrombocytopenia Syndrome Bunyavirus Strains Originating from Intragenic Recombination
Authors: He Cheng-Qiang , Ding Nai-Zheng 
Published: August 2012

ABSTRACT
This study analyzes available severe fever with thrombocytopenia syndrome virus (SFTSV) genomes and reports that a sublineage of lineage I bears a unique M segment recombined from two of three prevailing SFTSV lineages. Through recombination, the sublineage has acquired nearly complete G1 associated with protective epitopes from lineage III, suggesting that this recombination has the capacity to induce antigenic shift of the virus. Therefore, this study provides some valuable implications for the vaccine design of SFTSV.
An Sp1/Sp3 Site in the Downstream Region of Varicella-Zoster Virus (VZV) oriS Influences Origin-Dependent DNA Replication and Flanking Gene Transcription and Is Important for VZV Replication
In Vitro
and in Human Skin
Authors: Khalil Mohamed I. , Robinson Makeda , Sommer Marvin , Arvin Ann , Hay John , Ruyechan William T. 
Published: August 2012

ABSTRACT

The distribution and orientation of origin-binding protein (OBP) sites are the main architectural contrasts between varicella-zoster virus (VZV) and herpes simplex virus (HSV) origins of DNA replication (oriS). One important difference is the absence of a downstream OBP site in VZV, raising the possibility that an alternative
cis
element may replace its function. Our previous work established that Sp1, Sp3, and YY1 bind to specific sites within the downstream region of VZV oriS; we hypothesize that one or both of these sites may be the alternative
cis
element(s). Here, we show that the mutation of the Sp1/Sp3 site decreases DNA replication and transcription from the adjacent ORF62 and ORF63 promoters following superinfection with VZV. In contrast, in the absence of DNA replication or in transfection experiments with ORF62, only ORF63 transcription is affected. YY1 site mutations had no significant effect on either process. Recombinant viruses containing these mutations were then constructed. The Sp1/Sp3 site mutant exhibited a significant decrease in virus growth in MeWo cells and in human skin xenografts, while the YY1 site mutant virus grew as well as the wild type in MeWo cells, even showing a late increase in VZV replication in skin xenografts following infection. These results suggest that the Sp1/Sp3 site plays an important role in both VZV origin-dependent DNA replication and ORF62 and ORF63 transcription and that, in contrast to HSV, these events are linked during virus replication.