bluuebunny/crossref_metadata_2025_split huggingface dataset:
Loop-Mediated Isothermal Amplification for Rapid and Reliable Diagnosis of Tuberculous Meningitis
Authors: Nagdev Khushboo J. , Kashyap Rajpal S. , Parida Manmohan M. , Kapgate Rajkumar C. , Purohit Hemant J. , Taori Girdhar M. , Daginawala Hatim F. 
Published: March 2011

ABSTRACTDiagnosis of tuberculous meningitis (TBM) is often difficult. A reliable, simple, and rapid diagnostic test that can be performed in any standard laboratory could be helpful in TBM diagnosis. In this study, a loop-mediated isothermal amplification assay (LAMP) was evaluated to rapidly detect and diagnose TBM infection and was compared to the performance of nested PCR. Six specific primers were used to recognize the IS6110genomic sequence fromMycobacterium tuberculosis, which included one forward outer primer, one reverse outer primer, two respective inner primers, and two loop primers. The optimum reaction temperature and time were 63°C and 60 min, respectively. Nested PCR was performed targeting the IS6110region fromM. tuberculosisusing a commercial kit. The LAMP method yielded a sensitivity of 88.23% and a specificity of 80%, compared to the nested-PCR assay, which yielded a sensitivity of 52.9% and a specificity of 90% for TBM diagnosis. Comparative experiments showed that the LAMP assay is a rapid, sensitive, and specific method to detect TBM infection and that it is superior to the nested-PCR assay. LAMP is very simple, and it can be performed in any laboratory and in rural settings.
Identification of Mycobacteria in Solid-Culture Media by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry
Authors: Saleeb Paul G. , Drake Steven K. , Murray Patrick R. , Zelazny Adrian M. 
Published: March 2011

ABSTRACT

Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) has recently been introduced into the clinical microbiology laboratory as a rapid and accurate method to identify bacteria and yeasts. In this paper we describe our work on the use of MALDI-TOF MS for the identification of mycobacterial isolates. We developed a protocol for protein extraction from mycobacteria and utilized it to construct a database containing 42 clinically relevant type and reference strains of mycobacteria. The database was used to identify 104 clinical isolates of mycobacteria. All members of the
Mycobacterium tuberculosis
complex were identified accurately at the complex level but could not be separated at the species level. All other organisms were identified at the species level, with the exception of one strain of
M. kansasii
(accurately identified but with a low spectral score) and three pairs of closely related strains:
M. abscessus
and
M. massiliense
,
M. mucogenicum
and
M. phocaicum
, and
M. chimaera
and
M. intracellulare
. These pairs of organisms can currently be identified only by multilocus gene sequence analysis. We conclude that MALDI-TOF MS analysis can be incorporated into the work flow of the microbiology laboratory for rapid and accurate identification of most strains of mycobacteria isolated from solid growth media.
Multilocus Sequence Typing Implicates Rodents as the Main Reservoir Host of Human-Pathogenic Borrelia garinii in Japan
Authors: Takano Ai , Nakao Minoru , Masuzawa Toshiyuki , Takada Nobuhiro , Yano Yasuhiro , Ishiguro Fubito , Fujita Hiromi , Ito Takuya , Ma Xiaohang , Oikawa Yozaburo , Kawamori Fumihiko , Kumagai Kunihiko , Mikami Toshiyuki , Hanaoka Nozomu , Ando Shuji , Honda Naoko , Taylor Kyle , Tsubota Toshio , Konnai Satoru , Watanabe Haruo , Ohnishi Makoto , Kawabata Hiroki 
Published: March 2011

ABSTRACTMultilocus sequence typing ofBorrelia gariniiisolates from humans and comparison with rodent and tick isolates were performed. Fifty-nine isolates were divided into two phylogenetic groups, and an association was detected between clinical and rodent isolates, suggesting that, in Japan, human-pathogenicB. gariniicomes from rodents via ticks.
Phenotypic Suppression of a Herpes Simplex Virus 1 ICP27 Mutation by Enhanced Transcription of the Mutant Gene
Authors: Strain Anna K. , Rice Stephen A. 
Published: March 2011

ABSTRACT
ICP27 is an essential herpes simplex virus 1 (HSV-1) regulatory protein that enhances viral gene expression. Although it is predominantly nuclear, it shuttles to the cytoplasm during infection using an N-terminal nuclear export signal (NES). We previously engineered an NES-negative ICP27 mutant, dLeu, that replicates poorly in cultured cells. In this study, we isolated dLeuR, a growth-competent revertant of dLeu. We show that dLeuR possesses one or more extragenic mutations that enhance ICP27 transcription, leading to overexpression of the mutant protein and restoration of viral growth. This work provides evidence of a novel pathway regulating transcription of the ICP27 gene.
Interplay between Modified Vaccinia Virus Ankara and Dendritic Cells: Phenotypic and Functional Maturation of Bystander Dendritic Cells
Authors: Pascutti María F. , Rodríguez Ana M. , Falivene Juliana , Giavedoni Luis , Drexler Ingo , Gherardi M. Magdalena 
Published: March 2011

ABSTRACTModified vaccinia virus Ankara (MVA) is an attenuated poxvirus strain, currently under evaluation as a vaccine vector in various clinical settings. It has been reported that human dendritic cells (DCs) mature after infection with MVA, but reports on the functionality of DCs have so far been controversial. In this work, we studied the phenotype and functionality of MVA-infected DCs. As previously reported, we found that human monocyte-derived DCs upregulated CD86 and HLA-DR in response to MVA infection. Moreover, infected DCs produced a broad array of chemokines and cytokines and were able to activate and induce gamma interferon (IFN-γ) production both in CD4+and in CD8+allogeneic T cells and in specific autologous peripheral blood lymphocytes (PBLs). Analysis of DC maturation following infection with a recombinant green fluorescent protein (GFP)-expressing MVA revealed that upregulation of CD86 expression was mainly observed in GFPneg(bystander) cells. While GFPpos(infected) DCs produced tumor necrosis factor alpha (TNF-α), they were unable to produce CXCL10 and were less efficient at inducing IFN-γ production in CEF-specific autologous PBLs. Maturation of bystander DCs could be achieved by incubation with supernatant from infected cultures or with apoptotic infected cells. Type I IFNs were partially responsible for the induction of CXCL10 on bystander DCs. Our findings demonstrate for the first time that, in MVA-infected DC cultures, the leading role with respect to functionality and maturation characteristics is achieved by the bystander DCs.
The Nonnucleoside Reverse Transcriptase Inhibitor MIV-150 in Carrageenan Gel Prevents Rectal Transmission of Simian/Human Immunodeficiency Virus Infection in Macaques
Authors: Singer R. , Derby N. , Rodriguez A. , Kizima L. , Kenney J. , Aravantinou M. , Chudolij A. , Gettie A. , Blanchard J. , Lifson J. D. , Piatak M. , Fernández-Romero J. A. , Zydowsky T. M. , Robbiani M. 
Published: March 2011

ABSTRACT

Development of a microbicide that prevents rectal transmission of human immunodeficiency virus (HIV) is a vital component in reducing HIV spread. We recently demonstrated that a formulation of the nonnucleoside reverse transcriptase inhibitor (NNRTI) MIV-150 in carrageenan reduced vaginal infection of macaques with simian immunodeficiency virus SIVmac239 with HIV-1
HxB2
reverse transcriptase (SHIV-RT). Herein, we performed the first testing of MIV-150–carrageenan against rectal infection. Rhesus macaques were treated rectally with MIV-150–carrageenan or methyl cellulose (MC) placebo gel up to 4 h prior to rectal challenge with 10
3
or 10
4
50% tissue culture infective doses (TCID
50
) of SHIV-RT. Infection was assessed by measuring plasma virus RNA as well as T and B cell responses. MIV-150–carrageenan protected all animals challenged with 10
3
TCID
50
when gel was applied either 30 min or 4 h prior to challenge, while 100% of the MC-treated animals became infected (
n
= 4 each;
P
< 0.03). Partial protection (2 of 4 animals) by MIV-150–carrageenan was observed for rectal challenge with 10-fold more virus applied 4 h after the gel. Sequencing of the RT gene from plasma virus RNA isolated at peak viremia confirmed that both of these animals (like infected MC controls) were infected with wild-type virus. Infection correlated with the development of SIV-specific T and B cell responses. MIV-150 was detected in the rectal fluids and tissues 4 h after gel application but was not detected in the blood at any time (0.5 to 24 h). These data are promising for the development of NNRTI-containing gels to prevent rectal HIV transmission.
Efficient Gene Transfer in Bacterial Cell Chains
Authors: Babic Ana , Berkmen Melanie B. , Lee Catherine A. , Grossman Alan D. 
Published: March 2011

ABSTRACTHorizontal gene transfer contributes to evolution and the acquisition of new traits. In bacteria, horizontal gene transfer is often mediated by conjugative genetic elements that transfer directly from cell to cell. Integrative and conjugative elements (ICEs; also known as conjugative transposons) are mobile genetic elements that reside within a host genome but can excise to form a circle and transfer by conjugation to recipient cells. ICEs contribute to the spread of genes involved in pathogenesis, symbiosis, metabolism, and antibiotic resistance. Despite its importance, little is known about the mechanisms of conjugation in Gram-positive bacteria or how quickly or frequently transconjugants become donors. We visualized the transfer of the integrative and conjugative element ICEBs1from aBacillus subtilisdonor to recipient cells in real time using fluorescence microscopy. We found that transfer of DNA from a donor to a recipient appeared to occur at a cell pole or along the lateral cell surface of either cell. Most importantly, we found that when acquired by 1 cell in a chain, ICEBs1spread rapidly from cell to cell within the chain by additional sequential conjugation events. This intrachain conjugation is inherently more efficient than conjugation that is due to chance encounters between individual cells. Many bacterial species, including pathogenic, commensal, symbiotic, and nitrogen-fixing organisms, harbor ICEs and grow in chains, often as parts of microbial communities. It is likely that efficient intrachain spreading is a general feature of conjugative DNA transfer and serves to amplify the number of cells that acquire conjugative mobile genetic elements.IMPORTANCEConjugative elements contribute to horizontal gene transfer and the acquisition of new traits. They are largely responsible for spreading antibiotic resistance in bacterial communities. To study the cell biology of conjugation, we visualized conjugative DNA transfer betweenBacillus subtiliscells in real time using fluorescence microscopy. In contrast to previous predictions that transfer would occur preferentially from the donor cell pole, we found that transfer of DNA from a donor to a recipient appeared to occur at a cell pole or along the lateral cell surface of either cell. Most importantly, we found that when acquired by 1 cell in a chain, the conjugative DNA spread rapidly from cell to cell within the chain through sequential conjugation events. Since many bacterial species grow naturally in chains, this intrachain transfer is likely a common mechanism for accelerating the spread of conjugative elements within microbial communities.
Convergence of Iterative Sequences for Fixed Point and Variational Inclusion Problems
Authors: Yu Li , Liang Ma 
Published: March 2011

AbstractAn iterative process is considered for finding a common element in the fixed point set of a strict pseudocontraction and in the zero set of a nonlinear mapping which is the sum of a maximal monotone operator and an inverse strongly monotone mapping. Strong convergence theorems of common elements are established in real Hilbert spaces.
Advances in the Biology and Treatment of Bone Disease in Multiple Myeloma
Authors: Raje Noopur , Roodman G. David 
Published: March 2011

Abstract
Osteolytic bone disease is pathognomonic of multiple myeloma (MM) and affects more than 80% of patients. Bone disease results in skeletal-related events (SRE) such as vertebral compression fractures, which may cause cord compression, hypercalcemia, pathologic fractures that require radiation or surgical fixation, and severe pain. All of these not only result in a negative impact on quality of life but also adversely impact overall survival. Osteolytic disease is a consequence of increased osteoclast (OC) activation along with osteoblast (OB) inhibition, resulting in altered bone remodeling. OC number and activity are increased in MM via cytokine deregulation within the bone marrow (BM) milieu, whereas negative regulators of OB differentiation suppress bone formation. Bisphosphonates are a well-established treatment of myeloma-related skeletal disease and are the current standard of care. However, complications arising from their long-term use have prompted studies of schedule optimization and alternate strategies. Several novel agents are currently under investigation for their positive effect on bone remodeling via OC inhibition. The identification of negative regulators of OB differentiation has prompted the use of anabolic agents. In addition to restoring bone remodeling, these drugs may inhibit tumor growth in vivo. Future studies will look to combine or sequence all of these agents with the goal of not only alleviating morbidity from bone disease but also capitalizing on the resultant antitumor activity. Clin Cancer Res; 17(6); 1278–86. ©2011 AACR.
Shifts in the Therapeutic Paradigm for Patients Newly Diagnosed with Multiple Myeloma: Maintenance Therapy and Overall Survival
Authors: Palumbo Antonio , Attal Michel , Roussel Murielle 
Published: March 2011

Abstract
High-dose therapy (HDT) with autologous stem cell transplantation (ASCT) is the standard of care for eligible newly diagnosed multiple myeloma (MM) patients. Several randomized studies showed a survival advantage for patients undergoing transplantation, compared with conventional chemotherapy. Introduction of new drugs in this setting has markedly increased survival rates within the last 10 years. Efforts to further improve response rates and survival in those patients are still needed, mainly by increasing the depth of tumor reduction and the duration of response through more effective induction, consolidation, and maintenance therapies. Nevertheless, this approach is currently challenged by the promising results of long-term treatment with novel agents. Recent data suggest that the upfront combination of a proteasome inhibitor plus 1 immunomodulatory compound (IMiD) is highly effective. The combination of bortezomib, thalidomide, and dexamethasone (VTD) has proven to be highly effective as a frontline treatment and is significantly superior to vincristine, doxorubicin, and dexamethasone (VAD) or thalidomide and dexamethasone (Thal-Dex) before and after ASCT with a very manageable toxicity pattern. The most promising 3-drug association might be bortezomib, lenalidomide, and dexamethasone (VRD). Adjunction of a 4th drug has not proven to be more efficient. In patients not eligible for ASCT, the introduction of novel agents has changed the management of multiple myeloma. The combinations of melphalan, prednisone, and thalidomide and of bortezomib, melphalan, and prednisone have shown improved progression-free survival and overall survival in comparison with melphalan and prednisone alone. Melphalan, prednisone, and thalidomide and bortezomib, melphalan, and prednisone are now the new standards of care for elderly patients. Preliminary results also support the role of the combination of melphalan, prednisone, and lenalidomide followed by maintenance therapy with lenalidomide in the treatment of elderly patients. Physicians now have a wider variety of treatment options to tailor the most appropriate and efficacious treatment according to their patients' characteristics. Clin Cancer Res; 17(6); 1253–63. ©2011 AACR.
A Randomized Phase II Study of Gefitinib Plus Simvastatin Versus Gefitinib Alone in Previously Treated Patients with Advanced Non–Small Cell Lung Cancer
Authors: Han Ji-Youn , Lee Soo-Hyun , Yoo Nam Jin , Hyung Lee Suk , Moon Yoon Joo , Yun Tak , Kim Heung Tae , Lee Jin Soo 
Published: March 2011

Abstract
Purpose: To evaluate the efficacy and safety of gefitinib plus simvastatin (GS) versus gefitinib alone (G) in previously treated patients with advanced non–small cell lung cancer (NSCLC).
Experimental Design: Between May 2006 and September 2008, 106 patients (51% men, 75% adenocarcinoma, 50% never smoker) were randomly assigned to G alone (250 mg/d, n = 54) or GS (250 and 40 mg/d, respectively, n = 52). One cycle was 4 weeks of treatment. Therapy was continued until disease progression or intolerable toxicity was observed. The primary endpoint was response rate (RR). Secondary endpoints included toxicity, progression-free survival (PFS), and overall survival (OS).
Results: The RR was 38.5% (95% CI, 25.3–51.7) for GS and 31.5% (95% CI, 19.1–43.9) for G. The median PFS was 3.3 months [M] (95% CI, 1.4–5.2M) for GS and 1.9M (95% CI, 1.0–2.8M) for G. The median OS was 13.6M (95% CI, 7.1–20.1M) for GS and 12.0M (95% CI, 7.8–16.2M) for G. In exploratory subgroup analysis, GS showed higher RR (40% vs. 0%, P = 0.043) and longer PFS (3.6M vs. 1.7M, P = 0.027) compared with G alone in patients with wild-type epidermal growth factor receptor (EGFR) nonadenocarcinomas. Adverse events in both arms were generally mild and mainly consisted of skin rashes.
Conclusions: Although no superiority of GS to G was demonstrated in this unselected NSCLC population, GS showed higher RR and longer PFS compared with G alone in patients with wild-type EGFR nonadenocarcinomas. Simvastatin may improve the efficacy of gefitinib in that subgroup of gefitinib-resistant NSCLC patients. Clin Cancer Res; 17(6); 1553–60. ©2011 AACR.
Glucose Metabolism Gene Variants Modulate the Risk of Pancreatic Cancer
Authors: Dong Xiaoqun , Li Yanan , Chang Ping , Tang Hongwei , Hess Kenneth R. , Abbruzzese James L. , Li Donghui 
Published: March 2011

Abstract
Long-term type 2 diabetes is a known risk factor for pancreatic cancer (PC). We hypothesized that genetic variants in glucose metabolism modify individual susceptibility to PC, especially those associated with diabetes. We retrospectively genotyped 26 single-nucleotide polymorphisms of 5 glucose metabolism genes: glucokinase (GCK), glutamine-fructose-6-phosphate transaminase 1 (GFPT1), glucose phosphate isomerase (GPI), hexokinase 2 (HK2), and O-linked N-acetylglucosamine transferase (OGT) in a case–control study of PC conducted at MD Anderson during 2004 to 2010. Initial genotyping was conducted in 706 patients with PC and 706 cancer-free controls by using the Sequenom method. A HK2 genotype (R844K) with low frequency of homozygous variant was further examined in additional 948 patients and 476 controls. In the combined set of 1,654 cases and 1,182 controls, we showed a significant association of the HK2 R844K GA/AA genotype with reduced PC risk (OR = 0.78; 95% CI, 0.64–0.94; P = 0.009) and a significant interaction with diabetes (Pinteraction &lt; 0.001). The HK2 R844K GA/AA genotype was associated with a reduced risk of PC among nondiabetic individuals (OR = 0.68; 95% CI, 0.56–0.83) but with increased risk among diabetic patients (OR = 3.69; 95% CI, 2.34–5.82). These risk associations remained statistically significant when the analysis was restricted to whites or after exclusion of recent onset diabetes. No significant main effect of other genes or significant interaction of genotype with other risk factors was observed. The findings show a potential role of HK2 gene, alone or in interaction with diabetes, in modifying the risk of PC. Cancer Prev Res; 4(5); 758–66. ©2011 AACR.
Transcriptome sequencing and annotation of the microalgae Dunaliella tertiolecta: Pathway description and gene discovery for production of next-generation biofuels
Authors: Rismani-Yazdi Hamid , Haznedaroglu Berat Z , Bibby Kyle , Peccia Jordan 
Published: March 2011

Abstract

Background
Biodiesel or ethanol derived from lipids or starch produced by microalgae may overcome many of the sustainability challenges previously ascribed to petroleum-based fuels and first generation plant-based biofuels. The paucity of microalgae genome sequences, however, limits gene-based biofuel feedstock optimization studies. Here we describe the sequencing and de novo transcriptome assembly for the non-model microalgae species, Dunaliella tertiolecta, and identify pathways and genes of importance related to biofuel production.

Results
Next generation DNA pyrosequencing technology applied to D. tertiolecta transcripts produced 1,363,336 high quality reads with an average length of 400 bases. Following quality and size trimming, ~ 45% of the high quality reads were assembled into 33,307 isotigs with a 31-fold coverage and 376,482 singletons. Assembled sequences and singletons were subjected to BLAST similarity searches and annotated with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology (KO) identifiers. These analyses identified the majority of lipid and starch biosynthesis and catabolism pathways in D. tertiolecta.

Conclusions
The construction of metabolic pathways involved in the biosynthesis and catabolism of fatty acids, triacylglycrols, and starch in D. tertiolecta as well as the assembled transcriptome provide a foundation for the molecular genetics and functional genomics required to direct metabolic engineering efforts that seek to enhance the quantity and character of microalgae-based biofuel feedstock.