bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome of Helicobacter pylori Strain XZ274, an Isolate from a Tibetan Patient with Gastric Cancer in China
Authors: Guo Ying , Wang Haiying , Li Yan , Song Yang , Chen Chen , Liao Yaling , Ren Li , Guo Chunliang , Tong Wende , Shen Wei , Chen Ming , Mao Xuhu , Guo Gang , Zou Quanming 
Published: July 2012

ABSTRACT

The infection rate of
Helicobacter pylori
is high all over the world, especially in the Chinese Tibetan Plateau. Here, we report the genome sequence of
Helicobacter pylori
strain XZ274 isolated from a Tibetan patient with gastric cancer. The strain contains 1,634,138 bp with 1,654 coding sequences and a pXZ274 plasmid of 22,406 bp with 26 coding sequences. This is the first complete genome sequence of
Helicobacter pylori
from the Tibetan Plateau in China.
“Spoligoriftyping,” a Dual-Priming-Oligonucleotide-Based Direct-Hybridization Assay for Tuberculosis Control with a Multianalyte Microbead-Based Hybridization System
Authors: Gomgnimbou Michel Kiréopori , Abadia Edgar , Zhang Jian , Refrégier Guislaine , Panaiotov Stefan , Bachiyska Elizabeta , Sola Christophe 
Published: July 2012

ABSTRACT

We developed “spoligoriftyping,” a 53-plex assay based on two preexisting methods, the spoligotyping and “rifoligotyping” assays, by combining them into a single assay. Spoligoriftyping allows simultaneous spoligotyping (i.e., clustered regularly interspaced short palindromic repeat [CRISPR]-based genotyping) and characterization of the main rifampin drug resistance mutations on the
rpoB
hot spot region in a few hours. This test partly uses the dual-priming-oligonucleotide (DPO) principle, which allows simultaneous efficient amplifications of
rpoB
and the CRISPR locus in the same sample. We tested this method on a set of 114 previously phenotypically and genotypically characterized multidrug-resistant (MDR)
Mycobacterium tuberculosis
or drug-susceptible
M. tuberculosis
DNA extracted from clinical isolates obtained from patients from Bulgaria, Nigeria, and Germany. We showed that our method is 100% concordant with
rpoB
sequencing results and 99.95% (3,911/3,913 spoligotype data points) correlated with classical spoligotyping results. The sensitivity and specificity of our assay were 99 and 100%, respectively, compared to those of phenotypic drug susceptibility testing. Such assays pave the way to the implementation of locally and specifically adapted methods of performing in a single tube both drug resistance mutation detection and genotyping in a few hours.
Comparison of the BD Max Methicillin-Resistant Staphylococcus aureus (MRSA) Assay and the BD GeneOhm MRSA Achromopeptidase Assay with Direct- and Enriched-Culture Techniques Using Clinical Specimens for Detection of MRSA
Authors: Dalpke Alexander H. , Hofko Marjeta , Zimmermann Stefan 
Published: July 2012

ABSTRACT

We evaluated the new, fully automated molecular BD Max methicillin-resistant
Staphylococcus aureus
(MRSA) assay for detection of methicillin-resistant
S. aureus
in a low-prevalence (4.1%) setting. Sensitivity, specificity, and positive and negative predictive values were 93.9%, 99.2%, 83.8%, and 99.7%, respectively. The assay reported fewer unresolved results than the BD GeneOhm MRSA ACP assay.
Transmembrane Protein Aptamers That Inhibit CCR5 Expression and HIV Coreceptor Function
Authors: Scheideman Elizabeth H. , Marlatt Sara A. , Xie Yanhua , Hu Yani , Sutton Richard E. , DiMaio Daniel 
Published: July 2012

ABSTRACT
We have exploited the ability of transmembrane domains to engage in highly specific protein-protein interactions to construct a new class of small proteins that inhibit HIV infection. By screening a library encoding hundreds of thousands of artificial transmembrane proteins with randomized transmembrane domains (termed “traptamers,” for transmembrane aptamers), we isolated six 44- or 45-amino-acid proteins with completely different transmembrane sequences that inhibited cell surface and total expression of the HIV coreceptor CCR5. The traptamers inhibited transduction of human T cells by HIV reporter viruses pseudotyped with R5-tropic gp120 envelope proteins but had minimal effects on reporter viruses with X4-tropic gp120. Optimization of two traptamers significantly increased their activity and resulted in greater than 95% inhibition of R5-tropic reporter virus transduction without inhibiting expression of CD4, the primary HIV receptor, or CXCR4, another HIV coreceptor. In addition, traptamers inhibited transduction mediated by a mutant R5-tropic gp120 protein resistant to maraviroc, a small-molecule CCR5 inhibitor, and they dramatically inhibited replication of an R5-tropic laboratory strain of HIV in a multicycle infection assay. Genetic experiments suggested that the active traptamers specifically interacted with the transmembrane domains of CCR5 and that some of the traptamers interacted with different portions of CCR5. Thus, we have constructed multiple proteins not found in nature that interfere with CCR5 expression and inhibit HIV infection. These proteins may be valuable tools to probe the organization of the transmembrane domains of CCR5 and their relationship to its biological activities, and they may serve as starting points to develop new strategies to inhibit HIV infection.
Cytoplasmic Trafficking, Endosomal Escape, and Perinuclear Accumulation of Adeno-Associated Virus Type 2 Particles Are Facilitated by Microtubule Network
Authors: Xiao Ping-Jie , Samulski R. Jude 
Published: July 2012

ABSTRACT
Understanding adeno-associated virus (AAV) trafficking is critical to advance our knowledge of AAV biology and exploit novel aspects of vector development. Similar to the case for most DNA viruses, after receptor binding and entry, AAV traverses the cytoplasm and deposits the viral genome in the cell nucleus. In this study, we examined the role of the microtubule (MT) network in productive AAV infection. Using pharmacological reagents (e.g., nocodazole), live-cell imaging, and flow cytometry analysis, we demonstrated that AAV type 2 (AAV2) transduction was reduced by at least 2-fold in the absence of the MT network. Cell surface attachment and viral internalization were not dependent on an intact MT network. In treated cells at 2 h postinfection, quantitative three-dimensional (3D) microscopy determined a reproducible difference in number of intracellular particles associated with the nuclear membrane or the nucleus compared to that for controls (6 to 7% versus 26 to 30%, respectively). Confocal microscopy analysis demonstrated a direct association of virions with MTs, further supporting a critical role in AAV infection. To investigate the underling mechanisms, we employed single-particle tracking (SPT) to monitor the viral movement in real time. Surprisingly, unlike other DNA viruses (e.g., adenovirus [Ad] and herpes simplex virus [HSV]) that display bidirectional motion on MTs, AAV2 displays only unidirectional movement on MTs toward the nuclei, with peak instantaneous velocities at 1.5 to 3.5 μm/s. This rapid and unidirectional motion on MTs lasts for about 5 to 10 s and results in AAV particles migrating more than 10 μm in the cytoplasm reaching the nucleus very efficiently. Furthermore, electron microscopy analysis determined that, unlike Ad and HSV, AAV2 particles were transported on MTs within membranous compartments, and surprisingly, the acidification of AAV2-containing endosomes was delayed by the disruption of MTs. These findings together suggest an as-yet-undescribed model in which after internalization, AAV2 exploits MTs for rapid cytoplasmic trafficking in endosomal compartments unidirectionally toward the perinuclear region, where most acidification events for viral escape take place.
Crystallographic Analysis of Rotavirus NSP2-RNA Complex Reveals Specific Recognition of 5′ GG Sequence for RTPase Activity
Authors: Hu Liya , Chow Dar-Chone , Patton John T. , Palzkill Timothy , Estes Mary K. , Prasad B. V. Venkataram 
Published: July 2012

ABSTRACT
Rotavirus nonstructural protein NSP2, a functional octamer, is critical for the formation of viroplasms, which are exclusive sites for replication and packaging of the segmented double-stranded RNA (dsRNA) rotavirus genome. As a component of replication intermediates, NSP2 is also implicated in various replication-related activities. In addition to sequence-independent single-stranded RNA-binding and helix-destabilizing activities, NSP2 exhibits monomer-associated nucleoside and 5′ RNA triphosphatase (NTPase/RTPase) activities that are mediated by a conserved H225 residue within a narrow enzymatic cleft. Lack of a 5′ γ-phosphate is a common feature of the negative-strand RNA [(−)RNA] of the packaged dsRNA segments in rotavirus. Strikingly, all (−)RNAs (of group A rotaviruses) have a 5′ GG dinucleotide sequence. As the only rotavirus protein with 5′ RTPase activity, NSP2 is implicated in the removal of the γ-phosphate from the rotavirus (−)RNA. To understand how NSP2, despite its sequence-independent RNA-binding property, recognizes (−)RNA to hydrolyze the γ-phosphate within the catalytic cleft, we determined a crystal structure of NSP2 in complex with the 5′ consensus sequence of minus-strand rotavirus RNA. Our studies show that the 5′ GG of the bound oligoribonucleotide interacts extensively with highly conserved residues in the NSP2 enzymatic cleft. Although these residues provide GG-specific interactions, surface plasmon resonance studies suggest that the C-terminal helix and other basic residues outside the enzymatic cleft account for sequence-independent RNA binding of NSP2. A novel observation from our studies, which may have implications in viroplasm formation, is that the C-terminal helix of NSP2 exhibits two distinct conformations and engages in domain-swapping interactions, which result in the formation of NSP2 octamer chains.
TNFRSF25 Agonistic Antibody and Galectin-9 Combination Therapy Controls Herpes Simplex Virus-Induced Immunoinflammatory Lesions
Authors: J Reddy Pradeep B. , Schreiber Taylor H. , Rajasagi Naveen K. , Suryawanshi Amol , Mulik Sachin , Veiga-Parga Tamara , Niki Toshiro , Hirashima Mitsuomi , Podack Eckhard R. , Rouse Barry T. 
Published: July 2012

ABSTRACTOcular infection with herpes simplex virus 1 (HSV-1) results in a chronic immunoinflamammtory reaction in the cornea, which is primarily orchestrated by CD4+T cells. Hence, targeting proinflammatory CD4+T cells or increasing the representation of cells that regulate their function is a relevant therapeutic strategy. In this report, we demonstrate that effective therapeutic control can be achieved using a combination of approaches under circumstances where monotherapy is ineffective. We use a convenient and highly effective monoclonal antibody (MAb) approach with MAbT25 to expand cells that express the tumor necrosis factor receptor superfamily member 25 (TNFRSF25). In naïve animals, these are predominantly cells that are Foxp3-positive regulatory T cells. MAbT25 treatment before or at the time of initial HSV infection was an effective means of reducing the severity of subsequent stromal keratitis lesions. However, MAbT25 treatment was not effective if given 6 days after infection since it expanded proinflammatory effector T cells, which also express TNFRSF25. Therefore, the MAbT25 procedure was combined with galectin-9 (Gal-9), an approach that compromises the activity of T cells involved in tissue damage. The combination therapy provided highly effective lesion control over that achieved by treatment with one of them. The beneficial outcome of the combination therapy was attributed to the expansion of the regulatory T cell population that additionally expressed activation markers such as CD103 needed to access inflammatory sites. Additionally, there was a marked reduction of CD4+gamma interferon-producing effector T cells responsible for orchestrating the tissue damage. The approach that we describe has potential application to control a wide range of inflammatory diseases, in addition to stromal keratitis, an important cause of human blindness.
Molecular characterisation of quinolone resistance in Escherichia coli from animals in Turkey
Authors: Cengiz M. , Sonal S. , Buyukcangaz E. , Sen A. , Arslan E. , Mat B. , Sahinturk P. , Gocmen H. 
Published: July 2012

The aim of this study were to detect the gyrA, parC and marR mutations and qnr genes (qnrA, qnrB and qnrS) in 120 strains of Escherichia coli isolated from animals. European Committee on Antimicrobial Susceptibility Testing and Clinical Laboratory Standards Institute disc diffusion and minimum inhibitory concentration (MIC) tests, respectively, were used to determine fluoroquinolone (FQ) resistance, and molecular methods were used to detect the mutations and the genes. E coli isolates with an MIC of ≥8 mg/l had mutation at Ser‐80 in parC in addition to mutations at Ser‐83, Asp‐87 or both in gyrA. The nucleotide change was detected in marR (Ser‐3 → Asn, Ala‐53 → Glu, Gly‐103 → Ser, Tyr‐137 → His). Only four E coli isolates (3.3 per cent) contained qnrA and qnrS, and qnrB was not detected. Two E coli isolates from healthy calves also contained qnrA and qnrS. The MICs of enrofloxacin and danofloxacin for qnr ‐containing E coli isolates ranged from 32 mg/l to 256 mg/l. The results of this study indicated that the FQ‐resistant E coli isolates presented an alteration in gyrA (Ser‐83 → Leu, Asp‐87 → Asn) and parC (Ser‐80 → Ile) with high MICs (8–256 mg/l), and there was a low prevalence of qnr genes among E coli isolated from animals.
Dendrochronological reconstruction of spruce budworm (Choristoneura fumiferana) outbreaks in southern Quebec for the last 400 years1This article is one of a selection of papers from the 7th International Conference on Disturbance Dynamics in Boreal Forests.
Authors: Boulanger Yan , Arseneault Dominique , Morin Hubert , Jardon Yves , Bertrand Philip , Dagneau Charles 
Published: July 2012

It is argued that spruce budworm ( Choristoneura fumiferana (Clemens)) (SBW) outbreaks have tended to be more frequent, severe, and spatially synchronized since the beginning of the 20th century. However, few studies have assessed the long-term (>200 years) variations in SBW outbreak dynamics. We reconstructed the SBW outbreak history at the northern limit of the temperate forest in southern Quebec using dendrochronological material from old buildings and five old-growth stands. Our regional tree-ring chronology (1551–1995) represents one of the longest and most replicated insect outbreak reconstructions in North America. Nine potential outbreaks were identified (1976–1991, 1946–1959, 1915–1929, 1872–1903, 1807–1817, 1754–1765, 1706–1717, 1664–1670, and 1630–1638) with three additional uncertain outbreaks (1647–1661, 1606–1619, and 1564–1578). Results suggested that southern Quebec has experienced frequent and synchronized outbreaks throughout the last 400 years. Although outbreak frequency was higher during the 20th century (approximately 30 years) as compared with the 1660–1850 period (approximately 50 years), similar or even higher outbreak frequency might have occurred prior to 1660 (approximately 28 years). We did not find any evidence that the recent outbreak dynamics in southern Quebec is outside its historical range of the last 400 years. Previous studies based on living trees may have underestimated outbreak frequency and synchrony prior to 1900.
Estimating the value of wood quality information in constrained optimization
Authors: Kangas A. , Hurttala H. , Mäkinen H. , Lappi J. 
Published: July 2012

In recent years, forest information has been evaluated increasingly through its value in decision making, not solely through its statistical accuracy. The value of forest information is rooted in the ability to make better decisions with better data. When the adopted option differs from the optimal, it incurs suboptimality losses, defined as the difference between the outcome (typically NPV) of the optimal and selected options. In this study, we analyse the value of timber quality information for the timber buyer selecting stands to be purchased with a given budget or demand constraint. In the basic constrained linear programming approach, the option selected as optimal with erroneous data may prove to be infeasible when evaluated with error-free data. To properly estimate the value of information, the costs of violating the constraints need to be included. We present a stochastic goal programming approach for solving this problem in which the violations are penalized with the interest of a loan, in the case of budget constraint, and with diminishing revenues, in the case of demand constraints. We show that information on timber quality has value to the buyer, increasing with the penalty. The value varied from 0 to about 80 €·ha–1, assuming only the timber quality assessments to be uncertain. Using the stochastic solution instead of expected value solution also has value for the buyer.
Wnt-Pathway Activation in Two Molecular Classes of Hepatocellular Carcinoma and Experimental Modulation by Sorafenib
Authors: Lachenmayer Anja , Alsinet Clara , Savic Radoslav , Cabellos Laia , Toffanin Sara , Hoshida Yujin , Villanueva Augusto , Minguez Beatriz , Newell Philippa , Tsai Hung-Wen , Barretina Jordi , Thung Swan , Ward Stephen C. , Bruix Jordi , Mazzaferro Vincenzo , Schwartz Myron , Friedman Scott L. , Llovet Josep M. 
Published: July 2012

Abstract
Purpose: Hepatocellular carcinoma (HCC) is a heterogeneous cancer with active Wnt signaling. Underlying biologic mechanisms remain unclear and no drug targeting this pathway has been approved to date. We aimed to characterize Wnt-pathway aberrations in HCC patients, and to investigate sorafenib as a potential Wnt modulator in experimental models of liver cancer.
Experimental Design: The Wnt-pathway was assessed using mRNA (642 HCCs and 21 liver cancer cell lines) and miRNA expression data (89 HCCs), immunohistochemistry (108 HCCs), and CTNNB1-mutation data (91 HCCs). Effects of sorafenib on Wnt signaling were evaluated in four liver cancer cell lines with active Wnt signaling and a tumor xenograft model.
Results: Evidence for Wnt activation was observed for 315 (49.1%) cases, and was further classified as CTNNB1 class (138 cases [21.5%]) or Wnt-TGFβ class (177 cases [27.6%]). CTNNB1 class was characterized by upregulation of liver-specific Wnt-targets, nuclear β-catenin and glutamine-synthetase immunostaining, and enrichment of CTNNB1-mutation-signature, whereas Wnt-TGFβ class was characterized by dysregulation of classical Wnt-targets and the absence of nuclear β-catenin. Sorafenib decreased Wnt signaling and β-catenin protein in HepG2 (CTNNB1 class), SNU387 (Wnt-TGFβ class), SNU398 (CTNNB1-mutation), and Huh7 (lithium-chloride-pathway activation) cell lines. In addition, sorafenib attenuated expression of liver-related Wnt-targets GLUL, LGR5, and TBX3. The suppressive effect on CTNNB1 class–specific Wnt-pathway activation was validated in vivo using HepG2 xenografts in nude mice, accompanied by decreased tumor volume and increased survival of treated animals.
Conclusions: Distinct dysregulation of Wnt-pathway constituents characterize two different Wnt-related molecular classes (CTNNB1 and Wnt-TGFβ), accounting for half of all HCC patients. Sorafenib modulates β-catenin/Wnt signaling in experimental models that harbor the CTNNB1 class signature. Clin Cancer Res; 18(18); 4997–5007. ©2012 AACR.
Evening Cortisol Is Associated With Intra-Individual Instability in Daytime Napping in Nursing Home Residents With Dementia
Authors: Woods Diana Lynn , Yefimova Maria 
Published: July 2012

Background: Circadian rhythm disruption, reflected in alterations in sleep–wake activity and daytime napping behavior, is consistently reported in nursing home (NH) residents with dementia. This disruption may be reflected in day-to-day instability. The concept of allostatic load (AL), a measure of cumulative biological burden over a lifetime, may be a helpful model for understanding cortisol diurnal rhythm and daytime napping activity in this population. The purpose of this study was to examine the association between intra-individual daytime napping episodes and basal cortisol diurnal rhythm in NH residents with dementia in the context of AL. Method: Using a within-individual longitudinal design ( N = 51), the authors observed and recorded daytime napping activity every 20 min for 10 hr per day across 4 consecutive days. The authors obtained saliva samples 4 times each day (upon participants’ waking and within 1 hr, 6 hr, and 12 hr of participants’ wake time) for cortisol analysis. Results: The authors categorized participants as high changers (HCs; day-to-day instability in napping activity) or low changers (LCs; day-to-day stability). There were no significant differences in resident characteristics between groups. There was a significant difference between HCs and LCs in napping episodes ( F = 4.86, p = .03), with an interaction effect of evening cortisol on napping episodes in the HC group ( F = 10.161, p = .001). Conclusions: NH residents with unstable day-to-day napping episodes are more responsive to alterations in evening cortisol, an index of a dysregulated hypothalamic-pituitary-adrenal (HPA) axis. They may also be more amenable to environmental intervention, an avenue for further research.
Reorientation Deficits Are Associated With Amnestic Mild Cognitive Impairment
Authors: Caffò Alessandro O. , De Caro Maria F. , Picucci Luciana , Notarnicola Alessandra , Settanni Annalisa , Livrea Paolo , Lancioni Giulio E. , Bosco Andrea 
Published: July 2012

Background/Aims: Spatial memory can be impaired in amnestic mild cognitive impairment (aMCI). The present study investigates categorical spatial memory deficits using a virtual navigation-based reorientation task. Methods: Twenty-eight amnestic single domain and 23 amnestic multiple domain patients were compared with 53 healthy elderly controls on the performance of the virtual reorientation test (VReoT). Results: The reorientation performance of participants in both aMCI groups was significantly worse than that of controls suggesting that VReoT detects spatial memory deficits. No significant difference emerged between the 2 groups of patients. A subsequent receiver–operating characteristic analysis showed that a score of 8 had a sensitivity of 80.4% and a specificity of 94.3% (area under the curve = 0.90). Conclusion: The VReoT seemed to be accurate in differentiating patients with aMCI from controls and may represent an evaluation supplement for spatial memory deficits in prodromal stages of Alzheimer’s dementia.
STAM Protocol in Dementia
Authors: Ceccato Enrico , Vigato Giovanna , Bonetto Chiara , Bevilacqua Albina , Pizziolo Paolo , Crociani Susanna , Zanfretta Emanuele , Pollini Lorenza , Caneva Paolo Alberto , Baldin Lorella , Frongillo Cristina , Signorini Andrea , Demoro Sara , Barchi Elisabetta 
Published: July 2012

Background: The Sound Training for Attention and Memory in Dementia (STAM-Dem) is a manualized music-based protocol designed to be used in the rehabilitation of cognitive functions in elderly patients with dementia (PWD). Method: This was a multicenter, single-blind, randomized, and controlled trial that involved 51 PWD. The objective was to test the STAM-Dem efficacy. Patients in the experimental group followed the STAM-Dem for 2 weekly sessions of 45 minutes for 12 weeks (in addition to standard care). Those in the control group continued with the normal “standard care” provided. Results: In the experimental group, the instruments immediate prose memory test (MPI), deferred prose memory test (MPD), attentional matrices, activities of daily living, Music Therapy Activity Scale (SVAM) and Geriatric Music Therapy Profile (GMP) increase significantly from pre to post-test ( P < .05). Conclusion: The protocol is feasible and data suggest that there was an effect on attentino (matrices) and prose memory skills (MPI and MPD). The effect size reveals a general improvement in the results of the experimental group.