bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel live-dead staining methodology to study malaria parasite viability
Authors: Pasini Erica M , van den Ierssel Denise , Vial Henri J , Kocken Clemens HM 
Published: June 2013

AbstractBackgroundMalaria is a major health and socio-economical problem in tropical and sub-tropical areas of the world. Several methodologies have been used to assess parasite viability during the adaption of field strains to culture or the assessment of drug potential, but these are in general not able to provide an accurate real-time assessment of whether parasites are alive or dead.MethodsDifferent commercial dyes and kits were assessed for their potential to allow for the real-time detection of whether a blood stage malaria parasite is dead or alive.ResultsHere, a methodology is presented based on the potential-sensitive mitochondrial probe JC-1, which allows for the real-time visualization of live (red staining) and/or dead (absence of red staining) blood stage parasitesin vitroandex vivo. This method is applicable across malaria parasite species and strains and allows to visualize all parasite blood stages including gametocytes. Further, this methodology has been assessed also for use in drug sensitivity testing.ConclusionsThe JC-1 staining approach is a versatile methodology that can be used to assess parasite viability during the adaptation of field samples to culture and during drug treatment. It was found to hold promise in the assessment of drugs expected to lead to delayed death phenotypes and it currently being evaluated as a method for the assessment of parasite viability during the adaptation of patient-derivedPlasmodium vivaxto long-termin vitroculture.
Delivery of small interfering RNAs in human cervical cancer cells by polyethylenimine-functionalized carbon nanotubes
Authors: Huang Yuan-Pin , Lin I-Jou , Chen Chih-Chen , Hsu Yi-Chiang , Chang Chi-Chang , Lee Mon-Juan 
Published: June 2013

Abstract
Carbon nanotubes are capable of penetrating the cell membrane and are widely considered as potential carriers for gene or drug delivery. Because the C-C and C=C bonds in carbon nanotubes are nonpolar, functionalization is required for carbon nanotubes to interact with genes or drugs as well as to improve their biocompatibility. In this study, polyethylenimine (PEI)-functionalized single-wall (PEI-NH-SWNTs) and multiwall carbon nanotubes (PEI-NH-MWNTs) were produced by direct amination method. PEI functionalization increased the positive charge on the surface of SWNTs and MWNTs, allowing carbon nanotubes to interact electrostatically with the negatively charged small interfering RNAs (siRNAs) and to serve as nonviral gene delivery reagents. PEI-NH-MWNTs and PEI-NH-SWNTs had a better solubility in water than pristine carbon nanotubes, and further removal of large aggregates by centrifugation produced a stable suspension of reduced particle size and improved homogeneity and dispersity. The amount of grafted PEI estimated by thermogravimetric analysis was 5.08% (w/w) and 5.28% (w/w) for PEI-NH-SWNTs and PEI-NH-MWNTs, respectively. For the assessment of cytotoxicity, various concentrations of PEI-NH-SWNTs and PEI-NH-MWNTs were incubated with human cervical cancer cells, HeLa-S3, for 48 h. PEI-NH-SWNTs and PEI-NH-MWNTs induced cell deaths in a dose-dependent manner but were less cytotoxic compared to pure PEI. As determined by electrophoretic mobility shift assay, siRNAs directed against glyceraldehyde-3-phosphate dehydrogenase (siGAPDH) were completely associated with PEI-NH-SWNTs or PEI-NH-MWNTs at a PEI-NH-SWNT/siGAPDH or PEI-NH-MWNT/siGAPDH mass ratio of 80:1 or 160:1, respectively. Furthermore, PEI-NH-SWNTs and PEI-NH-MWNTs successfully delivered siGAPDH into HeLa-S3 cells at PEI-NH-SWNT/siGAPDH and PEI-NH-MWNT/siGAPDH mass ratios of 1:1 to 20:1, resulting in suppression of the mRNA level of GAPDH to an extent similar to that of DharmaFECT, a common transfection reagent for siRNAs. Our results indicate that the PEI-NH-SWNTs and PEI-NH-MWNTs produced in this study are capable of delivering siRNAs into HeLa-S3 cells to suppress gene expression and may therefore be considered as novel nonviral gene delivery reagents.
On the solution of high order stable time integration methods
Authors: Axelsson Owe , Blaheta Radim , Sysala Stanislav , Ahmad Bashir 
Published: June 2013

Abstract
Evolution equations arise in many important practical problems. They are frequently stiff, i.e. involves fast, mostly exponentially, decreasing and/or oscillating components. To handle such problems, one must use proper forms of implicit numerical time-integration methods. In this paper, we consider two methods of high order of accuracy, one for parabolic problems and the other for hyperbolic type of problems. For parabolic problems, it is shown how the solution rapidly approaches the stationary solution. It is also shown how the arising quadratic polynomial algebraic systems can be solved efficiently by iteration and use of a proper preconditioner.
Mutations in variable domains of the HIV-1 envelope gene can have a significant impact on maraviroc and vicriviroc resistance
Authors: Asin-Milan Odalis , Chamberland Annie , Wei Yi , Haidara Alpha , Sylla Mohamed , Tremblay Cécile L 
Published: June 2013

Abstract

Background
Resistance to CCR5 inhibitors, such as maraviroc and vicriviroc is characterized by reduction of maximal percent inhibition which indicates the use of an inhibitor-bound conformation of CCR5 for human immunodeficiency virus-1(HIV-1) entry. It is accompanied by substitutions in gp120 and gp41. Variable domain 3 (V3) plays the most important role, but substitutions outside V3 could also be involved in phenotype resistance. In this work, we investigated how mutations in variable regions of the viral envelope protein gp120 can contribute to CCR5 inhibitor resistance.

Methods
Resistant isolates were selected by passaging CC1/85 and BaL viruses with sub-inhibitory MVC and VCV concentrations. Mutations in gp160 were identified and mutants containing V2 (V169M), V3 (L317W) and V4 (I408T) were constructed.

Results
MVC and VCV susceptibility and viral tropism were assessed by single cycle assay. Mutant I408T showed 4-fold change (FC) increase in the half maximal inhibitory concentration (IC50) to MVC, followed by L317W (1.52-FC), V169M (1.23-FC), V169M/I408T (4-FC) L317W/I408T (3-FC), V169M/L317W (1.30-FC), and V169M/L317W/I408T (3.31-FC). MPI reduction was observed for mutants I408T (85%), L317W (95%), V169M/I408T (84%), L317W/I408T (85%) and V169M/L317W/I408T (83%). For VCV, I408T increased the IC50 by 2-FC and few mutants showed MPI reduction less than 95%: I408T (94%), L317W/I408T (94%) and V169M/L317W/I408T (94%). All mutants remained R5-tropic and presented decreased infectivity.

Conclusions
These results suggest that mutations in the V4 loop of HIV-1 may contribute to MVC and VCV resistance alone or combined with mutations in V2 and V3 loops.
Intranasal immunization with a helper-dependent adenoviral vector expressing the codon-optimized fusion glycoprotein of human respiratory syncytial virus elicits protective immunity in BALB/c mice
Authors: Fu Yuan-Hui , He Jin-Sheng , Qiao Wei , Jiao Yue-Ying , Hua Ying , Zhang Ying , Peng Xiang-Lei , Hong Tao 
Published: June 2013

Abstract

Background
Human respiratory syncytial virus (RSV) is a serious pediatric pathogen of the lower respiratory tract. Currently, there is no clinically approved vaccine against RSV infection. Recent studies have shown that helper-dependent adenoviral (HDAd) vectors may represent effective and safe vaccine vectors. However, viral challenge has not been investigated following mucosal vaccination with HDAd vector vaccines.

Methods
To explore the role played by HDAd as an intranasally administered RSV vaccine vector, we constructed a HDAd vector encoding the codon optimized fusion glycoprotein (Fsyn) of RSV, designated HDAd-Fsyn, and delivered intranasally HDAd-Fsyn to mice.

Results
RSV-specific humoral and cellular immune responses were generated in BALB/c mice, and serum IgG with neutralizing activity was significantly elevated after a homologous boost with intranasal (i.n.) application of HDAd-Fsyn. Humoral immune responses could be measured even 14 weeks after a single immunization. Immunization with i.n. HDAd-Fsyn led to effective protection against RSV infection on challenge.

Conclusion
The results indicate that HDAd-Fsyn can induce powerful systemic immunity against subsequent i.n. RSV challenge in a mouse model and is a promising candidate vaccine against RSV infection.
A reported death case of a novel bunyavirus in Shanghai, China
Authors: Pan Hao , Hu Jiayu , Liu Shelan , Shen Hong , Zhu Yiyi , Wu Jiabing , Zhang Xi , Zhou Xin , Wang Chengmin , Qu Jing , Yuan Zheng’an 
Published: June 2013

Abstract
This paper describes the first case of infection with a recently described novel bunyavirus, severe fever with thrombocytopenia syndrome virus (SFTSV), in Shanghai, China. The case is originally from Chizhou City, Anhui province within an endemic area for SFTSV. We describe the etiology, epidemiological characteristics, clinical diagnosis and treatment of this fatal case. This case is unique because major cause of death was renal failure, whereas other reported cases have been due to hemorrhage. The investigation and response to this case provides meaningful insight for the early and rapid diagnosis, treatment, prevention and control of severe fever with thrombocytopenia syndrome virus in non-endemic regions in China and globally.
Primary pulmonary blastoma of monophasic variety- diagnosis and management
Authors: Mistry Jitendra H , Pawar Sumita B , Mehta Harshad , Popov Aron Frederik , Mohite Prashant Nanasaheb 
Published: June 2013

Abstract
Pulmonary blastoma is a rare primary lung neoplasm, in that monophasic variety is far too rare. There are no specific clinical features seen for pulmonary blastoma; computed tomography and histopathology are diagnostic. Surgical excision is the treatment of choice; however, adjuvant chemotherapy and radiotherapy may be required in large and aggressive tumors.
Inferring chemical reaction patterns using rule composition in graph grammars
Authors: Andersen Jakob L , Flamm Christoph , Merkle Daniel , Stadler Peter F 
Published: June 2013

Abstract

Background
Modeling molecules as undirected graphs and chemical reactions as graph rewriting operations is a natural and convenient approach to modeling chemistry. Graph grammar rules are most naturally employed to model elementary reactions like merging, splitting, and isomerisation of molecules. It is often convenient, in particular in the analysis of larger systems, to summarize several subsequent reactions into a single composite chemical reaction.

Results
We introduce a generic approach for composing graph grammar rules to define a chemically useful rule compositions. We iteratively apply these rule compositions to elementary transformations in order to automatically infer complex transformation patterns. As an application we automatically derive the overall reaction pattern of the Formose cycle, namely two carbonyl groups that can react with a bound glycolaldehyde to a second glycolaldehyde. Rule composition also can be used to study polymerization reactions as well as more complicated iterative reaction schemes. Terpenes and the polyketides, for instance, form two naturally occurring classes of compounds of utmost pharmaceutical interest that can be understood as “generalized polymers” consisting of five-carbon (isoprene) and two-carbon units, respectively.

Conclusion
The framework of graph transformations provides a valuable set of tools to generate and investigate large networks of chemical networks. Within this formalism, rule composition is a canonical technique to obtain coarse-grained representations that reflect, in a natural way, “effective” reactions that are obtained by lumping together specific combinations of elementary reactions.
Efficacy of falls prevention interventions: protocol for a systematic review and network meta-analysis
Authors: Tricco Andrea C , Cogo Elise , Holroyd-Leduc Jayna , Sibley Kathryn M , Feldman Fabio , Kerr Gillian , Majumdar Sumit R , Jaglal Susan , Straus Sharon E 
Published: June 2013

Abstract

Background
Falls are a leading cause of morbidity and mortality in older adults. Although numerous trials of falls prevention interventions have been completed, there is extensive variation in their intervention components and clinical context, such that the key elements of an effective falls prevention program remain unclear to patients, clinicians, and policy-makers. Our objective is to identify the most effective interventions and combinations of interventions that prevent falls though a systematic review and meta-analysis, including a network meta-analysis.

Methods/Design
We will search for published (e.g., MEDLINE, EMBASE, Cochrane Central Register of Controlled Trials, Ageline) and unpublished (e.g., trial registries, dissertations) randomised clinical trials (RCTs) in all languages examining interventions to prevent falls compared to usual care or other falls prevention interventions among adults aged ≥65 years from all settings (e.g., community, acute care, long-term care, and rehabilitation). The primary outcomes are number of injurious falls and number of hospitalizations due to falls. Secondary outcomes include falls rate, number of fallers, number of emergency room visits due to falls, number of physician visits due to falls, number of fractures, costs, and number of intervention-related harms (e.g., muscle soreness related to exercise).
We will calibrate our eligibility criteria amongst the team and two independent team members will screen the literature search results in duplicate. Conflicts will be resolved through team discussion. A similar process will be used for data abstraction and quality appraisal with the Cochrane risk of bias tool.
Our results will be synthesized descriptively and a random effects meta-analysis will be conducted if the studies are deemed methodologically, clinically, and statistically (e.g., I2<60%) similar. If appropriate, a network meta-analysis will be conducted, which will allow the comparison of interventions that have not been compared in head-to-head RCTs, as well as the effectiveness of interventions.

Discussion
We will identify the most effective interventions and combinations of interventions that prevent falls in older people. Our results will be used to optimize falls prevention strategies, and our goal is to ultimately improve the health of seniors internationally.

Systematic review registration
PROSPERO registry number: CRD42013004151
Clinical risk factors for late intestinal toxicity after radiotherapy: a systematic review protocol
Authors: Qin Qiyuan , Huang Qingshan , Zhong Qinghua , Fan Xinjuan , Chen Dianke , Wang Lei 
Published: June 2013

Abstract

Background
Late intestinal toxicity after radiotherapy (LITAR) not only limits the radiation dose, which subsequently leads to unfavorable clinical outcomes, but also significantly lowers the quality of life in an increasing number of cancer survivors. Therefore, identifying clinical risk factors for LITAR is important for establishing a predictive model in the clinical setting of decision-making for these patients. This review aims to systematically summarize and clarify the clinical factors that can be potentially associated with an increased risk of moderate/severe LITAR in patients with abdominal or pelvic malignancies.

Methods/design
MEDLINE, EMBASE, Web of Science, Cochrane Central Register of Controlled Trials, Scopus, Google Scholar and Chinese BioMed will be systematically searched to identify appropriate studies. Citations of the retrieved studies and recent reviews will also be searched separately by case.
The enrolled studies should at least have the following information: (1) a clear definition and information on the LITAR severity; (2) assess clinical factors for moderate/severe toxicity with adjusted risk estimates; (3) have a cohort, case–control, randomized controlled trial and controlled clinical trial study design.
Two authors will independently review the abstract and full text of retrieved studies, extract data from eligible studies and assess the risk of bias. Disagreements will be discussed among reviewers until a consensus is reached. The effect of identified risk factors will be displayed in forest plots. If the information is sufficient, results will be synthesized by a meta-analysis with the random effects model to pool the estimate of risk posed by clinical factors. Subgroup and sensitivity analysis will be used to explore the sources of heterogeneity.

Discussion
This review will summarize the evidence of clinical risk factors for moderate/severe LITAR. The results may help guide decision-making and minimize the side effects of therapeutic modalities in the clinical setting.

Systematic review registration
This review has been registered at PROSPERO. The registration no. isCRD42013003744.
Psychrotrophic yeast Yarrowia lipolytica NCYC 789 mediates the synthesis of antimicrobial silver nanoparticles via cell-associated melanin
Authors: Apte Mugdha , Sambre Devashree , Gaikawad Shital , Joshi Swanand , Bankar Ashok , Kumar Ameeta Ravi , Zinjarde Smita 
Published: June 2013

Abstract
A psychrotrophic marine strain of the ascomycetous yeast Yarrowia lipolytica (NCYC 789) synthesized silver nanoparticles (AgNPs) in a cell-associated manner. These nanostructures were characterized by UV-Visible spectroscopy and scanning electron microscope-energy dispersive spectrometer (SEM-EDS) analysis. The brown pigment (melanin) involved in metal-interactions was obtained from the cells. This extracted pigment also mediated the synthesis of silver nanoparticles that were characterized by a variety of analytical techniques. The melanin-derived nanoparticles displayed antibiofilm activity. This paper thus reports the synthesis of AgNPs by the biotechnologically important yeast Y. lipolytica; proposes a possible mechanism involved in the synthetic process and describes the use of the bio-inspired nanoparticles as antibiofilm agents.
A geophysical investigation of the active Hockley Fault System near Houston, Texas
Authors: Khan Shuhab D. , Stewart Robert R. , Otoum Maisam , Chang Li 
Published: June 2013

Sedimentation and deformation toward the Gulf of Mexico Basin cause faulting in the coastal regions. In particular, many active (but non-seismic) faults underlie the Houston metropolitan area. Using geophysical data, we have examined the Hockley Fault System in northwest Harris County. Airborne LiDAR is an effective tool to identify fault scarps and we have used it to identify several new faults and assemble an updated map for the faults in Houston and surrounding areas. Two different LiDAR data sets (from 2001 to 2008) provide time-lapse images and suggest elevation changes across the Hockley Fault System at the rate of 10.9 mm/yr. This rate is further supported by GPS data from a station located on the downthrown side of the Hockley Fault System indicating movement at 13.8 mm/yr. To help illuminate the subsurface character of the faults, we undertook geophysical surveys (ground-penetrating radar, seismic reflection, and gravity) across two strands of the Hockley Fault System. Ground-penetrating radar data show discontinuous events to a depth of 10 m at the main fault location. Seismic data, from a vibroseis survey along a 1-km line perpendicular to the fault strike, indicate faulting to at least 300-m depth. The faults have a dip of about 70°. Gravity data show distinct changes across the fault. However, there are two contrasting Bouguer anomalies depending on the location of the transects and their underlying geology. Our geophysical surveys were challenged by urban features (especially traffic and access). However, the survey results consistently locate the fault and hold significant potential to understand its deformational features as well as assist in associated building zoning.
Neurokinin B Activates Arcuate Kisspeptin Neurons Through Multiple Tachykinin Receptors in the Male Mouse
Authors: de Croft Simon , Boehm Ulrich , Herbison Allan E. 
Published: June 2013

AbstractKisspeptin neurons located in the arcuate nucleus (ARN) coexpress dynorphin and neurokinin B (NKB) and may interact to influence gonadotropin secretion. Using a kisspeptin-green fluorescent protein mouse model, the present study examined whether the neuropeptides kisspeptin, dynorphin, and NKB modulate the electrical activity of ARN kisspeptin neurons in the adult male mouse. Cell-attached recordings showed that kisspeptin itself had no effect on kisspeptin neuron firing. Dynorphin and the κ-opioid receptor agonist U50-488 evoked a potent suppression of all ARN kisspeptin neuron firing that was blocked completely by the κ-opioid receptor antagonist nor-Binaltorphimine. Both NKB and Senktide, a neurokinin 3 receptor agonist, exerted a potent stimulatory action on ∼95% of ARN kisspeptin neurons. Although the selective neurokinin 3 receptor antagonists SB222200 and SR142801 blocked the effects of Senktide on kisspeptin neurons, they surprisingly had no effect on NKB activation of firing. Studies with selective neurokinin 1 receptor (SDZ-NKT343) and neurokinin 2 receptor (GR94800) antagonists revealed that the activation of kisspeptin neurons by NKB was only blocked completely by a cocktail of antagonists against all 3 tachykinin receptors. Whole-cell recordings revealed that individual kisspeptin neurons were activated directly by all 3 tachykinins substance, P, neurokinin A, and NKB. These experiments show that dynorphin and NKB have opposing actions on the electrical activity of kisspeptin neurons supporting the existence of an interconnected network of kisspeptin neurons in the ARN. However, the effects of NKB result from an unexpected activation of multiple tachykinin receptors.
transparent, a gene affecting stripe formation in Zebrafish, encodes the mitochondrial protein Mpv17 that is required for iridophore survival
Authors: Krauss Jana , Astrinides Pantilis , Frohnhöfer Hans Georg , Walderich Brigitte , Nüsslein-Volhard Christiane 
Published: June 2013

SummaryIn the skin of adult zebrafish, three pigment cell types arrange into alternating horizontal stripes, melanophores in dark stripes, xanthophores in light interstripes and iridophores in both stripes and interstripes. The analysis of mutants and regeneration studies revealed that this pattern depends on interactions between melanophores and xanthophores; however, the role of iridophores in this process is less understood. We describe the adult viable and fertile mutant transparent (tra), which shows a loss or strong reduction of iridophores throughout larval and adult stages. In addition, in adults only the number of melanophores is strongly reduced, and stripes break up into spots. Stripes in the fins are normal. By cell transplantations we show that tra acts cell-autonomously in iridophores, whereas the reduction in melanophores in the body occurs secondarily as a consequence of iridophore loss. We conclude that differentiated iridophores are required for the accumulation and maintenance of melanophores during pigment pattern formation. The tra mutant phenotype is caused by a small deletion in mpv17, an ubiquituously expressed gene whose protein product, like its mammalian and yeast homologs, localizes to mitochondria. Iridophore death might be the result of mitochondrial dysfunction, consistent with the mitochondrial DNA depletion syndrome observed in mammalian mpv17 mutants. The specificity of the tra phenotype is most likely due to redundancy after gene multiplication, making this mutant a valuable model to understand the molecular function of Mpv17 in mitochondria.