bluuebunny/crossref_metadata_2025 huggingface dataset:
Benchmarking short sequence mapping tools
Authors: Hatem Ayat , Bozdağ Doruk , Toland Amanda E , Çatalyürek Ümit V
Published: June 2013

Background

The development of next-generation sequencing instruments has led to the generation of millions of short sequences in a single run. The process of aligning these reads to a reference genome is time consuming and demands the development of fast and accurate alignment tools. However, the current proposed tools make different compromises between the accuracy and the speed of mapping. Moreover, many important aspects are overlooked while comparing the performance of a newly developed tool to the state of the art. Therefore, there is a need for an objective evaluation method that covers all the aspects. In this work, we introduce a benchmarking suite to extensively analyze sequencing tools with respect to various aspects and provide an objective comparison.

Results

We applied our benchmarking tests on 9 well known mapping tools, namely, Bowtie, Bowtie2, BWA, SOAP2, MAQ, RMAP, GSNAP, Novoalign, and mrsFAST (mrFAST) using synthetic data and real RNA-Seq data. MAQ and RMAP are based on building hash tables for the reads, whereas the remaining tools are based on indexing the reference genome. The benchmarking tests reveal the strengths and weaknesses of each tool. The results show that no single tool outperforms all others in all metrics. However, Bowtie maintained the best throughput for most of the tests while BWA performed better for longer read lengths. The benchmarking tests are not restricted to the mentioned tools and can be further applied to others.

Conclusion

The mapping process is still a hard problem that is affected by many factors. In this work, we provided a benchmarking suite that reveals and evaluates the different factors affecting the mapping process. Still, there is no tool that outperforms all of the others in all the tests. Therefore, the end user should clearly specify his needs in order to choose the tool that provides the best results.
Late-onset secondary pigmentary glaucoma following foldable intraocular lenses implantation in the ciliary sulcus: a long-term follow-up study
Authors: Chang Shirley HL , Wu Wei-Chi , Wu Shiu-Chen
Published: June 2013

Background

To review the long-term outcomes of eyes with secondary pigmentary glaucoma associated with the implantation of foldable intraocular lenses (IOL) in the ciliary sulcus.

Methods

The study retrospectively reviewed a series of cases who developed secondary pigmentary glaucoma after cataract operations. Data were collected from cases that were referred between 2002 and 2011.

Results

Ten eyes of 10 patients who developed secondary pigmentary glaucoma after foldable IOLs implantation in the sulcus were included in this study.

Intraocular pressure (IOP) elevation was present in 2 eyes (20%) within the first 2 weeks following the initial cataract operation. The onset of glaucoma was delayed in the other 8 eyes (80%); the average onset time in these eyes was 21.9 ± 17.1 months after the initial cataract operation. Six eyes (60%) received surgical treatment because of large fluctuations and poor control of IOPs. Only 3 eyes (30%) achieved final visual acuities better than 20/40.

Conclusion

Secondary pigmentary glaucoma accompanying the implantation of a foldable IOL in the ciliary sulcus may present as acute IOP elevation during the early postoperative period or, more commonly, late onset of IOP elevation accompanied by advanced glaucomatous optic nerve damage. Despite treatment, the visual prognosis for these patients can be poor. Placing a foldable IOL in the ciliary sulcus could pose a threat to the vision of the patients and long-term follow-up of IOP in these patients is necessary.
The effectiveness of critical time intervention for abused women and homeless people leaving Dutch shelters: study protocol of two randomised controlled trials
Authors: Lako Danielle AM , de Vet Renée , Beijersbergen Mariëlle D , Herman Daniel B , van Hemert Albert M , Wolf Judith RLM
Published: June 2013

Background

One of the main priorities of Dutch organisations providing shelter services is to develop evidence-based interventions in the care for abused women and homeless people. To date, most of these organisations have not used specific intervention models and the interventions which have been implemented rarely have an empirical and theoretical foundation. The present studies aim to examine the effectiveness of critical time intervention (CTI) for abused women and homeless people.

Methods

In two multi-centre randomised controlled trials we investigate whether CTI, a time-limited (nine month) outreach intervention, is more effective than care-as-usual for abused women and homeless people making the transition from shelter facilities to supported or independent housing. Participants were recruited in 19 women’s shelter facilities and 22 homeless shelter facilities across The Netherlands and randomly allocated to the intervention group (CTI) or the control group (care-as-usual). They were interviewed four times in nine months: once before leaving the shelter, and then at three, six and nine months after leaving the shelter. Quality of life (primary outcome for abused women) and recurrent loss of housing (primary outcome for homeless people) as well as secondary outcomes (e.g. care needs, self-esteem, loneliness, social support, substance use, psychological distress and service use) were assessed during the interviews. In addition, the model integrity of CTI was investigated during the data collection period.

Discussion

Based on international research CTI is expected to be an appropriate intervention for clients making the transition from institutional to community living. If CTI proves to be effective for abused women and homeless people, shelter services could include this case management model in their professional standards and improve the (quality of) services for clients.

Trial registration

NTR3463 and NTR3425
Toxicological evaluation of Terminalia paniculata bark extract and its protective effect against CCl4-induced liver injury in rodents
Authors: Talwar Sahil , Jagani Hitesh V , Nayak Pawan G , Kumar Nitesh , Kishore Anoop , Bansal Punit , Shenoy Rekha R , Nandakumar Krishnadas
Published: June 2013

Background

Based on the reported antioxidant and anti-inflammatory potential of Terminalia paniculata, the bark aqueous extract (TPW) was investigated against liver damage.

Methods

Intrinsic cytotoxicity was tested on normal human liver (Chang) cell lines, followed by acute and sub-chronic toxicity studies in mice. TPW was then evaluated against CCl4-induced liver toxicity in rats. Liver enzymes (AST, ALT, and ALP) and antioxidant markers were assessed. The effect of TPW on isolated hepatic cells, post-CCl4 administration, was assessed by isolated mitochondrial membrane staining. The actions of TPW on apoptotic pathway in CCl4-treated Chang cells were also elucidated.

Results

TPW was found to be safe at all doses tested in both in vitro and in vivo toxicity studies. TPW (400 mg/kg, p.o.) significantly (*p <0.05) improved liver enzyme activity as compared to CCl4. Also, it improved antioxidant status (GSH, GST, MDA and total thiol) and preserved hepatic cell architecture. TPW pre-treatment significantly attenuated the levels of phospho-p53, p53, cleaved caspase-3, phospho-Bad, Bad and cleaved PARP in CCl4-treated Chang cells, improving the viability considerably.

Conclusion

The findings support a protective role for Terminalia paniculata in pathologies involving oxidative stress.
Homofermentative production of optically pure L-lactic acid from xylose by genetically engineered Escherichia coli B
Authors: Zhao Jinfang , Xu Liyuan , Wang Yongze , Zhao Xiao , Wang Jinhua , Garza Erin , Manow Ryan , Zhou Shengde
Published: June 2013

Background

Polylactic acid (PLA), a biodegradable polymer, has the potential to replace (at least partially) traditional petroleum-based plastics, minimizing “white pollution”. However, cost-effective production of optically pure L-lactic acid is needed to achieve the full potential of PLA. Currently, starch-based glucose is used for L-lactic acid fermentation by lactic acid bacteria. Due to its competition with food resources, an alternative non-food substrate such as cellulosic biomass is needed for L-lactic acid fermentation. Nevertheless, the substrate (sugar stream) derived from cellulosic biomass contains significant amounts of xylose, which is unfermentable by most lactic acid bacteria. However, the microorganisms that do ferment xylose usually carry out heterolactic acid fermentation. As a result, an alternative strain should be developed for homofermentative production of optically pure L-lactic acid using cellulosic biomass.

Results

In this study, an ethanologenic Escherichia coli strain, SZ470 (ΔfrdBC ΔldhA ΔackA ΔpflB ΔpdhR ::pflBp6-acEF-lpd ΔmgsA), was reengineered for homofermentative production of L-lactic acid from xylose (1.2 mole xylose = > 2 mole L-lactic acid), by deleting the alcohol dehydrogenase gene (adhE) and integrating the L-lactate dehydrogenase gene (ldhL) of Pediococcus acidilactici. The resulting strain, WL203, was metabolically evolved further through serial transfers in screw-cap tubes containing xylose, resulting in the strain WL204 with improved anaerobic cell growth. When tested in 70 g L-1 xylose fermentation (complex medium), WL204 produced 62 g L-1 L-lactic acid, with a maximum production rate of 1.631 g L-1 h-1 and a yield of 97% based on xylose metabolized. HPLC analysis using a chiral column showed that an L-lactic acid optical purity of 99.5% was achieved by WL204.

Conclusions

These results demonstrated that WL204 has the potential for homofermentative production of L-lactic acid using cellulosic biomass derived substrates, which contain a significant amount of xylose.
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

Background

Malaria 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.

Methods

Different 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.

Results

Here, 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.

Conclusions

The 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

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

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

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

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

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

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

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

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

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

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.
An algorithm for 3D acoustic time-Laplace-Fourier-domain hybrid full waveform inversion
Authors: Kim Youngseo , Shin Changsoo , Calandra Henri , Min Dong-Joo
Published: June 2013

When full waveform inversion (FWI) is performed in the Laplace-Fourier domain, Laplace-Fourier-domain wave modeling, using finite-difference or finite-element methods, is performed to compute the gradient direction. In this case, a complex impedance matrix is composed and factored by direct matrix solvers. Alternatively, iterative matrix solvers may be used. However, solving 3D problems with such methods requires excessive computer memory or computing time, which causes problems in the application of the Laplace-Fourier-domain FWI. To avoid computational overburden in 3D problems, we propose a time-Laplace-Fourier hybrid FWI, in which forward and backward modeling are performed in the time domain and other procedures are conducted in the Laplace-Fourier domain. Our hybrid FWI is applied to two groups of frequencies. Inversions for the first and second groups of frequencies correspond to the Laplace-domain FWI and the Laplace-Fourier-domain FWI, respectively. The graphic processing unit is used to speed up the hybrid inversion algorithm. To verify the feasibility of this technique, the 3D hybrid FWI is applied to the data recorded along the A1 line of the synthetic SEG/EAGE 3D salt model and 3D wide-azimuth real exploration data. Numerical examples show that the hybrid FWI yields reasonable subsurface velocity structures that contribute to the enhancement of reverse-time migration images.
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.
MASW surveys in landfill sites in Australia
Authors: Suto Koya
Published: June 2013

Multichannel analysis of surface waves (Park et al., 1999), commonly called MASW, is a seismic technique used to map the near-surface S-wave velocity structure. It has been applied to a range of geotechnical engineering problems, such as detection of cavities (Miller et al., 1999), the search for bedrock structure (Carnevale et al., 2005), examining water seepage (Ivanov et al., 2006), and monitoring ground improvement (Burke and Schofield, 2008). As a by-product of urban development, industrial and domestic refuge is amassed and deposited in various places, ranging from naturally low ground to abandoned quarries. These places are called landfill sites. As urban development progresses, the landfill sites reach their capacity and become unsuitable for further filling. At that point, a variety of approaches are considered as a means of increasing the capacity. When housing developments creep up to the fill site, more refuse is not welcomed and the land use is reconsidered.
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

Kisspeptin 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

In 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.
IR–UV Double Resonance Spectroscopy as Implemented by Polarized Laser Schemes: Probing Orientations of Vibrational Transition Dipole Moments
Authors: Urashima Shu-hei , Miyazaki Mitsuhiko , Fujii Masaaki , Saigusa Hiroyuki
Published: June 2013

IR–UV double resonance spectroscopy based on polarized laser schemes is developed in order to gain information on the orientations of vibrational transition dipole moments. Polarization dependence of IR band shape is presented for the two amino stretching modes of aniline.
Serum heparan sulfate concentration in healthy subjects
Authors: Kaznowska-Bystryk Iwona , Żeleźnik Sylwia , Matros Olga , Solski Janusz
Published: June 2013

Heparan sulfate is one of the essential components of extracellular matrices and plasma membrane. They take part in the interaction with protein ligands, which affects the metabolism, transport, information transfer, support and regulation in all organ systems. The aim of the study was to examine the physiological HS level in the serum of the healthy subjects, as well as to check if this level is age- and sex- related.
The research was conducted on 30 healthy subjects: 16 women and 14 men, aged from 23 to 65 years, with the average of 30 years. Quantificational determination of HS was performed with the use of Heparan Sulfate ELISA kit. Concentrations of total cholesterol, HDL-cholesterol and triglycerides were measured with the use of standard enzymatic methods. The LDL-cholesterol was analyzed by direct method, and non-HDL-cholesterol was calculated. Based on the conducted research, it can be concluded that higher HS serum concentrations were observed in the group of healthy men compared to women group, and in the older ≥30 year-old group. The determination of serum HS concentration should consider gender and age differences in the result interpretation. Changes in HS serum concentrations are not correlated with the changes in the lipid profile parameters. For complete determining of existing statistical correlations between HS concentration, age, gender and the lipid profile parameters study results require confirmation on a greater number of cases.
Tea – natural source of fluoride compounds
Authors: Sikorska-Jaroszyńska Małgorzata H.J. , Mielnik-Błaszczak Maria , Krawczyk Dorota , Wróbel Rafał , Błaszczak Jerzy
Published: June 2013

Tea has come to be regarded as a very popular drink, and is nowadays consumed in almost the same amounts as water. Tea has antioxidant properties, influences the organism’s antioxidant status and prevents oxidative stress. Tea constitutes a very rich fluoride source. In the paper the influence of fluorides on human organism, soft and hard dental tissues and occurrence of dental and skeletal fluorosis was discussed.
Ozone, bacterial biofilm and dental caries – a review of literature
Authors: Sikorska-Jaroszyńska Małgorzata H.J. , Mielnik-Błaszczak Maria , Krawczyk Dorota , Wróbel Rafał , Błaszczak Jerzy
Published: June 2013

Ozone is an allotrope of oxygen in the form of triatomic molecules (O3). Recently, ozone and ozone therapy have become an object of ever increasing interest in the sphere of medicine and dentistry. In the paper the mechanisms of action, ozone’s influence on human organism and the role in medicine are discussed.
Assessment of oxidative stress parameters in rats pretreated with Ukrain and amitriptyline
Authors: Gawrńska-Grzywacz Monika , Herbet Mariola , Szcząchor Monika , Jagiełło-Wójtowicz Ewa
Published: June 2013

Our research aimed to evaluate the oxidant-antioxidant balance in rats exposed to the Ukrain and AMI drugs. The effect of 14-day administration of these drugs on selected parameters of oxidative stress in blood of rats has been investigated. The activity of antioxidant enzymes, namely glutathione peroxidase (GPX) and reductase (GR), and Total Antioxidant Status (TAS) were determined. It was noted that combined 14-day use of Ukrain (14 or 28 mg/kg) and AMI (10 mg/kg) significantly increased TAS and did not affect the activity of GPX and GR in comparison to groups receiving only Ukrain or AMI alone. While Ukrain administered to rats for 14 days in the above doses did not affect either the activity of the enzymes assayed or the level of TAS. After 2-week treatment with AMI at a dose of 10 mg/kg any statistically significant change of the enzymes activitiy or TAS concentration was not reported either, compared with the control group. The results indicate the beneficial effect of the combination of Ukrain and AMI drugs on the oxidant-antioxidant balance and increasing the antioxidant status in rats.
Validation of the doxycycline hydrochloride determination by high-performance liquid chromatography technique
Authors: Kurzawa Marzanna , Filipiak-Szok Anna , Czubachowski Tomasz , Szłyk Edward
Published: June 2013

A sensitive and reproducible chromatographic method was developed and validated for the quantification of doxycycline hydrochloride in veterinary product – Doxycyclinum 50%. The analysis was performed on HPLC (Shimadzu) apparatus with diode array detector. The separation was provided with C18 column (4.6mm×100 mm, 3 μm particle size) at mobile phase flow rate 1ml/min and detection at 254 nm. The method was tested in the range 50-150% nominal DOXY concentration resulting good linearity with correlation coefficient r=0.9999. The estimated LOD and LOQ elaborated method amounted to 0.46 and 1.55 mg/L. The recovery values were from 99.70 to 100.9% with RSD 0.78%. It was confirmed that the reagents used for testing of samples and solvents do not interfere with the active substance. Moreover, the significant influence of temperature and flow rate on the retention time was ascertained. The carried out research demonstrates that the method is validated and the obtained results are accurate and reproducible. The elaborated method can be suitable to routine analysis in quality control laboratory.
Formulation and stability evaluation of hydrogels with ketoconazole
Authors: Wróblewska Magdalena , Winnicka Katarzyna
Published: June 2013

This study is focused on designing hydrogels with ketoconazole (KET) based on two polymers - Carbopol 980 or hydroxyethyl cellulose (HEC). Hydrogels were stored for 6 months at different temperature and relative humidity conditions (4ºC ± 2ºC, 25ºC ± 2ºC and 60% ± 5% RH, 40ºC ± 2ºC and 75% ± 5% RH). It was found that hydrogels made of Carbopol 980 exhibited more favourable physicochemical properties and better stability . In HEC hydrogels stored at 40ºC ± 2ºC and 75% ± 5% RH a decrease of pH, differences in the content and sedimentation of KET were observed. In vitro release study showed that amount of released KET from designed hydrogels was definitely higher than from registered product.
Dynamics and efficiency of photoinduced charge transport in DNA:
Toward the elusive molecular wire
Authors: Lewis Frederick D. , Wasielewski Michael R.
Published: June 2013

Experimental investigations of photoinduced charge transport in synthetic DNA
capped hairpins possessing electron acceptor and donor stilbene chromophores at
either end have established the mechanism, dynamics, and efficiency of charge
transport in DNA. The mechanism for charge transport in repeating A-T base pairs
(A-tracts) was found to change from single-step superexchange at short distances
to multistep incoherent hole hopping at longer distances. The rate constants for
base-to-base hole hopping in longer A- and G-tract sequences are 1.2
× 109 s–1 and 4.3 × 109 s–1,
respectively, considerably slower than the rate constants associated with
molecular wires. Even slower rate constants are observed for alternating or
random base sequences such as those encountered in natural DNA. The efficiency
of charge separation in capped hairpins with A-tract sequences is also low as a
consequence of the competition of hole hopping with charge recombination.
Significantly higher efficiencies for charge separation are possible using
diblock purine base sequences consisting of two or three adenines followed by a
larger number of guanines. The short A-block serves as a molecular rectifier,
slowing down charge recombination. More efficient charge separation can also be
achieved using non-natural bases or by using the triplet acceptor anthraquinone
for hole injection.
Writers, artists, mothers: Author figures in the short fiction of Mary Lavin
Authors: D’hoker Elke
Published: June 2013

This article traces the development of figures of the author in the short fiction of the Irish writer Mary Lavin against the background of her anomalous position as woman, writer and mother in the conservative and patriarchal context of mid-century Ireland. Through a detailed reading
of six stories, the article shows how after staging a confident author figure in the early ‘A Story with a Pattern’, Lavin turns to dramatizing the tension between her roles as mother and artist in a series of oppositional characters in stories such as ‘The Becker Wives’,
‘Eterna’ and ‘In a Café’. Her artist figures, modelled after the Romantic conception of the author as exceptionally gifted outsiders, are unable to attain ‘ordinary’ lives as wives or mothers; while Lavin’s ‘alter egos’ in the so-called
widow stories are depicted only in a domestic context. Only in two stories written at the end of her career does Lavin again stage an author figure who combines the roles of mother and writer, thus offering an alternative to the Romantic image of the author that has long dominated Irish literary
culture.
Angela Carter as fiction: Refiguring the real author as Performative Author
Authors: Ryan-Sautour Michelle
Published: June 2013

In a 2006 article in The Independent, Christina Patterson echoes Gore Vidal by stating ‘Death, as any biographer knows, can be an excellent career move’. Commenting on a brief revival of Angela Carter’s work in 2006 concomitant with Emma Rice’s bringing of Nights
at the Circus to the stage, and Vintage’s reissuing of six of her works with new introductions, Patterson refers to Carter’s ‘whole new lease on life’ suggesting the metamorphic potential and curious temporality of the authorial figure with regard to reader reception.
The Vintage editions suggest, as Stephen Benson observes, the ‘legend’ of the ‘Carter effect’, identified by The British Academy Humanities Research Board, which distributes postgraduate studentships. This ‘Carter’ effect was also fostered by the theatricality
of Carter’s authorial performances. Sarah Gamble has observed the ‘screen’ of authorial identity upon which readers are led to project impressions, which functions as a ‘hall of mirrors’ in relation to penetrating to the authentic author. Such attempts at authorial
effacement and control are certainly not unusual. However, Carter’s postmodern enactment of the play of surfaces in the realm of authorial identity appears to heighten the consequent shifting of boundaries between fiction and life staged in her fiction. This article will address the
interaction between the games with identity inscribed in Carter’s short stories and the complex identity and temporality of the Performative Author.