bluuebunny/crossref_metadata_2025_split huggingface dataset:
Induction of high-titer IgG antibodies against multiple leukemia-associated antigens in CML patients with clinical responses to K562/GVAX immunotherapy
Authors: Qin L , Smith B D , Tsai H-L , Yaghi N K , Neela P H , Moake M , Fu J , Kasamon YL , Prince G T , Goswami M , Rosner G L , Levitsky H I , Hourigan C S 
Published: September 2013

AbstractThe ability to target myeloid leukemia with immunotherapy would represent a significant therapeutic advance. We report here immunological analysis of clinical trials of primary and secondary vaccination with K562/GM-CSF immunotherapy in adult chronic phase chronic myeloid leukemia patients (CML-CP) with suboptimal responses to imatinib mesylate. Using serological analysis of recombinant cDNA expression libraries of K562 with autologous vaccinated patient serum, we have identified 12 novel chronic myeloid leukemia-associated antigens (LAAs). We show that clinical responses following K562/GM-CSF vaccination are associated with induction of high-titer antibody responses to multiple LAAs. We observe markedly discordant patterns of baseline and induced antibody responses in these identically vaccinated patients. No single antigen was recognized in all responses to vaccination. We demonstrate that an additional ‘booster’ vaccination series can be given safely to those with inadequate responses to initial vaccination, and is associated with more frequent induction of IgG responses to antigens overexpressed in K562 vaccine compared with primary CML-CP. Finally, those with induced immune responses to the same LAAs often shared HLA subtypes and patients with clinical responses following vaccination recognized a partially shared but non-identical spectrum of antigens; both findings have potentially significant implications for cancer vaccine immunotherapy.
Integrated dual‐grating inteferometric detection with polymer microbeams for bio‐chemical sensing in liquid environment
Authors: Feng Jin‐yang , Ye Xiong‐ying , Shang Yuan‐fang , Wu Kang , Chen Feng 
Published: September 2013

An interferometric displacement detection method of polymer microbeams based on integrated dual‐grating was developed for bio‐chemical sensing in a liquid environment. Sensing microstructures made of polyimide (PI) with four symmetrically arranged L‐shaped beams suspending a central plate were designed and fabricated on a glass substrate using a surface micromachining process. With these structures, deflection changes of the microbeams were transduced to out‐of‐plane movements of the central plate, which were then measured from the interference of light spots diffracted from the integrated gratings using a charge coupled device image measurement setup. To extend the displacement detection range, two adjacent metal gratings corresponding to a microbeam were formed inside and outside a groove with a depth of 55 nm, respectively, to achieve a phase shift of about π/2 in liquid. The detected noise of aluminium (Al) microcantilevers in ethanol slightly increased compared with that in air, and the noise of PI microbeams in phosphate‐buffered saline was about three times larger than that of Al cantilevers in ethanol. The preliminary experimental results in ethanol show that the detection method based on polymer microbeams integrated with dual‐gratings is feasible in a liquid environment. Antibody–antigen binding detection was also conducted with a rabbit immunoglobulin G (IgG) immobilised chip in 100 μg/ml goat anti‐rabbit IgG solution.
Silver selenide nanoparticles: synthesis, characterisation and effect of preparation conditions under ultrasound radiation
Authors: Jafari Maryam , Salavati‐Niasari Masoud , Sobhani Azam 
Published: September 2013

A convenient sonochemical process for the preparation of silver selenide (Ag2Se) nanoparticles by using different complexing agents [NH3, citric acid, potassium thiocyanate (KSCN)] and hydrazine as reductant agent is developed. It was found that pure Ag2Se nanoparticles were prepared in the presence of KSCN after 90 minutes of sonication. The products were characterised by X‐ray diffraction, scanning electron microscopy and energy‐dispersive X‐ray spectroscopy analysis. Photoluminescence was used to study the optical properties of Ag2Se samples.
The Effects of Ethanol Preservation on Fish Fin Stable Isotopes: Does Variation in C:N Ratio and Body Size Matter?
Authors: Vizza Carmella , Sanderson Beth L. , Burrows Douglas G. , Coe Holly J. 
Published: September 2013

AbstractAlthough chemical preservation of stable isotope samples has been studied in a variety of species and tissue types, the effects of ethanol preservation on fish fin tissue have not been examined. Using caudal fin samples from juvenile Chinook Salmon Oncorhynchus tshawytscha and Rainbow Trout O. mykiss or steelhead (the anadromous form of Rainbow Trout), we investigated how storage time (2, 4, and 6 months), fin composition (C:N ratio), and fish body size (50–130 mm FL) influence preservation‐induced changes in δ13C and δ15N. In both species, we found that treatment fins (frozen and later preserved in ethanol) exhibited higher δ13C than did paired reference fins (frozen). The changes in δ15N, however, were smaller in magnitude and less consistent. Preservation‐induced increases in fin δ13C, but not δ15N, were significantly correlated with the change in C:N ratio (treatment–reference) in both species. In addition, these increases in δ13C were more highly correlated with body size in O. mykiss than in Chinook Salmon. Storage time had a significant effect on the shift in treatment fin δ13C and a small, but insignificant, effect on δ15N in O. mykiss. However, storage time was not a significant factor for explaining the isotopic shifts observed in Chinook Salmon fin tissue. This is the first study to document variation in preservation‐induced changes in δ13C within a species and to link this variation to C:N ratio. Future studies using species‐specific and tissue‐specific models to correct for preservation‐induced shifts in stable isotope ratios should be aware that these models do not account for intraspecific variation in tissue composition.
Length–Length and Width–Length Conversion of Longnose Skate and Big Skate Off the Pacific Coast: Implications for the Choice of Alternative Measurement Units in Fisheries Stock Assessment
Authors: Downs Donna E. , Cheng Yuk W. 
Published: September 2013

AbstractMost traditional fisheries models have size or stage–age relationships as their foundation. Two long‐established metrics used are FL and TL. Body length measurements are linked to age, maturity, and fecundity. Obtaining FL or TL measurements are not always convenient, especially for larger fish (>100 cm TL). Two skate species, Longnose Skate Raja rhina and Big Skate R. binoculata, were collected from commercial fishery landings along the coast of Washington State and length–length or width–length conversions were investigated for four metrics of size: TL, tail only length (TOL), interspiracular width (ISW), and interorbital width (IOW). Relationships between TL and alternative measures were examined using model II regression analyses and confirmed a strong linear relationship in all cases (R 2 > 0.94). It is likely that both TL and TOL measures have errors due to worn‐off tail portions; conversely, the ISW is nonlaborious and convenient to obtain. The ISW metric has a smaller coefficient of variation compared with IOW if we assume that both metrics have the same distribution of measurement errors. We recommend ISW as the preferred alternative metric in the assessment of large skate. The ISW will probably yield measurements that are equivalent, or potentially superior, to traditional metrics because the measurement is taken from body parts devoid of worn‐off portions.Received December 30, 2011; accepted June 13, 2013
The Myth of Mediterranean Familism
Authors: Calzada Ines , Brooks Clem 
Published: September 2013

ABSTRACT
This article seeks to re-open the consensus concerning the interrelationship between family values and public support for government versus private family provision. We offer new results from analyses of 2001 data from the International Social Survey Programme for a wide range of countries and world regions. Refining conventional scholarly wisdom, Southern European publics' have high levels of traditional family values, but mainly in contrast to other European countries; familism is also notably strong in Eastern Europe and several of the English-speaking democracies. Even more surprising, family values support is strongly and positively associated with support for public child care provision. We discuss implications of results for understanding the nature of public attitudes and familism in cross-national perspective, and the limits of theorizing identifying family values as the primary cause of welfare state development in Southern Europe.
Abundance and Distribution of Sharks in Northeast Florida Waters and Identification of Potential Nursery Habitat
Authors: McCallister Michael , Ford Ryan , Gelsleichter James 
Published: September 2013

Abstract
Sharks are considered top predators in many marine ecosystems and can play an important role in structuring community ecology. As a result, it is necessary to understand the factors that influence their abundance and distribution. This is particularly important as fishery managers develop management plans for sharks that identify areas that serve as essential fish habitat, especially nursery habitat. However, our understanding of shark habitat use in northeast Florida waters is limited. The goal of this study was to characterize the abundance and distribution of sharks in northeast Florida estuaries and to examine the effect of abiotic factors on shark habitat use. A bottom longline survey conducted from 2009 to 2011 indicated that 11 shark species use the estuarine waters of northeast Florida during the summer months. Atlantic Sharpnose Sharks Rhizoprionodon terraenovae, Blacktip Sharks Carcharhinus limbatus, and Bonnetheads Sphyrna tiburo were the most abundant species and made up 81.4% of the total catch. Site, month, and bottom water temperature were the most important factors determining the presence and abundance of sharks and suggest both regional and seasonal variations in the use of northeast Florida waters. Depth, salinity, and dissolved oxygen were also important factors. Our data show that these waters serve as a nursery for Atlantic Sharpnose and Blacktip Sharks, with young-of-the-year and juveniles being present in the summer months. Limited tag–return data reveal that juvenile sharks remain in these waters throughout the summer and that some return in subsequent summers. This is the first study to characterize the abundance and distribution of sharks and identify potential nursery areas in northeast Florida estuaries.
Received October 10, 2012; accepted March 7, 2013
INSECT: IN-silico SEarch for Co-occurring Transcription factors
Authors: Rohr Cristian O. , Parra R. Gonzalo , Yankilevich Patricio , Perez-Castro Carolina 
Published: September 2013

Abstract
Motivation: Transcriptional regulation occurs through the concerted actions of multiple transcription factors (TFs) that bind cooperatively to cis-regulatory modules (CRMs) of genes. These CRMs usually contain a variable number of transcription factor-binding sites (TFBSs) involved in related cellular and physiological processes. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) has been effective in detecting TFBSs and nucleosome location to identify potential CRMs in genome-wide studies. Although several attempts were previously reported to predict the potential binding of TFs at TFBSs within CRMs by comparing different ChIP-seq data, these have been hampered by excessive background, usually emerging as a consequence of experimental conditions. To understand these complex regulatory circuits, it would be helpful to have reliable and updated user-friendly tools to assist in the identification of TFBSs and CRMs for gene(s) of interest.
Results: Here we present INSECT (IN-silico SEarch for Co-occurring Transcription factors), a novel web server for identifying potential TFBSs and CRMs in gene sequences. By combining several strategies, INSECT provides flexible analysis of multiple co-occurring TFBSs, by applying differing search schemes and restriction parameters.
Availability and implementation: INSECT is freely available as a web server at http://bioinformatics.ibioba-mpsp-conicet.gov.ar/INSECT
Contact: cperezcastro@ibioba-mpsp-conicet.gov.ar or pyankilevich@ibioba-mpsp-conicet.gov.ar
Supplementary information: Supplementary data are available at Bioinformatics online.
OntoQuery: easy-to-use web-based OWL querying
Authors: Tudose Ilinca , Hastings Janna , Muthukrishnan Venkatesh , Owen Gareth , Turner Steve , Dekker Adriano , Kale Namrata , Ennis Marcus , Steinbeck Christoph 
Published: September 2013

Abstract
Summary: The Web Ontology Language (OWL) provides a sophisticated language for building complex domain ontologies and is widely used in bio-ontologies such as the Gene Ontology. The Protégé-OWL ontology editing tool provides a query facility that allows composition and execution of queries with the human-readable Manchester OWL syntax, with syntax checking and entity label lookup. No equivalent query facility such as the Protégé Description Logics (DL) query yet exists in web form. However, many users interact with bio-ontologies such as chemical entities of biological interest and the Gene Ontology using their online Web sites, within which DL-based querying functionality is not available. To address this gap, we introduce the OntoQuery web-based query utility.
Availability and implementation: The source code for this implementation together with instructions for installation is available at http://github.com/IlincaTudose/OntoQuery. OntoQuery software is fully compatible with all OWL-based ontologies and is available for download (CC-0 license). The ChEBI installation, ChEBI OntoQuery, is available at http://www.ebi.ac.uk/chebi/tools/ontoquery.
Contact: hastings@ebi.ac.uk
PAVIS: a tool for

P

eak

A

nnotation and

Vis

ualization
Authors: Huang Weichun , Loganantharaj Rasiah , Schroeder Bryce , Fargo David , Li Leping 
Published: September 2013

Abstract
Summary: We introduce a web-based tool, Peak Annotation and Visualization (PAVIS), for annotating and visualizing ChIP-seq peak data. PAVIS is designed with non-bioinformaticians in mind and presents a straightforward user interface to facilitate biological interpretation of ChIP-seq peak or other genomic enrichment data. PAVIS, through association with annotation, provides relevant genomic context for each peak, such as peak location relative to genomic features including transcription start site, intron, exon or 5′/3′-untranslated region. PAVIS reports the relative enrichment P-values of peaks in these functionally distinct categories, and provides a summary plot of the relative proportion of peaks in each category. PAVIS, unlike many other resources, provides a peak-oriented annotation and visualization system, allowing dynamic visualization of tens to hundreds of loci from one or more ChIP-seq experiments, simultaneously. PAVIS enables rapid, and easy examination and cross-comparison of the genomic context and potential functions of the underlying genomic elements, thus supporting downstream hypothesis generation.
Availability and Implementation: PAVIS is publicly accessed at http://manticore.niehs.nih.gov/pavis.
Contact: li3@niehs.nih.gov
Supplementary information: Supplementary data are available at Bioinformatics online
Economic recovery from natural disaster
Authors: Sardana G.D. , Dasanayaka W.S.B. 
Published: September 2013

PurposeThis paper aims to analyse as to how the benefits to Tsunami affected small industry were misplaced and carried wrong priorities. Besides the support provided was insufficient for an effective recovery. There existed many governance‐related problems. Overall recovery was at a low figure of 64.8 percent. The occurrence of the natural disaster of this high magnitude leaves a trail of lessons to be learnt by both the government agencies and also the donor community. There was no shortage of either the funds or the commodities, but it was sadly the governance and the sensitivity to the suffering of the people.Design/methodology/approachThe study employed the proven methodologies of a survey of available literature, web sites, and publications to obtain secondary data and information on industry especially the micro and SMEs in areas of disaster damage occurred because of Tsunami. The second methodology of research is in areas of collection of data on industry at national level and categorization for selection of sample size. Interviews formed an important source of information. Interviews were conducted with relevant stakeholders conducting various rehabilitation and re‐establishment programmes.FindingsMicro and SMEs are important for economic development of Sri Lanka. These carry a strategic importance to generate employment. As such rehabilitation of industry affected by Tsunami is vital. Tsunami could have been used by the government, development agencies and donors as opportunity for rebuilding on modern lines. The main damage was caused to the plant and machinery. A right expenditure should have been in the direction of procurement of tools, equipment and machinery for the affected units. Unfortunately the help could not be organized to reach the right industry, in right quantity, and right way. Surprisingly, it was not because of shortage of funds.Originality/valueThe present case leaves lessons for development agencies, government departments and welfare associations. No such extensive study seems to have carried out.
Teacher improvement through peer teacher evaluation in Kenyan schools
Authors: Wilfrida Arnodah Itolondo 
Published: September 2013

Purpose
– This article aims to assess the awareness among educators of strategies put in place for peer teacher evaluation (PTE), and training opportunities availed to them in relation to PTE.

Design/methodology/approach
– The study was conducted in secondary schools in three selected districts of Western Province of Kenya using a descriptive survey design. Data were collected from school principals, senior teachers, heads of departments and teachers using questionnaires, interview schedules and a document analysis guide.

Findings
– The findings generally revealed that though all schools where PTE was practised had made some attempts to organise some awareness programmes, they were not focused as evidenced in the varied reasons that were provided to show why they were organised. The study also established that less than half of the teachers had been exposed to in-service training opportunities.

Research limitations/implications
– There is scarce literature based on empirical studies focusing on school-based teacher evaluation (SBTE). Most of the studies the author was able to access were descriptive and on teacher evaluation in general. Consequently, most recent studies in Kenya, for example, tend to focus on topical issues like HIV/AIDS, gender, Free primary education and how they impact on curriculum implementation while what goes on in the classrooms is ignored.

Practical implications
– Identifying and analysing awareness strategies and in-service teacher training related factors that hinder and/or promote PTE may help in strengthening the practice if the recommendations of this study are implemented. Findings of this study if accessed may provide information to policy makers both at national, local and school levels in Kenya on the practice of PTE. National and local policy gives legality to PTE while school policy directs the process and procedures for the practice at school level. This study also provides a theoretical knowledge that precedes the practice of PTE.

Social implications
– Peer Teacher Evaluation embraces characteristics such as collaboration, collegiality and dialogue and so can enhance positive working relationships among teachers. Teachers in the classroom are known to maintain cultural norms of privacy and individualism. Peer Teacher Evaluation being teachers evaluating each other, therefore, removes the culture of privacy and individualism. If well practised, it may promote rapport and trust among teachers.

Originality/value
– The study analysed the level of awareness and in-service training of teachers on PTE which is one of the modes of SBTE in secondary schools with the purpose of coming up with suggestions that may help bring about improvement in the practice in order to strengthen it in schools.
Title by registration or conquest
Authors: Dixon Martin 
Published: September 2013

PurposeThe purpose of this paper is to analyse whether title to land is secure in England and Wales when registered under the Land Registration Act 2002, in particular when a title is registered without the proprietor being able to establish good title under pre‐registration rules of property law.Design/methodology/approachThis paper analyses reported judgments, with particular emphasis on the decision in Walker v. Burton [2012].FindingsThe paper identifies an uncertainty at the heart of the registration system: the uncertainty as to the extent to which a registered title may be rectified to remove the proprietor. This is acute when it appears that the registered proprietor has no claim to the land other than by reason of his registration. There may be a difference in this regard between intangible property titles and tangible titles.Originality/valueThe Land Registration Act 2002 is meant to replace registration of title with title by registration. The real force of this is only now being realised and there are few reported judgements, and less consistency, working out what this means in practice.
Management agreements in multi‐unit housing developments
Authors: Nathanael Gibbons Thomas 
Published: September 2013

PurposeThis paper applies existing theoretical models on management agreements for multi‐unit housing to a particular legislative provision and its application in a decided case. It then critiques that decision and makes recommendations for policymakers based on the application and scope of the provision. The paper aims to discuss these issues.Design/methodology/approachA socio‐legal approach is taken, based on a case study of a statutory provision discussed in a decided case.FindingsThis paper identifies new phenomena in relation to management agreements for multi‐unit housing and makes recommendations for policymakers based on the case study. These recommendations relate to the wording of similar statutory provisions and to developers' duties to future owners.Research limitations/implicationsThe case study is limited to a single legislative provision and single decided case, though some references are made to overseas jurisdictions.Practical implicationsThe findings will help guide policymakers in other jurisdictions.Originality/valueThrough extending existing models relating to body corporate management agreements and “developer abuse” to a case study relating to legislative reform, this paper shows the usefulness and limitations of a particular type of reform. This will assist those applying existing models to other jurisdictions and also provide guidance for policymakers.