bluuebunny/crossref_metadata_2025_split huggingface dataset:
Determination of the optimal tubulin isotype target as a method for the development of individualized cancer chemotherapy
Authors: Ravanbakhsh Siamak , Gajewski Melissa , Greiner Russell , Tuszynski Jack A 
Published: May 2013

AbstractBackgroundAs microtubules are essential for cell growth and division, its constituent protein β-tubulin has been a popular target for various treatments, including cancer chemotherapy. There are several isotypes of human β-tubulin and each type of cell expresses its characteristic distribution of these isotypes. Moreover, each tubulin-binding drug has its own distribution of binding affinities over the various isotypes, which further complicates identifying the optimal drug selection. An ideal drug would preferentially bind only the tubulin isotypes expressed abundantly by the cancer cells, but not those in the healthy cells. Unfortunately, as the distributions of the tubulin isotypes in cancer cells overlap with those of healthy cells, this ideal scenario is clearly not possible. We can, however, seek a drug that interferessignificantlywith the isotype distribution of the cancer cell, but has onlyminorinteractions with those of the healthy cells.MethodsWe describe a quantitative methodology for identifying thisoptimal tubulin isotype profilefor an ideal cancer drug, given the isotype distribution of a specific cancer type, as well as the isotype distributions in various healthy tissues, and the physiological importance of each such tissue.ResultsWe report the optimal isotype profiles for different types of cancer with various routes of delivery.ConclusionsOur algorithm, which defines the best profile for each type of cancer (given the drug delivery route and some specified patient characteristics), will help to personalize the design of pharmaceuticals for individual patients. This paper is an attempt to explicitly consider the effects of the tubulin isotype distributions in both cancer and normal cell types, for rational chemotherapy design aimed at optimizing the drug’s efficacy with minimal side effects.
Comparison of a loop-mediated isothermal amplification for orf virus withquantitative real-time PCR
Authors: Wang Guangxiang , Shang Youjun , Wang Yanhua , Tian Hong , Liu Xiangtao 
Published: May 2013

Abstract

Background
Orf virus (ORFV) causes orf (also known as contagious ecthyma or contagiouspapular dermatitis), a severe infectious skin disease in goats, sheep andother ruminants. Therefore, a rapid, highly specific and accurate method forthe diagnosis of ORFV infections is essential to ensure that the appropriatetreatments are administered and to reduce economic losses.

Methods
A loop-mediated isothermal amplification (LAMP) assay based on theidentification of the F1L gene was developed for the specific detection ofORFV infections. The sensitivity and specificity of the LAMP assay wereevaluated, and the effectiveness of this method was compared with that ofreal-time PCR.

Results
The sensitivity of this assay was determined to be 10 copies of a standardplasmid. Furthermore, no cross-reactivity was found with either capripoxvirus or FMDV. The LAMP and real-time PCR assays were both able to detectintracutaneous- and cohabitation-infection samples, with a concordance of97.83%. LAMP demonstrated a sensitivity of 89.13%.

Conclusion
The LAMP assay is a highly efficient and practical method for detecting ORFVinfection. This LAMP method shows great potential for monitoring theprevalence of orf, and it could prove to be a powerful supplemental tool forcurrent diagnostic methods.
Summary of papers presented at the 2012 seventh international cough symposium
Authors: Dicpinigaitis Peter V , Fontana Giovanni A , Lee Lu-Yuan , Tatar Milos 
Published: May 2013

Abstract
Twenty six papers were presented as posters in the Seventh International Symposium on Cough; 12 papers were presented in the Basic Science of Cough session, and 14 papers presented in the Clinical Science of Cough session. These papers explored a wide spectrum of cough-related areas including pathophysiological mechanisms, treatment and detection of cough, and symptom assessment and perception, and were grouped into several general themes for facilitate the discussion. Studies presented in these posters have provided new information that should improve our knowledge on the basic physiology and pharmacology of cough, and the peripheral and central neural mechanisms involved in the generation of the cough motor pattern. In addition, in the clinical science section, studies reporting potential new anti-tussive agents and further characterisation of cough symptoms and perception have provided a base for the fruitful strategies for the development of novel anti-tussive therapies and cough management.
Detection of capripoxvirus DNA using a novel loop-mediated isothermal amplification assay
Authors: Murray Lee , Edwards Lorraine , Tuppurainen Eeva SM , Bachanek-Bankowska Katarzyna , Oura Chris AL , Mioulet Valerie , King Donald P 
Published: May 2013

Abstract

Background

Sheep poxvirus (SPPV), Goat poxvirus (GTPV) and Lumpy skin disease virus (LSDV) are the most serious poxviruses of ruminants. They are double stranded DNA viruses of the genus Capripoxvirus, (subfamily Chordopoxvirinae) within the family Poxviridae. The aim of this study was to develop a Loop-mediated isothermal AMPlification (LAMP) assay for the detection of Capripoxvirus (CaPV) DNA.

Results
A single LAMP assay targeting a conserved region of the CaPV P32 gene was selected from 3 pilot LAMP assays and optimised by adding loop primers to accelerate the reaction time. This LAMP assay successfully detected DNA prepared from representative CaPV isolates (SPPV, GTPV and LSDV), and did not cross-react with DNA extracted from other mammalian poxviruses. The analytical sensitivity of the LAMP assay was determined to be at least 163 DNA copies/μl which is equivalent to the performance reported for diagnostic real-time PCR currently used for the detection of CaPV. LAMP reactions were monitored with an intercalating dye using a real-time PCR machine, or by agarose-gel electrophoresis. Furthermore, dual labelled LAMP products (generated using internal LAMP primers that were conjugated with either biotin or fluorescein) could be readily visualised using a lateral-flow device.

Conclusions
This study provides a simple and rapid approach to detect CaPV DNA that may have utility for use in the field, or in non-specialised laboratories where expensive equipment is not available.
LSSP-PCR of Trypanosoma cruzi: how the single primer sequence affects the kDNA signature
Authors: Segatto Marcela , Rodrigues Claudiney Melquíades , Machado Carlos Renato , Franco Glória Regina , Pena Sérgio Danilo Junho , Macedo Andréa Mara 
Published: May 2013

Abstract

Background
Low-stringency single specific primer PCR (LSSP-PCR) is a highly sensitive and discriminating technique that has been extensively used to genetically characterize Trypanosoma cruzi populations in the presence of large amounts of host DNA. To ensure high sensitivity, in most T. cruzi studies, the variable regions of the naturally amplified kinetoplast DNA (kDNA) minicircles were targeted, and this method translated the intraspecific polymorphisms of these molecules into specific and reproducible kDNA signatures. Although the LSSP-PCR technique is reproducible under strict assay conditions, the complex banding pattern generated can be significantly altered by even a single-base change in the target DNA. Our survey of the literature identified eight different primers with similar, if not identical, names that have been used for kDNA amplification and LSSP-PCR of T. cruzi. Although different primer sequences were used in these studies, many of the authors cited the same reference report to justify their primer choice. We wondered whether these changes in the primer sequence could affect also the parasite LSSP-PCR profiles.

Findings
To answer this question we compared the kDNA signatures obtained from three different and extensively studied T. cruzi populations with the eight primers found in the literature. Our results clearly demonstrate that even minimal modifications in the oligonucleotide sequences, especially in the 3′ or 5′ end, can significantly change the kDNA signature of a T. cruzi strain.

Conclusions
These results highlight the necessity of careful preservation of primer nomenclature and sequence when reproducing an LSSP-PCR work to avoid confusion and allow comparison of results among different laboratories.
Expression and cellular trafficking of GP82 and GP90 glycoproteins during Trypanosoma cruzi metacyclogenesis
Authors: Bayer-Santos Ethel , Cunha-e-Silva Narcisa Leal , Yoshida Nobuko , Franco da Silveira José 
Published: May 2013

Abstract

Background
The transformation of noninfective epimastigotes into infective metacyclic trypomastigotes (metacyclogenesis) is a fundamental step in the life cycle of Trypanosoma cruzi, comprising several morphological and biochemical changes. GP82 and GP90 are glycoproteins expressed at the surface of metacyclic trypomastigote, with opposite roles in mammalian cell invasion. GP82 is an adhesin that promotes cell invasion, while GP90 acts as a negative regulator of parasite internalization. Our understanding of the synthesis and intracellular trafficking of GP82 and GP90 during metacyclogenesis is still limited. Therefore, we decided to determine whether GP82 and GP90 are expressed only in fully differentiated metacyclic forms or they start to be expressed in intermediate forms undergoing differentiation.

Methods
Parasite populations enriched in intermediate forms undergoing differentiation were analyzed by quantitative real-time PCR, Western blot, flow cytometry and immunofluorescence to assess GP82 and GP90 expression.

Results
We found that GP82 and GP90 mRNAs and proteins are expressed in intermediate forms and reach higher levels in fully differentiated metacyclic forms. Surprisingly, GP82 and GP90 presented distinct cellular localizations in intermediate forms compared to metacyclic trypomastigotes. In intermediate forms, GP82 is localized in organelles at the posterior region and colocalizes with cruzipain, while GP90 is localized at the flagellar pocket region.

Conclusions
This study discloses new aspects of protein expression and trafficking during T. cruzi differentiation by showing that the machinery involved in GP82 and GP90 gene expression starts to operate early in the differentiation process and that different secretion pathways are responsible for delivering these glycoproteins toward the cell surface.
The histone deacetylase inhibitor sodium valproate causes limited transcriptional change in mouse embryonic stem cells but selectively overrides Polycomb-mediated Hoxb silencing
Authors: Boudadi Elsa , Stower Hannah , Halsall John A , Rutledge Charlotte E , Leeb Martin , Wutz Anton , O’Neill Laura P , Nightingale Karl P , Turner Bryan M 
Published: May 2013

Abstract

Background
Histone deacetylase inhibitors (HDACi) cause histone hyperacetylation and H3K4 hypermethylation in various cell types. They find clinical application as anti-epileptics and chemotherapeutic agents, but the pathways through which they operate remain unclear. Surprisingly, changes in gene expression caused by HDACi are often limited in extent and can be positive or negative. Here we have explored the ability of the clinically important HDACi valproic acid (VPA) to alter histone modification and gene expression, both globally and at specific genes, in mouse embryonic stem (ES) cells.

Results
Microarray expression analysis of ES cells exposed to VPA (1 mM, 8 h), showed that only 2.4% of genes showed a significant, >1.5-fold transcriptional change. Of these, 33% were down-regulated. There was no correlation between gene expression and VPA-induced changes in histone acetylation or H3K4 methylation at gene promoters, which were usually minimal. In contrast, all Hoxb genes showed increased levels of H3K9ac after exposure to VPA, but much less change in other modifications showing bulk increases. VPA-induced changes were lost within 24 h of inhibitor removal. VPA significantly increased the low transcription of Hoxb4 and Hoxb7, but not other Hoxb genes. Expression of Hoxb genes increased in ES cells lacking functional Polycomb silencing complexes PRC1 and PRC2. Surprisingly, VPA caused no further increase in Hoxb transcription in these cells, except for Hoxb1, whose expression increased several fold. Retinoic acid (RA) increased transcription of all Hoxb genes in differentiating ES cells within 24 h, but thereafter transcription remained the same, increased progressively or fell progressively in a locus-specific manner.

Conclusions

Hoxb genes in ES cells are unusual in being sensitive to VPA, with effects on both cluster-wide and locus-specific processes. VPA increases H3K9ac at all Hoxb loci but significantly overrides PRC-mediated silencing only at Hoxb4 and Hoxb7. Hoxb1 is the only Hoxb gene that is further up-regulated by VPA in PRC-deficient cells. Our results demonstrate that VPA can exert both cluster-wide and locus-specific effects on Hoxb regulation.
Separation of the defect-free Fe3O4-Au core/shell fraction from magnetite-gold composite nanoparticles by an acid wash treatment
Authors: Montazeri Hojatollah , Amani Amir , Shahverdi Hamid Reza , Haratifar Emad al din , Shahverdi Ahmad Reza 
Published: May 2013

Abstract
Some undesired nanoparticles, such as malformed structures or incomplete core/shell Fe3O4-Au nanocomposites, might be formed when Fe3O4-Au core/shell nanocomposites are being synthesized. These impurities should be separated before any applications are performed. In this investigation, magnetic cores (Fe3O4) were synthesized using a conventional fabrication method involving coprecipitation of Fe2+ and Fe3+. Carboxyl-capped magnetite-gold composite nanoparticles, measuring ≤50 nm, were then synthesized using a plant extract (Eucalyptus camaldulensis). The prepared carboxyl-capped magnetite-gold composite nanoparticles were further subjected to acid treatment for 18 h and characterized with different instrumentation methods. The results of the investigation showed that acid treatment can be applied successfully to separate defect-free Fe3O4-Au core/shell nanoparticles from different types of Fe3O4-Au nanocomposites, without any considerable changes in their physiochemical properties.
Discontinuous locomotion and prey sensing in the leech
Authors: Harley Cynthia M. , Rossi Matthew , Cienfuegos Javier , Wagenaar Daniel 
Published: May 2013

SUMMARYThe medicinal leech, Hirudo verbana, is an aquatic predator that utilizes water waves to locate its prey. However, to reach their prey, the leeches must move within the same water that they are using to sense prey. This requires that they either move ballistically towards a pre-determined prey location or that they account for their self-movement and continually track prey. We found that leeches do not localize prey ballistically. Instead, they require continual sensory information to track their prey. Indeed, in the event that the prey moves, leeches will approach the prey's new location. While leeches need to continually sense water disturbances to update their percept of prey location, their own behavior is discontinuous – approaching prey involves switching between swimming, crawling and non-locomoting. Each of these behaviors may allow for different sensory capabilities and may require different sensory filters. Here, we examined the sensory capabilities of leeches during each of these behaviors. We found that while one could expect the non-locomoting phases to direct subsequent behaviors, crawling phases were more effective than non-locomotor phases for providing direction. During crawling bouts, leeches adjusted their heading so as to become more directed towards the stimulus. This was not observed during swimming. Furthermore, in the presence of prey-like stimuli, leeches crawled more often and for longer periods of time.
Marked Biological Variance in Endocrine and Biochemical Markers in Childhood: Establishment of Pediatric Reference Intervals Using Healthy Community Children from the CALIPER Cohort
Authors: Bailey Dana , Colantonio David , Kyriakopoulou Lianna , Cohen Ashley H , Chan Man Khun , Armbruster David , Adeli Khosrow 
Published: May 2013

BACKGROUNDReference intervals are indispensable in evaluating laboratory test results; however, appropriately partitioned pediatric reference values are not readily available. The Canadian Laboratory Initiative for Pediatric Reference Intervals (CALIPER) program is aimed at establishing the influence of age, sex, ethnicity, and body mass index on biochemical markers and developing a comprehensive database of pediatric reference intervals using an a posteriori approach.METHODSA total of 1482 samples were collected from ethnically diverse healthy children ages 2 days to 18 years and analyzed on the Abbott ARCHITECT i2000. Following the CLSI C28-A3 guidelines, age- and sex-specific partitioning was determined for each analyte. Nonparametric and robust methods were used to establish the 2.5th and 97.5th percentiles for the reference intervals as well as the 90% CIs.RESULTSNew pediatric reference intervals were generated for 14 biomarkers, including α-fetoprotein, cobalamin (vitamin B12), folate, homocysteine, ferritin, cortisol, troponin I, 25(OH)-vitamin D [25(OH)D], intact parathyroid hormone (iPTH), thyroid-stimulating hormone, total thyroxine (TT4), total triiodothyronine (TT3), free thyroxine (FT4), and free triiodothyronine. The influence of ethnicity on reference values was also examined, and statistically significant differences were found between ethnic groups for FT4, TT3, TT4, cobalamin, ferritin, iPTH, and 25(OH)D.CONCLUSIONSThis study establishes comprehensive pediatric reference intervals for several common endocrine and immunochemical biomarkers obtained in a large cohort of healthy children. The new database will be of global benefit, ensuring appropriate interpretation of pediatric disease biomarkers, but will need further validation for specific immunoassay platforms and in local populations as recommended by the CLSI.
Current and Future Practices for the Testing of Multi-Component Geosynthetic Clay Liners
Authors: von Maubeuge Kent P. , Kline J. P. 
Published: May 2013

Description
Fifteen peer-reviewed papers address a decade of significant changes in manufacturing technology, design utilization, and market acceptance of multi-component geosynthetic clay liner materials. They are characterized by specially-engineered surface coatings, film attachments, bentonite modifications, and other components that enhance performance in specific ways.
This new publication helps to better identify changing material characteristics and designs, commonalities among these changes, and testing and standardization needs to better support the engineering community in regards to geosynthetic clay liners.
Pluralerwerb im Deutschen bei ­russisch- und türkischsprachigen Kindern im Vergleich mit anderen Migranten und monolingualen Muttersprachlern
Authors: Zaretsky Eugen , Neumann Katrin , Euler Harald A. , Lange Benjamin P. 
Published: May 2013

Abstract
The article focuses on the differences and common characteristics of the plural acquisition in German by children with Russian and Turkish mother tongues, compared with other immigrant children and Germans. Although not absolutely identical, the overgeneralization patterns of all groups appear to be very similar and obviously dependent only on the proficiency in German, without clear influences of the foreign linguistic background, the only exception being e-overgeneralizations in Russian children. Whereas immigrant children tend to account mostly for the frequency of the plural allomorphs in the input when choosing a plural marker, German children have already internalized the gender based distribution of some plural allomorphs.
Selektive Ableitung und Stimulation für ein blutdrucksenkendes Implantat unter Verwendung von Vielkanal-Cuff-Elektroden
Authors: Plachta Dennis T. T. , Cota Oscar , Stieglitz Thomas , Gierthmühlen Mortimer 
Published: May 2013

Zusammenfassung
Mit der Möglichkeit, blutdruckrelevante Fasern des N. vagus zu identifizieren und selektiv zu stimulieren, hat die Vagusnervstimulation das Potential, als Alternative zur Behandlung des therapierefraktären Blutdruckes etabliert zu werden. Die Selektivität dieser Stimulation ist essentiell, da eine unselektive Stimulation des gesamten N. vagus zu kardialen und gastrointestinalen Nebenwirkungen führen kann, die für eine chronische Therapie inakzeptabel sind. Durch den Einsatz von Vielkanal-Polyimid-Dünnfilm-Cuff-Elektroden ist es möglich, barorezeptiven Fasern im Vagusnerv zu lokalisieren und selektiv zu stimulieren. Hierzu werden die abgeleiteten neuronalen Signale in Echtzeit mit simultan aufgezeichneten EKG und Blutdrucksignalen korreliert, um diejenigen Elektroden zu identifizieren, welche den barorezeptiven Fasern am nächsten liegen. Der hierfür entwickelte Algorithmus basiert auf der kohärenten Mittelung und setzt keine dauerstabile Elektroden-Gewebe-Impedanz voraus. Die den blutdruckrelevanten Fasern am nächsten gelegenen Elektroden werden in tri- oder pentapolarer Konfiguration verwendet, um die Fasern selektiv zu stimulieren und über Aktivierung des Baroreflexes eine Blutdrucksenkung ohne relevante Bradykardie zu erreichen.
Beyond the Scope of this Paper
Authors: Hughes Hilary E. , Bridges-Rhoads Sarah C. 
Published: May 2013

While qualitative researchers include reflexive analyses about their research processes in publications, they are generally less forthcoming about their writing processes. Here we suggest that reflection on the thinking that happens in the writing process itself is a key analytic practice researchers can use to understand and transform the world. We invite readers to examine with us how productivity as a discourse in doctoral education relegates the act of writing to just another task to be completed, one more stage within the hierarchical processes of what we call PhDness. Using multiple texts as reflexive accounts of our writing as inquiry practices, written throughout and after our phenomenological and poststructural dissertation work, respectively, we demonstrate how writing not included in the final dissertation served as a necessary space to think potential action.