bluuebunny/crossref_metadata_2025 huggingface dataset:
Multidisciplinary team management in thoracic oncology: more than just a concept?
Authors: Powell Helen A. , Baldwin David R.
Published: February 2014

Multidisciplinary team (MDT) management in thoracic oncology has been introduced over the past two decades with the aim of improving outcomes for patients. While MDT management has become the standard of care in some countries, not all healthcare systems have adopted this practice. In this article we review the history and implementation of MDT care in thoracic oncology and explore the evidence for, and challenges associated with, this system of working.

There are many advantages of an MDT both to the patient, the clinicians and the wider population, but it is difficult to demonstrate a beneficial effect on outcomes such as treatment rates or survival given the substantial number of coexistent changes in the management of thoracic malignancies over the same time period. There are also some disadvantages associated with MDT working, particularly the costs of setting up the service and the time commitment from each of the healthcare professionals involved. Barriers to effective MDT working include poor attendance by some specialists, inadequate preparation and poor quality information about the patient. Variation in quality of MDTs has been reported so it is important that practice is monitored and areas for improvement identified.
Clinical implications in the shift of syndecan-1 expression from the cell membrane to the cytoplasm in bladder cancer
Authors: Miyake Makito , Lawton Adrienne , Dai Yunfeng , Chang Myron , Mengual Lourdes , Alcaraz Antonio , Goodison Steve , Rosser Charles J
Published: February 2014

Background

To determine the diagnostic and prognostic capability of urinary and tumoral syndecan-1 (SDC-1) levels in patients with cancer of the urinary bladder.

Methods

SDC-1 levels were quantitated by enzyme-linked immunosorbent assay (ELISA) in 308 subjects (102 cancer subjects and 206 non-cancer subjects) to assess its diagnostic capabilities in voided urine. The performance of SDC-1 was evaluated using the area under the curve of a receiver operating characteristic curve. In addition, immunohistochemical (IHC) staining assessed SDC-1 protein expression in 193 bladder specimens (185 cancer subjects and 8 non-cancer subjects). Outcomes were correlated to SDC-1 levels.

Results

Mean urinary levels of SDC-1 did not differ between the cancer subjects and the non-cancer subjects, however, the mean urinary levels of SDC-1 were reduced in high-grade compared to low-grade disease (p < 0.0001), and in muscle invasive bladder cancer (MIBC) compared to non-muscle invasive bladder cancer (NMIBC) (p = 0.005). Correspondingly, preliminary data note a shift from a membranous cellular localization of SDC-1 in normal tissue, low-grade tumors and NMIBC, to a distinctly cytoplasmic localization in high-grade tumors and MIBC was observed in tissue specimens.

Conclusion

Alone urinary SDC-1 may not be a diagnostic biomarker for bladder cancer, but its urinary levels and cellular localization were associated with the differentiation status of patients with bladder tumors. Further studies are warranted to define the potential role for SDC-1 in bladder cancer progression.
Application of Bother in patient reported outcomes instruments across cultures
Authors: Gawlicki Mary C , McKown Shawn M , Talbert Matthew J , Brandt Barbara A
Published: February 2014

Background

The objective of this study was to determine the applicability of the termbother,as used in Patient Reported Outcomes (PRO) instruments that will be translated into foreign languages from English for the United States.Botheris versatile in English for the U.S., in that it can describe negative mental states and physical sensations, as well as social disturbances.Botherhas many different meanings across cultures, due to this versatility. Alternatives forbotherwere explored for future PRO instrument development.

Methods

A PRO instrument used to evaluate the degree ofbotherresulting from psoriasis was analyzed. This disease can negatively impact patients physically, emotionally and socially. Translations ofbotherwere analyzed to determine its meaning when translated into other languages. Cognitive debriefing was conducted on psoriasis patients with the instrument containingbother.Following cognitive debriefing, a questionnaire was distributed to linguists and cognitive debriefing subjects to collect definitions ofbotherin each target language, and detail any difficulty with translation.

To establish alternatives tobotherand demonstrate the breakdown of concepts withinbother, translations of the Dermatology Quality of Life Index (DLQI) were analyzed. This instrument was selected for its focus on psoriasis and use of terminology that lacks the ambiguity ofbother.

Results

An analysis of back-translations revealed thatbotheryielded a back-translation that was conceptually different from the source 20% of the time (5/26). Analysis of alternative terminology found in the DLQI revealed much greater conceptual equivalence when translated into other languages.

Conclusion

When developing the wording of PRO instruments, the terminology chosen should be applicable across languages to allow for international pooling and comparison of data. While all linguists and subjects of cognitive debriefing understoodbotherto have a negative connotation, a large variety of definitions and synonyms provided across languages showed a lack of conceptual equivalence. Ambiguity of the term across cultures may result in variation in translation, impacting subsequent international data pooling. Analysis of alternatives revealed that measurement of unambiguous terminology produces the greatest conceptual equivalency across languages and cultures.
A comparison of various noncommuting conditions in metric fixed point theory and their applications
Authors: Agarwal Ravi P , Bisht Ravindra K , Shahzad Naseer
Published: February 2014

This paper presents a survey that aims to provide a brief historical account of the development through the definitions and comparison of weaker forms of commuting mappings set brought together from some applications oriented point of view.

MSC:47H10, 54H25, 41A50.
A primary-school-based study to reduce the prevalence of childhood obesity – the EdAl (Educació en Alimentació) study: a randomized controlled trial
Authors: Tarro Lucia , Llauradó Elisabet , Albaladejo Rosa , Moriña David , Arija Victoria , Solà Rosa , Giralt Montse
Published: February 2014

Background

Obesity is one of the main determinants of avoidable disease burden.

To implement a program by university students acting as “health promoting agents” (HPAs) and to evaluate the effects on obesity prevalence of the primary-school-based program that promotes healthy lifestyle, including dietary and physical activity recommendations over 28 months.

Methods

Two school clusters were randomly assigned to intervention (24 schools, 1,222 pupils) or control (14 schools, 717 pupils); 78% of pupils were Western European. Mean age (±SD) was 8.4 ± 0.6 years (49.9% females) at baseline. Generalized linear mixed models were used to analyze differences in primary outcome between both groups. Data collected included body mass index (BMI) every year. Dietary habits and lifestyle questionnaires were filled in by the parents at baseline and at the end of the study. The interventions focused on eight lifestyle topics covered in 12 activities (1 hour/activity/session) implemented by HPAs over 3 school academic years.

Results

At 28 months, obesity prevalence in boys was decreased −2.36% in the intervention group (from 9.59% to 7.23%) and increased 2.03% (from 7.40% to 9.43%) in the control group; the difference was 4.39% (95% CI 3.48 to 5.30; P = 0.01). The boys in the intervention group had an effective reduction of −0.24 units in the change of BMI z-score (from 0.01 to −0.04), compared to control (from −0.10 to 0.09); 5.1% more intervention pupils undertook physical activity >5 hours/week than control pupils (P = 0.02).

Fish consumption was a protector (odds ratio 0.39; 95% CI 0.23 to 0.67) while “fast-food” consumption was a risk factor for childhood obesity (odds ratio: 2.27; 95% CI 1.08 to 4.77).

Conclusions

Our school-based program, conducted by HPA students, successfully reduced childhood obesity prevalence in boys.

Trial registration

International Standard Randomized Controlled Trial Number: ISRCTN29247645.
Stirring time effect of silver nanoparticles prepared in glutathione mediated by green method
Authors: Balavandy Sepideh Keshan , Shameli Kamyar , Biak Dayang Radiah Binti Awang , Abidin Zurina Zainal
Published: February 2014

Background

This study aims to investigate the influence of different stirring time for synthesis of silver nanoparticles in glutathione (GSH) aqueous solution. The silver nanoparticles (Ag-NPs) were prepared by green synthesis method using GSH as reducing agent and stabilizer, under moderate temperature at different stirring times. Silver nitrate (AgNO3) was taken as the metal precursor while Ag-NPs were prepared in the over reaction time.

Results

Formation of Ag-NPs was determined by UV–vis spectroscopy where surface plasmon absorption maxima can be observed at 344–354 nm from the UV–vis spectrum. The synthesized nanoparticles were also characterized by X-ray diffraction (XRD). The peaks in the XRD pattern confirmed that the Ag-NPs possessed a face-centered cubic and peaks of contaminated crystalline phases were unable to be located. Transmission electron microscopy (TEM) revealed that Ag-NPs synthesized were in spherical shape. Zeta potential results indicate that the stability of the Ag-NPs is increases at the 72 h stirring time of reaction comparison to GSH. The Fourier transform infrared (FT-IR) spectrum suggested the complexation present between GSH and Ag-NPs. The use of green chemistry reagents, such as peptide, provides green and economic features to this work.

Conclusions

Ag-NPs were successfully synthesized in GSH aqueous solution under moderate temperature at different stirring times. The study clearly showed that the Ag-NPs synthesized in the long times of stirring, thus, the kinetic of GSH reaction is very slow. TEM results shows that with the increase of stirring times the mean particle size of Ag-NPs become increases. The FT-IR spectrum suggested the complexation present between GSH and Ag-NPs. These suggest that Ag-NPs can be employed as an effective bacteria inhibitor and can be applied in medical field.
Reliability and concurrent validity of a novel method allowing for in‐shoe measurement of navicular drop
Authors: Christensen Birgitte H , Andersen Kathrine S , Pedersen Kristina S , Bengtsen Britt S , Simonsen Ole , Kappel Simon L , Rathleff Michael S
Published: February 2014

Background

Increased navicular drop is associated with increased risk of lower extremity overuse injuries and foot orthoses are often prescribed to reduce navicular drop. For laboratory studies, transparent shoes may be used to monitor the effect of orthoses but no clinically feasible methods exist. We have developed a stretch‐sensor that allows for in‐shoe measurement of navicular drop but the reliability and validity is unknown. The purpose of this study was to investigate: 1) the reliability of the stretch‐sensor for measuring navicular drop, and 2) the concurrent validity of the stretch‐sensor compared to the static navicular drop test.

Methods

Intra‐ and inter‐rater reliability was tested on 27 participants walking on a treadmill on two separate days. The stretch‐sensor was positioned 20 mm posterior to the tip of the medial malleolus and 20 mm posterior to the navicular tuberosity. The participants walked six minutes on the treadmill before navicular drop was measured. Reliability was quantified by the Intraclass Correlation Coefficient (ICC 2.1) and agreement was quantified by Limits of Agreement (LOA). To assess concurrent validity, static navicular drop was measured with the stretch‐sensor and compared with static navicular drop measured with a ruler on 27 new participants. Linear regression was used to measure concurrent validity.

Results

The reliability of the stretch‐sensor was acceptable for barefoot measurement (intra‐ and inter‐rater ICC: 0.76‐0.84) but lower for in‐shoe measurement (ICC: 0.65). There was a significant association between static navicular drop measured with the stretch‐sensor compared with a ruler (r = 0.745, p < 0.001).

Conclusion

This study suggests that the stretch‐sensor has acceptable reliability for dynamic barefoot measurement of navicular drop. Furthermore, the stretch‐sensor shows concurrent validity compared with the static navicular drop test as performed by Brody. This new simple method may hold promise for both clinical assessment and research but more work is needed before the method can be recommended.
Defining the molecular pathologies in cloaca malformation: similarities between mouse and human
Authors: Runck Laura A. , Method Anna , Bischoff Andrea , Levitt Marc , Peña Alberto , Collins Margaret H. , Gupta Anita , Shanmukhappa Shiva , Wells James M. , Guasch Géraldine
Published: February 2014

Anorectal malformations are congenital anomalies that form a spectrum from the most benign type with excellent functional prognosis, to very complex, such as cloaca in females in which the rectum, vagina and urethra fail to develop separately and instead drain via a single common channel into the perineum. The severity of this phenotype suggests that the defect occurs early during embryonic development of the organs derived from the cloaca. Due to the inability to directly investigate human cloaca development, current research has relied on the use of mouse models of anorectal malformations. However, even studies of mouse embryos lack analysis of the earliest stages of cloaca patterning and morphogenesis. Here we compared human and mouse cloaca development and retrospectively identified that early mis-patterning of the embryonic cloaca may underlie the most severe forms of anorectal malformation in humans. In mouse, we identified that defective Shh signaling results in early dorsal-ventral epithelial abnormalities prior to the reported defects in septation. This is manifested by the absence of Sox2 and aberrant expression of Keratins in the cloaca of Shh knockout mice. Shh knockout embryos additionally develop a hypervascular stroma, which is defective in BMP signaling. These epithelial and stromal defects persist later creating an indeterminate epithelium with molecular alterations in the common channel. We then used these animals to perform a broad comparison with patients with mild to severe forms of anorectal malformations including cloaca. We found striking parallels with the Shh mouse model including nearly identical defective molecular identity of the epithelium and surrounding stroma. Our work strongly suggests that early cloacal epithelial differentiation defects may be the underlying cause of severe forms of anorectal malformations in humans. Moreover, deranged hedgehog and BMP signaling is correlated with severe anorectal malformations in both mouse and humans.
Adhesive interactions of N-cadherin limit the recruitment of microtubules to cell–cell contacts through organization of actomyosin
Authors: Plestant Charlotte , Strale Pierre-Olivier , Seddiki Rima , Nguyen Emmanuelle , Ladoux Benoit , Mège René-Marc
Published: February 2014

Adhesive interactions of cadherins induce crosstalk between adhesion complexes and the actin cytoskeleton, allowing strengthening of adhesions and cytoskeletal organization. The underlying mechanisms are not completely understood, and microtubules (MTs) might be involved, as for integrin-mediated cell–extracellular-matrix adhesions. Therefore, we investigated the relationship between N-cadherin and MTs by analyzing the influence of N-cadherin engagement on MT distribution and dynamics. MTs progressed less, with a lower elongation rate, towards cadherin adhesions than towards focal adhesions. Increased actin treadmilling and the presence of an actomyosin contractile belt, suggested that actin relays inhibitory signals from cadherin adhesions to MTs. The reduced rate of MT elongation, associated with reduced recruitment of end-binding (EB) proteins to plus ends, was alleviated by expression of truncated N-cadherin, but was only moderately affected when actomyosin was disrupted. By contrast, destabilizing actomyosin fibers allowed MTs to enter the adhesion area, suggesting that tangential actin bundles impede MT growth independently of MT dynamics. Blocking MT penetration into the adhesion area strengthened cadherin adhesions. Taken together, these results establish a crosstalk between N-cadherin, F-actin and MTs. The opposing effects of cadherin and integrin engagement on actin organization and MT distribution might induce bias of the MT network during cell polarization.
Mutations in Cx30 that are linked to skin disease and non-syndromic hearing loss exhibit several distinct cellular pathologies
Authors: Berger Amy C. , Kelly John J. , Lajoie Patrick , Shao Qing , Laird Dale W.
Published: February 2014

Connexin 30 (Cx30), a member of the large gap-junction protein family, plays a role in the homeostasis of the epidermis and inner ear through gap junctional intercellular communication (GJIC). Here, we investigate the underlying mechanisms of four autosomal dominant Cx30 gene mutations that are linked to hearing loss and/or various skin diseases. First, the T5M mutant linked to non-syndromic hearing loss formed functional gap junction channels and hemichannels, similar to wild-type Cx30. The loss-of-function V37E mutant associated with Clouston syndrome or keratitis-ichthyosis-deafness syndrome was retained in the endoplasmic reticulum and significantly induced apoptosis. The G59R mutant linked to the Vohwinkel and Bart-Pumphrey syndromes was retained primarily in the Golgi apparatus and exhibited loss of gap junction channel and hemichannel function but did not cause cell death. Lastly, the A88V mutant, which is linked to the development of Clouston syndrome, also significantly induced apoptosis but through an endoplasmic-reticulum-independent mechanism. Collectively, we discovered that four unique Cx30 mutants might cause disease through different mechanisms that also likely include their selective trans-dominant effects on coexpressed connexins, highlighting the overall complexity of connexin-linked diseases and the importance of GJIC in disease prevention.
A cascade of ER exit site assembly that is regulated by p125A and lipid signals
Authors: Klinkenberg David , Long Kimberly R. , Shome Kuntala , Watkins Simon C. , Aridor Meir
Published: February 2014

The inner and outer layers of COPII mediate cargo sorting and vesicle biogenesis. Sec16A and p125A (officially known as SEC23IP) proteins interact with both layers to control coat activity, yet the steps directing functional assembly at ER exit sites (ERES) remain undefined. By using temperature blocks, we find that Sec16A is spatially segregated from p125A-COPII-coated ERES prior to ER exit at a step that required p125A. p125A used lipid signals to control ERES assembly. Within p125A, we defined a C-terminal DDHD domain found in phospholipases and PI transfer proteins that recognized PA and phosphatidylinositol phosphates in vitro and was targeted to PI4P-rich membranes in cells. A conserved central SAM domain promoted self-assembly and selective lipid recognition by the DDHD domain. A basic cluster and a hydrophobic interface in the DDHD and SAM domains, respectively, were required for p125A-mediated functional ERES assembly. Lipid recognition by the SAM–DDHD module was used to stabilize membrane association and regulate the spatial segregation of COPII from Sec16A, nucleating the coat at ERES for ER exit.
The Hippo-YAP signaling pathway and contact inhibition of growth
Authors: Gumbiner Barry M. , Kim Nam-Gyun
Published: February 2014

The Hippo-YAP pathway mediates the control of cell proliferation by contact inhibition as well as other attributes of the physical state of cells in tissues. Several mechanisms sense the spatial and physical organization of cells, and function through distinct upstream modules to stimulate Hippo-YAP signaling: adherens junction or cadherin–catenin complexes, epithelial polarity and tight junction complexes, the FAT-Dachsous morphogen pathway, as well as cell shape, actomyosin or mechanotransduction. Soluble extracellular factors also regulate Hippo pathway signaling, often inhibiting its activity. Indeed, the Hippo pathway mediates a reciprocal relationship between contact inhibition and mitogenic signaling. As a result, cells at the edges of a colony, a wound in a tissue or a tumor are more sensitive to ambient levels of growth factors and more likely to proliferate, migrate or differentiate through a YAP and/or TAZ-dependent process. Thus, the Hippo-YAP pathway senses and responds to the physical organization of cells in tissues and coordinates these physical cues with classic growth-factor-mediated signaling pathways. This Commentary is focused on the biological significance of Hippo-YAP signaling and how upstream regulatory modules of the pathway interact to produce biological outcomes.
Src kinases and ERK activate distinct responses to Stitcher receptor tyrosine kinase signaling during wound healing in Drosophila
Authors: Tsarouhas Vasilios , Yao Liqun , Samakovlis Christos
Published: February 2014

Metazoans have evolved efficient mechanisms for epidermal repair and survival following injury. Several cellular responses and key signaling molecules that are involved in wound healing have been identified in Drosophila, but the coordination of cytoskeletal rearrangements and the activation of gene expression during barrier repair are poorly understood. The Ret-like receptor tyrosine kinase (RTK) Stitcher (Stit, also known as Cad96Ca) regulates both re-epithelialization and transcriptional activation by Grainy head (Grh) to induce restoration of the extracellular barrier. Here, we describe the immediate downstream effectors of Stit signaling in vivo. Drk (Downstream of receptor kinase) and Src family tyrosine kinases bind to the same docking site in the Stit intracellular domain. Drk is required for the full activation of transcriptional responses but is dispensable for re-epithelialization. By contrast, Src family kinases (SFKs) control both the assembly of a contractile actin ring at the wound periphery and Grh-dependent activation of barrier-repair genes. Our analysis identifies distinct pathways mediating injury responses and reveals an RTK-dependent activation mode for Src kinases and their central functions during epidermal wound healing in vivo.
Claudin-6, -10d, and -10e contribute to seawater acclimation in the euryhaline puffer fishTetraodon nigroviridis
Authors: Bui Phuong , Kelly Scott P.
Published: February 2014

Expression profiles of claudin-6, -10d, and -10e in the euryhaline teleost fish Tetraodon nigroviridis revealed claudin-6 in brain, eye, gill, and skin tissue, while claudin-10d and -10e were found in brain, gill and skin only. In fishes, the gill and skin are important tissue barriers that interface directly with surrounding water, but these organs generally function differently in osmoregulation. Therefore, roles for gill and skin claudin-6, -10d, and -10e in the osmoregulatory strategies of Tetraodon were investigated. In the gill epithelium claudin-6, -10d, and -10e co-localized with Na+-K+-ATPase immunoreactive (NKA-ir) ionocytes and differences in sub-cellular localization could be observed in hypo- (freshwater, FW) versus hyperosmotic (seawater, SW) environments. Claudin-10d and -10e abundance increased in the gills of fish acclimated to SW versus FW while claudin-6 abundance decreased in SW. Taken together with our knowledge of claudin-6 and -10 function in other vertebrates, data support the idea that in SW-acclimated Tetraodon, these claudins are abundant in gill ionocytes where they contribute to the formation of a Na+ shunt and 'leaky' epithelium, both of which are characteristic of salt secreting SW fish gills. Skin claudin-10d and -10e abundance also increased in fish acclimated to SW versus those in FW, but so did claudin-6. In skin, claudin-6 was found to co-localize with NKA-ir cells, but claudin-10d and -10e did not. This study provides direct evidence that the gill epithelium contains salinity responsive tight junction proteins that are abundant primarily in ionocytes. These same proteins also appear to play a role in the osmoregulatory physiology of the epidermis.
Highly Diastereoselective Synthesis of Chiral Furans with a Quaternary Carbon Substituent at the 2-Position Using 8-Phenylmenthol as the Chiral Auxiliary
Authors: Katori Aki , Sashihara Yoshiaki , Iwamoto Akihisa , Kojima Satoshi , Yamamoto Yohsuke
Published: February 2014

The reaction of cis-4-oxo-2-pentenal and 8-phenylmenthyl 2-oxocyclopentane-1-carboxylate in the presence of a fluorinated cosolvent afforded the corresponding furan product with a high diastereoselectivity of up to 96% de. Other cyclic β-ketoesters reacted in a likewise diastereoselective manner.
1st Mexican Sclerotherapy Consensus
Authors: Ramírez C. , Lemoine C. , Cázares H. , Ramírez A. , Jiménez E. , Rendón F. , Castañeda R. , Arias L. , Vega F.
Published: February 2014

Hintergrund: Sklerotherapie existiert seit 1516 und ist eine anerkannte Therapie, die weltweit zum Einsatz kommt. Mexikanische Ärzte nahmen an vielen Konsensen teil, um mannigfaltige Absprachen, Referenzen, Methoden und Verfahren zusammenzutragen, die zur Erstel-lung eines solchen Dokuments universelle Akzeptanz finden, u.a. den European Consensus of Sclerotherapy 2003 und dessen letzte Auflage aus dem Jahre 2006, den argentinischen und lateinamerikanischen Konsensus 2012 sowie verschiedene Quellen der Fachliteratur.

Zielsetzung: Unter Berücksichtigung der weltweit anerkannten Fachliteratur und der Erfahrungen von Sklerose-Experten wurde ein Dokument entwickelt, das Konzepte, Prioritäten, Unterschiede und Variationen im Hinblick auf Diagnose, Einsatz, Therapie und andere Themen im Zusammenhang mit Sklerotherapie vereint. Damit soll eine unter akademischen, medizinischen, rechtlichen und praktischen Gesichtspunkten wertvolle Informationsquelle geschaffen werden.

Methode: Folgende Punkte wurden berücksichtigt: Indikationen, Kontraindikationen, Arten von Sklerosierungsmitteln und verwendete Konzentrationen, Lage des Patienten, Verabreichungsweg, Vorbereitung und Konservierung von Sklerosierungsmitteln, erforderliche Instrumente, Injektionsvolumina, Verabreichungsparameter, Kompression und besondere Hinweise.

Die vorhandene Literatur wurde konsultiert hinsichtlich der abgehandelten Themen. Es wurde ein Expertengremium zusammengestellt, das eigene Erfahrungsberichte zur Verfügung stellte. Vor diesem Hintergrund wurden Antworten in Form klinischer Richtlinien formuliert oder allgemeine Empfehlungen abgegeben und Betrachtungen zur Variabilität der Konzepte zum Ausdruck gebracht, um konkrete Antworten auf die spezifischen Fragen zu bieten. Außerdem wird ein Abschnitt mit Betrachtungen integriert, in dem mögliche anerkannte Varianten zu jeder einzelnen Fragestellung erklärt werden. Im Haupttext wird der 100%ige Konsens bezüglich einer Thematik dargestellt, während die blauem Balken von Experten vorgeschlagene Varian-ten aufzeigen. Da die aufgeführten Punkte vor dem Hintergrund von in Mexiko verfügbaren Substanzen diskutiert werden, werden nicht alle Sklerosierungsmittel oder Instrumente besprochen.
BioJS InterMine List Analysis: A BioJS component for displaying graphical or statistical analysis of collections of items from InterMine endpoints
Authors: Kalderimis Alexis , Stepan Radek , Sullivan Julie , Lyne Rachel , Lyne Michael , Micklem Gos
Published: February 2014

Summary: The InterMineTable component is a reusable JavaScript component as part of the BioJS project. It enables users to embed powerful table-based query facilities in their websites with access to genomic data-warehouses such as http://www.flymine.org, which allow users to perform flexible queries over a wide range of integrated data types.

Availability:  http://github.com/alexkalderimis/im-tables-biojs; http://github.com/biojs/biojs; http://dx.doi.org/10.5281/zenodo.8301.
HeatMapViewer: interactive display of 2D data in biology
Authors: Yachdav Guy , Hecht Maximilian , Pasmanik-Chor Metsada , Yeheskel Adva , Rost Burkhard
Published: February 2014

Summary: The HeatMapViewer is a BioJS component that lays-out and renders two-dimensional (2D) plots or heat maps that are ideally suited to visualize matrix formatted data in biology such as for the display of microarray experiments or the outcome of mutational studies and the study of SNP-like sequence variants. It can be easily integrated into documents and provides a powerful, interactive way to visualize heat maps in web applications. The software uses a scalable graphics technology that adapts the visualization component to any required resolution, a useful feature for a presentation with many different data-points. The component can be applied to present various biological data types. Here, we present two such cases – showing gene expression data and visualizing mutability landscape analysis.

Availability: https://github.com/biojs/biojs; http://dx.doi.org/10.5281/zenodo.7706.
treeWidget: a BioJS component to visualise phylogenetic trees
Authors: Schreiber Fabian
Published: February 2014

Summary: Phylogenetic trees are widely used to represent the evolution of gene families. As the history of gene families can be complex (including lots of gene duplications), its visualisation can become a difficult task. A good/accurate visualisation of phylogenetic trees - especially on the web - allows easier understanding and interpretation of trees to help to reveal the mechanisms that shape the evolution of a specific set of gene/species. Here, I present treeWidget, a modular BioJS component to visualise phylogenetic trees on the web. Through its modularity, treeWidget can be easily customized to allow the display of sequence information, e.g. protein domains and alignment conservation patterns.

Availability: http://github.com/biojs/biojs; http://dx.doi.org/10.5281/zenodo.7707
The BioJS article collection of open source components for biological data visualisation
Authors: Corpas Manuel
Published: February 2014

Data-driven research has gained momentum in the life sciences. Visualisation of these data is essential for quick generation of hypotheses and their translation into useful knowledge. BioJS is a new proposed standard for JavaScript-based components to visualise biological data. BioJS is an open source community project that to date provides 39 different components contributed by a global community. Here, we present the BioJS F1000Research collection series. A total of 12 components and a project status article are published in bulk. This collection does not intend to be an all-encompassing, comprehensive source of BioJS articles, but an initial set; future submissions from BioJS contributors are welcome.
A Note on the Ichoua, Gendreau, and Potvin (2003) Travel Time Model
Authors: Ghiani Gianpaolo , Guerriero Emanuela
Published: February 2014

In this paper we exploit some properties of the travel time model proposed by Ichoua, Gendreau, and Potvin [Ichoua S, Gendreau M, Potvin J-Y (2003) Vehicle dispatching with time-dependent travel times. Eur. J. Oper. Res. 144:379–396], on which most of the current time-dependent vehicle-routing literature relies. First, we prove that any continuous piecewise-linear travel time model, satisfying the FIFO property, can be generated by an appropriate model. We also show that the model parameters can be obtained by solving a system of linear equations for each arc. Then such parameters are proved to be nonnegative, which allows us to interpret them as (dummy) speeds. Finally, we illustrate the procedure through a numerical example. As a by-product, we are able to link the travel time models of a road graph and the associated complete graph over which vehicle-routing problems are usually formulated.
Gravitational Radiation from Post-Newtonian Sources and Inspiralling Compact Binaries
Authors: Blanchet Luc
Published: February 2014

To be observed and analyzed by the network of gravitational wave detectors on ground (LIGO, VIRGO, etc.) and by the future detectors in space (eLISA, etc.), inspiralling compact binaries — binary star systems composed of neutron stars and/or black holes in their late stage of evolution — require high-accuracy templates predicted by general relativity theory. The gravitational waves emitted by these very relativistic systems can be accurately modelled using a high-order post-Newtonian gravitational wave generation formalism. In this article, we present the current state of the art on post-Newtonian methods as applied to the dynamics and gravitational radiation of general matter sources (including the radiation reaction back onto the source) and inspiralling compact binaries. We describe the post-Newtonian equations of motion of compact binaries and the associated Lagrangian and Hamiltonian formalisms, paying attention to the self-field regularizations at work in the calculations. Several notions of innermost circular orbits are discussed. We estimate the accuracy of the post-Newtonian approximation and make a comparison with numerical computations of the gravitational self-force for compact binaries in the small mass ratio limit. The gravitational waveform and energy flux are obtained to high post-Newtonian order and the binary’s orbital phase evolution is deduced from an energy balance argument. Some landmark results are given in the case of eccentric compact binaries — moving on quasi-elliptical orbits with non-negligible eccentricity. The spins of the two black holes play an important role in the definition of the gravitational wave templates. We investigate their imprint on the equations of motion and gravitational wave phasing up to high post-Newtonian order (restricting to spin-orbit effects which are linear in spins), and analyze the post-Newtonian spin precession equations as well as the induced precession of the orbital plane.
The role of stem cells in osteoarthritis
Authors: Singh A. , Goel S. C. , Gupta K. K. , Kumar M. , Arun G. R. , Patil H. , Kumaraswamy V. , Jha S.
Published: February 2014

Introduction

Osteoarthritis (OA) is a progressively debilitating disease that affects mostly cartilage, with associated changes in the bone. The increasing incidence of OA and an ageing population, coupled with insufficient therapeutic choices, has led to focus on the potential of stem cells as a novel strategy for cartilage repair.

Methods

In this study, we used scaffold-free mesenchymal stem cells (MSCs) obtained from bone marrow in an experimental animal model of OA by direct intra-articular injection. MSCs were isolated from 2.8 kg white New Zealand rabbits. There were ten in the study group and ten in the control group. OA was induced by unilateral transection of the anterior cruciate ligament of the knee joint. At 12 weeks post-operatively, a single dose of 1 million cells suspended in 1 ml of medium was delivered to the injured knee by direct intra-articular injection. The control group received 1 ml of medium without cells. The knees were examined at 16 and 20 weeks following surgery. Repair was investigated radiologically, grossly and histologically using haematoxylin and eosin, Safranin-O and toluidine blue staining.

Results

Radiological assessment confirmed development of OA changes after 12 weeks. Rabbits receiving MSCs showed a lower degree of cartilage degeneration, osteophyte formation, and subchondral sclerosis than the control group at 20 weeks post-operatively. The quality of cartilage was significantly better in the cell-treated group compared with the control group after 20 weeks.

Conclusions

Bone marrow-derived MSCs could be promising cell sources for the treatment of OA. Neither stem cell culture nor scaffolds are absolutely necessary for a favourable outcome. Cite this article: Bone Joint Res 2014;3:32–7.
As the crow flies: Conventions and symbolism in Seven Minutes in the Warsaw Ghetto
Authors: Shaw Nathan
Published: February 2014

In feature-length Holocaust cinema, viewers witness two hours of harrowing events, before being pacified with an ending providing some comfort and relief; often undermining what has gone before. However, in short-film Seven Minutes in the Warsaw Ghetto, this structure is reversed, fitting perfectly with the medium to provide a stronger, lasting impact.
Analytical Investigations of Kinetic and Heat Transfer in Slow Pyrolysis of a Biomass Particle
Authors: Ojolo S.J , Osheku C.A. , Sobamowo M.G
Published: February 2014

The utilization of biomass for heat and power generation has aroused the interest of most researchers especially those of energy .In converting solid fuel to a usable form of energy, pyrolysis plays an integral role. Understanding this very important phenomenon in the thermochemical conversion processes and representing it with appropriate mathematical models is vital in the design of pyrolysis reactors and biomass gasifiers. Therefore, this study presents analytical solutions to the kinetic and the heat transfer equations that describe the slow pyrolysis of a biomass particle. The effects of Biot number, temperature and residence time on biomass particle decomposition were studied. The results from the proposed analytical models are in good agreement with the reported experimental results. The developed analytical solutions to the heat transfer equations which have been stated to be “analytically involved” showed average percentage error and standard deviations 0.439 and 0.103 from the experimental results respectively as compared with previous model in literature which gives average percentage error and standard deviations 0.75 and 0.106 from the experimental results respectively. This work is of great importance in the design of some pyrolysis reactors/units and in the optimal design of the biomass gasifiers.
Antioxidant Effect on Oxidation Stability of Blend Fish Oil Biodiesel with Vegetable Oil Biodiesel and Petroleum Diesel Fuel
Authors: Hossain M. , Sujan S.M.A , Jamal M.S.
Published: February 2014

Two different phenolic synthetic antioxidants were used to improve the oxidation stability of fish oil biodiesel blends with vegetable oil biodiesel and petroleum diesel. Butylhydroxytoluene (BHT) most effective for improvement of the oxidation stability of petro diesel, whereas  tert butylhydroquinone (TBHQ) showed good performance in fish oil biodiesel. Fish oil/Rapeseed oil biodiesel mixed showed some acceptable results in higher concentration of antioxidants. TBHQ showed better oxidation stability than BHT in B100 composition. In fish oil biodiesel/diesel mixed fuel, BHT was more effective antioxidant than TBHQ to increase oxidation stability because BHT is more soluble than TBHQ. The stability behavior of biodiesel/diesel blends with the employment of the modified Rancimat method (EN 15751). The performance of antioxidants was evaluated for treating fish oil biodiesel/Rapeseed oil biodiesel for B100, and blends with two type diesel fuel (deep sulfurization diesel and automotive ultra-low sulfur or zero sulfur diesels). The examined blends were in proportions of 5, 10, 15, and 20% by volume of fish oil biodiesel.
Financial Measures for Electric Vehicles:Supporting the Integration of Renewable Energy in the Mobility Sector in Germany
Authors: Bickert Stefan
Published: February 2014

Electric vehicles (EV) are able to support the transition of sectors towards sustainability. The operation of these vehicles with renewable energies saves local and global emissions. Furthermore, fluctuating renewable energies can be integrated in existing energy systems by using electric vehicles for grid services. Thus, implementation of advantages requires market establishment of electric vehicles. The article provides a review on potentials of market development by comparing and studying costs of electric and conventional vehicles as well as effects of financial measures on costs of EV. These cost comparisons are based on market data and predictions of cost developments for private consumers in Germany. Costs are analysed by an economic model of Total Cost of Ownership (TCO), aiming to display financial proportionality between vehicles in different years of acquisition (2010 to 2030). In a further step, external financial measures are analysed and integrated in the cost model as one possibility to enhance and secure the market introduction. Findings demonstrate that higher costs of acquisition of electric vehicles cannot be compensated by lower costs of operation. While mobility costs of conventionally vehicles stay constant or even increase during the considered years, mobility costs of electric vehicles significantly decrease especially in the upcoming years. In all cases mobility costs of electric vehicles exceed costs of conventional vehicles, but differences are reduced from 19€ct in 2010 to 3€ct in 2030. Cost decreases of the battery have high influence on the increasing financial comparability of EV. Concerning financial measures especially a differentiation of energy prices and a compensation of grid services can help to decrease total costs of EV and to manage a shift from fossil energy resources to electricity in the mobility sector. The existing tax exemption for EV compensates only a little fraction (about 6%) of the cost difference. This highlights the importance of research on incentive schemes to support market integration of EV and thereby the integration of renewable energies in the mobility sector. This integration is supported by the possibility of storing surplus fluctuating renewable energy in the batteries of EV.
Optimization of Concentration and EM4 Augmentation for Improving Bio-Gas Productivity from Jatropha curcas Linn Capsule Husk
Authors: G.A Praptiningsih , Hendroko Roy , Wahono Satriyo K , Sasmito Andi , O. Nelwan Leopold , Nindita Anggi , Liwang Tony
Published: February 2014

Most literature suggests that two-phase digestion is more efficient than single-phase. The series of two-phase digestion studies have been conducted from 2011 to 2013 at the research farm of PT Bumimas Ekapersada, West Java, Indonesia. This paper reports on a research on optimation of concentration and augmentation of EM-4 (effective microorganism-4), a local commercial decomposer, as efforts to stabilize a biogas technology which made from husk capsules of Jatropha curcas Linn (DH-JcL). The studies of increasing organic loading rate (OLR) for the two-phase digestion was conducted to improve efficiency.  The concentration variable studied was 1: 8 (1 part DH-JCL and 8 parts water), compared to 1: 12 as a control. The augmentation treatment is the addition of EM-4 by 5% (v/v). It was also examined the augmentation of F2-EM4 (150 times duplication of EM-4) due to cost consideration. The studies were conducted in the laboratory which using a liter and two liters of glass digester and glass wool as immobilized growth. The results of this study support the previous studies: the optimum concentration was 1: 8, EM-4 was able to increase biogas production in two-phase digestion, yet biogas production decrease at single-phase. F2-EM4’s ability to support production of biogas were equivalent to that of EM-4.
N-homocysteinylation of apolipoprotein A-I impairs the protein’s antioxidant ability but not its cholesterol efflux capacity
Authors: Miyazaki Akari , Sagae Nozomi , Usami Yoko , Sato Megumi , Kameda Takahiro , Yoshimoto Akira , Ishimine Nau , Matsuda Kazuyuki , Sugano Mitsutoshi , Hara Masayuki , Honda Takayuki , Tozuka Minoru
Published: February 2014

A high homocysteine (Hcy) level is a risk factor for atherosclerosis. Hcy can be added to proteins through a process known as N-homocysteinylation. This is thought to be a potential cause of atherosclerosis induction. We previously reported that N-homocysteinylated apolipoprotein A-I (N-Hcy-apoA-I) was identified in normal human plasma. In this study, the effect of N-homocysteinylation on the functions of apoA-I was examined. A kinetic study using dimyristoyl phosphatidylcholine (DMPC) liposomes indicated that N-Hcy-apoA-I showed increased lipid-binding activity compared to wild-type apoA-I. Two reconstituted high-density lipoprotein (rHDL) particles of different sizes (approximately 8.2 nm and 7.6 nm in diameter) were produced by mixing apoA-I and 1-palmitoyl-2-oleoyl phosphatidylcholine (POPC). However, an increased ratio of large to small particles was found in rHDL prepared with N-Hcy-apoA-I. The normal apoA-I antioxidant ability, estimated by the suppression of conjugated diene formation in low-density lipoprotein (LDL) induced by copper sulfate oxidation, was considerably impaired when using N-Hcy-apoA-I. Although N-Hcy-apoA-I functioned as an oxidant, no significant difference was observed in the cholesterol efflux capacity from THP-1 macrophages between wild-type apoA-I and N-Hcy-apoA-I. These results suggest that N-Hcy-apoA-I might be proatherogenic due to its oxidative behavior but not an attenuation of cholesterol efflux capacity.
The History of Science and Ancient Mesopotamia
Authors: Rochberg Francesca
Published: February 2014

This paper views the relevance of cuneiform texts to the history of science from inside, i.e., from the perspective of the available sources, as well as from outside, i.e., from the perspective of historians of science outside the field of Assyriology. It reviews some of the methodological problems that beset the reconstruction of science in the ancient Near East as well as a way forward, which acknowledges localism and pluralism as well the compelling continuity from cuneiform traditions of knowledge to later counterparts (astronomy, astrology, magic, astral-medicine). Cuneiform texts will not instantiate a universal or transcultural science but are essential if science is to be seen as embedded in culture and history.
Use of Hand-Spray Plaster as a Coating for Soil Bulk Volume Measurement
Authors: Liu Xianfeng , Buzzi Olivier
Published: February 2014

This paper presents a new coating material [hand-spray plaster (HSP)] used to measure the bulk volume of soil specimens having irregular shapes. The new method has been validated against two benchmark methods, namely, the wax and plastic bag methods, by conducting swelling and shrinkage tests on intact Maryland clay. The results show that the new method yields similar values of volume but with much reduced data scattering. The HSP method is also far easier to use than the other two methods. Finally, the stiffness of the coating has been measured and its restraining effect has been found to be negligible. Some of the benefits of using the HSP method are: (1) limited fluid retention by the specimen post-immersion for volume measurement, (2) reduced water-intake rate with elimination of cracking upon swelling caused by high-suction gradients, (3) absence of the restraining effect on specimens upon swelling, and (4) accurate determination of the swelling and shrinkage curves with only one specimen per curve.
Surveying the Temporal Structure of Sounds Used in Music Perception
Authors: Schutz Michael , Vaisberg Jonathan M.
Published: February 2014

Recent work from our lab illustrates amplitude envelope’s crucial role in both perceptual (Schutz, 2009) and cognitive (Schutz & Stefanucci, 2010) processing. Consequently, we surveyed the amplitude envelopes of sounds used in Music Perception, categorizing them as either flat (i.e., trapezoidal shape), percussive (aka “damped” or “decaying”), other, or undefined. Curiously, the undefined category represented the largest percentage of sounds observed, with 35% lacking definition of this important property (approximately 27% were percussive, 27% flat, and 11% other). This omission of relevant information was not indicative of general inattention to methodological detail. Studies using tones with undefined amplitude envelopes generally defined other properties such as spectral structure (85%), duration (80%), and even model of headphones/speakers (65%) at high rates. Consequently, this targeted omission is intriguing, and suggests amplitude envelope is an area ripe for future research.