bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluating the Effects of Carbon Nanoreactor Diameter and Internal Structure on the Pathways of the Catalytic Hydrosilylation Reaction
Authors: Solomonsz William A. , Rance Graham A. , Khlobystov Andrei N.
Published: January 2014

Three different types of carbon nanoreactors, double‐walled nanotubes (DWNT), multi‐walled nanotubes (MWNT) and graphitised carbon nanofibers (GNF) have been appraised for the first time as containers for the reactions of phenylacetylene hydrosilylation catalysed by a confined molecular catalyst [Rh4(CO)12]. Interactions of [Rh4(CO)12] with carbon nanoreactors determining the ratio of β‐addition products are unchanged for all nanoreactors and are virtually unaffected by the confinement of [Rh4(CO)12] inside carbon nanostructures. Conversely, the relative concentrations of reactants affecting the ratio of addition and dehydrogenative silylation products is very sensitive to nanoscale confinement, with all nanoreactors demonstrating significant effects on the distribution of reaction products as compared to control experiments with the catalyst in bulk solution or adsorbed on the outer surface of nanoreactors. Surprisingly, the widest nanoreactors (GNF) change the reaction pathway most significantly, which is attributed to the graphitic step‐edges inside GNF providing effective anchoring points for the catalyst and creating local environments with greatly altered concentrations of reactants as compared to bulk solution. Possessing diameters significantly wider than molecules, GNF impose no restrictions on the transfer of reactants while providing the strongest confinement effects for the reaction. Furthermore, GNF facilitate the effective recyclability of the catalyst and thus represents a superior nanoreactor system to carbon nanotubes.
Stretchable Energy Storage and Conversion Devices
Authors: Yan Chaoyi , Lee Pooi See
Published: January 2014

Stretchable electronics are a type of mechanically robust electronics which can be bended, folded, crumpled and stretched and represent the emerging direction towards next‐generation wearable and implantable devices. Unlike existing electronics based on rigid Si technologies, stretchable devices can conform to the complex non‐coplanar surfaces and provide unique functionalities which are unreachable with simple extension of conventional technologies. Stretchable energy storage and conversion devices are the key components for the fabrication of complete and independent stretchable systems. In this review, we present the recent progresses in the developments of stretchable power sources including supercapacitors, batteries and solar cells. Representative structural and material designs to impart stretchability to the originally rigid devices are discussed. Advantages and drawbacks associated with the fabrication methods are also analysed. Summaries of the research progresses along with future development directions for this exciting field are also presented.
What Have We Learnt About the Mechanisms of Rapid Water Transport, Ion Rejection and Selectivity in Nanopores from Molecular Simulation?
Authors: Thomas Michael , Corry Ben , Hilder Tamsyn A.
Published: January 2014

Nanopores have demonstrated an extraordinary ability to allow water molecules to pass through their interiors at rates far exceeding expectations based on continuum theory. Moreover, simulation studies suggest that particular nanoscale pores have the potential to discriminate between water and salts as well as to distinguish between a range of different ion types. Some of the unusual features of transport in these nanopores have been elucidated with molecular dynamics simulation, specifically the spontaneous filling and rapid transport of water, the rejection of ions and the selection between ions. The main focus of this review, however, is the physical mechanisms which act to produce such remarkable behaviour at this scale, drawing on the many studies that have been conducted in the last decade. Since molecular dynamics simulations allow the motion of individual atoms to be followed over time, they have the potential to provide fundamental insight into the reasons why transport in nanoscale pores differs from expectations based on macroscopic theory. Gaining an understanding of the mechanisms of transport in these tiny pores should guide future experiments in this area aimed at developing novel technologies and improving existing membrane separation techniques.
SERS Biosensor Using Metallic Nano‐Sculptured Thin Films for the Detection of Endocrine Disrupting Compound Biomarker Vitellogenin
Authors: Srivastava Sachin K. , Shalabney Atef , Khalaila Isam , Grüner Christoph , Rauschenbach Bernd , Abdulhalim Ibrahim
Published: January 2014

A biosensor chip is developed for the detection of a protein biomarker of endocrine disrupting compounds, vitellogenin (Vg) in aquatic environment. The sensor chip is fabricated by immobilizing anti‐Vg antibody on 4‐Aminothiophenol (4‐ATP) coated nanosculptured thin films (nSTFs) of silver on Si substrates. The biosensor is based on the SERS of 4‐ATP, enhanced by the Ag nSTFs. Before the fabrication of the sensor, the performance of the enhancement is optimized with respect to the porosity of nSTFs. Further, the biosensor is developed on the nSTF with optimized enhancement. The SERS signals are recorded from the sensor chip for varying concentrations of Vg. A control experiment is performed on another similar protein Fetuin to confirm the specificity of the sensor. The repeatability and reusability of the sensor, along with its shelf life are also checked. The limit of detection of the sensor is found to be 5 pg mL‐1 of Vg in PBS within our experimental window. Apart from high sensitivity, specificity and reusability, the present sensor provides additional advantages of miniaturization, requirement of very small volumes of the analyte solution (15 μL) and fast response as compared to conventional techniques e.g., ELISA, as its response time is less than 3 minutes.
Effect of Mg–Ti Deoxidation on the Formation Behavior of Equiaxed Crystals During Rapid Solidification of Iron Alloys
Authors: Park Jun Seok , Park Joo Hyun
Published: January 2014

The effect of Mg–Ti deoxidation on the solidification structure of advanced high strength steel was investigated by observing the solidification structure and also the inclusion particles. The effect of precipitation of TiN, MgO, and “TiN–MgO” hybrid inclusion on the formation of fine equiaxed crystals was evaluated. The composition of inclusions was observed to change in the order of MgO → “MgO(core) + TiN(surface)” → Ti2O3 by reaction time, which corresponded to the change of solidification structure as “columnar → equiaxed → columnar.” This could be understood from the concept of lattice disregistry in between delta iron and MgO (3.97%), TiN (3.91%), and Ti2O3 (18.9%). However, even with very low disregistry between delta iron and MgO, the MgO itself did not work as an effective catalyst, indicating that there is another criterion for determining a good catalyst. The mechanism of the formation of TiN on MgO surface was schematically described. The precipitation of TiN on MgO surface was feasible although the content of Ti and N was lower than the equilibrium solubility product for the formation of TiN. Because disregistry between TiN and MgO is very low (0.05%), the precipitation of TiN on the surface of MgO is energetically more favorable.
Microstructure‐Based Modeling of Deformation in Steels Based on Constitutive Relationships from Micropillar Compression
Authors: Guo En‐Yu , Singh Sudhanshu S. , Xie Hu‐xiao , Williams Jason J. , Jing Tao , Chawla Nikhilesh
Published: January 2014

Microstructure‐based finite element modeling was performed on different microstructures of an austenitic‐ferritic cast duplex stainless steel using the constitutive behavior of individual phase obtained from micropillar compression tests. A qualitative analysis of equivalent plastic strain and von Mises stress was conducted in plane stress and plane strain conditions. The simulated results reveal that the morphology and the area fraction of the second phase can affect the mechanical properties. The stress values and the equivalent plastic strain in the shear bands are higher in plane strain loading than plane stress loading condition. Stress is concentrated mostly in ferrite phase. The evolution of stress during deformation is found to be dependent on the morphologies of ferrite phase in austenite matrix.
Inclusion Development in Steel During Ladle Metallurgical Treatment ‐ A Process Simulation Model – Part: Industrial Validation
Authors: Scheller Piotr R. , Shu Qifeng
Published: January 2014

Steel cleanliness strongly affects the properties of the products. There is an ever increasing requirement of strict control of inclusion composition and amount during ladle treatment. A comprehensive model for inclusion development in gas stirred ladles developed by the authors is validated in the industrial ladle treatment processes. It can be used for the process simulation and optimization. The important factors, like stirring intensity, reaction between steel and slag as well as refractory material, and the conditions needed for separation and floatation of non‐metallic inclusions are taken into account. FactSage and SimuSage packages are employed as the thermodynamics database and simulation tools, respectively. The evolution of steel and slag composition along with the amount and composition of inclusions during the ladle treatment are calculated and compared with results from the industrial process. The comparison between model predictions and actual plant data shows good agreement as well for 210 t heats as for 30 t heats and different steel grades. The present model is a useful tool for simulation and optimization of ladle metallurgical treatments in industry.
Asymmetric Mukaiyama Aldol Reactions Using Chiral Diamine–Coordinated Sn(II) Triflate: Development and Application to Natural Product Synthesis
Authors: Shiina Isamu
Published: January 2014

In 1989, the asymmetric Mukaiyama aldol reaction mediated by a Lewis acid consisting of a chiral diamine and Sn(II) triflate was reported. The asymmetric Mukaiyama aldol reaction is now widely used as a versatile tool for the construction of highly advanced, multifunctionalized molecules. In this Personal Account, the history of the development of this powerful methodology and the application of the asymmetric Mukaiyama aldol reaction in the synthesis of natural products are reviewed.
The role of Pten/Akt signaling pathway involved in BPA‐induced apoptosis of rat sertoli cells
Authors: Wang Chengmin , Fu Wenjuan , Quan Chao , Yan Maosheng , Liu Changjiang , Qi Suqin , Yang Kedi
Published: January 2014

Bisphenol‐A (BPA), one of endocrine‐disrupting chemicals, is a male reproductive toxicant. Previous studies have revealed the direct cytotoxicity of BPA in many cultured cells, such as mitotic aneuploidy in embryonic cells and somatic cells, and apoptosis in neurons and testicular Sertoli cells. To understand the action of BPA and assess its risk, the Pten/Akt pathway was investigated in cultured Sertoli cells to elucidate the mechanism of the reproductive effects of BPA. The results showed that over 50 μM BPA treatment could decrease the viability of Sertoli cells and cause more apoptosis. In addition, BPA could induce the increase in mRNA levels of Pten and Akt. The protein level of Pten was increased; however, the protein levels of phospho‐Akt and procaspase‐3 were decreased after BPA exposure. Taken together, observed results suggested that the Pten/Akt pathway might be involved in the apoptotic effects of BPA on Sertoli cells. © 2014 Wiley Periodicals, Inc. Environ Toxicol 30: 793–802, 2015.
Brood cover and food resources for wild turkeys following silvicultural treatments in mature upland hardwoods
Authors: McCord John M. , Harper Craig A. , Greenberg Cathryn H.
Published: January 2014

Closed‐canopy, upland hardwood forests with limited understory development provide suboptimal habitat for wild turkey (Meleagris gallopavo) broods and may lead to low recruitment. Various forest management practices have been used to stimulate understory development within upland hardwoods, but evaluation of such practices on cover and food resources for wild turkey broods is incomplete. Therefore, we compared effects of 7 silvicultural treatments (repeated fire, shelterwood harvest, shelterwood harvest with one fire, retention cut, retention cut with repeated fire, retention cut with herbicide, and retention cut with herbicide and repeated fire) on cover and food resources for wild turkey broods in mature upland hardwoods of the Ridge and Valley Physiographic Province, Tennessee, USA, during 2000–2009. Canopy reduction treatments enhanced understory conditions for wild turkey broods. Eight years following initial treatment, light infiltration in retention cuts with repeated fire was 6 times greater than that within control, 5 times greater than that within shelterwood harvests, and twice that within shelterwood harvests with one prescribed fire. Woody species dominated understory composition following all treatments and controls. Understory disturbance (prescribed fire and broadcast herbicide treatments) reduced density of stems >1.4 m tall and <11.4 cm diameter at breast height (dbh) and created less visual obstruction above 1 m compared with canopy reduction treatments without understory disturbance. Following canopy reduction without repeated prescribed fire, woody vegetation exceeded ideal height for wild turkey broods after 3 growing seasons and light infiltration returned to control levels within 7 years. Soft mast production was greatest following treatments that included canopy reduction, but varied by year and site. Invertebrate biomass did not increase following any treatment, but all treatment areas contained enough invertebrates to meet the protein requirement for a wild turkey brood (10.1 poults) for 28 days on <30 ha. Where wild turkey is a focal species and understory structure in mature upland hardwoods is limiting for broods, we recommend reducing canopy coverage to 60–70% and using low‐intensity fire every 3–5 years to enhance and maintain brood cover and increase food availability. © 2014 The Wildlife Society.
Evaluating wild Turkey movement ecology: An example using first‐passage time analysis
Authors: Byrne Michael E. , Guthrie Joshua D. , Hardin Jason , Collier Bret A. , Chamberlain Michael J.
Published: January 2014

Recent advances in animal tracking technology have increased interest in the field of animal movement ecology. Numerous methods have been developed to extract information from animal movement paths that can be used to link movement behavior to external stimuli such as habitat and climatic conditions. Given the recent development of Global Positioning System (GPS) technology suitable for use on wild turkeys (Meleagris gallapavo), we advocate the adoption of new methodologies to design novel research on wild turkey ecology. Here we provide a worked example using first‐passage time on male Rio Grande wild turkeys (M. g. intermedia) tracked via GPS in South Texas, USA, during April 2009 to illustrate one methodological option on which research can be based. From our example, we infer behavioral decisions in response to habitat variables that varied during the diurnal cycle; turkeys were more likely to exhibit localized movements during midday in open areas near food and water resources. We contend that by taking advantage of GPS technology and focusing research questions on movement behavior, wild turkey research can progress toward answering mechanistic questions regarding turkey habitat use. This shift in research focus will provide much‐needed information to managers that is currently lacking at both local and regional scales. © 2014 The Wildlife Society.
NFκB and STAT3 synergistically activate the expression of FAT10, a gene counteracting the tumor suppressor p53
Authors: Choi Yongwook , Kim Jong Kyoung , Yoo Joo-Yeon
Published: January 2014

Chronic inflammation is one of the main causes of cancer, yet the molecular mechanism underlying this effect is not fully understood. In this study, we identified FAT10 as a potential target gene of STAT3, the expression of which is synergistically induced by NFκB co‐stimulation. STAT3 binding stabilizes NFκB on the FAT10 promoter and leads to maximum induction of FAT10 gene expression. Increased FAT10 represses the transcriptional activity of the tumor suppressor p53, a protein that accelerates the protein degradation of FAT10. This FAT10‐p53 double‐negative regulation is critical in the control of tumorigenesis, as overexpressed FAT10 facilitates the tumor progression in the solid tumor model. In conclusion, transcriptional synergy between STAT3 and NFκB functions to put weight on FAT10 in the mutually inhibitory FAT10‐p53 regulatory loop and thus favors tumorigenesis under inflammatory conditions.
Molecular correlates of platinum response in human high‐grade serous ovarian cancer patient‐derived xenografts
Authors: Topp Monique D. , Hartley Lynne , Cook Michele , Heong Valerie , Boehm Emma , McShane Lauren , Pyman Jan , McNally Orla , Ananda Sumitra , Harrell Marisol , Etemadmoghadam Dariush , Galletta Laura , Alsop Kathryn , Mitchell Gillian , Fox Stephen B. , Kerr Jeffrey B. , Hutt Karla J. , Kaufmann Scott H. ,   Australian Ovarian Cancer Study, Swisher Elizabeth M. , Bowtell David D. , Wakefield Matthew J. , Scott Clare L.
Published: January 2014

Introduction

Improvement in the ability to target underlying drivers and vulnerabilities of high‐grade serous ovarian cancer (HG‐SOC) requires the development of molecularly annotated pre‐clinical models reflective of clinical responses.

Methods

We generated patient‐derived xenografts (PDXs) from consecutive, chemotherapy‐naïve, human HG‐SOC by transplanting fresh human HG‐SOC fragments into subcutaneous and intra‐ovarian bursal sites of NOD/SCID IL2Rγnull recipient mice, completed molecular annotation and assessed platinum sensitivity.

Results

The success rate of xenografting was 83%. Of ten HG‐SOC PDXs, all contained mutations in TP53, two were mutated for BRCA1, three for BRCA2, and in two, BRCA1 was methylated. In vivo cisplatin response, determined as platinum sensitive (progression‐free interval ≥100 d, n = 4), resistant (progression‐free interval <100 d, n = 3) or refractory (n = 3), was largely consistent with patient outcome. Three of four platinum sensitive HG‐SOC PDXs contained DNA repair gene mutations, and the fourth was methylated for BRCA1. In contrast, all three platinum refractory PDXs overexpressed dominant oncogenes (CCNE1, LIN28B and/or BCL2).

Conclusions

Because PDX platinum response reflected clinical outcome, these annotated PDXs will provide a unique model system for preclinical testing of novel therapies for HG‐SOC.
Regulation of the localisation and function of the oncogene LYRIC/AEG‐1 by ubiquitination at K486 and K491
Authors: Luxton Hayley J. , Barnouin Karin , Kelly Gavin , Hanrahan Sarah , Totty Nick , Neal David E. , Whitaker Hayley C.
Published: January 2014

The pivotal role of LYRIC/AEG‐1 in malignant transformation, tumourigenesis and chemo‐resistance has previously been demonstrated in different cell types and sub‐cellular compartments. The localisation of LYRIC/AEG‐1 appears crucial to its function and is regulated by three lysine‐rich nuclear localisation signal regions, one of which was previously demonstrated to be modified by ubiquitin. Here we show that mutation of LYRIC/AEG‐1 at K486 and K491 results in a loss of ubiquitination. A K486/491R double mutant that is incapable of ubiquitination shows reduced binding to the NFκB subunit p65 or importin‐β resulting in a distinctive peri‐nuclear localisation of LYRIC/AEG‐1. We also provide evidence to suggest that TOPORS, an E3 ligase that also regulates p53 modification may be responsible for LYRIC/AEG‐1 ubiquitin modification. Overall we demonstrate that specific sites of LYRIC/AEG‐1 ubiquitination are essential for regulating LYRIC/AEG‐1 localisation and functionally interacting proteins.
Not much happened: The impact of gender quotas in Poland
Authors: Millard Frances
Published: January 2014

Poland maintained its open-list PR system but introduced gender quotas in the 2011 parliamentary elections in order to increase the number of women deputies. Yet this change had only a limited impact on women’s representation. The 2011 election confirms that ‘favorable’ electoral laws provide opportunities for women, but they cannot guarantee that women will be elected. In particular, the use of quotas alone is not sufficient to ensure high levels of women’s representation. The most important factors in explaining the Polish result were 1) the absence of a ‘zipper’, a list ordering that alternates men and women candidates, thus ensuring high list-places for women 2) the parties’ favoring of men in their list placement 3) the relative size of the political parties and 4) voters’ support for list leaders and incumbent deputies. Despite a disappointing outcome, quotas may be seen as beneficial in increasing women’s presence and the potential for further evolution of the electoral system.
Synkopen – sinnvolle Diagnostik zur Identifizierung maligner Synkopen
Authors: Schaer Beat , Kühne Michael
Published: January 2014

Synkopen sind ein häufiges Problem sowohl in der Hausarztpraxis als auch auf Notfallstationen. Die Differenzierung zwischen kardialer und nicht-kardialer Ätiologie ist für die Prognose und das Procedere entscheidend. Verschiedene kardiologische Abklärungsmethoden und ihre Wertigkeit wie auch ein Algorithmus zur sinnvollen Synkopenabklärung werden dargelegt.
Vorhofflimmern – Medikamentöse Therapie bei Rhythmus- oder Frequenzkontrolle
Authors: Müller-Burri Stephan Andreas
Published: January 2014

Die medikamentöse Therapie von Patienten mit Vorhofflimmern umfasst neben einer dem individuellen Risiko des Patienten angepassten Thromboembolieprophylaxe die Frequenz- und Rhythmuskontrolle. Während eine suffiziente Frequenzkontrolle für alle Patienten von Bedeutung ist und in der Regel mit gutem Erfolg mit einer medikamentösen Behandlung erreicht werden kann, ist die Rhythmuskontrolle die Strategie der Wahl für Patienten, welche trotz suffizienter Frequenzkontrolle immer noch durch das Vorhofflimmern gestört sind und bei welchen aufgrund der klinischen Gesamtsituation mit einer vernünftigen Erfolgschance gerechnet werden kann. Die ungenügende Effizienz und die vielen und oft schwerwiegenden Nebenwirkungen der Antiarrhythmika sind der Grund, dass die pharmakologische Rhythmuskontrolle nicht selten durch invasive Therapieoptionen wie die Katheterablation ergänzt oder ersetzt werden muss.
Aktuelle Therapie des Vorhofflatterns
Authors: Kobza Richard
Published: January 2014

Nach Vorhofflimmern ist Vorhofflattern die häufigste anhaltende Arrhythmie. Die Therapieziele zur Behandlung von Vorhofflattern beinhalten die Verhinderung von systemischen Thrombo-Embolien, die ventrikuläre Frequenzkontrolle sowie die Wiederherstellung und Erhaltung von Sinusrhythmus (Rhythmuskontrolle). In der Akutbehandlung von Vorhofflattern ist die medikamentöse Therapie weiterhin unbestritten, jedoch hat sich das kathetertechnische Behandlungsverfahren mittels Hochfrequenzstromablation als kurative Therapie der ersten Wahl im klinischen Alltag bei rezidivierendem symptomtischem oder hämodynamisch relevantem typischem Vorhofflattern durchgesetzt. Die Thrombo-Embolie-Prophylaxe sollte bei Vorhofflattern analog wie beim Vorhofflimmern durchgeführt werden.
Paroxysmale supraventrikuläre Tachykardien – Mechanismen, Diagnostik und Therapie
Authors: Tanner Hildegard
Published: January 2014

Supraventrikuläre Tachykardien sind definitionsgemäß Tachykardien, die ihren Ursprungsort oberhalb der His-Bündel-Bifurkation haben. Der Ausdruck supraventrikulär ist aber ungenau und historisch bedingt. Die häufigsten supraventrikulären Tachykardien im eigentlichen Sinn umfassen die AV-Knoten-Reentry-Tachykardie und die AV-Reentry-Tachykardie, wobei die letztere die Ventrikel als integraler Bestandteil der kreisenden Erregung braucht und somit also nicht rein supraventrikulär ist. Die häufigste supraventrikuläre Tachykardie überhaupt ist aber die Sinustachykardie, die in der Regel physiologisch ist, gefolgt von Vorhofflimmern und Vorhofflattern. Da Vorhofflimmern und Vorhofflattern in dieser Ausgabe der Therapeutischen Umschau gesondert besprochen werden, liegt der Fokus dieser Übersichtsarbeit in der Diskussion von Mechanismen, Diagnostik und Therapie der AV-Knoten-Reentry-Tachykardie, der AV-Reentry-Tachykardie via akzessorische Leitungsbahn und am Rande auch der fokalen atrialen Tachykardie.
Behandlung bradykarder Rhythmusstörungen – wer benötigt einen Herzschrittmacher?
Authors: Seiler Jens
Published: January 2014

Bradykarde Rhythmusstörungen haben ihre Ursache in einer gestörten Impulsbildung im Sinusknoten und/oder in einer gestörten Erregungsleitung. Klinisch lassen sich Bradyarrhythmien subklassifizieren als Störungen der Sinusknotenfunktion und atrioventrikuläre (AV)-Blockierungen sowie funktionelle Bradykardien. Während anhaltende Arrhythmien mittels Standard-EKG zu diagnostizieren sind, sind zur Diagnose von intermittierenden Arrhythmien häufig Langzeit-EKGs und/oder Zusatztests erforderlich. Symptomatische bradykarde Rhythmusstörungen sind nach Ausschluss reversibler Ursachen die Standardindikation für die Herzschrittmachertherapie. Da die Sinusknotendysfunktion mit einer günstigen Prognose assoziiert ist, ist bei dieser Erkrankung eine Schrittmacherimplantation nur bei Symptomen gerechtfertigt. Bei AV-Blockierungen 3. Grades und 2. Grades Mobitz Typ II ist aus prognostischen Erwägungen auch bei asymptomatischen Patienten die Schrittmachertherapie indiziert. Rezidivierende unvorhersehbare neurokardiogene Synkopen auf der Basis eines kardioinhibitorischen Reflexes stellen in speziellen klinischen Situationen eine Schrittmacherindikation dar. Herzschrittmacherimplantationen werden seit über einem halben Jahrhundert durchgeführt und können heutzutage dank der enormen technologischen Entwicklung in Lokalanästhesie ambulant durchgeführt werden. Allerdings sind Komplikationen der Schrittmachertherapie weiterhin nicht selten.
Niedrigschwellige Betreuungsangebote für Menschen mit Demenz aus Sicht pflegender Angehöriger
Authors: Hochgraeber Iris , Dortmann Olga , Bartholomeyczik Sabine , Holle Bernhard
Published: January 2014

Niedrigschwellige Betreuungsangebote sind eine Möglichkeit, durch eine stundenweise Betreuung von Personen mit Demenz (PmD), pflegende Angehörige zu entlasten. Ziel der Studie ist es, die Aspekte von Niedrigschwelligkeit (Zugang, Flexibilität, Erreichbarkeit, Kostengünstigkeit) sowie die inhaltlichen und organisatorischen Aspekte niedrigschwelliger Angebote aus Sicht der pflegenden Angehörigen zu untersuchen. In einer explorativen Querschnittstudie wurde die Einschätzung von Angehörigen von PmD, welche ein niedrigschwelliges Betreuungsangebot in Anspruch nehmen, zu diesen Angeboten mittels standardisierter Fragebögen in zwei Regionen Nordrhein-Westfalens erhoben und deskriptiv ausgewertet. Die Ergebnisse zeigen, dass für die 53 befragten Angehörigen die inhaltliche Gestaltung der Betreuung v. a. mit Blick auf das Wohlbefinden der PmD von Bedeutung ist, während organisatorische Aspekte sowie die Niedrigschwelligkeit der Angebote als weniger wichtig empfunden werden. Die subjektiv eingeschätzte Belastung der pflegenden Angehörigen spielt dabei keine Rolle. Für die Entscheidung der pflegenden Angehörigen zur Inanspruchnahme scheint von Bedeutung zu sein, dass der Betreuungsschwerpunkt auf den Bedürfnissen der Menschen mit Demenz liegt, und dieser transparent dargestellt wird.
Vergleichende Qualitätsmessungen Teil 3: Funnel Plots
Authors: Kottner Jan , Lahmann Nils
Published: January 2014

Kennzahlenbasierte Qualitätsvergleiche von Einrichtungen sind verbreitet. Neben der Standardisierung und Risikoadjustierung muss die zufallsbedingte Variabilität in den Daten adäquat berücksichtigt werden. Rankings ohne Berücksichtigung der Präzision führen zu Fehlinterpretationen und fördern Datenmanipulationen. Konfidenzintervalle um die Kennzahlen der Einzeleinrichtungen sind eine Möglichkeit, die Präzision zu berücksichtigen. Funnel Plots als Spezialform von Regelkarten basieren auf der Theorie der Statistischen Prozesskontrolle (SPC). Darin werden die Kennzahlen in Beziehung zur Gruppengröße gesetzt. Warn- und Kontrollgrenzen, die sich 2 bzw. 3 Standardabweichungen vom Mittelwert aller Kennzahlen befinden, laufen mit steigender Fallzahl aufeinander zu und bilden einen Trichter. Kennzahlen innerhalb der Kontrollgrenzen weisen eine natürlicherweise zu erwartende Variabilität (common cause variation), Kennzahlen außerhalb der Kontrollgrenzen spezielle Variabilität (special cause variation) auf. Der Rankinggedanke ist aufgehoben. Funnel Plots bieten datenbasierte Kriterien, die Leistung von Einrichtungen im Qualitätsmanagement-Kontext zu bewerten.
Personal exposure to particulate matter in commuters using different transport modes (bus, bicycle, car and subway) in an assigned route in downtown Santiago, Chile
Authors: Suárez Liliana , Mesías Stephanie , Iglesias Verónica , Silva Claudio , Cáceres Dante D. , Ruiz-Rudolph Pablo
Published: January 2014

Commuters' exposure to PM2.5and ultrafine particles above background levels was observed in Santiago, Chile, which varied with transport mode.
Integrated DNA and RNA extraction and purification on an automated microfluidic cassette from bacterial and viral pathogens causing community-acquired lower respiratory tract infections
Authors: Van Heirstraeten Liesbet , Spang Peter , Schwind Carmen , Drese Klaus S. , Ritzi-Lehnert Marion , Nieto Benjamin , Camps Marta , Landgraf Bryan , Guasch Francesc , Corbera Antoni Homs , Samitier Josep , Goossens Herman , Malhotra-Kumar Surbhi , Roeser Tina
Published: January 2014

Fully automated LOC can reproduce and outperform benchtop NA-sample preparation starting with swab samples.
A multilayer concentric filter device to diminish clogging for separation of particles and microalgae based on size
Authors: Chen Chih-Chung , Chen Yu-An , Liu Yi-Ju , Yao Da-Jeng
Published: January 2014

This paper presents a size-based microfluidic multilayer concentric filter device capable of clog diminishing by using a small lab centrifuge.
Fluctuation of multiple metabolic pathways is required for Escherichia coli in response to chlortetracycline stress
Authors: Lin Xiangmin , Kang Liqun , Li Hui , Peng Xuanxian
Published: January 2014

Bacterial antibiotic resistance has become a worldwide challenge with the overuse and misuse of drugs.
Are proteins a redundant ontology? Epistemological limitations in the analysis of multistate species
Authors: Corfe Bernard M. , Evans Caroline A.
Published: January 2014

Do proteins really exist? Post-translational modification data depositions represent an insurmountable epistemological challenge. A framework to describe “proteins” as metabolic pathways or networks, in a conceptual continuum with metabolites, is proposed.
Highly conductive PEDOT electrodes for harvesting dynamic energy through piezoelectric conversion
Authors: Park Teahoon , Kim Byeonggwan , Kim Younghoon , Kim Eunkyoung
Published: January 2014

Highly conductive, transparent, surface energy matched, and flexible PEDOT electrodes for all organic piezoelectric devices show an enhanced piezoelectric conversion efficiency.
Preparation of a novel chloromethylated polystyrene-2-amino-1,3,4-thiadiazole chelating resin and its adsorption properties and mechanism for separation and recovery of Pt(iv) from aqueous solutions
Authors: Xiong Chunhua , Zheng Yuqiang , Feng Yujie , Yao Caiping , Ma Chunan , Zheng Xuming , Jiang Jianxiong
Published: January 2014

A novel chelating material PS-ATD resin applied to the efficient separation and recovery of platinum from aqueous solutions.
A simple carbazole-N-benzimidazole bipolar host material for highly efficient blue and single layer white phosphorescent organic light-emitting diodes
Authors: Pan Biao , Wang Bo , Wang Yixing , Xu Peng , Wang Lei , Chen Jiangshan , Ma Dongge
Published: January 2014

A new simple carbazole-N-benzimidazole bipolar luminogenmNBICzwas constructed and utilized as a host for an FIrpic-doped blue single layer white device.
Cobalt adipate, Co(C6H8O4): antiferromagnetic structure, unusual thermal expansion and magnetoelastic coupling
Authors: Saines Paul J. , Barton Phillip T. , Jura Marek , Knight Kevin S. , Cheetham Anthony K.
Published: January 2014

Anisotropic negative thermal expansion, driven by magnetoelastic coupling, has been found in cobalt adipate and interpreted through understanding its antiferromagnetic structure.
All-conjugated cationic copolythiophene “rod–rod” block copolyelectrolytes: synthesis, optical properties and solvent-dependent assembly
Authors: Thomas Amandine , Houston Judith E. , Van den Brande Niko , De Winter Julien , Chevrier Michèle , Heenan Richard K. , Terry Ann E. , Richeter Sébastien , Mehdi Ahmad , Van Mele Bruno , Dubois Philippe , Lazzaroni Roberto , Gerbaux Pascal , Evans Rachel C. , Clément Sébastien
Published: January 2014

The optical and thermal properties and solvent-dependent assembly of all-conjugated cationic copolythiophene block copolyelectrolytes are investigated.
Natural variation of rice strigolactone biosynthesis is associated with the deletion of two
MAX1
orthologs
Authors: Cardoso Catarina , Zhang Yanxia , Jamil Muhammad , Hepworth Jo , Charnikhova Tatsiana , Dimkpa Stanley O. N. , Meharg Caroline , Wright Mark H. , Liu Junwei , Meng Xiangbing , Wang Yonghong , Li Jiayang , McCouch Susan R. , Leyser Ottoline , Price Adam H. , Bouwmeester Harro J. , Ruyter-Spira Carolien
Published: January 2014

Significance

Strigolactones are a new class of plant hormones regulating plant shoot and root architecture in response to the environment. Also present in root exudates, strigolactones stimulate the germination of parasitic plant seeds. This report describes a genomic polymorphism—associated with the
Indica
/
Japonica
subspecies divide in rice that has a major impact on the biosynthesis of strigolactones, plant tillering, and germination of the parasitic plant
Striga hermonthica
—consisting of the deletion of two strigolactone biosynthetic genes orthologous to
Arabidopsis MAX1
. Both of these genes rescued the
Arabidopsis max1-1
highly branched mutant phenotype and increased the strigolactone level when overexpressed in the
Indica
rice variety Bala. This finding is of great interest for plant physiologists, plant evolutionary biologists, and breeders.
Dynamic regulation of β1 subunit trafficking controls vascular contractility
Authors: Leo M. Dennis , Bannister John P. , Narayanan Damodaran , Nair Anitha , Grubbs Jordan E. , Gabrick Kyle S. , Boop Frederick A. , Jaggar Jonathan H.
Published: January 2014

Significance

Plasma membrane ion channels composed of pore-forming and auxiliary subunits regulate physiological functions in virtually all cell types. A conventional view is that ion channels assemble with their auxiliary subunits prior to surface trafficking of the multiprotein complex. Arterial myocytes express large-conductance Ca
2+
-activated potassium (BK) channel α and auxiliary β1 subunits that modulate contractility and blood pressure and flow. The data here show that although most BKα subunits are plasma membrane-resident, β1 subunits are primarily intracellular in arterial myocytes. Nitric oxide, an important vasodilator, stimulates rapid surface trafficking of β1 subunits, which associate with, and activate, BK channels, leading to vasodilation. Thus, we show that rapid auxiliary subunit trafficking is a unique mechanism to control functional surface ion channel activity.
Coarse-grained simulations of the gating current in the voltage-activated Kv1.2 channel
Authors: Kim Ilsoo , Warshel Arieh
Published: January 2014

Significance

Structure-based modeling of gating currents in voltage activation of ion channels presents a major challenge. A part of the challenge involves the difficulties of modeling explicitly the charge motion in the electrolytes between the membrane and the electrodes. The present work overcomes some of the above challenge by using a coarse-grained model in simulating the activation of the Kv1.2 channel. The model yields realistic gating charges and free energy landscapes and allows us to simulate the time dependence of the fast gating current and to elucidate its relationship to the landscape involved in the activation process.
Comparison of approaches for parameter identifiability analysis of biological systems
Authors: Raue Andreas , Karlsson Johan , Saccomani Maria Pia , Jirstrand Mats , Timmer Jens
Published: January 2014

Motivation: Modeling of dynamical systems using ordinary differential equations is a popular approach in the field of Systems Biology. The amount of experimental data that are used to build and calibrate these models is often limited. In this setting, the model parameters may not be uniquely determinable. Structural or a priori identifiability is a property of the system equations that indicates whether, in principle, the unknown model parameters can be determined from the available data.

Results: We performed a case study using three current approaches for structural identifiability analysis for an application from cell biology. The approaches are conceptually different and are developed independently. The results of the three approaches are in agreement. We discuss strength and weaknesses of each of them and illustrate how they can be applied to real world problems.

Availability and implementation: For application of the approaches to further applications, code representations (DAISY, Mathematica and MATLAB) for benchmark model and data are provided on the authors webpage.

Contact:  andreas.raue@fdm.uni-freiburg.de
ECplot: an online tool for making standardized plots from large datasets for bioinformatics publications
Authors: Fok Alex Chun-Hong , Mok Sunny Siu-Nam , Lee Sau Dan , Yip Kevin Y.
Published: January 2014

Motivation and results: We have implemented ECplot, an online tool for plotting charts from large datasets. This tool supports a variety of chart types commonly used in bioinformatics publications. In our benchmarking, it was able to create a Box-and-Whisker plot with about 67 000 data points and 8 MB total file size within several seconds. The design of the tool makes common formatting operations easy to perform. It also allows more complex operations to be achieved by advanced XML (Extensible Markup Language) and programming options. Data and formatting styles are stored in separate files, such that style templates can be made and applied to new datasets. The text-based file formats based on XML facilitate efficient manipulation of formatting styles for a large number of data series. These file formats also provide a means to reproduce published figures from raw data, which complement parallel efforts in making the data and software involved in published analysis results accessible. We demonstrate this idea by using ECplot to replicate some complex figures from a previous publication.

Availability and implementation: ECplot and its source code (under MIT license) are available at https://yiplab.cse.cuhk.edu.hk/ecplot/.

Contact:  kevinyip@cse.cuhk.edu.hk
Combinatorial therapy discovery using mixed integer linear programming
Authors: Pang Kaifang , Wan Ying-Wooi , Choi William T. , Donehower Lawrence A. , Sun Jingchun , Pant Dhruv , Liu Zhandong
Published: January 2014

Motivation: Combinatorial therapies play increasingly important roles in combating complex diseases. Owing to the huge cost associated with experimental methods in identifying optimal drug combinations, computational approaches can provide a guide to limit the search space and reduce cost. However, few computational approaches have been developed for this purpose, and thus there is a great need of new algorithms for drug combination prediction.

Results: Here we proposed to formulate the optimal combinatorial therapy problem into two complementary mathematical algorithms, Balanced Target Set Cover (BTSC) and Minimum Off-Target Set Cover (MOTSC). Given a disease gene set, BTSC seeks a balanced solution that maximizes the coverage on the disease genes and minimizes the off-target hits at the same time. MOTSC seeks a full coverage on the disease gene set while minimizing the off-target set. Through simulation, both BTSC and MOTSC demonstrated a much faster running time over exhaustive search with the same accuracy. When applied to real disease gene sets, our algorithms not only identified known drug combinations, but also predicted novel drug combinations that are worth further testing. In addition, we developed a web-based tool to allow users to iteratively search for optimal drug combinations given a user-defined gene set.

Availability: Our tool is freely available for noncommercial use at http://www.drug.liuzlab.org/.

Contact: zhandong.liu@bcm.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
G-BLASTN: accelerating nucleotide alignment by graphics processors
Authors: Zhao Kaiyong , Chu Xiaowen
Published: January 2014

Motivation: Since 1990, the basic local alignment search tool (BLAST) has become one of the most popular and fundamental bioinformatics tools for sequence similarity searching, receiving extensive attention from the research community. The two pioneering papers on BLAST have received over 96 000 citations. Given the huge population of BLAST users and the increasing size of sequence databases, an urgent topic of study is how to improve the speed. Recently, graphics processing units (GPUs) have been widely used as low-cost, high-performance computing platforms. The existing GPU-BLAST is a promising software tool that uses a GPU to accelerate protein sequence alignment. Unfortunately, there is still no GPU-accelerated software tool for BLAST-based nucleotide sequence alignment.

Results: We developed G-BLASTN, a GPU-accelerated nucleotide alignment tool based on the widely used NCBI-BLAST. G-BLASTN can produce exactly the same results as NCBI-BLAST, and it has very similar user commands. Compared with the sequential NCBI-BLAST, G-BLASTN can achieve an overall speedup of 14.80X under ‘megablast’ mode. More impressively, it achieves an overall speedup of 7.15X over the multithreaded NCBI-BLAST running on 4 CPU cores. When running under ‘blastn’ mode, the overall speedups are 4.32X (against 1-core) and 1.56X (against 4-core). G-BLASTN also supports a pipeline mode that further improves the overall performance by up to 44% when handling a batch of queries as a whole. Currently G-BLASTN is best optimized for databases with long sequences. We plan to optimize its performance on short database sequences in our future work.

Availability:  http://www.comp.hkbu.edu.hk/∼chxw/software/G-BLASTN.html

Contact:  chxw@comp.hkbu.edu.hk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Women on Board: Female Board Membership as a Form of Elite Democratization
Authors: Heemskerk Eelke Michiel , Fennema Meindert
Published: January 2014

Corporate elites have been all-male bastions until the twenty-first century. The recent inclusion of women in the corporate elite needs explanation because it is an abrupt change in recruitment practices. We consider female presence in corporate boards as a sign of the democratization of elite social networks. Building on a case study of the Netherlands that covers the last four decades, we show that the corporate elite has become more open to nonmembers of traditional elites. In the process, women have also entered the boardroom. Initially, these were predominantly female politicians, but more recently many large corporations have recruited foreign females. We argue that the incremental feminization of the corporate elite was in the beginning—that is in the 1970s—initiated by the state but was subsequently pushed forward by the internationalization of corporate governance. We have traced the professional background of all female board members of the largest firms in the Netherlands over the period 1969–2011. We show that the female board members do not form a homogeneous group. The first wave of female directors had a political background, the second wave had an academic background, whereas the third wave was recruited from within the corporations. In this third wave, foreign female directors became predominant. Elites open up their ranks and privileged positions to women, but they do so reluctantly and under outside pressure.
MLL fusion proteins link transcriptional coactivators to previously active CpG-rich promoters
Authors: Okuda Hiroshi , Kawaguchi Marie , Kanai Akinori , Matsui Hirotaka , Kawamura Takeshi , Inaba Toshiya , Kitabayashi Issay , Yokoyama Akihiko
Published: January 2014

Mixed-lineage leukemia (MLL) maintains the expression of cellular memory genes during development, while leukemic MLL fusion proteins aberrantly maintain expression of hematopoietic stem cell program genes such as HOXA9 to cause leukemia. However, the molecular mechanism of gene activation is unclear. Here we show that only two functional modules are necessary and sufficient for target recognition: those that bind to non-methylated CpGs and di-/tri-methylated histone H3 lysine 36 (H3K36me2/3). An artificial protein composed of the two targeting modules and an interaction domain for AF4-family coactivators can functionally substitute for MLL fusion proteins. Because H3K36me2/3 markers are indicative of active transcription, MLL fusion proteins target previously active CpG-rich genes and activate transcription by recruiting coactivators thereto. Our results indicate that such chromatin context-dependent gene activation is the fundamental mechanism by which MLL fusion proteins maintain the expression of the cellular memory/hematopoietic stem cell program genes.
MLV integration site selection is driven by strong enhancers and active promoters
Authors: LaFave Matthew C. , Varshney Gaurav K. , Gildea Derek E. , Wolfsberg Tyra G. , Baxevanis Andreas D. , Burgess Shawn M.
Published: January 2014

Retroviruses integrate into the host genome in patterns specific to each virus. Understanding the causes of these patterns can provide insight into viral integration mechanisms, pathology and genome evolution, and is critical to the development of safe gene therapy vectors. We generated murine leukemia virus integrations in human HepG2 and K562 cells and subjected them to second-generation sequencing, using a DNA barcoding technique that allowed us to quantify independent integration events. We characterized >3 700 000 unique integration events in two ENCODE-characterized cell lines. We find that integrations were most highly enriched in a subset of strong enhancers and active promoters. In both cell types, approximately half the integrations were found in <2% of the genome, demonstrating genomic influences even narrower than previously believed. The integration pattern of murine leukemia virus appears to be largely driven by regions that have high enrichment for multiple marks of active chromatin; the combination of histone marks present was sufficient to explain why some strong enhancers were more prone to integration than others. The approach we used is applicable to analyzing the integration pattern of any exogenous element and could be a valuable preclinical screen to evaluate the safety of gene therapy vectors.