bluuebunny/crossref_metadata_2025 huggingface dataset:
Auswirkung von Lärm auf die Gesundheit
Authors: Röösli Martin
Published: December 2013

Mehr als die Hälfte der Bevölkerung fühlt sich durch Umweltlärm belästigt, dennoch wird das Thema kaum in der Hausarztpraxis thematisiert. Übermäßige Lärmbelastung hat direkte physiologische und indirekte Auswirkungen durch die Auslösung von Stress. Neben Schlafstörungen und Belästigungen zeigen mehrere epidemiologische Studien einen Zusammenhang zwischen der Lärmbelastung am Wohnort und dem Auftreten von Bluthochdruck sowie ischämischen Herzkrankheiten. Neue Untersuchungen deuten auch darauf hin, dass metabolische Effekte durch Lärm vermittelt sein könnten, was in Übereinstimmung mit gängigen Stresswirkungsmodellen steht. Es empfiehlt sich daher, in der Hausarztpraxis vor allem bei Bluthochdruckpatienten und Personen mit hohem kardiometabolischen Risiko auch das Thema Lärm anzusprechen und allenfalls Expositionsreduktionsmaßnahmen zu ergreifen.
Deutsche Übersetzung des Suicidal Patient Observation Charts (SPOC) – ein Instrument für die Praxis
Authors: Löhr Michael , Schulz Michael , Hemkendreis Bruno , Björkdahl Anna , Nienaber André
Published: December 2013

Die Pflege suizidaler Patientinnen und Patienten in psychiatrischen Einrichtungen ist eine komplexe und anspruchsvolle Aufgabe. Eine direkte und unmittelbare fürsorgliche und therapeutische Begleitung, auch als Intensivbetreuung beschrieben, wird auch in den Leitlinien empfohlen (DGPPN, 2012), und kann als eine häufig genutzte Intervention in der Pflege von akut suizidalen Patientinnen und Patienten angesehen werden. Intensivbetreuungen beinhalten ein breites Spektrum an Möglichkeiten, eine Beziehung zwischen dem intensiv Betreuenden und der Patientin bzw. dem Patienten herzustellen. Die Originalversion des SPOC wurde in Schweden entwickelt, mit dem Ziel, die Qualität der systematischen Dokumentation während einer Intensivbetreuung von suizidalen Patientinnen und Patienten zu verbessern. Sie ist ein Instrument zur systematischen Erfassung von beobachtbaren Verhaltensweisen und wahrgenommenen Stimmungen im Zusammenhang mit akuter Suizidalität, indem sie den Blick auf mögliche und die Suizidalität beeinflussende Stimmungszustände, z. B. «unruhig, ängstlich» und andere Einflussfaktoren wie z. B. «plötzliche Veränderung der Stimmungslage (Affektlabilität)» lenkt. Diese Form der Dokumentation soll im weiteren Prozess die Kommunikation über die Intensivbetreuung und wahrgenommene Stimmungen oder Aktivitäten sowohl im interprofessionellen Team als auch direkt mit der Patientin bzw. dem Patienten selbst unterstützen und verbessern, z. B. wer was zu welcher Zeit dokumentiert hat. Das SPOC umfasst 28 Items und 24 Betreuungsperioden. Das Ziel dieses Beitrags ist es, den wissenschaftlichen Übersetzungsprozess der englischen Version des SPOC in die deutsche Sprache darzulegen. Der wissenschaftliche Übersetzungsprozess beinhaltet zwei Vorwärts- und zwei Rückwärtsübersetzungen. Im abschließenden fünften Schritt wurde die Pre-Version durch 52 Pflegende inhaltsvalidiert. Dadurch konnten differierende Interpretationen durch sprachkulturelle Anpassungen reduziert werden. Mit der deutschen SPOC-Version liegt das Instrument nun auch für die deutschsprachige psychiatrische Pflegepraxis vor.
The Effects of Intergroup Climate on Immigrants’ Acculturation Preferences
Authors: Christ Oliver , Asbrock Frank , Dhont Kristof , Pettigrew Thomas F. , Wagner Ulrich
Published: December 2013

The effect of the intergroup climate on acculturation preferences among host-majority and immigrant group members has been long acknowledged in the acculturation literature. Only recently, however, research has started to directly examine the effect of the intergroup climate on acculturation preferences. In the present research, we aimed to contribute to this new and important line of research by adopting a multilevel approach to examine the effect of the intergroup climate (social context level of analysis) on immigrants’ acculturation preferences (individual level of analysis) over and above individual-level predictors of acculturation preferences. Based on recent cross-sectional survey data from Germany, we examined the acculturation preferences (cultural maintenance and maintenance of intergroup relations) of members of immigrant groups (immigrants from non-Western countries; N individual level = 317) living in different districts in Germany (N district-level = 179). On the social context level, we used the mean prejudice- and acculturation preferences-scores of the German respondents (N = 3,495) as proxies for the intergroup climate within these districts. Results of multilevel path analysis showed that on the context level, a negative intergroup climate (i.e., a higher amount of prejudice of the German respondents within the districts) was related to a stronger desire for cultural maintenance among the immigrants. The potential implications of a hostile intergroup climate for the acculturation process are discussed.
OK‐432 synergizes with IFN‐γ to confer dendritic cells with enhanced antitumor immunity
Authors: Pan Ke , Lv Lin , Zheng Hai‐Xia , Zhao Jing‐Jing , Pan Qiu‐Zhong , Li Jian‐Jun , Weng De‐Sheng , Wang Dan‐Dan , Jiang Shan‐Shan , Chang Alfred E , Li Qiao , Xia Jian‐Chuan
Published: December 2013

Generation of functional dendritic cells (DCs) with boosted immunity after the withdrawal of initial activation/maturation conditions remains a significant challenge. In this study, we investigated the impact of a newly developed maturation cocktail consisting of OK‐432 and interferon‐gamma (IFN‐γ) on the function of human monocyte‐derived DCs (MoDCs). We found that OK‐432 plus IFN‐γ stimulation could induce significantly stronger expression of surface molecules, production of cytokines, as well as migration of DCs compared with OK‐432 stimulation alone. Most importantly, DCs matured with OK‐432 plus IFN‐γ‐induced maintained secretion of interleukin‐12 (IL‐12)p70 in secondary culture after stimulus withdrawal. Functionally, OK‐432 plus IFN‐γ‐conditioned DCs induce remarkable Th1 and Tc1 responses more effectively than OK‐432 alone, even more than the use of α‐type‐1 cytokine cocktail. As a result, DCs matured with OK‐432 plus IFN‐γ can prime stronger cytotoxic lymphocyte (CTL) and natural killer (NK) cell response against tumor cells in vitro. Peripheral blood mononuclear cells activated by DCs matured with OK‐432 plus IFN‐γ also showed greater tumor growth inhibition in vivo in null mice. Molecular mechanistic analysis showed that DC maturation using IFN‐γ in concert with OK‐432 involves the activation of p38 and nuclear factor‐kappa B (NF‐κB) pathways. This study provided a novel strategy to generate more potent immune segments in DC vaccine.
Timescales and bottlenecks in miRNA‐dependent gene regulation
Authors: Hausser Jean , Syed Afzal Pasha , Selevsek Nathalie , van Nimwegen Erik , Jaskiewicz Lukasz , Aebersold Ruedi , Zavolan Mihaela
Published: December 2013

MiRNAs are post‐transcriptional regulators that contribute to the establishment and maintenance of gene expression patterns. Although their biogenesis and decay appear to be under complex control, the implications of miRNA expression dynamics for the processes that they regulate are not well understood. We derived a mathematical model of miRNA‐mediated gene regulation, inferred its parameters from experimental data sets, and found that the model describes well time‐dependent changes in mRNA, protein and ribosome density levels measured upon miRNA transfection and induction. The inferred parameters indicate that the timescale of miRNA‐dependent regulation is slower than initially thought. Delays in miRNA loading into Argonaute proteins and the slow decay of proteins relative to mRNAs can explain the typically small changes in protein levels observed upon miRNA transfection. For miRNAs to regulate protein expression on the timescale of a day, as miRNAs involved in cell‐cycle regulation do, accelerated miRNA turnover is necessary.
A disk-aromatic bowl cluster B30: toward formation of boron buckyballs
Authors: Tai Truong Ba , Duong Long Van , Pham Hung Tan , Mai Dang Thi Tuyet , Nguyen Minh Tho
Published: December 2013

The B30cluster is a bowl-shape structure, rather than a double-ring tubular form and exhibits disk-aromatic features similar to those of B19−and B202−. It suggests a consistent route for the formation of boron buckyballs such as B80and B92from multiple B30units.
Quencher-free molecular beacons as probes for oligonucleotides containing CAG repeat sequences
Authors: Kim Ki Tae , Veedu Rakesh N. , Seo Young Jun , Kim Byeang Hyean
Published: December 2013

Quencher-free molecular beacons allow the sensitive probing of DNA and RNA CAG repeat oligonucleotides with significant increases in fluorescence intensity of 16- and 43.5-fold, respectively.
One-pot synthesis of mesoporous ZrPW solid acid catalyst for liquid phase benzylation of anisole
Authors: Miao Zhichao , Song Huanling , Zhao Huahua , Xu Leilei , Chou Lingjun
Published: December 2013

Mesoporous zirconium phosphotungstate with large specific surface area, large pore volume, uniform pore size distribution, and tunable W/Zr ratios was successfully prepared.
Metal–organic frameworks MIL-88A hexagonal microrods as a new photocatalyst for efficient decolorization of methylene blue dye
Authors: Xu Wen-Tao , Ma Lin , Ke Fei , Peng Fu-Min , Xu Geng-Sheng , Shen Yu-Hua , Zhu Jun-Fa , Qiu Ling-Guang , Yuan Yu-Peng
Published: December 2013

Metal–organic framework MIL-88A displays an active MB dye degradation performance.
Ground and excited state electronic spectra of perylenediimide dimers with flexible and rigid geometries in DNA conjugates
Authors: Neelakandan Prakash P. , Zeidan Tarek A. , McCullagh Martin , Schatz George C. , Vura-Weis Josh , Kim Chul Hoon , Wasielewski Michael R. , Lewis Frederick D.
Published: December 2013

Ground and excited state spectra of co-facial PDI dimers embedded in DNA constructs depend on the geometry imposed by the construct.
Organic–inorganic hybrid polyhedra that can serve as supermolecular building blocks
Authors: Zhang Zhenjie , Wojtas Lukasz , Zaworotko Michael J.
Published: December 2013

Small cubicuboctahedral hybrid nanoballs can serve as octahedral supermolecular building blocks for the generation of primitive cubic nets.
Electroluminescent properties of lanthanide pentafluorophenolates
Authors: Pushkarev Anatoly P. , Ilichev Vasily A. , Maleev Alexander A. , Fagin Anatoly A. , Konev Alexey N. , Shestakov Alexander F. , Rumyantzev Roman V. , Fukin Georgy K. , Bochkarev Mikhail N.
Published: December 2013

An unusual change in emission color with increasing applied voltage is observed in OLEDs based on Tb(OC6F5)3(phen)2. The phenomenon is caused by shifting of the recombination zone from the HTL/complex interface towards the bulk complex.
Binary mixed homopolymer brushes grafted on nanorod particles: A self-consistent field theory study
Authors: Ma Xin , Yang Yingzi , Zhu Lei , Zhao Bin , Tang Ping , Qiu Feng
Published: December 2013

We employ the self-consistent field theory to study phase structures of brush-rod systems composed of two chemically distinct linear homopolymers. The polymer chains are uniformly grafted on the surface of a nanorod particle of finite length and comparable radius to the polymer radius of gyration. A “masking” technique treating the cylindrical boundary is introduced to solve the modified diffusion equations with an efficient and high-order accurate pseudospectral method involving fast Fourier transform on an orthorhombic cell. A rich variety of structures for the phase separated brushes is predicted. Phase diagrams involving a series of system parameters, such as the aspect ratio of the nanorod, the grafting density, and the chain length are constructed. The results indicate that the phase structure of the mixed brush-rod system can be tailored by varying the grafted chain length and/or the aspect ratio of the rod to benefit the fabrication of polymeric nanocomposites.
A semiconductor opening switch based generator with pulse repetitive frequency of 4 MHz
Authors: Wang Gang , Su Jiancang , Ding Zhenjie , Yuan Xuelin , Pan Yafeng
Published: December 2013

A MHz repetitive and nanosecond pulsed power generator based on the semiconductor opening switch (SOS) is developed, in which the pulse compression unit utilizes several Radio Frequency (RF) MOSFETs and a saturable Linear Transformer Driver (LTD). The RF MOSFETs are employed to obtain the forward pumping current pulses with the duration of tens of nanoseconds; the saturable LTD is used to raise the pulse voltage, to compress the pulse width and to pump SOS reversely. The SOS assembly cuts off the reverse current in a few nanoseconds, leading to a narrow output pulse on an external load. The experimental results show that the amplitude of the output pulse on a 106 Ω resistive load is about 3.8 kV and the width is 2 ns. Due to the repetitive ability of the RF MOSFETs, the generator can operate at a repetitive frequency of higher than 4 MHz in burst mode.
Polytope expansion of Lie characters and applications
Authors: Walton Mark A.
Published: December 2013

The weight systems of finite-dimensional representations of complex, simple Lie algebras exhibit patterns beyond Weyl-group symmetry. These patterns occur because weight systems can be decomposed into lattice polytopes in a natural way. Since lattice polytopes are relatively simple, this decomposition is useful, in addition to being more economical than the decomposition into single weights. An expansion of characters into polytope sums follows from the polytope decomposition of weight systems. We study this polytope expansion here. A new, general formula is given for the polytope sums involved. The combinatorics of the polytope expansion are analyzed; we point out that they are reduced from those of the Weyl character formula (described by the Kostant partition function) in an optimal way. We also show that the weight multiplicities can be found easily from the polytope multiplicities, indicating explicitly the equivalence of the two descriptions. Finally, we demonstrate the utility of the polytope expansion by showing how polytope multiplicities can be used in the calculation of tensor product decompositions, and subalgebra branching rules.
Degradation of InGaN/GaN laser diodes investigated by micro-cathodoluminescence and micro-photoluminescence
Authors: Meneghini M. , Carraro S. , Meneghesso G. , Trivellin N. , Mura G. , Rossi F. , Salviati G. , Holc K. , Weig T. , Schade L. , Karunakaran M. A. , Wagner J. , Schwarz U. T. , Zanoni E.
Published: December 2013

We present an investigation of the degradation of InGaN/GaN laser diodes grown on a GaN substrate. The results indicate that: (i) Ageing induces a significant increase in the threshold current (Ith) of the lasers, which is attributed to an increase in non-radiative recombination; (ii) Ith increase is correlated to a decrease in the micro-cathodoluminescence signal measured (after the removal of the top metallization) in the region under the ridge; (iii) micro-photoluminescence measurements indicate that constant current stress increases non-radiative recombination within the quantum wells (and not only within the barriers), and induces an increase in the emission wavelength of the degraded region.
Extending Romanovski polynomials in quantum mechanics
Authors: Quesne C.
Published: December 2013

Some extensions of the (third-class) Romanovski polynomials (also called Romanovski/pseudo-Jacobi polynomials), which appear in bound-state wavefunctions of rationally extended Scarf II and Rosen-Morse I potentials, are considered. For the former potentials, the generalized polynomials satisfy a finite orthogonality relation, while for the latter an infinite set of relations among polynomials with degree-dependent parameters is obtained. Both types of relations are counterparts of those known for conventional polynomials. In the absence of any direct information on the zeros of the Romanovski polynomials present in denominators, the regularity of the constructed potentials is checked by taking advantage of the disconjugacy properties of second-order differential equations of Schrödinger type. It is also shown that on going from Scarf I to Scarf II or from Rosen-Morse II to Rosen-Morse I potentials, the variety of rational extensions is narrowed down from types I, II, and III to type III only.
Electronic structures and magnetic moments of Co3FeN thin films grown by molecular beam epitaxy
Authors: Ito Keita , Sanai Tatsunori , Zhu Siyuan , Yasutomi Yoko , Toko Kaoru , Honda Syuta , Ueda Shigenori , Takeda Yukiharu , Saitoh Yuji , Imai Yoji , Kimura Akio , Suemasu Takashi
Published: December 2013

We evaluated electronic structures and magnetic moments in Co3FeN epitaxial films on SrTiO3(001). The experimentally obtained hard x-ray photoemission spectra of the Co3FeN film have a good agreement with those calculated. Site averaged spin magnetic moments deduced by x-ray magnetic circular dichroism were 1.52 μB per Co atom and 2.08 μB per Fe atom at 100 K. They are close to those of Co4N and Fe4N, respectively, implying that the Co and Fe atoms randomly occupy the corner and face-centered sites in the Co3FeN unit cell.
Multifunctional Bi2ZnOB2O6 single crystals for second and third order nonlinear optical applications
Authors: Iliopoulos K. , Kasprowicz D. , Majchrowski A. , Michalski E. , Gindre D. , Sahraoui B.
Published: December 2013

Bi2ZnOB2O6 nonlinear optical single crystals were grown by means of the Kyropoulos method from stoichiometric melt. The second and third harmonic generation (SHG/THG) of Bi2ZnOB2O6 crystals were investigated by the SHG/THG Maker fringes technique. Moreover, SHG microscopy studies were carried out providing two-dimensional SHG images as a function of the incident laser polarization. The high nonlinear optical efficiency combined with the possibility to grow high quality crystals make Bi2ZnOB2O6 an excellent candidate for photonic applications.
Controlled synthesis of nickel ferrite nanocrystals with tunable properties using a novel induction thermal plasma method
Authors: Bastien Samuel , Braidy Nadi
Published: December 2013

Nickel ferrite spinel nanopowders were synthesised using a solution spray radio-frequency inductively coupled plasma reactor over a wide range of compositions (NixFe3-xO4, x ≤ 1), with metastable powders produced for x = 0, 0.25, and 0.5. X-ray fluorescence and X-ray diffraction coupled to Rietveld refinement show that this synthesis technique offers an excellent level of control over both the chemical and crystallographic composition of the nanopowder through the control of the input Fe/Ni ratio. The technique produces highly crystalline nanopowders without the need for post-synthesis annealing. A bulk Fe/Ni ratio ≥2 yields a pure spinel NixFe3-xO4 phase, whereas Fe/Ni ratio <2 results in the excess Ni partitioning to a secondary bunsenite (Nix,Fe1-x)O phase. Morphological analysis using transmission electron microscopy shows that two types of particles are produced in different parts of the reactor: a highly faceted powder with the truncated octahedron morphology and a smaller-sized random agglomerate. The faceted particles have a log-normal particle size distribution, with an average size of about 30 nm while the agglomerates have a characteristic length of ∼3–5 nm.
Optimization of tunneling magnetoresistance of MgO based tunnel junctions by tuning the stage impedance for radio frequency sputtering of the barrier
Authors: Kaiser C. , Maddex D. , Pakala M. , Leng Q.
Published: December 2013

In this article, we describe a method to maximize the tunneling magnetoresistance of magnetic tunnel junctions with MgO tunneling barrier by optimizing the stage impedance for the RF MgO deposition. The impedance can be varied continuously using a matchbox that is in place to apply a RF bias to the stage. It is measured by means of a network analyzer connected to a dummy wafer on the stage. For positive stage reactance, both resistance area product and tunneling magnetoresistance are observed to drop, related to the stage impedance resonating with the plasma sheath capacitance. At high negative stage reactance, resputtering is minimized and tunneling magnetoresistance maximized.
Femtosecond laser excitation of multiple spin waves and composition dependence of Gilbert damping in full-Heusler Co2Fe1−xMnxAl films
Authors: Cheng Chuyuan , Meng Kangkang , Li Shufa , Zhao Jianhua , Lai Tianshu
Published: December 2013

Spin-wave dynamics in 30 nm thick Co2Fe1−xMnxAl full-Heusler films is investigated using time-resolved magneto-optical polar Kerr spectroscopy under an external field perpendicular to films. Damon-Eshbach (DE) and the first-order perpendicular standing spin-wave (PSSW) modes are observed simultaneously in four samples with x = 0, 0.3, 0.7, and 1. The frequency of DE and PSSW modes does not apparently depend on composition x, but damping of DE mode significantly on x and reaches the minimum as x = 0.7. The efficient coherent excitation of DE spin wave exhibits the promising application of Co2Fe0.3Mn0.7Al films in magnonic devices.
On the importance of AlGaN electron blocking layer design for GaN-based light-emitting diodes
Authors: Sheng Xia Chang , Simon Li Z. M. , Sheng Yang
Published: December 2013

There has been confusion regarding the usefulness of AlGaN electron blocking layer (EBL) in GaN-based light-emitting diodes (LEDs) with some published experimental data indicating that the LEDs without EBL performed better than those with it. InGaN/GaN LEDs have been investigated numerically to analyze its actual effect in these devices. Simulation results show that hole blocking effect of EBL mainly determines the effectiveness of using it which is more sensitive to its Al composition, band offset ratio, and polarization charges. It is found that the choice of Al composition is critical for EBL to improve the optical performance of GaN-based LEDs.
Chemistry Nobel honors computer simulation of biomolecules
Authors: Miller Johanna L.
Published: December 2013

Experiments alone aren’t always enough to understand why proteins and other large molecules do what they do.
Ernst Mach on bodies and buckets
Authors: Staley Richard
Published: December 2013

The scientist-philosopher’s critique of Newtonian mechanics was informed, in part, by a startling phenomenon he experienced as the train he was riding negotiated a sharp bend.
Effects of organic and inorganic selenium supplementation during late pregnancy on colostrum and serum Se status, performance and passive immunity in Merghoz goats
Authors: Kachuee R. , Moeini M. , Souri M.
Published: December 2013

This study was conducted to determine the effects of organic and inorganic selenium (Se) supplementation during late pregnancy on serum Se status, colostrum, performance and passive immunity in Merghoz goats in Iran. Thirty Merghoz goats (30 ± 3 kg) were given the same basal diet containing 0.11 mg Se/kg DM and were randomly allocated to one of three dietary treatments in a randomised complete block design. Four weeks before the expected kidding, the basal diets were supplemented with 0 (control), 0.3 mg Se/head.day in the form of L-selenomethionin (Se-Met) and 0.3 mg Se/head.day in the form of sodium selenite. Blood samples were collected from the goats in three phases: (1) a couple of days before starting the supplementation; (2) before the expected kidding; and (3) on the day of kidding. Blood samples were also taken from the newborn kids from the jugular vein at birth and 7 days of age. The serum Se and immunoglobulin G (IgG) concentrations, the white blood cells (WBC) and differential leukocyte counts were measured. The reproductive parameters such as the number of kids born per kidding, total weight of kids born per goat mating, the pregnancy period and kid birthweights were determined. The results indicated that the serum Se concentration increased in supplemented goats compared with controls. The Se concentrations also significantly increased in the colostrum of treated goats (P < 0.05). Similarly, serum Se concentrations in kids of treated goats were increased at birth. On the other hand, colostrum and daily milk production were not affected by Se supplementation. Likewise, the change in the mean serum IgG levels was not different among goats and kids (P > 0.05). However, the WBC, neutrophil and lymphocyte counts were higher in the kids of goats in the Se-Met group compared with the control group on the day of birth and 7 days of age (P < 0.05). It seemed that Se-Met could have influenced the lamb’s immunity at birth and 7 days of age. By contrast, selenite has not affected the performance and passive immunity in Merghoz goats.
Suppression of DNA-damage checkpoint signaling by Rsk-mediated phosphorylation of Mre11
Authors: Chen Chen , Zhang Liguo , Huang Nai-Jia , Huang Bofu , Kornbluth Sally
Published: December 2013

Significance

We have identified a pathway that links MAPK/ribosomal s6 kinase (Rsk) signaling to the inhibition of the response to a double-stranded break (DSB) in DNA, potentially explaining radioresistance in tumors with high rapidly accelerated fibrosarcoma (Raf)/MAPK/Rsk activity. The locus of this regulation was identified as meiotic recombination 11, whose phosphorylation by Rsk prevented its DNA binding and consequent activation of the central DSB checkpoint regulator, ataxia telangiectasia mutant.
DELLA proteins regulate arbuscule formation in arbuscular mycorrhizal symbiosis
Authors: Floss Daniela S. , Levy Julien G. , Lévesque-Tremblay Véronique , Pumplin Nathan , Harrison Maria J.
Published: December 2013

Significance

Arbuscular mycorrhizal (AM) symbiosis is a mutualistic interaction formed between most land plants and soil fungi. During symbiosis the fungus develops branched hyphae, known as arbuscules, inside the root cortical cells. Arbuscules are critical to the symbiosis and function in phosphate delivery to the plant. Here we show that arbuscule formation is regulated by DELLA proteins. DELLA proteins are negative regulators of gibberellic acid (GA) signaling and repress plant growth and development. Our data provide insights into regulation of arbuscule formation and identify a potential mechanism by which the plant can coordinate the symbiosis with its growth and nutrient status.
H19
lncRNA controls gene expression of the Imprinted Gene Network by recruiting MBD1
Authors: Monnier Paul , Martinet Clémence , Pontis Julien , Stancheva Irina , Ait-Si-Ali Slimane , Dandolo Luisa
Published: December 2013

Significance

The
H19
imprinted gene produces a long noncoding RNA (lncRNA) exclusively expressed from the maternal allele. It is involved in the control of embryonic growth and regulates nine genes of an Imprinted Gene Network (IGN). Our goal was to decipher the molecular mechanisms that drive this control of the IGN. We show that this lncRNA represses several target genes through interaction with the methyl-CpG–binding domain protein 1 MBD1. This protein is involved in the maintenance of repressive H3K9me3 histone marks. The
H19
RNA is required for the recruitment of MBD1 to some of its targets, including the adjacent insulin-like growth factor 2 gene, and acts by a fine-tuned regulation on the expression levels of these growth-controlling genes of the IGN.
Lower and upper stem–single-stranded RNA junctions together determine the Drosha cleavage site
Authors: Ma Hongming , Wu Yonggan , Choi Jang-Gi , Wu Haoquan
Published: December 2013

Significance

MicroRNA genes are transcribed as long primary microRNAs (pri-miRNAs) and then processed by the Drosha–DGCR8 (DiGeorge syndrome critical region gene 8) complex into ∼60-nt pre-miRNAs, which is the key step of miRNA biogenesis. How exactly the Drosha–DGCR8 complex recognizes pri-miRNAs and selects the processing site is not well understood. Here we developed a unique approach to examining the details of how this complex chooses the processing site in human cells. Our study yields new knowledge of how the Drosha–DGCR8 complex determines its processing sites and also provides an explanation for how 5′ isomiRs are generated in some miRNAs, which is another interesting but not clearly understood phenomenon in miRNA biogenesis.
Consumer diversity across kingdoms supports multiple functions in a coastal ecosystem
Authors: Hensel Marc J. S. , Silliman Brian R.
Published: December 2013

Significance

Societies value most natural ecosystems because they provide many different individual benefits all at once. However, species extinctions have threatened ecosystems' ability to function this way. Our study provides a real-world example that the loss of key species from a salt marsh can have profound impacts on the overall performance of an ecosystem. Our findings also suggest that the ability for nature to perform well at multiple levels may depend on having many distantly related species present, increasing the chances of maximizing different functions and services. Salt marshes provide many services to humans, including water filtration and coastal buffering, and this study shows that these processes are likely enhanced by the presence of a diverse community of consumers.
Mutant KRAS is a druggable target for pancreatic cancer
Authors: Zorde Khvalevsky Elina , Gabai Racheli , Rachmut Itzhak Haim , Horwitz Elad , Brunschwig Zivia , Orbach Ariel , Shemi Adva , Golan Talia , Domb Abraham J. , Yavin Eylon , Giladi Hilla , Rivkin Ludmila , Simerzin Alina , Eliakim Rami , Khalaileh Abed , Hubert Ayala , Lahav Maor , Kopelman Yael , Goldin Eran , Dancour Alan , Hants Yael , Arbel-Alon Sagit , Abramovitch Rinat , Shemi Amotz , Galun Eithan
Published: December 2013

Significance

Pancreatic cancer is still one of the major challenges in clinical oncology. Mutant KRAS is a driving oncogene in the majority of human pancreatic cancer cases. We have made an effort to meet this challenge by developing a therapeutic platform for local and prolonged delivery of siRNA. Our results show that the siRNA targeted against KRAS mutations with a local prolonged release system knocks down KRAS expression in vitro and in vivo, leading to an antitumor effect. Our report describes an applicable and efficient delivery method of siRNA that overcomes the major obstacles of toxicity and organ accessibility. Notably our approach enabled the conversion of KRAS from a nondruggable to a potentially druggable cancer target.
Ascites analysis by a microfluidic chip allows tumor-cell profiling
Authors: Peterson Vanessa M. , Castro Cesar M. , Chung Jaehoon , Miller Nathan C. , Ullal Adeeti V. , Castano Maria D. , Penson Richard T. , Lee Hakho , Birrer Michael J. , Weissleder Ralph
Published: December 2013

Significance

Serial molecular analyses of tumor cells during treatment- and biopsy-driven clinical trials are emerging norms for many cancers. Yet surgical and image-guided biopsies are expensive and invasive, explaining why alternative sources for tumor cells are being sought. In ovarian cancer (and other abdominopelvic cancers), abdominal fluid buildup (ascites) occurs frequently. We demonstrate that ascites tumor cells (ATCs) present a valuable source of tumor cells, rendering ascites another form of “liquid biopsy.” We evaluated 85 ovarian cancer-related markers and developed a unique, low cost miniaturized microfluidic ATC chip for on-chip enrichment and molecular profiling using small amounts of ascites. This approach could expand the utility of ATCs within cytotoxic and/or molecularly targeted ovarian cancer therapeutic trials.
Pentameric complex of viral glycoprotein H is the primary target for potent neutralization by a human cytomegalovirus vaccine
Authors: Freed Daniel C. , Tang Qi , Tang Aimin , Li Fengsheng , He Xi , Huang Zhao , Meng Weixu , Xia Lin , Finnefrock Adam C. , Durr Eberhard , Espeseth Amy S. , Casimiro Danilo R. , Zhang Ningyan , Shiver John W. , Wang Dai , An Zhiqiang , Fu Tong-Ming
Published: December 2013

Significance

Congenital human cytomegalovirus (HCMV) infection is an important cause of newborn disability, and developing a vaccine against congenital HCMV is a top priority. However, despite decades of efforts, a vaccine remains elusive. Previous vaccines lacked an antigen called pentameric glycoprotein H (gH) complex, essential for the virus to infect epithelial/endothelial cells, and these vaccines induced poor neutralizing antibodies. To support a unique vaccine concept featuring the pentameric gH complex, we established 45 mAbs from a rabbit immunized with an experimental vaccine. Over 50% of the mAbs have antiviral activity, and potent clones target the pentameric gH complex, thus establishing this antigen as the key for potent antiviral antibodies by vaccination. Our result contributes to the understanding of immune attributes of an effective vaccine against HCMV.
Protein O-mannosylation is crucial for E-cadherin–mediated cell adhesion
Authors: Lommel Mark , Winterhalter Patrick R. , Willer Tobias , Dahlhoff Maik , Schneider Marlon R. , Bartels Markus F. , Renner-Müller Ingrid , Ruppert Thomas , Wolf Eckhard , Strahl Sabine
Published: December 2013

Significance

Cell–cell adhesion is essential for embryonic development, tissue morphogenesis, and tissue repair, as well as for tumor invasion and metastasis. Thus, it is of fundamental importance to identify the molecular factors that affect this process. Here we demonstrate that O-mannosylation, an essential posttranslational protein modification, is crucial for the formation of adherens junctions between cells of the early mouse embryo, with O-mannosylation–deficient embryos dying at the morula-to-blastocyst transition. Moreover, we identified O-mannosyl glycans on E-cadherin, the major cell–cell adhesion protein of embryos, and demonstrated that these glycans are crucial for E-cadherin–mediated cell adhesion. Because O-mannosylation is a conserved feature of the classical cadherins, this protein modification most likely affects many more biological processes than previously thought.
Multiple modes of regulation of the human Ino80 SNF2 ATPase by subunits of the INO80 chromatin-remodeling complex
Authors: Chen Lu , Conaway Ronald C. , Conaway Joan W.
Published: December 2013

Significance

SNF2 family ATPases are ATP-dependent motors with roles in diverse nuclear processes. Regulation of the catalytic activity of SNF2 family ATPases via their associated proteins is a key element determining their functions. Thus, illuminating the mechanisms of action of SNF2 regulatory proteins is a priority of current studies. Here, we show subunits of the human INO80 chromatin-remodeling complex act by different mechanisms: Ies2 activates INO80 catalytic activity, while Ies6 and Arp5 function in nucleosome recognition.
Two-dimensional Raman-terahertz spectroscopy of water
Authors: Savolainen Janne , Ahmed Saima , Hamm Peter
Published: December 2013

Significance

The discussion about the structure of water becomes increasingly more controversial, and appears to be stuck because the major techniques used to study it (small-angle X-ray scattering emphasizing the structure, multidimensional infrared spectroscopy emphasizing the dynamics, and molecular dynamics simulations using questionable force fields) do not seem to provide mutually converging results. This calls for a different experimental approach, which we offer here with 2D Raman-terahertz spectroscopy. The work extends multidimensional vibrational spectroscopy into the far-IR regime where thermally excited soft modes are found that are directly responsible for molecular dynamics (in contrast with the high-frequency spectator modes investigated in 2D-IR spectroscopy, which per se are quiet at room temperature and sense the environment only indirectly).
On simplicial resolutions of framed links
Authors: Lei Fengchun , Li Fengling , Wu Jie
Published: December 2013

In this paper, we investigate the simplicial groups obtained from the link groups of naive cablings on any given framed link. Our main result states that the resulting simplicial groups have the homotopy type of the loop space of a wedge of

3
3

-spheres. This gives simplicial group models for some loop spaces using link groups.
Topological augmentation to infer hidden processes in biological systems
Authors: Sunnåker Mikael , Zamora-Sillero Elias , López García de Lomana Adrián , Rudroff Florian , Sauer Uwe , Stelling Joerg , Wagner Andreas
Published: December 2013

Motivation: A common problem in understanding a biochemical system is to infer its correct structure or topology. This topology consists of all relevant state variables—usually molecules and their interactions. Here we present a method called topological augmentation to infer this structure in a statistically rigorous and systematic way from prior knowledge and experimental data.

Results: Topological augmentation starts from a simple model that is unable to explain the experimental data and augments its topology by adding new terms that capture the experimental behavior. This process is guided by representing the uncertainty in the model topology through stochastic differential equations whose trajectories contain information about missing model parts. We first apply this semiautomatic procedure to a pharmacokinetic model. This example illustrates that a global sampling of the parameter space is critical for inferring a correct model structure. We also use our method to improve our understanding of glutamine transport in yeast. This analysis shows that transport dynamics is determined by glutamine permeases with two different kinds of kinetics. Topological augmentation can not only be applied to biochemical systems, but also to any system that can be described by ordinary differential equations.

Availability and implementation: Matlab code and examples are available at: http://www.csb.ethz.ch/tools/index.

Contact:  mikael.sunnaker@bsse.ethz.ch; andreas.wagner@ieu.uzh.ch

Supplementary information:  Supplementary data are available at Bioinformatics online.
LipidGO: database for lipid-related GO terms and applications
Authors: Fan Mengyuan , Low Hong Sang , Zhou Hufeng , Wenk Markus R. , Wong Limsoon
Published: December 2013

Motivation: Lipid, an essential class of biomolecules, is receiving increasing attention in the research community, especially with the development of analytical technique like mass spectrometry. Gene Ontology (GO) is the de facto standard function annotation scheme for gene products. Identification of both explicit and implicit lipid-related GO terms will help lipid research in many ways, e.g. assigning lipid function in protein function prediction.

Results: We have constructed a Web site ‘LipidGO’ that facilitates browsing and searching lipid-related GO terms. An expandable hierarchical GO tree is constructed that allows users to find lipid-related GO terms easily. To support large-scale analysis, a user is able to upload a list of gene products or a list of GO terms to find out which of them is lipid related. Finally, we demonstrate the usefulness of ‘LipidGO’ by two applications: (i) identifying lipid-related gene products in model organisms and (ii) discovering potential novel lipid-related molecular functions

Availability and implementation: LipidGO is available at http://compbio.ddns.comp.nus.edu.sg/%7elipidgo/index.php.

Contact:  wongls@comp.nus.edu.sg

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Novel Secretory Protein Ss-Caf1 of the Plant-Pathogenic Fungus Sclerotinia sclerotiorum Is Required for Host Penetration and Normal Sclerotial Development
Authors: Xiao Xueqiong , Xie Jiatao , Cheng Jiasen , Li Guoqing , Yi Xianhong , Jiang Daohong , Fu Yanping
Published: December 2013

To decipher the mechanism of pathogenicity in Sclerotinia sclerotiorum, a pathogenicity-defective mutant, Sunf-MT6, was isolated from a T-DNA insertional library. Sunf-MT6 could not form compound appressorium and failed to induce lesions on leaves of rapeseed though it could produce more oxalic acid than the wild-type strain. However, it could enter into host tissues via wounds and cause typical necrotic lesions. Furthermore, Sunf-MT6 produced fewer but larger sclerotia than the wild-type strain Sunf-M. A gene, named Ss-caf1, was disrupted by T-DNA insertion in Sunf-MT6. Gene complementation and knockdown experiments confirmed that the disruption of Ss-caf1 was responsible for the phenotypic changes of Sunf-MT6. Ss-caf1 encodes a secretory protein with a putative Ca2+-binding EF-hand motif. High expression levels of Ss-caf1 were observed at an early stage of compound appressorium formation and in immature sclerotia. Expression of Ss-caf1 without signal peptides in Nicotiana benthamiana via Tobacco rattle virus-based vectors elicited cell death. These results suggest that Ss-caf1 plays an important role in compound appressorium formation and sclerotial development of S. sclerotiorum. In addition, Ss-Caf1 has the potential to interact with certain host proteins or unknown substances in host cells, resulting in subsequent host cell death.
Using growth curves to forecast regional resource recovery: approaches, analytics and consistency tests
Authors: Sorrell Steve , Speirs Jamie
Published: December 2013

There is growing concern about the depletion of hydrocarbon resources and the risk of near-term peaks in production. These concerns hinge upon contested estimates of the recoverable resources of different regions and the associated forecasts of regional production. Beginning with Hubbert, an influential group of analysts have usedgrowth curvesboth to estimate recoverable resources and to forecast future production. Despite widespread use, these ‘curve-fitting’ techniques remain a focus of misunderstanding and dispute. The aim of this paper is to classify and explain these techniques and to identify both their relative suitability in different circumstances and the expected level of confidence in their results. The paper develops a mathematical framework that maps curve-fitting techniques onto the available data for conventional oil and highlights the critical importance of the so-called ‘reserve growth’. It then summarizes the historical origins, contemporary application and strengths and weaknesses of each group of curve-fitting techniques and uses illustrative data from a number of oil-producing regions to explore the extent to which these techniques provide consistent estimates of recoverable resources. The paper argues that the applicability of curve-fitting techniques is more limited than adherents claim, the confidence bounds on the results are wider than commonly assumed and the techniques have a tendency to underestimate recoverable resources.
Recovery rates, enhanced oil recovery and technological limits
Authors: Muggeridge Ann , Cockin Andrew , Webb Kevin , Frampton Harry , Collins Ian , Moulds Tim , Salino Peter
Published: December 2013

Enhanced oil recovery (EOR) techniques can significantly extend global oil reserves once oil prices are high enough to make these techniques economic. Given a broad consensus that we have entered a period of supply constraints, operators can at last plan on the assumption that the oil price is likely to remain relatively high. This, coupled with the realization that new giant fields are becoming increasingly difficult to find, is creating the conditions for extensive deployment of EOR. This paper provides a comprehensive overview of the nature, status and prospects for EOR technologies. It explains why the average oil recovery factor worldwide is only between 20% and 40%, describes the factors that contribute to these low recoveries and indicates which of those factors EOR techniques can affect. The paper then summarizes the breadth of EOR processes, the history of their application and their current status. It introduces two new EOR technologies that are beginning to be deployed and which look set to enter mainstream application. Examples of existing EOR projects in the mature oil province of the North Sea are discussed. It concludes by summarizing the future opportunities for the development and deployment of EOR.
Decline and depletion rates of oil production: a comprehensive investigation
Authors: Höök Mikael , Davidsson Simon , Johansson Sheshti , Tang Xu
Published: December 2013

Two of the most fundamental concepts in the current debate about future oil supply are oilfield
decline rates
and
depletion rates
. These concepts are related, but not identical. This paper clarifies the definitions of these concepts, summarizes the underlying theory and empirically estimates decline and depletion rates for different categories of oilfield. A database of 880 post-peak fields is analysed to determine typical depletion levels, depletion rates and decline rates. This demonstrates that the size of oilfields has a significant influence on decline and depletion rates, with generally high values for small fields and comparatively low values for larger fields. These empirical findings have important implications for oil supply forecasting.
The expression of long-term potentiation: reconciling the preists and the postivists
Authors: MacDougall Matthew J. , Fine Alan
Published: December 2013

Long-term potentiation (LTP) of excitatory synaptic transmission in the hippocampus has been investigated in great detail over the past 40 years. Where and how LTP is actually expressed, however, remain controversial issues. Considerable evidence has been offered to support both pre- and postsynaptic contributions to LTP expression. Though it is widely held that postsynaptic expression mechanisms are the primary contributors to LTP expression, evidence for that conclusion is amenable to alternative explanations. Here, we briefly review some key contributions to the ‘locus’ debate and describe data that support a dominant role for presynaptic mechanisms. Recognition of the state-dependency of expression mechanisms, and consideration of the consequences of the spatial relationship between postsynaptic glutamate receptors and presynaptic vesicular release sites, lead to a model that may reconcile views from both sides of the synapse.
Expression mechanisms underlying long-term potentiation: a postsynaptic view, 10 years on
Authors: Granger Adam J. , Nicoll Roger A.
Published: December 2013

This review focuses on the research that has occurred over the past decade which has solidified a postsynaptic expression mechanism for long-term potentiation (LTP). However, experiments that have suggested a presynaptic component are also summarized. It is argued that the pairing of glutamate uncaging onto single spines with postsynaptic depolarization provides the final and most elegant demonstration of a postsynaptic expression mechanism for NMDA receptor-dependent LTP. The fact that the magnitude of this LTP is similar to that evoked by pairing synaptic stimulation and depolarization leaves little room for a substantial presynaptic component. Finally, recent data also require a revision in our thinking about the way AMPA receptors (AMPARs) are recruited to the postsynaptic density during LTP. This recruitment is independent of subunit type, but does require an adequate reserve pool of extrasynaptic receptors.
GluA2-dependent AMPA receptor endocytosis and the decay of early and late long-term potentiation: possible mechanisms for forgetting of short- and long-term memories
Authors: Hardt Oliver , Nader Karim , Wang Yu-Tian
Published: December 2013

The molecular processes involved in establishing long-term potentiation (LTP) have been characterized well, but the decay of early and late LTP (E-LTP and L-LTP) is poorly understood. We review recent advances in describing the mechanisms involved in maintaining LTP and homeostatic plasticity. We discuss how these phenomena could relate to processes that might underpin the loss of synaptic potentiation over time, and how they might contribute to the forgetting of short-term and long-term memories. We propose that homeostatic downscaling mediates the loss of E-LTP, and that metaplastic parameters determine the decay rate of L-LTP, while both processes require the activity-dependent removal of postsynaptic GluA2-containing AMPA receptors.