bluuebunny/crossref_metadata_2025 huggingface dataset:
Simulating streamflow and dissolved organic matter export from a forested watershed
Authors: Xu Na , Saiers James E. , Wilson Henry F. , Raymond Peter A.
Published: April 2012

Stream water concentrations of dissolved organic matter (DOM) exhibit large temporal variations during precipitation on forested, headwater catchments. We present a modeling framework appropriate for describing streamflow and event‐driven export of DOM from small, forested watersheds. Our model links parametrically simple formulations for rainfall‐runoff generation and soil water carbon dynamics. The rainfall‐runoff formulation is developed by modifying the catchment model of Kirchner (2009) to account for hysteresis in the relationship between stream discharge and catchment water storage. Time series computations of catchment water storage are used by the soil carbon model to approximate the effects of leaching, adsorption, and mineralization on soil water DOM concentrations and the export of DOM from the terrestrial reservoir to the stream. Our findings show that this model is capable of reproducing hourly variations of stream discharge (ranging from 0.01 to 0.38 mm h−1) and stream water DOM concentrations (ranging from 1.8 to 14 mg C L−1) measured in a forested headwater stream in north central Massachusetts. Our analysis highlights the strong linkage between soil carbon dynamics and hydrological processes that govern catchment water storage and flow paths connecting the terrestrial system to the stream.
QSAR & DOCKING APPROACH - POTENTIAL WAY TO NEW DRUG DEVELOPMENT
Authors: Ajeet Ajeet
Published: April 2012

With today's need for discovering and developing new drug molecules, it is necessary to accept ways to save time and wet lab essentials. To this end, the QSAR and molecular docking approach is used widely by us. This poster describes steps for developing a new or modified moiety of a drug molecule.
Network-based analyses of Huntington’s Disease
Authors: Kalathur Ravi , Futschik Matthias
Published: April 2012

The use of high-throughput technologies has provided us with large amounts of data for _Huntington's disease_ (HD), especially at the gene and protein levels. As phenotypic changes in HD may not just be due to the activity of individual genes but interrelated alterations of whole molecular networks, it is important to systematically analyse and represent accumulated data in a network-based approach.

Methods:

To analyse and visualise protein interaction networks through a dedicated database to HD, we have established "HDNetDB": http://hdnetdb.sysbiolab.eu. This platform will not only help to understand molecular mechanisms better, but also assist in identifying potential molecular markers involved in HD.We further identified both pathways as well as gene ontology (GO) annotations that are enriched in HD and constructed networks of the pathways and enriched GO annotations.

Results:

Our integrative network based methodology helped us to identify pathways and networks that are specific to the HD and may lead to the identification of novel molecular targets. Follow-up analyses of molecular changes will distinguish between potential causes and effects in HD. We hope that the constructed database will help researchers worldwide to find a cure for HD.
Development of Java based graphical user interface for Diagnosis of Hepatitis UsingI Mixture of Expert
Authors: Shankaracharya M , Kumari Suchitra , Vidyarthi Ambarish
Published: April 2012

Hepatitis is deadly, and the fifth leading cause of death after heart disease, stroke, chest disease and cancer. Worldwide, 1.5 million deaths per year have been estimated. Detection of hepatitis is a big problem for general practitioners. An expert doctor commonly makes decisions by evaluating the current test results of a patient or by comparing the patient with others with the same condition with reference to the previous decisions. Many machine learning and data mining techniques have been designed for the automatic diagnosis of hepatitis. However, no one tool is available to the general population for the diagnosis of Hepatitis. Hence, a graphical user interface-enabled tool needs to be developed, through which medical practitioners can feed patient data easily and find hepatitis diagnoses instantly and accurately.

Methods:

In this study a hepatitis dataset was taken from the UCI machine repository database with a total of 20 attributes of two classes, Affected and Not Affected.

Results and Conclusion:

The models have been generated with a mixture of experts as a classification method for the diagnosis of hepatitis. Very good accuracy has been observed in the generated models. Finally, the model having the least minimum square error was selected. This model was then linked with GUI for the design of tools for hepatitis prediction.
Optogenetic control of genetically-targeted pyramidal neuron activity in prefrontal cortex
Authors: Baratta Michael , Nakamura Shinya , Dobelis Peter , Pomrenze Matthew , Dolzani Samuel , Cooper Donald
Published: April 2012

A salient feature of prefrontal cortex organization is the vast diversity of cell types that support the temporal integration of events required for sculpting future responses. A major obstacle in understanding the routing of information among prefrontal neuronal subtypes is the inability to manipulate the electrical activity of genetically defined cell types over behaviorally relevant timescales and activity patterns. To address these constraints, we present here a simple approach for selective activation of prefrontal excitatory neurons in both in vitro and in vivo preparations. Rat prelimbic pyramidal neurons were genetically targeted to express a light--activated nonselective cation channel, channelrhodopsin--2, or a light--driven inward chloride pump, halorhodopsin, which enabled them to be rapidly and reversibly activated or inhibited by pulses of light. These light responsive tools provide a spatially and temporally precise means of studying how different cell types contribute to information processing in cortical circuits. Our customized optrodes and optical commutators for in vivo recording allow for efficient light delivery and recording and can be requested at www.neuro--cloud.net/nature-precedings/baratta.
Dispersal Pattern of Injectate after Lumbar Interlaminar Epidural Spinal Injection Evaluated with Computerized Tomography
Authors: Paisley Kevin , Jeffries Joel , Monroe Mark , Choma Ted
Published: April 2012

Study Design

Retrospective analysis of lumbar computed tomographic epidurograms.

Objective

To evaluate the dispersal pattern of injectate after interlaminar lumbar epidural steroid injections.

Prior studies have evaluated the dispersal patterns of injectate after lumbar epidural steroid injections using fluoroscopy with varying results. To date, there have been no studies evaluating the dispersal pattern utilizing computerized tomography.

Methods

Ten epidurograms were analyzed after lumbar interlaminar epidural steroid injection. The epidurograms were examined, evaluating the dispersal pattern in longitudinal flow as well as circumferential flow. In addition, pain values were assessed with the visual analogue scale.

Results

Mean diffusion in the rostral direction was 9.8 cm (standard deviation 4.0 cm, range 4.0 to 15.0 cm). Mean diffusion in the caudal direction was 5.4 cm (standard deviation 1.4 cm, range 3.0 to 8.0 cm). Both rostral and caudal flow had a p value < 0.001. The circumferential flow was 360 degrees in 9 of 10 cases. In addition, there was significant ( p = 0.006) reduction in pain.

Conclusion

Interlaminar lumbar epidural steroid injections are an effective treatment modality for various spine-related conditions. The injectate diffuses throughout the epidural space with nearly uniform circumferential flow as well as significant rostral and caudal flow.
Bilateral Three-Level Lumbar Spondylolysis Repaired by Hook-Screw Technique
Authors: Sharifi Guive , Jahanbakhshi Amin , Daneshpajouh Behnam , Rahimizadeh Abolfazl
Published: April 2012

We report a case of bilateral three-level lumbar spondylolysis that was directly repaired by use of hook-screw technique. The patient complained of low back pain for 2 years that progressively worsened and was exacerbated with standing and walking. He also mentioned bilateral sciatalgia. The neurological examination was normal. Interestingly, we found bilateral lumbar spondylolysis in L3, L4, and L5 levels in imaging studies. After proving that spondylolysis was the source of the low back pain by local anesthetic agent injection, we used a direct technique for correction of spondylolysis by use of a hook-screw device plus decortications of lysis area and iliac crest autograft. We assessed the patient after surgery to evaluate pain recovery and fusion rate. The results were favorable and proved the efficacy of the hook-screw technique for treatment of symptomatic multilevel lumbar spondylolysis.
Strain relaxation in single crystal SrTiO3 grown on Si (001) by molecular beam epitaxy
Authors: Choi Miri , Posadas Agham , Dargis Rytis , Shih Chih-Kang , Demkov Alexander A. , Triyoso Dina H. , David Theodore N. , Dubourdieu Catherine , Bruley John , Jordan-Sweet Jean
Published: April 2012

An epitaxial layer of SrTiO3 grown directly on Si may be used as a pseudo-substrate for the integration of perovskite oxides onto silicon. When SrTiO3 is initially grown on Si (001), it is nominally compressively strained. However, by subsequent annealing in oxygen at elevated temperature, an SiOx interlayer can be formed which alters the strain state of SrTiO3. We report a study of strain relaxation in SrTiO3 films grown on Si by molecular beam epitaxy as a function of annealing time and oxygen partial pressure. Using a combination of x-ray diffraction, reflection high energy electron diffraction, and transmission electron microscopy, we describe the process of interfacial oxidation and strain relaxation of SrTiO3 on Si (001). Understanding the process of strain relaxation of SrTiO3 on silicon will be useful for controlling the SrTiO3 lattice constant for lattice matching with functional oxide overlayers.
Relaxation of a magnetized two ion species dusty plasma
Authors: Iqbal M. , Shukla P. K.
Published: April 2012

A possibility of relaxation of an electronegative dusty plasma composed of two flowing ion species with stationary dust particles is explored. It is shown that magnetic field in such a system has the potential to self-organize giving rise to multiple Beltrami fields. When all the inertial and noninertial forces are taken into account, the relaxed state comes out to be a triple curl Beltrami field. On ignoring the inertia of lighter ions relative to heavy ones, double curl Beltrami field appears as a relaxed state which is equivalent to the superposition of two Beltrami fields. It shows the importance of inertia of plasma components in the formation of relaxed magnetic field structures. It is also shown numerically that scale separation allows the simultaneous existence of magnetic field and velocities varying at vastly different length scales. This gives rise to a dynamo mechanism at relaxed equilibrium. The study bears a strong relevance to the formation of multi scale structures in electronegative dusty plasmas, found in space and laboratory.
Response to “Comment on ‘Debye shielding in a nonextensive plasma’” [Phys. Plasmas 19, 034701 (2012)]
Authors: Ait Gougam Leila , Tribeche Mouloud
Published: April 2012

We demonstrate that our used assumption concerning the Lagrange multiplier associated with the constraint on the internal energy in maximum Tsallis entropy principle, is well justified in the context of plasma physics. Moreover, it is pointed out that one has to critically analyze the commonly accepted “ion sound” formulation of the Bohm sheath criterion.
Resolution of identity approach for the Kohn-Sham correlation energy within the exact-exchange random-phase approximation
Authors: Bleiziffer Patrick , Heßelmann Andreas , Görling Andreas
Published: April 2012

Two related methods to calculate the Kohn-Sham correlation energy within the framework of the adiabatic-connection fluctuation-dissipation theorem are presented. The required coupling-strength-dependent density-density response functions are calculated within exact-exchange time-dependent density-functional theory, i.e., within time-dependent density-functional response theory using the full frequency-dependent exchange kernel in addition to the Coulomb kernel. The resulting resolution-of-identity exact-exchange random-phase approximation (RI-EXXRPA) methods in contrast to previous EXXRPA methods employ an auxiliary basis set (RI basis set) to improve the computational efficiency, in particular, to reduce the formal scaling of the computational effort with respect to the system size N from N6 to N5. Moreover, the presented RI-EXXRPA methods, in contrast to previous ones, do not treat products of occupied times unoccupied orbitals as if they were linearly independent. Finally, terms neglected in previous EXXRPA methods can be included, which leads to a method designated RI-EXXRPA+, while the method without these extra terms is simply referred to as RI-EXXRPA. Both EXXRPA methods are shown to yield total energies, reaction energies of small molecules, and binding energies of noncovalently bonded dimers of a quality that is similar and in some cases even better than that obtained with quantum chemistry methods such as Møller-Plesset perturbation theory of second order (MP2) or with the coupled cluster singles doubles method. In contrast to MP2 and to conventional density-functional methods, the presented RI-EXXRPA methods are able to treat static correlation.
A cryogen-free dilution refrigerator based Josephson qubit measurement system
Authors: Tian Ye , Yu H. F. , Deng H. , Xue G. M. , Liu D. T. , Ren Y. F. , Chen G. H. , Zheng D. N. , Jing X. N. , Lu Li , Zhao S. P. , Han Siyuan
Published: April 2012

We develop a small-signal measurement system on cryogen-free dilution refrigerator which is suitable for superconducting qubit studies. Cryogen-free refrigerators have several advantages such as less manpower for system operation and large sample space for experiment, but concern remains about whether the noise introduced by the coldhead can be made sufficiently low. In this work, we demonstrate some effective approaches of acoustic isolation to reduce the noise impact. The electronic circuit that includes the current, voltage, and microwave lines for qubit coherent state measurement is described. For the current and voltage lines designed to have a low pass of dc-100 kHz, we show that the measurements of Josephson junction's switching current distribution with a width down to 1 nA, and quantum coherent Rabi oscillation and Ramsey interference of the superconducting qubit can be successfully performed.
Dual frequency open-loop electric potential microscopy for local potential measurements in electrolyte solution with high ionic strength
Authors: Kobayashi Naritaka , Asakawa Hitoshi , Fukuma Takeshi
Published: April 2012

Recent development of open-loop electric potential microscopy (OL-EPM) has enabled to measure local potential distribution at a solid/liquid interface. However, the operating environment of OL-EPM has been limited to a weak electrolyte solution (<1 mM). This has significantly limited its application range in biology and chemistry. To overcome this limitation, we have developed dual frequency (DF) mode OL-EPM. In the method, an ac bias voltage consisting of two frequency components at f1 and f2 is applied between a tip and sample. The local potential is calculated from the amplitudes of the f1 and |f1 − f2| components of the electrostatic force. In contrast to the conventional single frequency (SF) mode OL-EPM, the detection of the 2f1 component is not required in DF mode. Thus, the maximum bias modulation frequency in DF mode is twice as high as that in SF mode. The high bias modulation frequency used in DF mode prevents the generation of electrochemical reactions and redistribution of ions and water, which enables to operate OL-EPM even in a strong electrolyte solution. In this study, we have performed potential measurements of nanoparticles on a graphite surface in 1 and 10 mM NaCl solution. The results demonstrate that DF mode OL-EPM allows measurements of local potential distribution in 10 mM electrolyte solution.
The critical growth velocity for planar-to-faceted interfaces transformation in SiGe crystals
Authors: Yang Xinbo , Fujiwara K. , Abrosimov N. V. , Gotoh R. , Nozawa J. , Koizumi H. , Kwasniewski A. , Uda S.
Published: April 2012

Crystal-melt interface morphological transformation of differently oriented SiGe crystals with different Ge concentrations was observed, and the effect of Ge concentration on critical growth velocity (Vc) for the interface morphological transformation was investigated. A planar-to-faceted morphological transformation for the 〈110〉, 〈112〉, and 〈100〉 interfaces was observed. Vc for planar-to-faceted transformation of the 〈110〉, 〈112〉, and 〈100〉 interfaces decreases nonlinearly with increasing Ge concentration. SiGe faceted interfaces can be attributed to the fact that the perturbation induced in a planar interface was amplified when the constitutional undercooled zone was formed at high growth velocities.
Surface morphological stabilization of stressed crystalline solids by simultaneous action of applied electric and thermal fields
Authors: Dasgupta Dwaipayan , Sfyris Georgios I. , Rauf Gungor M. , Maroudas Dimitrios
Published: April 2012

We examine the surface morphological stability of electrically and thermally conducting crystalline elastic solids in uniaxial tension under the simultaneous action of an electric field and a temperature gradient. We use linear stability analysis of a surface mass transport model that accounts for surface electromigration and thermomigration induced by the applied fields and for surface diffusional anisotropy. We find that a properly oriented applied thermal gradient can reduce the critical electric-field strength requirement for stabilization of the planar surface morphology. The temperature dependence of the solid material’s properties does not affect the critical strength requirement of the applied fields.
Langevin dynamics simulation of polymer-assisted virus-like assembly
Authors: Mahalik J. P. , Muthukumar M.
Published: April 2012

Starting from a coarse grained representation of the building units of the minute virus of mice and a flexible polyelectrolyte molecule, we have explored the mechanism of assembly into icosahedral structures with the help of Langevin dynamics simulations and the parallel tempering technique. Regular icosahedra with appropriate symmetry form only in a narrow range of temperature and polymer length. Within this region of parameters where successful assembly would proceed, we have systematically investigated the growth kinetics. The assembly of icosahedra is found to follow the classical nucleation and growth mechanism in the absence of the polymer, with the three regimes of nucleation, linear growth, and slowing down in the later stage. The calculated average nucleation time obeys the laws expected from the classical nucleation theory. The linear growth rate is found to obey the laws of secondary nucleation as in the case of lamellar growth in polymer crystallization. The same mechanism is seen in the simulations of the assembly of icosahedra in the presence of the polymer as well. The polymer reduces the nucleation barrier significantly by enhancing the local concentration of subunits via adsorbing them on their backbone. The details of growth in the presence of the polymer are also found to be consistent with the classical nucleation theory, despite the smallness of the assembled structures.
Titanium and magnesium Co-alloyed hematite thin films for photoelectrochemical water splitting
Authors: Tang Houwen , Yin Wan-Jian , Matin M. A. , Wang Heli , Deutsch Todd , Al-Jassim Mowafak M. , Turner John A. , Yan Yanfa
Published: April 2012

Using a combination of density functional theory calculation and materials synthesis and characterization we examine the properties of charge-compensated Ti and Mg co-alloyed hematite thin films for the application of photoelectrochemical (PEC) water splitting. We find that the charge-compensated co-alloying results in the following effects: (1) It enhances the solubility of Mg and Ti, which leads to reduced electron effective mass and therefore increased electron mobility; (2) It tunes the carrier density and therefore allows the optimization of electrical conductivity; and (3) It reduces the density of charged defects and therefore reduces carrier recombination. As a result, the Ti and Mg co-alloyed hematite thin films exhibit improved water oxidation photocurrent magnitudes as compared to pure hematite thin films. Our results suggest that charge-compensated co-alloying is a plausible approach for engineering hematite for the application of PEC water splitting.
Threshold voltage modulation mechanism of AlGaN/GaN metal-insulator-semiconductor high-electron mobility transistors with fluorinated Al2O3 as gate dielectrics
Authors: Chen Chao , Liu Xingzhao , Zhang Jihua , Tian Benlang , Jiang Hongchuan , Zhang Wanli , Li Yanrong
Published: April 2012

The enhancement-mode (E-mode) AlGaN/GaN metal-insulator-semiconductor high-electron mobility transistors (MISHEMTs) were realized by using fluorinated Al2O3 as gate dielectrics. The variations in binding-energy spectrum and valance-band spectrum in fluorinated-Al2O3/AlGaN/GaN are studied in this Letter, providing insights to mechanism underlying drastic threshold voltage (Vth) modulation of AlGaN/GaN MISHEMTs with fluorinated Al2O3 gate dielectrics. It was found that not the surface potential but rather the negative charges in Al2O3 gate dielectrics are the primary factor responsible for conversion from depletion-mode (D-mode) to E-mode AlGaN/GaN MISHEMTs by using fluorinated Al2O3 as gate dielectrics.
Absence of photoemission from the Fermi level in potassium intercalated picene and coronene films: Structure, polaron, or correlation physics?
Authors: Mahns Benjamin , Roth Friedrich , Knupfer Martin
Published: April 2012

The electronic structure of potassium intercalated picene and coronene films has been studied using photoemission spectroscopy. Picene has additionally been intercalated using sodium. Upon alkali metal addition core level as well as valence band photoemission data signal a filling of previously unoccupied states of the two molecular materials due to charge transfer from potassium. In contrast to the observation of superconductivity in Kxpicene and Kxcoronene (x ∼ 3), none of the films studied shows emission from the Fermi level, i.e., we find no indication for a metallic ground state. Several reasons for this observation are discussed.
Amelioration of interface state response using band engineering in III-V quantum well metal-oxide-semiconductor field-effect transistors
Authors: Yuan Ze , Nainani Aneesh , Bennett Brian R. , Brad Boos J. , Ancona Mario G. , Saraswat Krishna C.
Published: April 2012

Performance degradation due to interfacial traps is generally considered as one of the main challenges for III-V metal-oxide-semiconductor field-effect-transistors (MOSFETs). In this work, we have investigated the suppression of interface state response using band engineering in III-V quantum well MOSFETs and experimentally verified the concept in the antimonide materials system using a gate-stack consisting of Al2O3/GaSb/InAlSb. It is shown that if the thickness of the interfacial layer of GaSb is scaled down to a few monolayers, the effective bandgap of the interfacial layer increases dramatically due to quantum confinement, which leads to the suppression of interface-trap response.
Spatial trade-offs in the digestive and reproductive systems of grape phylloxera
Authors: Andrews K. B. , Kemper D. , Powell K. S. , Cooper P. D.
Published: April 2012

Trade-offs between reproduction and other energy-requiring activities are present in insects. However, feeding and reproduction are not often thought to be trade-offs, although in small insects space may be limiting for both ingestion of food and egg development. This study characterised the structure of the digestive system of radicicolae Daktulosphaira vitifoliae (Hemiptera: Phylloxeridae) to investigate how feeding and egg development occur in this species. Using light and electron microscopy, the midgut of D. vitifoliae was observed to be composed of anterior and posterior regions, separated by a hindgut connection. The midgut is compressed during the development of parthenogenetically produced eggs in adults; individual eggs are ~30% of the adult length and in volume internally occupy 3–5% of the body cavity. The midgut posterior chamber is suggested to be essential for the continual supply of energy during periods of reduced food intake. The presence of the hindgut and an anal opening indicated that waste excretion through the anus was physiologically possible, although honeydew excretion was not observed. The structure of the digestive system of radicicolae D. vitifoliae is atypical, containing adaptations that may assist the survival of the monophagous insect during dispersal events to a new Vitis food source.
Notes on coordination, game theory and the evolutionary basis of language*
Authors: Ross Don
Published: April 2012

It is widely appreciated that establishment and maintenance of coordination are among the key evolutionary promoters and stabilizers of human language. In consequence, it is also generally recognized that game theory is an important tool for studying these phenomena. However, the best known game theoretic applications to date tend to assimilate linguistic communication with signaling. The individualistic philosophical bias in Western social ontology makes signaling seem more challenging than it really is, and thus focuses attention on theoretical problems – for example, coordination on lexical meaning – that actual evolution did not need to solve by improving humans’ strategic or social intelligence relative to the endowments of other primates. At the same time, issues of genuine evolutionary significance related to language, especially those around the tensions between individual and collective agency, and around intergenerational accumulation of knowledge, are obscured. This in turn leads to underestimation of the potential contribution that game theory can make to enlightening models of the evolution of human language. JEL classification: A11, A12, B52, C73, D02, D03, D82, Z13
Carving language for social coordination
Authors: Fusaroli Riccardo , Tylén Kristian
Published: April 2012

Human social coordination is often mediated by language. Through verbal dialogue, people direct each other’s attention to properties of their shared environment, they discuss how to jointly solve problems, share their introspections, and distribute roles and assignments. In this article, we propose a dynamical framework for the study of the coordinative role of language. Based on a review of a number of recent experimental studies, we argue that shared symbolic patterns emerge and stabilize through a process of local reciprocal linguistic alignment. Such patterns in turn come to facilitate and refine social coordination by enabling the alignment, joint construction and navigation of conceptual models and actions. Implications of the framework are illustrated and discussed in relation to a case study where dyads of interlocutors interact verbally to reach joint decisions in a perceptual discrimination task. Keywords: social coordination; language; communication; linguistic alignment; symbolic patterns; affordances; emergence; evolution; adaptivity; interaction
Migrating fibroblasts reorient directionality by a metastable, PI3K-dependent mechanism
Authors: Welf Erik S. , Ahmed Shoeb , Johnson Heath E. , Melvin Adam T. , Haugh Jason M.
Published: April 2012

Mesenchymal cell migration as exhibited by fibroblasts is distinct from amoeboid cell migration and is characterized by dynamic competition among multiple protrusions, which determines directional persistence and responses to spatial cues. Localization of phosphoinositide 3-kinase (PI3K) signaling is thought to play a broadly important role in cell motility, yet the context-dependent functions of this pathway have not been adequately elucidated. By mapping the spatiotemporal dynamics of cell protrusion/retraction and PI3K signaling monitored by total internal reflection fluorescence microscopy, we show that randomly migrating fibroblasts reorient polarity through PI3K-dependent branching and pivoting of protrusions. PI3K inhibition did not affect the initiation of newly branched protrusions, nor did it prevent protrusion induced by photoactivation of Rac. Rather, PI3K signaling increased after, not before, the onset of local protrusion and was required for the lateral spreading and stabilization of nascent branches. During chemotaxis, the branch experiencing the higher chemoattractant concentration was favored, and, thus, the cell reoriented so as to align with the external gradient.
Multivariate proteomic profiling identifies novel accessory proteins of coated vesicles
Authors: Borner Georg H.H. , Antrobus Robin , Hirst Jennifer , Bhumbra Gary S. , Kozik Patrycja , Jackson Lauren P. , Sahlender Daniela A. , Robinson Margaret S.
Published: April 2012

Despite recent advances in mass spectrometry, proteomic characterization of transport vesicles remains challenging. Here, we describe a multivariate proteomics approach to analyzing clathrin-coated vesicles (CCVs) from HeLa cells. siRNA knockdown of coat components and different fractionation protocols were used to obtain modified coated vesicle-enriched fractions, which were compared by stable isotope labeling of amino acids in cell culture (SILAC)-based quantitative mass spectrometry. 10 datasets were combined through principal component analysis into a “profiling” cluster analysis. Overall, 136 CCV-associated proteins were predicted, including 36 new proteins. The method identified >93% of established CCV coat proteins and assigned >91% correctly to intracellular or endocytic CCVs. Furthermore, the profiling analysis extends to less well characterized types of coated vesicles, and we identify and characterize the first AP-4 accessory protein, which we have named tepsin. Finally, our data explain how sequestration of TACC3 in cytosolic clathrin cages causes the severe mitotic defects observed in auxilin-depleted cells. The profiling approach can be adapted to address related cell and systems biological questions.
Protective Immunity Does Not Correlate with the Hierarchy of  Virus-specific Cytotoxic T Cell Responses to Naturally Processed Peptides
Authors: Gallimore Awen , Dumrese Tilman , Hengartner Hans , Zinkernagel Rolf M. , Rammensee Hans-Georg
Published: April 2012

Infection of C57BL/6 mice with lymphocytic choriomeningitis virus (LCMV) stimulates major histocompatibility complex class I–restricted cytotoxic T cells (CTLs), which normally resolve the infection. Three peptide epitopes derived from LCMV have been shown to bind the mouse class I molecule H-2 Db and to stimulate CTL responses in LCMV-infected mice. This report describes the identity and abundance of each CTL epitope after their elution from LCMV-infected cells. Based on this information, peptide abundance was found to correlate with the magnitude of each CTL response generated after infection with LCMV. Subsequent experiments, performed to determine the antiviral capacity of each CTL specificity, indicate that the quantitative hierarchy of CTL activity does not correlate with the ability to protect against LCMV infection. This report, therefore, indicates that immunodominant epitopes should be defined, not only by the strength of the CTL response that they stimulate, but also by the ability of the CTLs to protect against infection.
Large third-order optical nonlinearity of Mg-doped PbS/PVA freestanding nanocomposite films
Authors: Krishnakumar V , Shanmugam G , Nagalakshmi R
Published: April 2012

Mg-doped PbS/PVA freestanding nanocomposite films were successfully prepared by a simple chemical route. X-ray diffraction patterns confirm the formation of all the films with cubic phase of PbS. Optical absorption spectra showed the blue shifted phenomena and the band gaps of Mg : PbS/PVA films increase with an increase in Mg concentration. The increase in resistivity with reducing particle size was examined for these films. The Z-scan results showed that the freestanding nanocomposite films exhibit the large nonlinear refractive index and absorption coefficients with negative sign and they are increased with Mg doping. Third-order nonlinear optical susceptibility and figure of merit were calculated and the maximum value is found to be about 3.405 × 10−5 esu and 2.067 × 10−9 esu m, respectively, for higher Mg-doped film which is three orders of magnitude larger than that observed in the substrate-supported films as reported earlier in the literature. The results show that the Mg : PbS/PVA films have great potential applications in future optical devices.
Dye-sensitized solar cell with a pair of carbon-based electrodes
Authors: Kyaw Aung Ko Ko , Tantang Hosea , Wu Tao , Ke Lin , Wei Jun , Demir Hilmi Volkan , Zhang Qichun , Sun Xiao Wei
Published: April 2012

We have fabricated a dye-sensitized solar cell (DSSC) with a pair of carbon-based electrodes using a transparent, conductive carbon nanotubes (CNTs) film modified with ultra-thin titanium-sub-oxide (TiOx) as the working electrode and a bilayer of conductive CNTs and carbon black as the counter electrode. Without TiOxmodification, the DSSC is almost nonfunctional whereas the power conversion efficiency (PCE) increases significantly when the working electrode is modified with TiOx. The performance of the cell could be further improved when the carbon black film was added on the counter electrode. The improved efficiency can be attributed to the inhibition of the mass recombination at the working electrode/electrolyte interface by TiOxand the acceleration of the electron transfer kinetics at the counter electrode by carbon black. The DSSC with a pair of carbon-based electrodes gives the PCE of 1.37%.
The fluvial history of Mars
Authors: Carr Michael H.
Published: April 2012

River channels and valleys have been observed on several planetary bodies in addition to the Earth. Long sinuous valleys on Venus, our Moon and Jupiter's moon Io are clearly formed by lava, and branching valleys on Saturn's moon Titan may be forming today by rivers of methane. But by far the most dissected body in our Solar System apart from the Earth is Mars. Branching valleys that in plan resemble terrestrial river valleys are common throughout the most ancient landscapes preserved on the planet. Accompanying the valleys are the remains of other indicators of erosion and deposition, such as deltas, alluvial fans and lake beds. There is little reason to doubt that water was the erosive agent and that early in Mars' history, climatic conditions were very different from the present cold conditions and such that, at least episodically, water could flow across the surface. In addition to the branching valley networks, there are large flood features, termed outflow channels. These are similar to, but dwarf, the largest terrestrial flood channels. The consensus is that these channels were also cut by water although there are other possibilities. The outflow channels mostly postdate the valley networks, although most are still very ancient. They appear to have formed at a time when surface conditions were similar to those that prevail today. There is evidence that glacial activity has modified some of the water-worn valleys, particularly in the 30–50° latitude belts, and ice may also be implicated in the formation of geologically recent, seemingly water-worn gullies on steep slopes. Mars also has had a long volcanic history, and long, sinuous lava channels similar to those on the Moon and Venus are common on and around the large volcanoes. These will not, however, be discussed further; the emphasis here is on the effects of running water on the evolution of the surface.
River sediments
Authors: Williams Martin
Published: April 2012

River history is reflected in the nature of the sediments carried and deposited over time. Using examples drawn from around the world, this account illustrates how river sediments have been used to reconstruct past environmental changes at a variety of scales in time and space. Problems arising from a patchy alluvial record and from influences external to the river basin can make interpretation difficult. The Nile is treated in some detail because its history is further complicated by tectonic, volcanic and climatic events in its headwaters and by enduring human impacts. It arose soon after 30 Ma. Since that time approximately 100 000 km
3
of rock have been eroded from its Ethiopian sources and deposited in the eastern Mediterranean, with minor amounts of sediment laid down along its former flood plains in Egypt and Sudan. From these fragmentary alluvial remains, a detailed history of Nile floods and droughts has been reconstructed for the last 15 kyr, and, with less detail, for the past 150 kyr, which shows strong accordance with global fluctuations in the strength of the summer monsoon, which are in turn perhaps modulated by changes in solar insolation caused by changes in the Earth's orbit and by variations in solar irradiance.
Noncanonical repression of translation initiation through small RNA recruitment of the RNA chaperone Hfq
Authors: Desnoyers Guillaume , Massé Eric
Published: April 2012

The RNA chaperone Hfq is mostly known to help small regulatory RNAs (sRNAs) interact with target mRNAs to block initiating ribosomes. In this model, whereas the sRNA is directly competing with initiating 30S ribosomal subunits, Hfq plays only an indirect role, allowing optimal sRNA–mRNA pairing. Here we report that Hfq is recruited by a sRNA, Spot42, to bind to a precise AU-rich region in the vicinity of the translation initiation region (TIR) of sdhC mRNA and competes directly with 30S ribosomal subunits. We show that the sRNA Spot42 binds sdhC too far upstream of the TIR to directly repress translation initiation in vitro and in vivo. Contrary to the canonical model of sRNA regulation, this suggests a new mechanism where Hfq is directly involved in the translational repression of the target mRNA and where the sRNA acts only as a recruitment factor.
Quantitative functions of Argonaute proteins in mammalian development
Authors: Wang Dongmei , Zhang Zhaojie , O'Loughlin Evan , Lee Thomas , Houel Stephane , O'Carroll Dónal , Tarakhovsky Alexander , Ahn Natalie G. , Yi Rui
Published: April 2012

Argonaute proteins (Ago1–4) are essential components of the microRNA-induced silencing complex and play important roles in both microRNA biogenesis and function. Although Ago2 is the only one with the slicer activity, it is not clear whether the slicer activity is a universally critical determinant for Ago2's function in mammals. Furthermore, functional specificities associated with different Argonautes remain elusive. Here we report that microRNAs are randomly sorted to individual Argonautes in mammals, independent of the slicer activity. When both Ago1 and Ago2, but not either Ago1 or Ago2 alone, are ablated in the skin, the global expression of microRNAs is significantly compromised and it causes severe defects in skin morphogenesis. Surprisingly, Ago3 is able to load microRNAs efficiently in the absence of Ago1 and Ago2, despite a significant loss of global microRNA expression. Quantitative analyses reveal that Ago2 interacts with a majority of microRNAs (60%) in the skin, compared with Ago1 (30%) and Ago3 (<10%). This distribution is highly correlated with the abundance of each Argonaute, as quantified by shotgun proteomics. The quantitative correlation between Argonautes and their associated microRNAs is conserved in human cells. Finally, we measure the absolute expression of Argonaute proteins and determine that their copy number is ∼1.4 × 105 to 1.7 × 105 molecules per cell. Together, our results reveal a quantitative picture for microRNA activity in mammals.
Generating Live Cell Data Using Total Internal Reflection Fluorescence Microscopy
Authors: Toomre Derek
Published: April 2012

Live cell fluorescent microscopy is important in elucidating dynamic cellular processes such as cell signaling, membrane trafficking, and cytoskeleton remodeling. Often, transient intermediate states are revealed only when imaged and quantitated at the single-molecule, vesicle, or organelle level. Such insight depends on the spatiotemporal resolution and sensitivity of a given microscopy method. Confocal microscopes optically section the cell and improve image contrast and axial resolution (>600 nm) compared with conventional epifluorescence microscopes. Another approach, which can selectively excite fluorophores in an even thinner optical plane (<100 nm) is total internal reflection fluorescence microscopy (TIRFM). The key principle of TIRFM is that a thin, exponentially decaying, evanescent field of excitation can be generated at the interface of two mediums of different refractive index (RI) (e.g., the glass coverslip and the biological specimen); as such, TIRFM is ill-suited to deep imaging of cells or tissue. However, for processes near the lower cell cortex, the sensitivity of TIRFM is exquisite. The recent availability of a very high numerical-aperture (NA) objective lens (>1.45) and turnkey TIRFM systems by all the major microscopy manufacturers has made TIRFM increasingly accessible and attractive to biologists, especially when performed in a quantitative manner and complemented with orthogonal genetic and molecular manipulations. This article discusses sample preparation for TIRFM, acquisition of time-lapse movies, and quantitative analysis. It also gives examples of imaging cytoskeleton dynamics and exo- and endocytosis using TIRFM.
Measuring Resting Membrane Potential Using the Fluorescent Voltage Reporters DiBAC4(3) and CC2-DMPE
Authors: Adams Dany S. , Levin Michael
Published: April 2012

Slow changes in steady-state (resting) transmembrane potential (Vmem) of non-excitable cells often encode important instructive signals controlling differentiation, proliferation, and cell:cell communication. Probing the function of such bioelectric gradients in vivo or in culture requires the ability to track Vmem, to characterize endogenous patterns of differential potential, map out isopotential cell groups (compartments or cell fields), and confirm the results of functional perturbation of Vmem. The use of fluorescent bioelectricity reporters (FBRs) has become more common as continuing research and innovation have produced better and more options. These dyes are now used routinely for cell sorting and for studies of cultured cells. Important advantages over single cell electrode measurements are offered by dyes, including: (1) subcellular resolution, (2) the ability to monitor multicellular areas and volumes in vivo, (3) simplicity of use, (4) ability to measure moving targets, and (5) ability to measure over long time periods. Thus, FBRs are suitable for longitudinal studies of systems that change and move over time, for example, embryos. Existing protocols focus on measurements of rapid action potentials in cultured cells or neurons. This article describes a dye pair that can be used to measure resting Vmem in cultured cells and in vivo in Xenopus laevis embryos and tadpoles (and is readily applied to other model systems, such as zebrafish, for studies of developmental bioelectricity). It is assumed that the reader is fully familiar with the process and terminology of fluorescence microscopy.
The Impact and Burden of Chronic Pain in the Workplace: A Qualitative Systematic Review
Authors: Patel Ajay S. , Farquharson Rachel , Carroll Dawn , Moore Andrew , Phillips Ceri J. , Taylor Rod S. , Barden Jodie
Published: April 2012

Background: Chronic pain (CP) poses a diverse and substantial burden for employees, employers, and society. The deleterious consequences of CP in the workplace are frequently underestimated.

Objective: To estimate the burden of CP in the European workplace.

Methods: A systematic review following PRISMA statement guidelines was conducted to identify studies reporting work‐related outcomes for people with CP. EMBASE, MEDLINE, EconLit, and Cochrane Library databases were searched up to 18th August 2010.

Results: We identified 91 observational studies. Few were specifically designed to investigate the association between CP, productivity, and employment. The focus for this review was studies clearly reporting outcomes relating to the burden of CP on employment status (n = 37), sickness absence (absenteeism,n = 47), and loss of productivity because of reduced ability at work (presenteeism,n = 8).

Conclusion: The body of evidence identified from the systematic review indicates that CP has a substantial negative impact on work‐related outcomes, supporting the importance of interventions to reduce the burden of CP. Well‐designed prospective studies specifically assessing the direct consequences of CP on employment are needed to confirm these findings.
A New Contact Force Model for Low Coefficient of Restitution Impact
Authors: Gharib Mohamed , Hurmuzlu Yildirim
Published: April 2012

Impact problems arise in many practical applications. The need for obtaining an accurate model for the inelastic impact is a challenging problem. In general, two approaches are common in solving the impact problems: the impulse-momentum and the compliance based methods. The former approach included the coefficient of restitution which provides a mechanism to solve the problem explicitly. While the compliance methods are generally tailored to solve elastic problems, researchers in the field have proposed several mechanisms to include inelastic losses. In this paper, we present correlations between the coefficient of restitution in the impulse-momentum based method and the contact stiffness in the compliance methods. We conducted numerical analysis to show that the resulting solutions are indeed identical for a specific range of impact conditions. The impulse-momentum based model is considered as a reference case to compare the post impact velocities. The numerical results showed that, the impulse-momentum and the compliance based methods can produce similar outcomes for specific range of coefficient of restitution if they satisfied a set of end conditions. The correlations lead to introduce a new contact force model with hysteresis damping for low coefficient of restitution impact.
Can epigenetic control explain pronounced within-plant heterogeneity of meiosis in a translocation trisome ofSecaleL.?
Authors: Sybenga J.
Published: April 2012

Meiotic metaphase I configuration frequencies were determined in different tillers of genetically related plants of rye ( Secale cereale L.) heterozygous for reciprocal translocation T248W (between chromosome arms 1RS and 6RS) and with an additional (telocentric) arm 1RS. Seventeen different configurations could be recognized, grouped into three categories. Very different configuration frequencies were found not only between sister plants from the same parents but also between tillers of the same plant grown under identical conditions (climate chambers at 15 °C and 20 °C). The heterogeneity reflects variation in chromosome pairing and crossing over, and is variable and unpredictable. Anthers within florets were homogeneous. Between tiller heterogeneity is insufficient to explain differences between sister plants. It is ascribed to random somatic variation in the conditions of the chromatin which, at meiosis, govern chromosome pairing. During sexual differentiation, these conditions are fixed and subsequent cell lineages have the same pairing and crossing over characteristics. As homology search is an activity of DNA, this control of pairing and crossing over, consistent over long cell lineages, may be considered to be epigenetic even when no realistic suggestions concerning its character can be given.