bluuebunny/crossref_metadata_2025 huggingface dataset:
Instituto de Sistemas Fotovoltaicos de Concentración concentration photovoltaics hybrid system first year of operation and improvements
Authors: Trujillo Serrano Pablo Jesus , Alamillo Davila Cesareo , Martínez Montes Maria , de la Rubia Oscar , Rubio Francisca , Masa‐Bote Daniel , Castillo‐Cagigal Manuel , Matallanas Eduardo , Caamaño‐Martín Estefania , Gutiérrez Alvaro
Published: February 2013

A photovoltaic (PV) hybrid system combines PV with other forms of electricity generation, usually a diesel generator. The system presented in this paper uses concentration photovoltaic (CPV) as the main generator in combination with a storage system and the grid, configured as the backup power supply. The load of the system consists of an air conditioning system of an office building. This paper presents the results obtained from the first months of operation of the CPV hybrid system installed at Instituto de Sistemas Fotovoltaicos de Concentración facilities together with exhaustive simulations in order to model the system behaviour and be able to improve the self‐consumption ratio. This system represents a first approach to the use of a CPV in office buildings complemented by an existing AC‐coupled hybrid system. The contribution of this paper to the analysis of this new system and the existing tools available for its simulation, at least a part of it, can be considered as a starting point for the development of these kinds of systems. Copyright © 2013 John Wiley & Sons, Ltd.
CdxHg(1−x)Te Alloy Colloidal Quantum Dots: Tuning Optical Properties from the Visible to Near‐Infrared by Ion Exchange
Authors: Gupta Shuchi , Zhovtiuk Olga , Vaneski Aleksandar , Lin Yan‐Cheng , Chou Wu‐Ching , Kershaw Stephen V. , Rogach Andrey L.
Published: February 2013

The energy gap between valence and conduction levels in colloidal semiconductor quantum dots can be tuned via the nanoparticle diameter when this is comparable to or less than the Bohr radius. In materials such as cadmium mercury telluride, which readily forms a single phase ternary alloy, this quantum confinement tuning can also be augmented by compositional tuning, which brings a further degree of freedom in the bandgap engineering. Here it is shown that compositional control of 2.3 nm diameter CdxHg(1−x)Te nanocrystals by exchange of Hg2+ in place of Cd2+ ions can be used to tune their optical properties across a technologically useful range, from 500 nm to almost 1200 nm. Data on composition‐dependent changes in the optical properties are provided, including bandgap, extinction coefficient, emission energy and spectral shape, Stokes shift, quantum efficiency, and radiative lifetimes as the exchange process occurs, which are highly relevant for those seeking to use these technologically important QD materials.
Magnetism and superconductivity in EuFe2As2 synthesized under high pressure
Authors: Tsvyashchenko A. V. , Sidorov V. A. , Fomicheva L. N. , Gofryk K. , Sadykov R. A. , Thompson J. D.
Published: February 2013

We have synthesized polycrystalline samples of EuFe2As2 by melting the stoichiometric mixture of constituent components at a high pressure (HP) of 8 GPa and measured the properties of HP‐synthesized samples at ambient and high pressure up to 6 GPa. SDW‐type antiferromagnetism appears below 150 K and Eu‐related antiferromagnetism appears below 16 K in all HP synthesized samples. Also, all HP‐synthesized samples exhibit superconductivity with Tc = 20–30 K at ambient pressure, though a zero‐resistance state has not been observed. This superconductivity is very robust against application of magnetic field (dHc2/dT = −3.2 T K−1) and pressure (a tiny signal of superconductivity is still detectable below 2.5 K at 5.8 GPa). SDW antiferromagnetism is suppressed under pressure and is not observed above 1.7 GPa and below 60 K. The temperature of the magnetic ordering of Eu2+ moments increases under pressure. Specific heat measurements in a magnetic field reveal an increase of this temperature in field, therefore indicating field‐induced ferromagnetism in the Eu sublattice.
Validity of the Patient Specific Functional Scale in Patients following Upper Extremity Nerve Injury
Authors: Novak Christine B. , Anastakis Dimitri J. , Beaton Dorcas E. , Mackinnon Susan E. , Katz Joel
Published: February 2013

Purpose

This study evaluated the validity of the Patient Specific Functional Scale (PSFS) in patients with upper extremity nerve injury.

Methods

Following Research Ethics Boards (REB) approval, we included English-speaking adults, with greater than 6 months after an upper extremity nerve injury. Patient reported questionnaires included: PSFS, 36-item short-form health survey (SF-36), Disabilities of the Arm, Shoulder and Hand (DASH), McGill Pain Questionnaire, Pain Catastrophizing Scale (PCS) and Pain Disability Index (PDI). Statistical analyses evaluated the relationships among the outcome measures and the independent variables (age, gender, nerve injured, time since injury, work status, worker's compensation/litigation). Linear regression was used to evaluate the variables that predicted the PSFS.

Results

There were 157 patients (53 women, 104 men); median time since injury of 14 months. The mean ± SD scores were: PSFS 3.1 ± 2.3, DASH 44 ± 22, PCS 16 ± 15, pain intensity 4.2 ± 3.0, pain rating index 13 ± 11, PDI 28.3 ± 17.6 and SF-36 component scores physical (41.8 ± 8.7) mental (45.9 ± 12.6). There were moderate correlations between the PSFS and the DASH, and the SF-36 physical role domain. The PSFS was significantly lower in brachial plexus injuries. The final model explained 20.7 % of the variance and independent variables were DASH, nerve injured and age. Conclusion This study provides evidence of construct validity of the PSFS for patients with upper extremity nerve injury. The PSFS is a valid method to assess functional limitations identified by the individual and can be completed in a shorter period of time than the DASH.
A Systematic Study of Mixed Surfactant Solutions of a Cationic Ester‐Bonded Dimeric Surfactant with Cationic, Anionic and Nonionic Monomeric Surfactants in Aqueous Media
Authors: Fatma Nazish , Ansari Wajid Husain , Panda Manorama , Kabir‐ud‐Din
Published: February 2013

A novel cationic biodegradable dimeric (gemini) surfactant, ethane‐1,2‐diyl bis(N,N‐dimethyl‐N‐hexadecylammoniumacetoxy) dichloride (16‐E2‐16), containing an ester‐linked spacer was synthesized. Its pure and mixed micellization properties with monomeric surfactants cetyl trimethyl ammonium chloride, cetyl pyridinium chloride, sodium dodecyl sulfate, sodium dodecyl benzene sulfonate, cetyl alcohol ethoxylate (20EO) and tert‐octylphenol ethoxylate (9.5EO) were investigated by surface tension measurements at 30 °C. The critical micelle concentration (CMC) of 16‐E2‐16 is well below that of cetyl trimethyl ammonium chloride containing the same number of carbon atoms in the hydrophobic tail per polar head. At different mole fractions of the gemini surfactant, the CMCs of the gemini‐conventional binary mixtures were determined and were found to be less than the ideal CMC values in all the cases indicating synergistic interactions. Aggregation number and Stern–Volmer constant, obtained by the fluorescence quenching technique, also support the synergistic behavior of the surfactant systems.
Longitudinal relations between personality traits and aspects of identity formation during adolescence
Authors: Hill Patrick L. , Allemand Mathias , Grob Sabine Zehnder , Peng Aristide , Morgenthaler Christoph , Käppler Christoph
Published: February 2013

The current study focused on three aspects of identity development relevant to the adolescent years: being an authentic person, perceiving control over and consistency in one's environment, and having consistent expectations from close others. In a two‐wave study of adolescents (n= 750), we examined how these aspects change over the course of a year, as well as whether these aspects correspond to the Big Five personality traits. Results indicated three important findings. First, all three aspects evidenced the capacity for change over a year, and appeared more malleable than personality traits. Second, youth higher on all aspects reported a more adaptive personality profile. Third, changes on these aspects coincide with those on personality traits over the year. Findings are discussed with respect to future directions for studying the interplay of identity and personality development.
New insights into the catalytic mechanism of vitamin K epoxide reductase (VKORC1) – The catalytic properties of the major mutations of rVKORC1 explain the biological cost associated to mutations
Authors: Matagrin Benjamin , Hodroge Ahmed , Montagut-Romans Adrien , Andru Julie , Fourel Isabelle , Besse Stéphane , Benoit Etienne , Lattard Virginie
Published: February 2013

The systematic use of antivitamin K anticoagulants (AVK) as rodenticides caused the selection of rats resistant to AVKs. The resistance is mainly associated to genetic polymorphisms in the Vkorc1 gene encoding the VKORC1 enzyme responsible for the reduction of vitamin K 2,3‐epoxide to vitamin K. Five major mutations, which are responsible for AVK resistance, have been described. Possible explanations for the biological cost of these mutations have been suggested. This biological cost might be linked to an increase in the vitamin K requirements. To analyze the possible involvement of VKORC1 in this biological cost, rVKORC1 and its major mutants were expressed in Pichia pastoris as membrane‐bound proteins and their catalytic properties were determined for vitamin K and 3‐OH‐vitamin K production. In this report, we showed that mutations at Leu‐120 and Tyr‐139 dramatically affect the vitamin K epoxide reductase activity. Moreover, this study allowed the detection of an additional production of 3‐hydroxyvitamin K for all the mutants in position 139. This result suggests the involvement of Tyr‐139 residue in the second half‐step of the catalytic mechanism corresponding to the dehydration of vitamin K epoxide. As a consequence, the biological cost observed in Y139C and Y139S resistant rat strains is at least partially explained by the catalytic properties of the mutated VKORC1 involving a loss of vitamin K from the vitamin K cycle through the formation of 3‐hydroxyvitamin K and a very low catalytic efficiency of the VKOR activity.
Use of Segmental Coordination Analysis of Nonparetic and Paretic Limbs During Obstacle Clearance in Community‐Dwelling Persons After Stroke
Authors: MacLellan Michael J. , Richards Carol L. , Fung Joyce , McFadyen Bradford J.
Published: February 2013

Objective

To use a segment coordination analysis to identify coordination differences between the paretic and nonparetic limbs for obstacle clearance in community‐dwelling persons after stroke.

Design

Within‐participant design.

Setting

Gait analysis laboratory.

Participants

Six community‐dwelling persons with a stroke (excluding cerebellar stroke).

Methods

Participants stepped over obstacles of 2 different heights (7.5% and 15% of leg length), leading alternately with their paretic and nonparetic limbs.

Main Outcome Measurements

Kinematic data were collected, and segment elevation angles (absolute segment angular position with respect to vertical) were calculated for the thigh, shank, and foot segments. Established mathematical techniques related to the planar law of intersegmental coordination (principal component analysis to quantify covariance and temporal phase relationships among elevation angles) were then applied to compare and contrast the coordination of these segment elevation angle trajectories between paretic and nonparetic limbs.

Results

Segment covariance in elevation angles followed the planar law of intersegmental coordination during level walking (ie, 3 elevation angles that form a plane and the variance explained by 2 principal components) for both paretic and nonparetic limbs. During obstacle clearance, however, relationships between covariance plane characteristics and phase differences for elevation angles of adjacent segments differed in the nonparetic limb, likely related to a need for greater limb elevation for obstacle clearance during paretic limb support or an altered foot trajectory, which resulted from preobstacle foot placement.

Conclusions

The present coordination analysis suggests the preservation of basic control mechanisms in the paretic limb during obstacle clearance after stroke and also reveals its specific motor control compensations. However, a larger study with differing levels of stroke severity must be conducted to understand how the evaluation of intersegmental coordination during walking could guide treatment of specific locomotor control deficits in stroke rehabilitation.
A Comparison of Two Balance Measures to Predict Discharge Performance From Inpatient Stroke Rehabilitation
Authors: O'Dell Michael W. , Au Jessica , Schwabe Eric , Batistick Holly , Christos Paul J.
Published: February 2013

Objective

To compare the admission Berg Balance Scale (BBS) and Postural Assessment Scale for Stroke (PASS) in predicting outcomes at discharge from an inpatient rehabilitation unit (IRU). We hypothesized that discharge outcomes would be better predicted by (1) the PASS compared with the BBS, and (2) by the PASS changing position subscore compared with the PASS maintain posture subscore.

Design

A retrospective study.

Setting

An IRU in an academic medical center.

Participants

Fifty‐five subjects with stroke and mean (standard deviation [SD]) age of 71.5 ± 13.8 years, admission functional independence measures (FIM) of 57.2 ± 17.2 points, and IRU length of stay of 17.3 ± 9.7 days.

Methodology/Main Outcome Measurements

Admission and discharge BBS and PASS scores, gait velocity (GV) at discharge, and selected FIM items at discharge were measured. GV was analyzed both as a continuous and categorical variable.

Results

The Spearman rank correlation coefficient (r) was strong between admission BBS and PASS (r = 0.90, P < .0001). Correlations between admission BBS and PASS and discharge GV were 0.32 (P = .03) and 0.28 (P = .06), respectively. Analysis of variance was significant for both balance measures when grouped by the discharge gait speed category (P < .0001). Pairwise comparisons were significant between GV‐A and the other 2 categories but not between GV‐B and GV‐C. The magnitude of the observed correlation with discharge GV was greater for PASS maintain posture subscore (r = 0.35, P = .02) than for PASS changing position subscore (r = 0.23, P = .13). Both subscores were significantly associated with both toileting and transfers (r = 0.43‐0.56, all at least P ≤ .001).

Conclusions

Contrary to our hypotheses, the BBS and PASS performed equally well in our study sample and were best at predicting patients discharged in the slowest GV category. There were few differences between the PASS subscores. Further research should compare how well admission BBS and PASS predict gait velocity, falls, and other functional parameters in the community after IRU discharge.
Nonoperative Treatment for Femoroacetabular Impingement: A Systematic Review of the Literature
Authors: Wall Peter D.H. , Fernandez Miguel , Griffin Damian R. , Foster Nadine E.
Published: February 2013

Objective

Femoroacetabular impingement (FAI) has been identified as a common cause of hip pain in young adults. However, it is not known whether an effective nonoperative treatment exists and whether there is any evidence to support such a treatment. The purpose of this review is to establish whether nonoperative treatments exist for FAI in the published literature and whether there is any evidence to support their use.

Type

A systematic review.

Literacy Survey

PubMed, Medline, EMBASE, CINAHL, AMED, and Cochrane Library databases were searched by using the following terms: femoroacetabular impingement, femoro‐acetabular impingement, and hip impingement. The search was limited to English only but with no time constraints.

Methodology

The review was undertaken at 2 academic institutions within the United Kingdom; any article that described or provided evidence that related to a nonoperative treatment for FAI was included. Fifty‐three articles met our criteria, of which, 48 were review and/or discussion based.

Synthesis

Five articles summarized primary experiments that described or evaluated nonoperative treatment, of which, 3 reported favorable outcomes. Many review and/or discussion articles (31 [65%]) indicated that a trial of conservative care was appropriate. Activity modification was most frequently recommended (39 [81%]), and nearly half promoted physical therapy as a treatment (23 [48%]).

Conclusion

The review literature appears to promote initial nonoperative treatment for FAI. Although the available literature with experimental data is limited, there is a suggestion that physical therapy and activity modification confer some benefit to patients. Nonoperative treatment regimens, particularly physical therapy, need to be evaluated more extensively and rigorously, preferably against operative care, to determine the true clinical effectiveness.
Diverse property rights, institutions and decentralisation: Forest management by village forest councils in Uttarakhand
Authors: Singh Satyajit
Published: February 2013

This study of decentralised institutions for forest management brings out the varied dimensions of local institutions and politics as they interface with property rights and decentralisation. Unlike the economic literature on decentralisation that is dominated by normative and prescriptive arguments on how a shift towards decentralisation should take place, this paper makes a case for re-centering of the political in the decentralisation literature. This political study of decentralisation does not prescribe decentralisation rules, but weighs the different social, economic and ecological outcomes under varied local conditions. It takes note of the diversity of local institutions and politics in the interpretation of formal rules, power relations, legal rights, moral claims, social custom, and the establishment of informal institutional arrangements. This is done in the context of questioning the typologies of neat property regimes that are broadly categorised as — open-access, state, private and common property - in the economic literature. These widely accepted typologies are tested at the local level and it is found that ownership does not necessarily refer to control and use of resources. The paper highlights the heterogeneity of property regimes under which the village communities manage the forests, and points out that specific state-society relations in particular villages determine the entitlements of the villagers. Importantly, the nature of collective action on decentralisation and negotiation of institutional design has an impact on the consequences at the local level. As the local reality is based on varied local resources, institutions, political processes and social capital, uniform national or state policies have very different local outcomes. This paper asks if it is possible to evolve policies that incorporate diverse institutional arrangements with a combination of different kinds of property rights under decentralised local governance management.
Application of phase-plane method in generating minimum time solution for stable walking of biped robot with specified pattern of motion
Authors: Sadigh Mohammad Jafar , Mansouri Saeed
Published: February 2013

Walking with a maximum speed is an interesting subject in the field of biped motion. Giving an answer to the question of “what is the maximum achievable speed of a certain biped walking with a physically acceptable pattern?” is the main objective of this work. In this paper, minimum time motion of biped was studied during one step that consists of single support phase (SSP) and double support phase (DSP). The minimum time problem is formulated with stability and non-slip conditions along with actuator limits expressed as some inequality constraints. In addition, certain kinematic constraints in terms of hip joint position are considered that ensure an acceptable walking pattern. A phase-plane technique is used to find the minimum time solution. A numerical simulation is given to shed some light on how the proposed method works. Validity and effectiveness of the method are verified by comparing the results with those of other researches.
The emission of compact jets powered by internal shocks
Authors: Malzac Julien
Published: February 2013

The emission of steady compact jets observed in the hard spectral state of X-ray binaries is likely to be powered by internal shocks caused by fluctuations of the outflow velocity. The dynamics of the internal shocks and the resulting spectral energy distribution (SED) of the jet is very sensitive to the shape of the Power Spectral Density (PSD) of the fluctuations of the jet Lorentz factor. I use Monte-Carlo simulations to investigate this dependence. It turns out that Lorentz factor fluctuations injected at the base of the jet with a flicker noise power spectrum (i.e. P(f) ∝ 1/f) naturally produce the canonical flat SED observed from radio to IR band in X-ray binary systems in the hard state. This model also predicts a strong, wavelength dependent, variability that resembles the observed one. In particular, strong sub-second variability is predicted in the infrared and optical bands.
Lense-Thirring QPO model testing by QPO phenomena in GX339-4 2010 outburst
Authors: Gao H. Q. , Qu J. L. , Zhang Z. , Zhou J. N.
Published: February 2013

Lense-Thirring QPO model is a promising model to explain QPO phenomena (Ingram et al. (2009)). In this model the QPO results from Lense-Thirring precession of a optical translucent inner hot flow in a truncated disc geometry. Now we check this model with different types QPO (see (Belloni et al. (2011)) for a recent review) of black hole transient (BHT) GX 339-4 2010 outburst and suggest type C QPOs are mainly coincident with this model prediction while type B QPOs are not.
Capacity, value neutrality and the ability to consider the future
Authors: Craigie Jillian
Published: February 2013

Calls for the adoption of a universal capacity approach to replace dedicated mental health law are motivated by the idea that the measures designed to protect patient autonomy in legislation such as the Mental Capacity Act 2005 should apply to everyone, including people with a psychiatric diagnosis. In this article it is argued that a diachronic perspective on questions of mental capacity is necessary if capacity law is to play this broader role, but that employing this perspective in assessments of capacity undermines central patient autonomy preserving features of the legislation, which presents a moral dilemma.
SO2photoexcitation mechanism links mass-independent sulfur isotopic fractionation in cryospheric sulfate to climate impacting volcanism
Authors: Hattori Shohei , Schmidt Johan A. , Johnson Matthew S. , Danielache Sebastian O. , Yamada Akinori , Ueno Yuichiro , Yoshida Naohiro
Published: February 2013

Natural climate variation, such as that caused by volcanoes, is the basis for identifying anthropogenic climate change. However, knowledge of the history of volcanic activity is inadequate, particularly concerning the explosivity of specific events. Some material is deposited in ice cores, but the concentration of glacial sulfate does not distinguish between tropospheric and stratospheric eruptions. Stable sulfur isotope abundances contain additional information, and recent studies show a correlation between volcanic plumes that reach the stratosphere and mass-independent anomalies in sulfur isotopes in glacial sulfate. We describe a mechanism, photoexcitation of SO2, that links the two, yielding a useful metric of the explosivity of historic volcanic events. A plume model of S(IV) to S(VI) conversion was constructed including photochemistry, entrainment of background air, and sulfate deposition. Isotopologue-specific photoexcitation rates were calculated based on the UV absorption cross-sections of32SO2,33SO2,34SO2, and36SO2from 250 to 320 nm. The model shows that UV photoexcitation is enhanced with altitude, whereas mass-dependent oxidation, such as SO2+ OH, is suppressed by in situ plume chemistry, allowing the production and preservation of a mass-independent sulfur isotope anomaly in the sulfate product. The model accounts for the amplitude, phases, and time development of Δ33S/δ34S and Δ36S/Δ33S found in glacial samples. We are able to identify the process controlling mass-independent sulfur isotope anomalies in the modern atmosphere. This mechanism is the basis of identifying the magnitude of historic volcanic events.
DNA damage in stem cells activates p21, inhibits p53, and induces symmetric self-renewing divisions
Authors: Insinga Alessandra , Cicalese Angelo , Faretta Mario , Gallo Barbara , Albano Luisa , Ronzoni Simona , Furia Laura , Viale Andrea , Pelicci Pier Giuseppe
Published: February 2013

DNA damage leads to a halt in proliferation owing to apoptosis or senescence, which prevents transmission of DNA alterations. This cellular response depends on the tumor suppressor p53 and functions as a powerful barrier to tumor development. Adult stem cells are resistant to DNA damage-induced apoptosis or senescence, however, and how they execute this response and suppress tumorigenesis is unknown. We show that irradiation of hematopoietic and mammary stem cells up-regulates the cell cycle inhibitor p21, a known target of p53, which prevents p53 activation and inhibits p53 basal activity, impeding apoptosis and leading to cell cycle entry and symmetric self-renewing divisions. p21 also activates DNA repair, limiting DNA damage accumulation and self-renewal exhaustion. Stem cells with moderate DNA damage and diminished self-renewal persist after irradiation, however. These findings suggest that stem cells have evolved a unique, p21-dependent response to DNA damage that leads to their immediate expansion and limits their long-term survival.
3′ fragment of miR173-programmed RISC-cleaved RNA is protected from degradation in a complex with RISC and SGS3
Authors: Yoshikawa Manabu , Iki Taichiro , Tsutsui Yasuhiro , Miyashita Kyoko , Poethig R. Scott , Habu Yoshiki , Ishikawa Masayuki
Published: February 2013

trans
-acting small interfering RNAs (tasiRNAs) are plant-specific endogenous siRNAs produced via a unique pathway whose first step is the microRNA (miRNA)-programmed RNA-induced silencing complex (RISC)–mediated cleavage of tasiRNA gene (
TAS
) transcripts. One of the products is subsequently transformed into tasiRNAs by a pathway that requires several factors including SUPPRESSOR OF GENE SILENCING3 (SGS3) and RNA-DEPENDENT RNA POLYMERASE6. Here, using in vitro assembled ARGONAUTE (AGO)1–RISCs, we show that SGS3 is recruited onto RISCs only when they bind target RNA. Following cleavage by miRNA173 (miR173)-programmed RISC, SGS3 was found in complexes containing cleaved
TAS2
RNA and RISC. The 3′ cleavage fragment (the source of tasiRNAs) was protected from degradation in this complex. Depletion of SGS3 did not affect
TAS2
RNA cleavage by miR173-programmed RISC, but did affect the stability of the 3′ cleavage fragment. When the 3′ nucleotide of 22-nt miR173 was deleted or the corresponding nucleotide in
TAS2
RNA was mutated, the complex was not observed and the 3′ cleavage fragment was degraded. Importantly, these changes in miR173 or
TAS2
RNA are known to lead to a loss of tasiRNA production in vivo. These results suggest that (
i
) SGS3 associates with AGO1–RISC via the double-stranded RNA formed by the 3′-terminal nucleotides of 22-nt miR173 and corresponding target RNA, which probably protrudes from the AGO1–RISC molecular surface, (
ii
) SGS3 protects the 3′ cleavage fragment of
TAS2
RNA from degradation, and (
iii
) the observed SGS3-dependent stabilization of the 3′ fragment of
TAS2
RNA is key to tasiRNA production.
The CORVET complex promotes tethering and fusion of Rab5/Vps21-positive membranes
Authors: Balderhaar Henning J. kleine , Lachmann Jens , Yavavli Erdal , Bröcker Cornelia , Lürick Anna , Ungermann Christian
Published: February 2013

Membrane fusion along the endocytic pathway occurs in a sequence of tethering, docking, and fusion. At endosomes and vacuoles, the CORVET (class C core vacuole/endosome tethering) and HOPS (homotypic fusion and vacuole protein sorting) tethering complexes require their organelle-specific Rabs for localization and function. Until now, despite the absence of experimental evidence, it has been assumed that CORVET is a membrane-tethering factor. To test this theory and understand the mechanistic analogies with the HOPS complex, we set up an in vitro system, and establish CORVET as a bona-fide tether for Vps21-positive endosome/vacuole membranes. Purified CORVET binds to SNAREs and Rab5/Vps21-GTP. We then demonstrate that purified CORVET can specifically tether Vps21-positive membranes. Tethering via CORVET is dose-dependent, stimulated by the GEF Vps9, and inhibited by Msb3, the Vps21-GAP. Moreover, CORVET supports fusion of isolated membranes containing Vps21. In agreement with its role as a tether, overexpressed CORVET drives Vps21, but not the HOPS-specific Ypt7 into contact sites between vacuoles, which likely represent vacuole-associated endosomes. We therefore conclude that CORVET is a tethering complex that promotes fusion of Rab5-positive membranes and thus facilitates receptor down-regulation and recycling at the late endosome.
Experimental demonstration of radicaloid character in a RuV=O intermediate in catalytic water oxidation
Authors: Moonshiram Dooshaye , Alperovich Igor , Concepcion Javier J. , Meyer Thomas J. , Pushkar Yulia
Published: February 2013

Water oxidation is the key half reaction in artificial photosynthesis. An absence of detailed mechanistic insight impedes design of new catalysts that are more reactive and more robust. A proposed paradigm leading to enhanced reactivity is the existence of oxyl radical intermediates capable of rapid water activation, but there is a dearth of experimental validation. Here, we show the radicaloid nature of an intermediate reactive toward formation of the O-O bond by assessing the spin density on the oxyl group by Electron Paramagnetic Resonance (EPR). In the study, an17O-labeled form of a highly oxidized, short-lived intermediate in the catalytic cycle of the water oxidation catalystcis,cis-[(2,2-bipyridine)2(H2O)RuIIIORuIII(OH2)(bpy)2]4+was investigated. It contains Ru centers in oxidation states [4,5], has at least one RuV= O unit, and shows |Axx| = 60G17O hyperfine splittings (hfs) consistent with the high spin density of a radicaloid. Destabilization of π-bonding in thed3RuV= O fragment is responsible for the high spin density on the oxygen and its high reactivity.
Shigella
impairs T lymphocyte dynamics in vivo
Authors: Salgado-Pabón Wilmara , Celli Susanna , Arena Ellen T. , Nothelfer Katharina , Roux Pascal , Sellge Gernot , Frigimelica Elisabetta , Bousso Philippe , Sansonetti Philippe J. , Phalipon Armelle
Published: February 2013

The Gram-negative enteroinvasive bacterium
Shigella flexneri
is responsible for the endemic form of bacillary dysentery, an acute rectocolitis in humans.
S. flexneri
uses a type III secretion system to inject effector proteins into host cells, thus diverting cellular functions to its own benefit. Protective immunity to reinfection requires several rounds of infection to be elicited and is short-lasting, suggesting that
S. flexneri
interferes with the priming of specific immunity. Considering the key role played by T-lymphocyte trafficking in priming of adaptive immunity, we investigated the impact of
S. flexneri
on T-cell dynamics in vivo. By using two-photon microscopy to visualize bacterium–T-cell cross-talks in the lymph nodes, where the adaptive immunity is initiated, we provide evidence that
S. flexneri
, via its type III secretion system, impairs the migration pattern of CD4
+
T cells independently of cognate recognition of bacterial antigens. We show that bacterial invasion of CD4
+
T lymphocytes occurs in vivo, and results in cell migration arrest. In the absence of invasion, CD4
+
T-cell migration parameters are also dramatically altered. Signals resulting from
S. flexneri
interactions with subcapsular sinus macrophages and dendritic cells, and recruitment of polymorphonuclear cells are likely to contribute to this phenomenon. These findings indicate that
S. flexneri
targets T lymphocytes in vivo and highlight the role of type III effector secretion in modulating host adaptive immune responses.
Drug-SNPing: an integrated drug-based, protein interaction-based tagSNP-based pharmacogenomics platform for SNP genotyping
Authors: Yang Cheng-Hong , Cheng Yu-Huei , Chuang Li-Yeh , Chang Hsueh-Wei
Published: February 2013

Summary: Many drug or single nucleotide polymorphism (SNP)-related resources and tools have been developed, but connecting and integrating them is still a challenge. Here, we describe a user-friendly web-based software package, named Drug-SNPing, which provides a platform for the integration of drug information (DrugBank and PharmGKB), protein–protein interactions (STRING), tagSNP selection (HapMap) and genotyping information (dbSNP, REBASE and SNP500Cancer). DrugBank-based inputs include the following: (i) common name of the drug, (ii) synonym or drug brand name, (iii) gene name (HUGO) and (iv) keywords. PharmGKB-based inputs include the following: (i) gene name (HUGO), (ii) drug name and (iii) disease-related keywords. The output provides drug-related information, metabolizing enzymes and drug targets, as well as protein–protein interaction data. Importantly, tagSNPs of the selected genes are retrieved for genotyping analyses. All drug-based and protein–protein interaction-based SNP genotyping information are provided with PCR-RFLP (PCR-restriction enzyme length polymorphism) and TaqMan probes. Thus, users can enter any drug keywords/brand names to obtain immediate information that is highly relevant to genotyping for pharmacogenomics research.

Availability and implementation: Drug-SNPing and its user manual are freely available at http://bio.kuas.edu.tw/drug-snping/.

Contact:  chuang@isu.edu.tw; yuhuei.cheng@gmail.com; changhw@kmu.edu.tw
Chemical rule-based filtering of MS/MS spectra
Authors: Reiz Beáta , Kertész-Farkas Attila , Pongor Sándor , Myers Michael P.
Published: February 2013

Motivation: Identification of proteins by mass spectrometry–based proteomics requires automated interpretation of peptide tandem mass spectrometry spectra. The effectiveness of peptide identification can be greatly improved by filtering out extraneous noise peaks before the subsequent database searching steps.

Results: Here we present a novel chemical rule-based filtering algorithm, termed CRF, which makes use of the predictable patterns (rules) of collision-induced peptide fragmentation. The algorithm selects peak pairs that obey the common fragmentation rules within plausible limits of mass tolerance as well as peak intensity and produces spectra that can be subsequently submitted to any search engine. CRF increases the positive predictive value and decreases the number of random matches and thus improves performance by 15–20% in terms of peptide annotation using search engines, such as X!Tandem. Importantly, the algorithm also achieves data compression rates of ∼75%.

Availability: The MATLAB source code and a web server are available at http://hydrax.icgeb.trieste.it/CRFilter/

Contact:  myers@icgeb.org

Supplementary information:  Supplementary data are available at Bioinformatics online.
A powerful Bayesian meta-analysis method to integrate multiple gene set enrichment studies
Authors: Chen Min , Zang Miao , Wang Xinlei , Xiao Guanghua
Published: February 2013

Motivation: Much research effort has been devoted to the identification of enriched gene sets for microarray experiments. However, identified gene sets are often found to be inconsistent among independent studies. This is probably owing to the noisy data of microarray experiments coupled with small sample sizes of individual studies. Therefore, combining information from multiple studies is likely to improve the detection of truly enriched gene classes. As more and more data become available, it calls for statistical methods to integrate information from multiple studies, also known as meta-analysis, to improve the power of identifying enriched gene sets.

Results: We propose a Bayesian model that provides a coherent framework for joint modeling of both gene set information and gene expression data from multiple studies, to improve the detection of enriched gene sets by leveraging information from different sources available. One distinct feature of our method is that it directly models the gene expression data, instead of using summary statistics, when synthesizing studies. Besides, the proposed model is flexible and offers an appropriate treatment of between-study heterogeneities that frequently arise in the meta-analysis of microarray experiments. We show that under our Bayesian model, the full posterior conditionals all have known distributions, which greatly facilitates the MCMC computation. Simulation results show that the proposed method can improve the power of gene set enrichment meta-analysis, as opposed to existing methods developed by Shen and Tseng (2010, Bioinformatics, 26, 1316–1323), and it is not sensitive to mild or moderate deviations from the distributional assumption for gene expression data. We illustrate the proposed method through an application of combining eight lung cancer datasets for gene set enrichment analysis, which demonstrates the usefulness of the method.

Availability:  http://qbrc.swmed.edu/software/

Contact:  Min.Chen@UTSouthwestern.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Prediction of contact matrix for protein–protein interaction
Authors: González Alvaro J. , Liao Li , Wu Cathy H.
Published: February 2013

Motivation: Prediction of protein–protein interaction has become an important part of systems biology in reverse engineering the biological networks for better understanding the molecular biology of the cell. Although significant progress has been made in terms of prediction accuracy, most computational methods only predict whether two proteins interact but not their interacting residues—the information that can be very valuable for understanding the interaction mechanisms and designing modulation of the interaction. In this work, we developed a computational method to predict the interacting residue pairs—contact matrix for interacting protein domains, whose rows and columns correspond to the residues in the two interacting domains respectively and whose values (1 or 0) indicate whether the corresponding residues (do or do not) interact.

Results: Our method is based on supervised learning using support vector machines. For each domain involved in a given domain–domain interaction (DDI), an interaction profile hidden Markov model (ipHMM) is first built for the domain family, and then each residue position for a member domain sequence is represented as a 20-dimension vector of Fisher scores, characterizing how similar it is as compared with the family profile at that position. Each element of the contact matrix for a sequence pair is now represented by a feature vector from concatenating the vectors of the two corresponding residues, and the task is to predict the element value (1 or 0) from the feature vector. A support vector machine is trained for a given DDI, using either a consensus contact matrix or contact matrices for individual sequence pairs, and is tested by leave-one-out cross validation. The performance averaged over a set of 115 DDIs collected from the 3 DID database shows significant improvement (sensitivity up to 85%, and specificity up to 85%), as compared with a multiple sequence alignment-based method (sensitivity 57%, and specificity 78%) previously reported in the literature.

Contact:  lliao@cis.udel.edu or wuc@cis.udel.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Protein signature-based estimation of metagenomic abundances including all domains of life and viruses
Authors: Klingenberg Heiner , Aßhauer Kathrin Petra , Lingner Thomas , Meinicke Peter
Published: February 2013

Motivation: Metagenome analysis requires tools that can estimate the taxonomic abundances in anonymous sequence data over the whole range of biological entities. Because there is usually no prior knowledge about the data composition, not only all domains of life but also viruses have to be included in taxonomic profiling. Such a full-range approach, however, is difficult to realize owing to the limited coverage of available reference data. In particular, archaea and viruses are generally not well represented by current genome databases.

Results: We introduce a novel approach to taxonomic profiling of metagenomes that is based on mixture model analysis of protein signatures. Our results on simulated and real data reveal the difficulties of the existing methods when measuring achaeal or viral abundances and show the overall good profiling performance of the protein-based mixture model. As an application example, we provide a large-scale analysis of data from the Human Microbiome Project. This demonstrates the utility of our method as a first instance profiling tool for a fast estimate of the community structure.

Availability:  http://gobics.de/TaxyPro.

Contact:  pmeinic@gwdg.de

Supplementary information:  Supplementary Material is available at Bioinformatics online.
Classification of mislabelled microarrays using robust sparse logistic regression
Authors: Bootkrajang Jakramate , Kabán Ata
Published: February 2013

Motivation: Previous studies reported that labelling errors are not uncommon in microarray datasets. In such cases, the training set may become misleading, and the ability of classifiers to make reliable inferences from the data is compromised. Yet, few methods are currently available in the bioinformatics literature to deal with this problem. The few existing methods focus on data cleansing alone, without reference to classification, and their performance crucially depends on some tuning parameters.

Results: In this article, we develop a new method to detect mislabelled arrays simultaneously with learning a sparse logistic regression classifier. Our method may be seen as a label-noise robust extension of the well-known and successful Bayesian logistic regression classifier. To account for possible mislabelling, we formulate a label-flipping process as part of the classifier. The regularization parameter is automatically set using Bayesian regularization, which not only saves the computation time that cross-validation would take, but also eliminates any unwanted effects of label noise when setting the regularization parameter. Extensive experiments with both synthetic data and real microarray datasets demonstrate that our approach is able to counter the bad effects of labelling errors in terms of predictive performance, it is effective at identifying marker genes and simultaneously it detects mislabelled arrays to high accuracy.

Availability: The code is available from http://cs.bham.ac.uk/∼jxb008.

Contact:  J.Bootkrajang@cs.bham.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
eMZed: an open source framework in Python for rapid and interactive development of LC/MS data analysis workflows
Authors: Kiefer Patrick , Schmitt Uwe , Vorholt Julia A.
Published: February 2013

Summary: The Python-based, open-source eMZed framework was developed for mass spectrometry (MS) users to create tailored workflows for liquid chromatography (LC)/MS data analysis. The goal was to establish a unique framework with comprehensive basic functionalities that are easy to apply and allow for the extension and modification of the framework in a straightforward manner. eMZed supports the iterative development and prototyping of individual evaluation strategies by providing a computing environment and tools for inspecting and modifying underlying LC/MS data. The framework specifically addresses non-expert programmers, as it requires only basic knowledge of Python and relies largely on existing successful open-source software, e.g. OpenMS.

Availability: The framework eMZed and its documentation are freely available at http://emzed.biol.ethz.ch/. eMZed is published under the GPL 3.0 license, and an online discussion group is available at https://groups.google.com/group/emzed-users.

Contact:  kiefer@micro.biol.ethz.ch

Supplementary information:  Supplementary data are available at Bioinformatics online.
Operating Room Fires
Authors: Mehta Sonya P. , Bhananker Sanjay M. , Posner Karen L. , Domino Karen B.
Published: February 2013

Background:

To assess patterns of injury and liability associated with operating room (OR) fires, closed malpractice claims in the American Society of Anesthesiologists Closed Claims Database since 1985 were reviewed.

Methods:

All claims related to fires in the OR were compared with nonfire-related surgical anesthesia claims. An analysis of fire-related claims was performed to identify causative factors.

Results:

There were 103 OR fire claims (1.9% of 5,297 surgical claims). Electrocautery was the ignition source in 90% of fire claims. OR fire claims more frequently involved older outpatients compared with other surgical anesthesia claims (P < 0.01). Payments to patients were more often made in fire claims (P < 0.01), but payment amounts were lower (median $120,166) compared to nonfire surgical claims (median $250,000, P < 0.01). Electrocautery-induced fires (n = 93) increased over time (P < 0.01) to 4.4% claims between 2000 and 2009. Most (85%) electrocautery fires occurred during head, neck, or upper chest procedures (high-fire-risk procedures). Oxygen served as the oxidizer in 95% of electrocautery-induced OR fires (84% with open delivery system). Most electrocautery-induced fires (n = 75, 81%) occurred during monitored anesthesia care. Oxygen was administered via an open delivery system in all high-risk procedures during monitored anesthesia care. In contrast, alcohol-containing prep solutions and volatile compounds were present in only 15% of OR fires during monitored anesthesia care.

Conclusions:

Electrocautery-induced fires during monitored anesthesia care were the most common cause of OR fires claims. Recognition of the fire triad (oxidizer, fuel, and ignition source), particularly the critical role of supplemental oxygen by an open delivery system during use of the electrocautery, is crucial to prevent OR fires. Continuing education and communication among OR personnel along with fire prevention protocols in high-fire-risk procedures may reduce the occurrence of OR fires.