bluuebunny/crossref_metadata_2025 huggingface dataset:
The angulation of the septal structures impacts ventricular imbalance in atrioventricular septal defects with a common atrioventricular junction
Authors: Ahmad Zaheer , Lim Zek , Roman Kevin , Haw Marcus , Anderson Robert H. , Vettukattil Joseph
Published: March 2015

Objective

Multiplanar re-formatting of full-volume three-dimensional echocardiography data sets offers new insights into the morphology of atrioventricular septal defects. We hypothesised that distortion of the alignment between the atrial and ventricular septums results in imbalanced venous return to the ventricles, with consequent proportional ventricular hypoplasia.

Methods

A single observer evaluated 31 patients, with a mean age of 52.09 months, standard deviation of 55, and with a range from 2 to 264 months, with atrioventricular septal defects, of whom 17 were boys. Ventricular imbalance, observed in nine patients, was determined by two-dimensional assessment, and confirmed at surgical inspection in selected cases when a univentricular strategy was undertaken. Offline analysis using multiplanar re-formatting was performed. A line was drawn though the length of the ventricular septum and a second line along the plane of the atrial septum, taking the angle between these two lines as the atrioventricular septal angle. We compared the angle between 22 patients with adequately sized ventricles, and those with ventricular imbalance undergoing univentricular repair.

Results

In the 22 patients undergoing biventricular repair, the septal angle was 0 in 14 patients; the other eight patients having angles ranging from 1 to 36, with a mean angle of 7.4°, and standard deviation of 11.1°.The mean angle in the nine patients with ventricle imbalance was 28.6°, with a standard deviation of 3.04°, and with a range from 26 to 35°. Of those undergoing univentricular repair, two patients died, with angles of 26 and 30°, respectively.

Conclusions

The atrioventricular septal angle derived via multiplanar formatting gives important information regarding the degree of ventricular hypoplasia and imbalance. When this angle is above 25°, patients are likely to have ventricular imbalance requiring univentricular repair.
Southwest's Four Corners Home to Largest U.S. Methane Signal
Authors: Betz Eric
Published: March 2015

Satellite data reveal fossil fuel harvesting operations in the Southwest's Four Corners are generating the country's largest methane signal viewable from space.
Dasgupta, Frankenberg, Perron, Shuster, and Tierney Receive 2014 James B. Macelwane Medals
Authors:   AGU
Published: March 2015

Rajdeep Dasgupta, Christian Frankenberg, J. Taylor Perron, David Lawrence Shuster, and Jessica Erin Tierney were awarded the 2014 James B. Macelwane Medal at the AGU Fall Meeting Honors Ceremony, held on 17 December 2014 in San Francisco, Calif. The medal is for “significant contributions to the geophysical sciences by an outstanding early career scientist.”
Asrar, Hsieh, Mandia, Overland, and Wysession Receive 2014 Ambassador Awards
Authors:   AGU
Published: March 2015

Ghassem R. Asrar, Paul A. Hsieh, Scott Mandia, James E. Overland, and Michael E. Wysession were awarded the 2014 Ambassador Awards at the AGU Fall Meeting Honors Ceremony. The award is in recognition of “outstanding contributions to the following area(s): societal impact, service to the Earth and space community, scientific leadership, and promotion of talent/career pool.”
New Section and Focus Group Honors for 2015
Authors: Paredes Beth
Published: March 2015

AGU Honors Program announces the creation of three new honors and awards.
A sublimation heat engine
Authors: Wells Gary G. , Ledesma-Aguilar Rodrigo , McHale Glen , Sefiane Khellil
Published: March 2015

Heat engines are based on the physical realization of a thermodynamic cycle, most famously the liquid–vapour Rankine cycle used for steam engines. Here we present a sublimation heat engine, which can convert temperature differences into mechanical work via the Leidenfrost effect. Through controlled experiments, quantified by a hydrodynamic model, we show that levitating dry-ice blocks rotate on hot turbine-like surfaces at a rate controlled by the turbine geometry, temperature difference and solid material properties. The rotational motion of the dry-ice loads is converted into electric power by coupling to a magnetic coil system. We extend our concept to liquid loads, generalizing the realization of the new engine to both sublimation and the instantaneous vapourization of liquids. Our results support the feasibility of low-friction in situ energy harvesting from both liquids and ices. Our concept is potentially relevant in challenging situations such as deep drilling, outer space exploration or micro-mechanical manipulation.
RETRACTED ARTICLE: Pre-activation of mesenchymal stem cells with TNF-α, IL-1β and nitric oxide enhances its paracrine effects on radiation-induced intestinal injury
Authors: Chen Hao , Min Xiao-Hui , Wang Qi-Yi , Leung Felix W. , Shi Liu , Zhou Yu , Yu Tao , Wang Chuan-Ming , An Geng , Sha Wei-Hong , Chen Qi-Kui
Published: March 2015

Conditioned medium from mesenchymal stem cells (MSC-CM) may represent a promising alternative to MSCs transplantation, however, the low concentrations of growth factors in non-activated MSC-CM hamper its clinical application. Recent data indicated that the paracrine potential of MSCs could be enhanced by inflammatory factors. Herein, we pre-activated bone-marrow-derived MSCs under radiation-induced inflammatory condition (MSCIEC-6(IR)) and investigated the evidence and mechanism for the differential effects of MSC-CMIEC-6(IR) and non-activated MSC-CM on radiation-induced intestinal injury (RIII). Systemic infusion of MSC-CMIEC-6(IR), but not non-activated MSC-CM, dramatically improved intestinal damage and survival of irradiated rats. Such benefits may involve the modulation of epithelial regeneration and inflammation, as indicated by the regeneration of intestinal epithelial/stem cells, the regulation of the pro-/anti-inflammatory cytokine balance. The mechanism for the superior paracrine efficacy of MSCIEC-6(IR) is related to a higher secretion of regenerative, immunomodulatory and trafficking molecules, including the pivotal factor IGF-1, induced by TNF-α, IL-1β and nitric oxide partially via a heme oxygenase-1 dependent mechanism. Together, our findings suggest that pre-activation of MSCs with TNF-α, IL-1β and nitric oxide enhances its paracine effects on RIII via a heme oxygenase-1 dependent mechanism, which may help us to maximize the paracrine potential of MSCs.
Carbon nanotube diameter control via catalytic Co nanoparticles electrodeposited in porous alumina membranes
Authors: Ke N. J. , Downard A. J. , Golovko V. B.
Published: March 2015

Co nanoparticles electrodeposited into porous alumina membranes catalyse growth of CNTs with diameters smaller than the membrane pores.
Stable organic dyes based on the benzo[1,2-b:4,5-b′]dithiophene donor for efficient dye-sensitized solar cells
Authors: Chen Yi-Fan , Liu Jun-Min , Huang Jian-Feng , Tan Li-Lin , Shen Yong , Xiao Li-Min , Kuang Dai-Bin , Su Cheng-Yong
Published: March 2015

A stable sensitizer incorporating the benzo[1,2-b:4,5-b′]dithiophene donor was used in dye-sensitized solar cells, showing the highest efficiency reported for amine-free organic dyes.
GlycoProfileAssigner: automated structural assignment with error estimation for glycan LC data
Authors: Duffy Fergal J. , Rudd Pauline M.
Published: February 2015

Motivation: Sequencing glycan structures is a difficult problem that requires the use of multiple experimental approaches. One powerful approach to glycan sequencing is the combination of liquid chromatography with sequential exoglycosidase digestions; however, interpreting this can be difficult and time-consuming. To aid this process, we introduce GlycoProfileAssigner, software for automated structural assignment of glycan profile data from liquid chromatography experiments.

Results: GlycoProfileAssigner has been tested on human IgG data, and can retrieve the correct structure in 14 out of 16 peaks tested.

Availability and Implementation: The programme and its source code is available at https://bitbucket.org/fergaljd/glycoprofileassigner

Contact: pauline.rudd@nibrt.ie

Supplementary information:  Supplementary data are available at Bioinformatics online.
An experimental demonstration of the critical depth principle
Authors: Diehl Sebastian , Berger Stella A. , Soissons Quentin , Giling Darren P. , Stibor Herwig
Published: March 2015

Sverdrup's critical depth hypothesis, which has had an almost canonical status in biological oceanography, has recently been challenged as a universal explanation for the formation of oceanic spring blooms, and several alternative hypotheses have been proposed. Arguments pro and contra alternative explanations have so far relied on theoretical considerations and purely observational data. In this paper, we propose that mesocosm experiments with natural plankton communities could make important contributions to the resolution of the issue. We first briefly review the foundations of the critical depth concept and derive an approximate relationship that relates optically scaled critical depth (=“critical optical depth”, i.e. the product of the light attenuation coefficient and the critical depth) to light-dependent phytoplankton production in the mixed surface layer. We describe how this relationship can be used to scale experimental mesocosms such that they reproduce ambient light conditions of natural water columns from the surface down to the critical depth and beyond. We illustrate the power of the approach with a mesocosm study in which we experimentally controlled the onset of the spring bloom of a lake plankton community through the manipulation of optically scaled mixed-layer depth. This experiment may be the first experimental demonstration of the critical depth principle acting on a natural plankton community. Compensation light intensity (=minimum average mixed-layer light intensity required to trigger a bloom of the ambient plankton community) could be constrained to be somewhat above 3.2 moles PAR m−2 d−1, corresponding to a critical optical depth of 10.5. We compare these numbers to estimates from marine systems and end with a discussion of how experiments could be designed to (i) more accurately determine the critical depth in a given system and (ii) resolve among competing hypotheses for vernal bloom onset.
Using age, triage score, and disposition data from emergency department electronic records to improve Influenza-like illness surveillance
Authors: Savard Noémie , Bédard Lucie , Allard Robert , Buckeridge David L
Published: February 2015

Objective Markers of illness severity are increasingly captured in emergency department (ED) electronic systems, but their value for surveillance is not known. We assessed the value of age, triage score, and disposition data from ED electronic records for predicting influenza-related hospitalizations.

Materials and Methods From June 2006 to January 2011, weekly counts of pneumonia and influenza (P&I) hospitalizations from five Montreal hospitals were modeled using negative binomial regression. Over lead times of 0–5 weeks, we assessed the predictive ability of weekly counts of 1) total ED visits, 2) ED visits with influenza-like illness (ILI), and 3) ED visits with ILI stratified by age, triage score, or disposition. Models were adjusted for secular trends, seasonality, and autocorrelation. Model fit was assessed using Akaike information criterion, and predictive accuracy using the mean absolute scaled error (MASE).

Results Predictive accuracy for P&I hospitalizations during non-pandemic years was improved when models included visits from patients ≥65 years old and visits resulting in admission/transfer/death (MASE of 0.64, 95% confidence interval (95% CI) 0.54–0.80) compared to overall ILI visits (0.89, 95% CI 0.69–1.10). During the H1N1 pandemic year, including visits from patients <18 years old, visits with high priority triage scores, or visits resulting in admission/transfer/death resulted in the best model fit.

Discussion Age and disposition data improved model fit and moderately reduced the prediction error for P&I hospitalizations; triage score improved model fit only during the pandemic year.

Conclusion Incorporation of age and severity measures available in ED records can improve ILI surveillance algorithms.
Parameterizing time in electronic health record studies
Authors: Hripcsak George , Albers David J , Perotte Adler
Published: February 2015

Background Fields like nonlinear physics offer methods for analyzing time series, but many methods require that the time series be stationary—no change in properties over time.

Objective Medicine is far from stationary, but the challenge may be able to be ameliorated by reparameterizing time because clinicians tend to measure patients more frequently when they are ill and are more likely to vary.

Methods We compared time parameterizations, measuring variability of rate of change and magnitude of change, and looking for homogeneity of bins of temporal separation between pairs of time points. We studied four common laboratory tests drawn from 25 years of electronic health records on 4 million patients.

Results We found that sequence time—that is, simply counting the number of measurements from some start—produced more stationary time series, better explained the variation in values, and had more homogeneous bins than either traditional clock time or a recently proposed intermediate parameterization. Sequence time produced more accurate predictions in a single Gaussian process model experiment.

Conclusions Of the three parameterizations, sequence time appeared to produce the most stationary series, possibly because clinicians adjust their sampling to the acuity of the patient. Parameterizing by sequence time may be applicable to association and clustering experiments on electronic health record data. A limitation of this study is that laboratory data were derived from only one institution. Sequence time appears to be an important potential parameterization.
The effect of non-Gaussianity on error predictions for the Epoch of Reionization (EoR) 21-cm power spectrum
Authors: Mondal Rajesh , Bharadwaj Somnath , Majumdar Suman , Bera Apurba , Acharyya Ayan
Published: February 2015

The Epoch of Reionization (EoR) 21-cm signal is expected to become increasingly non-Gaussian as reionization proceeds. We have used seminumerical simulations to study how this affects the error predictions for the EoR 21-cm power spectrum. We expect ${\rm SNR}=\sqrt{N_k}$ for a Gaussian random field where Nk is the number of Fourier modes in each k bin. We find that non-Gaussianity is important at high SNR where it imposes an upper limit [SNR]l. For a fixed volume V, it is not possible to achieve SNR > [SNR]l even if Nk is increased. The value of [SNR]l falls as reionization proceeds, dropping from ∼500 at $\bar{x}_{{\rm H\,{\small {i}}}}= 0.8{\rm -}0.9$ to ∼10 at $\bar{x}_{{\rm H\,{\small {i}}}}= 0.15$ for a [150.08 Mpc]3 simulation. We show that it is possible to interpret [SNR]l in terms of the trispectrum, and we expect $[{\rm SNR}]_l \propto \sqrt{V}$ if the volume is increased. For SNR ≪ [SNR]l we find ${\rm SNR}= \sqrt{N_k}/A$ with A ∼ 0.95–1.75, roughly consistent with the Gaussian prediction. We present a fitting formula for the SNR as a function of Nk, with two parameters A and [SNR]l that have to be determined using simulations. Our results are relevant for predicting the sensitivity of different instruments to measure the EoR 21-cm power spectrum, which till date have been largely based on the Gaussian assumption.
Probing the precise location of the radio core in the TeV blazar Mrk 501 with VERA at 43 GHz
Authors: Koyama Shoko , Kino Motoki , Doi Akihiro , Niinuma Kotaro , Hada Kazuhiro , Nagai Hiroshi , Honma Mareki , Akiyama Kazunori , Giroletti Marcello , Giovannini Gabriele , Orienti Monica , Isobe Naoki , Kataoka Jun , Paneque David , Kobayashi Hideyuki , Asada Keiichi
Published: February 2015

We investigate the position of the radio core in a blazar by multi-epoch astrometric observations at 43 GHz. Using the VLBI Exploration of Radio Astrometry (VERA), we have conducted four adjacent observations in 2011 February and another four in 2011 October, and succeeded in measuring the position of the radio core in the TeV blazar Mrk 501 relative to a distant compact quasar NRAO 512. During our observations, we find that (1) there is no positional change within ∼0.2 mas or ∼2.0 pc de-projected with ±1 σ error for the weighted-mean phase-referenced positions of the Mrk 501 core relative to NRAO 512 over four adjacent days, and (2) there is an indication of position change for the 3C 345 core relative to NRAO 512. By applying our results to the standard internal shock model for blazars, we constrain the bulk Lorenz factors of the ejecta.
Favorable Outcome of Hurthle Cell Carcinoma of the Thyroid Treated With Total Thyroidectomy, Radioiodine, and Selective Use of External-Beam Radiotherapy
Authors: Zavitsanos Peter , Amdur Robert J. , Drew Peter A. , Cusi Kenneth , Werning John W. , Morris Christopher G.
Published: February 2015

Objectives:

There is controversy about the prognosis of Hurthle cell carcinoma of the thyroid. The purpose of this project is to report the outcome of a well-defined group of patients treated at a single institution in the modern era.

Methods:

Sixteen patients met the following inclusion criteria: Treatment with curative intent at our institution between January 1, 1997, and December 31, 2010. Primary treatment with total thyroidectomy with or without neck dissection. Age >18 years at the time of thyroidectomy. Confirmation by a pathologist of the diagnosis of a primary Hurthle cell carcinoma of the thyroid based on ≥75% Hurthle cells with extension through the tumor capsule. No areas of poorly differentiated (insular) or undifferentiated (anaplastic) carcinoma. Stage T1-3, NX-1b, M0. All patients received radioiodine immediately after thyroidectomy (remnant ablation, n=14) or as adjuvant for a recurrence (n=2). External-beam radiotherapy to the neck as adjuvant therapy after thyroidectomy was used in 2 patients and after resection of a neck recurrence in 1 patient.

Results:

Five-year actuarial rates with a median 6 years of follow up on surviving patients were as follows:

Overall and cancer-specific survival: 92% (1 death from Hurthle cell carcinoma). Relapse-free survival (no visible tumor and unstimulated thyroglobulin ≤1.0): 65%.

Conclusions:

Our experience suggests that the outcome of Hurthle cell carcinoma of the thyroid is favorable in adults with stage T1-3 NX-1b M0 disease who are managed with total thyroidectomy, radioiodine, and—in selected cases—external-beam radiotherapy. We do not have the ability to compare our results to other management strategies.
Radiotherapy for Brain Metastases From Renal Cell Carcinoma in the Targeted Therapy Era
Authors: Bates James E. , Youn Paul , Peterson Carl R. , Usuki Kenneth Y. , Walter Kevin A. , Okunieff Paul , Milano Michael T.
Published: February 2015

Objectives:

Radiotherapy remains the standard approach for brain metastases from renal cell carcinoma (RCC). Kinase inhibitors (KI) have become standard of care for metastatic RCC. They also increase the radiosensitivity of various tumor types in preclinical models. Data are lacking regarding the effect of KIs among RCC patients undergoing radiotherapy for brain metastases. We report our experience of radiotherapy for brain metastatic RCC in the era of targeted therapy and analyzed effects of concurrent KI therapy.

Methods:

We retrospectively analyzed 25 consecutive patients who received radiotherapy for brain metastases from RCC with whole-brain radiotherapy (WBRT), stereotactic radiosurgery (SRS), or both. Kaplan-Meier rates of overall survival (OS) and brain progression-free survival (BPFS) were calculated and univariate analyses performed.

Results:

Lower diagnosis-specific graded prognostic assessment (DS-GPA) score and multiple intracranial metastases were associated with decreased OS and BPFS on univariate analysis; DS-GPA is also a prognostic factor on multivariate analysis. There was no significant difference in OS or BPFS for SRS compared with WBRT or WBRT and SRS combined. The concurrent use of KI was not associated with any change in OS or BPFS.

Conclusions:

This hypothesis-generating analysis suggests among patients with brain metastatic RCC treated with the most current therapies, those selected to undergo SRS did not experience significantly different survival or control outcomes than those selected to undergo WBRT. From our experience to date, limited in patient numbers, there seems to be neither harm nor benefit in using concurrent KI therapy during radiotherapy. Given that most patients progress systemically, we would recommend considering KI use during brain radiotherapy in these patients.
Postoperative Functional Evaluation of Percutaneous Vertebroplasty Compared With Percutaneous Kyphoplasty for Vertebral Compression Fractures
Authors: Zhao Da-Hang , Chen Ke , Zhu Jiang , Yang Xin , Dong Feng , Wang Wen-Bo
Published: February 2015

Both percutaneous vertebroplasty (PVP) and percutaneous kyphoplasty (PKP) have shown their superiorities in the treatment of vertebral compression fractures (VCFs), yet, few studies have compared their postoperative functional outcomes in patients with VCFs; the authors therefore conducted this meta-analysis to explore the postoperative functional recovery efficacies of PVP and PKP in the treatment of VCFs. Computerized bibliographic databases were applied to identify relevant articles comparing the therapeutic effect of PVP and PKP in the treatment of VCFs. Standardized mean difference and its 95% confidence interval were calculated. Statistical analyses were conducted with the STATA statistical software. Postoperative Oswestry Disability Index investigation outcomes revealed a significant difference between the PVP group and PKP group. Subgroup analysis by the 8 dimensions of the SF-36 health survey presented a statistical significance in general health between the PVP group and PKP group. The application of PKP has the superiority in postoperative functional recovery of VCFs as compared with PVP, especially in efficaciously extending kyphosis angle, improving vertebral body height and decreasing complication rate.
Sulfitobacter

undariae sp. nov., isolated from a brown algae reservoir
Authors: Park Sooyeon , Jung Yong-Taek , Won Sung-Min , Park Ji-Min , Yoon Jung-Hoon
Published: February 2015

A Gram-stain-negative, aerobic, non-spore-forming, non-flagellated and coccoid, ovoid or rod-shaped bacterial strain, W-BA2T, was isolated from a brown algae reservoir in Wando of South Korea. Strain W-BA2T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of approximately 2.0–3.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain W-BA2T fell within the clade comprising the type strains of species of the genus

Sulfitobacter

, clustering coherently with the type strains of

Sulfitobacter donghicola

and

Sulfitobacter guttiformis

showing sequence similarity values of 98.0–98.1 %. Sequence similarities to the type strains of the other species of the genus

Sulfitobacter

were 96.0–97.4 %. Strain W-BA2T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The major polar lipids of strain W-BA2T were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid. The DNA G+C content of strain W-BA2T was 55.0 mol% and its DNA–DNA relatedness values with the type strains of

Sulfitobacter donghicola

,

Sulfitobacter guttiformis

and

Sulfitobacter mediterraneus

were 16–23 %. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain W-BA2T is separated from other species of the genus

Sulfitobacter

. On the basis of the data presented, strain W-BA2T is considered to represent a novel species of the genus

Sulfitobacter

, for which the name Sulfitobacter undariae sp. nov. is proposed. The type strain is W-BA2T ( = KCTC 42200T = NBRC 110523T).
Polaribacter

undariae sp. nov., isolated from a brown alga reservoir
Authors: Park Sooyeon , Park Ji-Min , Jung Yong-Taek , Lee Kang Hyun , Yoon Jung-Hoon
Published: February 2015

A Gram-stain-negative, non-flagellated, non-gliding, aerobic and rod-shaped or ovoid bacterial strain, designated W-BA7T, was isolated from a brown alga reservoir on the South Sea in South Korea. This strain grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of approximately 2.0 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain W-BA7T belonged to the genus

Polaribacter

, clustering coherently with the type strain of

Polaribacter sejongensis,
showing 99.3 % sequence similarity. Strain W-BA7T exhibited 16S rRNA gene sequence similarity of 93.4–98.6 % to the type strains of the other species of the genus

Polaribacter

. Strain W-BA7T contained MK-6 as the predominant menaquinone and iso-C15 : 0 3-OH and anteiso-C15 : 0 as the major fatty acids. The major polar lipids of strain W-BA7T were phosphatidylethanolamine, three unidentified lipids, one unidentified glycolipid, one unidentified aminolipid and one unidentified aminophospholipid. The DNA G+C content of strain W-BA7T was 31.9 mol%, and the mean DNA–DNA relatedness with the type strains of four phylogenetically related species of the genus

Polaribacter

was 12–27 %. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain W-BA7T is separated from recognized species of the genus

Polaribacter

. On the basis of the data presented, strain W-BA7T is considered to represent a novel species of the genus

Polaribacter

, for which the name Polaribacter undariae sp. nov. is proposed. The type strain is W-BA7T ( = KCTC 42175T = CECT 8670T).
Sequence-based model of gap gene regulatory network
Authors: Kozlov Konstantin N , Gursky Vitaly V , Kulakovskiy Ivan V , Samsonova Maria G
Published: February 2015

Background: The detailed analysis of transcriptional regulation is crucially important for understanding biological processes. The gap gene network in Drosophila attracts large interest among researches studying mechanisms of transcriptional regulation. It implements the most upstream regulatory layer of the segmentation gene network. The knowledge of molecular mechanisms involved in gap gene regulation is far less complete than that of genetics of the system. Mathematical modeling goes beyond insights gained by genetics and molecular approaches. It allows us to reconstruct wild-type gene expression patterns in silico, infer underlying regulatory mechanism and prove its sufficiency. Results: We developed a new model that provides a dynamical description of gap gene regulatory systems, using detailed DNA-based information, as well as spatial transcription factor concentration data at varying time points. We showed that this model correctly reproduces gap gene expression patterns in wild type embryos and is able to predict gap expression patterns in Kr mutants and four reporter constructs. We used four-fold cross validation test and fitting to random dataset to validate the model and proof its sufficiency in data description. The identifiability analysis showed that most model parameters are well identifiable. We reconstructed the gap gene network topology and studied the impact of individual transcription factor binding sites on the model output. We measured this impact by calculating the site regulatory weight as a normalized difference between the residual sum of squares error for the set of all annotated sites and the set, from which the site of interest was left out. Conclusions: The reconstructed topology of the gap gene network is in agreement with previous modeling results and data from literature. We showed that 1) the regulatory weights of transcription factor binding sites show very weak correlation with their PWM score; 2) sites with low regulatory weight are important for the model output; 3) functional important sites are not exclusively located in cis-regulatory elements, but are rather dispersed through regulatory region. It is of importance that some of the sites with high functional impact in hb, Kr and kni regulatory regions coincide with strong sites annotated and verified in Dnase I footprint assays. Keywords: transcription; thermodynamics; reaction-diffusion; drosophila
Tandem repeat variation in human and great ape populations and its impact on gene expression divergence
Authors: Sonay Tugce Bilgin , Carvalho Tiago , Robinson Mark , Greminger Maja , Krützen Michael , Comas David , Highnam Gareth , Mittelman David , Sharp Andrew , Marques-Bonet Tomas , Wagner Andreas
Published: February 2015

Tandem repeats (TR) are stretches of DNA that are highly variable in length and mutate rapidly, and thus an important source of genetic variation. This variation is highly informative for population and conservation genetics, and has also been associated with several pathological conditions and with gene expression regulation. However, genome-wide surveys of TR variation have been scarce due to the technical difficulties derived from short-read technology. Here, we explored the genome-wide diversity of TRs in a panel of 83 human and nonhuman great ape genomes, and their impact on gene expression evolution. We found that populations and species diversity patterns can be efficiently captured with short TRs (repeat unit length 1-5 base pairs) with potential applications in conservation genetics. We also examined the potential evolutionary role of TRs in gene expression differences between humans and primates by using 30,275 larger TRs (repeat unit length 2-50 base pairs). About one third of the 13,035 one-to-one orthologous genes contained TRs within 5 kilobase pairs of their transcription start site, and had higher expression divergence than genes without such TRs. The same observation held for genes with repeats in their 3′ untranslated region, in introns, and in exons. Using our polymorphism data for the shortest TRs, we found that genes with polymorphic repeats in their promoters showed higher expression divergence in humans and chimpanzees compared to genes with fixed or no TRs in the promoters. Our findings highlight the potential contribution of TRs to recent human evolution through gene regulation.
Activation of Symbiosis Signaling by Arbuscular Mycorrhizal Fungi in Legumes and Rice
Authors: Sun Jongho , Miller J. Benjamin , Granqvist Emma , Wiley-Kalil Audrey , Gobbato Enrico , Maillet Fabienne , Cottaz Sylvain , Samain Eric , Venkateshwaran Muthusubramanian , Fort Sébastien , Morris Richard J. , Ané Jean-Michel , Dénarié Jean , Oldroyd Giles E.D.
Published: February 2015

Establishment of arbuscular mycorrhizal interactions involves plant recognition of diffusible signals from the fungus, including lipochitooligosaccharides (LCOs) and chitooligosaccharides (COs). Nitrogen-fixing rhizobial bacteria that associate with leguminous plants also signal to their hosts via LCOs, the so-called Nod factors. Here, we have assessed the induction of symbiotic signaling by the arbuscular mycorrhizal (Myc) fungal-produced LCOs and COs in legumes and rice (Oryza sativa). We show that Myc-LCOs and tetra-acetyl chitotetraose (CO4) activate the common symbiosis signaling pathway, with resultant calcium oscillations in root epidermal cells of Medicago truncatula and Lotus japonicus. The nature of the calcium oscillations is similar for LCOs produced by rhizobial bacteria and by mycorrhizal fungi; however, Myc-LCOs activate distinct gene expression. Calcium oscillations were activated in rice atrichoblasts by CO4, but not the Myc-LCOs, whereas a mix of CO4 and Myc-LCOs activated calcium oscillations in rice trichoblasts. In contrast, stimulation of lateral root emergence occurred following treatment with Myc-LCOs, but not CO4, in M. truncatula, whereas both Myc-LCOs and CO4 were active in rice. Our work indicates that legumes and non-legumes differ in their perception of Myc-LCO and CO signals, suggesting that different plant species respond to different components in the mix of signals produced by arbuscular mycorrhizal fungi.
Value management and innovation
Authors: Jay C.I. , Bowen P.A.
Published: March 2015

Purpose

– The purpose of this paper is to provide a holistic and comprehensive historical perspective of the evolution of value management, and to illustrate the impact that value analysis can have on innovation within organizations.

Design/methodology/approach

– A review of published material from credible sources describing the evolution of the value management methodology, and a desktop analysis of 35 documented value management case studies illustrating the role of value management in innovation.

Findings

– Published descriptions of the evolution of value management are incomplete and fragmented. A holistic and comprehensive historical perspective of value management as a value-adding methodology is provided. Mapped against a model for innovation, value management is shown to contribute substantially to innovation within organizations across a variety of contexts. Value management is currently evolving into a powerful approach to strategic planning.

Practical implications

– This paper illustrates the contribution of value management to innovation across a variety of industries and contexts.

Originality/value

– The paper provides a holistic and comprehensive historical perspective of the evolution of value management as a methodology, and demonstrates by mapping selected case studies onto a model of innovation impact, that the method is a powerful and versatile approach to obtaining innovative solutions to organizational problems.
Emergence of carbapenem non‐susceptible multidrug resistant Acinetobacter baumannii strains of clonal complexes 103B and 92B harboring OXA‐type carbapenemases and metallo‐β‐lactamases in Southern India
Authors: Saranathan Rajagopalan , Vasanth Vaidyanathan , Vasanth Thamodharan , Shabareesh Pidathala Raghavendra Venkata , Shashikala P. , Devi Chandrakesan Sheela , Kalaivani Ramakrishnan , Asir Johny , Sudhakar Pagal , Prashanth K
Published: February 2015

The molecular epidemiology and carbapenem resistance mechanisms of clinical isolates of Acinetobacter baumannii obtained from a south Indian tertiary care hospital were investigated by repetitive extragenic palindromic sequence PCR (REP‐PCR) and multi‐locus sequence typing (MLST). Analysis of resistant determinants was achieved by PCR screening for the presence of genes encoding OXA‐carbapenemases, metallo‐β‐lactamases (MBLs) and efflux pumps. REP‐PCR generated around eight clusters of high heterogeneity; of these, two major clusters (I and V) appeared to be clonal in origin. Analysis of representative isolates from different clusters by MLST revealed that most of the isolates belonged to sequence type 103 of CC103B. Second most prevalent ST belonged to clonal complex (CC) 92B which is also referred to as international clone II. Most of the isolates were multi‐drug resistant, being susceptible only to polymyxin‐B and newer quinolones. Class D β‐lactamases such as blaOXA‐51‐like (100%), blaOXA‐23‐like (56.8%) and blaOXA‐24‐like (14.8%) were found to be predominant, followed by a class B β‐lactamase, namely blaIMP‐1 (40.7%); none of the isolates had blaOXA‐58 like, blaNDM‐1 or blaSIM‐1. Genes of efflux‐pump adeABC were predominant, most of isolates being biofilm producers that were PCR‐positive for autoinducer synthase gene (>94%). Carbapenem non‐susceptible isolates were highly diverse and present throughout the hospital irrespective of type of ward or intensive care unit. Although previous reports have documented diverse resistant mechanisms in A. baumannii, production of MBL and OXA‐type of carbapenamases were found to be the predominant mechanism(s) of carbapenem resistance identified in strains isolated from Southern India.
Parasitoid wasps indirectly suppress seed production by stimulating consumption rates of their seed‐feeding hosts
Authors: Xi Xinqiang , Eisenhauer Nico , Sun Shucun
Published: February 2015

In parasitoid–herbivore–plant food chains, parasitoids may be simultaneously linked with both herbivore hosts and plants, as occurs when herbivores attacked by parasitoids continue to consume plants although they are destined to die. This peculiar property may cause parasitoids to confer a differential trophic cascading effect on plants than that known for typical predators.

We hypothesized that larval koinobiont parasitoids would confer an immediate negative effect on plant seed production by stimulating consumption of their seed‐predator hosts. We tested this hypothesis in an alpine parasitic food chain of plant seeds, pre‐dispersal seed predators (tephritid fly larvae) and koinobiont parasitoids using field observations, a field experiment and a microcosm study.

We first compared observed seed production in (i) non‐infected capitula, (ii) capitula infected only by seed predators (tephritid flies) and (iii) capitula infected by both seed predators and their parasitoids in five Asteraceae species. Consistent with our hypothesis, seed loss in the capitula with both seed predators and parasitoids was significantly greater than in the capitula infested only by seed predators.

This effect was replicated in a controlled field experiment focusing on the most common parasitoid–seed predator–plant interaction chain in our system, in which confounding factors (e.g. density and phenology) were excluded. Here, we show that parasitoids indirectly decreased plant seed production by changing the behaviour of seed predators.

In a microcosm study, we show that larval parasitoids significantly extended the growth period and increased the terminal size of their host tephritid maggots. Thus, parasitoids suppressed plant seed production by stimulating the growth and consumption of the fly maggots.

In contrast to the typical predator‐induced trophic cascade, we highlight the significance of parasitoids indirectly decreasing plant fitness by stimulating consumption by seed predators. Future studies on trophic interactions should consider the net effect of both increased consumption by seed predators and their death after development of parasitoids.
Expanding the conceptual toolkit of organ gifting
Authors: M. Shaw Rhonda
Published: February 2015

In jurisdictions where the sale of body tissue and organs is illegal, organ transplantation is often spoken of as a gift of life. In the social sciences and bioethics this concept has been subject to critique over the course of the last two decades for failing to reflect the complexities of organ and tissue exchange. I suggest that a new ethical model of organ donation and transplantation is needed to capture the range of experiences in this domain. The proposed model is both analytical and empirically oriented, and draws on research findings linking a series of qualitative sociological studies undertaken in New Zealand between 2007 and 2013. The studies were based on document analysis, field notes and 127 semi‐structured in‐depth interviews with people from different cultural and constituent groups directly involved in organ transfer processes. The aim of the article is to contribute to sociological knowledge about organ exchange and to expand the conceptual toolkit of organ donation to include the unconditional gift, the gift relation, gift exchange, body project, and body work. The rationale for the proposed model is to provide an explanatory framework for organ donors and transplant recipients and to assist the development of ethical guidelines and health policy discourse.
Hydrocarbon Generation and Expulsion of the Upper Triassic T3x5 Source Rocks in the Western Sichuan Depression: Assessment for Unconventional Natural Gas
Authors: Yingchun GUO , Yan SONG , Xiongqi PANG , Youwei WANG , Kerning YANG , Boyuan LI
Published: March 2015

Tight‐sand gas in the Jurassic and shale gas within the fifth member of Xujiahe Formation (T3x5) in the Western Sichuan Basin (WSD) are currently regarded as the most prolific emerging unconventional gas plays in China. This study conducted a conventional evaluation of T3x5 source rocks in the WSD, and investigated their hydrocarbon generation and expulsion characteristics, including intensity, efficiency and amount. The results show that, the T3x5 source rocks are thick (generally >200 m), and have a high total organic content (TOC), ranging from 2.5 to 4.5 wt%. It is thus indivative of a great hydrocarbon generation potential when they underwent high thermal evolution (Ro>1.2%) in the area. In addition, an improved method of hydrocarbon generation potential is applied, indicating that the source rocks reached a hydrocarbon expulsion threshold with vitrinite reflectance (Ro) reaching 1.06%, and that the comprehensive hydrocarbon expulsion efficiency is about 60%. The amount of hydrocarbon generation and expulsion from T3x5 source rocks is 3.14×1010 t and 1.86×1010 t, respectively, with a residual amount of 1.28×1010 t within them. Continuous‐type tight‐sand gas is predicted to have developed in the Jurassic in the Chengdu Sag of the WSD because of the good source‐reservoir configuration; the Jurassic sandstone reservoirs are tight, and the gas expelled from the T3x5 source rocks migrates for very short distances vertically and horizontally. The amount of gas accumulation in the Jurassic reservoirs derived from T3x5 source rocks is up to 9.3×108 t. Geological resources of shale gas are up to 1.05×1010 t. Small differences between the amounts calculated by the volumetric method and those obtained by hydrocarbon generation potential method may be due to other gas accumulations present within interbedded sands associated with gas shales.
Human leukocyte antigen (HLA)‐G gene polymorphism in patients with non‐small cell lung cancer
Authors: Kowal Aneta , Wiśniewski Andrzej , Kuśnierczyk Piotr , Jankowska Renata
Published: February 2015

Background

Lung cancer represents the highest morbidity and mortality caused by neoplasms in the world; therefore researchers continue to search for new tools to diagnose and treat the disease. The aim of the study was to establish the role of single nucleotide polymorphisms (SNP) in the promoter region of the human leukocyte antigen (HLA)‐G gene in patients with non‐small cell lung cancer.

Methods

We enrolled 143 patients with a mean age of 63 years, diagnosed with non‐small cell lung cancer, in the study. Adenocarcinomas made up 33% of the cases. Patients in stage III or IV of the tumor node metastasis staging system made up 59%. Two polymorphic sites in the promoter region of the HLA‐G gene were genotyped (−725C>G>T and −716T>G).

Results

All genotyped SNPs were in Hardy‐Weinberg equilibrium. No proof of a relationship between genotype −725C>G>T or −716T>G and the risk of lung cancer compared with healthy volunteers from the literature was found. We also found no correlation between the two SNPs and survival time, histological type of cancer, T stage, the presence of remote metastases or performance status according to the Eastern Cooperative Oncology Group (ECOG) scale. The only association we found was genotype −725C>G>T and the degree of lymph node metastases (N stage).

Conclusions

SNPs of the promoter of the HLA‐G gene may have an impact on the development of lymph node metastases. In the study we did not prove a relationship between the examined SNPs and the course of the disease because of the small patient groups studied.
One‐year outcome after prehospital intubation
Authors: PAKKANEN T. , VIRKKUNEN I. , SILFVAST T. , RANDELL T. , HUHTALA H. , YLI‐HANKALA A.
Published: February 2015

Background

The aim of physician staffed emergency medical services (EMS) is to supplement other EMS units in the care of prehospital patients. The need for advanced airway management in critical prehospital patients can be considered as one indicator of the severity of the patient's condition. Our primary aim was to study the long‐term outcome of critically ill patients (excluding cardiac arrest) who were intubated by EMS physicians in the prehospital setting.

Methods

Data of 845 patients, whose airways were secured by the EMS physicians during a 5‐year (2007–2011) period, were retrospectively evaluated. After exclusions, the outcome of 483 patients (8.9% of all patients treated by EMS) was studied. Evaluation was based on hospital patient records 1 year after the incident. For assessment of neurological outcome, a modified Glasgow Outcome Score (GOS) was used. Time and cause of death were recorded.

Results

55.3% of the study patients had a good neurological recovery (GOS 4–5) with independent life 1 year after the event. The overall 1‐year mortality (GOS 1) was 35.0%. Poor neurological outcome (GOS 2–3) was found in 9.7% of the patients. Patients with intoxication or convulsions survived best, while those with suspected intracranial pathology had the worst prognosis. Of all survivors, 85% recovered well.

Conclusion

The majority of the study patients had a favourable neurological recovery with independent life at 1 year after the incident. More than 80% of all deaths occurred within 30 days of the incident.
Arterial pressure during cardiopulmonary bypass is not associated with acute kidney injury
Authors: KANDLER K. , JENSEN M. E. , NILSSON J. C. , MØLLER C. H. , STEINBRÜCHEL D. A.
Published: February 2015

Background

Acute kidney injury (AKI) after cardiac surgery is common and is associated with increased mortality. We wanted to investigate if the arterial pressure or the use of norepinephrine during cardiopulmonary bypass were associated with AKI.

Methods

A retrospective analysis of patients who underwent coronary artery bypass grafting with or without concomitant procedures was conducted. AKI was defined using the RIFLE criteria. Data on arterial pressure and use of norepinephrine during cardiopulmonary bypass were entered in a binary logistic regression model to control for possible perioperative confounders.

Results

A total of 623 patients were included. Mean age was 68.3 ± 9.7 years and 81% were males. AKI was observed in 198 patients (32%). Mean arterial pressure was 47 ± 6 mmHg and 45 ± 6 mmHg (P = 0.008) in the AKI and no‐AKI group, respectively. Norepinephrine was used more frequently and in higher amounts, during cardiopulmonary bypass, in patients who developed AKI. These differences in arterial pressures and use of norepinephrine between the groups were not found to be significant when entered in the binary logistic regression model.

Conclusion

No independent relationship between arterial pressure or use of norepinephrine and AKI was found.