bluuebunny/crossref_metadata_2025 huggingface dataset:
Gene expression inference with deep learning
Authors: Chen Yifei , Li Yi , Narayan Rajiv , Subramanian Aravind , Xie Xiaohui
Published: December 2015

Motivation

Large-scale gene expression profiling has been widely used to characterize cellular states in response to various disease conditions, genetic perturbations, etc. Although the cost of whole-genome expression profiles has been dropping steadily, generating a compendium of expression profiling over thousands of samples is still very expensive. Recognizing that gene expressions are often highly correlated, researchers from the NIH LINCS program have developed a cost-effective strategy of profiling only ῀1,000 carefully selected landmark genes and relying on computational methods to infer the expression of remaining target genes. However, the computational approach adopted by the LINCS program is currently based on linear regression, limiting its accuracy since it does not capture complex nonlinear relationship between expression of genes.

Results

We present a deep learning method (abbreviated as D-GEX) to infer the expression of target genes from the expression of landmark genes. We used the microarray-based GEO dataset, consisting of 111K expression profiles, to train our model and compare its performance to those from other methods. In terms of mean absolute error averaged across all genes, deep learning significantly outperforms linear regression with 15.33% relative improvement. A gene-wise comparative analysis shows that deep learning achieves lower error than linear regression in 99.97% of the target genes. We also tested the performance of our learned model on an independent RNA-Seq-based GTEx dataset, which consists of 2,921 expression profiles. Deep learning still outperforms linear regression with 6.57% relative improvement, and achieves lower error in 81.31% of the target genes.

Availability

D-GEX is available athttps://github.com/uci-cbcl/D-GEX.

Contact

xhx@ics.uci.edu
Characterizing the Adult and Larval Transcriptome of the Multicolored Asian Lady Beetle, Harmonia axyridis
Authors: Havens Lindsay A , MacManes Matthew D
Published: December 2015

The reasons for the evolution and maintenance of striking visual phenotypes are as widespread as the species that display these phenotypes. While study systems such as Heliconius and Dendrobatidae have been well characterized and provide critical information about the evolution of these traits, a breadth of new study systems, in which the phenotype of interest can be easily manipulated and quantified, are essential for gaining a more general understanding of these specific evolutionary processes. One such model is the multicolored Asian lady beetle, Harmonia axyridis, which displays significant elytral spot and color polymorphism. Using transcriptome data from two life stages, adult and larva, we characterize the transcriptome, thereby laying a foundation for further analysis and identification of the genes responsible for the continual maintenance of spot variation in H. axyridis.
Architecting a distributed bioinformatics platform with iRODS and iPlant Agave API
Authors: Wang Liya , Van Buren Peter , Ware Doreen
Published: December 2015

Over the past few years, cloud-based platforms have been proposed to address storage, management, and computation of large-scale data, especially in the field of genomics. However, for collaboration efforts involving multiple institutes, data transfer and management, interoperability and standardization among different platforms have imposed new challenges. This paper proposes a distributed bioinformatics platform that can leverage local clusters with remote computational clusters for genomic analysis using the unified bioinformatics workflow. The platform is built with a data server configured with iRODS, a computation cluster authenticated with iPlant Agave system, and web server to interact with the platform. A Genome-Wide Association Study workflow is integrated to validate the feasibility of the proposed approach.
Reinstatement of an extinguished fear conditioned response in infant rats
Authors: Revillo Damian A. , Trebucq Gastón , Paglini Maria G. , Arias Carlos
Published: December 2015

Although it is currently accepted that the extinction effect reflects new context-dependent learning, this is not so clear during infancy, because some studies did not find recovery of the extinguished conditioned response (CR) in rodents during this ontogenetic stage. However, recent studies have shown the return of an extinguished CR in infant rats. The present study analyzes the possibility of recovering an extinguished CR with a reinstatement procedure in a fear conditioning paradigm, on PD17 (Experiments 1–4) and on PD24 (Experiment 5), while exploring the role of the olfactory content of the context upon the reinstatement effect during the preweanling period. Preweanling rats expressed a previously extinguished CR after a single experience with an unsignaled US. Furthermore, this result was only found when subjects were trained and tested in contexts that included an explicit odor, but not in standard experimental cages. Finally, Experiment 5 demonstrated the reinstatement effect on PD24 in a standard context. These results support the notion that extinction during infancy has the same characteristics as those described for extinction that occurs in adulthood. Instead of postulating a different mechanism for extinction during infancy, we propose that it may be more accurate to view the problem in terms of the variables that may differentially modulate the extinction effect according to the stages of ontogeny.
Synapsin is required to “boost” memory strength for highly salient events
Authors: Kleber Jörg , Chen Yi-Chun , Michels Birgit , Saumweber Timo , Schleyer Michael , Kähne Thilo , Buchner Erich , Gerber Bertram
Published: December 2015

Synapsin is an evolutionarily conserved presynaptic phosphoprotein. It is encoded by only one gene in the Drosophila genome and is expressed throughout the nervous system. It regulates the balance between reserve and releasable vesicles, is required to maintain transmission upon heavy demand, and is essential for proper memory function at the behavioral level. Task-relevant sensorimotor functions, however, remain intact in the absence of Synapsin. Using an odor–sugar reward associative learning paradigm in larval Drosophila, we show that memory scores in mutants lacking Synapsin (syn97) are lower than in wild-type animals only when more salient, higher concentrations of odor or of the sugar reward are used. Furthermore, we show that Synapsin is selectively required for larval short-term memory. Thus, without Synapsin Drosophila larvae can learn and remember, but Synapsin is required to form memories that match in strength to event salience—in particular to a high saliency of odors, of rewards, or the salient recency of an event. We further show that the residual memory scores upon a lack of Synapsin are not further decreased by an additional lack of the Sap47 protein. In combination with mass spectrometry data showing an up-regulated phosphorylation of Synapsin in the larval nervous system upon a lack of Sap47, this is suggestive of a functional interdependence of Synapsin and Sap47.
Possible overlapping time frames of acquisition and consolidation phases in object memory processes: a pharmacological approach
Authors: Akkerman Sven , Blokland Arjan , Prickaerts Jos
Published: December 2015

In previous studies, we have shown that acetylcholinesterase inhibitors and phosphodiesterase inhibitors (PDE-Is) are able to improve object memory by enhancing acquisition processes. On the other hand, only PDE-Is improve consolidation processes. Here we show that the cholinesterase inhibitor donepezil also improves memory performance when administered within 2 min after the acquisition trial. Likewise, both PDE5-I and PDE4-I reversed the scopolamine deficit model when administered within 2 min after the learning trial. PDE5-I was effective up to 45 min after the acquisition trial and PDE4-I was effective when administered between 3 and 5.5 h after the acquisition trial. Taken together, our study suggests that acetylcholine, cGMP, and cAMP are all involved in acquisition processes and that cGMP and cAMP are also involved in early and late consolidation processes, respectively. Most important, these pharmacological studies suggest that acquisition processes continue for some time after the learning trial where they share a short common time frame with early consolidation processes. Additional brain concentration measurements of the drugs suggest that these acquisition processes can continue up to 4–6 min after learning.
BL2D-SMC, the supramolecular crystallography beamline at the Pohang Light Source II, Korea
Authors: Shin Jong Won , Eom Kisu , Moon Dohyun
Published: December 2015

BL2D-SMC at the Pohang Light Source II is a supramolecular crystallography beamline based on a bending magnet. The beamline delivers high-flux tunable X-rays with energies from 8.3 to 20.7 keV and a 100 µm (horizontal) × 85 µm (vertical) full width at half-maximum focal spot. Experiments involving variable temperature, photo-excitation and gas sorption are supported by ancillary equipment and software in the beamline. The design of the beamline, its role and the main components are described.
Imaging lung tissue oscillations using high-speed X-ray velocimetry
Authors: Thurgood Jordan , Dubsky Stephen , Uesugi Kentaro , Curtis Michael , Samarage Chaminda R. , Thompson Bruce , Zosky Graeme , Fouras Andreas
Published: December 2015

This work utilized synchrotron imaging to achieve a regional assessment of the lung's response to imparted oscillations. The forced oscillation technique is increasingly being used in clinical and research settings for the measurement of lung function. During the forced oscillation technique, pressure oscillations are imparted to the lungsviathe subjects' airway opening and the response is measured. This provides information about the mechanical properties of the airways and lung tissue. The quality of measurements is dependent upon the input signal penetrating uniformly throughout the lung. However, the penetration of these signals is not well understood. The development and use of a novel image-processing technique in conjunction with synchrotron-based imaging was able to regionally assess the lungs' response to input pressure oscillation signals in anaesthetized mice. The imaging-based technique was able to quantify both the power and distribution of lung tissue oscillations during forced oscillations of the lungs. It was observed that under forced oscillations the apices had limited lung tissue expansion relative to the base. This technique could be used to optimize input signals used for the forced oscillation technique or potentially as a diagnostic tool itself.
Crystal structure of the co-crystal butylparaben–isonicotinamide (1/1)
Authors: Bhardwaj Rajni M. , Yang Huaiyu , Florence Alastair J.
Published: December 2015

The title 1:1 co-crystal, C11H14O3·C6H6N2O [systematic name: butyl 4-hydroxybenzoate–isonicotinamide (1/1)], crystallizes with one molecule of butylparaben (BPN) and one molecule of isonicotinamide (ISN) in the asymmetric unit. In the crystal, BPN and ISN molecules form hydrogen-bonded (O—H...N and N—H...O) dimers of paired BPN and ISN molecules. These dimers are further connected to each otherviaN—H...O=C hydrogen bonds, creating ribbons in [011] which further stack along theaaxis to form a layered structure with short C...C contacts of 3.285 (3) Å. Packing interactions within the crystal structure were assessed using PIXEL calculations.
Crystal structure of 2-(5-methoxy-1-benzofuran-3-yl)acetic acid
Authors: Gowda Ramakrishna , Gowda K. V. Arjuna , Reddy M. Keshava , Basanagouda Mahantesha
Published: December 2015

The benzofuran residue in the title compound, C11H10O4, is essentially planar (the r.m.s. deviation for the nine non-H atoms = 0.011 Å). While the methoxy group is coplanar with the fused ring system [C—C—O—C torsion angle = 3.1 (3)°], the acetic acid residue occupies a position almost prime [C—C—C—C = 77.0 (2)°]. In the crystal, centrosymmetrically related molecules are linked by O—H...O hydrogen bonds to form eight-membered {...HOCO}2synthons. The dimeric aggregates assemble into supramolecular layers in theabplaneviabenzene-C—H...O(ring) interactions.
Crystal structure of 4-methylsulfanyl-2-(2H-tetrazol-2-yl)pyrimidine
Authors: Thomann Andreas , Huch Volker , Hartmann Rolf W.
Published: December 2015

The title compound, C6H6N6S, crystallized with two independent molecules (AandB) in the asymmetric unit. The conformation of the two molecules differs slightly. While the tetrazole ring is inclined to the pyrimidene ring by 5.48 (7) and 4.24 (7)° in moleculesAandB, respectively, the N—C—S—C torsion angles of the thiomethyl groups differ byca180°. In the crystal, theAandBmolecules are linkedviaa C—H...N hydrogen bond. They stack along theb-axis direction forming columns within which there are weak π–π interactions present [shortest inter-centroid distance = 3.6933 (13) Å].
Crystal structure of tris(trans-1,2-diaminocyclohexane-κ2N,N′)cobalt(III) trichloride monohydrate
Authors: Gallagher Megan K. , Oliver Allen G. , Lappin A. Graham
Published: December 2015

The synthesis of the title hydrated complex salt, [Co(C6H14N2)3]Cl3·H2O, from racemictrans-1,2-diaminocyclohexane and [CoCl(NH3)5]Cl2and its structural characterization are presented in this paper. The product was synthesized in the interest of understanding the hydrogen-bonding patterns of coordination complexes. Previous characterizations of the product in theI-42dspace group have not yielded coordinates; thus, this paper provides the first coordinates for this complex in this space group. The octahedrally coordinated cation adopts twofold rotation symmetry, with outer-sphere chloride counter-ions and solvent water molecules forming a hydrogen-bonded network with amine H atoms.
Crystal structure ofN-{4-[(6-chloropyridin-3-yl)methoxy]phenyl}-2,6-difluorobenzamide
Authors: Liang Ying , Shi Li-Qiao , Yang Zi-Wen
Published: December 2015

In the title compound, C19H13ClF2N2O2, the conformation of the N—H bond in the amide segment isantito the C=O bond. The molecule is not planar, with dihedral angles between the central benzene ring and the outer benzene and pyridyl rings of 73.35 (7) and 81.26 (6)°, respectively. A weak intramolecular C—H...O hydrogen bond occurs. In the crystal, N—H...N, C—H...O and C—H...F hydrogen bonds lead to the formation of dimers. The N—H...N inversion dimers are linked by π–π contacts between adjacent pyridine rings [centroid–centroid = 3.8541 (12) Å] and C—H...π interactions. These contacts combine to stack the molecules along theaaxis.
Crystal structure of (Z)-7,8-dichloro-4-(2-oxopropylidene)-4,5-dihydro-1H-1,5-benzodiazepin-2(3H)-one
Authors: Lahmidi Sanae , Essaghouani Abdelhanine , Essassi El Mokhtar , Saadi Mohamed , El Ammari Lahcen
Published: December 2015

In the title compound, C12H10Cl2N2O2, the seven-membered heterocycle displays a half-chair conformation. The mean plane through the oxopropylidene group makes a dihedral angle of 36.44 (9)° with the fused benzene ring. An intramolecular N—H...O hydrogen bond to close anS(6) loop is noted. An important feature of the molecular packing are N—H...O hydrogen bonds that lead to the formation of helical supramolecular chains along thebaxis.
Crystal structure of a new hybrid compound based on an iodidoplumbate(II) anionic motif
Authors: Mokhnache Oualid , Boughzala Habib
Published: December 2015

Crystals of the one-dimensional organic–inorganic lead iodide-based compoundcatena-poly[bis(piperazine-1,4-diium) [[tetraiodidoplumbate(II)]-μ-iodido] iodide monohydrate], (C4N2H12)2[PbI5]I·H2O, were obtained by slow evaporation at room temperature of a solution containing lead iodide and piperazine in a 1:2 molar ratio. Inorganic lead iodide chains, organic (C4N2H12)2+cations, water molecules of crystallization and isolated I−anions are connected through N—H...·I, N—H...OWand OW—H...I hydrogen-bond interactions. Zigzag chains of corner-sharing [PbI6]4−octahedra with composition [PbI4/1I2/2]3−running parallel to theaaxis are present in the structure packing.
Crystal structure of 2-bromo-3-dimethylamino-N,N,N′,N′,4-pentamethyl-4-(trimethylsilyloxy)pent-2-eneamidinium bromide
Authors: Tiritiris Ioannis , Kress Ralf , Kantlehner Willi
Published: December 2015

The reaction of the orthoamide 1,1,1-tris(dimethylamino)-4-methyl-4-(trimethylsilyloxy)pent-2-yne with bromine in benzene, yields the title salt, C15H33BrN3OSi+·Br−. The C—N bond lengths in the amidinium unit are 1.319 (6) and 1.333 (6) Å, indicating double-bond character, pointing towards charge delocalization within the NCN plane. The C—Br bond length of 1.926 (5) Å is characteristic for a C—Br single bond. Additionally, there is a bromine–bromine interaction [3.229 (3) Å] present involving the anion and cation. In the crystal, weak C—H...Br interactions between the methyl H atoms of the cation and the bromide ions are present.
Crystal structure of (1Z,2E)-cinnamaldehyde oxime
Authors: Bugenhagen Bernhard , Al Soom Nuha , Al Jasem Yosef , Thiemann Thies
Published: December 2015

The title compound, C9H9NO, crystallized with two independent molecules (AandB) in the asymmetric unit. The conformation of the two molecules differs slightly with the phenyl ring in moleculeA, forming a dihedral angle of 15.38 (12)° with the oxime group (O—N=C), compared to the corresponding angle of 26.29 (11)° in moleculeB. In the crystal, theAandBmolecules are linked head-to-head by O—H...N hydrogen bonds, forming –A–B–A–B– zigzag chains along [010]. Within the chains and between neighbouring chains there are C—H...π interactions present, forming a three-dimensional structure.
White box, black box and self-organization
Authors: Kasianiuk Krzysztof
Published: December 2015

Purpose

– The purpose of this paper is to present two system identification models – “white box” and “black box” – as useful tools that help understand self-organization processes within and outside the organizations facilitated by leaders. Every leader is presented as a “systems designer” who plays a fundamental role in the process of self-organization, both within and outside the organization under study.

Design/methodology/approach

– First, “white box” and “black box” system identification models are presented as a basis for an integrated model of the “system” and its “environment.” Next, the ideas of “closed” and “open” systems as the prerequisites of self-organization processes are described. Finally, two basic leadership tactics as well as their combination are characterized and discussed.

Findings

– Two system identification models give a complementary view to the reality, as they combine both reductionist and holistic perspectives. The argument presented in the paper shows that there is a far reaching complementarity of the two system identification models.

Practical implications

– Since leaders need to comprehend complex adaptive processes taking place in the organizations and in their environment, they search for the best strategy to approach this task. The tactics presented in the paper could serve as a cognitive tools that help approach the reality leaders are immersed in.

Originality/value

– The paper utilizes two categories that are well recognized in systems theory and cybernetics, combines them with the idea of self-organization and puts it all in the context of leadership. It provides an integrated, yet relatively simple cognitive scheme that may be of theoretical and practical use.
An optimization model of the acceptable consensus and its economic significance
Authors: Gong Zaiwu , Xu Xiaoxia , Forrest Jeffrey , Yang Yingjie
Published: December 2015

Purpose

– The purpose of this paper is to construct an optimal resource reallocation model of the limited resource by a moderator for reaching the greatest consensus, and show how to reallocate the limited resources by using optimization methodology once the consensus opinion is reached. Moreover, this paper also devotes to theoretically exploring when or what is the condition that the group decision-making (GDM) system is stable; and when new opinions enter into the GDM, how the level of consensus changes.

Design/methodology/approach

– By minimizing the differences between the individuals’ opinions and the collective consensus opinion, this paper constructs a consensus optimization model and shows that the objective weights of the individuals are actually the optimal solution to this model.

Findings

– If all individual deviations of the decision makers (DMs) from the consensus balance each other out, the information entropy theorem shows this GDM is most stable, and economically each individual DM gets the same optimal unit of compensation. Once the consensus opinion is determined and each individual opinion of the DMs is under an acceptable consensus level, the consensus is still acceptable even if additional DMs are added, and the moderator’s cost is still no more than a fixed upper limitation.

Originality/value

– The optimization model based on acceptable consensus is constructed in this paper, and its economic significance, including the theoretical and practical significance, is emphatically analyzed: it is shown that the weight information of the optimization model carries important economic significance. Besides, some properties of the proposed model are discussed by analyzing its particular solutions: the stability of the consensus system is explored by introducing information entropy theory and variance distribution; in addition, the effect of adding new DMs on the stability of the acceptable consensus system is discussed by analyzing the convergence of consensus level: it is also built up the condition that once the consensus opinion is determined, the consensus degree will not decrease even when additional DMs are added to the GDM.
The interaction matrix: from individual goal-setting to the four modes of coexistence
Authors: Nechansky Helmut
Published: December 2015

Purpose

– The purpose of this paper is to show how individual acts of goal-setting of two persons or systems A and B determine, which modes of coexistence become possible in an interaction of the two.

Design/methodology/approach

– Some person or system A can approach another person or system B with an inclination to realize one of four goal-setting processes: first, A sets goals for B; second, A sets no own goals; third, A pursues own goals alone; and fourth, A and B develop mutual goals. And an interaction of A and B can lead to just four modes of coexistence: first, conflict – A and B fight; second, hierarchy – A submits to B; third, independence in niches – A and B do not interact; and fourth, cooperation – A and B work together.

Findings

– Placing the inclinations of A and B to realize one of the four goal-setting processes in a 4×4 matrix leads to the interaction matrix. It shows that individual goal-setting processes predetermine and limit the available modes of coexistence, i.e. cause certain patterns of interactions.

Practical implications

– The interaction matrix can be applied to all interactions between persons, groups and social units generally.

Originality/value

– The paper introduces a theoretical framework covering all options of goal-orientated behavior. It explains the interrelation between individual goal-setting of persons and systems and the resulting behavioral options in interactions. It is applicable to all behavioral sciences.
2-tuple linguistic Muirhead mean operators for multiple attribute group decision making and its application to supplier selection
Authors: Qin Jindong , Liu Xinwang
Published: December 2015

Purpose

– The purpose of this paper is to develop some 2-tuple linguistic aggregation operators based on Muirhead mean (MM), which is combined with multiple attribute group decision making (MAGDM) and applied the proposed MAGDM model for supplier selection under 2-tuple linguistic environment.

Design/methodology/approach

– The supplier selection problem can be regarded as a typical MAGDM problem, in which the decision information should be aggregated. In this paper, the authors investigate the MAGDM problems with 2-tuple linguistic information based on traditional MM operator. The MM operator is a well-known mean type aggregation operator, which has some particular advantages for aggregating multi-dimension arguments. The prominent characteristic of the MM operator is that it can capture the whole interrelationship among the multi-input arguments. Motivated by this idea, in this paper, the authors develop the 2-tuple linguistic Muirhead mean (2TLMM) operator and the 2-tuple linguistic dual Muirhead mean (2TLDMM) operator for aggregating the 2-tuple linguistic information, respectively. Some desirable properties and special cases are discussed in detail. Based on which, two approaches to deal with MAGDM problems under 2-tuple linguistic information environment are developed. Finally, a numerical example concerns the supplier selection problem is provided to illustrate the effectiveness and feasibility of the proposed methods.

Findings

– The results show that the proposed can solve the MAGDM problems within the context of 2-tuple linguistic information, in which the attributes are existing interaction phenomenon. Some 2-tuple aggregation operators based on MM have been developed. A case study of supplier selection is provided to illustrate the effectiveness and feasibility of the proposed methods. The results show that the proposed methods are useful to aggregate the linguistic decision information in which the attributes are not independent so as to select the most suitable supplier.

Practical implications

– The proposed methods can solve the 2-tuple linguistic MAGDM problem, in which the interactions exist among the attributes. Therefore, it can be used to supplier selection problems and other similar management decision problems.

Originality/value

– The paper develop some 2-tuple aggregation operators based on MM, and further present two methods based on the proposed operators for solving MAGDM problems. It is useful to deal with multiple attribute interaction decision-making problems and suitable to solve a variety of management decision-making applications.
The Burden of Major Adverse Cardiac Events and Antiplatelet Prevention in Patients with Coronary or Peripheral Arterial Disease
Authors: Khoury Hanane , Lavoie Louis , Welner Sharon , Folkerts Kerstin
Published: December 2015

Background

Patients with a history of a cardiovascular (CV) disease are at high risk of suffering secondary major adverse cardiac events (MACE), namely death, nonfatal myocardial infarction (MI), stroke, symptomatic pulmonary embolism, CV and all‐cause hospitalization, and bleeding.

Methods

A comprehensive review of the literature was conducted to review the epidemiology and burden of MACE in patients with coronary or peripheral arterial disease (CAD or PAD) in Europe and other ex‐US regions. Relevant articles published between 2003 and 2013 were retrieved from PubMed and other sites.

Results

MACE incidence and prevalence in patients with CAD or PAD were increased by at least 1.4‐fold compared with matched controls with no CV disease. In patients with CAD, MACE mostly occurred within 30 days of primary percutaneous coronary intervention; incidence decreased with time. Increased oxidative stress in coronary and peripheral arteries, diabetes, and chronic kidney disease were identified as the main risk factors for MACE in patients with CAD and PAD. Registry data showed that, although preventive antiplatelet therapy was prescribed at high rates, a large proportion (9–56%) of patients did not receive treatment. Furthermore, adherence to treatment declined over time, potentially leading to disease worsening.

Conclusion

Despite gaps in the literature, this assessment showed that MACE's risk is substantial among patients with CAD or PAD and that the use of preventive therapies is suboptimal. Development of additional preventive therapies for these patients is warranted.
Fine structure of diffused pseudobranchial neurosecretory cells associated with carotid labyrinth in an air‐breathing catfish Clarias batrachus
Authors: Sengar Manvendra , Yadav Laxmi , Gopesh Anita , Zaccone Daniele , Lauriano Eugenia Rita , Capillo Gioiele
Published: December 2015

Fish are known to have branchial chemoreceptors and even extrabranchial chemoreceptors to meet the challenges of aquatic environment. The pseudobranchial neurosecretory system associated with carotid labyrinth (CL) is one such example. CL – a chemosensory organ is well known in amphibians. The homologous structure also exists in fish. Clusters of neurosecretory cells, close to the CL and the first two efferent branchial arteries occur in catfish and a few other groups of teleosts. These cells belong to the pseudobranchial neurosecretory system (PNS). To reveal the ultrastructure of CL and the pseudobranchial neurosecretory cells (PNSCs), environmental scanning electron microscope (ESEM) and transmission electron microscope (TEM) investigations were made in an Asian air‐breathing catfish Clarias batrachus. Under ESEM, the PNS appeared as a mass of cells innervated by nerves and supplied by blood capillaries. The CL appeared to have a network of blood capillaries. The transmission electron microscopic investigations showed pear shaped PNSCs having different sizes of dense cored vesicles (DCVs), numerous mitochondria, nerve varicosities, indicating a secretory function of the cells. The CL shows a close association with PNSCs and smooth muscles. Although the exact function of the CL and associated PNSCs in the biology of fish is far from clear, their morphology suggests they are involved in a stress response such as to hypoxia.
Tolerance as a function of disapproval and respect: The case of Muslims
Authors: Simon Bernd , Schaefer Christoph Daniel
Published: December 2015

The article assesses a disapproval–respect model of tolerance according to which tolerance is made possible when disapproval of others' beliefs, preferences, or practices is balanced by respect for them as equal fellow citizens. Employing a sample of Muslims living in Germany, we predicted and found that such respect was more predictive of outgroup toleration when respondents disapproved rather than approved of the outgroups' beliefs, preferences, or practices. Moreover, respondents who displayed the critical combination of extreme disapproval and full respect indeed showed outgroup toleration. A parallel pattern of results was observed for willingness to engage in intergroup cooperation. Practical implications are discussed.
Regulatory T and B lymphocytes in a spontaneous autoimmune polyneuropathy
Authors: Quan S , Sheng J R , Abraham P M , Soliven B
Published: December 2015

B7-2–/– non-obese diabetic (NOD) mice develop a spontaneous autoimmune polyneuropathy (SAP) that mimics the progressive form of chronic inflammatory demyelinating polyradiculoneuropathy (CIDP). In this study, we focused on the role of regulatory T cells (Tregs) and regulatory B cells (Bregs) in SAP. We found that deletion of B7-2 in female NOD mice led to a lower frequency and number of Tregs and Bregs in spleens and lymph nodes. Tregs but not Bregs suppressed antigen-stimulated splenocyte proliferation, whereas Bregs inhibited the T helper type 1 (Th1) cytokine response. Both Tregs and Bregs induced an increase in CD4+interleukin (IL)−10+ cells, although less effectively in the absence of B7-2. Adoptive transfer studies revealed that Tregs, but not Bregs, suppressed SAP, while Bregs attenuated disease severity when given prior to symptom onset. B cell deficiency in B cell-deficient (muMT)/B7-2–/– NOD mice prevented the development of SAP, which would indicate that the pathogenic role of B cells predominates over its regulatory role in this model. We conclude that Bregs and Tregs control the immunopathogenesis and progression of SAP in a non-redundant fashion, and that therapies aimed at expansion of Bregs and Tregs may be an effective approach in autoimmune neuropathies.
Mechanisms of Reference Frame Selection in Spatial Term Use: Computational and Empirical Studies
Authors: Schultheis Holger , Carlson Laura A.
Published: December 2015

Previous studies have shown that multiple reference frames are available and compete for selection during the use of spatial terms such as “above.” However, the mechanisms that underlie the selection process are poorly understood. In the current paper we present two experiments and a comparison of three computational models of selection to shed further light on the nature of reference frame selection. The three models are drawn from different areas of human cognition, and we assess whether they may be applied to a reference frame selection by examining their ability to account for both existing and new empirical data comprising acceptance rates, response times, and response time distributions. These three models are the competitive shunting model (Schultheis,), the leaky competing accumulator (LCA) model (Usher & McClelland,), and a lexical selection model (Howard, Nickels, Coltheart, & Cole‐Virtue,). Model simulations show that only the LCA model satisfactorily accounts for the empirical observations. The key properties of this model that seem to drive its success are its bounded linear activation function, its number and type of processing stages, and its use of decay. Uncovering these critical properties has important implications for our understanding not only of spatial term use, in particular, but also of conflict and selection in human cognition more generally.
Changes in abundances of forest understorey birds on Africa's highest mountain suggest subtle effects of climate change
Authors: Dulle Hamadi I. , Ferger Stefan W. , Cordeiro Norbert J. , Howell Kim M. , Schleuning Matthias , Böhning‐Gaese Katrin , Hof Christian
Published: December 2015

Aim

Understanding how species respond to climate and land use change is of prime importance for biodiversity conservation. However, studies using historical, empirical data to understand species responses to climate change and anthropogenic habitat disturbance remain scarce, especially for tropical mountain ecosystems. Here, we compare historical to recent mist net data to study changes in abundance of forest understorey birds along two elevational gradients.

Location

Mount Kilimanjaro, Tanzania.

Methods

We investigate patterns of understorey bird abundance along elevational and disturbance gradients on two slopes of Mt. Kilimanjaro between 1991 and 2011. To understand species responses to climate change and disturbance, we use a trait‐based approach. Specifically, we test whether and how species' traits (temperature, habitat and dietary preferences) affect species responses to environmental change.

Results

We found that over the 20‐year time interval, mean minimum temperature increased across all sites along the elevational gradient, while levels of habitat disturbance remained similar. Mean abundance of understorey bird species increased significantly, especially at higher elevations and on the southern slope. Temporal increases were not related to species' temperature preferences and were detected for habitat generalists as well as herbivorous and omnivorous species, but not for forest specialists and insectivores.

Main conclusions

Our results suggest subtle effects of climate change on bird abundances which would not have been detectable if we had examined elevational range shifts or changes in species richness. Both warm‐ and cold‐adapted species appear to have benefited from increases in minimum temperatures at high elevations. This was not the case for forest specialists and insectivores which remained stable between sampling periods. This demonstrates that different groups of birds vary in their response to ongoing climatic changes. Our results underline the importance of tropical mountain ecosystems not only as global biodiversity hotspots, but also as safe havens for biodiversity in the face of global climate change.
Contemporary niche contraction affects climate change predictions for elephants and giraffes
Authors: Martínez‐Freiría Fernando , Tarroso Pedro , Rebelo Hugo , Brito José C.
Published: December 2015

Aim

Climate change assessments are largely based on correlative species distribution models (SDMs) that are sensible to spatial biases or incompleteness of input distribution data. We tested whether changes on the species' climatic niche resulting from recent human‐induced range contractions have a significant influence on SDM predictions of future species distributions.

Location

Africa.

Methods

For this study, we selected two highly detectable species with acknowledged human‐induced range contractions, namely the African savanna elephant (Loxodonta africana) and giraffe (Giraffa camelopardalis). We used presence data until the 1970s to describe each species' historical distribution, while more recent data characterized the contemporary distribution. We compared the temporal variation between these species distributions using multivariate analyses and the combination of four different SDM algorithms to predict historical, contemporary and future distributional ranges under climate change scenarios.

Results

We show how range contraction differentially reduces the climatic variability associated with the species niche and has an important influence on the predictions of suitable climatic space and species vulnerability trend under climate change scenarios. Future predictions of the distribution of the elephant were mainly affected by the loss of occupied area at the margins of the historical distributions, resulting in a lesser predicted extent when using the contemporary dataset. As for the giraffe models, there were more dramatic consequences with large areas of West Africa failing to be predicted as suitable in the contemporary models, probably as a result from the loss of climatic information due to the species almost complete disappearance from that region.

Main conclusions

Our findings support the importance of considering historical distributional ranges of species in climate change studies in order to account for their full climatic niche and to derive more reliable predictions of future distribution. This is particularly important in species for which distributional ranges have been strongly affected by human activities.
Three‐Dimensional Echocardiography in the Evaluation of Right Ventricular Global and Regional Systolic Function in Patients with Atrial Septal Defect before and after Percutaneous Closure
Authors: Kong Dehong , Cheng Leilei , Dong Lili , Pan Cuizhen , Yao Haohua , Zhou Daxin , Shu Xianhong
Published: December 2015

Objective

To evaluate right ventricular (RV) global and regional systolic function in patients with atrial septal defect (ASD) before and after percutaneous closure using real time three‐dimensional echocardiography (RT3DE).

Methods

RT3DE was performed in 81 patients with ASD within 24 hours before and after percutaneous closure to obtain RV global and regional ejection fraction (EF) in three compartments (inflow, body, and outflow). RV fractional area change (FAC), tricuspid annular plane systolic excursion (TAPSE), peak tricuspid systolic velocity (S), and pulmonary vascular resistance (PVR) were recorded. Forty matched normal adults were included as controls.

Results

When compared with controls, RV global and regional EF were decreased in preclosure patients (P < 0.001). FAC was lower while TAPSE and S were higher in preclosure patients than in controls (P < 0.05). After closure, RV systolic function parameters were all reduced (P < 0.001). Regional EF in the body compartment was the lowest among the three compartments in ASD patients (P < 0.05). Procedural percentage changes of RV global EF and regional EF in the inflow compartment were lower than those of two‐dimensional systolic function parameters (P < 0.05). RV global and regional EF in the inflow compartment were negatively correlated with PVR in patients after closure (r = −0.601, −0.543, P < 0.001).

Conclusions

RV global and regional systolic functions are impaired in open and closed ASD. RT3DE‐derived systolic function parameters are negatively correlated with RV after load. RT3DE has potential value in the evaluation of RV systolic function in patients with ASD.
Haematological malignancy in the intensive care unit: microbiology results and mortality
Authors: van Beers Eduard Johannes , Müller Marcella Catharina Antoinetta , Vlaar Alexander Petrus Johannes , Spanjaard Lodewijk , van den Bergh Walter Marcel ,   HEMA‐ICU Study Group
Published: December 2015

Background

Mortality prediction models of patients with a haematological malignancy admitted to an intensive care unit (ICU) do not include the presence of neutropenia and microbiology results. We performed a registry‐based retrospective study of haematology patients admitted to the ICU to investigate the relation between neutropenia, microbiology results and outcome of these patients.

Methods

Neutropenia and microbiology culture results within 24 h before or after ICU admission of patients with a haematological malignancy admitted between 2004 and 2010 were described and analysed for association with 28‐day mortality.

Results

We identified 234 individual patients with a current malignant haematological condition, of which 27% were neutropenic and 21% had a positive blood culture at admission. Most prevalent from blood cultured species were Escherichia coli and coagulase‐negative staphylococci. The overall 28‐day mortality was 38%. In patients with a positive blood culture but no neutropenia, 28‐day mortality was 28% and in patients with neutropenia but without positive blood culture, it was 36%. The 28‐day mortality of patients with both neutropenia and a positive blood culture was 55% with an adjusted (for APACHE‐II score) hazard ratio (HR) of 1.8 (95%CI 1.0–3.4) compared to other hematologic patients admitted to the ICU.

Conclusion

In patients with haematological malignancy admitted to the ICU, culture results are diverse. The combination of neutropenia and positive blood culture is associated with increased 28‐day mortality. We suggest this could be of additional value when assessing mortality risk in this patient group.
Individual Entrepreneurial Exit and Earnings in Subsequent Paid Employment
Authors: Luzzi Alessandra , Sasson Amir
Published: December 2015

We study earnings of individuals who exit entrepreneurship for paid employment. We find mean (median) positive rewards from entrepreneurship in subsequent paid employment relative to matched employees. Rewards are higher for former entrepreneurs hired in highly innovative sectors. We also find that the performance of the exited firm is a strong predictor of the earnings premium for former entrepreneurs when the firm performed well, while we do not find median discounts for entrepreneurs exiting low performing firms. We use registry data that encompass the population of firms and individuals in the Norwegian economy.
Multiaxial fatigue life modelling using hybrid approach of critical plane and genetic algorithm
Authors: Kamal M. , Rahman M. M.
Published: December 2015

This paper presents a new hybrid approach for multiaxial fatigue life estimation, based on continuum damage mechanics theory and a genetic algorithm with critical plane model formulation. The hybrid model employs a genetic algorithm based setup for calibration with standard proportional and non‐proportional profiles to predict fatigue life for complex loading profiles. The model is evaluated using experimental fatigue life data for SS304 steel. Calibration using simplified profiles is in agreement with the requirement for cost‐effective experimental fatigue life testing. In‐phase and out‐of‐phase loads are used for calibration, and fatigue life is predicted for more complicated profiles. The results show good agreement between the estimated and experimental fatigue life, and calibration through simple loading histories to predict fatigue life for complex histories appears to be an effective solution using the proposed model. A brief comparison is presented with fatigue life estimation performance of the proposed model with models available in commercial codes. Proposed model found to be more consistent in fatigue life prediction against various loading conditions.
Diabetes mellitus and white matter hyperintensity
Authors: Tamura Yoshiaki , Araki Atsushi
Published: December 2015

White matter hyperintensity (WMH) is a brain lesion detected as a high‐intensity area in magnetic resonance imaging T2 and fluid‐attenuated inversion recovery images, and it has been suggested that WMH reflects damage to small vessels in periventricular and subcortical areas. Although WMH has been linked to the incidence of stroke, more recently it has been clarified that WMH is also associated with progression of cognitive decline and functional disability, which are components of so‐called geriatric syndrome. In addition to hypertension, which is the classical risk factor for WMH, evidence has been accumulating to suggest that diabetes mellitus could also be associated with WMH progression, and some studies have shown that WMH severity is correlated with cognitive decline in patients with diabetes. The factors that accelerate WMH formation in elderly patients with diabetes remain poorly defined. It is considered that insulin resistance is an exacerbating factor, but the effects of hypertension, dyslipidemia or other vascular risk factors have yet be clarified, and further studies are required. Geriatr Gerontol Int 2015; 15 (Suppl. 1): 34–42.
Hypertension, haematuria and renal functioning in haemophilia – a cross‐sectional study in Europe
Authors: Holme P. A. , Combescure C. , Tait R.C. , Berntorp E. , Rauchensteiner S. , de Moerloose P. ,   the ADVANCE Working Group
Published: December 2015

Background and objectives

This cross‐sectional, epidemiological study sought to assess the prevalence and extent of potential risk factors for hypertension, particularly renal function related to haematuria and their associations in people with haemophilia.

Methodology

Demographic and medical data were collected at a single time‐point in patients with haemophilia over 40 years of age from 16 European centres. Associations with diagnosis of hypertension were tested in univariate and multivariate analyses.

Results

We enrolled 532 patients (median age 52 years, range 40–98) with haemophilia A (n = 467) or haemophilia B (n = 65). Haemophilia was severe (<0.01 IU mL−1) in 313 patients (59%). Hypertension was diagnosed in 239 patients (45%). In multivariate analyses, age and body mass index (BMI) were significantly and independently associated with hypertension (adjusted odds ratio (OR) 18.1, P < 0.001, in elderly patients and OR = 25.1, P < 0.001, in patients with BMI >30 kg m−2). Estimated glomerular filtration rate (eGFR) <70 mL min−1 (OR = 2.7, P = 0.047) was significantly associated with hypertension, but mean eGFR was significantly higher for severe than mild haemophilia. Further variables with OR > 2.8 were diabetes (OR = 2.8, P = 0.04), coronary artery disease (OR = 3.3, P = 0.052) and family history of hypertension (OR = 4.4, P < 0.001). Neither severity of haemophilia nor history of haematuria was significantly associated with hypertension in univariate or multivariate analyses.

Conclusion

As in the general population, age and BMI were major risk factors for hypertension in people with haemophilia. Renal dysfunction was associated with hypertension, but the prevalence of renal dysfunction was not extensive and furthermore not significantly correlated with haematuria. The associations of other variables with hypertension require further studies to confirm causal relationships over time.