bluuebunny/crossref_metadata_2025 huggingface dataset:
Integrating multiple resources to identify specific transcriptional cooperativity with a Bayesian approach
Authors: Hu Pengzhan , Shen Zhongchao , Tu Haibo , Zhang Li , Shi Tieliu
Published: November 2013

Motivation: Limited cohort of transcription factors is capable to structure various gene-expression patterns. Transcriptional cooperativity (TC) is deemed to be the main mechanism of complexity and precision in regulatory programs. Although many data types generated from numerous experimental technologies are utilized in an attempt to understand combinational transcriptional regulation, complementary computational approach that can integrate diverse data resources and assimilate them into biological model is still under development.

Results: We developed a novel Bayesian approach for integrative analysis of proteomic, transcriptomic and genomic data to identify specific TC. The model evaluation demonstrated distinguishable power of features derived from distinct data sources and their essentiality to model performance. Our model outperformed other classifiers and alternative methods. The application that contextualized TC within hepatocarcinogenesis revealed carcinoma associated alterations. Derived TC networks were highly significant in capturing validated cooperativity as well as revealing novel ones. Our methodology is the first multiple data integration approach to predict dynamic nature of TC. It is promising in identifying tissue- or disease-specific TC and can further facilitate the interpretation of underlying mechanisms for various physiological conditions.

Contact:  tieliushi01@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Background Lamb waves in the Earth's atmosphere
Authors: Nishida Kiwamu , Kobayashi Naoki , Fukao Yoshio
Published: November 2013

Lamb waves of the Earth's atmosphere in the millihertz band have been considered as transient phenomena excited only by large events. Here, we show the first evidence of background Lamb waves in the Earth's atmosphere from 0.2 to 10 mHz, based on the array analysis of microbarometer data from the USArray in 2012. The observations suggest that the probable excitation source is atmospheric turbulence in the troposphere. Theoretically, their energy in the troposphere tunnels into the thermosphere at a resonant frequency via thermospheric gravity wave, where the observed amplitudes indeed take a local minimum. The energy leak through the frequency window could partly contribute to thermospheric wave activity.
Comprehensive analysis of the functional microRNA–mRNA regulatory network identifies miRNA signatures associated with glioma malignant progression
Authors: Li Yongsheng , Xu Juan , Chen Hong , Bai Jing , Li Shengli , Zhao Zheng , Shao Tingting , Jiang Tao , Ren Huan , Kang Chunsheng , Li Xia
Published: November 2013

Glioma is the most common and fatal primary brain tumour with poor prognosis; however, the functional roles of miRNAs in glioma malignant progression are insufficiently understood. Here, we used an integrated approach to identify miRNA functional targets during glioma malignant progression by combining the paired expression profiles of miRNAs and mRNAs across 160 Chinese glioma patients, and further constructed the functional miRNA–mRNA regulatory network. As a result, most tumour-suppressive miRNAs in glioma progression were newly discovered, whose functions were widely involved in gliomagenesis. Moreover, three miRNA signatures, with different combinations of hub miRNAs (regulations≥30) were constructed, which could independently predict the survival of patients with all gliomas, high-grade glioma and glioblastoma. Our network-based method increased the ability to identify the prognostic biomarkers, when compared with the traditional method and random conditions. Hsa-miR-524-5p and hsa-miR-628-5p, shared by these three signatures, acted as protective factors and their expression decreased gradually during glioma progression. Functional analysis of these miRNA signatures highlighted their critical roles in cell cycle and cell proliferation in glioblastoma malignant progression, especially hsa-miR-524-5p and hsa-miR-628-5p exhibited dominant regulatory activities. Therefore, network-based biomarkers are expected to be more effective and provide deep insights into the molecular mechanism of glioma malignant progression.
A dominant allele controls development into female mimic male and diminutive female ruffs
Authors: Lank David B. , Farrell Lindsay L. , Burke Terry , Piersma Theunis , McRae Susan B.
Published: November 2013

Maintaining polymorphisms for genes with effects of ecological significance may involve conflicting selection in males and females. We present data from a captive population of ruffs (Philomachus pugnax) showing that a dominant allele controls development into both small, ‘female mimic’ males (‘faeders’), and a previously undescribed class of small ‘female faeders’. Most male ruffs have elaborate breeding plumage and display behaviour, but 0.5–1.5% are faeders, which lack both. Females from a captive population previously lacking faeders were bred with two founder faeder males and their faeder sons. The faeders’ offspring had a quadrimodal size distribution comprising normal-sized males and females, faeders and atypically small females. By contrast, ornamented males fathered only normal-sized offspring. We conclude that both founding faeders were heterozygous for a faeder allele absent from the original population. This allele is dominant to previously described genes that determine development into independent versus satellite ornamented males. Unlike those genes, the faeder allele is clearly expressed in females. Small body size is a component of the male faeder mating strategy, but provides no obvious benefit to females. Bisexual expression of the gene provides the opportunity to quantify the strength of sexually antagonistic selection on a Mendelian trait.
Pelagic larval duration predicts extinction risk in a freshwater fish clade
Authors: Douglas Morgan , Keck Benjamin P. , Ruble Crystal , Petty Melissa , Shute J. R. , Rakes Patrick , Hulsey C. Darrin
Published: November 2013

Pelagic larval duration (PLD) can influence evolutionary processes ranging from dispersal to extinction in aquatic organisms. Using estimates of PLD obtained from species of North American darters (Percidae: Etheostomatinae), we demonstrate that this freshwater fish clade exhibits surprising variation in PLD. Comparative analyses provide some evidence that higher stream gradients favour the evolution of shorter PLD. Additionally, similar to patterns in the marine fossil record in which lower PLD is associated with greater extinction probability, we found a reduced PLD in darter lineages was evolutionarily associated with extinction risk. Understanding the causes and consequences of PLD length could lead to better management and conservation of organisms in our increasingly imperiled aquatic environments.
The impact of simulated chronic nitrogen deposition on the biomass and N
2
-fixation activity of two boreal feather moss–cyanobacteria associations
Authors: Gundale Michael J. , Bach Lisbet H. , Nordin Annika
Published: November 2013

Bryophytes achieve substantial biomass and play several key functional roles in boreal forests that can influence how carbon (C) and nitrogen (N) cycling respond to atmospheric deposition of reactive nitrogen (N
r
). They associate with cyanobacteria that fix atmospheric N
2
, and downregulation of this process may offset anthropogenic N
r
inputs to boreal systems. Bryophytes also promote soil C accumulation by thermally insulating soils, and changes in their biomass influence soil C dynamics. Using a unique large-scale (0.1 ha forested plots), long-term experiment (16 years) in northern Sweden where we simulated anthropogenic N
r
deposition, we measured the biomass and N
2
-fixation response of two bryophyte species, the feather mosses
Hylocomium splendens
and
Pleurozium schreberi
. Our data show that the biomass declined for both species; however, N
2
-fixation rates per unit mass and per unit area declined only for
H. splendens
. The low and high treatments resulted in a 29% and 54% reduction in total feather moss biomass, and a 58% and 97% reduction in total N
2
-fixation rate per unit area, respectively. These results help to quantify the sensitivity of feather moss biomass and N
2
fixation to chronic N
r
deposition, which is relevant for modelling ecosystem C and N balances in boreal ecosystems.
Energy localization and frequency analysis in the locust ear
Authors: Malkin Robert , McDonagh Thomas R. , Mhatre Natasha , Scott Thomas S. , Robert Daniel
Published: November 2013

Animal ears are exquisitely adapted to capture sound energy and perform signal analysis. Studying the ear of the locust, we show how frequency signal analysis can be performed solely by using the structural features of the tympanum. Incident sound waves generate mechanical vibrational waves that travel across the tympanum. These waves shoal in a tsunami-like fashion, resulting in energy localization that focuses vibrations onto the mechanosensory neurons in a frequency-dependent manner. Using finite element analysis, we demonstrate that two mechanical properties of the locust tympanum, distributed thickness and tension, are necessary and sufficient to generate frequency-dependent energy localization.
Mathematical modelling of atheroma plaque formation and development in coronary arteries
Authors: Cilla Myriam , Peña Estefanía , Martínez Miguel A.
Published: November 2013

Atherosclerosis is a vascular disease caused by inflammation of the arterial wall, which results in the accumulation of low-density lipoprotein (LDL) cholesterol, monocytes, macrophages and fat-laden foam cells at the place of the inflammation. This process is commonly referred to as plaque formation. The evolution of the atherosclerosis disease, and in particular the influence of wall shear stress on the growth of atherosclerotic plaques, is still a poorly understood phenomenon. This work presents a mathematical model to reproduce atheroma plaque growth in coronary arteries. This model uses the Navier–Stokes equations and Darcy's law for fluid dynamics, convection–diffusion–reaction equations for modelling the mass balance in the lumen and intima, and the Kedem–Katchalsky equations for the interfacial coupling at membranes, i.e. endothelium. The volume flux and the solute flux across the interface between the fluid and the porous domains are governed by a three-pore model. The main species and substances which play a role in early atherosclerosis development have been considered in the model, i.e. LDL, oxidized LDL, monocytes, macrophages, foam cells, smooth muscle cells, cytokines and collagen. Furthermore, experimental data taken from the literature have been used in order to physiologically determine model parameters. The mathematical model has been implemented in a representative axisymmetric geometrical coronary artery model. The results show that the mathematical model is able to qualitatively capture the atheroma plaque development observed in the intima layer.
Do natural landscapes reduce future discounting in humans?
Authors: van der Wal Arianne J. , Schade Hannah M. , Krabbendam Lydia , van Vugt Mark
Published: November 2013

An important barrier to enduring behavioural change is the human tendency to discount the future. Drawing on evolutionary theories of life history and biophilia, this study investigates whether exposure to natural versus urban landscapes affects people's temporal discount rates. The results of three studies, two laboratory experiments and a field study reveal that individual discount rates are systematically lower after people have been exposed to scenes of natural environments as opposed to urban environments. Further, this effect is owing to people placing more value on the future after nature exposure. The finding that nature exposure reduces future discounting—as opposed to exposure to urban environments—conveys important implications for a range of personal and collective outcomes including healthy lifestyles, sustainable resource use and population growth.
Chimpanzee fauna isotopes provide new interpretations of fossil ape and hominin ecologies
Authors: Nelson Sherry V.
Published: November 2013

Carbon and oxygen stable isotopes within modern and fossil tooth enamel record the aspects of an animal's diet and habitat use. This investigation reports the first isotopic analyses of enamel from a large chimpanzee community and associated fauna, thus providing a means of comparing fossil ape and early hominin palaeoecologies with those of a modern ape. Within Kibale National Park forest, oxygen isotopes differentiate primate niches, allowing for the first isotopic reconstructions of degree of frugivory versus folivory as well as use of arboreal versus terrestrial resources. In a comparison of modern and fossil community isotopic profiles, results indicate thatSivapithecus, a Miocene ape from Pakistan, fed in the forest canopy, as do chimpanzees, but inhabited a forest with less continuous canopy or fed more on leaves.Ardipithecus, an early hominin from Ethiopia, fed both arboreally and terrestrially in a more open habitat than inhabited by chimpanzees.
Cysteine desulphurase-encoding gene sufS2 is required for the repressor function of RirA and oxidative resistance in Agrobacterium tumefaciens
Authors: Bhubhanil Sakkarin , Niamyim Phettree , Sukchawalit Rojana , Mongkolsuk Skorn
Published: November 2013

The Agrobacterium tumefaciens genome contains a cluster of genes that are predicted to encode Fe–S cluster assembly proteins, and this cluster is known as the sufS2BCDS1XA operon. sufS2 is the first gene in the operon, and it was inactivated to determine its physiological function. The sufS2 mutant exhibited a small colony phenotype, grew slower than the wild-type strain and was more sensitive to various oxidants including peroxide, organic hydroperoxide and superoxide. The sufS2 gene was negatively regulated by iron response regulator (Irr) and rhizobial iron regulator (RirA) under low and high iron conditions, respectively, and was inducible in response to oxidative stress. The oxidant-induced expression of sufS2 was controlled by Irr, RirA and an additional but not yet identified mechanism. sufS2 was required for RirA activity in the repression of a sufS2 promoter-lacZ fusion. RirA may use Fe–S as its cofactor. sufS2 disruption may cause a defect in the Fe–S supply and could thereby affect the RirA activity. The three conserved cysteine residues (C91, C99 and C105) in RirA were predicted to coordinate with the Fe–S cluster and were shown to be essential for RirA repression of the sufS2-lacZ fusion. These results suggested that sufS2 is important for the survival of A. tumefaciens.
Heterogeneity in iron-doped titania flower-like nanocrystalline aggregates: detection of brookite and anatase/rutile size–strain modeling
Authors: Kremenovic Aleksandar , Grujic Brojcin Mirjana , Welsch Anna-Maria , Colomban Philippe
Published: November 2013

Detailed investigations of Raman spectra and X-ray powder diffraction (XRPD) patterns of rutile-rich and anatase/brookite-poor flower-like nanocrystalline aggregates of Fe-doped TiO2shed new light with regard to its microstructure and heterogeneity. The brookite phase has been detected from the Raman spectra, and the presence of different phases in pure and doped samples is discussed. The phonon confinement model (PCM) was applied to Raman spectra, and the Warren–Averbach and simplified integral breadth methods were applied to XRPD patterns in order to obtain information about the nanocrystallite size and strain of rutile and anatase. The applied methods (i.e.XRPD size–strain analysis and the PCM fit of Raman spectra), when used in combination and together with other experimental techniques like high-resolution transmission electron microscopy, could be very useful in nanomaterial characterization.
Longitudinal pore alignment in anodic alumina films grown on polycrystalline metal substrates
Authors: Roslyakov Ilya V. , Eliseev Andrey A. , Yakovenko Ekaterina V. , Zabelin Alexander V. , Napolskii Kirill S.
Published: November 2013

A quantitative analysis of longitudinal pore alignment in anodic alumina films grown on polycrystalline metal substrates was performed on the basis of small-angle X-ray diffraction mapping. The very high sensitivity of the diffraction pattern to the orientation of the anodic alumina film allowed the average pore alignment within the irradiated area to be determined, with an accuracy better than 0.1°. It is shown that pores deviate from the orientation orthogonal to the metal surface by a small angle that is constant within a single-crystal grain. Strong correlation between the longitudinal pore alignment within the anodic alumina film and the grain structure of the aluminium substrate indicates the important role of the crystallographic orientation of the metal in the pore growth process.
HipGISAXS: a high-performance computing code for simulating grazing-incidence X-ray scattering data
Authors: Chourou Slim T. , Sarje Abhinav , Li Xiaoye S. , Chan Elaine R. , Hexemer Alexander
Published: November 2013

This article describes the development of a flexible grazing-incidence small-angle X-ray scattering (GISAXS) simulation code in the framework of the distorted wave Born approximation that effectively utilizes the parallel processing power provided by graphics processors and multicore processors. The code, entitledHigh-Performance GISAXS, computes the GISAXS image for any given superposition of user-defined custom shapes or morphologies in a material and for various grazing-incidence angles and sample orientations. These capabilities permit treatment of a wide range of possible sample structures, including multilayered polymer films and nanoparticles on top of or embedded in a substrate or polymer film layers. In cases where the material displays regions of significant refractive index contrast, an algorithm has been implemented to perform a slicing of the sample and compute the averaged refractive index profile to be used as the reference geometry of the unperturbed system. A number of case studies are presented, which demonstrate good agreement with the experimental data for a variety of polymer and hybrid polymer/nanoparticle composite materials. The parallelized simulation code is well suited for addressing the analysis efforts required by the increasing amounts of GISAXS data being produced by high-speed detectors and ultrafast light sources.
Ordered and twinned structure in hexagonal-based potassium tungsten bronze nanosheets
Authors: Jia Shuangfeng , Sang Hongqian , Zhang Wenjing , Zhang Han , Zheng He , Liao Lei , Wang Jianbo
Published: November 2013

Non-stoichiometric hexagonal-based potassium tungsten bronze (KxWO3) nanosheets were synthesized by oxidizing tungsten foil in potassium hydroxide. The tungsten bronze nanosheets exhibited an ordered monoclinic superstructure as revealed by X-ray diffraction patterns. Further detailed structural investigation by employing electron microscopy techniques showed the coexistence of 120° rotation twinning variants in the superstructure phase, which may result from the rotation symmetry reduction induced by the ordered arrangements of K vacancies during crystal growth.
Can Laue microdiffraction be used to solve and refine complex inorganic structures?
Authors: Dejoie Catherine , McCusker Lynne B. , Baerlocher Christian , Kunz Martin , Tamura Nobumichi
Published: November 2013

The white-beam Laue diffraction experiment is an attractive alternative to the more conventional monochromatic one for single-crystal structure analysis, because it takes full advantage of the X-ray energy spectrum of a synchrotron source and requires no rotation of the crystal in the beam. Therefore, it could be used for structural characterizations underin situoroperandoconditions. The potential of Laue diffraction was recognized and exploited by the protein community many years ago, and the methodology, which involved positioning and rotating the crystal in the beam, has been successfully applied to the determination of both protein and small-molecule crystal structures. Here, it is proposed that the specificities of Laue diffraction are exploited to study randomly oriented stationary microcrystals of inorganic materials. In order to determine the best strategy for collecting a reasonable quantity of data from stationary crystals, a series of simulations on four model structures for three experimental setups have been performed. It is shown that the structures of the four samples can be solved with the dual-space method inSHELX, even though the data sets are highly incomplete and much of the low-resolution part is missing. The experimental setup and data collection strategy for measuring such microcrystals have been developed on BL12.3.2 at the Advanced Light Source in Berkeley. The intensities of reflections with one and two harmonics can be extracted reliably by exploiting the tunable low-energy threshold of a Pilatus detector. In this way, the number of usable reflections can be increased from 75 to 95%. Such Laue microdiffraction data have been measured and used successfully to refine the structures of the model samples.
Small-angle X-ray scattering and light scattering study of hybrid nanoparticles composed of thermoresponsive triblock copolymer F127 and thermoresponsive statistical polyoxazolines with hydrophobic moieties
Authors: Bogomolova Anna , Hruby Martin , Panek Jiri , Rabyk Maria , Turner Stuart , Bals Sara , Steinhart Milos , Zhigunov Alexander , Sedlacek Ondrej , Stepanek Petr , Filippov Sergey K.
Published: November 2013

A combination of new thermoresponsive statistical polyoxazolines, poly[(2-butyl-2-oxazoline)-stat-(2-isopropyl-2-oxazoline)] [pBuOx-co-piPrOx], with different hydrophobic moieties and F127 surfactant as a template system for the creation of thermosensitive nanoparticles for radionuclide delivery has recently been tested [Pánek, Filippov, Hrubý, Rabyk, Bogomolova, Kučka & Stěpánek (2012).Macromol. Rapid Commun.33, 1683–1689]. It was shown that the presence of the thermosensitive F127 triblock copolymer in solution reduces nanoparticle size and polydispersity. This article focuses on a determination of the internal structure and solution properties of the nanoparticles in the temperature range from 288 to 312 K. Here, it is demonstrated that below the cloud point temperature (CPT) the polyoxazolines and F127 form complexes that co-exist in solution with single F127 molecules and large aggregates. When the temperature is raised above the CPT, nanoparticles composed of polyoxazolines and F127 are predominant in solution. These nanoparticles could be described by a spherical shell model. It was found that the molar weight and hydrophobicity of the polymer do not influence the size of the outer radius and only slightly change the inner radius of the nanoparticles. At the same time, molar weight and hydrophobicity did affect the process of nanoparticle formation. In conclusion, poly(2-oxazoline) molecules are fully incorporated inside of F127 micelles, and this result is very promising for the successful application of such systems in radionuclide delivery.
Fast quantitative analysis of strong uniaxial texture using a March–Dollase approach
Authors: Zolotoyabko Emil
Published: November 2013

Interrelations between the degree of uniaxial preferred orientation and the intensities and widths of selected X-ray diffraction peaks are analyzed within the March–Dollase approach. Simple analytical expressions are developed which relate the degree of preferred orientation to the rocking curve width of the strongest diffraction peak or the intensity ratio of two diffraction peaks, one of them being originated in the preferably orientated atomic planes.
Soft-X-ray ARPES facility at the ADRESS beamline of the SLS: concepts, technical realisation and scientific applications
Authors: Strocov V. N. , Wang X. , Shi M. , Kobayashi M. , Krempasky J. , Hess C. , Schmitt T. , Patthey L.
Published: November 2013

Soft-X-ray angle-resolved photoelectron spectroscopy (ARPES) with photon energies around 1 keV combines the momentum space resolution with increasing probing depth. The concepts and technical realisation of the new soft-X-ray ARPES endstation at the ADRESS beamline of SLS are described. The experimental geometry of the endstation is characterized by grazing X-ray incidence on the sample to increase the photoyield and vertical orientation of the measurement plane. The vacuum chambers adopt a radial layout allowing most efficient sample transfer. High accuracy of the angular resolution is ensured by alignment strategies focused on precise matching of the X-ray beam and optical axis of the analyzer. The high photon flux of up to 1013 photons s−1(0.01% bandwidth)−1delivered by the beamline combined with the optimized experimental geometry break through the dramatic loss of the valence band photoexcitation cross section at soft-X-ray energies. ARPES images with energy resolution up to a few tens of meV are typically acquired on the time scale of minutes. A few application examples illustrate the power of our advanced soft-X-ray ARPES instrumentation to explore the electronic structure of bulk crystals with resolution in three-dimensional momentum, access buried heterostructures and study elemental composition of the valence states using resonant excitation.
Energetic adjustments in freely breeding‐fasting king penguins: does colony density matter?
Authors: Viblanc Vincent A. , Saraux Claire , Malosse Nelly , Groscolas René
Published: November 2013

For seabirds that forage at sea but breed while fasting on land, successful reproduction depends on the effective management of energy stores. Additionally, breeding often means aggregating in dense colonies where social stress may affect energy budgets.

Male king penguins (Aptenodytes patagonicus) fast for remarkably long periods (up to 1·5 months) while courting and incubating ashore. Although their fasting capacities have been well investigated in captivity, we still know very little about the energetics of freely breeding birds.

We monitored heart rate (HR, a proxy to energy expenditure), body temperature and physical activity of male king penguins during their courtship and first incubation shift in a colony of some 24 000 freely breeding pairs. Males were breeding either under low but increasing colony density (early breeders) or at high and stable density (late breeders).

In early breeders, daily mean and resting HR decreased during courtship but increased again 3 days before egg laying and during incubation. In late breeders, HR remained stable throughout this same breeding period. Interestingly, the daily increase in resting HR we observed in early breeders was strongly associated with a marked increase in colony density over time. This finding remained significant even after controlling for climate effects.

In both early and late breeders, courtship and incubation were associated with a progressive decrease in physical activity, whereas core body temperature remained unchanged.

We discuss the roles of decreased physical activity and thermoregulatory strategies in sustaining the long courtship–incubation fast of male king penguins. We also draw attention to a potential role of conspecific density in affecting the energetics of breeding‐fasting seabirds, that is, a potential energy cost to coloniality.
Non‐native acylated homoserine lactones reveal that LuxIR quorum sensing promotes symbiont stability
Authors: Studer Sarah V. , Schwartzman Julia A. , Ho Jessica S. , Geske Grant D. , Blackwell Helen E. , Ruby Edward G.
Published: November 2013

Quorum sensing, a group behaviour coordinated by a diffusible pheromone signal and a cognate receptor, is typical of bacteria that form symbioses with plants and animals. LuxIR‐type N‐acyl L‐homoserine (AHL) quorum sensing is common in Gram‐negative Proteobacteria, and many members of this group have additional quorum‐sensing networks. The bioluminescent symbiont Vibrio fischeri encodes two AHL signal synthases: AinS and LuxI. AinS‐dependent quorum sensing converges with LuxI‐dependent quorum sensing at the LuxR regulatory element. Both AinS‐ and LuxI‐mediated signalling are required for efficient and persistent colonization of the squid host, Euprymna scolopes. The basis of the mutualism is symbiont bioluminescence, which is regulated by both LuxI‐ and AinS‐dependent quorum sensing, and is essential for maintaining a colonization of the host. Here, we used chemical and genetic approaches to probe the dynamics of LuxI‐ and AinS‐mediated regulation of bioluminescence during symbiosis. We demonstrate that both native AHLs and non‐native AHL analogues can be used to non‐invasively and specifically modulate induction of symbiotic bioluminescence via LuxI‐dependent quorum sensing. Our data suggest that the first day of colonization, during which symbiont bioluminescence is induced by LuxIR, is a critical period that determines the stability of the V. fischeri population once symbiosis is established.
HmsC, a periplasmic protein, controls biofilm formation via repression of HmsD, a diguanylate cyclase in Yersinia pestis
Authors: Ren Gai‐Xian , Yan Hai‐Qin , Zhu Hui , Guo Xiao‐Peng , Sun Yi‐Cheng
Published: November 2013

Yersinia pestis, the cause of plague, forms a biofilm in the foregut of its flea vector to enhance transmission. Biofilm formation in Y. pestis is controlled by the intracellular levels of the second messenger molecule cyclic diguanylate (c‐di‐GMP). HmsT and Y3730, the two diguanylate cyclases (DGC) in Y. pestis, are responsible for the synthesis of c‐di‐GMP. Y3730, which we name here as HmsD, has little effect on in vitro biofilms, but has a major effect on biofilm formation in the flea. The mechanism by which HmsD plays differential roles in vivo and in vitro is not understood. In this study, we show that hmsD is part of a three‐gene operon (y3729‐31), which we designate as hmsCDE. Deletion of hmsC resulted in increased, hmsD‐dependent biofilm formation, while deletion or overexpression of hmsE did not affect biofilm formation. Localization experiments suggest that HmsC resides in the periplasmic space. In addition, we provide evidence that HmsC might interact directly with the periplasmic domain of HmsD and cause the proteolysis of HmsD. We propose that HmsC senses the environmental signals, which in turn regulates HmsD, and controls the c‐di‐GMP synthesis and biofilm formation in Y. pestis.
Careful science? Bodywork and care practices in randomised clinical trials
Authors: Jespersen Astrid P. , Bønnelycke Julie , Eriksen Hanne H.
Published: November 2013

Concern about obesity has prompted numerous public health campaigns that urge people to be more physically active. The campaigns often include normative statements and attempt to impose restrictions on individuals' lives without considering the complexities of daily life. We suggest that broadening the focus to reflect everyday practices would foster better targeted public health campaigns. This article is based on our participation inFINE, a multidisciplinary Danish research project. The core methodology ofFINEwas a randomised controlled trial in which 61 moderately overweight men were put into different exercise groups. In this article we analyse the scientific work of the trial as representing entangled processes of bodywork, where data are extracted and objectified bodies are manipulated and care practices address the emotional, social and mundane aspects of the participants' everyday lives. Care practices are an inherent part of producing scientific facts but they are removed from the recognised results of scientific practice and thus from common public health recommendations. However, knowledge about the strategic use of care practices in lifestyle interventions is important for public health initiatives and future efforts should incorporate this aspect.
The role of thiopurine metabolites in inflammatory bowel disease and rheumatological disorders
Authors: Friedman Antony B. , Sparrow Miles P. , Gibson Peter R.
Published: November 2013

Thiopurines have been a cornerstone of medical management of patients with inflammatory bowel disease (IBD) and many rheumatological disorders. The thiopurines are metabolized to their end products, 6‐methymercaptopurine (6MMP) and the 6‐thioguanine nucleotides (6TGN), with 6TGN being responsible for thiopurine efficacy by causing apoptosis and preventing activation and proliferation of T‐lymphocytes. In IBD, conventional weight‐based dosing with thiopurines leads to an inadequate response in many patients. Utilizing measurement of these metabolites and then employing dose optimization strategies has led to markedly improved outcomes in IBD. Switching between thiopurines as well as the addition of low‐dose allopurinol can overcome adverse events and elevate 6TGN levels into the therapeutic window. There is a paucity of data on thiopurine metabolites in rheumatological diseases and further research is required.
Stability of soil microbial structure and activity depends on microbial diversity
Authors: Tardy Vincent , Mathieu Olivier , Lévêque Jean , Terrat Sébastien , Chabbi Abad , Lemanceau Philippe , Ranjard Lionel , Maron Pierre‐Alain
Published: November 2013

Despite the central role of microbes in soil processes, empirical evidence concerning the effect of their diversity on soil stability remains controversial. Here, we addressed the ecological insurance hypothesis by examining the stability of microbial communities along a gradient of soil microbial diversity in response to mercury pollution and heat stress. Diversity was manipulated by dilution extinction approach. Structural and functional stabilities of microbial communities were assessed from patterns of genetic structure and soil respiration after the stress. Dilution led to the establishment of a consistent diversity gradient, as revealed by 454 sequencing of ribosomal genes. Diversity stability was enhanced in species‐rich communities whatever the stress whereas functional stability was improved with increasing diversity after heat stress, but not after mercury pollution. This discrepancy implies that the relevance of ecological insurance for soil microbial communities might depend on the type of stress. Our results also suggest that the significance of microbial diversity for soil functional stability might increase with available soil resources. This could have strong repercussions in the current ‘global changes’ context because it suggests that the combined increased frequencies of extreme climatic events, nutrient loading and biotic exploitation may amplify the functional consequences of diversity decrease.
Separating the Shirkers from the Workers? Making Sure Respondents Pay Attention on Self‐Administered Surveys
Authors: Berinsky Adam J. , Margolis Michele F. , Sances Michael W.
Published: November 2013

Good survey and experimental research requires subjects to pay attention to questions and treatments, but many subjects do not. In this article, we discuss “Screeners” as a potential solution to this problem. We first demonstrate Screeners’ power to reveal inattentive respondents and reduce noise. We then examine important but understudied questions about Screeners. We show that using a single Screener is not the most effective way to improve data quality. Instead, we recommend using multiple items to measure attention. We also show that Screener passage correlates with politically relevant characteristics, which limits the generalizability of studies that exclude failers. We conclude that attention is best measured using multiple Screener questions and that studies using Screeners can balance the goals of internal and external validity by presenting results conditional on different levels of attention.
Sociable robots, jazz music, and divination: Contingency as a cultural resource for negotiating problems of intentionality
Authors: WILF EITAN
Published: November 2013

In practices that range from mechanical divination in Central Africa to gamelike interactions among jazz students and the development of a jazz‐improvising humanoid robot marimba player in the United States, contextually meaningful contingency is widely used as a cultural resource for negotiating problems of intentionality. Whereas anthropologists have been concerned with the use of contingency mostly as a cultural resource for increasing predictability of intentions in conflictual situations, I highlight contexts pervaded by modern normative ideals of creativity in which predictability of intentions constitutes a problem, for which contextually meaningful contingency is used as a solution.
Senses of care: Embodying inequality and sustaining personhood in the home care of older adults in Chicago
Authors: BUCH ELANA D.
Published: November 2013

In paid home care—one of the fastest‐growing occupations in the United States—low‐wage workers help elderly clients living in their own homes remain independent by embodying and then reproducing the elders’ lifetimes of experience. Exploring the bodily and moral consequences of everyday home care practices in Chicago, I show that in this context, sustaining independent personhood depended on and intensified unequal social relations. To sustain clients’ personhood, workers developed a deeply embodied empathy that enabled them to imagine and re‐create the elders’ social and sensory worlds. Home care practices involved unreciprocated circulations of bodily experience that led some workers to feel that the needs and preferences of their clients took priority over their own comfort and well‐being. Care workers’ bodily practices thus became one way in which social hierarchies shaped individual subjectivities and came to seem morally legitimate.
Religious cosmopolitanisms: Media, transnational Santería, and travel between the United States and Cuba
Authors: BELISO‐DE JESUS AISHA
Published: November 2013

Santería religious travel and media circulations between Cuba and the United States have created new multilateral transnational linkages since the mid‐1990s. U.S.‐based Santería travelers and the Cuban priests who engage with them draw on global–local theoretical models in their interactions, in which video recording of rituals, a putatively prohibited practice in Santería, is becoming increasingly common. I suggest that ontological formations are shifting understandings and uses of religious media. Videos are used as sources of ritual knowledge and as part of rituals themselves and are thought of as ways to virtually and spiritually “travel.” I show how U.S. and Cuban practitioners draw on shared but uneven “religious cosmopolitanisms,” whereby they reconfigure notions of “mobility” through travel‐by‐video and infuse transnational experiences with new spiritual–religious meanings.
The hybrid state: Crime and citizenship in urban Jamaica
Authors: JAFFE RIVKE
Published: November 2013

In inner‐city neighborhoods in Kingston, Jamaica, criminal “dons” have taken on a range of governmental functions. While such criminal actors have sometimes been imagined as heading “parallel states,” I argue that they are part of a hybrid state, an emergent political formation in which multiple governmental actors—in this case, criminal organizations, politicians, police, and bureaucrats—are entangled in a relationship of collusion and divestment, sharing control over urban spaces and populations. Extending recent scholarship on variegated sovereignty and neoliberal shifts in governance, I consider the implications of this diversification of governmental actors for the ways that citizenship is experienced and enacted. The hybrid state both produces and relies on distinct political subjectivities. It is accompanied by a reconfigured, hybrid citizenship, in which multiple practices and narratives related to rule and belonging, to rights and responsibilities, are negotiated by a range of actors.
Omnibus Risk Assessment via Accelerated Failure Time Kernel Machine Modeling
Authors: Sinnott Jennifer A. , Cai Tianxi
Published: November 2013

Integrating genomic information with traditional clinical risk factors to improve the prediction of disease outcomes could profoundly change the practice of medicine. However, the large number of potential markers and possible complexity of the relationship between markers and disease make it difficult to construct accurate risk prediction models. Standard approaches for identifying important markers often rely on marginal associations or linearity assumptions and may not capture non-linear or interactive effects. In recent years, much work has been done to group genes into pathways and networks. Integrating such biological knowledge into statistical learning could potentially improve model interpretability and reliability. One effective approach is to employ a kernel machine (KM) framework, which can capture nonlinear effects if nonlinear kernels are used (Scholkopf and Smola, 2002; Liu et al., 2007, 2008). For survival outcomes, KM regression modeling and testing procedures have been derived under a proportional hazards (PH) assumption (Li and Luan, 2003; Cai, Tonini, and Lin, 2011). In this article, we derive testing and prediction methods for KM regression under the accelerated failure time (AFT) model, a useful alternative to the PH model. We approximate the null distribution of our test statistic using resampling procedures. When multiple kernels are of potential interest, it may be unclear in advance which kernel to use for testing and estimation. We propose a robust Omnibus Test that combines information across kernels, and an approach for selecting the best kernel for estimation. The methods are illustrated with an application in breast cancer.
Bayesian Latent-Class Mixed-Effect Hybrid Models for Dyadic Longitudinal Data with Non-Ignorable Dropouts
Authors: Ahn Jaeil , Liu Suyu , Wang Wenyi , Yuan Ying
Published: November 2013

The analysis of longitudinal dyadic data is challenging due to the complicated correlations within and between dyads, as well as possibly non-ignorable dropouts. Based on a mixed-effects hybrid model, we propose an approach to analyze longitudinal dyadic data with non-ignorable dropouts. We factorize the joint distribution of the measurement and dropout processes into three components: the marginal distribution of random effects, the conditional distribution of the dropout process given the random effects, and the conditional distribution of the measurement process given the random effects and missing data patterns. We model the conditional dropout process using a discrete survival model, and the conditional measurement process using a latent-class pattern-mixture model. These models account for the dyadic interdependence using the “actor” and “partner” effects and dyad-specific random effects. We use the latent-dropout-class approach to address the problem of a large number of missing data patterns caused by the dyadic data structure. We evaluate the performance of the proposed method using a simulation study, and apply our method to a longitudinal dyadic data set that arose from a prostate cancer trial.
Model selection for minimum‐diameter partitioning
Authors: Brusco Michael J. , Steinley Douglas
Published: November 2013

The minimum‐diameter partitioning problem (MDPP) seeks to produce compact clusters, as measured by an overall goodness‐of‐fit measure known as the partition diameter, which represents the maximum dissimilarity between any two objects placed in the same cluster. Complete‐linkage hierarchical clustering is perhaps the best‐known heuristic method for the MDPP and has an extensive history of applications in psychological research. Unfortunately, this method has several inherent shortcomings that impede the model selection process, such as: (1) sensitivity to the input order of the objects, (2) failure to obtain a globally optimal minimum‐diameter partition when cutting the tree at K clusters, and (3) the propensity for a large number of alternative minimum‐diameter partitions for a given K. We propose that each of these problems can be addressed by applying an algorithm that finds all of the minimum‐diameter partitions for different values of K. Model selection is then facilitated by considering, for each value of K, the reduction in the partition diameter, the number of alternative optima, and the partition agreement among the alternative optima. Using five examples from the empirical literature, we show the practical value of the proposed process for facilitating model selection for the MDPP.
Methyl jasmonate sensitizes human bladder cancer cells to gambogic acid‐induced apoptosis through down‐regulation of EZH2 expression by miR‐101
Authors: Wang Yongjun , Xiang Wei , Wang Miao , Huang Tao , Xiao Xingyuan , Wang Liang , Tao Dan , Dong Liyun , Zeng Fuqing , Jiang Guosong
Published: November 2013

Background and Purpose

Gambogic acid (GA) and methyl jasmonate (MJ) are increasingly being recognized as novel natural anticancer compounds. Here, we investigated the antitumour effects of GA in combination with MJ on human bladder cancer cells.

Experimental Approach

Cell viability was detected by cell counting kit‐8 assay. Cell apoptosis was assessed by Hoechst 33258 staining and flow cytometry. Protein levels were determined by immunoblotting and expressions of mRNA and miRNAs by RT‐PCR. Differential expressions of a group of downstream genes were identified using microarray analysis.

Key Results

MJ significantly sensitized bladder cancer cells to GA‐induced growth inhibition and apoptosis while sparing normal fibroblasts. MJ enhanced GA‐induced activation of caspase‐3 and caspase‐9, and down‐regulated the expression of XIAP. Furthermore, treatment of bladder cancer cells with a combination of GA and MJ induced synergistic inhibition of the enhancer of zeste homologue 2 (EZH2) expression, whereas miR‐101 expression was up‐regulated. Conversely, knockdown of miR‐101 restored this decreased expression of EZH2 and suppressed the inhibitory effect of GA and MJ on the growth of bladder cancer cells. Microarray analysis showed that genes closely associated with bladder cancer development were significantly down‐regulated by GA and MJ. In a s.c. xenograft mouse model of human bladder carcinoma, the combination of GA and MJ exerted an increased antitumour effect compared with GA alone.

Conclusion and Implications

MJ sensitizes bladder cancer cells to GA‐induced apoptosis by down‐regulating the expression of EZH2 induced by miR‐101. Thus, the combination of selective anti‐cancer agents MJ and GA could provide a novel strategy for treating human bladder cancer.
TRP channels in lower urinary tract dysfunction
Authors: Franken J , Uvin P , De Ridder D , Voets T
Published: November 2013

Lower urinary tract dysfunction (LUTd) represents a major healthcare problem. Although it is mostly not lethal, associated social disturbance, medical costs, loss of productivity and especially diminished quality of life should not be underestimated. Although more than 15% of people suffer from a form of LUTd to some extent, pathophysiology often remains obscure. In the past 20 years, transient receptor potential (TRP) channels have become increasingly important in this field of research. These intriguing ion channels are believed to be the main molecular sensors that generate bladder sensation. Therefore, they are intensely pursued as new drug targets for both curative and symptomatic treatment of different forms of LUTd. TRPV1 was the first of its class to be investigated. Actually, even before this channel was cloned, it had already been targeted in the bladder, with clinical trials of intravesical capsaicin instillations. Several other polymodally gated TRP channels, particularly TRPM8, TRPA1 and TRPV4, also appear to play a prominent role in bladder (patho)physiology. With this review, we provide a brief overview of current knowledge on the role of these TRP channels in LUTd and their potential as molecular targets for treatment.

Linked Articles

This article is part of a themed section on the pharmacology of TRP channels. To view the other articles in this section visit http://dx.doi.org/10.1111/bph.2014.171.issue‐10