bluuebunny/crossref_metadata_2025 huggingface dataset:
Fabrication and testing of porous Ti microneedles for drug delivery
Authors: Yan Xiao‐Xiao , Liu Jing‐Quan , Jiang Shui‐Dong , Yang Bin , Yang Chun‐Sheng
Published: December 2013

Porous metal microneedles were fabricated by an incorporated process of cutting and wet etching. Each microneedle is comprised of many connecting microholes that can deliver drugs into organisms conveniently and efficiently. The microneedle height is larger than 400 μm, the pitch distance is about 800 μm and the microholes in each microneedle are about 20 μm in diameter. In force testing, the microneedles could resist large shear forces and pierce into skins easily; in the in vivo experiment, the insulin was efficiently injected into rats by a patch of the microneedles. The testing and the experiment demonstrated that the microneedles could deliver drugs into organisms to treat diseases without fracture.
Can Customer Satisfaction and Dissatisfaction Coexist? An Issue of Telecommunication Service in China
Authors: Chen Aihui , Lu Yaobin , Gupta Sumeet , Xiaolin Qi
Published: December 2013

Although the telecommunication industry in China is growing at a fast pace, and firms are making strong efforts to provide customers with various services, customer switching continues to be high. Satisfaction has been considered as one of the most important antecedent of customer loyalty. However, little attention has been paid to dissatisfaction, a qualitatively different construct from satisfaction, which also influences loyalty. Relying on the two-factor and three-factor theory, this research proposes a theoretical framework to demonstrate the coexistence of customer satisfaction and dissatisfaction, and investigates the different antecedents and influences of satisfaction and dissatisfaction on customer loyalty. Through an exploratory study, we derived 11 telecom service attributes and further classified them into three categories, namely, hygiene factors, bivalent factors, and motivating factors. Each of these categories has a distinct effect on shaping customers’ satisfaction and dissatisfaction. The PLS analysis of the survey data collected from 679 respondents provides insights into the complex interrelationships between 11 telecom service attributes, functional perception, motivating perception, customer satisfaction, customer dissatisfaction, and customer loyalty constructs. This study has a few interesting implications for researchers and telecom industry managers.
Energy requirements for maintenance and growth of entire male Bali cattle in East Timor
Authors: Yuliaty  , Low S. , Fisher J. , Dryden G. McL.
Published: December 2013

The metabolisable energy (ME) requirements for maintenance and growth of entire male Bali cattle (Bos javanicus) were determined by regressing liveweight change on ME intake. Cattle were fed either a diet (DM basis) of 52.5% urea-treated rice straw plus 47.5% fresh leucaena forage (Expt 1), or fresh leucaena forage alone (Expt 2). In each experiment, liveweight change and feed intake were measured over 4 weeks, after a 1-week introductory period, and feed constituent digestibilities were measured during the final week. In Expt 1, 10 bulls between 1.5 and 3 years of age and weighing 123.7 ± 11.79 kg (mean ± s.d.) were allocated to DM intakes estimated to provide 0.75, 1.0, 1.25, 1.5, 1.75, or 2.0 times the estimated ME requirement for maintenance (based on calculations made from published CSIRO equations for tropical cattle species other than B. javanicus), with either one or two bulls per treatment. In Expt 2, the bulls were given treatments estimated to provide 0.85, 1.0, 1.4, 1.8, or 2.2 times the ME requirement for maintenance, with two bulls allocated to each treatment. The measured ME requirements for maintenance were 0.42 ± 0.369 and 0.40 ± 0.153 MJ/kg LW0.75.day (coefficient ± standard error, Expts 1 and 2, respectively). The ME requirement for ‘production’ (i.e. positive liveweight change of male Bali cattle under the specific conditions of the experiment) was calculated to be 39.2 MJ/kg liveweight gain in Expt 2. The calculated efficiency of use of dietary ME for production in Expt 2, was 0.34
A Nano-Silver Enhancement Effect on the Luminescence of a Ligand–Eu3+ Complex via a SiO2 Spacer
Authors: Wang Rui , Tang Jianguo , Kong Na , Wang Yao , Liu Jixian , Liu Jingquan
Published: December 2013

Luminescent rare earth complex (REC) nanocomposites, Eu(TTA)3Phen attached onto Ag@SiO2 nanoshells, were fabricated by facile wet chemistry and self-assembly techniques. Transmission electron microscopy, and fourier transform infrared and UV–Vis spectroscopy were used to investigate the step-by-step fabrication. The luminescence of REC was significantly enhanced using a silver core (size: 45 nm) surrounded by a 20-nm thick silica shell. Thicker or thinner silica shells afforded tuning of the metal-enhanced luminescence. The thiophene-TTA-containing REC fluorophore was able to etch the silver core, resulting in hollow silica shells, consequently displaying no luminescence enhancing capabilities. The etching efficiency was proportional to the concentration of Eu(TTA)3Phen, and decreased with increasing shell thickness.
Role of free-ranging mammals in the deposition of Escherichia coli into a Texas floodplain
Authors: Parker Israel D. , Lopez Roel R. , Padia Reema , Gallagher Meghan , Karthikeyan Raghupathy , Cathey James C. , Silvy Nova J. , Davis Donald S.
Published: December 2013

Context The role of wildlife in faecal pollution of water bodies (deposition of Escherichia coli (E. coli)) is not well understood. Current water-quality and land-use planning research largely relies on unreliable wildlife data (e.g. poor sourcing of abundance estimates, population density estimates applied to multiple fundamentally different areas, suspect or insufficiently described data collection techniques) Aims Our goal for the present research was to investigate deposition of E. coli into a floodplain by free-ranging mammals. Objectives of the research were to determine the density of important free-ranging meso- and large mammals in the study area, determine faecal E. coli loads for each species, and evaluate spatial data on species-specific faecal deposition. Methods We conducted our research in south-eastern Texas, USA, on two cattle ranches bisected by Cedar Creek (44-km long). Cedar Creek has elevated E. coli concentrations. We conducted mark–recapture and mark–resight population density estimates (2008/09) for meso- and large mammals in the study areas. We collected faecal samples from all captured wildlife. We also conducted transects through the study area to determine faecal-deposition patterns. Key results We found that raccoons (Procyon lotor), wild pigs (Sus scrofa), Virginia opossums (Didelphis virginiana) and white-tailed deer (Odocoileus virginianus) all had substantial faecal E. coli loads and population densities, thus implying an important role in E. coli deposition into the study floodplain. All species were widely distributed through the floodplain. Conclusions Free-ranging mammals contribute E. coli to floodplains and potentially affect water quality. We determined that four species commonly found in floodplains throughout North America all contributed E. coli to the study floodplain, thus implying mammal E. coli contributions in many locations and this is potentially important for E. coli management. Implications Improved locally specific mammal population estimates and estimates of locally derived E. coli concentration will improve floodplain and water-quality models that often depend on data of various quality. Additionally, our analyses demonstrated the need for continued research into the role of wildlife in E. coli deposition.
Estimating lizard population density: an empirical comparison between line-transect and capture–recapture methods
Authors: Ruiz de Infante Anton J. , Rotger A. , Igual J. M. , Tavecchia G.
Published: December 2013

Context
In most natural populations, exhaustive counts are not possible and estimates need to be derived from partial sampling by using analytical methods that account for biological processes, sampling errors and detection probability. The methods available have contrasting pitfalls and payoffs in relation to the assumptions made but are seldom contrasted on the same population.

Aims
We compared density estimates derived by different sampling methods. Despite the real density being unknown, the ‘soft’ validation of density estimates might help to better understand the possible pitfalls and payoffs of each method. This was done in three closed populations and with three different habitat typologies to disentangle the effects of different capture-detection processes to those introduced by the method itself.

Methods
We considered the problem of estimating population density of the endemic Balearic lizard, Podarcis lilfordi, in three island populations. We compared estimates derived by distance sampling (LT) in three types of habitat with those calculated from a simultaneous 3-day capture–mark–recapture study. Capture histories of marked individuals were used to estimate density using spatially explicit capture–recapture models (SECR) and a capture–mark–recapture model without spatial data (CMR). Moreover, we empirically assessed the influence of survey duration by extending the survey in the largest island to five occasions. The real population density was unknown and absolute accuracy of each method cannot be assessed; nevertheless, relative estimates might be informative.

Key results
LT estimates had the greatest coefficient of variation in vegetated habitats, corresponding to possible departures from model assumptions. SECR estimates differed among islands and were from 12% to 37% lower than those derived by LT but only in the largest islands with high and dense vegetation. CMR estimates depended on the number of occasions whereas SECR did not and showed lower variance. LT and SECR estimates showed differences across islets.

Conclusions
Line-transect and capture–recapture methods gave comparable results but the interaction between recapture processes and habitat types should be considered when inferring density to the whole area. We found density estimates between 1500 and 2500 individuals ha–1, being a higher value than those found for lizards in continental regions.

Implications
Pitfalls and payoffs of each method are discussed to optimise experimental design in estimating population density.
Multimodel assessment of water scarcity under climate change
Authors: Schewe Jacob , Heinke Jens , Gerten Dieter , Haddeland Ingjerd , Arnell Nigel W. , Clark Douglas B. , Dankers Rutger , Eisner Stephanie , Fekete Balázs M. , Colón-González Felipe J. , Gosling Simon N. , Kim Hyungjun , Liu Xingcai , Masaki Yoshimitsu , Portmann Felix T. , Satoh Yusuke , Stacke Tobias , Tang Qiuhong , Wada Yoshihide , Wisser Dominik , Albrecht Torsten , Frieler Katja , Piontek Franziska , Warszawski Lila , Kabat Pavel
Published: December 2013

Water scarcity severely impairs food security and economic prosperity in many countries today. Expected future population changes will, in many countries as well as globally, increase the pressure on available water resources. On the supply side, renewable water resources will be affected by projected changes in precipitation patterns, temperature, and other climate variables. Here we use a large ensemble of global hydrological models (GHMs) forced by five global climate models and the latest greenhouse-gas concentration scenarios (Representative Concentration Pathways) to synthesize the current knowledge about climate change impacts on water resources. We show that climate change is likely to exacerbate regional and global water scarcity considerably. In particular, the ensemble average projects that a global warming of 2 °C above present (approximately 2.7 °C above preindustrial) will confront an additional approximate 15% of the global population with a severe decrease in water resources and will increase the number of people living under absolute water scarcity (<500 m
3
per capita per year) by another 40% (according to some models, more than 100%) compared with the effect of population growth alone. For some indicators of moderate impacts, the steepest increase is seen between the present day and 2 °C, whereas indicators of very severe impacts increase unabated beyond 2 °C. At the same time, the study highlights large uncertainties associated with these estimates, with both global climate models and GHMs contributing to the spread. GHM uncertainty is particularly dominant in many regions affected by declining water resources, suggesting a high potential for improved water resource projections through hydrological model development.
Assessing agricultural risks of climate change in the 21st century in a global gridded crop model intercomparison
Authors: Rosenzweig Cynthia , Elliott Joshua , Deryng Delphine , Ruane Alex C. , Müller Christoph , Arneth Almut , Boote Kenneth J. , Folberth Christian , Glotter Michael , Khabarov Nikolay , Neumann Kathleen , Piontek Franziska , Pugh Thomas A. M. , Schmid Erwin , Stehfest Elke , Yang Hong , Jones James W.
Published: December 2013

Significance

Agriculture is arguably the sector most affected by climate change, but assessments differ and are thus difficult to compare. We provide a globally consistent, protocol-based, multimodel climate change assessment for major crops with explicit characterization of uncertainty. Results with multimodel agreement indicate strong negative effects from climate change, especially at higher levels of warming and at low latitudes where developing countries are concentrated. Simulations that consider explicit nitrogen stress result in much more severe impacts from climate change, with implications for adaptation planning.
Production and stabilization of the trimeric influenza hemagglutinin stem domain for potentially broadly protective influenza vaccines
Authors: Lu Yuan , Welsh John P. , Swartz James R.
Published: December 2013

Significance

The discovery of neutralizing antibodies that block influenza infection by binding to the hemagglutinin (HA) stem domain raised the hope for broadly protective vaccines. These could avoid the need for annual vaccinations and reduce pandemic threats, and the stem subdomain of the trimeric HA ectodomain would be an ideal antigen. However, its production has proven extremely difficult. Here, we describe a simple procedure resulting in high yields of HA stem trimer recognized identically by a panel of neutralizing antibodies as compared with recognition of the full-length HA ectodomain. Cell-free protein synthesis is followed by a simple refolding procedure to produce a rationally mutated stem in which newly exposed protein surfaces are modified and trimerization is induced and covalently stabilized.
Circadian clock-dependent and -independent rhythmic proteomes implement distinct diurnal functions in mouse liver
Authors: Mauvoisin Daniel , Wang Jingkui , Jouffe Céline , Martin Eva , Atger Florian , Waridel Patrice , Quadroni Manfredo , Gachon Frédéric , Naef Felix
Published: December 2013

Significance

Circadian clocks orchestrate daily rhythms in behavior and physiology using temporal regulation of gene expression to control core clock genes and rhythmic output programs. Although transcription regulation was shown to drive extensive diurnal mRNA rhythms, less is known about the proteins. Here, we provide a proteome-wide study of rhythmic protein accumulation in mouse liver, showing that proteins preferentially accumulate in the morning and during the night. About one-half of these rhythmic proteins could not be explained by rhythmic mRNAs, suggesting that translational or posttranslational regulation plays an important role. Moreover, such rhythms involved many secreted proteins and were clock-independent. Hence, these findings indicate that feeding behavior might determine the rhythmic functions of circulating proteins in the blood.
Imaging the wave functions of adsorbed molecules
Authors: Lüftner Daniel , Ules Thomas , Reinisch Eva Maria , Koller Georg , Soubatch Serguei , Tautz F. Stefan , Ramsey Michael G. , Puschnig Peter
Published: December 2013

Significance

In quantum mechanics, the electrons in a molecule are described by a mathematical object termed the wave function or molecular orbital. This function determines the chemical and physical properties of matter and consequently there has been much interest in measuring orbitals, despite the fact that strictly speaking they are not quantum-mechanical observables. We show how the amplitude and phase of orbitals can be measured in good agreement with wave functions from ab initio calculations. Not only do such measurements allow wave functions of complex molecules and nanostructures to be determined, they also open up a window into critical discussions of theoretical orbital concepts.
Aggregation-triggering segments of SOD1 fibril formation support a common pathway for familial and sporadic ALS
Authors: Ivanova Magdalena I. , Sievers Stuart A. , Guenther Elizabeth L. , Johnson Lisa M. , Winkler Duane D. , Galaleldeen Ahmad , Sawaya Michael R. , Hart P. John , Eisenberg David S.
Published: December 2013

Significance

Pathological deposition of mutated Cu/Zn superoxide dismutase (SOD1) accounts for ∼20% of the familial ALS (fALS) cases. Insoluble protein aggregates, immunoreactive for SOD1, have been found in both fALS and sporadic ALS (sALS) patients. To study the molecular origin of SOD1 aggregation, we used a computational approach to discover four segments from SOD1 that form fibril-like aggregates. We found that two of these,
101
DSVISLS
107
and
147
GVIGIAQ
153
, are likely to trigger the aggregation of full-length SOD1, suggesting common molecular determinants of fALS and sALS.
Swimming against the tide: the Macro-Economic Research Group in the South African transition 1991–94
Authors: Freund William
Published: December 2013

This article focuses on the establishment and disowning of the Macro-Economic Research Group (MERG) by the African National Congress in the lead-up to the formation of the democratic dispensation of 1994 and the first elections, overwhelmingly won by the African National Congress (ANC), which still forms the national government of South Africa. Considerable emphasis is placed on the politics of the ANC and to a lesser extent the general situation of the South African economy rather than by dissecting economic debates alone. MERG was a relatively lone substantial voice calling for real structural and institutional changes in the economy, ultimately rejected by the ANC at the behest of business. Two decades after the end of apartheid, it has become a hallmark of liberal criticism of the government to denounce it as following the worked-out agenda of a radical agenda underlying the anti-apartheid rhetoric while the African National Congress clothes itself in the liberation language of the Freedom Charter and sometimes even the supposed first-stage National Democratic Revolution that will precede socialism reflecting the discourse of the South African Communist Party. The following discussion aims to clarify what actually happened in terms of macro-economic policy debates in the transitional years 1990–94 and the consequences.
Marikana, turning point in South African history
Authors: Alexander Peter
Published: December 2013

Equating a ‘turning point’ with what William Sewell terms an ‘event’, it is argued that Marikana is a turning point in South African history. The massacre was a rupture that led to a sequence of further occurrences, notably a massive wave of strikes, which are changing structures that shape people's lives. We have not yet reached the end of this chain of occurrences, and the scale of the turning point remains uncertain. In common with other events, Marikana has revealed structures unseen in normal times, providing an exceptional vantage point, allowing space for collective creativity, and enabling actors to envisage alternative futures.
Endosomal WASH and exocyst complexes control exocytosis of MT1-MMP at invadopodia
Authors: Monteiro Pedro , Rossé Carine , Castro-Castro Antonio , Irondelle Marie , Lagoutte Emilie , Paul-Gilloteaux Perrine , Desnos Claire , Formstecher Etienne , Darchen François , Perrais David , Gautreau Alexis , Hertzog Maud , Chavrier Philippe
Published: December 2013

Remodeling of the extracellular matrix by carcinoma cells during metastatic dissemination requires formation of actin-based protrusions of the plasma membrane called invadopodia, where the trans-membrane type 1 matrix metalloproteinase (MT1-MMP) accumulates. Here, we describe an interaction between the exocyst complex and the endosomal Arp2/3 activator Wiskott-Aldrich syndrome protein and Scar homolog (WASH) on MT1-MMP–containing late endosomes in invasive breast carcinoma cells. We found that WASH and exocyst are required for matrix degradation by an exocytic mechanism that involves tubular connections between MT1-MMP–positive late endosomes and the plasma membrane in contact with the matrix. This ensures focal delivery of MT1-MMP and supports pericellular matrix degradation and tumor cell invasion into different pathologically relevant matrix environments. Our data suggest a general mechanism used by tumor cells to breach the basement membrane and for invasive migration through fibrous collagen-enriched tissues surrounding the tumor.
Jab1 regulates Schwann cell proliferation and axonal sorting through p27
Authors: Porrello Emanuela , Rivellini Cristina , Dina Giorgia , Triolo Daniela , Del Carro Ubaldo , Ungaro Daniela , Panattoni Martina , Feltri Maria Laura , Wrabetz Lawrence , Pardi Ruggero , Quattrini Angelo , Previtali Stefano Carlo
Published: December 2013

Axonal sorting is a crucial event in nerve formation and requires proper Schwann cell proliferation, differentiation, and contact with axons. Any defect in axonal sorting results in dysmyelinating peripheral neuropathies. Evidence from mouse models shows that axonal sorting is regulated by laminin211– and, possibly, neuregulin 1 (Nrg1)–derived signals. However, how these signals are integrated in Schwann cells is largely unknown. We now report that the nuclear Jun activation domain–binding protein 1 (Jab1) may transduce laminin211 signals to regulate Schwann cell number and differentiation during axonal sorting. Mice with inactivation of Jab1 in Schwann cells develop a dysmyelinating neuropathy with axonal sorting defects. Loss of Jab1 increases p27 levels in Schwann cells, which causes defective cell cycle progression and aberrant differentiation. Genetic down-regulation of p27 levels in Jab1-null mice restores Schwann cell number, differentiation, and axonal sorting and rescues the dysmyelinating neuropathy. Thus, Jab1 constitutes a regulatory molecule that integrates laminin211 signals in Schwann cells to govern cell cycle, cell number, and differentiation. Finally, Jab1 may constitute a key molecule in the pathogenesis of dysmyelinating neuropathies.
ProbeSelect: selecting differentially expressed probes in transcriptional profile data
Authors: Hosur Raghavendra , Szak Suzanne , Thai Alice , Allaire Norm , Bienkowska Jadwiga
Published: December 2013

Summary: Transcriptional profiling still remains one of the most popular techniques for identifying relevant biomarkers in patient samples. However, heterogeneity in the population leads to poor statistical evidence for selection of most relevant biomarkers to pursue. In particular, human transcriptional differences can be subtle, making it difficult to tease out real differentially expressed biomarkers from the variability inherent in the population. To address this issue, we propose a simple statistical technique that identifies differentially expressed probes in heterogeneous populations as compared with controls.

Availability and implementation: The algorithm has been implemented in Java and available at www.sourceforge.net/projects/probeselect.

Contact:  jbienkowska@gmail.com or jadwiga@csail.mit.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
DIVE: a data intensive visualization engine
Authors: Bromley Dennis , Rysavy Steven J. , Su Robert , Toofanny Rudesh D. , Schmidlin Tom , Daggett Valerie
Published: December 2013

Summary: Modern scientific investigation is generating increasingly larger datasets, yet analyzing these data with current tools is challenging. DIVE is a software framework intended to facilitate big data analysis and reduce the time to scientific insight. Here, we present features of the framework and demonstrate DIVE’s application to the Dynameomics project, looking specifically at two proteins.

Availability and implementation: Binaries and documentation are available at http://www.dynameomics.org/DIVE/DIVESetup.exe.

Contact:  daggett@uw.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
ORCA: a COBRA toolbox extension for model-driven discovery and analysis
Authors: Mao Longfei , Verwoerd Wynand S.
Published: December 2013

Summary: Over past decades, constraint-based modelling has emerged as an important approach to obtain referential information about mechanisms behind biological phenotypes and identify physiological and perturbed metabolic states at genome-scale. However, application of this novel approach to systems biology in biotechnology is still hindered by the functionalities of the existing modelling software. To augment the usability of the constraint-based approach for various use scenarios, we present ORCA, a Matlab package, which extends the scope of established Constraint-Based Reconstruction and Analysis metabolic modelling and includes three unique functionalities: (i) a framework method integrating three analyses of multi-objective optimization, robustness analysis and fractional benefit analysis, (ii) metabolic pathways identification with futile loop elimination and (iii) a dynamic flux balance analysis framework incorporating kinetic constraints.

Availability and implementation: ORCA is freely available to academic users and is downloadable from https://sourceforge.net/projects/exorca/; a mini-tutorial is supplied in the package for training purposes as well as a software manual.

Contact:  Longfei.mao@lincolnuni.ac.nz

Supplementary information:  Supplementary data are available at Bioinformatics online.
NeuroPID: a predictor for identifying neuropeptide precursors from metazoan proteomes
Authors: Ofer Dan , Linial Michal
Published: December 2013

Motivation: The evolution of multicellular organisms is associated with increasing variability of molecules governing behavioral and physiological states. This is often achieved by neuropeptides (NPs) that are produced in neurons from a longer protein, named neuropeptide precursor (NPP). The maturation of NPs occurs through a sequence of proteolytic cleavages. The difficulty in identifying NPPs is a consequence of their diversity and the lack of applicable sequence similarity among the short functionally related NPs.

Results: Herein, we describe Neuropeptide Precursor Identifier (NeuroPID), a machine learning scheme that predicts metazoan NPPs. NeuroPID was trained on hundreds of identified NPPs from the UniProtKB database. Some 600 features were extracted from the primary sequences and processed using support vector machines (SVM) and ensemble decision tree classifiers. These features combined biophysical, chemical and informational–statistical properties of NPs and NPPs. Other features were guided by the defining characteristics of the dibasic cleavage sites motif. NeuroPID reached 89–94% accuracy and 90–93% precision in cross-validation blind tests against known NPPs (with an emphasis on Chordata and Arthropoda). NeuroPID also identified NPP-like proteins from extensively studied model organisms as well as from poorly annotated proteomes. We then focused on the most significant sets of features that contribute to the success of the classifiers. We propose that NPPs are attractive targets for investigating and modulating behavior, metabolism and homeostasis and that a rich repertoire of NPs remains to be identified.

Availability: NeuroPID source code is freely available at http://www.protonet.cs.huji.ac.il/neuropid

Contact:  michall@cc.huji.ac.il

Supplementary information:  Supplementary data are available at Bioinformatics online.
Pathogenic Th2-type follicular helper T cells contribute to the development of lupus inFas-deficient mice
Authors: Futatsugi-Yumikura Shizue , Matsushita Kazufumi , Fukuoka Ayumi , Takahashi Suzuka , Yamamoto Nayu , Yonehara Shin , Nakanishi Kenji , Yoshimoto Tomohiro
Published: December 2013

Fas mutant mice are well recognized as autoimmune mouse models, which develop symptoms similar to human systemic lupus erythematosus. Although disease severity in Fas mutant mice is greatly affected by the genetic background, the mechanisms affecting pathological heterogeneity among different strains of Fas mutant mice are poorly understood. In this study, we examined the phenotypic differences between Fas-deficient (Fas−/−) mice on the BALB/c and C57BL/6 backgrounds to gain insight into the etiological and pathological heterogeneity of monogenic autoimmune diseases. Fas−/− mice on the BALB/c background (BALB/c-Fas−/−) developed more severe autoimmune disease with high serum auto-antibodies and renal disease compared with those on the C57BL/6 background (C57BL/6-Fas−/−). Splenic B cells were highly activated, and germinal center formation was enhanced in BALB/c-Fas−/− but not in C57BL/6-Fas−/− mice. Follicular helper T (Tfh) cells were equally abundant in the spleens from both strains of Fas−/− mice. However, Tfh cells from BALB/c-Fas−/− mice produced much higher amounts of B-cell-activating cytokines, including IL-4 and IL-10, a phenotype reminiscent of Th2-type Tfh cells described in human studies. Our results revealed a qualitative difference in Tfh cells between the two strains of Fas−/− mice. We propose that the pathogenic Th2-type Tfh cells in BALB/c-Fas−/− mice contribute to the excessive activation of B cells, resulting in high serum immunoglobulin levels and the severe lupus phenotype, which may account for the differential outcomes of human monogenic autoimmune diseases.
Human 4E-T represses translation of bound mRNAs and enhances microRNA-mediated silencing
Authors: Kamenska Anastasiia , Lu Wei-Ting , Kubacka Dorota , Broomhead Helen , Minshall Nicola , Bushell Martin , Standart Nancy
Published: December 2013

A key player in translation initiation is eIF4E, the mRNA 5′ cap-binding protein. 4E-Transporter (4E-T) is a recently characterized eIF4E-binding protein, which regulates specific mRNAs in several developmental model systems. Here, we first investigated the role of its enrichment in P-bodies and eIF4E-binding in translational regulation in mammalian cells. Identification of the conserved C-terminal sequences that target 4E-T to P-bodies was enabled by comparison of vertebrate proteins with homologues in Drosophila (Cup and CG32016) and Caenorhabditis elegans by sequence and cellular distribution. In tether function assays, 4E-T represses bound mRNA translation, in a manner independent of these localization sequences, or of endogenous P-bodies. Quantitative polymerase chain reaction and northern blot analysis verified that bound mRNA remained intact and polyadenylated. Ectopic 4E-T reduces translation globally in a manner dependent on eIF4E binding its consensus Y30X4Lϕ site. In contrast, tethered 4E-T continued to repress translation when eIF4E-binding was prevented by mutagenesis of YX4Lϕ, and modestly enhanced the decay of bound mRNA, compared with wild-type 4E-T, mediated by increased binding of CNOT1/7 deadenylase subunits. As depleting 4E-T from HeLa cells increased steady-state translation, in part due to relief of microRNA-mediated silencing, this work demonstrates the conserved yet unconventional mechanism of 4E-T silencing of particular subsets of mRNAs.
The influence of viral RNA secondary structure on interactions with innate host cell defences
Authors: Witteveldt Jeroen , Blundell Richard , Maarleveld Joris J. , McFadden Nora , Evans David J. , Simmonds Peter
Published: December 2013

RNA viruses infecting vertebrates differ fundamentally in their ability to establish persistent infections with markedly different patterns of transmission, disease mechanisms and evolutionary relationships with their hosts. Although interactions with host innate and adaptive responses are complex and persistence mechanisms likely multi-factorial, we previously observed associations between bioinformatically predicted RNA secondary formation in genomes of positive-stranded RNA viruses with their in vivo fitness and persistence. To analyse this interactions functionally, we transfected fibroblasts with non-replicating, non-translated RNA transcripts from RNA viral genomes with differing degrees of genome-scale ordered RNA structure (GORS). Single-stranded RNA transcripts induced interferon-β mediated though RIG-I and PKR activation, the latter associated with rapid induction of antiviral stress granules. A striking inverse correlation was observed between induction of both cellular responses with transcript RNA structure formation that was independent of both nucleotide composition and sequence length. The consistent inability of cells to recognize RNA transcripts possessing GORS extended to downstream differences from unstructured transcripts in expression of TNF-α, other interferon-stimulated genes and induction of apoptosis. This functional association provides novel insights into interactions between virus and host early after infection and provides evidence for a novel mechanism for evading intrinsic and innate immune responses.
Genetic analysis of the Replication Protein A large subunit family in Arabidopsis reveals unique and overlapping roles in DNA repair, meiosis and DNA replication
Authors: Aklilu Behailu B. , Soderquist Ryan S. , Culligan Kevin M.
Published: December 2013

Replication Protein A (RPA) is a heterotrimeric protein complex that binds single-stranded DNA. In plants, multiple genes encode the three RPA subunits (RPA1, RPA2 and RPA3), including five RPA1-like genes in Arabidopsis. Phylogenetic analysis suggests two distinct groups composed of RPA1A, RPA1C, RPA1E (ACE group) and RPA1B, RPA1D (BD group). ACE-group members are transcriptionally induced by ionizing radiation, while BD-group members show higher basal transcription and are not induced by ionizing radiation. Analysis of rpa1 T-DNA insertion mutants demonstrates that although each mutant line is likely null, all mutant lines are viable and display normal vegetative growth. The rpa1c and rpa1e single mutants however display hypersensitivity to ionizing radiation, and combination of rpa1c and rpa1e results in additive hypersensitivity to a variety of DNA damaging agents. Combination of the partially sterile rpa1a with rpa1c results in complete sterility, incomplete synapsis and meiotic chromosome fragmentation, suggesting an early role for RPA1C in promoting homologous recombination. Combination of either rpa1c and/or rpa1e with atr revealed additive hypersensitivity phenotypes consistent with each functioning in unique repair pathways. In contrast, rpa1b rpa1d double mutant plants display slow growth and developmental defects under non-damaging conditions. We show these defects in the rpa1b rpa1d mutant are likely the result of defective DNA replication leading to reduction in cell division.
Functional domains of the 50S subunit mature late in the assembly process
Authors: Jomaa Ahmad , Jain Nikhil , Davis Joseph H. , Williamson James R. , Britton Robert A. , Ortega Joaquin
Published: December 2013

Despite the identification of many factors that facilitate ribosome assembly, the molecular mechanisms by which they drive ribosome biogenesis are poorly understood. Here, we analyze the late stages of assembly of the 50S subunit using Bacillus subtilis cells depleted of RbgA, a highly conserved GTPase. We found that RbgA-depleted cells accumulate late assembly intermediates bearing sub-stoichiometric quantities of ribosomal proteins L16, L27, L28, L33a, L35 and L36. Using a novel pulse labeling/quantitative mass spectrometry technique, we show that this particle is physiologically relevant and is capable of maturing into a complete 50S particle. Cryo-electron microscopy and chemical probing revealed that the central protuberance, the GTPase associating region and tRNA-binding sites in this intermediate are unstructured. These findings demonstrate that key functional sites of the 50S subunit remain unstructured until late stages of maturation, preventing the incomplete subunit from prematurely engaging in translation. Finally, structural and biochemical analysis of a ribosome particle depleted of L16 indicate that L16 binding is necessary for the stimulation of RbgA GTPase activity and, in turn, release of this co-factor, and for conversion of the intermediate to a complete 50S subunit.
Molecular evolution of protein-RNA mimicry as a mechanism for translational control
Authors: Katz Assaf , Solden Lindsey , Zou S. Betty , Wiley Navarre William , Ibba Michael
Published: December 2013

Elongation factor P (EF-P) is a conserved ribosome-binding protein that structurally mimics tRNA to enable the synthesis of peptides containing motifs that otherwise would induce translational stalling, including polyproline. In many bacteria, EF-P function requires post-translational modification with (R)-β-lysine by the lysyl-tRNA synthetase paralog PoxA. To investigate how recognition of EF-P by PoxA evolved from tRNA recognition by aminoacyl-tRNA synthetases, we compared the roles of EF-P/PoxA polar contacts with analogous interactions in a closely related tRNA/synthetase complex. PoxA was found to recognize EF-P solely via identity elements in the acceptor loop, the domain of the protein that interacts with the ribosome peptidyl transferase center and mimics the 3'-acceptor stem of tRNA. Although the EF-P acceptor loop residues required for PoxA recognition are highly conserved, their conservation was found to be independent of the phylogenetic distribution of PoxA. This suggests EF-P first evolved tRNA mimicry to optimize interactions with the ribosome, with PoxA-catalyzed aminoacylation evolving later as a secondary mechanism to further improve ribosome binding and translation control.
Transcriptional regulation by BglJ–RcsB, a pleiotropic heteromeric activator in Escherichia coli
Authors: Salscheider Silja Lucia , Jahn Andreas , Schnetz Karin
Published: December 2013

The bacterial Rcs phosphorelay signals perturbations of the bacterial cell envelope to its response regulator RcsB, which regulates transcription of multiple loci related to motility, biofilm formation and various stress responses. RcsB is unique, as its set of target loci is modulated by interaction with auxiliary regulators including BglJ. The BglJ–RcsB heteromer is known to activate the HNS repressed leuO and bgl loci independent of RcsB phosphorylation. Here, we show that BglJ–RcsB activates the promoters of 10 additional loci (chiA, molR, sfsB, yecT, yqhG, ygiZ, yidL, ykiA, ynbA and ynjI). Furthermore, we mapped the BglJ–RcsB binding site at seven loci and propose a consensus sequence motif. The data suggest that activation by BglJ–RcsB is DNA phasing dependent at some loci, a feature reminiscent of canonical transcriptional activators, while at other loci BglJ–RcsB activation may be indirect by inhibition of HNS-mediated repression. In addition, we show that BglJ–RcsB activates transcription of bgl synergistically with CRP where it shifts the transcription start by 20 bp from a position typical for class I CRP-dependent promoters to a position typical for class II CRP-dependent promoters. Thus, BglJ–RcsB is a pleiotropic transcriptional activator that coordinates regulation with global regulators including CRP, LeuO and HNS.
Depression Subtypes in Pediatric Inflammatory Bowel Disease
Authors: Szigethy Eva M. , Youk Ada O. , Benhayon David , Fairclough Diane L. , Newara Melissa C. , Kirshner Margaret A. , Bujoreanu Simona I. , Mrakotsky Christine , Bousvaros Athos , Srinath Arvind I. , Keljo David J. , Kupfer David J. , DeMaso David R.
Published: December 2013

Objective:

The association between inflammatory bowel disease (IBD) and depression provides a unique opportunity to understand the relation between systemic inflammation and depressive symptom profiles.

Methods:

Youth (n = 226) ages 9 to 17 years with comorbid IBD and depression underwent psychiatric assessment and evaluation of IBD activity. Latent profile analysis (LPA) identified depressive subgroups based on similar responses to the Children's Depression Rating Scale‐Revised. Demographic factors, depression severity, anxiety, IBD activity, inflammatory markers, IBD‐related medications, and illness perception were evaluated as predictors of profile membership.

Results:

Mean age was 14.3 years; 75% had Crohn disease; 31% were taking systemic corticosteroids. Mean depressive severity was moderate, whereas IBD activity, which reflects inflammation, was mild. LPA identified 3 subgroups: Profile‐1 (mild, 75%) had diverse low‐grade depressive symptoms and highest quality of life; Profile‐2 (somatic, 19%) had severe fatigue, appetite change, anhedonia, decreased motor activity, and depressed mood with concurrent high‐dose steroid therapy and the highest IBD activity; and Profile‐3 (cognitive, 6%) had the highest rates of self‐reported depressive symptoms, ostomy placements, and anxiety with IBD symptoms in the relative absence of inflammation.

Conclusions:

Evidence was found for 3 depression profiles in youth with IBD and depression. Our analyses determined that patients with predominantly somatic or cognitive symptoms of depression comprised 25% of our cohort. These findings may be used to design subgroup‐specific interventions for depression in adolescents with IBD and other physical illnesses associated with systemic inflammation.
Evaluation and Treatment of Functional Constipation in Infants and Children
Authors: Tabbers M.M. , DiLorenzo C. , Berger M.Y. , Faure C. , Langendam M.W. , Nurko S. , Staiano A. , Vandenplas Y. , Benninga M.A.
Published: December 2013

Background:

Constipation is a pediatric problem commonly encountered by many health care workers in primary, secondary, and tertiary care. To assist medical care providers in the evaluation and management of children with functional constipation, the North American Society for Pediatric Gastroenterology, Hepatology, and Nutrition and the European Society for Pediatric Gastroenterology, Hepatology, and Nutrition were charged with the task of developing a uniform document of evidence‐based guidelines.

Methods:

Nine clinical questions addressing diagnostic, therapeutic, and prognostic topics were formulated. A systematic literature search was performed from inception to October 2011 using Embase, MEDLINE, the Cochrane Database of Systematic Reviews and Cochrane Central Register of Controlled Clinical Trials, and PsychInfo databases. The approach of the Grading of Recommendations Assessment, Development and Evaluation was applied to evaluate outcomes. For therapeutic questions, quality of evidence was assessed using the Grading of Recommendations, Assessment, Development, and Evaluation system. Grading the quality of evidence for the other questions was performed according to the classification system of the Oxford Centre for Evidence‐Based Medicine. During 3 consensus meetings, all recommendations were discussed and finalized. The group members voted on each recommendation, using the nominal voting technique. Expert opinion was used where no randomized controlled trials were available to support the recommendation.

Results:

This evidence‐based guideline provides recommendations for the evaluation and treatment of children with functional constipation to standardize and improve their quality of care. In addition, 2 algorithms were developed, one for the infants <6 months of age and the other for older infants and children.

Conclusions:

This document is intended to be used in daily practice and as a basis for further clinical research. Large well‐designed clinical trials are necessary with regard to diagnostic evaluation and treatment.
EEG Abnormalities Are Associated With Increased Risk of Transplant or Poor Outcome in Children With Acute Liver Failure
Authors: Hussain Elora , Grimason Michele , Goldstein Joshua , Smith Craig M. , Alonso Estella , Whitington Peter F. , Wainwright Mark S.
Published: December 2013

Objectives:

There are limited data on the incidence of seizures and utility of brain imaging and electroencephalogram (EEG) to predict outcome of children with acute liver failure (ALF). We investigated the association between hepatic encephalopathy (HE) scores, abnormal EEG or neuroimaging, and short‐term outcome.

Methods:

Single‐center retrospective observational study of infants and children with ALF who underwent continuous EEG monitoring and brain imaging within 24 hours of admission to the intensive care unit (ICU).

Results:

A total of 19 patients with ALF with a mean age of 6.8 ± 1.5 years were evaluated. The majority of cases (74%) were indeterminate. Of the total, 10 patients (53%) survived to discharge without liver transplant (LT), 5 (26%) received LT, and 4 (21%) died without LT. Seizures occurred in only 2 cases (19%). Patients who had an abnormal EEG on admission (n = 7) were significantly more likely to die or require LT (P < 0.05, Fisher exact test). Patients with either an admission HE score ≤2, or liver injury unit score <222, combined with a normal or mildly abnormal EEG were more likely to survive without LT. Neuroimaging was normal in the majority of cases (87%) and was not associated with outcome.

Conclusions:

Children with a moderate or severe abnormality of EEG background on admission were significantly more likely to require LT or to die. Children with an HE score ≤2, and a normal or only mildly abnormal EEG, were significantly more likely to survive without needing LT. These findings are an initial step toward distinguishing patients with ALF who may recover spontaneously from those who will require LT.
Neumann nodal domains
Authors: McDonald Ross B. , Fulling Stephen A.
Published: December 2013

As an alternative to nodal domains in the usual sense, we propose a partition of the domain of a real-valued eigenfunction in

by trajectories of the gradient, linking saddle points to extrema. Its most elementary properties are listed and exemplified. The main point is that the problem of avoided crossings is largely eliminated.
The importance of population growth and regulation in human life history evolution
Authors: Baldini Ryan
Published: December 2013

Explaining the evolution of human life history characteristics remains an outstanding problem to evolutionary anthropologists. Progress is hindered by common misunderstandings of how selection works in age-structured populations. I review two important results of life history theory related to demography. First, different life history strategies evolve under density-independent and density-dependent population growth. Second, and more poorly appreciated, different kinds of density-dependence also select for different life history strategies; assuming zero population growth alone is insufficient to determine the optimal strategy. I show that these facts are more than methodological niceties by reanalyzing the model by Kaplan et al. (2000) and showing that the results depend strongly on the form of population regulation assumed. This analysis suggests that progress in human life history theory requires better understanding of the demography of our ancestors. I close with a discussion of empirical implications.