bluuebunny/crossref_metadata_2025 huggingface dataset:
Computational Modeling of the Regulatory Network Organizing the Wound Response in Arabidopsis thaliana
Authors: Kim Jan T. , Camargo Anyela , Devoto Alessandra , Moulton Vincent , Turner John
Published: September 2012

Plants are frequently wounded by mechanical impact or by insects, and their ability to adequately respond to wounding is essential for their survival and reproductive success. The wound response is mediated by a signal transduction and regulatory network. Molecular studies in Arabidopsis have identified the COI1 gene as a central component of this network. Current models of these networks qualitatively describe the wound response, but they are not directly assessed using quantitative gene expression data. We built a model comprising the key components of the Arabidopsis wound response using the transsys framework. For comparison, we constructed a null model that is devoid of any regulatory interactions, and various alternative models by rewiring the wound response model. All models were parametrized by computational optimization to generate synthetic gene expression profiles that approximate the empirical data set. We scored the fit of the synthetic to the empirical data with various distance measures, and used the median distance after optimization to directly and quantitatively assess the wound response model and its alternatives. Discrimination of candidate models depends substantially on the measure of gene expression profile distance. Using the null model to assess quality of the distance measures for discrimination, we identify correlation of log-ratio profiles as the most suitable distance. Our wound response model fits the empirical data significantly better than the alternative models. Gradual perturbation of the wound response model results in a corresponding gradual decline in fit. The optimization approach provides insights into biologically relevant features, such as robustness. It is a step toward enabling integrative studies of multiple cross-talking pathways, and thus may help to develop our understanding how the genome informs the mapping of environmental signals to phenotypic traits.
Indications of Stratified Turbulence in a Mechanistic GCM
Authors: Brune Sebastian , Becker Erich
Published: September 2012

The horizontal kinetic energy spectrum and its budget are analyzed on the basis of a general circulation model with simplistic parameterizations of radiative and latent heating. A spectral truncation at total wavenumber 330 is combined with a level spacing of either ~200 m or ~1.5 km from the midtroposphere to the lower stratosphere. The subgrid-scale parameterization consists of a Smagorinsky-type anisotropic diffusion scheme that is scaled by a Richardson criterion for dynamic instability and combined with a stress-tensor-based hyperdiffusion that acts only on the very smallest resolved scales. Simulations with both vertical resolutions show a transition from the synoptic −3 to the mesoscale slope in the upper-tropospheric kinetic energy spectrum. Analysis of the spectral budget indicates that the mesoscale slope can be interpreted as stratified turbulence, as has been proposed in recent works of Lindborg and others, only when a high vertical resolution is applied. In this case, the mesoscale kinetic energy around 300–150 hPa is dominated by the nonrotational flow, and the forward horizontal energy cascade is accompanied by an equally strong forward spectral flux due to adiabatic conversion. This adiabatic conversion mainly results from a vertical potential energy flux that originates in the midtroposphere, where the mesoscale adiabatic conversion is negative. For a conventionally coarse vertical resolution, however, the mesoscale slope in the troposphere is dominated by the rotational flow, and the spectral flux due to adiabatic conversion is not comparable to that associated with horizontal advection.
The Effect of Phase-Correlated Returns and Spatial Smoothing on the Accuracy of Radar Refractivity Retrievals
Authors: Nicol J. C. , Illingworth A. J.
Published: September 2012

Radar refractivity retrievals have the potential to accurately capture near-surface humidity fields from the phase change of ground clutter returns. In practice, phase changes are very noisy and the required smoothing will diminish large radial phase change gradients, leading to severe underestimates of large refractivity changes (ΔN). To mitigate this, the mean refractivity change over the field (〈ΔN〉field) must be subtracted prior to smoothing. However, both observations and simulations indicate that highly correlated returns (e.g., when single targets straddle neighboring gates) result in underestimates of 〈ΔN〉field when pulse-pair processing is used. This may contribute to reported differences of up to 30 N units between surface observations and retrievals. This effect can be avoided if 〈ΔN〉field is estimated using a linear least squares fit to azimuthally averaged phase changes. Nevertheless, subsequent smoothing of the phase changes will still tend to diminish the all-important spatial perturbations in retrieved refractivity relative to 〈ΔN〉field; an iterative estimation approach may be required. The uncertainty in the target location within the range gate leads to additional phase noise proportional to ΔN, pulse length, and radar frequency. The use of short pulse lengths is recommended, not only to reduce this noise but to increase both the maximum detectable refractivity change and the number of suitable targets. Retrievals of refractivity fields must allow for large ΔN relative to an earlier reference field. This should be achievable for short pulses at S band, but phase noise due to target motion may prevent this at C band, while at X band even the retrieval of ΔN over shorter periods may at times be impossible.
The Social Stratification of Older Adults’ Preparations for End-of-Life Health Care
Authors: Carr Deborah
Published: September 2012

I use data from the Wisconsin Longitudinal Study ( n = 4,971) to evaluate the extent to which socioeconomic status affects three health-related (living will, durable power of attorney for health care, and discussions) and one financial (will) component of end-of-life planning. Net worth is positively associated with all four types of planning, after demographic, health, and psychological characteristics are controlled. Low rates of health-related planning among persons with low or negative assets are largely accounted for by the fact that they are less likely to execute a will, an action that triggers health-related preparations. Rates of health-related planning alone are higher among recently hospitalized persons, whereas financial planning only is more commonly done by homeowners and those with richer assets. The results suggest that economically advantaged persons engage in end-of-life planning as a two-pronged strategy entailing financial and health-related preparations. Implications for health policy, practice, and theory are discussed.
Monitoring Early First-Grade Reading Progress
Authors: Clemens Nathan H. , Shapiro Edward S. , Wu Jiun-Yu , Taylor Aaron B. , Caskie Grace L.
Published: September 2012

This study compared the validity of progress monitoring slope of nonsense word fluency (NWF) and word identification fluency (WIF) with early first-grade readers. Students ( N = 80) considered to be at risk for reading difficulty were monitored with NWF and WIF on a 1-2 week basis across 11 weeks. Reading skills at the end of first grade were assessed using measures of passage reading fluency, real and pseudoword reading efficiency, and basic comprehension. Latent growth models indicated that although slope on both measures significantly predicted year-end reading skills, models including WIF accounted for more variance in spring reading skills than NWF, and WIF slope was more strongly associated with reading outcomes than NWF slope. Analyses of student growth plots suggested that WIF slope was more positively associated with later reading skills and discriminated more clearly between students according to successful or unsuccessful year-end reading outcomes. Although both measures may be used to monitor reading growth of at-risk students in early first grade, WIF may provide a clearer index of reading growth. Implications for data-based decision-making are discussed.
The Power of a Smile to Move You
Authors: de Lemus Soledad , Spears Russell , Moya Miguel
Published: September 2012

Extending evidence that nonverbal complementary behavior can occur in dyads to the intergroup domain, the authors predicted that women assume a relatively submissive (narrow) posture when confronted with a male instructor adopting a dominant (broad) posture, but only when he smiles (affiliation motive) and when gender is salient. Male affiliation (smiling vs. not smiling) and gender salience were manipulated in Study 1 by focusing on sex differences (vs. individual differences) in presentation style, strengthened by the instructor making a sexist remark. As predicted, women adopted a more submissive posture when gender was salient and the male instructor smiled. In Study 2, male posture was manipulated (dominant vs. submissive) to examine postural complementarity in women. Study 3 replicated the postural effect, especially when the sexist remark is present. This effect was mediated by the instructor’s perceived warmth. Implications for gender, benevolent sexism, and intergroup power relations are discussed.
The Contact Caveat
Authors: Barlow Fiona Kate , Paolini Stefania , Pedersen Anne , Hornsey Matthew J. , Radke Helena R. M. , Harwood Jake , Rubin Mark , Sibley Chris G.
Published: September 2012

Contact researchers have largely overlooked the potential for negative intergroup contact to increase prejudice. In Study 1, we tested the interaction between contact quantity and valence on prejudice toward Black Australians ( n = 1,476), Muslim Australians ( n = 173), and asylum seekers ( n = 293). In all cases, the association between contact quantity and prejudice was moderated by its valence, with negative contact emerging as a stronger and more consistent predictor than positive contact. In Study 2, White Americans ( n = 441) indicated how much positive and negative contact they had with Black Americans on separate measures. Although both quantity of positive and negative contact predicted racism and avoidance, negative contact was the stronger predictor. Furthermore, negative (but not positive) contact independently predicted suspicion about Barack Obama’s birthplace. These results extend the contact hypothesis by issuing an important caveat: Negative contact may be more strongly associated with increased racism and discrimination than positive contact is with its reduction.
The Language of Psychological Change
Authors: North Rebecca J. , Meyerson Rachel L. , Brown Danielle N. , Holahan Charles J.
Published: September 2012

This study uses linguistic analysis to investigate psychological changes associated with an emotion regulation strategy integrating psychological acceptance and positive reappraisal, as compared to two established strategies. Two hundred and sixty-nine undergraduate participants wrote for 4 consecutive days, 20 minutes each day, about the biggest problem in their lives and were randomly assigned to use one of three emotion regulation strategies: (a) acceptance + positive reappraisal, (2) emotional disclosure, or (3) positive reappraisal. Linguistic analyses were conducted to examine changes in attentional focus and insightful and causal thinking in the writings. Results indicated that participants who integrated acceptance and positive reappraisal wrote less about the past and more about the future, and used more insight words, over the course of writing relative to the other two conditions. In addition, they used a decreasing amount of first-person singular pronouns (e.g., “I”) and increased more in their use of first-person plural pronouns (e.g., “we”). Implications of these language findings for understanding underlying psychological changes are discussed.
Process and performance evaluation of ultrasonic, induction and resistance welding of advanced thermoplastic composites
Authors: Villegas Irene Fernandez , Moser Lars , Yousefpour Ali , Mitschang Peter , Bersee Harald EN
Published: September 2012

The possibility of assembling through welding is one of the major features of thermoplastic composites and it positively contributes to their cost-effectiveness in manufacturing. This article presents a comparative evaluation of ultrasonic, induction and resistance welding of individual carbon fibre-reinforced polyphenylene sulphide (PPS) thermoplastic composite samples that comprises an analysis of the static and dynamic mechanical behaviour of the joints as well as of the main process variables. The induction welding process as used in this research benefitted from the conductive nature of the reinforcing fibres. Hence, no susceptor was placed at the welding interface. Resistance welding used a fine-woven stainless-steel mesh as the heating element and low welding pressures and times were applied to prevent current leakage. Triangular energy directors moulded on a separate tape of PPS resin were used to concentrate ultrasonic heat at the welding interface. The static single-lap shear strength of the joints was found similar for induction and ultrasonic welding. A 15% drop in the static mechanical properties of the resistance welded joints was attributed to incomplete welded overlaps following current leakage prevention. However, the fatigue performance relative to the static one was similar for the three sorts of joints. A comparative analysis of process variables such as welding time, required power and energy was also carried out.
Don’t Judge a Book by Its Cover, Revisited
Authors: Segal-Caspi Lihi , Roccas Sonia , Sagiv Lilach
Published: September 2012

Research has documented a robust stereotype regarding personality attributes related to physical attractiveness (the “what is beautiful is good” stereotype). But do physically attractive women indeed possess particularly attractive inner attributes? Studying traits and values, we investigated two complementary questions: how perceived attractiveness relates to perceived personality, and how it relates to actual personality. First, 118 women reported their traits and values and were videotaped reading the weather forecast. Then, 118 judges rated the traits, values, and attractiveness of the women. As hypothesized, attractiveness correlated with attribution of desirable traits, but not with attribution of values. By contrast, attractiveness correlated with actual values, but not actual traits: Attractiveness correlated with tradition and conformity values (which were contrasted with self-direction values) and with self-enhancement values (which were contrasted with universalism values). Thus, despite the widely accepted “what is beautiful is good” stereotype, our findings suggest that the beautiful strive for conformity rather than independence and for self-promotion rather than tolerance.
The impact of rural residency on the expression and outcome of systemic lupus erythematosus: data from a multiethnic Latin American cohort
Authors: Pons-Estel GJ , Saurit V , Alarcón GS , Hachuel L , Boggio G , Wojdyla D , Alfaro-Lozano JL , de la Torre I García , Massardo L , Esteva-Spinetti MH , Guibert-Toledano M , Gómez LA Ramirez , Costallat LT Lavras , del Pozo MJ Sauza , Silveira LH , Cavalcanti F , Pons-Estel BA
Published: September 2012

Objective: The objective of this paper is to examine the role of place of residency in the expression and outcomes of systemic lupus erythematosus (SLE) in a multi-ethnic Latin American cohort. Patients and methods: SLE patients (<two years of diagnosis) from 34 centers constitute this cohort. Residency was dichotomized into rural and urban, cut-off: 10,000 inhabitants. Socio-demographic, clinical/laboratory and mortality rates were compared between them using descriptive tests. The influence of place of residency on disease activity at diagnosis and renal disease was examined by multivariable regression analyses. Results: Of 1426 patients, 122 (8.6%) were rural residents. Their median ages (onset, diagnosis) were 23.5 and 25.5 years; 85 (69.7%) patients were Mestizos, 28 (22.9%) Caucasians and 9 (7.4%) were African-Latin Americans. Rural residents were more frequently younger at diagnosis, Mestizo and uninsured; they also had fewer years of education and lower socioeconomic status, exhibited hypertension and renal disease more frequently, and had higher levels of disease activity at diagnosis; they used methotrexate, cyclophosphamide pulses and hemodialysis more frequently than urban patients. Disease activity over time, renal damage, overall damage and the proportion of deceased patients were comparable in rural and urban patients. In multivariable analyses, rural residency was associated with high levels of disease activity at diagnosis (OR 1.65, 95% CI 1.06–2.57) and renal disease occurrence (OR 1.77, 95% CI 1.00–3.11). Conclusions: Rural residency associates with Mestizo ethnicity, lower socioeconomic status and renal disease occurrence. It also plays a role in disease activity at diagnosis and kidney involvement but not on the other end-points examined.
Association between the CD226 rs763361 polymorphism and susceptibility to autoimmune diseases: a meta-analysis
Authors: Song GG , Bae S-C , Choi SJ , Ji JD , Lee YH
Published: September 2012

Objective: The aim of this study was to explore whether the CD226 rs763361 polymorphism confers susceptibility to autoimmune diseases. Methods: A meta-analysis was conducted on the associations between the CD226 rs763361 polymorphism and autoimmune diseases using: 1) allele contrast, and 2) the recessive, 3) dominant and 4) additive models. Results: Ten articles that included 17 comparative studies on a total of 8900 patients and 10,295 controls were included in the meta-analysis. These studies were performed on seven European, five Asian and five South American sample populations. Meta-analysis of all study subjects revealed an association between the CD226 rs763361 T allele and the susceptibility to autoimmune diseases (odds ratio; OR 1.162, 95% confidence interval; CI 1.097–1.230, p < 1.0 × 10–8). Stratification by ethnicity indicated an association between the CD226 rs763361 T allele and autoimmune disease in Europeans and South Americans (OR 1.134, 95% CI 1.079–1.191, p = 6.7 × 10–7; OR 1.308, 95% CI 1.160–1.475, p = 1.1 × 10–5) and between the CD226 rs763361 TT genotype and autoimmune disease in Asians (OR 1.366, 95% CI 1.130–1.650, p = 0.001). Disease-specific meta-analysis showed an association between systemic lupus erythematosus (SLE) and the CD226 rs763361 T allele (OR 1.150, 95% CI 1.040–1.271, p = 0.006), but no association between rheumatoid arthritis and the CD226 rs763361 polymorphism (OR for the T allele 1.207, 95% CI 0.913–1.596, p = 0.187). On the other hand, associations were found between the CD226 rs763361 T allele and systemic sclerosis (SSc) and type 1 diabetes (T1D) (OR 1.126, 95% CI 1.020–1.244, p = 0.019; OR 1.353, 95% CI 1.102–1.660, p = 0.004). Conclusions: This meta-analysis demonstrates the CD226 rs763361 polymorphism confers susceptibility to autoimmune disease in Europeans, South Americans and Asians, and in particular, shows that the CD226 rs763361 polymorphism is associated with SLE, SSc and T1D. These results support the existence of an association between the CD226 gene and a subgroup of autoimmune diseases.
Syntactic trees and small-world networks: syntactic development as a dynamical process
Authors: Barceló-Coblijn Lluís , Corominas-Murtra Bernat , Gomila Antoni
Published: September 2012

Language has been argued to exhibit a complex system behavior. In our approach, the syntactic relations of dependency between words have been represented as networks. In a previous study, two English infants’ corpora of utterances were analyzed longitudinally, offering a view of the ontogeny of syntax. Abrupt changes were detected in the growth pattern of the Giant Connected Component – the largest connected set of nodes in a graph. In the present study, we have further analyzed and compared three more infants, from the CHILDES database, learning three different languages: Dutch, German and Spanish. Our results show, along with previous work with English-speaking infants, that all three infants’ syntactic networks change their topology in a similar way, from tree-like networks to small-world networks. This change happens at a similar period in all three infants (between ~700 and ~800 days), regardless of the language they acquire. Our study also shows that the hubs – the most connected nodes in these small-world networks – are always the so-called functional words, which, according to linguistic theory, just contribute to the syntactic structure of human language. The emergence of these hubs happens abruptly, following a logarithmic growth pattern. This developmental pattern challenges usage-based theories of language acquisition and suggests that syntactic development is driven by the growth of the lexicon.
A numerical approach for nonsmooth ordinary differential equations
Authors: Erfanian Hamid Reza , Skandari MH Noori , Kamyad AV
Published: September 2012

In this paper, the authors proposed an approach for solving nonsmooth continuous and discontinuous ordinary differential equations which is based on a generalization of the Taylor expansion. First is considered a generalized derivative for nonsmooth functions with a single variable which is proposed by Kamyad et al. Then, the generalized Taylor expansion of nonsmooth functions is introduced and used to state an approach. Finally, some numerical examples of nonsmooth ordinary differential equations are solved.
Robotically controlled sloshing suppression in point-to-point liquid container transfer
Authors: Reyhanoglu Mahmut , Hervas Jaime Rubio
Published: September 2012

This paper studies the sloshing suppression problem in point-to-point liquid container transfer via a Prismatic–Prismatic–Revolute robot. A multi-mass–spring model is introduced for the characterization of the most prominent liquid-sloshing modes. The control inputs are two forces and a torque applied to the prismatic joints and the revolute joint, respectively. The control objective is to control the robot end-effector movement while suppressing the sloshing modes. A nonlinear mathematical model that reflects all of these specifications is first derived. Then, a Lyapunov-based nonlinear feedback controller is designed to achieve the control objective. Finally, a simulation example is included to demonstrate the effectiveness of the controller.
Police Workforce Structures
Authors: Wilson Jeremy M. , Heinonen Justin A.
Published: September 2012

Research has long focused on the size of police agencies, giving little attention to the composition of the workforce itself. Literature in fields such as the military, healthcare, organizational psychology, and business, highlights the importance of workforce structures in meeting both organizational and staff needs. Using data from a national survey, we examine personnel cohorts (i.e., distribution of junior, midlevel, and senior sworn staff) as an element of workforce structure in the largest, U.S. municipal police organizations. We describe the importance of cohort structures for enhancing performance (meeting both organizational and individual needs) and assess variation in cohort structures. We discuss the cohorts in light of their effects on personnel management, and highlight the importance of existing cohort structures when considering major personnel decisions such as hiring freezes, furloughs, layoffs, and buyouts. We summarize future research that could advance theory and policy regarding workforce structures in police and other criminal justice organizations.
Using Mimicry to Elicit Answers to Intimate Questions in Survey Research
Authors: Guéguen Nicolas , Martin Angélique , Meineri Sebastien , Simon Julien
Published: September 2012

Mimicry is generally associated with a feeling of similarity that often results in a positive perception of the mimicker. We hypothesized that participants would become less reluctant to respond to highly intimate questions when these questions were administered by a mimicking interviewer. A female confederate approached female students for their participation in a survey on sexual behavior in which the questions became increasingly intimate. During the survey, confederates mimicked or did not mimic the participants. It was found that participants in the mimicry condition responded to more questions than did nonparticipants.
Reliability of Position Generator Measures across Different Occupational Lists
Authors: Verhaeghe Pieter-Paul , Putte Bart Van de , Roose Henk
Published: September 2012

The position generator is a widely used research tool to measure individual social capital. Although the position generator is said to be reliable, there are only a few broad guidelines to construct the instrument and there is no standard list of occupational items. Furthermore, the reliability of the position generator across different occupational lists has not yet been tested. This article examines the reliability of 13 position generator measures across different occupational lists by means of a parallel test experiment. We found that only the volume measure has good reliability. Reliability of the social class–based position generator measures is fair to good, and reliability of the occupational prestige/status–based position generator measures is poor. These latter types of measures are the ones most often used.
Constitutional Change and American Pivotal Politics
Authors: Dougherty Keith , Moeller Justin
Published: September 2012

Recent studies of legislative gridlock espouse the importance of institutional design in separation-of-powers games. However, few scholars have focused on the effects of the adoption of the U.S. Constitution on legislative gridlock. This article attempts to fill that gap by determining whether the Constitution improved the marginal effect of the gridlock interval on the ability to change policy. Results suggest that policy is more responsive to the range of pivotal players (in both the negative and the positive direction) under the Constitution than under the Articles of Confederation, providing empirical evidence that it may be the superior design.
Anatomic Popliteal Entrapment Syndrome is Often a Difficult Diagnosis
Authors: Politano Amani D. , Bhamidipati Castigliano M. , Tracci Margaret C. , Upchurch Gilbert R. , Cherry Kenneth J.
Published: September 2012

Anatomic popliteal artery entrapment can be challenging to diagnose. Four cases are described in which initial diagnosis and treatment failed to identify and correct the anatomic defect responsible for patients’ symptoms. In 3 of these cases, initial assessment and diagnosis was exertional compartment syndrome, yet compartment release did not resolve the complaint. Following accurate diagnosis, surgical release of aberrant popliteal fossa anatomy provided all 4 patients with lasting symptom resolution, though 1 patient with bilateral operations has had relief of only 1 side. In the diagnostic algorithm for these patients, angiography with forced plantarflexion against resistance aids in eliciting the pathognomonic images of arterial occlusion in this disorder.
When Hispanic Students Are Not Expected to Succeed
Authors: Murakami Elizabeth T. , Garza Encarnacion , Merchant Betty
Published: September 2012

This case focuses on culturally responsive leadership. Culturally responsive leadership is defined here by the way the principal manifests his or her advocacy for the children he or she serves. In this principal’s case, the authors analyze characteristics of culturally responsive leadership in an inner-city elementary school with a majority of Hispanic students. During her tenure as a principal at Stephens, Ms. Martinez sharply raised the academic performance of students. However, far from idyllic, her experience in the school involved courage and resilience.
A Retrospective Comparison of First Metatarsophalangeal Joint Arthrodesis Using a Locked Plate and Compression Screw Technique
Authors: Hyer Christopher F. , Scott Ryan T. , Swiatek Michael
Published: September 2012

Introduction: The historic primary treatment for end-stage first metatarsophalangeal (MTP) joint arthritis has been fusion. Traditionally, this has been accomplished by metaphyseal apposition between the proximal phalanx and metatarsal using crossed compression screws. Recently, locked plates have been introduced that help support this technique by offering added stability. We present our experience with 45 first MTP fusions in 45 feet using a locked plate and compression screw. Methods: A retrospective review of 45 patients who met the study criteria with a hallux rigidus correction using a locked plate with a compression screw was performed. Charts and radiographs were independently reviewed by 2 authors not involved in the index procedures to assess outcomes. Results: There was a 93% fusion rate (42/45 feet) with 3 nonunions. The mean time to union was 51.1 days (range = 29-116 days, SD = 24.4). The mean patient age was 58.1 years (range = 29-80 years, SD = 10.1). The mean time to partial weight bearing was 7.0 days (range = 0-53 days, SD = 13.8) and the mean time to full weight bearing was 62.0 days (range = 29-57 days, SD = 17.9). Discussion: We report on the results of first MTP fusion using a compression screw and locked plate technique. The results show that this is an effective means of creating a first MTP joint arthrodesis.

Levels of Evidence: Therapeutic, Level IV, Case series
Effect of doping level on physical properties of antimony doped nanocrystalline tin oxide films fabricated using low cost spray technique
Authors: Muruganantham G , Ravichandran K , Saravanakumar K , Philominathan P , Sakthivel B
Published: September 2012

Antimony doped nanocrystalline tin oxide (SnO2∶Sb) films have been fabricated using a low cost and simple fabrication technique using a perfume atomiser. The X-ray diffraction patterns of the antimony doped tin oxide (ATO) films show that the films are polycrystalline with tetragonal cassiterite structure having (110) plane parallel to the surface of the substrate. The preferred orientation remains constant for all the doping levels (0·5–3·0 at-%) and the degree of preferred orientation increases with increasing doping concentration in the starting solution. The intensity of the (110) plane steadily increases as the doping concentration of antimony increases. The fine quality of AFM images show that the films have homogeneous and uniform surface. The sheet resistance is found to decrease with increasing antimony doping level, attain a minimum value (6·34 Ω sq−1) when the doping concentration is 2·5 at-% and then increase for further doping.
Absence of LTB4/BLT1 axis facilitates generation of mouse GM-CSF–induced long-lasting antitumor immunologic memory by enhancing innate and adaptive immune systems
Authors: Yokota Yosuke , Inoue Hiroyuki , Matsumura Yumiko , Nabeta Haruka , Narusawa Megumi , Watanabe Ayumi , Sakamoto Chika , Hijikata Yasuki , Iga-Murahashi Mutsunori , Takayama Koichi , Sasaki Fumiyuki , Nakanishi Yoichi , Yokomizo Takehiko , Tani Kenzaburo
Published: August 2012

BLT1 is a high-affinity receptor for leukotriene B4 (LTB4) that is a potent lipid chemoattractant for myeloid leukocytes. The role of LTB4/BLT1 axis in tumor immunology, including cytokine-based tumor vaccine, however, remains unknown. We here demonstrated that BLT1-deficient mice rejected subcutaneous tumor challenge of GM-CSF gene-transduced WEHI3B (WGM) leukemia cells (KO/WGM) and elicited robust antitumor responses against second tumor challenge with WEHI3B cells. During GM-CSF–induced tumor regression, the defective LTB4/BLT1 signaling significantly reduced tumor-infiltrating myeloid-derived suppressor cells, increased the maturation status of dendritic cells in tumor tissues, enhanced their CD4+ T-cell stimulation capacity and migration rate of dendritic cells that had phagocytosed tumor-associated antigens into tumor-draining lymph nodes, suggesting a positive impact on GM-CSF–sensitized innate immunity. Furthermore, KO/WGM mice displayed activated adaptive immunity by attenuating regulatory CD4+ T subsets and increasing numbers of Th17 and memory CD44hiCD4+ T subsets, both of which elicited superior antitumor effects as evidenced by adoptive cell transfer. In vivo depletion assays also revealed that CD4+ T cells were the main effectors of the persistent antitumor immunity. Our data collectively underscore a negative role of LTB4/BLT1 signaling in effective generation and maintenance of GM-CSF–induced antitumor memory CD4+ T cells.
Endogenous antigen presentation impacts on T-box transcription factor expression and functional maturation of CD8+ T cells
Authors: Smith Corey , Elhassen Diah , Gras Stephanie , Wynn Katherine K. , Dasari Vijayendra , Tellam Judy , Tey Siok-Keen , Rehan Sweera , Liu Yu Chih , Rossjohn Jamie , Burrows Scott R. , Khanna Rajiv
Published: September 2012

T-box transcription factors T-bet (Tbx21) and Eomesodermin (Eomes) are critical players in CD8+ cytotoxic T lymphocyte effector function and differentiation, but how the expression of these transcription factors is regulated remains poorly defined. Here we show that dominant T cells directed toward human CMV, expressing significantly higher levels of T-bet with graded loss of Eomes expression (T-bethiEomeshi/lo), are more efficient in recognizing endogenously processed peptide-major histocompatibility complexes (pMHC) compared with subdominant virus-specific T cells expressing lower levels of T-bet and high levels of Eomes (T-betintEomeshi). Paradoxically, the T-bethiEomeshi/lo dominant populations that efficiently recognized endogenous antigen demonstrated lower intrinsic avidity for pMHC, whereas T-betintEomeshi subdominant populations were characterized by higher pMHC avidity and less efficient recognition of virus-infected cells. Importantly, differential endogenous viral antigen recognition by CMV-specific CD8+ T cells also correlated with the differentiation status and expression of perforin, granzyme B and K. Furthermore, we demonstrate that the expression of T-bet correlates with clonal expansion, differentiation status, and expression of perforin, granzyme B and K in antigen-specific T cells. These findings illustrate how endogenous viral antigen presentation during persistent viral infection may influence the transcriptional program of virus-specific T cells and their functional profile in the peripheral blood of humans.
The expanding role(s) of eosinophils in health and disease
Authors: Jacobsen Elizabeth A. , Helmers Richard A. , Lee James J. , Lee Nancy A.
Published: August 2012

Surprisingly, the role(s) of eosinophils in health and disease is often summarized by clinicians and basic research scientists as a pervasive consensus opinion first learned in medical/graduate school. Eosinophils are rare white blood cells whose activities are primarily destructive and are only relevant in parasitic infections and asthma. However, is this consensus correct? This review argues that the wealth of available studies investigating the role(s) of eosinophils in both health and disease demonstrates that the activities of these granulocytes are far more expansive and complex than previously appreciated. In turn, this greater understanding has led to the realization that eosinophils have significant contributory roles in a wide range of diseases. Furthermore, published studies even implicate eosinophil-mediated activities in otherwise healthy persons. We suggest that the collective reports in the literature showing a role for eosinophils in an ever-increasing number of novel settings highlight the true complexity and importance of this granulocyte. Indeed, discussions of eosinophils are no longer simple and more often than not now begin with the question/statement “Did you know …?”
Platelet factor 4 binding to lipid A of Gram-negative bacteria exposes PF4/heparin-like epitopes
Authors: Krauel Krystin , Weber Claudia , Brandt Sven , Zähringer Ulrich , Mamat Uwe , Greinacher Andreas , Hammerschmidt Sven
Published: September 2012

The positively charged chemokine platelet factor 4 (PF4) forms immunogenic complexes with heparin and other polyanions. Resulting antibodies can induce the adverse drug effect heparin-induced thrombocytopenia. PF4 also binds to bacteria, thereby exposing the same neoantigen(s) as with heparin. In this study, we identified the negatively charged lipopolysaccharide (LPS) as the PF4 binding structure on Gram-negative bacteria. We demonstrate by flow cytometry that mutant bacteria with progressively truncated LPS structures show increasingly enhanced PF4 binding activity. PF4 bound strongest to mutants lacking the O-antigen and core structure of LPS, but still exposing lipid A on their surfaces. Strikingly, PF4 bound more efficiently to bisphosphorylated lipid A than to monophosphorylated lipid A, suggesting that phosphate residues of lipid A mediate PF4 binding. Interactions of PF4 with Gram-negative bacteria, where only the lipid A part of LPS is exposed, induce epitopes on PF4 resembling those on PF4/heparin complexes as shown by binding of human anti-PF4/heparin antibodies. As both the lipid A on the surface of Gram-negative bacteria and the amino acids of PF4 contributing to polyanion binding are highly conserved, our results further support the hypothesis that neoepitope formation on PF4 after binding to bacteria is an ancient host defense mechanism.
The transpulmonary pressure gradient for the diagnosis of pulmonary vascular disease
Authors: Naeije Robert , Vachiery Jean-Luc , Yerly Patrick , Vanderpool Rebecca
Published: August 2012

The transpulmonary pressure gradient (TPG), defined by the difference between mean pulmonary arterial pressure (Ppa) and left atrial pressure (Pla; commonly estimated by pulmonary capillary wedge pressure:Ppcw) has been recommended for the detection of intrinsic pulmonary vascular disease in left-heart conditions associated with increased pulmonary venous pressure. In these patients, a TPG of >12 mmHg would result in a diagnosis of “out of proportion” pulmonary hypertension. This value is arbitrary, because the gradient is sensitive to changes in cardiac output and both recruitment and distension of the pulmonary vessels, which decrease the upstream transmission ofPla. Furthermore, pulmonary blood flow is pulsatile, with systolicPpaand meanPpadetermined by stroke volume and arterial compliance. It may, therefore, be preferable to rely on a gradient between diastolicPpaandPpcw. The measurement of a diastolicPpa/Ppcwgradient (DPG) combined with systemic blood pressure and cardiac output allows for a step-by-step differential diagnosis between pulmonary vascular disease, high output or high left-heart filling pressure state, and sepsis. The DPG is superior to the TPG for the diagnosis of “out of proportion” pulmonary hypertension.
The study of risk in pulmonary arterial hypertension
Authors: Rubin Lewis J. , Simonneau Gerald , Badesch David , Galiè Nazzareno , Humbert Marc , Keogh Anne , Massaro Joseph , Matucci Cerinic Marco , Sitbon Olivier , Kymes Steven
Published: September 2012

A growing body of published evidence exists on the risk factors for disease progression in pulmonary arterial hypertension (PAH). The Scientific Steering Committee for the Study of Risk in PAH was established to bring together leading clinical and statistical experts in PAH and risk modelling, for the purpose of advancing the understanding of the risk of development and progression of PAH. Herein, we discuss the impact of this information on three key areas: 1) clinical decision-making; 2) policy and reimbursement; and 3) future trials and research.
Pulmonary alveolar microlithiasis: two case reports and review of the literature
Authors: Lina M. Jönsson Åsa , Simonsen Ulf , Hilberg Ole , Bendstrup Elisabeth
Published: September 2012

Pulmonary alveolar microlithiasis is a rare diffuse lung disease characterised by deposition of calcium phosphate within the alveolar airspaces. The disease is usually discovered from birth up to 40 yrs of age and is often diagnosed incidentally during radiography of the chest for other reasons. Many patients are asymptomatic and the majority of patients either have normal or restrictive pulmonary function. The clinical course of the disease varies. While it remains static in some patients, it progresses into pulmonary fibrosis, respiratory failure and cor pulmonale in others. With the exception of lung transplantation, there is no known effective treatment for the disease. Although the aetiology remains unclear, mutations of the solute carrier family 34 (sodium phosphate), member 2 gene (theSLC34A2gene), which encodes a sodium/phosphate co-transporter, are considered to be the cause of the disease.

We present two cases of pulmonary alveolar microlithiasis with different mutations in theSLC34A2gene that have not been previously described, and a review of the literature.
On the translations of quasimonotone maps and monotonicity
Authors: Farajzadeh AP , Karamian A , Plubtieng S
Published: August 2012

We show that given a convex subset K of a topological vector space X and a multivalued map

T
:
K
⇉

X
∗

, if there exists a nonempty subset S of

X
∗

with the surjective property on K and

T
+
w

is quasimonotone for each

w
∈
S

, then T is monotone. Our result is a new version of the result obtained by N. Hadjisavvas (Appl. Math. Lett. 19:913-915, 2006).
Reconstructing differentially co-expressed gene modules and regulatory networks of soybean cells
Authors: Zhu Mingzhu , Deng Xin , Joshi Trupti , Xu Dong , Stacey Gary , Cheng Jianlin
Published: September 2012

Background

Current experimental evidence indicates that functionally related genes show coordinated expression in order to perform their cellular functions. In this way, the cell transcriptional machinery can respond optimally to internal or external stimuli. This provides a research opportunity to identify and study co-expressed gene modules whose transcription is controlled by shared gene regulatory networks.

Results

We developed and integrated a set of computational methods of differential gene expression analysis, gene clustering, gene network inference, gene function prediction, and DNA motif identification to automatically identify differentially co-expressed gene modules, reconstruct their regulatory networks, and validate their correctness. We tested the methods using microarray data derived from soybean cells grown under various stress conditions. Our methods were able to identify 42 coherent gene modules within which average gene expression correlation coefficients are greater than 0.8 and reconstruct their putative regulatory networks. A total of 32 modules and their regulatory networks were further validated by the coherence of predicted gene functions and the consistency of putative transcription factor binding motifs. Approximately half of the 32 modules were partially supported by the literature, which demonstrates that the bioinformatic methods used can help elucidate the molecular responses of soybean cells upon various environmental stresses.

Conclusions

The bioinformatics methods and genome-wide data sources for gene expression, clustering, regulation, and function analysis were integrated seamlessly into one modular protocol to systematically analyze and infer modules and networks from only differential expression genes in soybean cells grown under stress conditions. Our approach appears to effectively reduce the complexity of the problem, and is sufficiently robust and accurate to generate a rather complete and detailed view of putative soybean gene transcription logic potentially underlying the responses to the various environmental challenges. The same automated method can also be applied to reconstruct differentially co-expressed gene modules and their regulatory networks from gene expression data of any other transcriptome.
Identification of the Streptococcus mutans LytST two-component regulon reveals its contribution to oxidative stress tolerance
Authors: Ahn Sang-Joon , Qu Ming-Da , Roberts Elisha , Burne Robert A , Rice Kelly C
Published: September 2012

Background

The S. mutans LrgA/B holin-like proteins have been shown to affect biofilm formation and oxidative stress tolerance, and are regulated by oxygenation, glucose levels, and by the LytST two-component system. In this study, we sought to determine if LytST was involved in regulating lrgAB expression in response to glucose and oxygenation in S. mutans.

Results

Real-time PCR revealed that growth phase-dependent regulation of lrgAB expression in response to glucose metabolism is mediated by LytST under low-oxygen conditions. However, the effect of LytST on lrgAB expression was less pronounced when cells were grown with aeration. RNA expression profiles in the wild-type and lytS mutant strains were compared using microarrays in early exponential and late exponential phase cells. The expression of 40 and 136 genes in early-exponential and late exponential phase, respectively, was altered in the lytS mutant. Although expression of comYB, encoding a DNA binding-uptake protein, was substantially increased in the lytS mutant, this did not translate to an effect on competence. However, a lrgA mutant displayed a substantial decrease in transformation efficiency, suggestive of a previously-unknown link between LrgA and S. mutans competence development. Finally, increased expression of genes encoding antioxidant and DNA recombination/repair enzymes was observed in the lytS mutant, suggesting that the mutant may be subjected to increased oxidative stress during normal growth. Although the intracellular levels of reaction oxygen species (ROS) appeared similar between wild-type and lytS mutant strains after overnight growth, challenge of these strains with hydrogen peroxide (H2O2) resulted in increased intracellular ROS in the lytS mutant.

Conclusions

Overall, these results: (1) Reinforce the importance of LytST in governing lrgAB expression in response to glucose and oxygen, (2) Define a new role for LytST in global gene regulation and resistance to H2O2, and (3) Uncover a potential link between LrgAB and competence development in S. mutans.
Association between insertion/deletion polymorphism in angiotensin-converting enzyme gene and acute lung injury/acute respiratory distress syndrome: a meta-analysis
Authors: Matsuda Akihisa , Kishi Taro , Jacob Asha , Aziz Monowar , Wang Ping
Published: September 2012

Background

A previous meta-analysis reported a positive association between an insertion/deletion (I/D) polymorphism in the angiotensin-converting enzyme gene (ACE) and the risk of acute lung injury (ALI)/acute respiratory distress syndrome (ARDS). Here, we updated this meta-analysis and additionally assessed the association of this polymorphism with ALI/ARDS mortality.

Methods

We searched electronic databases through October 2011 for the terms “angiotensin-converting enzyme gene”, “acute lung injury”, and “acute respiratory distress syndrome,” and reviewed all studies that reported the relationship of the I/D polymorphism in ACE with ALI/ARDS in humans. Seven studies met the inclusion criteria, comprising 532 ALI/ARDS patients, 3032 healthy controls, and 1432 patients without ALI/ARDS. We used three genetic models: the allele, dominant, and recessive models.

Results

The ACE I/D polymorphism was not associated with susceptibility to ALI/ARDS for any genetic model. However, the ACE I/D polymorphism was associated with the mortality risk of ALI/ARDS in Asian subjects ( P
allele < 0.0001, P
dominant = 0.001, P
recessive = 0.002). This finding remained significant after correction for multiple comparisons.

Conclusions

There is a possible association between the ACE I/D polymorphism genotype and the mortality risk of ALI/ARDS in Asians.