bluuebunny/crossref_metadata_2025 huggingface dataset:
A Mixed Methods Portrait of Urban Instrumental Music Teaching
Authors: Fitzpatrick Kate R.
Published: September 2011

The purpose of this mixed methods study was to learn about the ways that instrumental music teachers in Chicago navigated the urban landscape. The design of the study most closely resembles Creswell and Plano Clark’s (2007) two-part Triangulation Convergence Mixed Methods Design, with the addition of an initial exploratory focus group component. Research questions focused on the contextual knowledge that the teachers held regarding their students and communities, the specialized skills they relied upon to be successful, the attitudes and beliefs they held toward teaching instrumental music in an urban school, and the challenges and rewards that they perceived from teaching in this context. The results suggest that the instrumental music teachers utilized their knowledge of the urban context to modify their general pedagogical approach, that they believed a specialized set of skills was required for success in the urban context, that they had relatively positive levels of job satisfaction and believed strongly in the development of their students’ potential, and that they faced serious challenges to the success of their programs but also perceived great reward from the personal and musical improvement of their students.
Without Bias? Government Policy That Creates Fair and Equitable Property Tax Assessments
Authors: Gilderbloom John I. , Hanka Matthew J. , Ambrosius Joshua D.
Published: September 2011

Ensuring accurate, unbiased residential property tax assessments is an important, and contentious, issue facing communities today, particularly in this era of fiscal and economic crisis. Furthermore, this question is critical because it involves important social justice issues. Past studies have shown inequities by race, class, and location with some neighborhoods paying more of their fair share in property taxes. This study looks at the reliability of tax-assessment data in a medium-sized American city—Louisville, Kentucky. In an effort to compare various housing data sources, this study contrasts three measures of neighborhood median housing value for 170 census tracts in Louisville in the year 2000: self-reported values (U.S. Census); sales prices (MLS); and tax assessments from the county’s property valuation administrator. We find that the effects of various neighborhood characteristics on the three property measures do not vary by measure. Furthermore, an assessments-to-sale ratio does not vary by traditional indicators of neighborhood distress including racial composition and proximity to the inner city. We conclude that assessments in Louisville are not biased by neighborhood and argue that several aspects of policy and administration present in Louisville make for more accountable and fair assessment practices—including tough state statutes, the election of the chief assessor, the use of aerial technology to view improvements, public transparency, the use of sales prices in reassessing properties, and the willingness to reassess downward communities hit hardest by the foreclosure crisis.
The Circadian Clock Influences Heart Performance
Authors: Wu Xi , Liu Zhiwei , Shi Guangsen , Xing Lijuan , Wang Xiaohan , Gu Xiwen , Qu Zhipeng , Dong Zhen , Xiong Jing , Gao Xiang , Zhang Chenyu , Xu Ying
Published: September 2011

Circadian clocks are believed to provide the selective advantage of anticipation, thus allowing organisms to respond efficiently to stimuli at the appropriate moment. Disrupted circadian rhythms have been found to affect a variety of basic physiological processes. However, the importance of the circadian clock in regulating heart performance remains undetermined. We hypothesized that the circadian clock plays a crucial role in heart performance through the anticipation of daily workload. Echocardiography was employed to monitor heart function and structure in mice in a noninvasive, real-time manner. In wild-type mice, both the ejection fraction (EF) and the shortening fraction (FS), two important markers of cardiac function, show diurnal variation. In addition, the amplitude of the EF and the FS enlarges in response to forced exercise in a time-dependent manner. The diurnal variations in EF and FS are altered in mice with disruptions in circadian clock genes and are significantly attenuated under an imposed light regimen. Furthermore, it shows that the overexpression of peroxisome proliferator–activated receptor gamma coactivator 1 alpha ( Pgc1α) under control of the muscle creatine kinase (MCK) promoter inhibited clock gene expression in the heart and muscle and decreased the expression of peroxisome proliferator–activated receptor alpha ( Pparα), metabolic genes glucose transporter ( Glut4), and acetyl-coA synthetase ( Acs1). Pgc1α overexpression abolished the diurnal variation of EF. We thus propose that PGC1α might play an important role in circadian-mediated, impaired cardiac function by regulating the circadian rhythm of metabolic genes.
Cardiac-Specific Mutation of Clock Alters the Quantitative Measurements of Physical Activities without Changing Behavioral Circadian Rhythms
Authors: Ko Michael L. , Shi Liheng , Tsai Ju-Yun , Young Martin E. , Neuendorff Nichole , Earnest David J. , Ko Gladys Y.-P.
Published: September 2011

Even though peripheral circadian oscillators in the cardiovascular system are known to exist, the daily rhythms of the cardiovascular system are mainly attributed to autonomic or hormonal inputs under the control of the central oscillator, the suprachiasmatic nucleus (SCN). In order to examine the role of peripheral oscillators in the cardiovascular system, we used a transgenic mouse where the Clock gene is specifically disrupted in cardiomyocytes. In this cardiomyocyte-specific CLOCK mutant (CCM) mouse model, the circadian input from the SCN remains intact. Both CCM and wild-type (WT) littermates displayed circadian rhythms in wheel-running behavior. However, the overall wheel-running activities were significantly lower in CCM mice compared to WT over the course of 5 weeks, indicating that CCM mice either have lower baseline physical activities or they have lower physical adaptation abilities because daily wheel running, like routine exercise, induces physical adaptation over a period of time. Upon further biochemical analysis, it was revealed that the diurnal oscillations of phosphorylation states of several kinases and protein expression of the L-type voltage-gated calcium channel (L-VGCC) α1D subunit found in WT hearts were abolished in CCM hearts, indicating that in mammalian hearts, the daily oscillations of the activities of these kinases and L-VGCCs were downstream elements of the cardiac core oscillators. However, the phosphorylation of p38 MAPK exhibited robust diurnal rhythms in both WT and CCM hearts, indicating that cardiac p38 could be under the influence of the central clock through neurohormonal signals or be part of the circadian input pathway in cardiomyocytes. Taken together, these results indicate that the cardiac core oscillators have an impact in regulating circadian rhythmicities and cardiac function.
Photic Resetting and Entrainment in CLOCK-Deficient Mice
Authors: Dallmann Robert , DeBruyne Jason P. , Weaver David R.
Published: September 2011

Mice lacking the CLOCK protein have a relatively subtle circadian phenotype, including a slightly shorter period in constant darkness, differences in phase resetting after 4-hour light pulses in the early and late night, and a variably advanced phase angle of entrainment in a light-dark (LD) cycle. The present series of experiments was conducted to more fully characterize the circadian phenotype of Clock−/− mice under various lighting conditions. A phase-response curve (PRC) to 4-hour light pulses in free-running mice was conducted; the results confirm that Clock−/− mice exhibit very large phase advances after 4-hour light pulses in the late subjective night but have relatively normal responses to light at other phases. The abnormal shape of the PRC to light may explain the tendency of CLOCK-deficient mice to begin activity before lights-out when housed in a 12-hour light:12-hour dark lighting schedule. To assess this relationship further, Clock−/− and wild-type control mice were entrained to skeleton lighting cycles (1L:23D and 1L:10D:1L:12D). Comparing entrainment under the 2 types of skeleton photoperiods revealed that exposure to 1-hour light in the morning leads to a phase advance of activity onset (expressed the following afternoon) in Clock−/− mice but not in the controls. Constant light typically causes an intensity-dependent increase in circadian period in mice, but this did not occur in CLOCK-deficient mice. The failure of Clock−/− mice to respond to the period-lengthening effect of constant light likely results from the increased functional impact of light falling in the phase advance zone of the PRC. Collectively, these experiments reveal that alterations in the response of CLOCK-deficient mice to light in several paradigms are likely due to an imbalance in the shape of the PRC to light.
Programs for Undergraduate Women in Science and Engineering
Authors: Fox Mary Frank , Sonnert Gerhard , Nikiforova Irina
Published: September 2011

We analyze programs for undergraduate women in science and engineering as strategic research sites in the study of disparities between women and men in scientific fields within higher education. Based on responses to a survey of the directors of the universe of these programs in the United States, the findings reveal key patterns in the programs’ (1) definitions of the issues of women in science and engineering, (2) their solutions to address the issues, (3) their goals and perceived success with goals, and (4) their organizational characteristics and relationship to the larger institutional environments. The findings—which are conceptually grounded in the distinction between structural/institutional and individual issues facing women in science—have implications for understanding gender, science, and higher education, and for initiatives undertaken to improve the condition of women in scientific fields. The findings may also inform strategic efforts to reduce gender disparity in other organizational contexts.
Youth Privilege
Authors: Utrata Jennifer
Published: September 2011

Relative to gender, race, and class, age relations are undertheorized. Yet age, like gender, is routinely accomplished in daily life. Grandmothers and adult daughters simultaneously do age and gender as they support one another in managing paid work and domestic responsibilities. Drawing on ethnographic data and interviews with 90 single mothers and 30 grandmothers (babushki) in Russia, I explore intergenerational negotiations for support. Both single mothers and grandmothers are held accountable for doing gendered age, but labor and marriage markets tip the balance in favor of single mothers. Single mothers re-create youth privilege, finding their lives simpler with a babushka. Some grandmothers embrace newer discourses of femininity, challenging assumptions about age and family status that oblige them to perform care work. But most grandmothers do whatever they can to help daughters, feeling more dependent than ever on them because of the uncertainties of capitalism and the state’s retrenchment. I contribute to theories of age and gender intersectionality by making visible both single mothers’ youth privilege and grandmothers’ unpaid, often devalued, care work.
Pyrolysis properties of exfoliated nanocomposite synthesized by vinyl acetate and organic montmorillonite through different processes
Authors: Hui-wang Cui , Guan-ben Du
Published: September 2011

Thermogravimetric analysis is always used to study the pyrolysis process of polymers and composites and can reflect their thermal degradation properties. In the article, an exfoliated nanocomposite was synthesized by vinyl acetate and organic montmorillonite through different processes. Linear macromolecular chains of polyvinyl acetate were formed in the layers of organic montmorillonite, and no chemical bond existed between them, but only physical effect. Organic montmorillonite was exfoliated into layers or sheets of nanoparticles, randomly dispersing in the matrix of polyvinyl acetate, so the different synthesis processes and the addition of organic montmorillonite had little effect on the structure of the exfoliated nanocomposite, but some certain effect on the pyrolysis properties. The pyrolysis was found to consist of eight phases, and those of polyvinyl acetate and the exfoliated nanocomposite were similar. The presence of organic montmorillonite had no obvious effect on the pyrolysis temperature, but mainly delayed the thermal degradation process. In addition, their pyrolysis kinetics was firstly analyzed by the Agrawal integral equation. The kinetic parameters, including the kinetics mechanism function, the activation energy, the frequency factor, the reaction order, the reaction rate constant, the form factor of heat flow curve, and the kinetic compensation effect equation, were obtained in detail.
Disability, Intersectionality and Deprivation
Authors: Pal G.C.
Published: September 2011

Social perspective on disability affirms that a large number of persons with disabilities struggle to lead a normal life because of stereotypical attitudes, social stigma, discrimination and neglect. Various socio-cultural conditions also interact with different types of disability in a complex manner to make the overall life qualitatively different. The critical issue is that the interface of disability with other social identities is more likely to compound problem, which by and large is overlooked. With the recognition that understanding the intersections of multiple forms of dis-crimination has a powerful human rights dimension and greater social significance for inclusion, this article is an attempt to examine the interface of disability and caste on living conditions of persons with disabilities. Drawing on data primarily from the latest National Sample Survey, the article throws light on the circumstances of the persons with disabilities across social groups, with a special focus on Dalits (scheduled castes) with disabilities. It is revealed that despite several special interventions for the social integration of dalits and persons with disabilities, dalits with disabilities are doubly disadvantaged. The article argues for the preferential support services and socio-psychological interventions for the group within the larger framework of inclusiveness.
Understanding Coping with Distress due to Physical Disability
Authors: Pande Namita , Tewari Shruti
Published: September 2011

This article presents findings of two studies that investigated coping with physical disability within the multivariate transactional model of stress. In the first study, 30 persons with locomotor disability were interviewed to explore the nature of stressors and coping strategies. In the second study, five scales were administered on a sample of 120 persons with locomotor disability to investigate the role of personal and situational variables in determining the extent of perceived distress and its relationship with coping. The manner in which anāsakti and positive life orientation moderated the relationship between perceived distress and coping was also investigated. The findings revealed that the major stressors which led to distress were ego-related stressors, inability to fulfil traditional gender roles, problems in interpersonal relationships with family and others, physical barriers and deformed body image. Education was found to be the strongest predictor of perceived distress and problem-focused coping was significantly related to lower levels of distress. Moderation analyses showed that with stronger belief in the philosophy of anāsakti and higher positive life orientation, lower levels of distress were strongly related to problem focused coping. The impli-cations of these findings for psycho-social rehabilitation of persons with physical disability are discussed.
Relationship Between Late-Life Hypertension, Blood Pressure, and Alzheimer’s Disease
Authors: Yang Yuan-Han , Roe Catherine M. , Morris John C.
Published: September 2011

Relationship between late-life hypertension and Alzheimer’s disease (AD) remains less clear. Both cross-sectional and longitudinal methods were used to examine whether systolic blood pressure (SBP), diastolic blood pressure (DBP), pulse pressure (PP), mean arterial pressure (MAP), and self-reported hypertension (S-HTN) in late life were associated with having and developing AD. The cross-sectional examination included 1768 individuals with AD and 818 nondemented individuals, and AD was not significantly associated with S-HTN or any of blood pressure measures (S-HTN: P = .236; SBP: P = .095; DBP: P = .429; PP: P = .145; MAP: P = .162). In the longitudinal examination, 594 nondemented individuals, 171 with and 423 without S-HTN at entry, were included. Diastolic blood pressure was significantly related to the development of AD ( P = .030) but not S-HTN ( P = .251), SBP ( P = .294) PP ( P = .919), and MAP ( P = .060). The association underscores the necessity of further investigation to outline the detailed mechanisms and biological relevance, if any, of late-life DBP to later AD.
Using Acceptance and Commitment Therapy With People With Psychosis
Authors: Bloy Sally , Oliver Joseph E. , Morris Eric
Published: September 2011

There is a small but increasing body of research to suggest that acceptance and commitment therapy (ACT) is useful for people experiencing psychosis. As an intervention, ACT does not specifically target symptom reduction but rather emphasizes more flexible responding in the presence of psychotic symptoms to encourage increases in value-driven behavior. A case study is presented, detailing use of ACT in working with someone experiencing long-standing distressing psychosis, specifically, paranoia, delusions, and associated emotional disturbance. Measures of general distress, severity, and intensity of delusional thoughts and depression were taken at two points prior to therapy starting and again post intervention. All measures showed improvements post therapy, although symptoms did not remit completely. However, the client reported significant increases in value-based activities. The results indicated that, although not a primary treatment target, ACT can help in reduction of symptoms. As expected, the intervention can also assist in increasing value-based behavior, in spite of the presence of ongoing psychotic symptoms.
Persistent spontaneous bacterial peritonitis: a common complication in patients with spontaneous bacterial peritonitis and a high score in the model for end-stage liver disease
Authors: Desai Archita P. , Reau Nancy , Reddy K. Gautham , Te Helen S. , Mohanty Smruti , Satoskar Rohit , DeVoss Amanda , Jensen Donald
Published: September 2011

Objectives:

Spontaneous bacterial peritonitis (SBP) is associated with a high mortality rate. After antibiotic therapy, improvement in fluid polymorphonuclear (PMN) cell count is expected within 2 days. However, our institution recognized cases unresponsive to standard treatment.

Methods:

To study these recalcitrant cases, we completed a retrospective chart review of patients admitted for SBP to the University of Chicago from 2002 to 2007. SBP was defined by an ascitic PMN cell count ≥250/ ml.

Results:

Of 55 patients with SBP, 15 did not show improvement in fluid PMN cell count to below 250/ ml with standard treatment, leading to a prevalence of 27%. The patients with persistent SBP were younger than those with nonpersistent SBP [mean (SD) 51.80 (9.84) compared with 58.13 (8.79); p = 0.0253]. Persistent SBP had a higher serum ascites albumin gradient (SAAG) [median (Q1, Q3) 1.85 (1.50, 2.41) compared with 1.10 (0.60, 1.60)] and a higher score in the model for end-stage liver disease (MELD) [mean (SD) 27.98 (8.09) compared with 22.22 (8.10)] than nonpersistent SBP patients; p = 0.027 and p = 0.023, respectively. In addition, persistent SBP patients were more likely to have a positive ascitic fluid culture than nonpersistent SBP patients [odds ratio (OR) (95% CI) 4.33 (1.21, 15.47); p = 0.024]. Importantly, in-hospital mortality in the persistent SBP group was 40%, compared with 22.5% in the nonpersistent SBP group [OR = 2.30 (0.64, 8.19); p = 0.20].

Conclusions:

The risk of persistent SBP is nearly 40% in patients with MELD score >25, SAAG >1.5 or positive ascitic fluid culture. Furthermore, patients who develop persistent SBP tend to experience a higher mortality rate. This study underscores the importance of further examination of this vulnerable population.
Soy foods: are they useful for optimal bone health?
Authors: Lanou Amy J.
Published: September 2011

Numerous studies have investigated the relationship between soy foods, soy protein, or isoflavone extracts and markers of bone health and osteoporosis prevention, and have come to conflicting conclusions. Research on dietary patterns, rather than on specific food ingredients or individual foods, may offer an opportunity for better understanding the role of soy foods in bone health. Evidence is reviewed regarding the question of whether soy foods contribute to a dietary pattern in humans that supports and promotes bone health. Soy foods are associated with improved markers of bone health and improved outcomes, especially among Asian women. Although the optimal amounts and types of soy foods needed to support bone health are not yet clear, dietary pattern evidence suggests that regular consumption of soy foods is likely to be useful for optimal bone health as an integral part of a dietary pattern that is built largely from whole plant foods.
Bazedoxifene: the evolving role of third-generation selective estrogen-receptor modulators in the management of postmenopausal osteoporosis
Authors: Komm Barry S. , Chines Arkadi A.
Published: September 2011

Osteoporosis is a significant public health concern, particularly for postmenopausal women. Current treatment options may not be appropriate for all women. Selective estrogen-receptor modulators (SERMs) are a class of molecules with tissue-selective activity. Bazedoxifene is currently in clinical development for the prevention and treatment of postmenopausal osteoporosis. In a 2-year, phase III, osteoporosis prevention study ( N = 1583), bazedoxifene 10, 20, and 40 mg was shown to preserve bone mineral density and decrease biochemical markers of bone turnover compared with placebo in postmenopausal women at risk for osteoporosis. In a pivotal 3-year, phase III, osteoporosis treatment study ( N = 7492), bazedoxifene 20 and 40 mg significantly reduced the incidence of new vertebral fractures compared with placebo ( p < 0.05 for both) in postmenopausal women with osteoporosis. In a post hoc subgroup analysis of women at higher risk for fracture ( n = 1772), bazedoxifene 20 mg significantly reduced the risk of nonvertebral fractures versus placebo ( p = 0.02) and raloxifene 60 mg ( p = 0.05). Bazedoxifene 20 mg has demonstrated sustained efficacy in reducing the risk of vertebral fractures over 5 and 7 years. Overall, bazedoxifene was generally safe and well tolerated, with favorable endometrial and breast safety profiles. As with other SERMs, the rate of deep vein thrombosis was higher in the bazedoxifene groups compared with placebo at 3 and 5 years. Considering its demonstrated efficacy and safety, bazedoxifene may be an appropriate osteoporosis therapy for women who cannot take or are unwilling to take bisphosphonates because of safety or tolerability issues. Bazedoxifene may also be appropriate for younger women at increased fracture risk who are concerned about the effects of long-term bisphosphonate therapy. This article reviews the results of key clinical trials of bazedoxifene for the prevention and treatment of postmenopausal osteoporosis and describes its role in clinical practice.
Comprehensive analysis of tumor microenvironment cytokines in Waldenstrom macroglobulinemia identifies CCL5 as a novel modulator of IL-6 activity
Authors: Elsawa Sherine F. , Novak Anne J. , Ziesmer Steven C. , Almada Luciana L. , Hodge Lucy S. , Grote Deanna M. , Witzig Thomas E. , Fernandez-Zapico Martin E. , Ansell Stephen M.
Published: September 2011

Although proinflammatory and chemotactic cytokines can profoundly affect the tumor microenvironment, and many of them have been shown to have therapeutic efficacy in preclinical models, the role of these molecules in Waldenström macroglobulinemia (WM) remains poorly understood. In this study, simultaneous analysis of WM patient sera and bone marrow biopsies identified a set of dysregulated cytokines including CCL5, G-CSF, and soluble IL-2 receptor, that were significantly elevated in WM patients whereas IL-8 and EGF levels were significantly lower in these patients compared with healthy controls. Interestingly, CCL5 levels positively correlated with features of disease aggressiveness such as elevated IgM levels and bone marrow involvement. Functional analysis of tumor microenvironment revealed a functional correlation between CCL5 levels and IL-6 levels, a proinflammatory cytokine with an important role in normal and malignant B-cell biology. Furthermore, CCL5 stimulated IL-6 secretion in WM stromal cells resulting in increased IgM secretion by WM malignant cells via the JAK/STAT signaling pathway. Thus, together these results define a novel signaling network in the WM tumor microenvironment controlling IgM secretion and suggest CCL5 as a potential target for the treatment of this disease.
What is the potential for bisexual men in China to act as a bridge of HIV transmission to the female population? Behavioural evidence from a systematic review and meta-analysis
Authors: Chow Eric PF , Wilson David P , Zhang Lei
Published: September 2011

Background

HIV prevalence among men who have sex with men (MSM) in China has rapidly increased in recent years. It is suggested that MSM could be a potential bridge of HIV transmission to the general female population. We investigated the bisexual behaviour of MSM in China through systematic review and meta-analysis.

Methods

We conducted a systematic review and meta-analyses on published peer-reviewed Chinese and English literature during 2001-2010 according to the PRISMA guidelines. Marital status and sexual behavioural indicators of MSM were presented graphically using forest plots. The pooled effect rates with 95% confidence intervals were also calculated. Meta-regression analyses were performed to examine the factors associated with high heterogeneities across the studies.

Results

Forty-three eligible articles (11 in English and 32 in Chinese) were identified. Our results showed that 17.0% (95% CI: 15.1-19.1%) of MSM in China are currently married to a woman and 26.3% (95% CI: 23.6-29.1%) of MSM had female sexual partners in the last six months. The pooled estimates for condom use rate between MSM and female sex partners was 41.4% (95% CI: 35.5-47.5%) at the last sex act; and 25.6% (95% CI: 23.0-28.4%) in the last six months. The consistent condom use rates with regular, non-commercial, casual and commercial female sex partners in the last six months were 23.3% (95% CI: 11.25-42.1%), 39.0% (95% CI: 28.8-50.3%) and 55.8% (95% CI: 41.4-69.4%), respectively.

Conclusions

A substantial proportion of Chinese MSM is currently married or had sexual relations with a female in the past six months. In addition, low condom usage was common between married MSM and their wives, hence posing a higher risk of transmitting HIV. Harm-reduction programs targeting married MSM and their female partners are necessary to curb the further spread of HIV infection to the general female population.
Overexpression of members of the microRNA-183 family is a risk factor for lung cancer: A case control study
Authors: Zhu Wangyu , Liu XiaoGuang , He JianYing , Chen DongDong , Hunag YanYan , Zhang Yong Kui
Published: September 2011

Background

Lung cancer is the leading cause of cancer-related deaths worldwide. Early detection is considered critical for lung cancer treatment. MicroRNAs (miRNAs) have shown promise as diagnostic and prognostic indicators. This study was to identify specific miRNAs with diagnostic and prognostic value for patients with lung cancer, and to explore the correlation between expression profiles of miRNAs and patient survival.

Methods

Gene expression of members of the miR-183 family (miR-96, miR-182, and miR-183) were examined in 70 paired samples from lung cancer patients (primary cancer and non-cancerous tissues and sera), as well as 44 serum samples from normal volunteers and lung cancer cell lines by quantitative real-time reverse transcription polymerase chain reaction (RT-qPCR). The correlation between the expression of miRNAs in tissues, sera, and patient overall survival were also examined by log-rank and Cox regression analysis.

Results

Expression levels of members of the miR-183 family in lung cancer tumor and sera were higher than that of their normal counterparts. The miR-96 expression in tumors was positively associated with its expression in sera. Log-rank and Cox regression analyses demonstrated that high expression of tumor and serum miRNAs of the miR-183 family were associated with overall poor survival in patients with lung cancer.

Conclusions

Our results suggest that the expressions of miR-96, miR-182, and miR-183 in tumor and sera may be considered potential novel biomarkers for the diagnosis and prognosis of lung cancer.
Split-Inteins for Simultaneous, site-specific conjugation of Quantum Dots to multiple protein targets In vivo
Authors: Charalambous Anna , Antoniades Ioanna , Christodoulou Neophytos , Skourides Paris A
Published: September 2011

Background

Proteins labelled with Quantum Dots (QDs) can be imaged over long periods of time with ultrahigh spatial and temporal resolution, yielding important information on the spatiotemporal dynamics of proteins within live cells or in vivo. However one of the major problems regarding the use of QDs for biological imaging is the difficulty of targeting QDs onto proteins. We have recently developed a DnaE split intein-based method to conjugate Quantum Dots (QDs) to the C-terminus of target proteins in vivo. In this study, we expand this approach to achieve site-specific conjugation of QDs to two or more proteins simultaneously with spectrally distinguishable QDs for multiparameter imaging of cellular functions.

Results

Using the DnaE split intein we target QDs to the C-terminus of paxillin and show that paxillin-QD conjugates become localized at focal adhesions allowing imaging of the formation and dissolution of these complexes. We go on to utilize a different split intein, namely Ssp DnaB mini-intein, to demonstrate N-terminal protein tagging with QDs. Combination of these two intein systems allowed us to simultaneously target two distinct proteins with spectrally distinguishable QDs, in vivo, without any cross talk between the two intein systems.

Conclusions

Multiple target labeling is a unique feature of the intein based methodology which sets it apart from existing tagging methodologies in that, given the large number of characterized split inteins, the number of individual targets that can be simultaneously tagged is only limited by the number of QDs that can be spectrally distinguished within the cell. Therefore, the intein-mediated approach for simultaneous, in vivo, site-specific (N- and C-terminus) conjugation of Quantum Dots to multiple protein targets opens up new possibilities for bioimaging applications and offers an effective system to target QDs and other nanostructures to intracellular compartments as well as specific molecular complexes.
The functional spectrum of low-frequency coding variation
Authors: Marth Gabor T , Yu Fuli , Indap Amit R , Garimella Kiran , Gravel Simon , Leong Wen Fung , Tyler-Smith Chris , Bainbridge Matthew , Blackwell Tom , Zheng-Bradley Xiangqun , Chen Yuan , Challis Danny , Clarke Laura , Ball Edward V , Cibulskis Kristian , Cooper David N , Fulton Bob , Hartl Chris , Koboldt Dan , Muzny Donna , Smith Richard , Sougnez Carrie , Stewart Chip , Ward Alistair , Yu Jin , Xue Yali , Altshuler David , Bustamante Carlos D , Clark Andrew G , Daly Mark , DePristo Mark , Flicek Paul , Gabriel Stacey , Mardis Elaine , Palotie Aarno , Gibbs Richard ,   the 1000 Genomes Project
Published: September 2011

Background

Rare coding variants constitute an important class of human genetic variation, but are underrepresented in current databases that are based on small population samples. Recent studies show that variants altering amino acid sequence and protein function are enriched at low variant allele frequency, 2 to 5%, but because of insufficient sample size it is not clear if the same trend holds for rare variants below 1% allele frequency.

Results

The 1000 Genomes Exon Pilot Project has collected deep-coverage exon-capture data in roughly 1,000 human genes, for nearly 700 samples. Although medical whole-exome projects are currently afoot, this is still the deepest reported sampling of a large number of human genes with next-generation technologies. According to the goals of the 1000 Genomes Project, we created effective informatics pipelines to process and analyze the data, and discovered 12,758 exonic SNPs, 70% of them novel, and 74% below 1% allele frequency in the seven population samples we examined. Our analysis confirms that coding variants below 1% allele frequency show increased population-specificity and are enriched for functional variants.

Conclusions

This study represents a large step toward detecting and interpreting low frequency coding variation, clearly lays out technical steps for effective analysis of DNA capture data, and articulates functional and population properties of this important class of genetic variation.
Do Survivorship Care Plans Make a Difference? A Primary Care Provider Perspective
Authors: Shalom Marina Mor , Hahn Erin E. , Casillas Jacqueline , Ganz Patricia A.
Published: September 2011

Survivorship care plans were highly valued by these primary care providers, increasing their knowledge about survivors' cancer history and influencing patient management.
Rhetorical Silence, Scholarly Absence, and Tradition Rethought
Authors: Holdstein Deborah H.
Published: September 2011

In this article, Deborah Holdstein exhorts scholars of rhetoric and composition to break new ground by searching for absences — missing topics, little-known but influential scholars, alternative canons — that would enhance the work in the field. Noting that certain topics or scholarly movements take root as original scholarship when in fact others had earlier tilled that scholarly ground, Holdstein uses the specific examples of Wallace W. Douglas and Jewish rhetoric to suggest that there is unique work yet to be done. Holdstein's perspective is shaped by her five-year term as editor of College Composition and Communication and her concern about derivative scholarship rather than work that truly challenges our assumptions.
Governance Matters
Authors: Leitch Vincent B.
Published: September 2011

These papers were given at the 2011 MLA panel on faculty governance. They present the topic's importance in the face of budget crises and institutional pressure.
Advertising Strategies in Electronic Retailing: A Differential Games Approach
Authors: Liu Dengpan , Kumar Subodha , Mookerjee Vijay S.
Published: September 2011

We consider advertising problems under an information technology (IT) capacity constraint encountered by electronic retailers in a duopolistic setting. There is a considerable amount of literature on advertising games between firms, yet introducing an IT capacity constraint fundamentally changes this problem. In the presence of information processing constraints, although advertising may still cause a customer to switch, it may not result in a sale, i.e., the customer may be lost by both firms. This situation could occur when customers have a limited tolerance for processing delays and leave the website of a firm because of slow response. In such situations, attracting more traffic to a firm's site (by increasing advertising expenditure) may not generate enough additional revenue to warrant this expenditure. We use a differential game formulation to obtain closed-form solutions for the advertising effort over time in the presence of IT capacity constraints. Based on these solutions, we present several useful managerial insights.
Avoiding Pitfalls in Applying Prediction Models, As Illustrated by the Example of Prostate Cancer Diagnosis
Authors: Cammann Henning , Jung Klaus , Meyer Hellmuth-A , Stephan Carsten
Published: September 2011

BACKGROUND

The use of different mathematical models to support medical decisions is accompanied by increasing uncertainties when they are applied in practice. Using prostate cancer (PCa) risk models as an example, we recommend requirements for model development and draw attention to possible pitfalls so as to avoid the uncritical use of these models.

CONTENT

We conducted MEDLINE searches for applications of multivariate models supporting the prediction of PCa risk. We critically reviewed the methodological aspects of model development and the biological and analytical variability of the parameters used for model development. In addition, we reviewed the role of prostate biopsy as the gold standard for confirming diagnoses. In addition, we analyzed different methods of model evaluation with respect to their application to different populations. When using models in clinical practice, one must validate the results with a population from the application field. Typical model characteristics (such as discrimination performance and calibration) and methods for assessing the risk of a decision should be used when evaluating a model's output. The choice of a model should be based on these results and on the practicality of its use.

To avoid possible errors in applying prediction models (the risk of PCa, for example) requires examining the possible pitfalls of the underlying mathematical models in the context of the individual case. The main tools for this purpose are discrimination, calibration, and decision curve analysis.
Specific Immunoassay Reveals Increased Serum Trypsinogen 3 in Acute Pancreatitis
Authors: Oiva Jani , Itkonen Outi , Koistinen Riitta , Hotakainen Kristina , Zhang Wang-Ming , Kemppainen Esko , Puolakkainen Pauli , Kylänpää Leena , Stenman Ulf-Håkan , Koistinen Hannu
Published: September 2011

BACKGROUND

Trypsinogen 3 is a minor trypsinogen isoform in the pancreas. In contrast with trypsin 1 and 2, trypsin 3 degrades pancreatic secretory trypsin inhibitor, which may lead to an excess of active trypsin and acute pancreatitis (AP). We developed an immunoassay for trypsinogen 3 and studied whether an assay of serum trypsinogen 3 is of clinical utility in the diagnosis of AP.

METHODS

Monoclonal antibodies were generated using recombinant human trypsinogen 3 as the antigen and used to establish a sandwich-type immunoassay. We analyzed serum trypsinogen 3 concentrations in 82 patients with AP and 63 patients with upper abdominal pain (controls). The reference interval was determined using serum samples from 172 apparently healthy individuals.

RESULTS

The measuring range of the trypsinogen 3 assay was 1.0–250 μg/L. Intra- and interassay CVs were <11%, and cross-reactivity with other trypsinogen isoenzymes was <0.1%. The median trypsinogen 3 concentration in serum from healthy individuals was <1.0 μg/L, and the upper reference limit was 4.4 μg/L. We observed increased trypsinogen 3 concentrations in patients with mild (median 9.5 μg/L) and severe (15.0 μg/L) AP; in both groups, the concentrations were significantly higher than in controls (median <1.0 μg/L) (P < 0.0001). In ROC analysis, the area under the curve of trypsinogen 3 for separation between AP and controls was 0.90 (P < 0.0001).

CONCLUSIONS

We established for the first time a specific immunoassay for trypsinogen 3 using monoclonal antibodies. Patients with AP were found to have increased serum concentrations of trypsinogen 3. The availability of this assay will be useful for studies of the clinical utility of trypsinogen 3.
A Practical Dynamic Modulus Testing Protocol
Authors: Li Xinjun , Christopher Williams R.
Published: September 2011

The dynamic modulus test is widely accepted by pavement agencies as the critical parameter for the recently proposed mechanistic empirical design procedure and the candidate of the simple performance test to accompany the Superpave volumetric mix design process. However, the specified dynamic modulus test procedure is time-consuming and costly. State pavement agencies are seeking a more practical test protocol. This paper presents a method for identifying a practical dynamic modulus testing procedure. The currently well-adopted method of calculating the dynamic method is discussed and compared to the more fundamental dynamic modulus calculation method by using actual experimental data from two different asphalt mixtures. It was found that the NCHRP report proposed method produces higher modulus values, but the difference is less than 10 %, as indicates that the simple peak to peak method can be used in the calculation without compromising accuracy. A comprehensive dynamic modulus test, which incorporates strain level, test temperature, and frequency, was performed on one asphalt mixture. Experimental data were analyzed with t-test at the 95 % level of confidence. The analysis results show no statistical difference between the dynamic modulus for the two studied strain levels and no permanent damage was found on tested specimens for all three test temperatures. Comparison of the master curves built by different temperature and frequency combinations illustrates redundancy in test temperature and frequency. A more practical dynamic modulus test procedure is proposed based upon the evaluation. This research shows that three test temperatures, 4.4°C, 21.1°C, and 37.8°C, and six frequencies, 25, 10, 5, 1, 0.5 and 0.1 Hz, plus one additional frequency of 0.01 Hz at 37.8°C are adequate to build a smooth master curve to satisfactorily characterize asphalt mixtures.
Cal-20
Authors: Black Matt
Published: September 2011

Photo essay on California’s twentieth congressional district.
It's Not about Winning, It's about Getting Better
Authors: Schroth Holly A.
Published: September 2011

“Jack is a consummate professional with a great moral compass, nationally respected credentials and an ability to win with a whistle or three-piece suit. In my 30-plus years in athletics, I can think of very few that rival Jack's capabilities as a coach and a person.”–Rick Greenspan, Cal Associate Athletic Director1
Clinical manifestation, disease course and response to enzyme replacement therapy in Hungarian patients with Pompe’s disease
Authors: Bereznai Benjamin , Trauninger Anita , György Ilona , Szakszon Katalin , Almássy Zsuzsanna , Pál Endre , Herczegfalvi Ágnes , Várdi Visy Katalin , Illés Zsolt , Molnár Mária Judit
Published: September 2011

Pompe’s disease is an autosomal recessive disease caused by deficiency of acid-alpha-glucosidase. Aims and Methods: Authors analyzed the phenotype of 11 Hungarian patients with Pompe’s disease and evaluated clinical parameters and response to enzyme replacement therapy during a long-term follow-up in 8 patients. Results: One patient with atypical infantile form presented with cardiomyopathy and a very slow progression of motor deficits; after 2 years of enzyme replacement therapy no disability was present at the age 6 years. Another patient was asymptomatic at the age of 2.5 years. The adult onset form was characterized by slight to prominent limb-girdle myopathy with an age of onset between 20 and 50 years. In 3 of such cases respiratory insufficiency was also present. Conclusions: Hungarian patients with Pompe’s disease presented with a wide phenotypic variability ranging from atypical early childhood form with slowly progressive course to late-onset limb-girdle myopathy with variable courses. Enzyme replacement therapy resulted in significant improvement in motor and respiratory functions in most of the patients. Orv. Hetil., 2011, 152, 1569–1575.
Electrons are round, π are squared
Authors: Palucka Tim
Published: September 2011

“In the most exquisite measurements yet, researchers declared the [electron] particle to be a perfect sphere to within one billionth of a billionth of a billionth of a centimetre.”—The Guardian, May 25, 2011
Transient Absorption for Characterization of Quantum Dot Intermediate Band Solar Cells
Authors: Kolla Praveen , Norman Andrew , Smith Steve
Published: September 2011

We use transient absorption methods to characterize the sequential two-photon absorption in a quantum-dot super-lattice based intermediate band solar cell (QD-IBSC). Using collinear, orthogonally polarized beams generated from an Optical Parametric Oscillator (OPO) at varying time delay, tuned stepwise from 1050nm to 1250nm, we use the solar cell photocurrent as a direct measure of the transient absorption by measuring the differential photo-current as a function of time delay between two energetically degenerate, 100fs pulses. For comparison, we measure the pulse autocorrelation in the same geometry using a GaAsP photodiode, where all observed photocurrent is derived from instantaneous two-photon absorption. Our measurements show that at high intensity, the measurement is dominated by instantaneous two photon absorption, with a simultaneous sequential two-photon photocurrent which persists beyond the pulse overlap. Our measurements demonstrate the method can reveal carrier dynamics in a working QD-IBSC, and their dependence on energy. The method could potentially give details of the band structure formed in the QD-IBSC. Such knowledge may benefit device development and future designs of IBSCs based on QD superlattices or alternative intermediate band materials or device structures.
Review Paper: The Helmholtz‐Kohlrausch effect
Authors: Donofrio Robert L.
Published: September 2011

Abstract— The Helmholtz‐Kohlrausch (H‐K) effect is the influence of color purity on the perceived brightness of a color object (or source). In addition to a review of the effect, a survey of color and brightness‐perception studies from 1825 to the present (including our own studies on disabling glare) is presented. Disabling glare is the blinding experience which results from a bright source in our field of view. There has been a great deal of work on the H‐K effect, and this paper is our personal view of the subject. The H‐K effect has lead to new color‐appearance models which help to describe the brightness/luminance discrepancies, and we will only touch on this subject. It will be shown how the H‐K effect affects many of the displays, mobile devices, and phones. Additionally, how the H‐K effect is involved with our perception at mesopic light levels encountered during night driving will be discussed.
Image correction based on homography in stereoscopic projection display
Authors: Liu Jun , Wang Qiong‐Hua , Xu Xiao‐Qing , Gu Jun
Published: September 2011

Abstract— Stereoscopic and autostereoscopic projection‐display systems use projector arrays to present stereoscopic images, and each projector casts one parallax image of a stereoscopic scene. Because of the position shift of the projectors, the parallax images have geometric deformation, which influences the quality of the displayed stereoscopic images. In order to solve this problem, a method based on homography is proposed. The parallax images are pre‐transformed before they are projected, and then the stereoscopic images without geometric distortion can be obtained. An autostereoscopic projection‐display system is developed to present the images with and without calibration. Experimental results show that this method works effectively.