bluuebunny/crossref_metadata_2025 huggingface dataset:
Method Variance and Marker Variables: A Review and Comprehensive CFA Marker Technique
Authors: Williams Larry J. , Hartman Nathan , Cavazotte Flavia
Published: April 2010

Lindell and Whitney introduced a partial correlation technique, now referred to as the correlational marker technique, for controlling method variance using a marker variable that is theoretically unrelated to substantive variables in a study. This article (a) first reviews their specific analysis plan, and then (b) reviews empirical studies that have followed all or part of this plan. The authors also (c) describe a structural equation method that has been applied to the analysis of marker variables and (d) review empirical studies using this analytical approach. Next, the authors (e) develop a comprehensive confirmatory factor analysis (CFA) marker technique analysis plan, and (f) demonstrate this plan with an empirical example. Finally, the authors (g) describe how marker variables can be examined along with other method variance processes, (h) discuss the important role of theory in the critical step of selecting marker variables, and (i) discuss assumptions and limitations of the Comprehensive CFA Marker Technique.
Using Mixed-Measurement Item Response Theory With Covariates (MM-IRT-C) to Ascertain Observed and Unobserved Measurement Equivalence
Authors: Tay Louis , Newman Daniel A. , Vermunt Jeroen K.
Published: April 2010

Traditional item response theory (IRT) measurement invariance approaches examine measurement equivalence (ME) between observed groups (e.g., race, gender, culture). By contrast, mixed-measurement item response theory (MM-IRT) ascertains ME among unobserved groups (i.e., latent classes [LC] of respondents distinguished by differences in scale use). Both approaches can be integrated by using the Mixed-Measurement Item Response Theory with Covariates (MM-IRT-C) model, in which covariates (i.e., observed characteristics) are modeled in conjunction with LCs, thereby elucidating if ME is attributable to observed and/or unobserved groupings. We first show how this technique can be used to ascertain ME over multiple observed characteristics (categorical and/or continuous) concomitantly, thereby advancing a more general approach to observed ME. Next, we illustrate how the full MM-IRT-C can be used to: (a) infer underlying latent measurement classes (LCs), (b) determine associations of LC membership with observed characteristics, and (c) determine if observed measurement nonequivalence occurs predominantly within a particular latent measurement class. This method is demonstrated using a measure of union citizenship behavior, with years of work experience and gender as covariates. The proposed framework extends organizational ME research from considering a single question (i.e., Is there ME between categorical observed groups?) to addressing eight, separate questions about observed and unobserved ME. The substantive and methodological contributions of this model for rethinking ME and its use in organizational research are discussed.
Un/Wrapping Shibuya: Place, Media, and Punctualization
Authors: Morris Brian
Published: April 2010

This article discusses cultural studies approaches to the role of media and communication technologies in the constitution of place. The discussion emerges out of the author’s ongoing study of the Shibuya district of Tokyo. Known for its trendsetting youth cultures and as a site of conspicuous consumption, Shibuya is also marked by an unusually intense proliferation of screen technologies, from the large scale (such as television screens embedded in building structures) to the miniature (individual mobile telephone screens). An examination of the articulation of these ubiquitous media technologies with a range of human and institutional actors in Shibuya provides broader insights into contemporary spatial practices and formations. It is argued that a combination of Law’s notion of “punctualization,” drawn from actor-network theory, and Hendy’s social anthropological concept of “un/wrapping” provides a generative framework for conceptualizing and describing the processual production and experience of Shibuya’s mediated place identity.
Locality differences of sickness absence in the context of health and social conditions of the inhabitants
Authors: Virtanen Pekka , Vahtera Jussi , Nygård Clas-Håkan
Published: April 2010

Background and aim: Earlier research has suggested that local communities develop different sickness absence practices, expressed in variation in the absence figures. This study aimed to test the hypothesis that the work places residing in a locality share similar sickness absence practice. Methods: Register data from the major public sector employers and from private industrial employers were used to compare the absence in two localities. Results: There were significant differences by locality in both branches and both in short and in long sickness absences. Population-level statistics showed a corresponding locality difference in recipients of sickness allowance benefits and in primary healthcare visits, but not in indicators of mortality and morbidity. Social problems were more common in the locality with high rate of absence. Conclusion: Area-specific practice, or habitus, as an independent determinant of sickness absence is discussed and an explicitly sociological context is recommended for debates about ‘‘best sickness absence practices’’ and corresponding intervention measures.
The Reverse Favorite-Longshot Bias in the National Hockey League: Do Bettors Still Score on Longshots?
Authors: Woodland Linda M. , Woodland Bill M.
Published: April 2010

The favorite—longshot bias, the tendency of bettors to underbet favorites and overbet longshots (underdogs), has received considerable attention in the economics and finance literature. Although the bias is prevalent in racetrack betting, with pari-mutuel odds, researchers have detected a reverse bias in two fixed-odds betting markets in the United States. A weak bias was documented for Major League Baseball for 22 seasons. It was also found to be present in the National Hockey League betting market and was of sufficient strength to allow for profitable wagering opportunities. This article analyzes 10 additional seasons of hockey wagering. The bias is sustained for the first three seasons but disappears in the last seven seasons as the market converges to efficiency. This contrasts with the baseball betting market, where the bias persists.
“I Mean It’s Awkward Anxiety”: Exploring the Role of Sociohistorical Context in Men’s Negotiation of Masculine Subjectivity
Authors: Weber Christina D.
Published: April 2010

In this article, the author explores the process of claiming masculine subjectivity through in-depth interviews conducted with two brothers who are adult children of a Vietnam Veteran. Drawn from a larger research project, these interviews serve as a case study that reveals the ways in which men navigate masculine subjectivity within a specific historical context. Drawing on Connell and Messerschmidt’s reformulation of hegemonic masculinity and Butler’s work on performativity, the author explores the dynamics of masculine subjectivity through the historical event of the Vietnam War. The author demonstrates how these men utilize both hegemonic masculinity and a subordinate form of masculinity found in the Vietnam Veteran as a way of negotiating their position as masculine subjects. The tension created by this negotiation ultimately produces a state of anxiety as they try to hold onto illusive idealized social narratives of masculine identity.
A Phan on Phish: Live Improvised Music in Five Performative Commitments
Authors: Blau Jnan A.
Published: April 2010

Explored as a series of five interrelated performative commitments, the author takes seriously the notion that live musical performance, especially when it is pervaded by an improvisational ethos, can be quite powerful and well worth close examination. In particular, the band Phish, with its devout subcultural following of “phans,” is mined as a rich site for critical, theoretical, and descriptive fodder. The author writes as both a phan and a scholar, drawing from his own experiences seeing Phish live on many occasions as well as from an interdisciplinary body of scholarly literature. The essay provides insight not only into the Phish phenomenon but also into the intersections of performance, communication, popular music, and critical cultural studies.
Singing “I Will Survive”: Performance as Evolving Relationship
Authors: McRae Chris
Published: April 2010

The 1978 disco hit “I Will Survive,” made popular by Gloria Gaynor, has personal significance for me as a listener and as a performer. In this essay, I trace my evolving relationship with this song from my childhood as I sang and listened to the song with my mother to my later performances of the song as a musician in different bands. In telling my story, I look to my various relationships with this song to argue for an analysis of music that complicates and considers the ways in which the listener, performer, and performance work together to shape the ways in which we come to interpret meanings and identities in the cultural performance of music.
Queer Punk Macha Femme: Leslie Mah’s Musical Performance in Tribe 8
Authors: Shoemaker Deanna
Published: April 2010

This essay analyzes the musical performances of Leslie Mah, biracial lead guitarist and backup vocalist for the legendary all-female, queercore punk band Tribe 8, whose members broke up in 2005 after fifteen years together. Inspired by the recent turn in performance studies toward studies of music as performance, this work employs multiple methods and objects to get at the complex totality of popular music’s performativity. Mah’s macha femme persona, playing style, and performance of identity as a lesbian woman of color within queercore punk music allow her to enter a carnivalesque realm of feminist menace, palpable rage, and unruly pleasure. Mah’s performance strategies and articulations of her queer and biracial identities in interviews are contextualized within feminist performance, riot grrrl, and punk music studies. Tribe 8’s lyrics, music, marketing, and band member personas provide cultural context for Mah’s distinctive performance of macha femme.
Call it Swing: A Jazz Blues Autoethnography
Authors: Spry Tami
Published: April 2010

This performative autoethnography utilizes jazz swing as a method to further activate the critical processes in qualitative research. In reflecting on my father’s 25 years as a jazz musician, I find his everyday lived methodology of swing provides an opportunity to explore the ways in which family inheritance collides with sociocultural practices of racial inequity and cultural appropriation. Autoethnographically re/inhabiting this space and sound with my father revealed a performative ethos, an empathetic epistemology of critical reflection activated by the transgressive discipline of jazz. Specifically, this performative ethos is applied to issues of racial accountability, embodied theorizing, and the ethical implications of an aesthetic/epistemic praxis in autoethnography. More broadly, I offer performative ethos as critical pedagogy assisting in living a critical life where issues of power and privilege are personally political and are written and rewritten daily with others in hope of utopia.
Ethnic differences in alpha-1 antitrypsin deficiency in the United States of America
Authors: de Serres Frederick J. , Blanco Ignacio , Fernández-Bustillo Enrique
Published: April 2010

Background: Our earlier publications have demonstrated that alpha-1 antitrypsin (AAT) deficiency is not a rare disorder in the United States with at least 33,728 PI*ZZ homozygote individuals at risk.

Method: Using data on the prevalences of the two most common deficiency alleles PI*S and PI*Z in the five major individual ethnic subgroups in the United States, the numbers of heterozygotes for PI*MS and PI*MZ, and compound heterozygotes/homozygotes for PI*SS, PI*SZ and PI*ZZ have been determined for each ethnic subgroup.

Results: When the data for the prevalence of AAT deficiency in individual cohorts are displayed as a function of ethnic subgroup, striking differences are found in the numbers in each of the five phenotypic classes of PI*S and PI*Z. This type of analysis has demonstrated striking differences in the risk for AAT deficiency in each of these five ethnic subgroups. This analysis as a function of ethnic subgroup also has demonstrated that there are higher numbers of each of the five PI*S and PI*Z deficiency classes, namely PI*MS, PI*SS, PI*MZ, PI*SZ and PI*ZZ.

Conclusions: This analysis has demonstrated that the highest risk for AAT deficiency is found in Whites, followed by Hispanics and Blacks with the lowest prevalence among Mexican Americans and no risk among Asians. The numbers for those at risk for AAT deficiency in the United States are well documented and in the present analysis there are, for example, a total of 48,904 PI*ZZ homozygotes at risk. The critical question for our healthcare professionals is ‘When will the medical community acknowledge that AAT deficiency is a prevalent and well-documented human genetic disorder and develop appropriate mechanisms for early diagnosis, medical follow-up and treatment both in the United States and worldwide?’
Optical coherence tomography as a potential readout in clinical trials
Authors: Greenberg Benjamin M. , Frohman Elliot
Published: April 2010

Optical coherence tomography (OCT) is a noninvasive tool used for measuring tissue at micrometer resolution. It has been extensively applied to ocular pathologies and is now being studied as a biomarker in various neurologic conditions. The retina represents a unique environment for study, with unmyelinated axons that directly synapse into the central nervous system. When trying to quantify axonal degradation in neurologic disease, the currently used imaging modalities are limited in sensitivity and specificity. Early data suggest that several neurologic conditions have pathologic changes in the retinal nerve fiber layer of the eye, creating a potential surrogate marker for neurodegeneration. OCT has the potential to become a noninvasive, reproducible test for axonal degeneration that could become an invaluable tool for measuring the efficacy of potential neuroprotective agents. If the natural history of neurodegeneration, as measured by OCT, can be documented in diseases such as Alzheimer’s, Parkinson’s and multiple sclerosis, then OCT can be used to measure alterations in the rate of degeneration when treatment is applied. Thus, OCT represents a new, promising technology for documenting outcomes in neuroprotection trials.
Extra-articular Snapping Hip: A Literature Review
Authors: Lewis Cara L.
Published: April 2010

Context:

Snapping hip, or coxa saltans, is a vague term used to describe palpable or auditory snapping with hip movements. As increasing attention is paid to intra-articular hip pathologies such as acetabular labral tears, it is important to be able to identify and understand the extra-articular causes of snapping hip.

Evidence Acquisition

The search terms snapping hip and coxa sultans were used in PubMed to locate suitable studies of any publication date (ending date, November 2008).

Results:

Extra-articular snapping may be caused laterally by the iliotibial band or anteriorly by the iliopsoas tendon. Snapping of the iliopsoas tendon usually requires contraction of the hip flexors and may be difficult to differentiate from intra-articular causes of snapping. Dynamic ultrasound can help detect abrupt tendon translation during movement, noninvasively supporting the diagnosis of extra-articular snapping hip. The majority of cases of snapping hip resolve with conservative treatment, which includes avoidance of aggravating activities, stretching, and anti-inflammatory medication. In recalcitrant cases, surgery to lengthen the iliotibial band or the iliopsoas tendon has produced symptom relief but may result in prolonged weakness.

Conclusions:

In treating active patients with snapping soft tissues around the hip, clinicians should recognize that the majority of cases resolve without surgical intervention, while being mindful of the potential for concomitant intra-articular and internal snapping hips.
Postoperative Rehabilitation Guidelines for Hip Arthroscopy in an Active Population
Authors: Voight Michael L. , Robinson Kevin , Gill Lance , Griffin Karen
Published: April 2010

Context:

With the evolution of hip arthroscopy has come an increased recognition of intra-articular hip pathologies and improved techniques for their management. Whereas mechanical problems can often be corrected through surgery, functional deficits must be corrected through the rehabilitation process. Therefore, the evolution of hip arthroscopy has necessitated a progression in hip rehabilitation to ensure optimal postsurgical results.

Evidence Acquisition:

Literature review was conducted with PubMed, EMBASE, and PEDro (1992 to 2009) with the terms hip, rehabilitation, and physical therapy.

Results:

Although it is generally accepted that rehabilitation after hip arthroscopy is important, there is limited evidence-based research to support the rehabilitative guidelines.

Conclusion:

The common goal of hip rehabilitation should remain focused on the return to pain-free function of the hip joint. Outcome data indicate that this goal is being met; however, further data are required to completely validate the long-term success of hip rehabilitation after arthroscopy.
Platelet-Rich Plasma: Where Are We Now and Where Are We Going?
Authors: Cole Brian J. , Seroyer Shane T. , Filardo Giuseppe , Bajaj Sarvottam , Fortier Lisa A.
Published: April 2010

Context:

Platelet-rich plasma (PRP) may affect soft tissue healing via growth factors released after platelet degranulation. Because of this potential benefit, clinicians have begun to inject PRP for the treatment of tendon, ligament, muscle, and cartilage injuries and early osteoarthritis.

Evidence Acquisition:

A PubMed search was performed for studies relating to PRP, growth factors, and soft tissue injuries from 1990 to 2010. Relevant references from these studies were also retrieved.

Results:

Soft tissue injury is a major source of disability that may often be complicated by prolonged and incomplete recovery. Numerous growth factors may potentiate the healing and regeneration of tendons and ligaments. The potential benefits of biologically enhanced healing processes have led to a recent interest in the use of PRP in orthopaedic sports medicine. There has been widespread anecdotal use of PRP for muscle strains, tendinopathy, and ligament injuries and as a surgical adjuvant to rotator cuff repair, anterior cruciate ligament reconstruction, and meniscal or labral repairs. Although the fascination with this emerging technology has led to a dramatic increase in its use, scientific data supporting this use are still in their infancy.

Conclusions:

The literature is replete with studies on the basic science of growth factors and their relation to the maintenance, proliferation, and regeneration of various tissues and tissue-derived cells. Despite the promising results of several animal studies, well-controlled human studies are lacking.
Sportsmen’s Groin—Diagnostic Approach and Treatment With the Minimal Repair Technique: A Single-Center Uncontrolled Clinical Review
Authors: Muschaweck Ulrike , Berger Luise Masami
Published: April 2010

Context:

Sportsmen’s groin, also called sports hernia and Gilmore groin, is one of the most frequent sports injuries in athletes and may place an athletic career at risk. It presents with acute or chronic groin pain exacerbated with physical activity. So far, there is little consensus regarding pathogenesis, diagnostic criteria, or treatment. There have been various attempts to explain the cause of the groin pain. The assumption is that a circumscribed weakness in the posterior wall of the inguinal canal, which leads to a localized bulge, induces a compression of the genital branch of the genitofemoral nerve, considered responsible for the symptoms.

Methods:

The authors developed an innovative open suture repair—the Minimal Repair technique—to fit the needs of professional athletes. With this technique, the circumscribed weakness of the posterior wall of the inguinal canal is repaired by an elastic suture; the compression on the nerve is abolished, and the cause of the pain is removed. In contrast with that of common open suture repairs, the defect of the posterior wall is not enlarged, the suture is nearly tension free, and the patient can return to full training and athletic activity within a shorter time. The outcome of patients undergoing operations with the Minimal Repair technique was compared with that of commonly used surgical procedures.

Results:

The following advantages of the Minimal Repair technique were found: no insertion of prosthetic mesh, no general anesthesia required, less traumatization, and lower risk of severe complications with equal or even faster convalescence. In 2009, a prospective cohort of 129 patients resumed training in 7 days and experienced complete pain relief in an average of 14 days. Professional athletes (67%) returned to full activity in 14 days (median).

Conclusion:

The Minimal Repair technique is an effective and safe way to treat sportsmen’s groin.
Reassessment of Disease Severity in Patients Following Severe Acute Exacerbations of Asthma
Authors: Bravo Rosalynn C. , Carroll Christopher L. , Schramm Craig M. , Bhandari Anita
Published: April 2010

Patients with asthma may have severe exacerbations. The impact of severe acute exacerbation on patient outcome has not been studied, however. The purpose of this study was to examine the long-term outcome of severe exacerbation of asthma on baseline disease severity in children. Data were collected retrospectively from all children with asthma older than 5 years who were admitted to the intensive care unit (ICU) with an acute exacerbation and were subsequently followed as outpatients. Patients were divided into 4 severity groups (intermittent, mild persistent, moderate persistent, and severe persistent) based on the severity of asthma prior to ICU admission, at the time of admission, and at 12-month follow-up. Thirty-nine patients were followed for 12 months after ICU admission. Pulmonology consultation was more likely to be obtained in patients with moderate and severe asthma at baseline as compared with those with intermittent or mild asthma ( P = .004). On follow-up, 59% had a change in classification of their asthma severity. Changes in asthma severity were more likely to occur at the time of ICU admission rather than at 12-month follow-up. There was no difference in the gender, race, age, or body mass index at the time of ICU admission between the group who had a change in asthma severity and the group with no change in severity. There was no difference in Modified Pulmonary Index Score, duration of hospitalization, or length of stay in the ICU between the 2 groups. Prior inhaled steroid dose was lower in patients who had a change in severity as compared with those who had not ( P = .018). Children with mild asthma were frequently reclassified to a more severe asthma category after an acute life-threatening episode of asthma. It is likely that this reclassification was due to underestimation of disease severity prior to the ICU admission, but the severe acute event itself may have contributed to increased severity classification.
Dimer-tetramer transition controls RUNX1/ETO leukemogenic activity
Authors: Wichmann Christian , Becker Yvonne , Chen-Wichmann Linping , Vogel Vitali , Vojtkova Anna , Herglotz Julia , Moore Sandra , Koch Joachim , Lausen Jörn , Mäntele Werner , Gohlke Holger , Grez Manuel
Published: April 2010

RUNX1/ETO, the fusion protein resulting from the chromosomal translocation t(8;21), is one of the most frequent translocation products in acute myeloid leukemia. Several in vitro and in vivo studies have shown that the homo-tetramerization domain of ETO, the nervy homology region 2 (NHR2), is essential for RUNX1/ETO oncogenic activity. We analyzed the energetic contribution of individual amino acids within the NHR2 to RUNX1/ETO dimer-tetramer transition and found a clustered area of 5 distinct amino acids with strong contribution to the stability of tetramers. Substitution of these amino acids abolishes tetramer formation without affecting dimer formation. Similar to RUNX1/ETO monomers, dimers failed to bind efficiently to DNA and to alter expression of RUNX1-dependent genes. RUNX1/ETO dimers do not block myeloid differentiation, are unable to enhance the self-renewal capacity of hematopoietic progenitors, and fail to induce leukemia in a murine transplantation model. Our data reveal the existence of an essential structural motif (hot spot) at the NHR2 dimer-tetramer interface, suitable for a molecular intervention in t(8;21) leukemias.
Processing and cross-presentation of individual HLA-A, -B, or -C epitopes from NY-ESO-1 or an HLA-A epitope for Melan-A differ according to the mode of antigen delivery
Authors: Robson Neil C. , McAlpine Tristan , Knights Ashley J. , Schnurr Max , Shin Amanda , Chen Weisan , Maraskovsky Eugene , Cebon Jonathan
Published: April 2010

The ability of dendritic cells (DCs) to cross-present protein tumor antigens to cytotoxic T lymphocytes (CTLs) underpins the success of therapeutic cancer vaccines. We studied cross-presentation of the cancer/testis antigen, NY-ESO-1, and the melanoma differentiation antigen, Melan-A by human DC subsets. Monocyte-derived DCs (MoDCs) efficiently cross-presented human leukocyte associated (HLA)–A2-restricted epitopes from either a formulated NY-ESO-1/ISCOMATRIX vaccine or when either antigen was mixed with ISCOMATRIX adjuvant. HLA-A2 epitope generation required endosomal acidification and was proteasome-independent for NY-ESO-1 and proteasome-dependent for Melan-A. Both MoDCs and CD1c+ blood DCs cross-presented NY-ESO-1–specific HLA-A2157-165–, HLA-B760-72–, and HLA-Cw392-100–restricted epitopes when formulated as an NY-ESO-1/ISCOMATRIX vaccine, but this was limited when NY-ESO-1 and ISCOMATRIX adjuvant were added separately to the DC cultures. Finally, cross-presentation of NY-ESO-1157-165/HLA-A2, NY-ESO-160-72/HLA-B7, and NY-ESO-192-100/HLA-Cw3 epitopes was proteasome-dependent when formulated as immune complexes (ICs) but only proteasome-dependent for NY-ESO-160-72/HLA-B7–restricted cross-presentation facilitated by ISCOMATRIX adjuvant. We demonstrate, for the first time, proteasome-dependent and independent cross-presentation of HLA-A–, B–, and C–restricted epitopes within the same full-length tumor antigen by human DCs. Our findings identify important differences in the capacities of human DC subsets to cross-present clinically relevant, full-length tumor antigens and how vaccine formulation impacts CTL responses in vivo.
A biophysical elucidation for less toxicity of Agglutinin than Abrin-a from the Seeds of Abrus Precatorius in consequence of crystal structure
Authors: Cheng Jack , Lu Tian-Huey , Liu Chao-Lin , Lin Jung-Yaw
Published: April 2010

X-ray crystal structure determination of agglutinin from abrus precatorius in Taiwan is presented. The crystal structure of agglutinin, a type II ribosome-inactivating protein (RIP) from the seeds of Abrus precatorius in Taiwan, has been determined from a novel crystalline form by the molecular replacement method using the coordinates of abrin-a as the template. The structure has space group P41212 with Z = 8, and been refined at 2.6 Å to R-factor of 20.4%. The root-mean-square deviations of bond lengths and angles from the standard values are 0.009 Å and 1.3°. Primary, secondary, tertiary and quaternary structures of agglutinin have been described and compared with those of abrin-a to a certain extent. In subsequent docking research, we found that Asn200 of abrin-a may form a critical hydrogen bond with G4323 of 28SRNA, while corresponding Pro199 of agglutinin is a kink hydrophobic residue bound with the cleft in a more compact complementary relationship. This may explain the lower toxicity of agglutinin than abrin-a, despite of similarity in secondary structure and the activity cleft of two RIPs.
Sequence variation and selection of small RNAs in domesticated rice
Authors: Wang Yu , Shen Dan , Bo Shiping , Chen Huan , Zheng Jian , Zhu Qian-Hao , Cai Daguang , Helliwell Chris , Fan Longjiang
Published: April 2010

Background

Endogenous non-coding small RNAs (21-24 nt) play an important role in post-transcriptional gene regulation in plants. Domestication selection is the most important evolutionary force in shaping crop genomes. The extent of polymorphism at small RNA loci in domesticated rice and whether small RNA loci are targets of domestication selection have not yet been determined.

Results

A polymorphism survey of 94 small RNA loci (88 MIRNAs, four TAS3 loci and two miRNA-like long hairpins) was conducted in domesticated rice, generating 2 Mb of sequence data. Many mutations (substitution or insertion/deletion) were observed at small RNA loci in domesticated rice, e.g. 12 mutation sites were observed in the mature miRNA sequences of 11 MIRNAs (12.5% of the investigated MIRNAs). Several small RNA loci showed significant signals for positive selection and/or potential domestication selection.

Conclusions

Sequence variation at miRNAs and other small RNAs is higher than expected in domesticated rice. Like protein-coding genes, non-coding small RNA loci could be targets of domestication selection and play an important role in rice domestication and improvement.
Historical spatial range expansion and a very recent bottleneck of Cinnamomum kanehiraeHay. (Lauraceae) in Taiwan inferred from nuclear genes
Authors: Liao Pei-Chun , Kuo Dai-Chang , Lin Chia-Chia , Ho Kuo-Chieh , Lin Tsan-Piao , Hwang Shih-Ying
Published: April 2010

Background

Species in the varied geographic topology of Taiwan underwent obvious demographic changes during glacial periods. Cinnamomum kanehirae has been exploited for timber and to obtain medicinal fungi for the past 100 years. Understanding anthropogenic factors influencing the demography of this species after the last glacial maximum (LGM) is critically important for the conservation of this species.

Results

Populations of C. kanehirae were classified into four geographic regions: northwestern (NW), west-central (WC), southwestern (SW), and southeastern (SE). In total, 113 individuals from 19 localities were sampled, and variations in the chalcone synthase gene (Chs) intron and leafy (Lfy) intron-2 sequences of nuclear DNA were examined in order to assess phylogeographic patterns, the timescales of demographic and evolutionary events, and recent anthropogenic effects. In total, 210 Chs and 170 Lfy sequences, which respectively constituted 36 and 35 haplotypes, were used for the analyses. Estimates of the migration rate (M) through time revealed a pattern of frequent gene flow during previous and the present interglacials. The isolation-by-distance test showed that there generally was no significant correlation between genetic and geographic distances. The level of among-region genetic differentiation was significant when comparing eastern to western populations. However, no significant among-region genetic differentiation was found in comparisons among the four geographic regions. Moreover, essentially no genetic structuring was found for the three regions west of the CMR. A fit of spatial range expansion was found for pooled and regional samples according to the non-significant values of the sum of squared deviations. Using the Bayesian skyline plot (BSP) method, a recent bottleneck after the LGM expansion was detected in both regional and pooled samples.

Conclusions

Common haplotype distributions among geographic regions and the relatively shallow genetic structuring displayed are the result of historical gene flows. Southward dispersals in an earlier time frame from the NW region and in a later time frame from the SE region were inferred. The BSP analysis suggested a postglacial expansion event. Recent trends, however, refer to a bottleneck due to human interventions observed for both pooled and regional C. kanehirae samples.
An EST resource for tilapia based on 17 normalized libraries and assembly of 116,899 sequence tags
Authors: Lee Bo-Young , Howe Aimee E , Conte Matthew A , D'Cotta Helena , Pepey Elodie , Baroiller Jean-Francois , di Palma Federica , Carleton Karen L , Kocher Thomas D
Published: April 2010

Background

Large collections of expressed sequence tags (ESTs) are a fundamental resource for analysis of gene expression and annotation of genome sequences. We generated 116,899 ESTs from 17 normalized and two non-normalized cDNA libraries representing 16 tissues from tilapia, a cichlid fish widely used in aquaculture and biological research.

Results

The ESTs were assembled into 20,190 contigs and 36,028 singletons for a total of 56,218 unique sequences and a total assembled length of 35,168,415 bp. Over the whole project, a unique sequence was discovered for every 2.079 sequence reads. 17,722 (31.5%) of these unique sequences had significant BLAST hits (e-value < 10-10) to the UniProt database.

Conclusion

Normalization of the cDNA pools with double-stranded nuclease allowed us to efficiently sequence a large collection of ESTs. These sequences are an important resource for studies of gene expression, comparative mapping and annotation of the forthcoming tilapia genome sequence.
Genetic variations regulate alternative splicing in the 5' untranslated regions of the mouse glioma-associated oncogene 1, Gli1
Authors: Palaniswamy Ramesh , Teglund Stephan , Lauth Matthias , Zaphiropoulos Peter G , Shimokawa Takashi
Published: April 2010

Background

Alternative splicing is one of the key mechanisms that generate biological diversity. Even though alternative splicing also occurs in the 5' and 3' untranslated regions (UTRs) of mRNAs, the understanding of the significance and the regulation of these variations is rather limited.

Results

We investigated 5' UTR mRNA variants of the mouse Gli1 oncogene, which is the terminal transcriptional effector of the Hedgehog (HH) signaling pathway. In addition to identifying novel transcription start sites, we demonstrated that the expression ratio of the Gli1 splice variants in the 5' UTR is regulated by the genotype of the mouse strain analyzed. The GT allele, which contains the consensus intronic dinucleotides at the 5' splice site of intron 1B, favors exon 1B inclusion, while the GC allele, having a weaker 5' splice site sequence, promotes exon 1B skipping. Moreover, the alternative Gli1 5' UTRs had an impact on translational capacity, with the shorter and the exon 1B-skipped mRNA variants being most effective.

Conclusions

Our findings implicate novel, genome-based mechanisms as regulators of the terminal events in the mouse HH signaling cascade.
Curcumin reduces α-synuclein induced cytotoxicity in Parkinson's disease cell model
Authors: Wang Min S , Boddapati Shanta , Emadi Sharareh , Sierks Michael R
Published: April 2010

Background

Overexpression and abnormal accumulation of aggregated α-synuclein (αS) have been linked to Parkinson's disease (PD) and other synucleinopathies. αS can misfold and adopt a variety of morphologies but recent studies implicate oligomeric forms as the most cytotoxic species. Both genetic mutations and chronic exposure to neurotoxins increase αS aggregation and intracellular reactive oxygen species (ROS), leading to mitochondrial dysfunction and oxidative damage in PD cell models.

Results

Here we show that curcumin can alleviate αS-induced toxicity, reduce ROS levels and protect cells against apoptosis. We also show that both intracellular overexpression of αS and extracellular addition of oligomeric αS increase ROS which induces apoptosis, suggesting that aggregated αS may induce similar toxic effects whether it is generated intra- or extracellulary.

Conclusions

Since curcumin is a natural food pigment that can cross the blood brain barrier and has widespread medicinal uses, it has potential therapeutic value for treating PD and other neurodegenerative disorders.
Early atherosclerosis and cardiac autonomic responses to mental stress: a population-based study of the moderating influence of impaired endothelial function
Authors: Chumaeva Nadja , Hintsanen Mirka , Hintsa Taina , Ravaja Niklas , Juonala Markus , Raitakari Olli T , Keltikangas-Järvinen Liisa
Published: April 2010

Background

Acute mental stress may contribute to the cardiovascular disease progression via autonomic nervous system controlled negative effects on the endothelium. The joint effects of stress-induced sympathetic or parasympathetic activity and endothelial function on atherosclerosis development have not been investigated. The present study aims to examine the interactive effect of acute mental stress-induced cardiac reactivity/recovery and endothelial function on the prevalence of carotid atherosclerosis.

Methods

Participants were 81 healthy young adults aged 24-39 years. Preclinical atherosclerosis was assessed by carotid intima-media thickness (IMT) and endothelial function was measured as flow-mediated dilatation (FMD) using ultrasound techniques. We also measured heart rate, respiratory sinus arrhythmia (RSA), and pre-ejection period (PEP) in response to the mental arithmetic and speech tasks.

Results

We found a significant interaction of FMD and cardiac RSA recovery for IMT (p = 0.037), and a significant interaction of FMD and PEP recovery for IMT (p = 0.006). Among participants with low FMD, slower PEP recovery was related to higher IMT. Among individuals with high FMD, slow RSA recovery predicted higher IMT. No significant interactions of FMD and cardiac reactivity for IMT were found.

Conclusions

Cardiac recovery plays a role in atherosclerosis development in persons with high and low FMD. The role of sympathetically mediated cardiac activity seems to be more important in those with impaired FMD, and parasympathetically mediated in those with relatively high FMD. The development of endothelial dysfunction may be one possible mechanism linking slow cardiac recovery and atherosclerosis via autonomic nervous system mediated effect.
Molecular mechanism of chemoresistance by miR-215 in osteosarcoma and colon cancer cells
Authors: Song Bo , Wang Yuan , Titmus Matthew A. , Botchkina Galina , Formentini Andrea , Kornmann Marko , Ju Jingfang
Published: April 2010

Background

Translational control mediated by non-coding microRNAs (miRNAs) plays a key role in the mechanism of cellular resistance to anti-cancer drug treatment. Dihydrofolate reductase (DHFR) and thymidylate synthase (TYMS, TS) are two of the most important targets for antifolate- and fluoropyrimidine-based chemotherapies in the past 50 years. In this study, we investigated the roles of miR-215 in the chemoresistance to DHFR inhibitor methotrexate (MTX) and TS inhibitor Tomudex (TDX).

Results

The protein levels of both DHFR and TS were suppressed by miR-215 without the alteration of the target mRNA transcript levels. Interestingly, despite the down-regulation of DHFR and TS proteins, ectopic expression of miR-215 resulted in a decreased sensitivity to MTX and TDX. Paradoxically, gene-specific small-interfering RNAs (siRNAs) against DHFR or TS had the opposite effect, increasing sensitivity to MTX and TDX. Further studies revealed that over-expression of miR-215 inhibited cell proliferation and triggered cell cycle arrest at G2 phase, and that this effect was accompanied by a p53-dependent up-regulation of p21. The inhibitory effect on cell proliferation was more pronounced in cell lines containing wild-type p53, but was not seen in cells transfected with siRNAs against DHFR or TS. Moreover, denticleless protein homolog (DTL), a cell cycle-regulated nuclear and centrosome protein, was confirmed to be one of the critical targets of miR-215, and knock-down of DTL by siRNA resulted in enhanced G2-arrest, p53 and p21 induction, and reduced cell proliferation. Additionally, cells subjected to siRNA against DTL exhibited increased chemoresistance to MTX and TDX. Endogenous miR-215 was elevated about 3-fold in CD133+HI/CD44+HI colon cancer stem cells that exhibit slow proliferating rate and chemoresistance compared to control bulk CD133+/CD44+ colon cancer cells.

Conclusions

Taken together, our results indicate that miR-215, through the suppression of DTL expression, induces a decreased cell proliferation by causing G2-arrest, thereby leading to an increase in chemoresistance to MTX and TDX. The findings of this study suggest that miR-215 may play a significant role in the mechanism of tumor chemoresistance and it may have a unique potential as a novel biomarker candidate.
Collection by trained pediatricians or parents of mid-turbinate nasal flocked swabs for the detection of influenza viruses in childhood
Authors: Esposito Susanna , Molteni Claudio G , Daleno Cristina , Valzano Antonia , Tagliabue Claudia , Galeone Carlotta , Milani Gregorio , Fossali Emilio , Marchisio Paola , Principi Nicola
Published: April 2010

This study evaluated the efficiency of pediatric mid-turbinate nasal flocked swabs used by parents in 203 children aged 6 months to 5 years with signs and symptoms of respiratory disease. Two nasal samples were collected from each child in a randomised sequence: one by a trained pediatrician and one by a parent. The real-time polymerase chain reaction influenza virus detection rates were similar in the samples collected using the two methods (Cohen's kappa = 0.86), as were the cycle threshold values. In comparison with the pediatrician-collected samples, the sensitivity and specificity of the parental collections were respectively 89.3% (95% confidence interval [CI]: 77.8-100%) and 97.7% (95% CI: 95.5-100%), and the positive and negative predictive values were respectively 86.2% (95% CI: 73.7-95.1%) and 98.2% (95% CI: 96.4-100%). The children were significantly more satisfied with the parental collections (median values ± standard deviation, 1.59 ± 0.55 vs 3.51 ± 0.36; p < 0.0001). These findings show that mid-turbinate nasal flocked swabs specifically designed for infants and children can be used by parents without reducing the influenza virus detection rate. Moreover, the direct involvement of parents significantly increases patient acceptance, thus simplifying collection and suggesting that this novel swab design should be considered for epidemiological surveys and vaccine efficacy studies.
Differential regulation of PGC-1α expression in rat liver and skeletal muscle in response to voluntary running
Authors: Matiello Renata , Fukui Rosa T , Silva Maria ER , Rocha Dalva M , Wajchenberg Bernardo L , Azhar Salman , Santos Rosa F
Published: April 2010

Background

The beneficial actions of exercise training on lipid, glucose and energy metabolism and insulin sensitivity appear to be in part mediated by PGC-1α. Previous studies have shown that spontaneously exercised rats show at rest enhanced responsiveness to exogenous insulin, lower plasma insulin levels and increased skeletal muscle insulin sensitivity. This study was initiated to examine the functional interaction between exercise-induced modulation of skeletal muscle and liver PGC-1α protein expression, whole body insulin sensitivity, and circulating FFA levels as a measure of whole body fatty acid (lipid) metabolism.

Methods

Two groups of male Wistar rats (2 Mo of age, 188.82 ± 2.77 g BW) were used in this study. One group consisted of control rats placed in standard laboratory cages. Exercising rats were housed individually in cages equipped with running wheels and allowed to run at their own pace for 5 weeks. At the end of exercise training, insulin sensitivity was evaluated by comparing steady-state plasma glucose (SSPG) concentrations at constant plasma insulin levels attained during the continuous infusion of glucose and insulin to each experimental group. Subsequently, soleus and plantaris muscle and liver samples were collected and quantified for PGC-1α protein expression by Western blotting. Collected blood samples were analyzed for glucose, insulin and FFA concentrations.

Results

Rats housed in the exercise wheel cages demonstrated almost linear increases in running activity with advancing time reaching to maximum value around 4 weeks. On an average, the rats ran a mean (Mean ± SE) of 4.102 ± 0.747 km/day and consumed significantly more food as compared to sedentary controls (P < 0.001) in order to meet their increased caloric requirement. Mean plasma insulin (P < 0.001) and FFA (P < 0.006) concentrations were lower in the exercise-trained rats as compared to sedentary controls. Mean steady state plasma insulin (SSPI) and glucose (SSPG) concentrations were not significantly different in sedentary control rats as compared to exercise-trained animals. Plantaris PGC-1α protein expression increased significantly from a 1.11 ± 0.12 in the sedentary rats to 1.74 ± 0.09 in exercising rats (P < 0.001). However, exercise had no effect on PGC-1α protein content in either soleus muscle or liver tissue. These results indicate that exercise training selectively up regulates the PGC-1α protein expression in high-oxidative fast skeletal muscle type such as plantaris muscle.

Conclusion

These data suggest that PGC-1α most likely plays a restricted role in exercise-mediated improvements in insulin resistance (sensitivity) and lowering of circulating FFA levels.
HSP60, a protein downregulated by IGFBP7 in colorectal carcinoma
Authors: Ruan Wenjing , Wang Yinghong , Ma Yu , Xing Xiaoming , Lin Jie , Cui Jing , Lai Maode
Published: April 2010

Background

In our previous study, it was well defined that IGFBP7 was an important tumor suppressor gene in colorectal cancer (CRC). We aimed to uncover the downstream molecules responsible for IGFBP7's behaviour in this study.

Methods

Differentially expressed protein profiles between PcDNA3.1(IGFBP7)-transfected RKO cells and the empty vector transfected controls were generated by two-dimensional gel electrophoresis (2-DE) and mass spectrometry (MS) identification. The selected differentially expressed protein induced by IGFBP7 was confirmed by western blot and ELISA. The biological behaviour of the protein was explored by cell growth assay and colony formation assay.

Results

Six unique proteins were found differentially expressed in PcDNA3.1(IGFBP7)-transfected RKO cells, including albumin (ALB), 60 kDa heat shock protein(HSP60), Actin cytoplasmic 1 or 2, pyruvate kinase muscle 2(PKM2), beta subunit of phenylalanyl-tRNA synthetase(FARSB) and hypothetical protein. The downregulation of HSP60 by IGFBP7 was confirmed by western blot and ELISA. Recombinant human HSP60 protein could increase the proliferation rate and the colony formation ability of PcDNA3.1(IGFBP7)-RKO cells.

Conclusion

HSP60 was an important downstream molecule of IGFBP7. The downregulation of HSP60 induced by IGFBP7 may be, at least in part, responsible for IGFBP7's tumor suppressive biological behaviour in CRC.