bluuebunny/crossref_metadata_2025 huggingface dataset:
Associations between Smoking, Alcohol Consumption, and Colorectal Cancer, Overall and by Tumor Microsatellite Instability Status
Authors: Poynter Jenny N. , Haile Robert W. , Siegmund Kimberly D. , Campbell Peter T. , Figueiredo Jane C. , Limburg Paul , Young Joanne , Le Marchand Loic , Potter John D. , Cotterchio Michelle , Casey Graham , Hopper John L. , Jenkins Mark A. , Thibodeau Stephen N. , Newcomb Polly A. , Baron John A. ,   for the Colon Cancer Family Registry
Published: October 2009

Introduction: Both smoking and alcohol consumption have been associated with modestly increased risks of colorectal cancer (CRC). Reports have suggested that these associations may differ by tumor molecular subtype, with stronger associations for microsatellite unstable (MSI-H) tumors.

Methods: We used a population-based case-unaffected sibling design including 2,248 sibships (2,253 cases; 4,486 siblings) recruited to the Colon Cancer Family Registry to evaluate the association between smoking, alcohol consumption, and CRC. Associations were assessed using conditional logistic regression, treating sibship as the matching factor.

Results: Although there were no statistically significant associations between any smoking variable and CRC overall, smoking did confer an increased risk of certain types of CRC. We observed an association between pack-years of smoking and rectal cancer [odds ratio (OR), 1.85; 95% confidence interval (CI), 1.23-2.79 for >40 pack-years versus nonsmokers; Ptrend = 0.03], and there was an increased risk of MSI-H CRC with increasing duration of smoking (OR, 1.94; 95% CI, 1.09-3.46 for >30 years of smoking versus nonsmokers). Alcohol intake was associated with a modest increase in risk for CRC overall (OR, 1.21; 95% CI, 1.03-1.44 for 12+ drinks per week versus nondrinkers), with more marked increases in risk for MSI-L CRC (OR, 1.85; 95% CI, 1.06-3.24) and rectal cancer (OR, 1.48; 95% CI, 1.08-2.02).

Conclusions: We found associations between cigarette smoking and increased risks of rectal cancer and MSI-H CRC. Alcohol intake was associated with increased risks of rectal cancer and MSI-L CRC. These results highlight the importance of considering tumor phenotype in studies of risk factors for CRC. (Cancer Epidemiol Biomarkers Prev 2009;18(10):2745–50)
Reduced Prediagnostic 25-Hydroxyvitamin D Levels in Women with Breast Cancer: A Nested Case-Control Study
Authors: Rejnmark Lars , Tietze Anna , Vestergaard Peter , Buhl Line , Lehbrink Melsene , Heickendorff Lene , Mosekilde Leif
Published: October 2009

Vitamin D status may affect risk of cancer. In a cross-sectional study with a nested case-control analysis, we determined whether risk of breast cancer is associated with prediagnostic plasma 25-hydroxyvitamin D (25OHD) levels and the effects of lifestyle characteristics known to influence vitamin D status on risk of breast cancer. We studied women without a prior history of breast cancer referred to a diagnostic mammography examination (n = 2,465). Cases were women diagnosed with an incident breast cancer (n = 142). Controls were women not diagnosed with a breast cancer matched to cases on age, menopausal status, and time of year of blood sampling (n = 420). Characteristics of cases and controls were assessed by a self-administrated questionnaire. Blood samples were collected prior to the diagnostic mammography examination. Cases had lower plasma 25OHD levels than controls. Compared with the lowest tertile of 25OHD levels, risk of breast cancer was significantly reduced among women in the highest tertile (relative risk, 0.52; 95% confidence interval, 0.32-0.85). Risk estimates were similar in women with an estrogen receptor–positive and estrogen receptor–negative breast cancer. Use of vitamin D supplements, sunbathing frequency, and fish intake was associated with 25OHD levels, but did not affect the risk of breast cancer. Accordingly, risk of breast cancer was inversely associated with 25OHD levels. Randomized controlled trials are warranted in order to assess whether a causal relationship exists. (Cancer Epidemiol Biomarkers Prev 2009;18(10):2655–60)
Sex-Specific Pediatric Percentiles for Ventricular Size and Mass as Reference Values for Cardiac MRI
Authors: Sarikouch Samir , Peters Brigitte , Gutberlet Matthias , Leismann; Birte , Kelter-Kloepping Andrea , Koerperich Hermann , Kuehne Titus , Beerbaum Philipp
Published: October 2009

Background—

Cardiac MRI is important in the treatment of children with congenital heart disease, but sufficient normative data are lacking. For ventricular volumes and mass, we sought to deliver reference centiles and to investigate sex effects.

Methods and Results—

We included 114 healthy children and adolescents, uniformly distributed spanning an age range of 4 to 20 years, as required by the Lambda-Mu-Sigma method to achieve a percentile distribution, thus avoiding arbitrary age categories. Subjects underwent axial volumetry (1.5-T scanner) using standardized 2D steady-state free-precession and flow protocols. Percentiles were computed for age 8 to 20 years (99 subjects) because breath-holds were more consistent in this group. When indexed for body surface area or height, the centile curves of ventricular volumetric parameters showed allometric increase until adolescence, when a plateau was reached, with values comparable to published adult reference data. In contrast, ventricular mass centiles increased without plateau. There was a significant sex difference, with centiles reflecting larger values in boys than in girls (
P
<0.05) when ventricular volumes were indexed to body surface area or height but not when indexed to weight (exception: mass). There was excellent agreement of axial and short-axis volumetry and of volumetric and flow-derived stroke volumes.

Conclusions—

Percentiles for ventricular volumes and mass in healthy children have been established to serve as reference values in pediatric heart disease. Significant sex differences were noted when indexing volumes to body surface area or height. Unisex centiles related to weight may be considered for chamber volumes albeit not for mass.
An unstable social environment affects sex ratio in guinea pigs: an adaptive maternal effect?
Authors: Von Engelhardt Nikolaus , Kaiser Sylvia , Sachser Norbert , Kemme Kristina , Groothuis Ton , Wewers Dirk
Published: October 2009

Evolutionary theory suggests that offspring sex should be adjusted to environmental conditions in order to maximize future reproductive success. In several animal taxa environmental factors indeed affect the secondary sex ratio. In humans, changes in the sex ratio at birth have been associated with population stressors like war, environmental disasters or economic strife during pregnancy. Here we compared litter sex ratios of female guinea pigs, exposed experimentally to a stable and an unstable social environment. In the latter group composition was changed every three days. Under unstable social conditions the sex ratio was significantly more biased towards daughters than in the stable social situation. This finding was consistent among four independent experiments, conducted independently from each other. Life expectancy can be dramatically reduced under conditions of social instability. Hence mothers in such conditions should bias their investment towards the sex that reaches sexual maturity first, which is the female sex in this species. Thus, to shift the offspring sex ratio towards more daughters under conditions of social instability may represent a maternal strategy to maximize future reproductive success.
The Synergistic Relationship between Soil Moisture and the Low-Level Jet and Its Role on the Prestorm Environment in the Southern Great Plains
Authors: Frye John D. , Mote Thomas L.
Published: October 2009

Changes in low-level moisture alter the convective parameters [e.g., convective available potential energy (CAPE), lifted index (LI), and convective inhibition (CIN)] as a result of alterations in the latent and sensible heat energy exchange. Two sources for low-level moisture exist in the southern Great Plains: 1) moisture advection by the low-level jet (LLJ) from the Gulf of Mexico and 2) evaporation and transpiration from the soils and vegetation in the region. The primary focus of this study is to examine the spatial distribution of soil moisture on a daily basis and to determine the effect it has on the convective parameters. The secondary objective is to investigate how the relationship between soil moisture and convective parameters is altered by the presence of an LLJ. The soil moisture data were obtained through newly developed procedures and advances in technology aboard the Tropical Rainfall Measuring Mission Microwave Imager. The convective parameter data were obtained through the North American Regional Reanalysis dataset. The study examined seven warm seasons (April–September) from 1998 to 2004 and found that the convective environment is more unstable (CAPE > 900 J kg−1, LI < −2°C) but more strongly capped (CIN > 70 J kg−1) on days with an LLJ present. Spearman’s rank correlation analysis showed a less stable atmosphere with increased soil moisture, after soil moisture reached 5%, on most days. Additional analysis determined that on all synoptic-type days the probability of reaching various thresholds of convective intensity increased as soil moisture values increased. The probabilities were even greater on days with an LLJ present than on the days without an LLJ present. An examination of four days representing each synoptic-type day indicates that on the daily scale the intensity of the convective environment is closely related to the high soil moisture and the presence of an LLJ.
A Qualitative Investigation of Korean Immigrant Women’s Lives
Authors: Yoon Eunju , Lee Dal Yob , Koo Young Ran , Yoo Sung-Kyung
Published: October 2009

Postimmigration adjustment experiences of 10 Korean immigrant women were examined using the consensual qualitative research method. Seven domains emerged: general life conditions; gender role; changes in family dynamics; ethnic/national identity, cultural competency, and belongingness; value changes; racial relationships; and support systems and attitudes toward counseling. Participants reported English barriers as one of the biggest challenges. They appreciated a better educational environment for children; a sense of liberation from patriarchal, collectivistic pressures (e.g., demands by in-laws, comparison with others); and strengthened family ties. They highlighted Korean immigrant women’s strengths and adaptability for family survival in the new environment. Participants reported lacking cultural competency or a sense of belongingness in the mainstream society but expected their children to succeed and have voices in the mainstream society. All participants experienced racism and developed coping strategies such as verbal confrontation. Concern about gossips in the small ethnic community was a barrier to seeking counseling.
Is Schwartz’s Value Survey an Interval Scale, and Does It Really Matter?
Authors: Lee Julie Anne , Soutar Geoffrey
Published: October 2009

Researchers often assume the numerical ratings approach used to measure values, such as Schwartz’s Value Survey (SVS), conforms to an interval scale. Correspondence analysis was used to examine this assumption by analyzing SVS data obtained from four Anglo (Australia, New Zealand, United Kingdom, and United States) and two Asian (South Korea and China) countries. The analysis suggested the SVS did not exhibit the characteristics of an interval scale, with responses across all countries producing larger intervals at the low end of the scale and smaller intervals from the mid to high end of the scale. Further analysis suggested there were significant differences in the traditional SVS means and the means suggested by the correspondence analysis. However, when correlations and Euclidian distances between SVS and correspondence analysis scores were examined, they were very high, suggesting the lack of interval scaling was unlikely to affect the relationships between the SVS value types and other constructs.
Cultural and Universal Routes to Authorship Ascription: Effects of Outcome Priming on Experienced Self-Agency in the Netherlands and Japan
Authors: Aarts Henk , Oikawa Masanori , Oikawa Haruka
Published: October 2009

The experience of self-agency is a fundamental feature of human experience. Recent research has suggested that self-agency experiences are driven by an unconscious authorship ascription process that relies on an online match between accessible outcome representations and the production of the outcome. Extending this work, this study explores the role of culture in the manifestation of this unconscious authorship ascription process by testing whether subliminal priming of the outcome of an action prior to occurrence increased experiences of self-agency in Dutch and Japanese participants. Results show that outcome priming enhances the experience of self-agency independently of cultural background. However, Dutch participants experienced higher levels of self-agency than did Japanese participants, and this cultural effect was mediated by differences in beliefs of self-determination.These findings suggest that the experience of self-agency has a universal, nonconscious component that operates independently from a more cultural one, reflecting differences in conscious beliefs about the role of the self in choice and control.
Making Practice Public: Teacher Learning in the 21st Century
Authors: Lieberman Ann , Pointer Mace Desiree
Published: October 2009

We propose that the advent and ubiquity of new media tools and social networking resources provide a means for professional, networked learning to “scale up.” We preface our discussion with a review of research that has led us to argue for professional learning communities, document the policies and practices of professional development in high-achieving countries internationally that have transformed the way teachers learn, and discuss online social networking as it is being used for teacher learning. Our 10-year experience at the Carnegie Foundation for the Advancement of Teaching gave us an opportunity to learn to make multimedia representations of practice for use in both preservice and professional development. We believe that making practice public in this way can be transformative.
Beyond Knowledge: Exploring Why Some Teachers Are More Thoughtfully Adaptive Than Others
Authors: Fairbanks Colleen M. , Duffy Gerald G. , Faircloth Beverly S. , Ye He  , Levin Barbara , Rohr Jean , Stein Catherine
Published: October 2009

As teacher educators, we have observed that knowledge alone does not lead to the kinds of thoughtful teaching we strive for. Puzzled by differences in the teaching practices of teacher candidates having similar professional knowledge, we explore what might account for these differences. We address what is necessary, beyond traditional forms of professional knowledge, to support the development of thoughtful teachers who are responsive to students and situations. We provide four perspectives, each drawn from areas in which we conduct our research, and suggest a need to move beyond knowledge in teacher education. Our aim is to explore questions about preparing thoughtful teachers and to challenge others to do the same. We postulate that self-knowledge and a sense of agency with the intent of purposefully negotiating personal and professional contexts may be as important, if not more important, than the more traditional conceptions of professional knowledge.
Waltz and World History: The Paradox of Parsimony
Authors: Buzan Barry , Little Richard
Published: October 2009

This article provides a critique of Waltz’s work from the perspective of world history. It shows how Waltz’s commitment to a highly parsimonious theoretical approach paradoxically both sets up the possibility of his theory being universally applicable, and undermines its prospects as a viable approach to understanding world history. Using the key concepts from Waltz’s work — units, systems, structure, process — we show the detailed grounds on which his theory fails to apply to such large swathes of time and place, so that its claims to universality fall, even though it can usefully be applied to some times and places. We also show its shortcomings in relation to the essential historical task of periodization. We argue that international relations needs to engage more with world history, and that the task of doing so will fall to approaches other than Waltz’s.
Left Behind: Neorealism’s Truncated Contextual Materialism and Republicanism
Authors: Deudney Daniel
Published: October 2009

Anarchy and the balance of power are the two core ideas in Waltz’s neorealism, and he explicitly draws them from early modern political theory, particularly Hobbes and Rousseau. Unfortunately, Waltz leaves behind a key variable in these early modern state-of-nature arguments: violence interdependence — the capacity of actors to harm one another (independent of distribution of power). This difference between the extreme insecurity of the state of nature and the tractable insecurity of the state of war derives from different degrees of violence interdependence. The variable is implicit but powerful in Hobbes, and explicit in Rousseau’s analysis of topographic fragmentation as a foundation for the European state system. As the effects of the industrial revolution made themselves felt, many theorists (the global geopoliticans, Carr and many liberals) continued to employ the variable Waltz dropped, and they generally argued that Europe had shifted from a state-of-war to a state-of-nature anarchy, thus posing the choice of catastrophe or integration. Herz and Morgenthau continue this argument in the nuclear era, reaching very different conclusions than Waltz. Similarly, the balance of power was conceived by early modern republican theorists as the counter to hierarchy, and this was transposed to the ‘system level’ via the device of referring to Europe as a whole as a ‘republic’ that was in part ‘by nature’. Other important republican power restraints (notably division, mixture and union) were dropped by Waltz but are developed by liberal globalist security theory.
Human Interconnectedness
Authors: Linklater Andrew
Published: October 2009

Kenneth Waltz’s structural realism abstracts the international political domain from other spheres of social interaction to explain recurrent patterns of competition and conflict across the millennia. There are similarities between the structural realist ‘grand narrative’ and the process-sociological approach developed by Norbert Elias. But the latter supported ‘high-level synthesis’ in the social sciences in order to understand how relations between material, ideational and emotional forces have contributed to the growth of human interconnectedness. The analysis contended that one of the purposes of the social sciences is to increase knowledge of how humans can gain control of the processes that bind them together in global networks of interdependence. Elias was opposed to partisan inquiry such as Kant’s notion of a universal history with a cosmopolitan intent. But a shared emphasis on how humans have developed the capacity to cause distant harm reveals how future grand narratives can combine the analysis of the growth of interconnectedness with the ethical argument for greater transnational solidarity.
Beyond Waltz’s Nuclear World: More Trust May be Better
Authors: Wheeler Nicholas J.
Published: October 2009

In 1981 Kenneth Waltz published a controversial Adelphi Paper, ‘The Spread of Nuclear Weapons: More May Be Better’, in which he turned the conventional wisdom on its head by arguing that the spread of nuclear weapons would not be a terrifying prospect. This article rejects the proposition that fear of nuclear destruction can serve as a permanent basis of international order, and argues that securing order depends upon the building of trust between nuclear-armed and arming powers. A key contribution here has been the theory and practice of security communities, which opens up the promise of replacing nuclear threats by a new international politics in which force has been delegitimated as an instrument of state policy. This article discusses the potential for nuclear trust-building through the example of the security community that developed between Argentina and Brazil in the 1980s. Both countries had the potential to develop nuclear weapons by the end of the 1970s, and there were concerns that their rivalry might lead to a regional nuclear arms race. Having explored the factors that promoted trust between Buenos Aires and Brasilia, the article considers the lessons that can be learned for nuclear trust-building elsewhere.
The Use of Female Commercial Sex Workers’ Services by Latino Day Laborers
Authors: Galván Frank H. , Ortiz Daniel J. , Martinez Victor , Bing Eric G.
Published: October 2009

This article reports the characteristics of Latino day laborers who have sex with female commercial sex workers (CSWs). A sample of 450 day laborers in Los Angeles was used. Multivariate logistic regression was used to determine the association of independent variables with the likelihood of having sex with a CSW. Overall, 26% of the 450 day laborers reported having had sex with a CSW in the previous 12 months. A lower likelihood of having sex with a CSW was found for those with more than 6 years of education and for those who were married and living with their spouses. A higher likelihood of having sex with a CSW was found for those who met the criteria for harmful drinking or drug dependence. Commercial sex work has been associated with sexually transmitted infections and other problems among clients of CSWs and warrants further attention by providers working with day laborers.
Safety Evaluation of a Peptide Product Derived From Sardine Protein Hydrolysates (Valtyron)
Authors: Osajima Katsuhiro , Ninomiya Toshio , Harwood Melody , Danielewska-Nikiel Barbara
Published: October 2009

The peptide product, Valtyron, is obtained via enzymatic hydrolysis of sardine muscle. Although the safety and efficacy of the sardine peptide product have been evaluated in human studies, sardine peptides have not been identified as the subject of toxicological testing. In this study, the sardine peptide product did not exhibit any mutagenic activity in Salmonella typhimurium or Escherichia coli WP2 uvrA. Likewise, the sardine peptide product was not associated with clastogenic properties in mouse bone marrow cells in a micronucleus assay. An oral rat LD50 value of greater than 10 000 mg per kilogram of body weight was determined for peptide α-1000, and in rats administered peptide α-1000 by gavage at levels up to 5000 mg per kilogram of body weight per day for 28 days, no compound-related differences were observed in standard toxicological parameters. The results of these studies support the safety of the sardine peptide product for use in food for human consumption as a dietary source of peptides available from sardines.
Primary DNA Damage Assessed With the Comet Assay and Comparison to the Absorbed Dose of Diagnostic X-rays in Children
Authors: Milković Đurđica , Garaj-Vrhovac Vera , Ranogajec-Komor Mária , Miljanić Saveta , Gajski Goran , Knežević Željka , Beck Natko
Published: October 2009

The aim of this work is to assess DNA damage in peripheral blood lymphocytes of children prior to and following airway X-ray examinations of the chest using the alkaline comet assay and to compare data with the measured absorbed dose. Twenty children with pulmonary diseases, between the ages of 5 and 14 years, are assessed. Absorbed dose measurements are conducted for posterior–anterior projection on the forehead, thyroid gland, gonads, chest, and back. Doses are measured using thermoluminescent and radiophotoluminescent dosimetry systems. Differences between tail lengths, tail intensity, and tail moments as well as for the long-tailed nuclei before and after exposures are statistically significant and are dependent on the individual. The results demonstrate the usefulness of the comet assay as a measure of X-ray damage to lymphocytes in a clinical setting. Doses measured with both dosimeters show satisfactory agreement (0.01 mSv) and are suitable for dosimetric measurements in X-ray diagnostics.
Acute Microinstillation Inhalation Exposure to Sarin Induces Changes in Respiratory Dynamics and Functions in Guinea Pigs
Authors: Conti Michele L. , Che Magnus M. , Boylan Megan , Sciuto Alfred M. , Gordon Richard K. , Nambiar Madhusoodana P.
Published: October 2009

This study investigates the toxic effects of sarin on respiratory dynamics following microinstillation inhalation exposure in guinea pigs. Animals are exposed to sarin for 4 minutes, and respiratory functions are monitored at 4 hours and 24 hours by whole-body barometric plethysmography. Data show significant changes in respiratory dynamics and function following sarin exposure. An increase in respiratory frequency is observed at 4 hours post exposure compared with saline controls. Tidal volume and minute volume are also increased in sarin-exposed animals 4 hours after exposure. Peak inspiratory flow increases, whereas peak expiratory flow increases at 4 hours and is erratic following sarin exposure. Animals exposed to sarin show a significant decrease in expiratory time and inspiratory time. End-inspiratory pause is unchanged whereas end-expiratory pause is slightly decreased 24 hours after sarin exposure. These results indicate that inhalation exposure to sarin alters respiratory dynamics and function at 4 hours, with return to normal levels at 24 hours post exposure.
Drug—Botanical Interactions: A Review of the Laboratory, Animal, and Human Data for 8 Common Botanicals
Authors: Shord Stacy S. , Shah Kanan , Lukose Alvina
Published: October 2009

Many Americans use complementary and alternative medicine (CAM) to prevent or alleviate common illnesses, and these medicines are commonly used by individuals with cancer.These medicines or botanicals share the same metabolic and transport proteins, including cytochrome P450 enzymes (CYP), glucuronosyltransferases (UGTs), and P-glycoprotein (Pgp), with over-the-counter and prescription medicines increasing the likelihood of drug—botanical interactions.This review provides a brief description of the different proteins, such as CYPs, UGTs, and Pgp.The potential effects of drug—botanical interactions on the pharmacokinetics and pharmacodynamics of the drug or botanical and a summary of the more common models used to study drug metabolism are described.The remaining portion of this review summarizes the data extracted from several laboratory, animal, and clinical studies that describe the metabolism, transport, and potential interactions of 8 selected botanicals. The 8 botanicals include black cohosh, Echinacea, garlic, Gingko biloba, green tea, kava, milk thistle, and St John’s wort; these botanicals are among some of the more common botanicals taken by individuals with cancer.These examples are included to demonstrate how to interpret the different studies and how to use these data to predict the likelihood of a clinically significant drug—botanical interaction.
Integrative Tumor Board: A Case Report and Discussion From Dana-Farber Cancer Institute
Authors: Lu Weidong , Ott Mary Jane , Kennedy Stacy , Mathay Maria B. , Doherty-Gilman Anne M. , Dean-Clower Elizabeth , Hayes Carolyn M. , Rosenthal David S.
Published: October 2009

A 34-year-old woman carrying a BRCA1 gene and a significant family history was diagnosed with T1c, N1 breast cancer. The tumor was estrogen receptor, progesterone receptor, and HER-2/Neu negative.The patient received dose-dense chemotherapy with Adriamycin and Cytoxan followed by Taxol, and left breast irradiation. Later, a bilateral S-GAP flap reconstruction with right prophylactic mastectomy and left mastectomy were performed. During her treatment, the patient had an integrative medicine consultation and was seen by a team of health care providers specializing in integrative therapies, including integrative nutrition, therapeutic massage, acupuncture, and yoga. Each modality contributed unique benefit in her care that led to a satisfactory outcome for the patient.A detailed discussion regarding her care from each modality is presented.The case elucidates the need for integrative approaches for cancer patients in a conventional medical setting.
Organizational Collaboration to Promote College Access: A P-20 Framework
Authors: Núñez Anne-Marie , Oliva Maricela
Published: October 2009

P-20 collaboration between the P-12 and higher education sectors has been increasing in recent years as a strategy to promote college access, particularly among underrepresented students.This article provides an overview of the current state of P-20 scholarship and practice in the field, offers an approach to conceptualizing the study and practice of P-20 collaboration, suggests strategies for refining research and practice in the field, and offers directions for future inquiry.
Parent Involvement in the College Planning Process: A Case Study of P-20 Collaboration
Authors: Fann Amy , McClafferty Jarsky Karen , McDonough Patricia M.
Published: October 2009

Parents who have not had opportunities to attend college themselves have neither experience with the process of college preparation and college going nor sufficient access to needed information.This article describes a collaborative venture between a university department of education and a cluster of local schools designed to help parents of first-generation students become active participants in their children’s college preparation and planning, shedding light on the importance of parental involvement in the college-going process.
The Short and Happy Life of Interdisciplinarity in Game Studies
Authors: Malaby Thomas M. , Burke Timothy
Published: October 2009

The rise of virtual worlds and their demonstrated potential to generate new economies, forms of belonging, and learning—all within spaces that are deeply game-like—makes new demands of our thinking about games and society. A number of scholars have recently begun to forge an approach distinct from past efforts, shifting their attention toward broader, contextual understandings of games, communities, and play. Seeking to treat such spaces neither as wholly determined by outside factors nor as utterly sui generis, they aim to account for the contingent and emergent relationship that these spaces have with other domains of human experience.
A Case of Mistaken Identity: Complete Androgen Insensitivity Syndrome
Authors: Moores Penelope , Rashid Mumtaz
Published: October 2009

Complete androgen insensitivity syndrome (CAIS) is a rare and complicated endocrine condition in which individuals inherit a female phenotype but a male karotype of 46XY. It occurs as a result of a defect on the X chromosome inhibiting the effect of androgens during embryological development. Although magnetic resonance imaging is considered the gold standard imaging technique in cases of CAIS, these patients will often present in the ultrasound department with primary amenorrhoea. This case highlights both the value and limitations of ultrasound in such circumstances. Also considered are the many complex and sensitive issues involved, and the multi-disciplinary approach required, in the treatment of individuals diagnosed with CAIS.
The Effect of Cuff Occlusion Protocols on Radial Strain and Arterial Haemodynamics
Authors: Rafati Mehravar , Mokhtari-Dizaji Manijhe , Saberi Hajir
Published: October 2009

The purpose of this study is to compare arterial vasodilation in response to two occlusive cuff positions and various protocols under reactive hyperaemic stimulus. For determining the optimal reactive hyperaemia protocol we studied 10 healthy young adults and calculated the relative strain and haemodynamic changes of the left brachial artery with motion estimation from sequential ultrasonic images and Doppler sonograms. The results from two occlusion cuff positions (left proximal upper arm and distal forearm) showed that brachial artery vasodilation was significantly greater under upper arm occlusion than under forearm occlusion. Results from optimizing reactive hyperaemia protocols showed that the optimum occlusion pressure was 150 mmHg, with an occlusion time of 5 min. The optimum time interval for recording ultrasonic images and estimating relative strain after releasing the cuff was 45-60 s. Use of these conditions resulted in higher vasodilation and larger blood flow changes. We conclude that the magnitudes of relative strain and blood velocity are related not only to the choice of the location of cuff inflation and the magnitude of occlusion pressure and time, but also to the time interval after the release of the occlusive cuff.
Prenatal Screening for Down Syndrome in Australia
Authors: Nisbet Debbie L , McLennan Andrew
Published: October 2009

Prenatal screening for Down syndrome should be offered to all pregnant women. The screening option chosen will be influenced by maternal preference, local availability of tests, and the gestation at which the pregnant woman presents. Screening tests take into account the effect of maternal age on Down syndrome risk. The combined first trimester screen using nuchal translucency and first trimester maternal serum screening can achieve a detection rate for Down syndrome of 90% with a 5% false positive rate, when performed by appropriately trained individuals. Midtrimester maternal serum screening is a good screening option for women unable to undergo the combined first trimester screen.
Oxidative modification of von Willebrand factor by neutrophil oxidants inhibits its cleavage by ADAMTS13
Authors: Chen Junmei , Fu Xiaoyun , Wang Yi , Ling Minhua , McMullen Brad , Kulman John , Chung Dominic W. , López José A.
Published: October 2009

Elevated plasma von Willebrand factor (VWF) and low ADAMTS13 activity have been reported in several inflammatory states, including sepsis and acute respiratory distress syndrome. One hallmark of inflammation is neutrophil activation and production of reactive oxygen species, including superoxide radical, hydrogen peroxide, and hypochlorous acid (HOCl). HOCl is produced from hydrogen peroxide and chloride ions through the action of myeloperoxidase. HOCl can oxidize methionine to methionine sulfoxide and tyrosine to chlorotyrosine. This is of interest because the ADAMTS13 cleavage site in VWF, the Tyr1605-Met1606 peptide bond, contains both oxidation-prone residues. We hypothesized that HOCl would oxidize either or both of these residues and possibly inhibit ADAMTS13-mediated cleavage. We therefore treated ADAMTS13 substrates with HOCl and examined their oxidative modification by mass spectrometry. Met1606 was oxidized to the sulfoxide in a concentration-dependent manner, with complete oxidation at 75μM HOCl, whereas only a miniscule percentage of Tyr1605 was converted to chlorotyrosine. The oxidized substrates were cleaved much more slowly by ADAMTS13 than the nonoxidized substrates. A similar result was obtained with multimeric VWF. Taken together, these findings indicate that reactive oxygen species released by activated neutrophils have a prothrombotic effect, mediated in part by inhibition of VWF cleavage by ADAMTS13.
Induction of B-cell development in adult mice reveals the ability of bone marrow to produce B-1a cells
Authors: Düber Sandra , Hafner Martin , Krey Martina , Lienenklaus Stefan , Roy Bishnudeo , Hobeika Elias , Reth Michael , Buch Thorsten , Waisman Ari , Kretschmer Karsten , Weiss Siegfried
Published: October 2009

To study B-cell development from bone marrow (BM), we generated recombination-activating gene 1 (Rag1)–targeted mice lacking mature lymphocytes. B-cell development can be induced in such mice by B cell–specific restoration of a functional Rag1 transcription unit. Follicular and marginal zone B cells populated the spleen when Rag1 expression was permitted. Notably, the peritoneal cavity was dominated by bona fide B-1a cells, as judged by surface markers and functional properties. These BM-derived B-1a cells exhibited a polyclonal VDJ repertoire with substantial N nucleotide insertions. Nevertheless, physiologic frequencies of phosphatidylcholine-specific B cells were detected. Importantly, the BM of young and 5-month-old mice was indistinguishable with regard to the potential to generate B-1a cells.
Primary radiotherapy showed favorable outcome in treating extranodal nasal-type NK/T-cell lymphoma in children and adolescents
Authors: Wang Zhao-Yang , Li Ye-Xiong , Wang Wei-Hu , Jin Jing , Wang Hua , Song Yong-Wen , Liu Qing-Feng , Wang Shu-Lian , Liu Yue-Ping , Qi Shu-Nan , Fang Hui , Liu Xin-Fan , Yu Zi-Hao
Published: October 2009

Extranodal nasal-type natural killer (NK)/T-cell lymphoma is rarely observed in children and adolescents. We aim to investigate the clinical features, prognosis, and treatment outcomes in these patients. Thirty-seven patients were reviewed. There were 19, 14, 2, and 2 patients with stage I, stage II, stage III, and stage IV diseases, respectively. Among the patients with stage I and II disease, 19 patients received initial radiotherapy with or without chemotherapy, and 14 patients received chemotherapy followed by radiotherapy. The 4 patients with stage III and IV disease received primary chemotherapy and radiation of the primary tumor. Children and adolescents with extranodal nasal-type NK/T-cell lymphoma usually presented with early-stage disease, high frequency of B symptoms, good performance, low-risk age-adjusted international prognostic index, and chemoresistance. The complete response rate after initial radiotherapy was 73.7%, which was significantly higher than the response rate after initial chemotherapy (16.7%; P = .002). The 5-year overall survival (OS) and progression-free survival (PFS) rates for all the patients were 77.0% and 68.5%, respectively. The corresponding OS and PFS rates for patients with stage I and II disease were 77.6% and 72.3%, respectively. Children and adolescents with early-stage extranodal nasal-type NK/T-cell lymphoma treated with primary radiotherapy had a favorable prognosis.
Riboswitch Detection Using Profile Hidden Markov Models
Authors: Singh Payal , Bandyopadhyay Pradipta , Bhattacharya Sudha , Krishnamachari A , Sengupta Supratim
Published: October 2009

Background

Riboswitches are a type of noncoding RNA that regulate gene expression by switching from one structural conformation to another on ligand binding. The various classes of riboswitches discovered so far are differentiated by the ligand, which on binding induces a conformational switch. Every class of riboswitch is characterized by an aptamer domain, which provides the site for ligand binding, and an expression platform that undergoes conformational change on ligand binding. The sequence and structure of the aptamer domain is highly conserved in riboswitches belonging to the same class. We propose a method for fast and accurate identification of riboswitches using profile Hidden Markov Models (pHMM). Our method exploits the high degree of sequence conservation that characterizes the aptamer domain.

Results

Our method can detect riboswitches in genomic databases rapidly and accurately. Its sensitivity is comparable to the method based on the Covariance Model (CM). For six out of ten riboswitch classes, our method detects more than 99.5% of the candidates identified by the much slower CM method while being several hundred times faster. For three riboswitch classes, our method detects 97-99% of the candidates relative to the CM method. Our method works very well for those classes of riboswitches that are characterized by distinct and conserved sequence motifs.

Conclusion

Riboswitches play a crucial role in controlling the expression of several prokaryotic genes involved in metabolism and transport processes. As more and more new classes of riboswitches are being discovered, it is important to understand the patterns of their intra and inter genomic distribution. Understanding such patterns will enable us to better understand the evolutionary history of these genetic regulatory elements. However, a complete picture of the distribution pattern of riboswitches will emerge only after accurate identification of riboswitches across genomes. We believe that the riboswitch detection method developed in this paper will aid in that process. The significant advantage in terms of speed, of our pHMM-based approach over the method based on CM allows us to scan entire databases (rather than 5'UTRs only) in a relatively short period of time in order to accurately identify riboswitch candidates.
Microarray platform consistency is revealed by biologically functional analysis of gene expression profiles
Authors: Li Zhiguang , Su Zhenqiang , Wen Zhining , Shi Leming , Chen Tao
Published: October 2009

Background

Several different microarray platforms are available for measuring gene expression. There are disagreements within the microarray scientific community for intra- and inter-platform consistency of these platforms. Both high and low consistencies were demonstrated across different platforms in terms of genes with significantly differential expression. Array studies for gene expression are used to explore biological causes and effects. Therefore, consistency should eventually be evaluated in a biological setting to reveal the functional differences between the examined samples, not just a list of differentially expressed genes (DEG). In this study, we investigated whether different platforms had a high consistency from the biologically functional perspective.

Results

DEG data without filtering the different probes in microarrays from different platforms generated from kidney samples of rats treated with the kidney carcinogen, aristolochic acid, in five test sites using microarrays from Affymetrix, Applied Biosystems, Agilent, and GE health platforms (two sites using Affymetrix for intra-platform comparison) were input into the Ingenuity Pathway Analysis (IPA) system for functional analysis. The functions of the DEG lists determined by IPA were compared across the four different platforms and two test sites for Affymetrix platform. Analysis results showed that there is a very high level of consistency between the two test sites using the same platform or among different platforms. The top functions determined by the different platforms were very similar and reflected carcinogenicity and toxicity of aristolochic acid in the rat kidney.

Conclusion

Our results demonstrate that highly consistent biological information can be generated from different microarray platforms.
Conformational changes and loose packing promote E. coli Tryptophanase cold lability
Authors: Kogan Anna , Gdalevsky Garik Y , Cohen-Luria Rivka , Goldgur Yehuda , Phillips Robert S , Parola Abraham H , Almog Orna
Published: October 2009

Background

Oligomeric enzymes can undergo a reversible loss of activity at low temperatures. One such enzyme is tryptophanase (Trpase) from Escherichia coli. Trpase is a pyridoxal phosphate (PLP)-dependent tetrameric enzyme with a Mw of 210 kD. PLP is covalently bound through an enamine bond to Lys270 at the active site. The incubation of holo E. coli Trpases at 2°C for 20 h results in breaking this enamine bond and PLP release, as well as a reversible loss of activity and dissociation into dimers. This sequence of events is termed cold lability and its understanding bears relevance to protein stability and shelf life.

Results

We studied the reversible cold lability of E. coli Trpase and its Y74F, C298S and W330F mutants. In contrast to the holo E. coli Trpase all apo forms of Trpase dissociated into dimers already at 25°C and even further upon cooling to 2°C. The crystal structures of the two mutants, Y74F and C298S in their apo form were determined at 1.9Å resolution. These apo mutants were found in an open conformation compared to the closed conformation found for P. vulgaris in its holo form. This conformational change is further supported by a high pressure study.

Conclusion

We suggest that cold lability of E. coli Trpases is primarily affected by PLP release. The enhanced loss of activity of the three mutants is presumably due to the reduced size of the side chain of the amino acids. This prevents the tight assembly of the active tetramer, making it more susceptible to the cold driven changes in hydrophobic interactions which facilitate PLP release. The hydrophobic interactions along the non catalytic interface overshadow the effect of point mutations and may account for the differences in the dissociation of E. coli Trpase to dimers and P. vulgaris Trpase to monomers.
Evaluating geographic imputation approaches for zip code level data: an application to a study of pediatric diabetes
Authors: Hibbert James D , Liese Angela D , Lawson Andrew , Porter Dwayne E , Puett Robin C , Standiford Debra , Liu Lenna , Dabelea Dana
Published: October 2009

Background

There is increasing interest in the study of place effects on health, facilitated in part by geographic information systems. Incomplete or missing address information reduces geocoding success. Several geographic imputation methods have been suggested to overcome this limitation. Accuracy evaluation of these methods can be focused at the level of individuals and at higher group-levels (e.g., spatial distribution).

Methods

We evaluated the accuracy of eight geo-imputation methods for address allocation from ZIP codes to census tracts at the individual and group level. The spatial apportioning approaches underlying the imputation methods included four fixed (deterministic) and four random (stochastic) allocation methods using land area, total population, population under age 20, and race/ethnicity as weighting factors. Data included more than 2,000 geocoded cases of diabetes mellitus among youth aged 0-19 in four U.S. regions. The imputed distribution of cases across tracts was compared to the true distribution using a chi-squared statistic.

Results

At the individual level, population-weighted (total or under age 20) fixed allocation showed the greatest level of accuracy, with correct census tract assignments averaging 30.01% across all regions, followed by the race/ethnicity-weighted random method (23.83%). The true distribution of cases across census tracts was that 58.2% of tracts exhibited no cases, 26.2% had one case, 9.5% had two cases, and less than 3% had three or more. This distribution was best captured by random allocation methods, with no significant differences (p-value > 0.90). However, significant differences in distributions based on fixed allocation methods were found (p-value < 0.0003).

Conclusion

Fixed imputation methods seemed to yield greatest accuracy at the individual level, suggesting use for studies on area-level environmental exposures. Fixed methods result in artificial clusters in single census tracts. For studies focusing on spatial distribution of disease, random methods seemed superior, as they most closely replicated the true spatial distribution. When selecting an imputation approach, researchers should consider carefully the study aims.