bluuebunny/crossref_metadata_2025 huggingface dataset:
Increased hospitalizations and death in patients with ESRD secondary to lupus
Authors: Sule S , Fivush B , Neu A , Furth S
Published: June 2012

Background: Systemic lupus erythematosus (SLE) is an autoimmune disease that can affect almost any organ system, including the kidneys. Using a large national dataset, our goal was to compare the morbidity as measured by hospitalization and mortality rates between hemodialysis patients with end-stage renal disease (ESRD) secondary to SLE to those with ESRD due to other causes. Methods: The risk of hospitalization was calculated by Poisson regression with clustering for repeated measures using the United States Renal Data System (USRDS) Hospitalization Analytic File in strata of pediatric and adult patients. Cox proportional hazard ratio was used to assess the mortality risk in hospitalized patients. Subjects were censored at transplantation or end of follow-up. Results: Adult patients with ESRD secondary to SLE were hospitalized more frequently than other adults (incidence rate ratio (IRR): 1.43, 95% confidence interval (CI): 1.15–1.77) and had a higher risk of death (hazard ratio (HR): 1.89, 95% CI: 1.66–2.5). Mortality was higher in hospitalized pediatric patients with SLE compared to pediatric patients with other causes of ESRD (HR: 2.01, 95% CI: 1.75–2.31) and adults with SLE (HR: 2.05, 95% CI: 1.79–2.34). Conclusion: Our study demonstrates that there is a trend toward increased hospitalization rates in pediatric and adult patients with SLE. Among these hospitalized patients with SLE, there is an increased risk of death due to cardiovascular disease.
Influencers of ethical beliefs and the impact on moral distress and conscientious objection
Authors: Davis Shoni , Schrader Vivian , Belcheir Marcia J
Published: June 2012

Considering a growing nurse shortage and the need for qualified nurses to handle increasingly complex patient care situations, how ethical beliefs are influenced and the consequences that can occur when moral conflicts of right and wrong arise need to be explored. The aim of this study was to explore influencers identified by nurses as having the most impact on the development of their ethical beliefs and whether these influencers might impact levels of moral distress and the potential for conscientious objection. Nurses whose ethical beliefs were most influenced by their religious beliefs scored higher in levels of moral distress and demonstrated greater differences in areas of conscientious objection than did nurses who developed their ethical beliefs from influencers such as family values, life and work experience, political views or the professional code of ethics.
Rewards for pairs of Q-learning agents conducive to turn-taking in medium-access games
Authors: Raffensperger Peter A , Bones Philip J , McInnes Allan I , Webb Russell Y
Published: June 2012

We describe a class of stateful games, which we call ‘medium-access games’, as a model for human and machine communication and demonstrate how to use the Nash equilibria of those games as played by pairs of agents with stationary policies to predict turn-taking behaviour in Q-learning agents based on the agents’ reward function. We identify which fixed policies exhibit turn-taking behaviour in medium-access games and show how to compute the Nash equilibria of such games by using Markov chain methods to calculate the agents’ expected rewards for different stationary policies. We present simulation results for an extensive range of reward functions for pairs of Q-learners playing medium-access games and we use our analysis for stationary agents to develop predictors for the emergence of turn-taking. We explain how to use our predictors to design reward functions for pairs of Q-learning agents that are conducive (or prohibitive) to the emergence of turn-taking in medium-access games. We focus on designing multi-agent reinforcement learning systems that deliberately produce coordinated turn-taking but we also intend our results to be useful for analysing emergent turn-taking behaviour. Based on our turn-taking related results, we suggest ways to use our methodology to designs rewards for quantifiable behaviours besides turn-taking.
Lymph Node Ratio
Authors: Yang Cuicui , Liu Fangfang , Li Shuai , Li Weidong , Zhai Lili , Ren Meijing , Li Yaqing , Lang Ronggang , Fan Yu , Zhang Xinmin , Fu Li
Published: June 2012

St. Gallen 2005 expert consensus guideline modified its criteria for the risk category of breast cancer (BC) patients by integrating a combination of lymph nodes with metastasis (positive lymph nodes [PLNs]) and HER-2/neu status of tumor. Recently, some studies have shown that lymph node ratio (LNR), defined as the ratio of axillary lymph nodes with tumor metastasis to the total lymph nodes dissected, was a better independent prognostic indicator than PLN and should be considered as an alternative to the status of regional lymph nodes in the staging of breast cancer (pN). In the current study, the authors retrospectively reviewed 1095 primary BC patients with PLN and assessed the prognostic effect of LNR measured by relapse-free survival and overall survival to explore the feasibility of LNR and HER-2/neu status in stratifying the risk category of BC. Our results indicate that although by univariate analysis and when assessed as single covariate in multivariate analysis, both PLN and LNR were independent prognostic factors, PLN lost its significance when combined with LNR as covariates. A cutoff value of LNR = 0.30 was identified to show high accuracy in separating patients based on their survivals. The risk categories defined by LNR combined with HER-2/neu status were compatible to those defined by the PLN in combination with HER-2/neu status. LNR was a strong prognostic predictor of node-positive BC patients, superior to PLN. It should be considered as a new factor to couple with HER-2/neu status in defining risk category of BC patients.
Natural, innate improvements in multiple sclerosis disability
Authors: Tremlett Helen , Zhu Feng , Petkau John , Oger Joel , Zhao Yinshan ,   and the BC MS Clinic Neurologists
Published: June 2012

Background:

Improvements in multiple sclerosis (MS) disability have recently been reported in immunomodulatory drug (IMD) clinical trials and observational studies. However, improvements have rarely been examined in natural history or IMD naive patients. We investigated annual and biennial improvements in Expanded Disability Status Scale (EDSS) scores in British Columbia, Canada.

Methods:

The British Columbian MS database was accessed for definite MS patients (1980–2009). Consecutive IMD-free EDSS scores one and two years apart (± 3 months) were examined; improvements (≥0.5,≥1,≥2 EDSS points) and sustained improvements (confirmed at one year) were described. The influence of patient characteristics on improvements was examined using logistic regression.

Results:

From 16,132 EDSS scores, 7653 yearly and 5845 biennial EDSS intervals were available for 2961 and 2382 patients respectively. Of the yearly intervals, 14.9% showed an improvement (≥0.5 points), 8.3% ≥1 point and 2.2% ≥2 point improvement, with nearly half being sustained. Corresponding worsenings were observed in 32.9%, 20.5% and 7.9% respectively, with stability in just over half (53%). Biennial findings were similar. Characteristics generally associated with improvements included: female sex, younger age, shorter disease duration, relapsing-onset and presence of moderate disability (compared with mild or advanced) and a previous episode of worsening (disassociated from a relapse). However, improvements were also observed after periods of stability and in primary-progressive MS.

Conclusion:

Improvements in MS disability over one or two years are not unusual. We suggest the term ‘innate improvements’. Our findings have implication for the design of clinical trials and observational studies in MS targeting improvements on the EDSS.
‘Citizens of fate’: Blood, disease and the question of mortality in Sadness by William Yang
Authors: Hamilton Margaret
Published: June 2012

William Yang’s performance Sadness challenges essentialised categories of identification by juxtaposing tales of his Chinese-Australian family with the journey of friends from his community dying of AIDS-related complications and infection. In doing so, Yang foregrounds the threat of mortality that attempts to stabilise identity politics for the ‘nation’. In the age of global media Yang resists multi-modal approaches to his medium to reclaim the theatrical space of narration. As a consequence, Yang’s Sadness affords an opportunity to rethink the imperatives intrinsic to the classification of social subjects in terms of racial, sexual and reproductive practices, and the relationship of the citizen-body to modes of cultural representation.
Global female masculinities
Authors: Halberstam Judith
Published: June 2012

In this essay, I discuss the subtle discursive shifts which have made transgenderism in the USA and Europe into simultaneously a mark of the historically specific definitional cleaving of homosexuality from gender variance, a trendy and stylistic shift from gender androgyny within lesbian communities to gender variance within gender-queer communities, a sign of an internal split within feminism between the stabilization of the category of woman and the undermining of the coherence of the category within queer theory. At the same time, I show how transgenderism has been installed within a “global gay” system as part of the hegemony of US taxonomies – the addition of “T” to the acronym “LGBT” allows for the neat division and explanation of a very wide range of translocal phenomena in terms of the US model. So, how are we to understand and explain the impact of transgenderism upon not only traditional gendering but also upon queer communities and even on the ebb and flow of sexual and gender definition globally?
‘Treating it as a normal business’: Researching the pornography industry
Authors: Voss Georgina
Published: June 2012

This article examines the lack of research on the pornography industry and the means of addressing this situation. Much contemporary pornography research invokes the apparent economic prowess of the pornography industry as justification for its work, yet focuses on the product and its reception rather than on the industry that produces it. In this article I identify and discuss the specific institutional challenges around studying pornography within business studies, and also the opportunities that arose through this work. The research methods used in this study of the North American pornography industry are presented and discussed, together with considerations around access, authentication, and stigma. I challenge the dependence by current scholars on secondary data about the industry by offering theoretical frameworks and methodological approaches with which to gather rich empirical material, thus furthering the wider field of pornography research.
The ‘real core’: The taste of Taiwanese men for Japanese adult videos
Authors: Wong Heung-wah , Yau Hoi-yan
Published: June 2012

Inspired by Simon Hardy who sees ‘pornographic realism’ as the defining characteristic of pornography, this article argues that Taiwanese men identify more with Japanese adult videos (AVs) especially bishōjo (beautiful young woman) AVs, the prototypical genre in Japanese AV industry, than other varieties, because they appear to these men as more ‘real’. However, this article goes further to move beyond the reality–representation divide by arguing that the so-called ‘reality’ is also discursively constituted. We first demonstrate how the ‘proper’ sex act of men in Taiwan is discursively constituted through Simon and Gagnon’s notion of ‘sexual script’. We then show how this discursively mediated male sex in Taiwan parallels neatly with the structure of the narrative of nine Japanese bishōjo AVs featuring Yuki Maiko, a prominent Japanese AV actress. We conclude that Japanese AVs in general and bishōjo AVs in particular will garner huge popularity among Taiwanese men because they appear to these men very ‘real’. That is to say, the distinction between pornographic representations of sex and the ‘real’ sex vanishes not because pornographic representations are getting more ‘real’ as Hardy has argued, but because the so-called ‘real’ sex is also culturally constituted.
Comfort for the people and liberation for the housewife: Gender, consumption and refrigerators in Argentina (1930–60)
Authors: Pérez Inés
Published: June 2012

The mass consumption of electric refrigerators in Argentina has been linked to several representations. On the one hand, it has occupied a central place in the rhetoric of ‘welfare democratization’ used by the Peronist government to present a ‘new Argentina.’ On the other hand, it took on a prominent role in the search for distinction by and within the growing middle class, and in the creation of social distance within the middle class. In both cases, the image of the housewife’s ‘liberation’ from daily chores because of new appliances condensed the ‘popularization of comfort’, the success of the social model that fostered it and success of head of the household who could provide a better life for his family. The increase in refrigerator consumption changed the visibility of domestic work in a paradoxical way: as it became a frequent topic in several discursive spaces, it suggested that the housewife’s work had been (or would be) replaced by new appliances. In this article, I examine the meanings ascribed to this appliance through its representation in 45 life narratives and the narratives' intertextual relationships with texts from the period. This analysis focuses on the ways in which the refrigerator became intertwined with the strategies of distinction used by those who could afford such a product. I also analyse the conditions that allowed the ‘popularization’ of refrigerators, as well as the discourses that made the product a ‘must-have’.
The Roles of District and National Opinion in 2010 Congressional Campaign Agendas
Authors: Pietryka Matthew T.
Published: June 2012

A primary goal of congressional elections is to create a link between constituent opinion and representative behavior. Explanations of congressional campaign agendas, however, have focused on national measures of issue salience and ownership, ignoring opinion within districts. Moreover, no study has systematically assessed the relative influence of issue salience and ownership. This article seeks to address these gaps using several public opinion surveys and a content analysis of 2010 House campaign websites. The analysis demonstrates significant across-district variation in citizens’ priorities and preferences, yet finds no discernible relationship between district opinion and campaign issue agendas. In contrast, the analysis suggests that campaign issue emphasis is positively associated with the issue’s national salience and party ownership, but salience appears to be the stronger predictor. Together, the results suggest that the 2010 candidates used their campaign issue agendas to forge a national strategy, rather than emphasize identification with their constituents.
Assessing the Stability of Psychological and Political Survey Measures
Authors: Gerber Alan S. , Huber Gregory A. , Doherty David , Dowling Conor M.
Published: June 2012

Recent research demonstrates growing scholarly interest in the relationship between personality characteristics and political attitudes and behaviors. In this article we present analysis using data from a national panel survey conducted in two waves—the first prior to the 2010 U.S. midterm election, the second after it. We assess the stability of a variety of personality measures and find high correlations between the pre- and postelection measures. We also leverage the fact that Republicans made substantial gains in Congress in the 2010 election to determine whether various personality measures are affected by the intersection of partisan attachments and political events and find little evidence that they are. The findings provide encouraging evidence for those interested in examining the relationship between personality and political attitudes using survey data.
Deciding When to Put Grandma in the Nursing Home
Authors: Klug Marilyn G. , Volkov Boris , Muus Kyle , Halaas Gwen Wagstrom
Published: June 2012

For caregivers of persons with dementia, estimating when that person should be placed in long-term care is difficult. Health care providers also find it hard to give an exact time as to when the person should be placed. Using data from 197 caregivers working with the Dementia Care Services Project in North Dakota, we show that asking the caregiver about their inclination to place can be equated to asking them for a specific time to place (κ = .616). Using the probability density function of time to place we were able to translate it into inclination. This inclination is easier information for the caregiver to provide and places fewer burdens on the caregiver and patient. It also provides the health care provider with a measure of time to help advise caregivers and recommend interventions and provide service organizations with measures of cost savings to support the impact of outreach and intervention.
Vascular Risk Factors and Cardiovascular Outcomes in the Alzheimer’s Disease Neuroimaging Initiative
Authors: Epstein Noam U. , Xie Hui , Ruland Sean D. , Pandey Dilip K.
Published: June 2012

Background: Vascular disease and medical factors are associated with cognitive decline and cardiovascular events. We examined the association between vascular risk factors and events in the Alzheimer’s Disease Neuroimaging Initiative cohort. Methods: The association between vascular risk factors and cardiovascular events in a cohort of 810 participants, including 400 with mild cognitive impairment, 184 with Alzheimer’s, and 226 controls was investigated using a longitudinal hazard model. Results: There were 31 events including 11 strokes, 7 myocardial infarctions, 5 revascularizations, and 8 deaths during an average follow-up of 31 months. Longitudinal cardiovascular event rates were low and similar between diagnostic groups. Conclusions: All baseline vascular risk factors that were expected to be associated with longitudinal cardiovascular events were, or were trending toward, associating with cardiovascular events except atrial fibrillation, depression, and apolipoprotein E genotype. Despite differences in baseline vascular risk factors, longitudinal cardiovascular event rates were similar between diagnostic groups.
Macrodactyly — options and outcomes
Authors: Hardwicke J. , Khan M. A. A. , Richards H. , Warner R. M. , Lester R.
Published: June 2012

We report the outcomes of 32 patients diagnosed with macrodactyly. The average age at presentation was 46 months and there was an equal distribution across the sexes, although there was a male predominance in the upper limb and female predominance in the lower limb. There were 20 cases of upper limb macrodactyly and 13 cases affecting the lower limb. Multiple digits were more commonly affected than isolated digits, with an average of 2.5 digits affected. Static disease required significantly fewer operations than progressive disease. The need for repeated procedures must be highlighted in cases of progressive macrodactyly. In the vast majority of cases the functional and cosmetic outcome is good, with good patient acceptance.
Tendon transfer for treatment of internal rotation contracture of the shoulder in brachial plexus birth palsy
Authors: Abdel-Ghani H. , Hamdy K. A. , Basha N. , Tarraf Y. N.
Published: June 2012

We retrospectively analyzed 63 patients with internal rotation contracture of the shoulder secondary to brachial plexus birth palsy treated with subscapularis sliding combined with either latissimus dorsi transfer (group A: n = 18) or latissimus dorsi and teres major transfer (group B: n = 45) to the rotator cuff. The mean age at time of surgery was 43 months (SD 21 months; range 8 months to 9 years). We used a modification of the Gilbert shoulder grading system for assessment. All patients showed statistically significant improvement of active shoulder abduction and external rotation without significant differences between the two groups. Significant external rotation contracture of the shoulder (inability to touch the abdomen with the wrist extended) occurred in 42 of 63 patients, and there was a greater incidence of external rotation contracture in group B. We conclude that surgery should be restricted to latissimus dorsi transfer without teres major transfer to avoid external rotation contractures. Our modification of the Gilbert grading system appears to be valid and applicable.
Delivery system for the enhanced efficiency of immunostimulatory nucleic acids
Authors: Smole Anže , Krajnik Alenka Kužnik , Oblak Alja , Pirher Nina , Jerala Roman
Published: June 2012

Toll-like receptors (TLRs) play a key role in the recognition of pathogen-associated molecular patterns, including immunostimulatory nucleic acids (INAs). INAs are recognized by TLRs in endosomes, leading to the activation of signalling pathways that activate the innate immune response. This feature makes INAs and their synthetic analogues useful as adjuvants in vaccines and in cancer treatment. We tested a delivery system for the improvement of the therapeutic effect of INAs which consists of a conjugate between transferrin (Tf) and poly-L-lysine (PLL). Tf is a ligand of the transferrin receptor (TfR) and is internalized via receptor-mediated endocytosis, while PLL binds negatively charged INAs. The TfPLL conjugate protected TLR3 ligand polyinosinic:polycytidylic acid [poly(I:C)] from RNase degradation and enhanced the uptake of poly(I:C) in HeLa cells. Co-localization between TfPLL-bound poly(I:C) and lysosomes demonstrated delivery into the endosomal pathway. Time dependence of the production of IL-6 in the primary cell line showed that TfPLL conjugate enabled a gradual release of poly(I:C) and stronger activation of TLR3 receptor in comparison with poly(I:C) alone. Only 3 h of stimulation by poly(I:C) + TfPLL complexes initiated a strong immune response in contrast to poly(I:C) alone. The poly(I:C) + TfPLL complexes have potential use for development of advanced vaccine adjuvants and targeted cancer immune therapy in cells that express higher levels of TfR.
Update on plication procedures for Peyronie’s disease and other penile deformities
Authors: Mobley Elizabeth M. , Fuchs Molly E. , Myers Jeremy B. , Brant William O.
Published: June 2012

Plication techniques are not a panacea for deformities associated with Peyronie’s disease or congenital curvature. However, they do provide certain advantages, both theoretic and real, over competing procedures such as grafting. Depending on the technique, plication procedures have minimal risk of de novo erectile dysfunction, minimal risk of injury to the dorsal neurovascular bundle, and may be used for a variety of angulation deformities, including multiplanar curvature and severe degrees of curvature. A variety of incisions may be used, including the classic circumcision with degloving but also ventral raphe, dorsal penile inversion, and penoscrotal. These may be helpful in preventing postoperative morbidity and in sparing the prepuce if desired. Plication may also be combined with procedures such as penile prosthesis for correction of residual curvature. Lastly, despite its complications, plication techniques are very well tolerated, are relatively simple to perform and result in the very high satisfaction rates.
BMI Changes Associated With Dietary Trends Among Brazilian Adolescents
Authors: Borges Camila Aparecida , Enes Carla Cristina , Slater Betzabeth , Conde Wolney Lisboa
Published: June 2012

Dietary patterns are a subject of growing interest considering the complex nature of dietary intake and its relationship with health outcomes. The aim of this study was to investigate the relationship between changes in adolescents’ BMI and their dietary trend pattern. This study is a follow-up of the children in the study titled “Dietary Intake and Physical Activity as Determinants of Changes in Body Mass Index in a Cohort of Adolescents Enrolled in Public Schools in Piracicaba, Sao Paulo,” and was conducted in public schools in Piracicaba, Sao Paulo, Brazil, with 372 adolescents participating in wave I (2004) and 268 participating in wave II (2005). Dietary intake was assessed using a semiquantitative food frequency questionnaire (SQFFQ), and height and weight measurements were also collected. The authors identified dietary patterns using principal component analysis. To describe dietary trends, they decided to match patterns across waves. Dietary patterns were gathered from 12 food groups. Relative risk was calculated by dividing the incidence of overweight among boys and girls across quintiles of dietary pattern scores. Matching C1 wave I and C1 wave II shows a multigroup trend pattern based on consumption of high levels of fruit, cereals, fatty foods, meat/eggs, milk, and vegetable groups. The relative risk for overweight was significantly lower for boys between the quintiles of this pattern (P < .05). The main results indicate that sustaining a healthy eating pattern for adolescents living without any nutritional intervention is of primary importance in maintaining or reducing BMI at this age.
Metaphors of the Adult Asthma Experience in a Suburban Area
Authors: McClelland Molly L. , Huttlinger Kathleen
Published: June 2012

Metaphor is one element of language capable of capturing human’s perception of reality. Nursing care can improve as patients’ perceptions of their illnesses are better understood. Realizing how patients with asthma, their family members, and the nurses caring for them perceive the asthma experience was the goal of this study. The authors used a qualitative research method implementing systematic metaphorical analysis to analyze the data. The authors identified an encompassing metaphor titled: Owning and Winning the Asthma War. The results of this study enhanced understanding of the asthma experience and contributed to metaphorical analysis as a valid way of knowing, understanding, and describing in nursing and human sciences.
ISAAC Malta
Authors: Fsadni Peter , Ellul Pierre , Montefort Maxine , Caruana Simone , Agius Muscat Hugo , Montefort Stephen
Published: June 2012

Introduction. Malta is one of the centers that participated in phases 1 and 3 of the International Study of Asthma and Allergies in Childhood (ISAAC). Aim. To investigate changes in the geographical distribution of wheezing in the Maltese Islands. Methods. ISAAC Malta phase 1 was carried out in 1994 with 3506 participants from 24 schools for the 5- to 8-year-old age group and 4184 participants from 25 schools for the 13- to 15-year-old age group. ISAAC Malta phase 3 in 2001 studied 3800 participants from 44 schools and 4139 children from 18 schools in the 5- to 8-year-old age group and 13- to 15-year-old age group, respectively. The ISAAC-standardized questionnaire was used, part of which included information regarding the place of dwelling of the individual participants. Results. In the younger age group there was an increase from 8.8% to 14.8% ( P < .0001) in the total prevalence of current wheezing between 1994 and 2001. Most geographical regions of the Maltese islands reported an increase in wheezing with the Central East (10.2% vs 23%, P < .0001), Grand Harbour (8.5% vs 21.2%, P < .005), East (8.6% vs 22.5%, P < .00001), and Central North (6.5% vs 16.3%, P < .0004) regions having the largest increases. The prevalence of current wheezing in the older age group remained stable (16% to 14.6%, P = .08). Conclusions. There seems to be some environmental trigger found in certain areas of the Maltese Islands that must be affecting the prevalence of wheezing in the younger age.
Antidiabetic Potentials of a Novel Polyherbal Preparation Formulated According to Principles of Siddha System of Medicine
Authors: Balaji Venkataraman , Williams Augustine Anne , Sathish Sampath , Mayilvanan Chinnaiyan , Narasimhan Akilavalli , Balasubramanian Karundevi
Published: June 2012

According to the principles of Siddha system of medicine, the following polyherbal preparation consisting of 5 plant parts in equal ratio namely, Asparagus racemosus, Emblica officinalis, Salacia oblonga, Syzygium aromaticum, and Tinospora cordifolia was formulated to treat experimental type 2 diabetic rats. So, using plants having aphrodisiac property in the formulation is a rational approach and first of its kind, as there have been no reports so far. Phenolics and other bioactive compounds present in polyherbal preparation may be responsible for lipid-lowering effects and strong antioxidant activity. Polyherbal preparation treatment reverted the activities of glycolytic and gluconeogenic enzymes that are disturbed in diabetic rats. It is concluded that polyherbal preparation treatment improves deranged lipid profile, antioxidant status, glycogen content, and decreases lipid peroxidation, which provides stability to membrane integrity and thus favors insulin receptor to achieve better glucose tolerance through a holistic approach.
Treatment-influenced associations of PML-RARα mutations, FLT3 mutations, and additional chromosome abnormalities in relapsed acute promyelocytic leukemia
Authors: Gallagher Robert E. , Moser Barry K. , Racevskis Janis , Poiré Xavier , Bloomfield Clara D. , Carroll Andrew J. , Ketterling Rhett P. , Roulston Diane , Schachter-Tokarz Esther , Zhou Da-cheng , Chen I-Ming L. , Harvey Richard , Koval Greg , Sher Dorie A. , Feusner James H. , Tallman Martin S. , Larson Richard A. , Powell Bayard L. , Appelbaum Frederick R. , Paietta Elisabeth , Willman Cheryl L. , Stock Wendy
Published: June 2012

Mutations in the all-trans retinoic acid (ATRA)–targeted ligand binding domain of PML-RARα (PRα/LBD+) have been implicated in the passive selection of ATRA-resistant acute promyelocytic leukemia clones leading to disease relapse. Among 45 relapse patients from the ATRA/chemotherapy arm of intergroup protocol C9710, 18 patients harbored PRα/LBD+ (40%), 7 of whom (39%) relapsed Off-ATRA selection pressure, suggesting a possible active role of PRα/LBD+. Of 41 relapse patients coanalyzed, 15 (37%) had FMS-related tyrosine kinase 3 internal tandem duplication mutations (FLT3-ITD+), which were differentially associated with PRα/LBD+ depending on ATRA treatment status at relapse: positively, On-ATRA; negatively, Off-ATRA. Thirteen of 21 patients (62%) had additional chromosome abnormalities (ACAs); all coanalyzed PRα/LBD mutant patients who relapsed off-ATRA (n = 5) had associated ACA. After relapse Off-ATRA, ACA and FLT3-ITD+ were negatively associated and were oppositely associated with presenting white blood count and PML-RARα type: ACA, low, L-isoform; FLT3-ITD+, high, S-isoform. These exploratory results suggest that differing PRα/LBD+ activities may interact with FLT3-ITD+ or ACA, that FLT3-ITD+ and ACA are associated with different intrinsic disease progression pathways manifest at relapse Off-ATRA, and that these different pathways may be short-circuited by ATRA-selectable defects at relapse On-ATRA. ACA and certain PRα/LBD+ were also associated with reduced postrelapse survival.
Ancient DNA studies: new perspectives on old samples
Authors: Rizzi Ermanno , Lari Martina , Gigli Elena , De Bellis Gianluca , Caramelli David
Published: June 2012

In spite of past controversies, the field of ancient DNA is now a reliable research area due to recent methodological improvements. A series of recent large-scale studies have revealed the true potential of ancient DNA samples to study the processes of evolution and to test models and assumptions commonly used to reconstruct patterns of evolution and to analyze population genetics and palaeoecological changes. Recent advances in DNA technologies, such as next-generation sequencing make it possible to recover DNA information from archaeological and paleontological remains allowing us to go back in time and study the genetic relationships between extinct organisms and their contemporary relatives. With the next-generation sequencing methodologies, DNA sequences can be retrieved even from samples (for example human remains) for which the technical pitfalls of classical methodologies required stringent criteria to guaranty the reliability of the results. In this paper, we review the methodologies applied to ancient DNA analysis and the perspectives that next-generation sequencing applications provide in this field.
A previously uncharacterized gene stm0551 plays a repressive role in the regulation of type 1 fimbriae in Salmonella enterica serotype Typhimurium
Authors: Wang Ke-Chuan , Hsu Yuan-Hsun , Huang Yi-Ning , Yeh Kuang-Sheng
Published: June 2012

Background

Salmonella enterica serotype Typhimurium produces surface-associated fimbriae that facilitate adherence of the bacteria to a variety of cells and tissues. Type 1 fimbriae with binding specificity to mannose residues are the most commonly found fimbrial type. In vitro, static-broth culture favors the growth of S. Typhimurium with type 1 fimbriae, whereas non-type 1 fimbriate bacteria are obtained by culture on solid-agar media. Previous studies demonstrated that the phenotypic expression of type 1 fimbriae is the result of the interaction and cooperation of the regulatory genes fimZ, fimY, fimW, and fimU within the fim gene cluster. Genome sequencing revealed a novel gene, stm0551, located between fimY and fimW that encodes an 11.4-kDa putative phosphodiesterase specific for the bacterial second messenger cyclic-diguanylate monophosphate (c-di-GMP). The role of stm0551 in the regulation of type 1 fimbriae in S. Typhimurium remains unclear.

Results

A stm0551-deleted stain constructed by allelic exchange constitutively produced type 1 fimbriae in both static-broth and solid-agar medium conditions. Quantative RT-PCR revealed that expression of the fimbrial major subunit gene, fimA, and one of the regulatory genes, fimZ, were comparably increased in the stm0551-deleted strain compared with those of the parental strain when grown on the solid-agar medium, a condition that normally inhibits expression of type 1 fimbriae. Following transformation with a plasmid possessing the coding sequence of stm0551, expression of fimA and fimZ decreased in the stm0551 mutant strain in both culture conditions, whereas transformation with the control vector pACYC184 relieved this repression. A purified STM0551 protein exhibited a phosphodiesterase activity in vitro while a point mutation in the putative EAL domain, substituting glutamic acid (E) with alanine (A), of STM0551 or a FimY protein abolished this activity.

Conclusions

The finding that the stm0551 gene plays a negative regulatory role in the regulation of type 1 fimbriae in S. Typhimurium has not been reported previously. The possibility that degradation of c-di-GMP is a key step in the regulation of type 1 fimbriae warrants further investigation.
Analysis of the P1promoter in response to UV-B radiation in allelic variants of high-altitude maize
Authors: Rius Sebastián Pablo , Grotewold Erich , Casati Paula
Published: June 2012

Background

Plants living at high altitudes are typically exposed to elevated UV-B radiation, and harbor mechanisms to prevent the induced damage, such as the accumulation of UV-absorbing compounds. The maize R2R3-MYB transcription factor P1 controls the accumulation of several UV-B absorbing phenolics by activating a subset of flavonoid biosynthetic genes in leaves of maize landraces adapted to high altitudes.

Results

Here, we studied the UV-B regulation of P1 in maize leaves of high altitude landraces, and we investigated how UV-B regulates P1binding to the CHS promoter in both low and high altitude lines. In addition, we analyzed whether the expansion in the P1 expression domain between these maize landraces and inbred lines is associated to changes in the molecular structure of the proximal promoter, distal enhancer and first intron of P1. Finally, using transient expression experiments in protoplasts from various maize genotypes, we investigated whether the different expression patterns of P1 in the high altitude landraces could be attributed to trans- or cis-acting elements.

Conclusions

Together, our results demonstrate that, although differences in cis-acting elements exist between the different lines under study, the different patterns of P1 expression are largely a consequence of effects in trans.
PeanutDB: an integrated bioinformatics web portal for Arachis hypogaea transcriptomics
Authors: Duan Xiaohong , Schmidt Emily , Li Pei , Lenox Douglas , Liu Lin , Shu Changlong , Zhang Jie , Liang Chun
Published: June 2012

Background

The peanut (Arachis hypogaea) is an important crop cultivated worldwide for oil production and food sources. Its complex genetic architecture (e.g., the large and tetraploid genome possibly due to unique cross of wild diploid relatives and subsequent chromosome duplication: 2n = 4x = 40, AABB, 2800 Mb) presents a major challenge for its genome sequencing and makes it a less-studied crop. Without a doubt, transcriptome sequencing is the most effective way to harness the genome structure and gene expression dynamics of this non-model species that has a limited genomic resource.

Description

With the development of next generation sequencing technologies such as 454 pyro-sequencing and Illumina sequencing by synthesis, the transcriptomics data of peanut is rapidly accumulated in both the public databases and private sectors. Integrating 187,636 Sanger reads (103,685,419 bases), 1,165,168 Roche 454 reads (333,862,593 bases) and 57,135,995 Illumina reads (4,073,740,115 bases), we generated the first release of our peanut transcriptome assembly that contains 32,619 contigs. We provided EC, KEGG and GO functional annotations to these contigs and detected SSRs, SNPs and other genetic polymorphisms for each contig. Based on both open-source and our in-house tools, PeanutDB presents many seamlessly integrated web interfaces that allow users to search, filter, navigate and visualize easily the whole transcript assembly, its annotations and detected polymorphisms and simple sequence repeats. For each contig, sequence alignment is presented in both bird’s-eye view and nucleotide level resolution, with colorfully highlighted regions of mismatches, indels and repeats that facilitate close examination of assembly quality, genetic polymorphisms, sequence repeats and/or sequencing errors.

Conclusion

As a public genomic database that integrates peanut transcriptome data from different sources, PeanutDB (http://bioinfolab.muohio.edu/txid3818v1) provides the Peanut research community with an easy-to-use web portal that will definitely facilitate genomics research and molecular breeding in this less-studied crop.
Immunophenotyping invasive breast cancer: paving the road for molecular imaging
Authors: Vermeulen Jeroen F , van Brussel Aram SA , van der Groep Petra , Morsink Folkert HM , Bult Peter , van der Wall Elsken , van Diest Paul J
Published: June 2012

Background

Mammographic population screening in The Netherlands has increased the number of breast cancer patients with small and non-palpable breast tumors. Nevertheless, mammography is not ultimately sensitive and specific for distinct subtypes. Molecular imaging with targeted tracers might increase specificity and sensitivity of detection. Because development of new tracers is labor-intensive and costly, we searched for the smallest panel of tumor membrane markers that would allow detection of the wide spectrum of invasive breast cancers.

Methods

Tissue microarrays containing 483 invasive breast cancers were stained by immunohistochemistry for a selected set of membrane proteins known to be expressed in breast cancer.

Results

The combination of highly tumor-specific markers glucose transporter 1 (GLUT1), epidermal growth factor receptor (EGFR), insulin-like growth factor-1 receptor (IGF1-R), human epidermal growth factor receptor 2 (HER2), hepatocyte growth factor receptor (MET), and carbonic anhydrase 9 (CAIX) 'detected' 45.5% of tumors, especially basal/triple negative and HER2-driven ductal cancers. Addition of markers with a 2-fold tumor-to-normal ratio increased the detection rate to 98%. Including only markers with >3 fold tumor-to-normal ratio (CD44v6) resulted in an 80% detection rate. The detection rate of the panel containing both tumor-specific and less tumor-specific markers was not dependent on age, tumor grade, tumor size, or lymph node status.

Conclusions

In search of the minimal panel of targeted probes needed for the highest possible detection rate, we showed that 80% of all breast cancers express at least one of a panel of membrane markers (CD44v6, GLUT1, EGFR, HER2, and IGF1-R) that may therefore be suitable for molecular imaging strategies. This study thereby serves as a starting point for further development of a set of antibody-based optical tracers with a high breast cancer detection rate.
Increased expression of MMP-9 and IL-8 are correlated with poor prognosis of Bladder Cancer
Authors: Reis Sabrina Thalita , Leite Katia Ramos M , Piovesan Luís Felipe , Pontes-Junior José , Viana Nayara Izabel , Abe Daniel Kanda , Crippa Alexandre , Moura Caio Martins , Adonias Sanarelly Pires , Srougi Miguel , Dall’Oglio Marcos Francisco
Published: June 2012

Background

Extracellular matrix homeostasis is strictly maintained by a coordinated balance between the expression of metalloproteinases (MMPs) and their inhibitors. The purpose of this study was to investigate whether the expression of MMP-9, MMP-2 and its specific inhibitors, are expressed in a reproducible, specific pattern and if the profiles are related to prognosis in Bladder Cancer (BC).

Methods

MMP-9, MMP-2 and its specific inhibitors expression levels were analyzed by quantitative real-time polymerase chain reaction (qRT-PCR) in fresh-frozen malignant tissue collected from 40 patients with BC submitted to transurethral resection of bladder. The control group consisted of normal bladder tissue from five patients who had undergone retropubic prostatectomy to treat benign prostatic hyperplasia.

Results

MMP-9 was overexpressed in 59.0 % of patients, and MMP-2, TIMP-1, TIMP-2, MMP-14, RECK and IL-8 was underexpressed in most of the patients. Regarding prognostic parameters we observed that high-grade tumors exhibited significantly higher levels of MMP-9 and IL-8 (p = 0.012, p = 0.003). Invasive tumors (pT1-pT2) had higher expression levels of MMP-9 than superficial tumors (pTa) (p = 0.026). The same was noted for IL-8 that was more expressed by invasive tumors (p = 0.015, p = 0.048). Most importantly tumor recurrence was related with higher levels of both MMP-9 (p = 0.003) and IL-8 (p = 0.005).

Conclusion

We have demonstrated that the overexpression of MMP-9 and higher expression of IL-8 are related to unfavorable prognostic factors of urothelial bladder cancer and tumor recurrence and may be useful in the follow up of the patients.
Identification of immunogenic proteins and generation of antibodies against SalmonellaTyphimurium using phage display
Authors: Meyer Torsten , Schirrmann Thomas , Frenzel André , Miethe Sebastian , Stratmann-Selke Janin , Gerlach Gerald F , Strutzberg-Minder Katrin , Dübel Stefan , Hust Michael
Published: June 2012

Background

Solely in Europoe, Salmonella Typhimurium causes more than 100,000 infections per year. Improved detection of livestock colonised with S. Typhimurium is necessary to prevent foodborne diseases. Currently, commercially available ELISA assays are based on a mixture of O-antigens (LPS) or total cell lysate of Salmonella and are hampered by cross-reaction. The identification of novel immunogenic proteins would be useful to develop ELISA based diagnostic assays with a higher specificity.

Results

A phage display library of the entire Salmonella Typhimurium genome was constructed and 47 immunogenic oligopeptides were identified using a pool of convalescent sera from pigs infected with Salmonella Typhimurium. The corresponding complete genes of seven of the identified oligopeptids were cloned. Five of them were produced in E. coli. The immunogenic character of these antigens was validated with sera from pigs infeced with S. Tyhimurium and control sera from non-infected animals. Finally, human antibody fragments (scFv) against these five antigens were selected using antibody phage display and characterised.

Conclusion

In this work, we identified novel immunogenic proteins of Salmonella Typhimurium and generated antibody fragments against these antigens completely based on phage display. Five immunogenic proteins were validated using a panel of positive and negative sera for prospective applications in diagnostics of Salmonela Typhimurium.
Acute Care of At-Risk Newborns (ACoRN): quantitative and qualitative educational evaluation of the program in a region of China
Authors: Singhal Nalini , Lockyer Jocelyn , Fidler Herta , Aziz Khalid , McMillan Douglas , Qiu Xiangming , Ma Xiaolu , Du Lizhong , Lee Shoo K
Published: June 2012

Background

The Acute Care of at-Risk Newborns (ACoRN) program was developed in Canada for trained health care providers for the identification and management of newborns who are at-risk and/or become unwell in the first few hours or days after birth. The ACoRN process follows an 8-step framework that enables the evaluation and management of babies irrespective of the experience or expertise of the caregiving individual or team. This study assesses the applicability of the program to Chinese pediatric practitioners.

Methods

Course content and educational materials were translated from English into Chinese by bilingual neonatal practitioners. Confidence and knowledge questionnaires were developed and reviewed for face and content validity by a team of ACoRN instructors. Bilingual Chinese instructors were trained at the tertiary perinatal centre in Hangzhou Zhejiang to deliver the course at 15 level II county hospitals. Participants completed pre- and post-course confidence and knowledge questionnaires and provided feedback through post-course focus groups.

Results

216 physicians and nurses were trained. Confidence and knowledge relating to neonatal stabilization improved significantly following the courses. Participants rated course utility and function between 4.2 and 4.6/5 on all items. Pre/post measures of confidence were significantly correlated with post course knowledge. Focus group data supported the perceived value of the program and recommended course adjustments to include pre-course reading, and increased content related to simulation, communication skills, and management of respiratory illness and jaundice.

Conclusions

ACoRN, a Canadian educational program, appears to be well received by Chinese health care providers and results in improved knowledge and confidence. International program adaptation for use by health care professionals requires structured and systematic evaluation to ensure that the program meets the needs of learners, reflects their learning styles, and can be applied in their setting.
Efficiency improvement of silicon solar cells enabled by ZnO nanowhisker array coating
Authors: Yu Xuegong , Wang Dong , Lei Dong , Li Genhu , Yang Deren
Published: June 2012

An efficient antireflection coating is critical for the improvement of silicon solar cell performance via increased light coupling. Here, we have grown well-aligned ZnO nanowhisker (NW) arrays on Czochralski silicon solar cells by a seeding-growth two-step process. It is found that the ZnO NWs have a great effect on the macroscopic antireflection effect and, therefore, improves the solar cell performance. The ZnO NW array-coated solar cells display a broadband reflection suppression from 500 to 1,100 nm, and the minimum reflectance smaller than 3% can easily be achieved. By optimizing the time of ZnO NW growth, it has been confirmed that an increase of 3% relatively in the solar cell efficiency can be obtained. These results are quite interesting for the application of ZnO nanostructure in the fabrication of high-efficiency silicon solar cells.