bluuebunny/crossref_metadata_2025 huggingface dataset:
Writing Usable Qualitative Health Research Findings
Authors: Sandelowski Margarete , Leeman Jennifer
Published: June 2012

Scholars in diverse health-related disciplines and specialty fields of practice routinely promote qualitative research as an essential component of intervention and implementation programs of research and of a comprehensive evidence base for practice. Remarkably little attention, however, has been paid to the most important element of qualitative studies—the findings in reports of those studies—and specifically to enhancing the accessibility and utilization value of these findings for diverse audiences of users. The findings in reports of qualitative health research are too often difficult to understand and even to find owing to the way they are presented. A basic strategy for enhancing the presentation of these findings is to translate them into thematic statements, which can then in turn be translated into the language of intervention and implementation. Writers of qualitative health research reports might consider these strategies better to showcase the significance and actionability of findings to a wider audience.
Critical Care Nurses’ Perception of Barriers and Supportive Behaviors in End-of-Life Care
Authors: Attia Amal Kadry , Abd-Elaziz Wafaa Wahdan , Kandeel Nahed Attia
Published: June 2012

Aim:

To investigate critical care nurses' perceptions of barriers and supportive behaviors in providing end of life (EOL) care to dying patients and their families.

Methods:

The study involved a convenient sample of 70 nurses who were involved in caring for critically ill patients. Data were collected using a structured interview sheet.

Results:

Barriers to providing EOL care were related to intensive care environment, family members, nurses' knowledge and skills, physicians' attitudes and treatment policy. Possible help to providing EOL care involved nurses' support to each other, patient and family-centered care, and families' support.

Conclusions:

There is a need to allow the family unlimited access to the dying patient, involve them in patient care and provide them with a private place for grieving.
Clock Without Hands
Authors: Brennan Frank
Published: June 2012

Carson McCullers was one of the greatest American writers of the 20th century. For much of her adult life she struggled with illness. In her final novel, Clock Without Hands, a central character was diagnosed with a serious illness. Themes of illness, mortality, and creativity are examined in the physical and psychospiritual journey of both the character and the author herself. Reflections are made on the practice of palliative care.
Talking About the Boss
Authors: Ellwardt Lea , Wittek Rafael , Wielers Rudi
Published: June 2012

This study developed and tested a relational theory of positive and negative gossip about managers. It is argued that spreading information about managers depends on trust in organizations, more specifically the employees’ generalized and interpersonal trust in managers and colleagues. Hypotheses were tested by conducting two studies in a medium-sized Dutch child care organization, namely, an employee survey ( N = 132) and a network study at two sites ( N = 58). Multiple regressions and cross-sectional social network analysis (exponential random graph modeling [ERGM]) revealed that negative gossip about managers increases when employees have low trust, nonfriendly relationships, and infrequent contact with the managers. This effect is further enhanced when contacts between employees are trusting and frequent. Implications for theories about management and organizations are discussed.
Cognitive Behavior Therapy as a Systemic Approach in Counseling
Authors: Robey Patricia A.
Published: June 2012

This article presents an interview with Dr. Arthur Freeman, an expert in cognitive behavior therapy (CBT). Freeman shares the process of his therapeutic training and the experiences that led him to choose CBT as the model for his work with clients. Freeman provides a brief explanation of CBT concepts and discusses the application of CBT in work with family systems, with couples, and with children.
Childhood Food Addiction and the Family
Authors: Carlisle Kristy L. , Buser Juleen K. , Carlisle Robert M.
Published: June 2012

Food addiction among children is a concerning issue. Few empirical studies have examined the relevance of food addiction among pediatric samples, but emerging evidence suggests that some children experience their eating patterns as addictive. The present review will discuss the issue of food addiction among children, and will also attend to the related concepts of binge eating and obesity. Several family factors that have been implicated as contributing to problematic eating practices among children will be discussed, including family functioning, parental modeling, parental pressure, and the impact of low socioeconomic status. Finally, implications for counselors who work with families struggling with food addiction will be presented.
Mixed Gastric Carcinoma With Intestinal and Cribriform Patterns
Authors: Lino-Silva Leonardo Saúl , Salcedo Hernández Rosa Angélica , Molina-Frías Ernesto
Published: June 2012

Gastric adenocarcinoma is characterized by marked heterogeneity at cytological and architectural level and frequently shows overlap between microscopic patterns. This article describes a peculiar pattern of gastric adenocarcinoma, previously unreported, that combines intestinal type adenocarcinoma with areas of cribriform pattern that resembles both architectural and cytological in situ ductal carcinoma of the breast and to the best of the authors’ knowledge, there are no earlier reports of this pattern in the stomach, which has been named “gastric carcinoma with cribriform component (CGA). The authors analyzed 12 cases of intestinal type adenocarcinoma with areas at least 20% of cribriform pattern (range from 20% to 90%) that was present in 9% of intestinal type gastric adenocarcinomas in their institution. There is slight predilection for male sex, and the median age of presentation is 55.8 years. The phenotype by immunohistochemistry is the same as with conventional (non-CGA) carcinomas. CGA shows more frequent lymphovascular invasion ( P = .039), perineural invasion ( P = .027) and resembles both in situ and invasive cribriform carcinoma of the breast. In clinical stage III the overall 3-year survival of CGA was worse than those with non-CGA component (38.6% vs 25%; 3-year survival, P = .010) and proves to be an independent adverse factor for overall survival in a multivariate analysis. Compared with conventional gastric carcinomas, CGA is deep infiltrating, has more nodal metastases, more lymphovascular and perineural invasion, and has decreased overall survival. Thus, proper recognition and report is important, even in small biopsies or small foci.
Development and Exploration of the Experiences With Classism Scale
Authors: Thompson Mindi N. , Subich Linda M.
Published: June 2012

The examination of barriers in relation to college students’ vocational choice and development is an important area of research, but the barrier of classism is relatively underexamined. This may be due to the deficiencies in measurement, so we describe herein the development of a new measure, the Experiences with Classism scale (EWCS). The EWCS was developed to extend prior qualitative work that highlighted the need to consider experiences with classism in the lives of undergraduate students. Results provided initial evidence for the usefulness of the EWCS to measure undergraduate students’ experiences with classism at a personal and systemic level. Across two studies, the EWCS was demonstrated to have high internal consistency reliability, to have a stable factor structure consisting of two factors, to correlate as expected with relevant demographic variables, and to fit within a nomological network of convergent and discriminant constructs. The EWCS was also demonstrated to predict self-reported experiences of depression, anxiety, stress, self-esteem, and psychological wellness. Implications for further research and practice are suggested.
Dry reciprocal sliding wear behavior of nanocrystalline Fe88Si12 alloy
Authors: Fu Licai , Yang Jun , Bi Qinling , Liu Weimin
Published: June 2012

Dry sliding wear behavior of nanocrystalline Fe88Si12 alloy has been investigated compared with coarse grained counterpart. The friction coefficient of the Fe88Si12 alloy changes slightly with grain size. But the wear resistance of the Fe88Si12 alloy improves as the grain size decreases to 40 nm, and then weakens when the grain size decreases from 40 nm to 10 nm. The grain size has significantly effect on the tribological behavior of Fe88Si12 alloy by modifying the hardness and the tribo-chemical interaction on the sliding zone during the wear process.
Importance of adaptive multimode lubrication mechanism in natural and artificial joints
Authors: Murakami Teruo
Published: June 2012

The healthy natural synovial joints maintain excellent load-carrying capacity and lubricating properties with extremely low friction and minimum wear even under heavily loaded conditions. The superior lubricating performance appears to be actualized by not single lubrication mode but the synergistic combination of various modes depending on the severity of operating conditions. This mechanism is called adaptive multimode lubrication and the application of this good working lubrication mechanism to artificial joints with soft layer is expected to contribute to remarkable improvement in longevity of joint prostheses. However, some of detailed mechanisms in natural synovial joints have not yet been clarified. In this article, the effectiveness of biphasic lubrication in natural synovial joints was examined by biphasic finite element analysis under both the on–off loading (migrating contact) and the continuous loading (continuous contact) to cartilage. Then, the method to suppress the gradual rising in friction for articular cartilage under the continuous loading is discussed. Finally, the effectiveness of fibre reinforcement in hydrogel artificial cartilage was examined in walking simulator test.
Towards an international culture: Gen Y students and SNS?
Authors: Lichy Jessica
Published: June 2012

This article reports the findings of a small-scale investigation into the Internet user behaviour of generation Y (Gen Y) students, with particular reference to social networking sites. The study adds to the literature on cross-cultural Internet user behaviour with specific reference to Gen Y and social networking. It compares how a cohort of international students makes use of SNS for academic work and for recreational purposes. The study also explores the notion of ‘second-level digital divide’ which holds that urban dwellers will use the Internet in a different way from suburban and rural dwellers. The findings point to broad areas of commonality among students and some disparity in their Internet user behaviour, indicating the importance of proceeding with caution when using technology-enhanced learning, to avoid over-generalizing the needs of the so-called Gen Y students.
Form Effects on DIBELS Next Oral Reading Fluency Progress- Monitoring Passages
Authors: Cummings Kelli D. , Park Yonghan , Bauer Schaper Holle A.
Published: June 2012

The purpose of this article is to describe passage effects on Dynamic Indicators of Basic Early Literacy Skills–Next Edition Oral Reading Fluency ( DIBELS Next ORF) progress-monitoring measures for Grades 1 through 6. Approximately 572 students per grade (total N with at least one data point = 3,092) read all three DIBELS Next winter benchmark passages in the prescribed order, and within 2 weeks read four additional progress-monitoring passages in a randomly assigned and counterbalanced order. All 20 progress-monitoring passages were read by students in Grades 1 through 4; 16 passages were read in Grade 5 and 12 passages were read in Grade 6. Results focus on the persistence of form effects in spite of a priori criteria used in passage development. The authors describe the utility of three types of equating methods (i.e., mean, linear, and equipercentile equating) in ameliorating these effects. Their conclusions focus on preferred equating methods with small samples, the impact of form effects on progress-monitoring decision making, and recommendations for future use of ORF passages for progress monitoring.
Clinical Characteristics of HIV-Infected Patients Who Survive after the Diagnosis of HIV Infection for More Than 10 Years in a Resource-Limited Setting
Authors: Kiertiburanakul Sasisopin , Luengroongroj Pawinee , Sungkanuparph Somnuek
Published: June 2012

A retrospective cohort study was conducted and 129 patients with a diagnosis of HIV infection for more than 10 years were identified. Half the patients were men and mean (standard deviation, SD) age at HIV diagnosis was 33.2 (9.2) years. One third had a diagnosis of AIDS at cohort entry with median (interquartile range, IQR) CD4 counts of 259 (112-430) cells/mm3. All received antiretroviral therapy with median (IQR) current CD4 counts of 502 (363-607) cells/mm3 and 95% had HIV RNA <50 copies/mL. For adverse events, 28% experienced drug resistance, 27% experienced hospitalization, 59% had dyslipidemia, 35% had creatinine >1.0 mg/dL, and 5% had glucose >126 mg/dL. In conclusion, immunological and virological responses can be achieved among patients with a diagnosis of HIV infection for more than 10 years even in a resource-limited setting. Adverse events are common. Preparation for monitoring and management of these adverse events is a crucial part of successful long-term HIV care.
Transformative, Mixed Methods Checklist for Psychological Research With Mexican Americans
Authors: Canales Genevieve
Published: June 2012

This is a description of the creation of a research methods tool, the Transformative, Mixed Methods Checklist for Psychological Research With Mexican Americans. For conducting literature reviews of and planning mixed methods studies with Mexican Americans, it contains evaluative criteria calling for transformative mixed methods, perspectives from Chicana/o (Mestiza/o) psychology, and Baca-Zinn and Dill’s Chicana multiracial feminism. It is useful to researchers, journal editors, teachers, and students in psychology and other social sciences. It may serve as a template in the development of comparable checklists for critiquing mixed methods studies with other cultural groups, including African Americans, American Indians, and Asian Americans.
Parents’ Expression and Discussion of Emotion in the Multilingual Family
Authors: Chen Stephen H. , Kennedy Morgan , Zhou Qing
Published: June 2012

Parents regularly use words to express and discuss emotion with their children, but does it matter which language they use to do so? In this article, we examine this question in the multilingual family context by integrating findings from both psychological and linguistic research. We propose that parents’ use of different languages for emotional expression or discussion holds significant implications for children’s emotional experience, understanding, and regulation. Finally, we suggest that an understanding of the implications of emotion-related language shifts is critical, particularly in adapting interventions within a rapidly diversifying society.
Self-Determination Theory Applied to Health Contexts
Authors: Ng Johan Y. Y. , Ntoumanis Nikos , Thøgersen-Ntoumani Cecilie , Deci Edward L. , Ryan Richard M. , Duda Joan L. , Williams Geoffrey C.
Published: June 2012

Behavior change is more effective and lasting when patients are autonomously motivated. To examine this idea, we identified 184 independent data sets from studies that utilized self-determination theory (SDT; Deci & Ryan, 2000) in health care and health promotion contexts. A meta-analysis evaluated relations between the SDT-based constructs of practitioner support for patient autonomy and patients’ experience of psychological need satisfaction, as well as relations between these SDT constructs and indices of mental and physical health. Results showed the expected relations among the SDT variables, as well as positive relations of psychological need satisfaction and autonomous motivation to beneficial health outcomes. Several variables (e.g., participants’ age, study design) were tested as potential moderators when effect sizes were heterogeneous. Finally, we used path analyses of the meta-analyzed correlations to test the interrelations among the SDT variables. Results suggested that SDT is a viable conceptual framework to study antecedents and outcomes of motivation for health-related behaviors.
Comparison of a multifilament stainless steel suture with FiberWire for flexor tendon repairs — an in vitro biomechanical study
Authors: McDonald E. , Gordon J. A. , Buckley J. M. , Gordon L.
Published: June 2012

Our goal was to investigate and compare the mechanical properties of multifilament stainless steel suture (MFSS) and polyethylene multi-filament core FiberWire in flexor tendon repairs. Flexor digitorum profundus tendons were repaired in human cadaver hands with either a 4-strand cruciate cross-lock repair or 6-strand modified Savage repair using 4-0 and 3-0 multifilament stainless steel or FiberWire. The multifilament stainless steel repairs were as strong as those performed with FiberWire in terms of ultimate load and load at 2 mm gap. This study suggests that MFSS provides as strong a repair as FiberWire. The mode of failure of the MFSS occurred by the suture pulling through the tendon, which suggests an advantage in terms of suture strength.
Collagen Gene Variants Previously Associated With Anterior Cruciate Ligament Injury Risk Are Also Associated With Joint Laxity
Authors: Bell Richard D. , Shultz Sandra J. , Wideman Laurie , Henrich Vincent C.
Published: June 2012

Background:

Genetic association studies demonstrate a relationship between several collagen gene variants and anterior cruciate ligament (ACL) injury, yet the mechanism of these relationships is still unclear. Joint laxity is a heritable trait; increased magnitudes of anterior knee laxity (AKL), genu recurvatum (GR), and general joint laxity (GJL) have been consistently associated with a greater risk of ACL injury. Joint laxity may constitute an important intermediate phenotype for the genetic association with ACL injury that can be measured clinically.

Hypothesis:

To determine if genetic variants within the COL1A1, COL5A1, and COL12A1 genes, previously associated with ACL injury, were also associated with greater magnitudes of AKL, GR, and GJL.

Study Design:

Descriptive laboratory study.

Methods:

Blood samples and measures of AKL, GR, and GJL were obtained from 124 (50 male, 74 female) healthy, recreationally active subjects. Genomic DNA was extracted from the blood samples and genotyped for single-nucleotide polymorphisms previously examined relative to ACL injury. Univariate analyses of variance compared the magnitude of each laxity variable across the 3 genotypes for each single-nucleotide polymorphism in both sex-combined and sex-specific models.

Results:

Specific genotypes were associated with greater GR in all subjects. Some genotypes were associated with greater magnitudes of GR, AKL, and GJL in females only.

Conclusions:

Gene variants previously associated with ACL injury risk were in large part also associated with joint laxity. Sex-specific genetic associations with joint laxity were consistent with those previously reported for ACL injury.

Clinical Relevance:

These data provide insight into potential pathways through which genotypic variants in collagen genes have the potential to alter ligament structure and behavior and, thus, ACL injury risk.
Promoting or Jeopardizing Lighter Carbon Footprints? Self-Affirmation Can Polarize Environmental Orientations
Authors: van Prooijen Anne-Marie , Sparks Paul , Jessop Donna C.
Published: June 2012

Research has shown that self-affirmation often leads to more adaptive responses to messages that focus on behavior-specific, individual threats. However, little is known about the effects of self-affirmation in the context of an ongoing collective threat, such as climate change. In the study reported here ( N = 90), the authors examined whether self-affirmation might polarize orientations toward environment-related actions when people rely on their established beliefs about climate change. The authors found that self-affirmation led to more constructive pro-environmental motives among participants with positive ecological worldviews but led to less constructive pro-environmental motives among participants with negative ecological worldviews. These findings suggest that in the absence of a persuasive threatening message, self-affirmation might serve to validate a person’s initial worldviews about environmental issues.
Identification of a 3-gene model as a powerful diagnostic tool for the recognition of ALK-negative anaplastic large-cell lymphoma
Authors: Agnelli Luca , Mereu Elisabetta , Pellegrino Elisa , Limongi Tania , Kwee Ivo , Bergaggio Elisa , Ponzoni Maurilio , Zamò Alberto , Iqbal Javeed , Piccaluga Pier Paolo , Neri Antonino , Chan Wing C. , Pileri Stefano , Bertoni Francesco , Inghirami Giorgio , Piva Roberto
Published: June 2012

Anaplastic large-cell lymphomas (ALCLs) are a group of clinically and biologically heterogeneous diseases including the ALK+ and ALK− systemic forms. Whereas ALK+ ALCLs are molecularly characterized and can be readily diagnosed, specific immunophenotypic or genetic features to define ALK− ALCL are missing, and their distinction from other T-cell non-Hodgkin lymphomas (T-NHLs) remains controversial. In the present study, we undertook a transcriptional profiling meta-analysis of 309 cases, including ALCL and other primary T-NHL samples. Pathway discovery and prediction analyses defined a minimum set of genes capable of recognizing ALK− ALCL. Application of quantitative RT-PCR in independent datasets from cryopreserved and formalin-fixed paraffin-embedded samples validated a 3-gene model (TNFRSF8, BATF3, and TMOD1) able to successfully separate ALK− ALCL from peripheral T-cell lymphoma not otherwise specified, with overall accuracy near 97%. In conclusion, our data justify the possibility of translating quantitative RT-PCR protocols to routine clinical settings as a new approach to objectively dissect T-NHL and to select more appropriate therapeutic protocols.
Single nucleotide polymorphisms and inherited risk of chronic lymphocytic leukemia among African Americans
Authors: Coombs Catherine C. , Rassenti Laura Z. , Falchi Lorenzo , Slager Susan L. , Strom Sara S. , Ferrajoli Alessandra , Weinberg J. Brice , Kipps Thomas J. , Lanasa Mark C.
Published: June 2012

The incidence of chronic lymphocytic leukemia (CLL) is significantly lower in African Americans than whites, but overall survival is inferior. The biologic basis for these observations remains unexplored. We hypothesized that germline genetic predispositions differ between African Americans and whites with CLL and yield inferior clinical outcomes among African Americans. We examined a discovery cohort of 42 African American CLL patients ascertained at Duke University and found that the risk allele frequency of most single nucleotide polymorphisms known to confer risk of development for CLL is significantly lower among African Americans than whites. We then confirmed our results in a distinct cohort of 68 African American patients ascertained by the CLL Research Consortium. These results provide the first evidence supporting differential genetic risk for CLL between African Americans compared with whites. A fuller understanding of differential genetic risk may improve prognostication and therapeutic decision making for all CLL patients.
Consensus properties for the deep coalescence problem and their application for scalable tree search
Authors: Lin Harris T , Burleigh J Gordon , Eulenstein Oliver
Published: June 2012

Background

To infer a species phylogeny from unlinked genes, phylogenetic inference methods must confront the biological processes that create incongruence between gene trees and the species phylogeny. Intra-specific gene variation in ancestral species can result in deep coalescence, also known as incomplete lineage sorting, which creates incongruence between gene trees and the species tree. One approach to account for deep coalescence in phylogenetic analyses is the deep coalescence problem, which takes a collection of gene trees and seeks the species tree that implies the fewest deep coalescence events. Although this approach is promising for phylogenetics, the consensus properties of this problem are mostly unknown and analyses of large data sets may be computationally prohibitive.

Results

We prove that the deep coalescence consensus tree problem satisfies the highly desirable Pareto property for clusters (clades). That is, in all instances, each cluster that is present in all of the input gene trees, called a consensus cluster, will also be found in every optimal solution. Moreover, we introduce a new divide and conquer method for the deep coalescence problem based on the Pareto property. This method refines the strict consensus of the input gene trees, thereby, in practice, often greatly reducing the complexity of the tree search and guaranteeing that the estimated species tree will satisfy the Pareto property.

Conclusions

Analyses of both simulated and empirical data sets demonstrate that the divide and conquer method can greatly improve upon the speed of heuristics that do not consider the Pareto consensus property, while also guaranteeing that the proposed solution fulfills the Pareto property. The divide and conquer method extends the utility of the deep coalescence problem to data sets with enormous numbers of taxa.
The maximum clique enumeration problem: algorithms, applications, and implementations
Authors: Eblen John D , Phillips Charles A , Rogers Gary L , Langston Michael A
Published: June 2012

Background

The maximum clique enumeration (MCE) problem asks that we identify all maximum cliques in a finite, simple graph. MCE is closely related to two other well-known and widely-studied problems: the maximum clique optimization problem, which asks us to determine the size of a largest clique, and the maximal clique enumeration problem, which asks that we compile a listing of all maximal cliques. Naturally, these three problems are

N
P

-hard, given that they subsume the classic version of the

N
P

-complete clique decision problem. MCE can be solved in principle with standard enumeration methods due to Bron, Kerbosch, Kose and others. Unfortunately, these techniques are ill-suited to graphs encountered in our applications. We must solve MCE on instances deeply seeded in data mining and computational biology, where high-throughput data capture often creates graphs of extreme size and density. MCE can also be solved in principle using more modern algorithms based in part on vertex cover and the theory of fixed-parameter tractability (FPT). While FPT is an improvement, these algorithms too can fail to scale sufficiently well as the sizes and densities of our datasets grow.

Results

An extensive testbed of benchmark graphs are created using publicly available transcriptomic datasets from the Gene Expression Omnibus (GEO). Empirical testing reveals crucial but latent features of such high-throughput biological data. In turn, it is shown that these features distinguish real data from random data intended to reproduce salient topological features. In particular, with real data there tends to be an unusually high degree of maximum clique overlap. Armed with this knowledge, novel decomposition strategies are tuned to the data and coupled with the best FPT MCE implementations.

Conclusions

Several algorithmic improvements to MCE are made which progressively decrease the run time on graphs in the testbed. Frequently the final runtime improvement is several orders of magnitude. As a result, instances which were once prohibitively time-consuming to solve are brought into the domain of realistic feasibility.
Transcriptome analysis of the honey bee fungal pathogen, Ascosphaera apis: implications for host pathogenesis
Authors: Cornman R Scott , Bennett Anna K , Murray K Daniel , Evans Jay D , Elsik Christine G , Aronstein Kate
Published: June 2012

Background

We present a comprehensive transcriptome analysis of the fungus Ascosphaera apis, an economically important pathogen of the Western honey bee (Apis mellifera) that causes chalkbrood disease. Our goals were to further annotate the A. apis reference genome and to identify genes that are candidates for being differentially expressed during host infection versus axenic culture.

Results

We compared A. apis transcriptome sequence from mycelia grown on liquid or solid media with that dissected from host-infected tissue. 454 pyrosequencing provided 252 Mb of filtered sequence reads from both culture types that were assembled into 10,087 contigs. Transcript contigs, protein sequences from multiple fungal species, and ab initio gene predictions were included as evidence sources in the Maker gene prediction pipeline, resulting in 6,992 consensus gene models. A phylogeny based on 12 of these protein-coding loci further supported the taxonomic placement of Ascosphaera as sister to the core Onygenales. Several common protein domains were less abundant in A. apis compared with related ascomycete genomes, particularly cytochrome p450 and protein kinase domains. A novel gene family was identified that has expanded in some ascomycete lineages, but not others. We manually annotated genes with homologs in other fungal genomes that have known relevance to fungal virulence and life history. Functional categories of interest included genes involved in mating-type specification, intracellular signal transduction, and stress response. Computational and manual annotations have been made publicly available on the Bee Pests and Pathogens website.

Conclusions

This comprehensive transcriptome analysis substantially enhances our understanding of the A. apis genome and its expression during infection of honey bee larvae. It also provides resources for future molecular studies of chalkbrood disease and ultimately improved disease management.
Transcriptional profiling by cDNA-AFLP analysis showed differential transcript abundance in response to water stress in Populus hopeiensis
Authors: Song Yuepeng , Wang Zeliang , Bo Wenhao , Ren Yuanyuan , Zhang Zhiyi , Zhang Deqiang
Published: June 2012

Background

Drought is one of the main environmental factors limiting tree growth and productivity of plantation forests worldwide. Populus hopeiensis Hu et Chow is one of the most important commercial plantation tree species in China. However, the genes controlling drought tolerance in this species have not been identified or characterized. Here, we conducted differential expression analyses and identified a number of genes that were up- or downregulated in P. hopeiensis during water stress. To the best of our knowledge, this is the first comprehensive study of differentially expressed genes in water-stressed P. hopeiensis.

Results

Using the cDNA-AFLP detection technique, we used 256 primer combinations to identify differentially expressed genes in P. hopeiensis during water stress. In total, 415 transcript derived-fragments (TDFs) were obtained from 10× deep sequencing of 473 selected TDFs. Of the 415 TDFs, 412 were annotated by BLAST searches against various databases. The majority of these genes encoded products involved in ion transport and compartmentalization, cell division, metabolism, and protein synthesis. The TDFs were clustered into 12 groups on the basis of their expression patterns. Of the 415 reliable TDFs, the sequences of 35 were homologous to genes that play roles in short or long-term resistance to drought stress. Some genes were further selected for validation of cDNA-AFLP expression patterns using real-time PCR analyses. The results confirmed the expression patterns that were detected using the cDNA-AFLP technique.

Conclusion

The cDNA-AFLP technique is an effective and powerful tool for identifying candidate genes that are differentially expressed under water stress. We demonstrated that 415 TDFs were differentially expressed in water-stressed poplar. The products of these genes are involved in various biological processes in the drought response of poplar. The results of this study will aid in the identification of candidate genes of future experiments aimed at understanding this response of poplar.
Comparative transcriptome analysis between planarian Dugesia japonica and other platyhelminth species
Authors: Nishimura Osamu , Hirao Yukako , Tarui Hiroshi , Agata Kiyokazu
Published: June 2012

Background

Planarians are considered to be among the extant animals close to one of the earliest groups of organisms that acquired a central nervous system (CNS) during evolution. Planarians have a bilobed brain with nine lateral branches from which a variety of external signals are projected into different portions of the main lobes. Various interneurons process different signals to regulate behavior and learning/memory. Furthermore, planarians have robust regenerative ability and are attracting attention as a new model organism for the study of regeneration. Here we conducted large-scale EST analysis of the head region of the planarian Dugesia japonica to construct a database of the head-region transcriptome, and then performed comparative analyses among related species.

Results

A total of 54,752 high-quality EST reads were obtained from a head library of the planarian Dugesia japonica, and 13,167 unigene sequences were produced by de novo assembly. A new method devised here revealed that proteins related to metabolism and defense mechanisms have high flexibility of amino-acid substitutions within the planarian family. Eight-two CNS-development genes were found in the planarian (cf. C. elegans 3; chicken 129). Comparative analysis revealed that 91% of the planarian CNS-development genes could be mapped onto the schistosome genome, but one-third of these shared genes were not expressed in the schistosome.

Conclusions

We constructed a database that is a useful resource for comparative planarian transcriptome studies. Analysis comparing homologous genes between two planarian species showed that the potential of genes is important for accumulation of amino-acid substitutions. The presence of many CNS-development genes in our database supports the notion that the planarian has a fundamental brain with regard to evolution and development at not only the morphological/functional, but also the genomic, level. In addition, our results indicate that the planarian CNS-development genes already existed before the divergence of planarians and schistosomes from their common ancestor.
Reprogramming of gene expression during compression wood formation in pine: Coordinated modulation of S-adenosylmethionine, lignin and lignan related genes
Authors: Villalobos David P , Díaz-Moreno Sara M , Said El-Sayed S , Cañas Rafael A , Osuna Daniel , Van Kerckhoven Sonia H E , Bautista Rocío , Claros Manuel Gonzalo , Cánovas Francisco M , Cantón Francisco R
Published: June 2012

Background

Transcript profiling of differentiating secondary xylem has allowed us to draw a general picture of the genes involved in wood formation. However, our knowledge is still limited about the regulatory mechanisms that coordinate and modulate the different pathways providing substrates during xylogenesis. The development of compression wood in conifers constitutes an exceptional model for these studies. Although differential expression of a few genes in differentiating compression wood compared to normal or opposite wood has been reported, the broad range of features that distinguish this reaction wood suggest that the expression of a larger set of genes would be modified.

Results

By combining the construction of different cDNA libraries with microarray analyses we have identified a total of 496 genes in maritime pine (Pinus pinaster, Ait.) that change in expression during differentiation of compression wood (331 up-regulated and 165 down-regulated compared to opposite wood). Samples from different provenances collected in different years and geographic locations were integrated into the analyses to mitigate the effects of multiple sources of variability. This strategy allowed us to define a group of genes that are consistently associated with compression wood formation. Correlating with the deposition of a thicker secondary cell wall that characterizes compression wood development, the expression of a number of genes involved in synthesis of cellulose, hemicellulose, lignin and lignans was up-regulated. Further analysis of a set of these genes involved in S-adenosylmethionine metabolism, ammonium recycling, and lignin and lignans biosynthesis showed changes in expression levels in parallel to the levels of lignin accumulation in cells undergoing xylogenesisin vivoandin vitro.

Conclusions

The comparative transcriptomic analysis reported here have revealed a broad spectrum of coordinated transcriptional modulation of genes involved in biosynthesis of different cell wall polymers associated with within-tree variations in pine wood structure and composition. In particular, we demonstrate the coordinated modulation at transcriptional level of a gene set involved in S-adenosylmethionine synthesis and ammonium assimilation with increased demand for coniferyl alcohol for lignin and lignan synthesis, enabling a better understanding of the metabolic requirements in cells undergoing lignification.
Pregnancy and liver adenoma management: PALM-study
Authors: van Aalten Susanna M , Bröker Mirelle E E , Busschbach J J V , de Koning Harry J , de Man Robert A , Steegers Eric A P , Steyerberg Ewout W , Terkivatan Turkan , IJzermans Jan N M
Published: June 2012

Background

Hepatocellular adenoma (HCA) in pregnant women requires special considerations because of the risk of hormone induced growth and spontaneous rupture, which may threaten the life of both mother and child. Due to scarcity of cases there is no evidence-based algorithm for the evaluation and management of HCA during pregnancy. Most experts advocate that women with HCA should not get pregnant or advise surgical resection before pregnancy. Whether it is justified to deny a young woman a pregnancy, as the biological behavior may be less threatening than presumed depends on the incidence of HCA growth and the subsequent clinical events during pregnancy.

We aim to investigate the management and outcome of HCA during pregnancy and labor based on a prospectively acquired online database in the Netherlands.

Methods/design

The Pregnancy And Liver adenoma Management (PALM) - study is a multicentre prospective study in three cohorts of pregnant patients. In total 50 pregnant patients, ≥ 18 years of age with a radiologically and/or histologically proven diagnosis of HCA will be included in the study. Radiological diagnosis of HCA will be based on contrast enhanced MRI. Lesions at inclusion must not exceed 5 cm. The study group will be compared to a healthy control group of 63 pregnant patients and a group of 63 pregnant patients with diabetes mellitus without HCA. During their pregnancy HCA patients will be closely monitored by means of repetitive ultrasound (US) at 14, 20, 26, 32 and 38 weeks of gestation and 6 and 12 weeks postpartum. Both control groups will undergo US of the liver at 14 weeks of gestation to exclude HCA lesions in the liver. All groups will be asked to fill out quality of life related questionnaires.

Discussion

The study will obtain information about the behaviour of HCA during pregnancy, the clinical consequences for mother and child and the impact of having a HCA during pregnancy on the health related quality of life of these young women. As a result of this study we will propose a decision-making model for the management of HCA during pregnancy.

Trial registration

Dutch trial register: NTR3034
Molecular epidemiology of extended-spectrum β-lactamase-producing Escherichia coli in the community and hospital in Korea: emergence of ST131 producing CTX-M-15
Authors: Park Sun Hee , Byun Ji-Hyun , Choi Su-Mi , Lee Dong-Gun , Kim Si-Hyun , Kwon Jae-Cheol , Park Chulmin , Choi Jung-Hyun , Yoo Jin-Hong
Published: June 2012

Background

The prevalence of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli has been increased not only in the hospital but also in the community worldwide. This study was aimed to characterize ESBL- producing E. coli isolates and to investigate the molecular epidemiology of community isolates in comparison with hospital isolates at a single center in Korea.

Methods

A total of 142 ESBL-producing E. coli isolates were collected at Daejeon St Mary’s Hospital in Korea from January 2008 to September 2009. The ESBLs were characterized by PCR sequencing using specific primers. The genetic relatedness was determined by pulsed field gel electrophoresis (PFGE) and multilocus sequence typing (MLST).

Results

Of 142 isolates, 139 were positive for CTX-M type ESBLs; CTX-M-14 (n = 69, 49.6 %), CTX-M-15 (n = 53, 38.1 %) and both CTX-M-14 and -15 (n = 17, 12.2 %). CTX-M-14 and CTX-M-15 were detected in both community and hospital isolates whereas isolates producing both CTX-M14 and-15 were mainly identified in the hospital. CTX-M producing E. coli isolates were genetically heterogeneous, revealing 75 distinct PFGE types. By MLST, 21 distinctive STs including 5 major STs (ST131, ST405, ST38, ST10, and ST648) were identified. Major STs were distributed in both community and hospital isolates, and ST131 was the predominant clone regardless of the locations of acquisition. No specific major STs were confined to a single type of ESBLs. However, ST131 clones were significantly associated with CTX-M-15 and the majority of them were multidrug-resistant. Distinctively, we identified a hospital epidemic caused by the dissemination of an epidemic strain, ST131-PFGE type 10, characterized by multidrug resistance and co-producing both CTX-Ms with OXA-1 or TEM-1b.

Conclusions

The epidemiology of ESBL-producing E. coli is a complex and evolving phenomenon attributed to the horizontal transfer of genetic elements and clonal spread of major clones, predominantly ST131. The multidrug resistant ST131 clone producing CTX-M-15 has emerged as a major clone in both the community and hospital, suggesting the widespread of this epidemic clone in Korea.
Estimating coverage of a women’s group intervention among a population of pregnant women in rural Bangladesh
Authors: Younes Layla , Houweling Tanja AJ , Azad Kishwar , Costello Anthony , Fottrell Edward
Published: June 2012

Background

Reducing maternal and child mortality requires focused attention on better access, utilisation and coverage of good quality health services and interventions aimed at improving maternal and newborn health among target populations, in particular, pregnant women. Intervention coverage in resource and data poor settings is rarely documented. This paper describes four different methods, and their underlying assumptions, to estimate coverage of a community mobilisation women’s group intervention for maternal and newborn health among a population of pregnant women in rural Bangladesh.

Methods

Primary and secondary data sources were used to estimate the intervention’s coverage among pregnant women. Four methods were used: (1) direct measurement of a proxy indicator using intervention survey data; (2) direct measurement among intervention participants and modelled extrapolation based on routine longitudinal surveillance of births; (3) direct measurement among participants and modelled extrapolation based on cross-sectional measurements and national data; and (4) direct measurement among participants and modelled extrapolation based on published national data.

Results

The estimated women’s group intervention’s coverage among pregnant women ranged from 30% to 34%, depending on method used. Differences likely reflect differing assumptions and methodological biases of the various methods.

Conclusion

In the absence of complete and timely population data, choice of coverage estimation method must be based on the strengths and limitations of available methods, capacity and resources for measurement and the ultimate end user needs. Each of the methods presented and discussed here is likely to provide a useful understanding of intervention coverage at a single point in time and Methods 1 and 2 may also provide more reliable estimates of coverage trends.

Footnotes

1Unpublished data from three focus group discussions with women’s group members and facilitators participating in the Women’s Groups intervention.
Genome-wide association study identifies a maternal copy-number deletion in PSG11 enriched among preeclampsia patients
Authors: Zhao Linlu , Triche Elizabeth W , Walsh Kyle M , Bracken Michael B , Saftlas Audrey F , Hoh Josephine , Dewan Andrew T
Published: June 2012

Background

Specific genetic contributions for preeclampsia (PE) are currently unknown. This genome-wide association study (GWAS) aims to identify maternal single nucleotide polymorphisms (SNPs) and copy-number variants (CNVs) involved in the etiology of PE.

Methods

A genome-wide scan was performed on 177 PE cases (diagnosed according to National Heart, Lung and Blood Institute guidelines) and 116 normotensive controls. White female study subjects from Iowa were genotyped on Affymetrix SNP 6.0 microarrays. CNV calls made using a combination of four detection algorithms (Birdseye, Canary, PennCNV, and QuantiSNP) were merged using CNVision and screened with stringent prioritization criteria. Due to limited DNA quantities and the deleterious nature of copy-number deletions, it was decided a priori that only deletions would be selected for assay on the entire case-control dataset using quantitative real-time PCR.

Results

The top four SNP candidates had an allelic or genotypic p-value between 10-5 and 10-6, however, none surpassed the Bonferroni-corrected significance threshold. Three recurrent rare deletions meeting prioritization criteria detected in multiple cases were selected for targeted genotyping. A locus of particular interest was found showing an enrichment of case deletions in 19q13.31 (5/169 cases and 1/114 controls), which encompasses the PSG11 gene contiguous to a highly plastic genomic region. All algorithm calls for these regions were assay confirmed.

Conclusions

CNVs may confer risk for PE and represent interesting regions that warrant further investigation. Top SNP candidates identified from the GWAS, although not genome-wide significant, may be useful to inform future studies in PE genetics.