bluuebunny/crossref_metadata_2025 huggingface dataset:
Crossing the Line: Framing Appropriate Responses in the Diversity Classroom
Authors: Kirk Delaney J. , Durant Rita
Published: June 2009

The assignment for the students was to write honestly about how they felt regarding specific current events dealing with diversity. However, what resulted was a kairos moment for the professor—an instance that called for her best response even when she did not know what that was—when a student crossed the line in terms of respectful communication. Our story picks up there and follows us through our own emotions and dialogues as we worked to make sense as to why the student responded as he did and how the emotionally charged issue could be turned into a teachable moment around language, boundaries, understanding, and acceptance.
Integrating Service-Learning into an Introduction to Entrepreneurship Course
Authors: McCrea Elizabeth A.
Published: June 2009

Despite fairly widespread recognition that entrepreneurship occurs in both profit and nonprofit enterprises, a review of experiential learning techniques in entrepreneurship education does not explicitly mention service-learning. This omission may be because of a perceived lack of relevance of the pedagogy to entrepreneurship, the belief that inexperienced students are not interested in or capable of the work, and/or faculty concern about the approach’s time-consuming nature. Yet service-learning can be a powerful pedagogy for teaching the skills and body of knowledge pertaining to entrepreneurship. This article chronicles the author’s experience integrating service-learning into an introductory undergraduate entrepreneurship course and offers it as a model for others to adapt to their own preferences and teaching context. It includes the author’s rationale for using service-learning, an abridged course syllabus, sample student reflection assignments, a project grading rubric, and other course materials. Client and student feedback as well as the author’s personal reflections on the learning experience are also provided.
Service-Learning and Integrated Course Redesign
Authors: Flannery Brenda L. , Pragman Claudia H.
Published: June 2009

This article describes the process of redesigning a Principles of Management course to integrate a service-learning metaproject. The metaproject was Campus Kitchen, a food recovery and delivery program operated on a handful of university campuses across the United States. We used L. Dee Fink’s integrated course design approach as well as systems theory thinking to structure the redesign. The redesign was comprehensive starting with a scan and an evaluation of the many broad and specific situational factors shaping the course. This information required us to rethink everything from how we structured the delivery of course content to how we assessed learning and project outcomes. The article concludes with our reflections about what we learned by using this exciting, yet demanding, pedagogy.
Developing Enlightened Leaders for Industry and Community
Authors: Rhee Kenneth S. , Honeycutt Sigler Tracey
Published: June 2009

What does it take to develop enlightened leaders who can transform their organizations and communities? The quest to develop enlightened leaders who are self-aware, learning centered, adaptable, interpersonally competent, and team oriented is a challenge faced by many management programs. The Master of Science program in Executive Leadership and Organization Change (ELOC) was designed to develop enlightened leaders who can demonstrate outstanding and transformative leadership in their organizations and communities. The ELOC program is an innovative executive-level master’s program designed to develop leadership and change management skills through the pedagogical framework of ACT (action learning, competency development, and teamwork). ELOC students participated in a public engagement practicum course in the first summer of their program. A description of the ELOC program as well as a description of the service-learning course is presented. Key components in the program and course that facilitated the desired executive leadership development are highlighted.
Cultural Structures of the Persian Parents’ Ratings of ADHD
Authors: Ghanizadeh Ahmad , Jafari Peyman
Published: June 2009

Objective: The objective was to study the cultural structure of Farsi-speaking parents’ ratings with diagnostic definitions of ADHD. Method: The children with ADHD and their parents were interviewed. The parents rated their children on the Farsi-speaking parents’ ADHD rating questionnaire. Results: The principal components analysis extracted the two factors of inattention and hyperactivity— impulsivity. The items “often has trouble playing or enjoying leisure activities quietly,” “Is often ‘on the go’ or often acts as if ‘driven by a motor,’” and “Often talks excessively” were loaded on the impulsivity, not the hyperactivity factor. Conclusion: The Farsi version of the items of the DSM-IV ADHD criteria consisted of two separate factors of hyperactivity—impulsivity and inattentiveness. In addition, the factor of hyperactivity—impulsivity consisted of two separate factors of hyperactivity and impulsivity. There are some differences in the items loading from previous studies in other cultures. (J. of Att. Dis. 2010; 13(4) 369-373)
Genetic and Environmental Risks for High Blood Pressure Among African American Mothers and Daughters
Authors: Taylor Jacquelyn Y. , Maddox Rosanna , Chun Yi Wu
Published: June 2009

Objective: To determine the relationship between genetic and environmental lifestyle factors (physical activity and sodium) on blood pressure (BP) among African-American women. Method: In this cross-sectional study involving 108 African-American mothers and daughters from a Midwestern area, investigators obtained BP measurements, information on minutes of physical activity, amount of sodium intake, and buccal swab saliva samples. Results: Of the 4 single nucleotide polymorphisms (SNPs) on the sodium bicarbonate cotransporter gene (SLC4A5), rs8179526 had a statistically significant interaction with cytosine/thymine (C/T) genotype by sodium status on systolic BP (SBP; p = .0077). For gene × physical activity interaction, 2 significant interactions (cytosine/adenine [C/A] genotype by physical activity and adenine/adenine [A/A] genotype by physical activity, p = .0107 and p = .0171, respectively) on SBP and 1 on diastolic BP (DBP; A/A genotype by physical activity, p = .0233) were found on rs1017783. Two significant guanine/adenine [G/A] genotype by physical activity interactions were found on rs6731545 for SBP and DBP (p = .0160 and p = .0492, respectively). Discussion: A gene × environmental interaction with rs8179526 has a protective effect on SBP in African-American women with high sodium intake. Participants with C/T genotype of rs8179526 who consumed greater than 2,300 mg of sodium had lower SBP than those who consumed less than recommended. Women with thymine/thymine (T/T) genotype of rs8179526 who consumed greater than 2,300 mg had lower SBP than those who consumed less. Awareness of both the protective and deleterious properties of rs8179526 in African-American women may one day assist in determining appropriate treatment plans.
Negotiating the neurochemical self: anti-depressant consumption in women's recovery from depression
Authors: Fullagar Simone
Published: June 2009

Anti-depressant treatment can be viewed as an exercise of biopower that is articulated through policies and practices aimed at the reduction of depression, population healthcare costs and effects on labour force productivity. Drawing upon a feminist governmentality perspective, this article examines the discourses that shaped women's experiences of anti-depressant medication in an Australian qualitative study on recovery from depression. The majority of women had been prescribed anti-depressants to treat a chemical imbalance in the brain, manage symptoms and restore normal functioning. One-third of participants identified anti-depressants as helpful in their recovery, while two-thirds were either highly ambivalent about, or critical of, medication as a solution to depression. Thirty-one women who identified the `positive' benefits of anti-depressants actively constituted themselves as biomedical consumers seeking to redress a chemical imbalance. The problem of depression, the emergence of molecular science and the push for pharmacological solutions are contributing to the discursive formation of new subject positions — such as the neurochemically deficient self. Three themes were identified in relation to medication use, namely restoring normality, signifying recovery success and control/uncertainty. Anti-depressant medication offered women a normalized pathway to successful recovery that stood in stark contrast to the biologically deficient and morally failing self. These women's stories importantly reveal the gender relations and paradoxes arising from biopolitical technologies that shape selfhood for women in advanced liberal societies.
The tenacity of the coronary candidate: how people with familial hypercholesterolaemia construct raised cholesterol and coronary heart disease
Authors: Weiner Kate
Published: June 2009

This article considers how people with familial hypercholesterolaemia (FH), an inherited high cholesterol condition, construct FH, high cholesterol and coronary heart disease (CHD). These data are used to explore some of the more prevalent claims about the expansion of genetic explanations for health and illness and its implications. The article draws on 31 interviews with people with FH undertaken at a large lipid clinic, a specialist outpatient clinic, in the north of England. I argue that interviewees tended to distinguish between their own `hereditary' high cholesterol and other people's `lifestyle induced' high cholesterol as a way to establish their own lack of culpability for their condition. At the same time, however, they strongly emphasized the need to take care of themselves, in particular by adhering to appropriate dietary and lifestyle regimes. Interviewees' accounts of CHD were not strongly framed in genetic terms, but tended to conform to established lay notions encapsulated by the idea of the `coronary candidate'. In sum, having FH does not seem to transform these people's understandings of the causes of high cholesterol or CHD. Their experiences were largely accommodated within existing lay frameworks. The analysis contributes to a growing reappraisal of transformative narratives about genetic knowledge.
Young women's use of medicines: autonomy and positioning in relation to family and peer norms
Authors: Hansen Dana Lee , Hansen Ebba Holme , Holstein Bjørn E.
Published: June 2009

Medicine use among youths is widespread and on the increase. This is especially true for young females, whose utilization of a variety of medications grows considerably during the teenage years. This user perspective study aims to obtain a greater understanding of what young women perceive as the norms for medicine use at home and among peers, and how these perceptions are reflected in their own use of medicine. In-depth interviews were conducted with 20 young Danish women between the ages of 16 and 20. During the interviews, participants described their perceptions regarding usual medicine taking practices and ideas about appropriate medicine use within their family and peer group. Young women possessed a keen awareness of medicine-related norms, although medicine use was a topic only rarely discussed with others. At the interface of these themes pertaining to family and peer norms, a unifying concept involving growing autonomy in medicine use emerged. This concept consisted of three parts: the great influence of family norms when autonomy was limited, growing autonomy under changing influences and assertion of autonomy and positioning of own behaviour relative to the norm. This study's findings indicate that despite increases in autonomy in medicine use, normative perceptions continued to serve as important reference points for informants' own medicine taking behaviour. Practitioners involved in the health care and promotion of youth may benefit from an increased awareness of the influential role that perceived norms in peer and family contexts can play in young women's use of medicine.
Ethnic return migration and hierarchical nationhood
Authors: Seol Dong-Hoon , Skrentny John D.
Published: June 2009

Though nationhood is typically understood to be an equalizing or horizontal concept, the phenomenon of ethnic return migration has shown that states as well as societies can draw hierarchical distinctions between persons of the same ancestry. We demonstrate two dimensions — legal and social — of this `hierarchical nationhood' by analysing the South Korean policy and citizen attitudes regarding Joseonjok, or ethnic Korean Chinese citizens moving to South Korea. On the legal dimension, the Korean state defines Joseonjok as foreigners, allowing them entry mainly for low-wage jobs and excluding them from social benefits, while preferring them over other foreigners. The legal dimension of hierarchy is also institutionalized in a more favourable visa for Korean Americans that excludes Joseonjok. The social dimension of hierarchical nationhood is shown by public opinion data of Korean citizens towards Joseonjok foreign workers and data on reported experiences of discrimination. Finally, the authors show how Korea's hierarchical nationhood is shaped by economic and geopolitical goals, and describe analogous cases in Asia and Europe.
Migrants and ethnic minorities in post-Communist Europe
Authors: Triandafyllidou Anna
Published: June 2009

Migration movements within Central and Eastern Europe and the development of related migrant diasporas are to date relatively underresearched topics. Also, little attention has been paid to the process of identity negotiation that takes place between post-1989 migrants, their co-ethnic minorities native to the host state and the host state national majority. This article looks into the development of diasporic identities among Ukrainian and Romanian migrants in Poland and Hungary, focusing particularly on members of the political elite of these recent migrations. The informants included in this study form part of a civically and politically active small elite among the recent migrants. They have a double importance for their diaspora group: they play a constitutive part in the making of the diaspora, as they are the ones to set up the diaspora institutions, and they are also the ones who bear the brunt for carving an identity space in the country of settlement: between the native majority and their co-ethnic native minority. Of particular interest is how these first-generation elite immigrants negotiate their national identity within the triangle of country of origin, country of settlement and co-ethnic national minority (native in the host country). The methodology of critical discourse analysis is used to analyse in-depth interviews with 10 first-generation immigrants in the two countries.
Dementia-Friendly Architecture: Environments That Facilitate Wayfinding in Nursing Homes
Authors: Marquardt Gesine , Schmieg Peter
Published: June 2009

Spatial disorientation is a prime reason for institutionalization. The autonomy of the residents and their quality of life, however, is strongly linked with their ability to reach certain places within their nursing home. The physical environment has a great potential for supporting a resident’s wayfinding abilities. For this study, data were collected from 30 German nursing homes. Skilled nurses rated the resident’s ability to perform 5 wayfinding tasks. The architectural characteristics of the homes were analyzed and their impact on the resulting scores was tested for statistical significance using the Mann-Whitney U test (P < .05). Results confirm that people with advancing dementia are increasingly dependent on a compensating environment. The significant factors include a small number of residents per living area, the straight layout of the circulation system without any changes in direction, and the provision of only 1 living/dining room. These and additional results were transformed into architectural guidelines.
Neutrophil morphology and migration are affected by substrate elasticity
Authors: Oakes Patrick W. , Patel Dipan C. , Morin Nicole A. , Zitterbart Daniel P. , Fabry Ben , Reichner Jonathan S. , Tang Jay X.
Published: June 2009

To reach sites of inflammation, neutrophils execute a series of adhesion and migration events that include transmigration through the vascular endothelium and chemotaxis through the vicinal extracellular matrix until contact is made with the point of injury or infection. These in vivo microenvironments differ in their mechanical properties. Using polyacrylamide gels of physiologically relevant elasticity in the range of 5 to 100 kPa and coated with fibronectin, we tested how neutrophil adhesion, spreading, and migration were affected by substrate stiffness. Neutrophils on the softest gels showed only small changes in spread area, whereas on the stiffest gels they showed a 3-fold increase. During adhesion and migration, the magnitudes of the distortions induced in the gel substrate were independent of substrate stiffness, corresponding to the generation of significantly larger traction stresses on the stiffer gels. Cells migrated more slowly but more persistently on stiffer substrates, which resulted in neutrophils moving greater distances over time despite their slower speeds. The largest tractions were localized to the posterior of migrating neutrophils and were independent of substrate stiffness. Finally, the phosphatidylinositol 3-kinase inhibitor LY294002 obviated the ability to sense substrate stiffness, suggesting that phosphatidylinositol 3-kinase plays a mechanistic role in neutrophil mechanosensing.
Fpocket: An open source platform for ligand pocket detection
Authors: Le Guilloux Vincent , Schmidtke Peter , Tuffery Pierre
Published: June 2009

Background

Virtual screening methods start to be well established as effective approaches to identify hits, candidates and leads for drug discovery research. Among those, structure based virtual screening (SBVS) approaches aim at docking collections of small compounds in the target structure to identify potent compounds. For SBVS, the identification of candidate pockets in protein structures is a key feature, and the recent years have seen increasing interest in developing methods for pocket and cavity detection on protein surfaces.

Results

Fpocket is an open source pocket detection package based on Voronoi tessellation and alpha spheres built on top of the publicly available package Qhull. The modular source code is organised around a central library of functions, a basis for three main programs: (i) Fpocket, to perform pocket identification, (ii) Tpocket, to organise pocket detection benchmarking on a set of known protein-ligand complexes, and (iii) Dpocket, to collect pocket descriptor values on a set of proteins. Fpocket is written in the C programming language, which makes it a platform well suited for the scientific community willing to develop new scoring functions and extract various pocket descriptors on a large scale level. Fpocket 1.0, relying on a simple scoring function, is able to detect 94% and 92% of the pockets within the best three ranked pockets from the holo and apo proteins respectively, outperforming the standards of the field, while being faster.

Conclusion

Fpocket provides a rapid, open source and stable basis for further developments related to protein pocket detection, efficient pocket descriptor extraction, or drugablity prediction purposes. Fpocket is freely available under the GNU GPL license at http://fpocket.sourceforge.net.
A core-attachment based method to detect protein complexes in PPI networks
Authors: Wu Min , Li Xiaoli , Kwoh Chee-Keong , Ng See-Kiong
Published: June 2009

Background

How to detect protein complexes is an important and challenging task in post genomic era. As the increasing amount of protein-protein interaction (PPI) data are available, we are able to identify protein complexes from PPI networks. However, most of current studies detect protein complexes based solely on the observation that dense regions in PPI networks may correspond to protein complexes, but fail to consider the inherent organization within protein complexes.

Results

To provide insights into the organization of protein complexes, this paper presents a novel core-attachment based method (COACH) which detects protein complexes in two stages. It first detects protein-complex cores as the "hearts" of protein complexes and then includes attachments into these cores to form biologically meaningful structures. We evaluate and analyze our predicted protein complexes from two aspects. First, we perform a comprehensive comparison between our proposed method and existing techniques by comparing the predicted complexes against benchmark complexes. Second, we also validate the core-attachment structures using various biological evidence and knowledge.

Conclusion

Our proposed COACH method has been applied on two different yeast PPI networks and the experimental results show that COACH performs significantly better than the state-of-the-art techniques. In addition, the identified complexes with core-attachment structures are demonstrated to match very well with existing biological knowledge and thus provide more insights for future biological study.
The histone methyltransferase SUV420H2 and Heterochromatin Proteins HP1 interact but show different dynamic behaviours
Authors: Souza Patricia P , Völkel Pamela , Trinel Dave , Vandamme Julien , Rosnoblet Claire , Héliot Laurent , Angrand Pierre-Olivier
Published: June 2009

Background

Histone lysine methylation plays a fundamental role in chromatin organization and marks distinct chromatin regions. In particular, trimethylation at lysine 9 of histone H3 (H3K9) and at lysine 20 of histone H4 (H4K20) governed by the histone methyltransferases SUV39H1/2 and SUV420H1/2 respectively, have emerged as a hallmark of pericentric heterochromatin. Controlled chromatin organization is crucial for gene expression regulation and genome stability. Therefore, it is essential to analyze mechanisms responsible for high order chromatin packing and in particular the interplay between enzymes involved in histone modifications, such as histone methyltransferases and proteins that recognize these epigenetic marks.

Results

To gain insights into the mechanisms of SUV420H2 recruitment at heterochromatin, we applied a tandem affinity purification approach coupled to mass spectrometry. We identified heterochromatin proteins HP1 as main interacting partners. The regions responsible for the binding were mapped to the heterochromatic targeting module of SUV420H2 and HP1 chromoshadow domain. We studied the dynamic properties of SUV420H2 and the HP1 in living cells using fluorescence recovery after photobleaching. Our results showed that HP1 proteins are highly mobile with different dynamics during the cell cycle, whereas SUV420H2 remains strongly bound to pericentric heterochromatin. An 88 amino-acids region of SUV420H2, the heterochromatic targeting module, recapitulates both, HP1 binding and strong association to heterochromatin.

Conclusion

FRAP experiments reveal that in contrast to HP1, SUV420H2 is strongly associated to pericentric heterochromatin. Then, the fraction of SUV420H2 captured and characterized by TAP/MS is a soluble fraction which may be in a stable association with HP1. Consequently, SUV420H2 may be recruited to heterochromatin in association with HP1, and stably maintained at its heterochromatin sites in an HP1-independent fashion.
A complex selection signature at the human AVPR1B gene
Authors: Cagliani Rachele , Fumagalli Matteo , Pozzoli Uberto , Riva Stefania , Cereda Matteo , Comi Giacomo P , Pattini Linda , Bresolin Nereo , Sironi Manuela
Published: June 2009

Background

The vasopressin receptor type 1b (AVPR1B) is mainly expressed by pituitary corticotropes and it mediates the stimulatory effects of AVP on ACTH release; commonAVPR1Bhaplotypes have been involved in mood and anxiety disorders in humans, while rodents lacking a functional receptor gene display behavioral defects and altered stress responses.

Results

Here we have analyzed the two exons of the gene and the data we present suggest thatAVPR1Bhas been subjected to natural selection in humans. In particular, analysis of exon 2 strongly suggests the action of balancing selection in African populations and Europeans: the region displays high nucleotide diversity, an excess of intermediate-frequency alleles, a higher level of within-species diversity compared to interspecific divergence and a genealogy with common haplotypes separated by deep branches. This relatively unambiguous situation coexists with unusual features across exon 1, raising the possibility that a nonsynonymous variant (Gly191Arg) in this region has been subjected to directional selection.

Conclusion

Although the underlying selective pressure(s) remains to be identified, we consider this to be among the first documented examples of a gene involved in mood disorders and subjected to natural selection in humans; this observation might add support to the long-debated idea that depression/low mood might have played an adaptive role during human evolution.
Organization and evolution of two SIDER retroposon subfamilies and their impact on the Leishmania genome
Authors: Smith Martin , Bringaud Frédéric , Papadopoulou Barbara
Published: June 2009

Background

We have recently identified two large families of extinct transposable elements termed Short Interspersed DEgenerated Retroposons (SIDERs) in the parasitic protozoan Leishmania major. The characterization of SIDER elements was limited to the SIDER2 subfamily, although members of both subfamilies have been shown to play a role in the regulation of gene expression at the post-transcriptional level. Apparent functional domestication of SIDERs prompted further investigation of their characterization, dissemination and evolution throughout the Leishmania genus, with particular attention to the disregarded SIDER1 subfamily.

Results

Using optimized statistical profiles of both SIDER1 and SIDER2 subgroups, we report the first automated and highly sensitive annotation of SIDERs in the genomes of L. infantum, L. braziliensis and L. major. SIDER annotations were combined to in-silico mRNA extremity predictions to generate a detailed distribution map of the repeat family, hence uncovering an enrichment of antisense-oriented SIDER repeats between the polyadenylation and trans-splicing sites of intergenic regions, in contrast to the exclusive sense orientation of SIDER elements within 3'UTRs. Our data indicate that SIDER elements are quite uniformly dispersed throughout all three genomes and that their distribution is generally syntenic. However, only 47.4% of orthologous genes harbor a SIDER element in all three species. There is evidence for species-specific enrichment of SIDERs and for their preferential association, especially for SIDER2s, with different metabolic functions. Investigation of the sequence attributes and evolutionary relationship of SIDERs to other trypanosomatid retroposons reveals that SIDER1 is a truncated version of extinct autonomous ingi-like retroposons (DIREs), which were functional in the ancestral Leishmania genome.

Conclusion

A detailed characterization of the sequence traits for both SIDER subfamilies unveils major differences. The SIDER1 subfamily is more heterogeneous and shows an evolutionary link with vestigial DIRE retroposons as previously observed for the ingi/RIME and L1Tc/NARTc couples identified in the T. brucei and T. cruzi genomes, whereas no identified DIREs are related to SIDER2 sequences. Although SIDER1s and SIDER2s display equivalent genomic distribution globally, the varying degrees of sequence conservation, preferential genomic disposition, and differential association to orthologous genes allude to an intricate web of SIDER assimilation in these parasitic organisms.
Probing the endosperm gene expression landscape in Brassica napus
Authors: Huang Yi , Chen Liang , Wang Liping , Vijayan Kannan , Phan Sieu , Liu Ziying , Wan Lianglu , Ross Andrew , Xiang Daoquan , Datla Raju , Pan Youlian , Zou Jitao
Published: June 2009

Background

In species with exalbuminous seeds, the endosperm is eventually consumed and its space occupied by the embryo during seed development. However, the main constituent of the early developing seed is the liquid endosperm, and a significant portion of the carbon resources for the ensuing stages of seed development arrive at the embryo through the endosperm. In contrast to the extensive study of species with persistent endosperm, little is known about the global gene expression pattern in the endosperm of exalbuminous seed species such as crucifer oilseeds.

Results

We took a multiparallel approach that combines ESTs, protein profiling and microarray analyses to look into the gene expression landscape in the endosperm of the oilseed crop Brassica napus. An EST collection of over 30,000 entries allowed us to detect close to 10,000 unisequences expressed in the endosperm. A protein profile analysis of more than 800 proteins corroborated several signature pathways uncovered by abundant ESTs. Using microarray analyses, we identified genes that are differentially or highly expressed across all developmental stages. These complementary analyses provided insight on several prominent metabolic pathways in the endosperm. We also discovered that a transcription factor LEAFY COTYLEDON (LEC1) was highly expressed in the endosperm and that the regulatory cascade downstream of LEC1 operates in the endosperm.

Conclusion

The endosperm EST collection and the microarray dataset provide a basic genomic resource for dissecting metabolic and developmental events important for oilseed improvement. Our findings on the featured metabolic processes and the LEC1 regulatory cascade offer new angles for investigation on the integration of endosperm gene expression with embryo development and storage product deposition in seed development.
Pleiotropic effects of the twin-arginine translocation system on biofilm formation, colonization, and virulence in Vibrio cholerae
Authors: Zhang Lijuan , Zhu Zhaoqin , Jing Huaiqi , Zhang Jingyun , Xiong Yanwen , Yan Meiying , Gao Shouyi , Wu Long-Fei , Xu Jianguo , Kan Biao
Published: June 2009

Background

The Twin-arginine translocation (Tat) system serves to translocate folded proteins, including periplasmic enzymes that bind redox cofactors in bacteria. The Tat system is also a determinant of virulence in some pathogenic bacteria, related to pleiotropic effects including growth, motility, and the secretion of some virulent factors. The contribution of the Tat pathway to Vibrio cholerae has not been explored. Here we investigated the functionality of the Tat system in V. cholerae, the etiologic agent of cholera.

Results

In V. cholerae, the tatABC genes function in the translocation of TMAO reductase. Deletion of the tatABC genes led to a significant decrease in biofilm formation, the ability to attach to HT-29 cells, and the ability to colonize suckling mouse intestines. In addition, we observed a reduction in the output of cholera toxin, which may be due to the decreased transcription level of the toxin gene in tatABC mutants, suggesting an indirect effect of the mutation on toxin production. No obvious differences in flagellum biosynthesis and motility were found between the tatABC mutant and the parental strain, showing a variable effect of Tat in different bacteria.

Conclusion

The Tat system contributes to the survival of V. cholerae in the environment and in vivo, and it may be associated with its virulence.
Epidemiologic heterogeneity of common mood and anxiety disorders over the lifecourse in the general population: a systematic review
Authors: Nandi Arijit , Beard John R , Galea Sandro
Published: June 2009

Background

Clinical evidence has long suggested there may be heterogeneity in the patterns and predictors of common mood and anxiety disorders; however, epidemiologic studies have generally treated these outcomes as homogenous entities. The objective of this study was to systematically review the epidemiologic evidence for potential patterns of heterogeneity of common mood and anxiety disorders over the lifecourse in the general population.

Methods

We reviewed epidemiologic studies examining heterogeneity in either the nature of symptoms experienced ("symptom syndromes") or in patterns of symptoms over time ("symptom trajectories"). To be included, studies of syndromes were required to identify distinct symptom subtypes, and studies of trajectories were required to identify distinct longitudinal patterns of symptoms in at least three waves of follow-up. Studies based on clinical or patient populations were excluded.

Results

While research in this field is in its infancy, we found growing evidence that, not only can mood and anxiety disorders be differentiated by symptom syndromes and trajectories, but that the factors associated with these disorders may vary between these subtypes. Whether this reflects a causal pathway, where genetic or environmental factors influence the nature of the symptom or trajectory subtype experienced by an individual, or whether individuals with different subtypes differed in their susceptibility to different environmental factors, could not be determined. Few studies addressed issues of comorbidity or transitions in symptoms between common disorders.

Conclusion

Understanding the diversity of these conditions may help us identify preventable factors that are only associated with some subtypes of these common disorders.
Integrated application of uniform design and least-squares support vector machines to transfection optimization
Authors: Pan Jin-Shui , Hong Mei-Zhu , Zhou Qi-Feng , Cai Jia-Yan , Wang Hua-Zhen , Luo Lin-Kai , Yang De-Qiang , Dong Jing , Shi Hua-Xiu , Ren Jian-Lin
Published: June 2009

Background

Transfection in mammalian cells based on liposome presents great challenge for biological professionals. To protect themselves from exogenous insults, mammalian cells tend to manifest poor transfection efficiency. In order to gain high efficiency, we have to optimize several conditions of transfection, such as amount of liposome, amount of plasmid, and cell density at transfection. However, this process may be time-consuming and energy-consuming. Fortunately, several mathematical methods, developed in the past decades, may facilitate the resolution of this issue. This study investigates the possibility of optimizing transfection efficiency by using a method referred to as least-squares support vector machine, which requires only a few experiments and maintains fairly high accuracy.

Results

A protocol consists of 15 experiments was performed according to the principle of uniform design. In this protocol, amount of liposome, amount of plasmid, and the number of seeded cells 24 h before transfection were set as independent variables and transfection efficiency was set as dependent variable. A model was deduced from independent variables and their respective dependent variable. Another protocol made up by 10 experiments was performed to test the accuracy of the model. The model manifested a high accuracy. Compared to traditional method, the integrated application of uniform design and least-squares support vector machine greatly reduced the number of required experiments. What's more, higher transfection efficiency was achieved.

Conclusion

The integrated application of uniform design and least-squares support vector machine is a simple technique for obtaining high transfection efficiency. Using this novel method, the number of required experiments would be greatly cut down while higher efficiency would be gained. Least-squares support vector machine may be applicable to many other problems that need to be optimized.
Effective and cheap removal of leukocytes and platelets from Plasmodium vivax infected blood
Authors: Sriprawat Kanlaya , Kaewpongsri Supaporn , Suwanarusk Rossarin , Leimanis Mara L , Lek-Uthai Usa , Phyo Aung Pyae , Snounou Georges , Russell Bruce , Renia Laurent , Nosten François
Published: June 2009

Background

Investigations of Plasmodium vivax are restricted to samples collected from infected persons or primates, because this parasite cannot be maintained in in vitro cultures. Contamination of P. vivax isolates with host leukocytes and platelets is detrimental to a range of ex vivo and molecular investigations. Easy-to-produce CF11 cellulose filters have recently provided us with an inexpensive method for the removal of leukocytes and platelets. This contrasted with previous reports of unacceptably high levels of infected red blood cell (IRBC) retention by CF11. The aims of this study were to compare the ability of CF11 cellulose filters and the commercial filter Plasmodipur at removing leukocyte and platelet, and to investigate the retention of P. vivax IRBCs by CF11 cellulose filtration.

Methods and Results

Side-by-side comparison of six leukocyte removal methods using blood samples from five healthy donor showed that CF11 filtration reduced the mean initial leukocyte counts from 9.4 × 103 per μl [95%CI 5.2–13.5] to 0.01 × 103 [95%CI 0.01–0.03]. The CF11 was particularly effective at removing neutrophils. CF11 treatment also reduced initial platelet counts from 211.6 × 103 per μl [95%CI 107.5–315.7] to 0.8 × 103 per μl [95%CI -0.7–2.2]. Analysis of 30 P. vivax blood samples before and after CF11 filtration showed only a minor loss in parasitaemia (≤ 7.1% of initial counts). Stage specific retention of P. vivax IRBCs was not observed.

Conclusion

CF11 filtration is the most cost and time efficient method for the production of leukocyte- and platelet-free P. vivax-infected erythrocytes from field isolates.
An exo-cell assay for examining real-time γ-secretase activity and inhibition
Authors: Shelton Christopher C , Tian Yuan , Frattini Mark G , Li Yue-Ming
Published: June 2009

γ-Secretase is an aspartyl protease that cleaves multiple substrates that are involved in broad biological processes ranging from stem cell development to neurodegeneration. The investigation of γ-secretase has been limited by currently available assays that require genetic or biochemical manipulation in the form of substrate transfection or membrane preparation. Here we report an exo-cell assay that is capable of characterizing γ-secretase activity in any cellular system without limitation. Using a highly active, recombinant substrate this assay can quickly and easily ascertain the status of γ-secretase activity in cell systems and patient samples. We have applied this method to determine the activity of γ-secretase in primary cell samples where transfection and/or membrane isolation are not viable options. Importantly, it allows for the detection of real time γ-secretase activity after inhibitor or drug treatment. The application of this assay to determine the role of γ-secretase in physiological and pathological conditions will greatly facilitate our characterization of this complex protease and help in the development and evaluation of γ-secretase-targeted therapies in Alzheimer's disease or a variety of neoplasms.
The bioactivity of plant extracts against representative bacterial pathogens of the lower respiratory tract
Authors: Bocanegra-García Virgilio , del Rayo Camacho-Corona María , Ramírez-Cabrera Mónica , Rivera Gildardo , Garza-González Elvira
Published: June 2009

Background

Lower respiratory tract infections are a major cause of illness and death. Such infections are common in intensive care units (ICU) and their lethality persists despite advances in diagnosis, treatment and prevention. In Mexico, some plants are used in traditional medicine to treat respiratory diseases or ailments such as cough, bronchitis, tuberculosis and other infections. Medical knowledge derived from traditional societies has motivated searches for new bioactive molecules derived from plants that show potent activity against bacterial pathogens. Therefore, the aim of this study was to evaluate the effect of hexanic, chloroformic (CLO), methanolic (MET) and aqueous extracts from various plants used in Mexican traditional medicine on various microorganisms associated with respiratory disease.

Methods

thirty-five extracts prepared from nine plants used in Mexican traditional medicine for the treatment of respiratory infections were evaluated against 15 control bacterial species and clinical isolates.

Results

Both chloroformic (CLO) and methanolic (MET) extracts of Larrea tridentata were active against Methicillin-resistant S. aureus, B. subtilis and L. monocytogenes. A MET extract of L. tridentata was also active against S. aureus, S. pneumoniae, S. maltophilia, E. faecalis and H. influenzae and the CLO extract was active against A. baumannii. An Aqueous extract of M. acumitata and a MET extract of N. officinale were active against S. pneumoniae. CLO and MET extracts of L. tridentata were active against clinical isolates of S. aureus, S. pneumoniae and E. faecalis.

Conclusion

Overall, our results support the potential use of L. tridentata as a source of antibacterial compounds.
Nerve growth factor and receptor expression in rheumatoid arthritis and spondyloarthritis
Authors: Barthel Christian , Yeremenko Nataliya , Jacobs Roland , Schmidt Reinhold E , Bernateck Michael , Zeidler Henning , Tak Paul-Peter , Baeten Dominique , Rihl Markus
Published: June 2009

Introduction

We previously described the presence of nerve growth factor receptors in the inflamed synovial compartment. Here we investigated the presence of the corresponding nerve growth factors, with special focus on nerve growth factor (NGF).

Methods

mRNA expression levels of four ligands (NGF, brain derived growth factor (BDNF), neurotrophin (NT)-3, NT-4) and their four corresponding receptors (tyrosine kinase (trk) A, trkB, trkC, NGFRp75) were determined in the synovial fluid (SF) cells of 9 patients with rheumatoid arthritis (RA) and 16 with spondyloarthritis (SpA) and compared with 7 osteoarthritis (OA) patients. NGF was also determined in synovial tissue (ST) biopsies of 10 RA and 10 SpA patients. The production of NGF by monocytes and lymphocytes was assessed by flow cytometry of SF cells, synovial tissue derived fibroblast-like synoviocytes (FLS) were assessed by ELISA on culture supernatant.

Results

SF cell analysis revealed a clear BDNF and NGF mRNA expression, with significantly higher NGF expression in RA and SpA patients than in the OA group. NGF expression was higher in ST samples of RA as compared to SpA. Using intracellular FACS analysis, we could demonstrate the presence of the NGF protein in the two inflammatory arthritis groups on both CD3+ T lymphocytes and CD14+ cells, i.e. monocytes/macrophages, whereas cultured FLS did not produce NGF in vitro.

Conclusions

Neurotrophins and especially NGF are expressed in the synovial fluid and tissue of patients with peripheral synovitis. The presence of neurotrophins as well as their receptors, in particular the NGF/trkA-p75 axis in peripheral synovitis warrants further functional investigation of their active involvement in chronic inflammatory arthritis.
The spatial distribution of radiodense breast tissue: a longitudinal study
Authors: Pinto Pereira Snehal M , McCormack Valerie A , Moss Sue M , dos Santos Silva Isabel
Published: June 2009

Introduction

Mammographic breast density is one of the strongest known markers of susceptibility to breast cancer. To date research into density has relied on a single measure (for example, percent density (PD)) summarising the average level of density for the whole breast, with no consideration of how the radiodense tissue may be distributed. This study aims to investigate the spatial distribution of density within the breast using 493 mammographic images from a sample of 165 premenopausal women (~3 medio-lateral oblique views per woman).

Methods

Each breast image was divided into 48 regions and the PD for the whole breast (overall PD) and for each one of its regions (regional PD) was estimated. The spatial autocorrelation (Moran's I value) of regional PD for each image was calculated to investigate spatial clustering of density, whether the degree of clustering varied between a woman's two breasts and whether it was affected by age and other known density correlates.

Results

The median Moran's I value for 165 women was 0.31 (interquartile range: 0.26, 0.37), indicating a clustered pattern. High-density areas tended to cluster in the central regions of the breast, regardless of the level of overall PD, but with considerable between-woman variability in regional PD. The degree of clustering was similar between a woman's two breasts (mean within-woman difference in Moran's I values between left and right breasts = 0.00 (95% confidence interval (CI) = -0.01, 0.01); P = 0.76) and did not change with aging (mean within-woman difference in I values between screens taken on average 8 years apart = 0.01 (95% CI = -0.01, 0.02); P = 0.30). Neither parity nor age at first birth affected the level of spatial autocorrelation of density, but increasing body mass index (BMI) was associated with a decrease in the degree of spatial clustering.

Conclusions

This study is the first to demonstrate that the distribution of radiodense tissue within the breast is spatially autocorrelated, generally with the high-density areas clustering in the central regions of the breast. The degree of clustering was similar within a woman's two breasts and between women, and was little affected by age or reproductive factors although it declined with increasing BMI.
Implementation of the Quality Oncology Practice Initiative at a University Comprehensive Cancer Center
Authors: Blayney Douglas W. , McNiff Kristen , Hanauer David , Miela Gretchen , Markstrom Denise , Neuss Michael
Published: June 2009

Purpose

The Quality Oncology Practice Initiative (QOPI) is a voluntary program developed by the American Society of Clinical Oncology (ASCO) to aid oncology practices in quality self-assessment. Few academic cancer centers have been QOPI participants.

Methods

We implemented the QOPI process at the University of Michigan Comprehensive Cancer Center, a large, hospital-based academic cancer center, and report our experience with five rounds of data collection. Patient medical records were selected using QOPI-specified procedures and abstracted locally; results were entered into an ASCO-maintained database and analyzed.

Results

Abstractors who were not directly involved with patient care required an average of 62.3 minutes per medical record (4.7 minutes per data element) to abstract data. We found that compliance with quality measures was uniformly high when measures were structured into our electronic medical record. Results from other measures, including those measuring chemotherapy administration in the last 2 weeks of life, were initially markedly different from those reported by other QOPI participants. Our practice changed toward the QOPI national practice norm after a presentation of the results at a faculty research conference. We found that other measures were consistently greater than 90%, including disease-specific diagnosis and treatment measures.

Conclusion

Measuring and showing performance data to physicians was sufficient to change some aspects of physician behavior. Improvement in other measures requires structural practice changes. QOPI, an oncologist-developed system, can be adapted for use in practice improvement at an academic medical center.