bluuebunny/crossref_metadata_2025 huggingface dataset:
Special Section: The Critical Role of the Dialectic in Viable Metatheory
Authors: Anchin Jack C.
Published: December 2008

Henriques (2008) persuasively argues that his Tree of Knowledge (ToK) System provides a more viable alternative to Wilson's (1998) consilience model as a framework for integrating knowledge generated by the natural sciences, social sciences, and humanities. I selectively deconstruct the ToK System to demonstrate that its capacity to solve problems through integrative solutions and to advance interdisciplinary conjunctions derives from its pervasive dialectical ontology and epistemology. Emphasis is on analyzing Behavioral Investment Theory, the Justification Hypothesis (the JH), and Henriques' solution to the problem of psychology—all essential to unifying the three great branches of learning. I also suggest directions for further development of the JH, rooted in the psychoanalytic classical—relational dialectic. Potent implications of Henriques' formulations for epistemological bridging within psychology and for multidisciplinary integration are discussed.
Special Section: Pruning the Tree of Knowledge
Authors: Katzko Michael W.
Published: December 2008

There are several intellectual projects embedded within the Tree of Knowledge (ToK) System and they tend to blur together at critical junctions. The aim of this commentary is to identify some of these strands of analysis and their implicit metaphysical presuppositions. It is argued that the presuppositions are not consistent across the different strands. The strands can continue to be pursued independently, insofar as they have distinct purposes. However, the incompatible presuppositions are surfacing in the effort to combine the strands into a single system of analysis.
On the Possibility of Unification
Authors: Goertzen Jason R.
Published: December 2008

In this article it is argued that—in spite of contrary semantic and substantive criticisms that have been put forward—the crisis in psychology is a real problem facing the discipline. The crisis is discussed as a nexus of philosophical tensions, which divide individuals, departments, and psychological organizations, and which are therefore primarily responsible for the fragmentation of psychology. Some of the major existing analyses of the crisis are critiqued, and it is subsequently concluded that even the major analyses themselves perpetuate the crisis since they fail to direct unification efforts to the underlying philosophical tensions without at least approaching them with unbracketed a priori theoretical commitments and assumptions. The article concludes with a discussion of the difficulties facing those psychologists who take on the program of research necessary for resolving the crisis in psychology.
Productivity of Rural Credit
Authors: Sriram M. S.
Published: December 2008

The policy intervention in agriculture has been credit driven. This is even more pronounced in the recent interventions made by the State in the package announced for distressed farmers, in doubling agricultural credit, providing subvention and putting an upper cap on interest rates for agricultural loans. We use existing literature and data to argue that the causality of agricultural output with increased doses of credit cannot be clearly established.

We argue that Indian agriculture is undergoing a fundamental change wherein the technology and inputs are moving out of the hands of the farmers to external suppliers. This, over a period of time may have resulted in the de–skilling of farmers and without adequate public investments in support services and without appropriate risk mitigation products, has created a near–crisis in agriculture. Thus, we argue that policy interventions have to be necessarily patient and holistic.

Looking specifically at the rural financial markets using some primary data, we argue that it is necessary to understand the rural financial markets from the demand side. We conclude the article by identifying some directions in which the policy intervention could move, keeping the overall rural economy in view rather than being focussed only on agriculture.
The Apna Bazar Cooperative
Authors: Chaudhary Rajinder
Published: December 2008

When debate on economic policy in the Third World countries like India is confined to ways of privatization and its critique, it is useful to document and highlight other forms of economic organization. Notionally, a cooperative is an alternate form of economic organization, but it is not discussed frequently in public debate or economic theory texts. One reason for this could be that at least in India, largely, cooperatives have a public image of either being a sham or being government–managed. The present study is part of an endeavour to critically examine this image and has led to documentation of some self–reliant, real cooperatives of long standing in a variety of settings. This is a case study of a 58 year old, self–reliant and member controlled consumer cooperative. Besides checking on its cooperative and self–reliant character, its structure and processes have also been documented in some detail to aid in its replication. This process has led to a more critical reading.
Court Reporters: A Viable Solution for the Challenges of Focus Group Data Collection?
Authors: Scott Shannon D. , Sharpe Heather , O'Leary Kathy , Dehaeck Ulrike , Hindmarsh Kathryn , Moore John Garry , Osmond Martin H.
Published: December 2008

Focus group interviews are a common approach to data collection in qualitative research projects. They are, however, a method with the potential for methodological and pragmatic difficulties, many of which stem from transcribing focus group data from an audiotape. An alternative to postinterview transcription is the use of a court reporter. Advantages found using court reporters were increased accuracy, timely receipt of transcripts, less distraction for focus group facilitators, guaranteed confidentiality, time saved reviewing transcripts, and convenience. Because court reporters do not traditionally work in health research, there might be issues with medical terminology that require diligence on the part of the researcher to ensure that jargon is appropriately identified and transcribed. Using court reporters in rural areas might be cost-prohibitive because of travel expenses. Court reporters offer a viable and worthwhile approach to data transcription, and in our experience, have provided our research team with rich and accurate data.
Unit Characteristics and Patient Satisfaction
Authors: Seago Jean Ann
Published: December 2008

The purpose of this study was to discover if there was relationship between nurse perception of autonomy, control over practice, or relationships with physicians and patient satisfaction with care related to pain management, teaching, or physical care on medical surgical units. The study design was correlational, descriptive, and cross-sectional. The hospital sample was a purposive convenience sample of acute care hospitals in California, with a total of 21 hospitals, 60 medical surgical nursing units, 314 nurses, and 470 patients. Findings indicated that higher patient functional status and having a doctor in the hospital 24 hours/day were related to patient satisfaction with pain management. Lower nurse perception of autonomy, having a doctor in the hospital 24 hours/day, and higher number of patient years of education were related to higher patient satisfaction with teaching. Lower total hours worked by the nurses was related to higher patient satisfaction with physical care.
Modeling the Effects of Diversity Experiences and Multiple Capitals on Latina/o College Students' Academic Self-Confidence
Authors: Núñez Anne-Marie
Published: December 2008

This study develops a model predicting academic self-confidence for 2nd-year Latina/o college students. Findings indicate that forms of academic, cultural, social, and intercultural capital (the capacity to negotiate diverse racial and ethnic environments) are positively associated with academic self-confidence. The prevalence of negative cross-racial interactions is negatively associated with academic self-confidence. The study's results suggest policy and programming implications to support the development of Latina/o students' academic self-confidence.
Are Federal Dollars Bearing Fruit?
Authors: Willison Scott , Bong Seok Jang
Published: December 2008

This study considers 4 years of national College Assistance Migrant Program (CAMP) data from programs located across the United States. Findings reveal that 81% of the migrant college students served by CAMP continue to study a 2nd year. Researchers found that the success of high-achieving programs can overshadow less effective ones and, thus, recommend that future program reviews be concerned with the whole as well as the parts. The development of program evaluation criteria is recommended.
The Vanishing Latino Male in Higher Education
Authors: Saenz Victor B. , Ponjuan Luis
Published: December 2008

Latino male students are “vanishing” from the American education pipeline, a trend that is especially evident at the secondary and postsecondary levels. The question of why Latino males are vanishing from America's colleges is complex, and this scholarly article explores some of the socio-cultural factors, peer dynamics, and labor force demands that may be conspiring to propagate this trend. The authors expound on various theoretical and empirical explanations for this persisting and troubling trend.
Latino Immigrant Access to Higher Education in a Bipolar Context of Reception
Authors: Flores Stella M. , Chapa Jorge
Published: December 2008

This study evaluates the recent political context in which foreign-born noncitizen immigrants in the United States exist, their traditional and new settlement locations of residence, and where they are most likely to use public policies that encourage college enrollment. Legislative trends indicate that state activity continues to evolve around the issue of college access for undocumented immigrants, whereas U.S. congressional activity on the federal version of this educational legislation and general immigration policy remains unresolved.
Increasing Latina/o Students' Baccalaureate Attainment
Authors: Oseguera Leticia , Locks Angela M. , Vega Irene I.
Published: December 2008

Notwithstanding years of retention efforts, graduation rates of Latinas/os remain alarmingly low. The purpose of this review is threefold. First, the authors go beyond traditional theory and highlight those scholars who shed new information on retention for Latina/o students. Second, they summarize factors that specifically affect Latina/o students. Third, promising practices for effectively retaining Latina/o students in higher education institutions are highlighted.
Treatment of Dilated Venous Bypass Grafts With an Expanded Polytetrafluoroethylene-covered Nitinol Endoprosthesis
Authors: van Vugt R. , Kruse R.R. , Fritschy W.M. , Moll F.L.
Published: December 2008

An above-knee femoropopliteal bypass graft constructed of great saphenous vein became dilated in 2 patients 12 and 25 years after surgery. Both patients had several concomitant disorders. The dilations were treated by insertion of an expanded polytetrafluoroethylene-covered nitinol endoprosthesis. There were no major procedural complications. One minor endoleak that developed immediately after endograft placement resolved within 6 weeks. The leg swelling subsided, and the endoprostheses have remained patent for 18 and 24 months, respectively. To our knowledge, these were the first cases in which an endoprosthesis was used to treat dilation of a venous bypass graft.
Communication, Coordination, and Camaraderie in World of Warcraft
Authors: Chen Mark G.
Published: December 2008

In applying traditional game theory to multiplayer computer games, not enough attention has been given to actual player practice in local settings. To do this, the author describes a team of players in the massively multiplayer online role-playing game World of Warcraft. This motley group learned how to defeat an end-game dungeon through collaborative improvements on communication and coordination. It focused on sustaining and building player relationships and learning together rather than the accepted norm of obtaining magical items. Trust was forged through a desire to ``hang out and have fun'' and was evidenced by the joviality of their communication. The group's ability to reflect and be consistent about its desires for camaraderie allowed it to recover from a poor performing night, which threatened to disband the group. The team's success depended on its ability to define and retain a coherent group identity and establish shared social incentives rather than individual incentives for participation.
Oh, We've Got Trouble! Right Here in Ravenna City
Authors: Tooms Autumn , Lugg Catherine A.
Published: December 2008

Currently in his second year as assistant principal, Jack Andrews is facing conflicting pressures of leadership related to his perception of career mobility and the tensions caused by a pervasively heterosexist, sexist, and homophobic culture in his school. This case raises questions regarding the purpose of school in terms of social justice, equality and liability, and curriculum outside of the lessons geared toward standardized testing. In addition, this case provokes reflection on the relationship between community values and the politics related to leadership and career mobility.
Victim Narratives, Legal Representation, and Domestic Violence Civil Protection Orders
Authors: Durfee Alesha
Published: December 2008

The objective of this study is to examine the relationship between the use of legal representation and domestic violence civil protection order hearing outcomes. In most jurisdictions, the protection order process has been bureaucratized and carefully structured to facilitate access for victims without legal representation; however, results of an analysis of protection order cases indicates that even with “victim-friendly” procedures and forms, individuals without legal representation are significantly less likely to have their requests for protection orders granted. The implications of these findings are discussed in the context of institutional inequalities in the American legal system.
Predicting Fear of Crime
Authors: Franklin Cortney A. , Franklin Travis W.
Published: December 2008

The current research tests the vulnerability, disorder, and social integration models to determine their relative predictive capacity across separate female and male citizen samples on fear of crime. Although previous literature typically includes gender as a control variable, the present analysis goes beyond this to determine whether the models function differently according to gender. Findings indicate that there are in fact significant differences in predictors of female and male fear of crime. Increased age reduces fear for women but not men, and increased income leads to higher levels of fear for men but lower levels for women. Theoretical implications and future research directions are discussed.
Intimate Partner Violence Perpetration Among College Students
Authors: Nabors Erin L. , Jasinski Jana L.
Published: December 2008

This study examines the relationships between college students' attitudes regarding gender roles and gendered violence and their perpetration of intimate partner violence. Although findings from previous studies demonstrate associations between gender role and gendered violence-related attitudes and intimate partner violence, research to date fails to fully explore these associations. In an attempt to fill this void, the current study looks at attitudes before and after perpetration is reported to determine whether attitudes precede or follow perpetration. Additionally, the study examines these relationships among a previously unexplored set of attitudes within the physical violence literature—those related to chivalry. Findings suggest that the relationships between attitudes and intimate partner violence are more complex than prior research indicates and differ for female and male college students.
Intersections of Immigration and Domestic Violence
Authors: Erez Edna , Adelman Madelaine , Gregory Carol
Published: December 2008

Feminist criminologists have helped to criminalize domestic violence in the United States and elsewhere. With this significant accomplishment, scholars also have critiqued the intended and unintended consequences of such reliance on the state for women's safety. One such critique reveals the intersectionality of social inequalities, social identities, and domestic violence. Here, the authors analyze the relationship between immigration and domestic violence based on interviews with 137 immigrant women in the United States from 35 countries. They find that immigration shapes how women understand domestic violence, their access to resources, and responses to domestic violence. This project documents observed dynamics of structural intersectionality for immigrant women as national origin and citizenship status are considered as another layer of identity politics and marginalization in relation to domestic violence.
“Being Shut Out in the Dark”
Authors: Skinner Tina , Taylor Helen
Published: December 2008

In Britain in the past 25 years there have been substantial changes in police responses to survivors of rape and sexual assault. Little is known about the impact of these changes on young survivors. In this article, the authors draw on interviews with nine youth aged 14 to 16 who reported a sexual offense to one police service in England. They discuss the degree of choice that young people get from the point of making the decision to report to the police through to the finalization of the case. Findings indicate that victims had limited choice at each stage of the criminal justice process. This is an outcome of a criminal justice system that continues to prioritize professional power over victims' needs and rights. The authors conclude by asserting the need for victims to be given the opportunity to participate actively in criminal justice processes.
Gendered Justice
Authors: Messing Jill Theresa , Heeren John W.
Published: December 2008

This research examines a newspaper sample of men and women who killed multiple people in a single domestic altercation during the years 1993 to 2002. As all these perpetrators of multiple domestic homicide are eligible to be capitally tried, differences in capital sentencing are examined using bivariate statistics and descriptive, case-oriented analyses. Women who kill their children using a knife or firearm are disproportionately sentenced to death, whereas men who kill in the context of a separation are granted leniency in regard to the death penalty. The interaction between the gender of the offender and the crime committed is discussed.
POLICEwomen or PoliceWOMEN?
Authors: Rabe-Hemp Cara E.
Published: December 2008

This work originates from a set of accounts given by female police officers to determine how they construct their identity and their image of themselves in relation to their gender, as they talk about their roles as police, and the broader roles of men and women in society. Despite policewomen's fight for equality in policing, women not only differentiated themselves from their male counterparts, but also described “doing gender” (West & Zimmerman, 1987) and “doing police work” collaboratively. Women actively resisted and adopted stereotypical norms of femininity and policing, broadening their opportunities for work in the male dominated occupation while reinforcing their traditional conception of gender difference.
Bringing Light to Finland: The Clerical Estate and Enlightenment Literature in Eighteenth-Century Finland
Authors: Ahokas Minna
Published: December 2008

In eighteenth-century Finland, the clergy was one of the dominant, elite groups that took part in all the forums of the early public sphere. In the Lutheran realm of Sweden, the history of reading is inseparable from the Lutheran Church's persistent teaching of the Catechism. Besides their role as preachers and teachers, several Finnish churchmen took an active role in the Finnish book trade as well. When, by the end of the eighteenth century, book production increased and secular literature challenged religious literature, the works of philosophers linked to Enlightenment were among the new literature that found its way into Finnish book collections so far dominated by religious books. Both preventive and post-publication censorship was used to prevent the import of dangerous literature, and the writings of French philosophers were repeatedly banned. Despite the censorship, Enlightenment literature remained accessible to the Finnish audience. The ideas of the Enlightenment aroused enthusiasm as well as suspicion in the clerical estate. Seen from a comparative perspective, the Enlightenment in Finland was never distinctively anticlerical. The book collections of the Finnish clergymen and professors of theology provide proof that their interests besides theology lay in different fields of natural science, philosophy, and secular literature. Among the religious literature, authors of the Enlightenment are frequently listed.
Forms and Methods of the Book Trade in Finland in the Seventeenth and Eighteenth Centuries
Authors: Laine Tuija
Published: December 2008

Traces the history of the first printing presses in Finland, and describes the method of publishing printed works through the subscription system. Examines the emergence of the publication of printed dissertations, as well as of convenient compendia and formats.
How to Observe the Librarian
Authors: Skouvig Laura
Published: December 2008

This article presents four perspectives for observing changes in librarianship in Denmark in the twentieth century. These perspectives give rise to the following questions: 1) How has librarianship renegotiated the concept of the professional according to demands from society and in the light of different definitions of the concept?; 2) Which identities have librarians held in the twentieth century?; 3) How has the identity of the public employee been articulated in the twentieth century?; 4) How have curricula from the Royal School of Library and Information Science defined librarians in relation to society? The article is not empirical in its scope but should be seen as a reflection on how to view observations on librarianship. The conclusion of the article presents aspects for further study. These further studies could be focused on the relation between librarianship and the articulation of the public employee.
Polyclonal T-cell reconstitution of X-SCID recipients after in utero transplantation of lymphoid-primed multipotent progenitors
Authors: Liuba Karina , Pronk Cornelis J. H. , Stott Simon R. W. , Jacobsen Sten-Eirik W.
Published: December 2008

Although successful in utero hematopoietic cell transplantation (IUHCT) of X-linked severe combined immune deficiency (X-SCID) with enriched stem and progenitor cells was achieved more than a decade ago, it remains applied only in rare cases. Although this in part reflects that postnatal transplantations have overall given good results, there are no direct comparisons between IUHCT and postnatal transplantations of X-SCID. The proposed tolerance of the fetal immune system to foreign human leukocyte antigen early in gestation, a main rationale behind IUHCT, has recently been challenged by evidence for a considerable immune barrier against in utero transplanted allogeneic bone marrow cells. Consequently, there is need for further exploring the application of purified stem and progenitor cells to overcome this barrier also in IUHCT. Herein, we demonstrate in a congenic setting that recently identified lymphoid-primed multipotent progenitors are superior to hematopoietic stem cells in providing rapid lymphoid reconstitution after IUHCT of X-SCID recipients, and sustain in the long-term B cells, polyclonal T cells, as well as short-lived B-cell progenitors and thymic T-cell precursors. We further provide evidence for IUHCT of hematopoietic stem cells giving superior B- and T-cell reconstitution in fetal X-SCID recipients compared with neonatal and adolescent recipients.
Functional analysis of novel SNPs and mutations in human and mouse genomes
Authors: Liu Chuan-Kun , Chen Yan-Hau , Tang Cheng-Yang , Chang Shu-Chuan , Lin Yi-Jung , Tsai Ming-Fang , Chen Yuan-Tsong , Yao Adam
Published: December 2008

Background

With the flood of information generated by the new generation of sequencing technologies, more efficient bioinformatics tools are needed for in-depth impact analysis of novel genomic variations. FANS (Functional Analysis of Novel SNPs) was developed to streamline comprehensive but tedious functional analysis steps into a few clicks and to offer a carefully designed presentation of results so researchers can focus more on thinking instead of typing and calculating.

Results

FANS http://fans.ngc.sinica.edu.tw/ harnesses the power of public information databases and powerful tools from six well established websites to enhance the efficiency of analysis of novel variations. FANS can process any point change in any coding region or GT-AG splice site to provide a clear picture of the disease risk of a prioritized variation by classifying splicing and functional alterations into one of nine risk subtypes with five risk levels.

Conclusion

FANS significantly simplifies the analysis operations to a four-step procedure while still covering all major areas of interest to researchers. FANS offers a convenient way to prioritize the variations and select the ones with most functional impact for validation. Additionally, the program offers a distinct improvement in efficiency over manual operations in our benchmark test.
WSPMaker: a web tool for calculating selection pressure in proteins and domains using window-sliding
Authors: Lee Yong Seok , Kim Tae-Hyung , Kang Tae-Wook , Chung Won-Hyong , Shin Gwang-Sik
Published: December 2008

Background

In the study of adaptive evolution, it is important to detect the protein coding sites where natural selection is acting. In general, the ratio of the rate of non-synonymous substitutions (Ka) to the rate of synonymous substitutions (Ks) is used to estimate either negative or positive selection for an entire gene region of interest. However, since each amino acid in a region has a different function and structure, the type and strength of natural selection may be different for each amino acid. Specifically, domain sites on the protein are indicative of structurally and functionally important sites. Therefore, Window-sliding tools can be used to detect evolutionary forces acting on mutation sites.

Results

This paper reports the development of a web-based tool, WSPMaker (Window-sliding Selection pressure Plot Maker), for calculating selection pressures (estimated by Ka/Ks) in the sub-regions of two protein-coding DNA sequences (CDSs). The program uses a sliding window on DNA with a user-defined window length. This enables the investigation of adaptive protein evolution and shows selective constraints of the overall/specific region(s) of two orthologous gene-coding DNA sequences. The method accommodates various evolutionary models and options such as the sliding window size. WSPmaker uses domain information from Pfam HMM models to detect highly conserved residues within orthologous proteins.

Conclusion

WSPMaker is a web tool for scanning and calculating selection pressures (estimated by Ka/Ks) in sub-regions of two protein-coding DNA sequences (CDSs).
The value of position-specific scoring matrices for assessment of protein allegenicity
Authors: Lim Shen Jean , Tong Joo Chuan , Chew Fook Tim , Tammi Martti T
Published: December 2008

Background

Bioinformatics tools are commonly used for assessing potential protein allergenicity. While these methods have achieved good accuracies for highly conserved sequences, they are less effective when the overall similarity is low. In this study, we assessed the feasibility of using position-specific scoring matrices as a basis for predicting potential allergenicity in proteins.

Results

Two simple methods for predicting potential allergenicity in proteins, based on general and group-specific allergen profiles, are presented. Testing results indicate that the performances of both methods are comparable to the best results of other methods. The group-specific profile approach, with a sensitivity of 84.04% and specificity of 96.52%, gives similar results as those obtained using the general profile approach (sensitivity = 82.45%, specificity = 96.92%).

Conclusion

We show that position-specific scoring matrices are highly promising for constructing computational models suitable for allergenicity assessment. These data suggest it may be possible to apply a targeted approach for allergenicity assessment based on the profiles of allergens of interest.
Evaluation of MHC-II peptide binding prediction servers: applications for vaccine research
Authors: Lin Hong Huang , Zhang Guang Lan , Tongchusak Songsak , Reinherz Ellis L , Brusic Vladimir
Published: December 2008

Background

Initiation and regulation of immune responses in humans involves recognition of peptides presented by human leukocyte antigen class II (HLA-II) molecules. These peptides (HLA-II T-cell epitopes) are increasingly important as research targets for the development of vaccines and immunotherapies. HLA-II peptide binding studies involve multiple overlapping peptides spanning individual antigens, as well as complete viral proteomes. Antigen variation in pathogens and tumor antigens, and extensive polymorphism of HLA molecules increase the number of targets for screening studies. Experimental screening methods are expensive and time consuming and reagents are not readily available for many of the HLA class II molecules. Computational prediction methods complement experimental studies, minimize the number of validation experiments, and significantly speed up the epitope mapping process. We collected test data from four independent studies that involved 721 peptide binding assays. Full overlapping studies of four antigens identified binding affinity of 103 peptides to seven common HLA-DR molecules (DRB1*0101, 0301, 0401, 0701, 1101, 1301, and 1501). We used these data to analyze performance of 21 HLA-II binding prediction servers accessible through the WWW.

Results

Because not all servers have predictors for all tested HLA-II molecules, we assessed a total of 113 predictors. The length of test peptides ranged from 15 to 19 amino acids. We tried three prediction strategies – the best 9-mer within the longer peptide, the average of best three 9-mer predictions, and the average of all 9-mer predictions within the longer peptide. The best strategy was the identification of a single best 9-mer within the longer peptide. Overall, measured by the receiver operating characteristic method (AROC), 17 predictors showed good (AROC > 0.8), 41 showed marginal (AROC > 0.7), and 55 showed poor performance (AROC < 0.7). Good performance predictors included HLA-DRB1*0101 (seven), 1101 (six), 0401 (three), and 0701 (one). The best individual predictor was NETMHCIIPAN, closely followed by PROPRED, IEDB (Consensus), and MULTIPRED (SVM). None of the individual predictors was shown to be suitable for prediction of promiscuous peptides. Current predictive capabilities allow prediction of only 50% of actual T-cell epitopes using practical thresholds.

Conclusion

The available HLA-II servers do not match prediction capabilities of HLA-I predictors. Currently available HLA-II prediction servers offer only a limited prediction accuracy and the development of improved predictors is needed for large-scale studies, such as proteome-wide epitope mapping. The requirements for accuracy of HLA-II binding predictions are stringent because of the substantial effect of false positives.
A protein interaction based model for schizophrenia study
Authors: Hsu Pei-Chun , Yang Ueng-Cheng , Shih Kuan-Hui , Liu Chih-Min , Liu Yu-Li , Hwu Hai-Gwo
Published: December 2008

Background

Schizophrenia is a complex disease with multiple factors contributing to its pathogenesis. In addition to environmental factors, genetic factors may also increase susceptibility. In other words, schizophrenia is a highly heritable disease. Some candidate genes have been deduced on the basis of their known function with others found on the basis of chromosomal location. Individuals with multiple candidate genes may have increased risk. However it is not clear what kind of gene combinations may produce the disease phenotype. Their collective effect remains to be studied.

Results

Most pathways except metabolic pathways are rich in protein-protein interactions (PPIs). Thus, the PPI network contains pathway information, even though the upstream-downstream relation of PPI is yet to be explored. Here we have constructed a PPI sub-network by extracting the nearest neighbour of the 36 reported candidate genes described in the literature. Although these candidate genes were discovered by different approaches, most of the proteins formed a cluster. Two major protein interaction modules were identified on the basis of the pairwise distance among the proteins in this sub-network. The large and small clusters might play roles in synaptic transmission and signal transduction, respectively, based on gene ontology annotation. The protein interactions in the synaptic transmission cluster were used to explain the interaction between the NRG1 and CACNG2 genes, which was found by both linkage and association studies. This working hypothesis is supported by the co-expression analysis based on public microarray gene expression.

Conclusion

On the basis of the protein interaction network, it appears that the NRG1-triggered NMDAR protein internalization and the CACNG2 mediated AMPA receptor recruiting may act together in the glutamatergic signalling process. Since both the NMDA and AMPA receptors are calcium channels, this process may regulate the influx of Ca2+. Reducing the cation influx might be one of the disease mechanisms for schizophrenia. This PPI network analysis approach combined with the support from co-expression analysis may provide an efficient way to propose pathogenetic mechanisms for various highly heritable diseases.
MiRTif: a support vector machine-based microRNA target interaction filter
Authors: Yang Yuchen , Wang Yu-Ping , Li Kuo-Bin
Published: December 2008

Background

MicroRNAs (miRNAs) are a set of small non-coding RNAs serving as important negative gene regulators. In animals, miRNAs turn down protein translation by binding to the 3' UTR regions of target genes with imperfect complementary pairing. The identification of microRNA targets has become one of the major challenges of miRNA research. Bioinformatics investigations on miRNA target have resulted in a number of target prediction tools. Although these tools are capable of predicting hundreds of targets for a given miRNA, many of them suffer from high false positive rates, indicating the need for a post-processing filter for the predicted targets. Once trained with experimentally validated true and false targets, machine learning methods appear to be ideal approaches to distinguish the true targets from the false ones.

Results

We present a miRNA target filtering system named MiRTif (miRNA:target interaction filter). The system is a support vector machine (SVM) classifier trained with 195 positive and 38 negative miRNA:target interaction pairs, all experimentally validated. Each miRNA:target interaction pair is divided into a seed and a non-seed region. The encoded feature vector contains various k-gram frequencies in the seed, the non-seed and the entire regions. Informative features are selected based on their discriminating abilities. Prediction accuracies are assessed using 10-fold cross-validation experiments. Our system achieves AUC (area under the ROC curve) of 0.86, sensitivity of 83.59%, and specificity of 73.68%. More importantly, the system correctly predicts majority of the false positive miRNA:target interactions (28 out of 38). The possibility of over-fitting due to the relatively small negative sample set has also been investigated using a set of non-validated and randomly selected targets (from miRBase).

Conclusion

MiRTif is designed as a post-processing filter that takes miRNA:target interactions predicted by other target prediction softwares such as TargetScanS, PicTar and miRanda as inputs, and determines how likely the given interaction is a real or a pseudo one. MiRTif can be accessed from http://bsal.ym.edu.tw/mirtif.
Human neural progenitors express functional lysophospholipid receptors that regulate cell growth and morphology
Authors: Hurst Jillian H , Mumaw Jennifer , Machacek David W , Sturkie Carla , Callihan Phillip , Stice Steve L , Hooks Shelley B
Published: December 2008

Background

Lysophospholipids regulate the morphology and growth of neurons, neural cell lines, and neural progenitors. A stable human neural progenitor cell line is not currently available in which to study the role of lysophospholipids in human neural development. We recently established a stable, adherent human embryonic stem cell-derived neuroepithelial (hES-NEP) cell line which recapitulates morphological and phenotypic features of neural progenitor cells isolated from fetal tissue. The goal of this study was to determine if hES-NEP cells express functional lysophospholipid receptors, and if activation of these receptors mediates cellular responses critical for neural development.

Results

Our results demonstrate that Lysophosphatidic Acid (LPA) and Sphingosine-1-phosphate (S1P) receptors are functionally expressed in hES-NEP cells and are coupled to multiple cellular signaling pathways. We have shown that transcript levels for S1P1 receptor increased significantly in the transition from embryonic stem cell to hES-NEP. hES-NEP cells express LPA and S1P receptors coupled to Gi/o G-proteins that inhibit adenylyl cyclase and to Gq-like phospholipase C activity. LPA and S1P also induce p44/42 ERK MAP kinase phosphorylation in these cells and stimulate cell proliferation via Gi/o coupled receptors in an Epidermal Growth Factor Receptor (EGFR)- and ERK-dependent pathway. In contrast, LPA and S1P stimulate transient cell rounding and aggregation that is independent of EGFR and ERK, but dependent on the Rho effector p160 ROCK.

Conclusion

Thus, lysophospholipids regulate neural progenitor growth and morphology through distinct mechanisms. These findings establish human ES cell-derived NEP cells as a model system for studying the role of lysophospholipids in neural progenitors.
Abelson tyrosine kinase links PDGFbeta receptor activation to cytoskeletal regulation of NMDA receptors in CA1 hippocampal neurons
Authors: Beazely Michael A , Weerapura Manjula , MacDonald John F
Published: December 2008

Background

We have previously demonstrated that PDGF receptor activation indirectly inhibits N-methyl-D-aspartate (NMDA) currents by modifying the cytoskeleton. PDGF receptor ligand is also neuroprotective in hippocampal slices and cultured neurons. PDGF receptors are tyrosine kinases that control a variety of signal transduction pathways including those mediated by PLCγ. In fibroblasts Src and another non-receptor tyrosine kinase, Abelson kinase (Abl), control PDGF receptor regulation of cytoskeletal dynamics. The mechanism whereby PDGF receptor regulates cytoskeletal dynamics in central neurons remains poorly understood.

Results

Intracellular applications of active Abl, but not heat-inactivated Abl, decreased NMDA-evoked currents in isolated hippocampal neurons. This mimics the effects of PDGF receptor activation in these neurons. The Abl kinase inhibitor, STI571, blocked the inhibition of NMDA currents by Abl. We demonstrate that PDGF receptors can activate Abl kinase in hippocampal neurons via mechanisms similar to those observed previously in fibroblasts. Furthermore, PDGFβ receptor activation alters the subcellular localization of Abl. Abl kinase is linked to actin cytoskeletal dynamics in many systems. We show that the inhibition of NMDA receptor currents by Abl kinase is blocked by the inclusion of the Rho kinase inhibitor, Y-27632, and that activation of Abl correlates with an increase in ROCK tyrosine phosphorylation.

Conclusion

This study demonstrates that PDGFβ receptors act via an interaction with Abl kinase and Rho kinase to regulated cytoskeletal regulation of NMDA receptor channels in CA1 pyramidal neurons.
Spontaneous intramural jejunal haematoma: a case report
Authors: Birla Rashmi P , Mahawar Kamal K , Saw Elena YW , Tabaqchali Mohamed A , Woolfall Philip
Published: December 2008

Background

Spontaneous intramural intestinal haematoma is a rare complication of anticoagulation therapy. A misdiagnosis may lead to an unnecessary and even hazardous surgical intervention.

Case presentation

An 85 year old lady presented to us with acute abdomen. She was on Warfarin and was found to have grossly deranged clotting parameters. Computed Tomography Scan revealed a long loop of markedly thick-walled proximal jejunum. A diagnosis of spontaneous intramural jejunal haematoma was made.

Conclusion

She was successfully treated with conservative management with Vitamin K and blood products.
On the use of dispersive APVO GPR curves for thin-bed properties estimation: Theory and application to fracture characterization
Authors: Deparis Jacques , Garambois Stéphane
Published: December 2008

The presence of a thin layer embedded in any formation creates complex reflection patterns caused by interferences within the thin bed. The generated reflectivity amplitude variations with offset have been increasingly used in seismic interpretation and more recently tested on ground-penetrating radar (GPR) data to characterize nonaqueous-phase liquid contaminants. Phase and frequency sensitivities of the reflected signals are generally not used, although they contain useful information. The present study aims to evaluate the potential of these combined properties to characterize a thin bed using GPR data acquired along a common-midpoint (CMP) survey, carried out to assess velocity variations in the ground. It has been restricted to the simple case of a thin bed embedded within a homogeneous formation, a situation often encountered in fractured media. Dispersive properties ofthe dielectric permittivity of investigated materials (homogeneous formation, thin bed) are described using a Jonscher parameterization, which permitted study of the dependency of amplitude and phase variation with offset (APVO) curves on frequency and thin-bed properties (filling nature, aperture). In the second part, we discuss and illustrate the validity of the thin-bed approximation as well as simplify assumptions and make necessary careful corrections to convert raw CMP data into dispersive APVO curves. Two different strategies are discussed to correct the data from propagation effects: a classical normal-moveout approach and an inverse method. Finally, the proposed methodology is applied to a CMP GPR data set acquired along a vertical cliff. It allowed us to extract the characteristics of a subvertical fracture with satisfying resolution and confidence. The study motivates interest to use dispersion dependency of the reflection coefficient variations for thin-bed characterization.
Stress-dependent anisotropy in transversely isotropic rocks: Comparison between theory and laboratory experiment on shale
Authors: Ciz Radim , Shapiro Serge A.
Published: December 2008

Understanding the effect of stress and pore pressure on seismic velocities is important for overpressure prediction and for 4D reflection seismic interpretation. A porosity-deformation approach (originally called the piezosensitivity theory) and its anisotropic extension describe elastic moduli of rocks as nonlinear functions of the effective stress. This theory assumes a presence of stiff and compliant parts of the pore space. The stress-dependent geometry of the compliant pore space predominantly controls stress-induced changes in elastic moduli. We show how to apply this theory to a shale that is transversely isotropic (TI) under unloaded conditions. The porosity-deformation approach shows that components of the compliance tensor depend on exponential functions of the principal components of the effective stress tensor. In the case of a hydrostatic loading of a TI rock, only the diagonal elements of this tensor, expressed in contracted notation, are significantly stress dependent. Two equal shear components of the compliance will depend on a combination of two stress exponentials. Exponents of the stress exponentials are controlled by components of the stress-sensitivity tensor. This tensor is an important physical characteristic directly related to the elastic nonlinearity of the porous rock. We simplify the porosity-deformation theory for TI rocks and provide corresponding explicit equations. We apply this theory to ultrasonic measurements on saturated shale samples from the North Sea. We show that the theory explains the compliance tensor, anellipticity, and three anisotropic parameters under a broad range of loads.
3D magnetic data-space inversion with sparseness constraints
Authors: Pilkington Mark
Published: December 2008

I have developed an inversion approach that determines a 3D susceptibility distribution that produces a given magnetic anomaly. The subsurface model consists of a 3D, equally spaced array of dipoles. The inversion incorporates a model norm that enforces sparseness and depth weighting of the solution. Sparseness is imposed by using the Cauchy norm on model parameters. The inverse problem is posed in the data space, leading to a linear system of equations with dimensions based on the number of data, [Formula: see text]. This contrasts with the standard least-squares solution, derived through operations within the [Formula: see text]-dimensional model space ([Formula: see text] being the number of model parameters). Hence, the data-space method combined with a conjugate gradient algorithm leads to computational efficiency by dealing with an [Formula: see text] system versus an [Formula: see text] one, where [Formula: see text]. Tests on synthetic data show that sparse inversion produces a much more focused solution compared with a standard model-space, least-squares inversion. The inversion of aeromagnetic data collected over a Precambrian Shield area again shows that including the sparseness constraint leads to a simpler and better resolved solution. The degree of improvement in model resolution for the sparse case is quantified using the resolution matrix.
Optimum design of perforated plug mufflers using a neural network and a genetic algorithm
Authors: Chang Y-C , Chiu M-C , Cheng M-M
Published: December 2008

Research on new techniques of perforated plug silencers has been well addressed. Most researchers have explored noise reduction effects based on a pure plane wave theory. However, the maximum noise reduction of a silencer under a space constraint, which frequently occurs in engineering problems, is rarely addressed. Therefore, the optimum design of mufflers becomes an essential issue. In this paper, to save the design time during the flexible optimum process, a simplified mathematical model of a muffler is constructed with a neural network with a series of real data — input design data (muffle dimensions) and output data (theoretical sound transmission loss (STL)) were approximated by a theoretical mathematical model (TMM) in advance. To assess the optimal mufflers, the neural network model (NNM) is used as an objective function in conjunction with a genetic algorithm (GA). Moreover, the numerical cases of sound elimination with respect to various parameter sets and pure tones (500, 1000, and 2000 Hz) are exemplified and discussed.

Before the GA operation is carried out, the approximation between TMM and real data is checked. In addition, both the TMM and NNM are compared. It is found that the TMM and the experimental data are in agreement. Moreover, the TMM and NNM conform.

Optimal results reveal that the maximum amount of the STL can be optimally obtained at the desired frequencies. Consequently, the optimum algorithm proposed in this study can provide an efficient method to develop optimal silencers in industry.