bluuebunny/crossref_metadata_2025 huggingface dataset:
Offenders with Mental Disorder on Five Continents: A Comparison of Approaches to Treatment and Demographic Factors Relevant to Measurement of Outcome
Authors: The SWANZDSAJCS Group Per Lindqvist  , Taylor PamelaJ. , Dunn Emma , Ogloff JamesR. P. , Skipworth Jeremy , Kramp Peter , Kaliski Sean , Yoshikawa Kazuo , Gagné Pierre , Thomson Lindsay
Published: September 2009

Specialist forensic mental health service development continues worldwide. Given their generally small size and slow patient turnover, aggregating multi-site data could aid in the study of their effectiveness, safety, and value for money. The study compares such context of care and treatment philosophies in nine countries. National databases on demographics, mental disorders, and offending were identified. Participating forensic mental health practitioners independently rated likely outcomes for standard cases of serious offenders with psychosis or personality disorder. Gender distribution was similar between populations, but there were differences in age distribution and proportions of ethnic groups. Rates of psychosis were similar, but there were considerable population-based differences in substance misuse disorder rates, other substance misuse indicators and in criminal conviction statistics. Case analysis confirmed shared preferences for mental health disposals for people with psychosis, and penal disposals otherwise, with differences only in process details. Criminal recidivism was thus found to be a poor comparative measure between these countries, as it was impossible to adjust fully for differences in crime classification and measurement. Clinical outcome measures may be less vulnerable to national differences, but prevalence and type of substance misuse must be rated precisely when sharing or comparing service outcome data between nations.
Preliminary Evidence of Adaptive Decision Making Techniques Used by Parole Board Members
Authors: Gobeil Renée , Serin RalphC.
Published: September 2009

Given wide-ranging interest in the predictors of recidivism, it is surprising that relatively little research has focused on a major factor influencing offenders' ability to re-offend—conditional release decisions. Using a correlational design and hypothetical offender vignettes, this study examined conditional release decisions in a sample of 31 parole board members from Canada and New Zealand. Results revealed marked inter-individual differences, not related to demographic characteristics, in the parole decisions reached, as well as in the amount and types of file information considered. Results also demonstrated variation in decisions by offender type, as well as in the frequency with which different file information was accessed. These patterns offered preliminary evidence of the use of adaptive decision making techniques among board members, with case reviews focusing on specific information known to be related to parole outcome. Though useful in the face of time pressures, such techniques may be inconsistent with legislated requirements.
Psychiatry Reforms and Increasing Criminal Behavior of the Severely Mentally Ill: Any Link?
Authors: Schanda Hans , Stompe Thomas , Ortwein-Swoboda Gerhard
Published: September 2009

During the last decades of the 20th century, general mental healthcare underwent fundamental changes in all countries of the Western world. Despite all doubtless improvements for the majority of the mentally ill, many countries report on a substantial increase of admissions of mentally disordered offenders to forensic hospitals. Possible relations between these findings and the introduction of psychiatry reforms are under permanent discussion. However, the more or less ubiquitous increase of forensic hospital beds seems to conflict with the heterogeneous economic and legal preconditions for the reforms and the remarkable differences concerning details of service provision, access to medical insurance and social support in various parts of the world. We tried to find an explanation for these findings and to formulate a hypothesis which is able to resolve the seeming contradictions. Epidemiological data from Austria on psychiatric service provision and data from criminal statistics since 1970 were taken from several national sources and analyzed with regard to possible associations. Lack of mental hospital beds, insufficient provision of outpatient care, increasing “liberalism” with regard to involuntary admission to inpatient treatment or a general trend towards risk containment were not able to sufficiently explain the increase of forensic hospital beds. Rather, the rising incidence and prevalence rates of mentally disordered offenders not guilty by reason of insanity (NGRI) were associated with a marked reduction of time under civil commitment in patients posing danger to others. However, this factor represents a mere epiphenomenon and has to be understood as a proxy for the changed attitude of mental health professionals towards a subgroup of violent patients whose sufficient treatment is not integrated into the therapeutic concepts of modern mental healthcare. This may be the consequence of the societal changes in all countries of the Western world during the last 50 years.
The Content and Quality of Forensic Mental Health Assessment: Validation of a Principles-Based Approach
Authors: Lander TammyD. , Heilbrun Kirk
Published: September 2009

The expanding practice of forensic mental health assessment (FMHA) has created a need for more detailed guidelines within the field. Toward that end, Heilbrun (2001) has described a set of principles developed using relevant legal, ethical, scientific, and professional authority. These principles have not yet been validated through the use of expert judgment. The current study examined the content of adult criminal FMHA reports ( N = 125) through applying these principles to the reports, and by obtaining a simultaneous measure of expert judgments for these reports on the dimensions of relevance, helpfulness, and overall quality from five experts: a judge, a law professor, a practicing attorney, a psychiatrist, and a psychologist. Report content reflected limited consistency with FMHA principles. There were significant correlations between number of FMHA principles and ratings of report relevance, helpfulness, and quality, providing the first empirical validation of these principles. The implications of these findings are discussed.
Involuntary Outpatient Commitment in Florida: Case Information and Provider Experience and Opinions
Authors: Christy Annette , Petrila John , McCranie Mark , Lotts Vivian
Published: September 2009

The use of involuntary outpatient commitment (IOC) is a significant international issue. Variations can be found in Australia, New Zealand, Scotland, Ontario (Canada), Switzerland, and the United States. Its use varies considerably by country and in the United States, between states. In Florida, the IOC statute has been used sparingly. This paper first presents information about the first fifty IOC cases in Florida including a description of the pre- and post-IOC order emergency commitments and state hospital admissions of these individuals. It then provides results from a survey of mental health professionals about their experience with and opinions about IOC. The majority of the individuals with IOC orders had at least one emergency commitment in the two years pre-IOC order ( n = 46; range 1–7) and in the two years post-IOC order ( n = 41; range 1–13). While 41 individuals experienced 68 total emergency commitments in the 180 days prior to the IOC order, 18 individuals had 24 emergency commitments in the 180 days after the order. Eleven had at least one state hospital admission pre-IOC order, with eight having such an admission post-IOC order. Results from the survey suggest that a number of issues have reduced the use of IOC, including difficulties in applying the statute, inadequate clinical resources, and skepticism regarding the practical effect of an IOC order on positive clinical outcomes. The implications of these results for policy development are discussed.
Psychopathy as a Predictor of Instrumental Violence Among Civil Psychiatric Patients
Authors: Hodges Heath , Heilbrun Kirk
Published: September 2009

Identifying the motivation for violent behavior is important in risk assessment and risk management. This study examined previously archived data from the MacArthur Violence Risk Assessment Study to investigate the relationship between psychopathy and instrumental violence committed by civil psychiatric patients following hospital discharge. Analyses compared the traditional two-factor model of the Psychopathy Checklist: Screening Version (PCL:SV) to Cooke and Michie's revised three-factor model and Hare's revised 4-facet model. Results indicated that higher total scores on all models were associated with increased risk for instrumental membership. This remained the case after controlling for variables related to instrumental violence. When examining the individual contribution of factors/facets in all three models, those reflecting antisocial traits (Factor II, facet 4) were the only significant predictors of instrumental membership. The implications of these findings are discussed.
The Effects of Different Forms of Risk Communication on Judicial Decision Making
Authors: Dolores JohnC. , Redding RichardE.
Published: September 2009

When mental health experts provide information to courts on the results of a risk assessment conducted on a defendant or patient, they engage in “risk communication.” We examined the effects of four different forms of risk communication (prediction, categorical, risk factors/risk management, or hybrid) on judges' ( n = 253) perceptions of risk assessment evidence introduced in a case where they must decide whether to release from the hospital an individual found not guilty by reason of insanity. Judges who received information in the risk factors/risk management form were more likely to release the patient than were those who received prediction-based or categorical risk information. Judges with greater experience hearing cases involving risk assessment evidence were also more likely to release. Moreover, judges who had positive attitudes towards risk assessment and social science evidence in general, were more likely to find the risk assessment evidence introduced in the particular case to be understandable, relevant, and dispositive. Implications of the results for how mental health experts communicate risk information to the courts are discussed.
The Palestine one-state solution: report on the conference held in Boston, Massachusetts, March 2009
Authors: Hafez Ziad
Published: September 2009

This is a report on a conference held at the University of Massachusetts in Boston about the ‘One-State Solution for Palestine’. The latter is a response and an alternative to the ‘Two-State Solution’ favoured by the United States and the international community. Such a solution is losing credibility in terms of its possible implementation by most Arab Palestinians and the vast majority of Arabs. The two-day conference hosted academicians and activists from Palestine, the United States, and Europe defending the ‘One-State Solution’. (For further information, see http://www.onestateforpalestineisrael.com/.)
Individuation frames inscribed in language: a comparative study of English and Japanese
Authors: Foster John
Published: September 2009

Might the forgetting of critical culture–language-bound metaphors be the eradication of personality? Could following the trail back through these metaphors provide one perspective on the individuation process described in Jungian psychology? The author utilizes the concept of spatial metaphor developed by Lakoff and Johnson and subjects this cognitive frame to the understanding of embodied intelligence as understood by Nietzsche, Deleuze and Merleau-Ponty. Specific language recorders in both English and Japanese are compared in an effort to assess comparable metaphors as they function, and begin to lose functionality, at the edges of language.
Understanding hydrogen-bond patterns in proteins using network motifs
Authors: Rahat Ofer , Alon Uri , Levy Yaakov , Schreiber Gideon
Published: September 2009

Summary: Protein structures can be viewed as networks of contacts (edges) between amino-acid residues (nodes). Here we dissect proteins into sub-graphs consisting of six nodes and their corresponding edges, with an edge being either a backbone hydrogen bond (H-bond) or a covalent interaction. Six thousand three hundred and twenty-two such sub-graphs were found in a large non-redundant dataset of high-resolution structures, from which 35 occur much more frequently than in a random model. Many of these significant sub-graphs (also called network motifs) correspond to sub-structures of α helices and β-sheets, as expected. However, others correspond to more exotic sub-structures such as 310 helix, Schellman motif and motifs that were not defined previously. This topological characterization of patterns is very useful for producing a detailed differences map to compare protein structures. Here we analyzed in details the differences between NMR, molecular dynamics (MD) simulations and X-ray structures for Lysozyme, SH3 and the lambda repressor. In these cases, the same structures solved by NMR and simulated by MD showed small but consistent differences in their motif composition from the crystal structures, despite a very small root mean square deviation (RMSD) between them. This may be due to differences in the pair-wise energy functions used and the dynamic nature of these proteins.

Availability: A web-based tool to calculate network motifs is available at http://bioinfo.weizmann.ac.il/protmot/.

Contact:  gideon.schreiber@weizmann.ac.il; koby.levy@weizmann.ac.il

Supplementary information:  Supplementary data are available at Bioinformatics online.
Bayesian detection of non-sinusoidal periodic patterns in circadian expression data
Authors: Chudova Darya , Ihler Alexander , Lin Kevin K. , Andersen Bogi , Smyth Padhraic
Published: September 2009

Motivation: Cyclical biological processes such as cell division and circadian regulation produce coordinated periodic expression of thousands of genes. Identification of such genes and their expression patterns is a crucial step in discovering underlying regulatory mechanisms. Existing computational methods are biased toward discovering genes that follow sine-wave patterns.

Results: We present an analysis of variance (ANOVA) periodicity detector and its Bayesian extension that can be used to discover periodic transcripts of arbitrary shapes from replicated gene expression profiles. The models are applicable when the profiles are collected at comparable time points for at least two cycles. We provide an empirical Bayes procedure for estimating parameters of the prior distributions and derive closed-form expressions for the posterior probability of periodicity, enabling efficient computation. The model is applied to two datasets profiling circadian regulation in murine liver and skeletal muscle, revealing a substantial number of previously undetected non-sinusoidal periodic transcripts in each. We also apply quantitative real-time PCR to several highly ranked non-sinusoidal transcripts in liver tissue found by the model, providing independent evidence of circadian regulation of these genes.

Availability: Matlab software for estimating prior distributions and performing inference is available for download from http://www.datalab.uci.edu/resources/periodicity/.

Contact:  dchudova@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Client-side integration of life science literature resources
Authors: Easty Richard , Nikolov Nikolay
Published: September 2009

Motivation: The online resources in the life sciences are characterized by a great fragmentation and one of the pressing issues of bioinformatics is making the integration of these resources a smoother and more flexible process than it is currently. Here we present i-cite, a browser extension, which implements a client-side model of integration which improves the navigation within the rapidly increasing life science literature and links terms from it to corresponding non-textual data.

Availability:  http://i-cite.org.

Contact:  nan23@cam.ac.uk
Relative contribution of sequence and structure features to the mRNA binding of Argonaute/EIF2C–miRNA complexes and the degradation of miRNA targets
Authors: Hausser Jean , Landthaler Markus , Jaskiewicz Lukasz , Gaidatzis Dimos , Zavolan Mihaela
Published: September 2009

How miRNAs recognize their target sites is a puzzle that many experimental and computational studies aimed to solve. Several features, such as perfect pairing of the miRNA seed, additional pairing in the 3′ region of the miRNA, relative position in the 3′ UTR, and the A/U content of the environment of the putative site, have been found to be relevant. Here we have used a large number of previously published data sets to assess the power that various sequence and structure features have in distinguishing between putative sites that do and those that do not appear to be functional. We found that although different data sets give widely different answers when it comes to ranking the relative importance of these features, the sites inferred from most transcriptomics experiments, as well as from comparative genomics, appear similar at this level. This suggests that miRNA target sites have been selected in evolution on their ability to trigger mRNA degradation. To understand at what step in the miRNA-induced response individual features play a role, we transfected human HEK293 cells with miRNAs and analyzed the association of Argonaute/EIF2C–miRNA complexes with target mRNAs and the degradation of these messages. We found that structural features of the target site are only important for Argonaute/EIF2C binding, while sequence features such as the A/U content of the 3′ UTR are important for mRNA degradation.
Predictable dynamic program of timing of DNA replication in human cells
Authors: Desprat Romain , Thierry-Mieg Danielle , Lailler Nathalie , Lajugie Julien , Schildkraut Carl , Thierry-Mieg Jean , Bouhassira Eric E.
Published: September 2009

The organization of mammalian DNA replication is poorly understood. We have produced high-resolution dynamic maps of the timing of replication in human erythroid, mesenchymal, and embryonic stem (ES) cells using TimEX, a method that relies on gaussian convolution of massive, highly redundant determinations of DNA copy-number variations during S phase to produce replication timing profiles. We first obtained timing maps of 3% of the genome using high-density oligonucleotide tiling arrays and then extended the TimEX method genome-wide using massively parallel sequencing. We show that in untransformed human cells, timing of replication is highly regulated and highly synchronous, and that many genomic segments are replicated in temporal transition regions devoid of initiation, where replication forks progress unidirectionally from origins that can be hundreds of kilobases away. Absence of initiation in one transition region is shown at the molecular level by single molecule analysis of replicated DNA (SMARD). Comparison of ES and erythroid cells replication patterns revealed that these cells replicate about 20% of their genome in different quarters of S phase. Importantly, we detected a strong inverse relationship between timing of replication and distance to the closest expressed gene. This relationship can be used to predict tissue-specific timing of replication profiles from expression data and genomic annotations. We also provide evidence that early origins of replication are preferentially located near highly expressed genes, that mid-firing origins are located near moderately expressed genes, and that late-firing origins are located far from genes.
The completion of the Mammalian Gene Collection (MGC)
Authors:   The MGC Project Team, Temple Gary , Gerhard Daniela S. , Rasooly Rebekah , Feingold Elise A. , Good Peter J. , Robinson Cristen , Mandich Allison , Derge Jeffrey G. , Lewis Jeanne , Shoaf Debonny , Collins Francis S. , Jang Wonhee , Wagner Lukas , Shenmen Carolyn M. , Misquitta Leonie , Schaefer Carl F. , Buetow Kenneth H. , Bonner Tom I. , Yankie Linda , Ward Ming , Phan Lon , Astashyn Alex , Brown Garth , Farrell Catherine , Hart Jennifer , Landrum Melissa , Maidak Bonnie L. , Murphy Michael , Murphy Terence , Rajput Bhanu , Riddick Lillian , Webb David , Weber Janet , Wu Wendy , Pruitt Kim D. , Maglott Donna , Siepel Adam , Brejova Brona , Diekhans Mark , Harte Rachel , Baertsch Robert , Kent Jim , Haussler David , Brent Michael , Langton Laura , Comstock Charles L.G. , Stevens Michael , Wei Chaochun , van Baren Marijke J. , Salehi-Ashtiani Kourosh , Murray Ryan R. , Ghamsari Lila , Mello Elizabeth , Lin Chenwei , Pennacchio Christa , Schreiber Kirsten , Shapiro Nicole , Marsh Amber , Pardes Elizabeth , Moore Troy , Lebeau Anita , Muratet Mike , Simmons Blake , Kloske David , Sieja Stephanie , Hudson James , Sethupathy Praveen , Brownstein Michael , Bhat Narayan , Lazar Joseph , Jacob Howard , Gruber Chris E. , Smith Mark R. , McPherson John , Garcia Angela M. , Gunaratne Preethi H. , Wu Jiaqian , Muzny Donna , Gibbs Richard A. , Young Alice C. , Bouffard Gerard G. , Blakesley Robert W. , Mullikin Jim , Green Eric D. , Dickson Mark C. , Rodriguez Alex C. , Grimwood Jane , Schmutz Jeremy , Myers Richard M. , Hirst Martin , Zeng Thomas , Tse Kane , Moksa Michelle , Deng Merinda , Ma Kevin , Mah Diana , Pang Johnson , Taylor Greg , Chuah Eric , Deng Athena , Fichter Keith , Go Anne , Lee Stephanie , Wang Jing , Griffith Malachi , Morin Ryan , Moore Richard A. , Mayo Michael , Munro Sarah , Wagner Susan , Jones Steven J.M. , Holt Robert A. , Marra Marco A. , Lu Sun , Yang Shuwei , Hartigan James , Graf Marcus , Wagner Ralf , Letovksy Stanley , Pulido Jacqueline C. , Robison Keith , Esposito Dominic , Hartley James , Wall Vanessa E. , Hopkins Ralph F. , Ohara Osamu , Wiemann Stefan
Published: September 2009

Since its start, the Mammalian Gene Collection (MGC) has sought to provide at least one full-protein-coding sequence cDNA clone for every human and mouse gene with a RefSeq transcript, and at least 6200 rat genes. The MGC cloning effort initially relied on random expressed sequence tag screening of cDNA libraries. Here, we summarize our recent progress using directed RT-PCR cloning and DNA synthesis. The MGC now contains clones with the entire protein-coding sequence for 92% of human and 89% of mouse genes with curated RefSeq (NM-accession) transcripts, and for 97% of human and 96% of mouse genes with curated RefSeq transcripts that have one or more PubMed publications, in addition to clones for more than 6300 rat genes. These high-quality MGC clones and their sequences are accessible without restriction to researchers worldwide.
Metabolite Sorting of a Germplasm Collection Reveals the Hydroxylase3 Locus as a New Target for Maize Provitamin A Biofortification
Authors: Vallabhaneni Ratnakar , Gallagher Cynthia E. , Licciardello Nicholas , Cuttriss Abby J. , Quinlan Rena F. , Wurtzel Eleanore T.
Published: September 2009

Vitamin A deficiency, a global health burden, can be alleviated through provitamin A carotenoid biofortification of major crop staples such as maize (Zea mays) and other grasses in the Poaceae. If regulation of carotenoid biosynthesis was better understood, enhancement could be controlled by limiting β-carotene hydroxylation to compounds with lower or no nonprovitamin A activity. Natural maize genetic diversity enabled identification of hydroxylation genes associated with reduced endosperm provitamin A content. A novel approach was used to capture the genetic and biochemical diversity of a large germplasm collection, representing 80% of maize genetic diversity, without having to sample the entire collection. Metabolite data sorting was applied to select a 10-line genetically diverse subset representing biochemical extremes for maize kernel carotenoids. Transcript profiling led to discovery of the Hydroxylase3 locus that coincidently mapped to a carotene quantitative trait locus, thereby prompting investigation of allelic variation in a broader collection. Three natural alleles in 51 maize lines explained 78% of variation and approximately 11-fold difference in β-carotene relative to β-cryptoxanthin and 36% of the variation and 4-fold difference in absolute levels of β-carotene. A simple PCR assay to track and identify Hydroxylase3 alleles will be valuable for predicting nutritional content in genetically diverse cultivars found worldwide.
The Variegated Mutants Lacking Chloroplastic FtsHs Are Defective in D1 Degradation and Accumulate Reactive Oxygen Species
Authors: Kato Yusuke , Miura Eiko , Ido Kunio , Ifuku Kentaro , Sakamoto Wataru
Published: September 2009

In the photosynthetic apparatus, a major target of photodamage is the D1 reaction center protein of photosystem II (PSII). Photosynthetic organisms have developed a PSII repair cycle in which photodamaged D1 is selectively degraded. A thylakoid membrane-bound metalloprotease, FtsH, was shown to play a critical role in this process. Here, the effect of FtsHs in D1 degradation was investigated in Arabidopsis (Arabidopsis thaliana) mutants lacking FtsH2 (yellow variegated2 [var2]) or FtsH5 (var1). Because these mutants are characterized by variegated leaves that sometimes complicate biochemical studies, we employed another mutation, fu-gaeri1 (fug1), that suppresses leaf variegation in var1 and var2 to examine D1 degradation. Two-dimensional blue native PAGE showed that var2 has less PSII supercomplex and more PSII intermediate lacking CP43, termed RC47, than the wild type under normal growth light. Moreover, our histochemical and quantitative analyses revealed that chloroplasts in var2 accumulate significant levels of reactive oxygen species, such as superoxide radical and hydrogen peroxide. These results indicate that the lack of FtsH2 leads to impaired D1 degradation at the step of RC47 formation in PSII repair and to photooxidative stress even under nonphotoinhibitory conditions. Our in vivo D1 degradation assays, carried out by nonvariegated var2 fug1 and var1 fug1 leaves, demonstrated that D1 degradation was impaired in different light conditions. Taken together, our results suggest the important role of chloroplastic FtsHs, which was not precisely examined in vivo. Attenuated D1 degradation in the nonvariegated mutants also suggests that leaf variegation seems to be independent of the PSII repair.
Genome-WideMedicago truncatulaSmall RNA Analysis Revealed Novel MicroRNAs and Isoforms Differentially Regulated in Roots and Nodules
Authors: Lelandais-Brière Christine , Naya Loreto , Sallet Erika , Calenge Fanny , Frugier Florian , Hartmann Caroline , Gouzy Jérome , Crespi Martin
Published: September 2009

Posttranscriptional regulation of a variety of mRNAs by small 21- to 24-nucleotide RNAs, notably the microRNAs (miRNAs), is emerging as a novel developmental mechanism. In legumes like the model Medicago truncatula, roots are able to develop a de novo meristem through the symbiotic interaction with nitrogen-fixing rhizobia. We used deep sequencing of small RNAs from root apexes and nodules of M. truncatula to identify 100 novel candidate miRNAs encoded by 265 hairpin precursors. New atypical precursor classes producing only specific 21- and 24-nucleotide small RNAs were found. Statistical analysis on sequencing reads abundance revealed specific miRNA isoforms in a same family showing contrasting expression patterns between nodules and root apexes. The differentially expressed conserved and nonconserved miRNAs may target a large variety of mRNAs. In root nodules, which show diverse cell types ranging from a persistent meristem to a fully differentiated central region, we discovered miRNAs spatially enriched in nodule meristematic tissues, vascular bundles, and bacterial infection zones using in situ hybridization. Spatial regulation of miRNAs may determine specialization of regulatory RNA networks in plant differentiation processes, such as root nodule formation.
The Rice α-Amylase Glycoprotein Is Targeted from the Golgi Apparatus through the Secretory Pathway to the Plastids
Authors: Kitajima Aya , Asatsuma Satoru , Okada Hisao , Hamada Yuki , Kaneko Kentaro , Nanjo Yohei , Kawagoe Yasushi , Toyooka Kiminori , Matsuoka Ken , Takeuchi Masaki , Nakano Akihiko , Mitsui Toshiaki
Published: September 2009

The well-characterized secretory glycoprotein, rice (Oryza sativa) α-amylase isoform I-1 (AmyI-1), was localized within the plastids and proved to be involved in the degradation of starch granules in the organelles of rice cells. In addition, a large portion of transiently expressed AmyI-1 fused to green fluorescent protein (AmyI-1-GFP) colocalized with a simultaneously expressed fluorescent plastid marker in onion (Allium cepa) epidermal cells. The plastid targeting of AmyI-1 was inhibited by both dominant-negative and constitutively active mutants of Arabidopsis thaliana ARF1 and Arabidopsis SAR1, which arrest endoplasmic reticulum-to-Golgi traffic. In cells expressing fluorescent trans-Golgi and plastid markers, these fluorescent markers frequently colocalized when coexpressed with AmyI-1. Three-dimensional time-lapse imaging and electron microscopy of high-pressure frozen/freeze-substituted cells demonstrated that contact of the Golgi-derived membrane vesicles with cargo and subsequent absorption into plastids occur within the cells. The transient expression of a series of C-terminal-truncated AmyI-1-GFP fusion proteins in the onion cell system showed that the region from Trp-301 to Gln-369 is necessary for plastid targeting of AmyI-1. Furthermore, the results obtained by site-directed mutations of Trp-302 and Gly-354, located on the surface and on opposite sides of the AmyI-1 protein, suggest that multiple surface regions are necessary for plastid targeting. Thus, Golgi-to-plastid traffic appears to be involved in the transport of glycoproteins to plastids and plastid targeting seems to be accomplished in a sorting signal–dependent manner.
Global Identification of Targets of theArabidopsisMADS Domain Protein AGAMOUS-Like15
Authors: Zheng Yumei , Ren Na , Wang Huai , Stromberg Arnold J. , Perry Sharyn E.
Published: September 2009

AGAMOUS-Like15 (AGL15) is a MADS domain transcriptional regulator that promotes somatic embryogenesis by binding DNA and regulating gene expression. Chromatin immunoprecipitation (ChIP) analysis previously identified DNA fragments with which AGL15 associates in vivo, and a low-throughput approach revealed a role for AGL15 in gibberellic acid catabolism that is relevant to embryogenesis. However, higher throughput methods are needed to identify targets of AGL15. Here, we mapped AGL15 in vivo binding sites using a ChIP-chip approach and the Affymetrix tiling arrays for Arabidopsis thaliana and found that ∼2000 sites represented in three biological replicates of the experiment are annotated to nearby genes. These results were combined with high-throughput measurement of gene expression in response to AGL15 accumulation to discriminate responsive direct targets from those further downstream in the network. LEAFY COTYLEDON2, FUSCA3, and ABA INSENSITIVE3, which encode B3 domain transcription factors that are key regulators of embryogenesis, were identified and verified as direct target genes of AGL15. Genes identified as targets of the B3 genes are also targets of AGL15, and we found that INDOLEACETIC ACID-INDUCED PROTEIN30 is involved in promotion of somatic embryo development. The data presented here and elsewhere suggest that much cross-regulation occurs in gene regulatory networks underpinning embryogenesis.
Silence as the Foundation of Learning
Authors: Caranfa Angelo
Published: September 2009

Past and present discussions on education all too frequently neglect the role that silence plays in learning. In this article I set out to demonstrate that silence is the very foundation of learning. My claim is that we must find ways of freeing silence in our pedagogical practices so that our discourse does not denigrate into mere empty words, but becomes a means towards self‐knowledge. My position is that no discourse can awaken self‐knowledge; what it can do, at best, is to help create an inner state of silence necessary for mental, moral, and spiritual growth of the human self. The essay is a defense of Socratic learning, complemented with the poetic discourse of Max Picard. Such a marriage alone can render education creative, most especially when it is applied to reading and writing.
Why and how terrestrial plants exchange gases with air
Authors: Cieslik S. , Omasa K. , Paoletti E.
Published: September 2009

This work is intended as a review of gas exchange processes between the atmosphere and the terrestrial vegetation, which have been known for more than two centuries since the discovery of photosynthesis. The physical and biological mechanisms of exchange of carbon dioxide, water vapour, volatile organic compounds emitted by plants and air pollutants taken up by them, is critically reviewed. The role of stomatal physiology is emphasised, as it controls most of these processes. The techniques used for measurement of gas exchange fluxes between the atmosphere and vegetation are outlined.
Solving the barriers to diabetes education through the use of multimedia
Authors: Isarankura‐Na‐Ayudhya Chartchalerm , Nantasenamat Chanin , Dansethakul Prabhop , Saetum Pradermchai , Laosrivijit Sirikul , Prachayasittikul Virapong
Published: September 2009

Diabetes mellitus is a chronic disease that affects > 180 million people worldwide. It is persistent in Thai communities in spite of much effort in prevention and control. This study examined the knowledge capacity of villagers in the Klongmai community of Nakhon Pathom, Thailand, regarding diabetes by way of action research. A health status assessment and a survey of the community were carried out and used as the basis for designing an educational video on diabetes that is accessible regardless of age and educational background. Evaluations of the pre‐ and poststudy questionnaires were carried out using statistical analysis. The results indicated that the devised educational materials were effective in encouraging the community's self‐awareness and perception of diabetes at the significance level of 0.05. Most importantly, the participants demonstrated proficiency in adapting the knowledge gained from the workshop to their own lifestyle.
Carpet weaving: an occupational risk for onychomycosis?
Authors: Kaçar N , Ergin Ş , Ergin Ç , Arslan Ş , Erdoğan BŞ
Published: September 2009

Background Some occupations carry a risk for fungal infections.

Objective To investigate the prevalence of onychomycosis in carpet weavers.

Methods Seventy‐seven weavers (the mean age ± SD = 32.97 ± 12.38) from three factories and 77 controls (the mean age ± SD = 38.32 ± 12.38) were examined for onychomycosis. Samples from nails and the carpets, which were being weaved, were taken for mycological investigations.

Results Direct microscopic examination of only two controls’ normal‐appearing nails was positive. Fungal growth was observed in the culture of four weavers’ normal‐appearing nails. It was watched over that most of the weavers had polished‐appearing nails and were using a glue containing cynoacrylate to restore their broken nails due to weaving.

Conclusion The fungal growth observed in weavers’ nails has been accepted as colonization. There is no data about the presence of fungi on normal‐appearing nails. So, we thought that the weavers with fungal colonization should be followed for the development of onychomycosis.
Soy intake and risk of endocrine‐related gynaecological cancer: a meta‐analysis
Authors: Myung S‐K , Ju W , Choi HJ , Kim SC ,   The Korean Meta‐Analysis (KORMA) Study Group
Published: September 2009

Background Epidemiology studies have reported associations between soy intake and the risk of endocrine‐related gynaecological cancers. However, to date there have been no quantitative meta‐analyses reported regarding this topic.

Objectives We investigated the quantitative associations between soy food intake and the risk of endometrial cancer and ovarian cancer by a meta‐analysis of case–control studies and cohort studies.

Search strategy We searched MEDLINE (PubMed), EMBASE and the Cochrane Library during October 2008 using common keywords related to soy intake and endometrial or ovarian cancer. Two evaluators independently reviewed and selected articles, based on predetermined selection criteria.

Selection criteria Included studies met all of the following criteria: (1) a case–control study or cohort study (to date, no randomized controlled trials have been reported); (2) investigated the associations between ‘soy or soy product intake’ and ‘endometrial cancer’ or ‘ovarian cancer’; (3) reported outcome measures with adjusted odds ratios (OR) or relative risks (RR) and 95% confidence intervals (CI).

Data collection and analysis We investigated the associations between the overall soy intake (highest versus lowest intake) and the risk of endocrine‐related gynaecological cancers (endometrial or ovarian cancer) as the main analysis. We also performed subgroup analyses by type of cancer (endometrial or ovarian), type of study design (case–control or cohort) and type of soy intake (soy foods or soy constituents).

Main results Out of 477 articles that met our initial criteria, a total of seven epidemiology studies consisting of five case–control studies and two cohort studies were included in the final analyses. Compared with the lowest soy intake, the OR for the highest soy intake was 0.61 (95% CI, 0.53–0.72) of all endocrine‐related cancers among seven studies; 0.70 for endometrial cancer (95% CI, 0.57–0.86) and 0.52 for ovarian cancer (95% CI, 0.42–0.66) in the fixed‐effects meta‐analyses. The subgroup analyses by study design showed similar findings among the case–control studies (OR, 0.62; 95% CI, 0.53–0.73) and the cohort studies (OR, 0.57; 95% CI, 0.36–0.90).

Author’s conclusions The results of the current study showed protective effects of soy intake on the risk for endocrine‐related gynaecological cancers. Additional larger prospective studies are now needed.
Regulation of PINK1 by NR2B‐containing NMDA receptors in ischemic neuronal injury
Authors: Shan Yuexin , Liu Baosong , Li Lijun , Chang Ning , Li Lei , Wang Hanbin , Wang Dianshi , Feng Hua , Cheung Carol , Liao Mingxia , Cui Tianyuan , Sugita Shuzo , Wan Qi
Published: September 2009

Dysfunction of PTEN‐induced kinase‐1 (PINK1) is implicated in neurodegeneration. We report here that oxygen‐glucose deprivation (OGD), anin vitroinsult mimicking ischemic neuron injury, resulted in a significant reduction of PINK1 protein expression in cultured cortical neurons. The decrease of PINK1 expression was blocked by the antagonists of NMDA receptors. We revealed that the overactivation of NR2B‐containing NMDA receptors (NR2BRs) was responsible for the OGD‐induced PINK1 reduction. The overactivated NR2BRs also inhibited the phosphorylation, but not the protein expression, of the cell survival‐promoting kinase Akt after OGD insult, indicating that OGD‐induced reduction of PINK1 protein is specific in the injury paradigm. We further showed that enhancing the protein expression of PINK1 antagonized OGD‐induced reduction of Akt phosphorylation, suggesting that Akt may be a downstream target of PINK1 in ischemic neuron injury. Importantly, we provided evidence that both NR2BR antagonist and PINK1 over‐expression protected against OGD‐induced neuronal death. These results suggest that the overactivation of NR2BRs may contribute to ischemic neuron death through suppressing PINK1‐dependent survival signaling. Thus, selectively antagonizing NR2BR signal pathway‐induced neurotoxicity may be a potential neuroprotection strategy.
Long‐Term Effects of Minimum Drinking Age Laws on Past‐Year Alcohol and Drug Use Disorders
Authors: Norberg Karen E. , Bierut Laura J. , Grucza Richard A.
Published: September 2009

Background: Many studies have found that earlier drinking initiation predicts higher risk of later alcohol and substance use problems, but the causal relationship between age of initiation and later risk of substance use disorder remains unknown.

Method: We use a “natural experiment” study design to compare the 12‐month prevalence ofDiagnostic and Statistical Manual, Fourth Edition,alcohol and substance use disorders among adult subjects exposed to different minimum legal drinking age laws minimum legal drinking age in the 1970s and 1980s. The sample pools 33,869 respondents born in the United States 1948 to 1970, drawn from 2 nationally representative cross‐sectional surveys: the 1991 National Longitudinal Alcohol Epidemiological Survey (NLAES) and the 2001 National Epidemiological Study of Alcohol and Related Conditions. Analyses control for state and birth year fixed effects, age at assessment, alcohol taxes, and other demographic and social background factors.

Results: Adults who had been legally allowed to purchase alcohol before age 21 were more likely to meet criteria for an alcohol use disorder [odds ratio (OR) 1.31, 95% confidence intervals (95% CI) 1.15 to 1.46,p < 0.0001] or another drug use disorder (OR 1.70, 95% CI 1.19 to 2.44,p = 0.003) within the past‐year, even among subjects in their 40s and 50s. There were no significant differences in effect estimates by respondent gender, black or Hispanic ethnicity, age, birth cohort, or self‐reported age of initiation of regular drinking; furthermore, the effect estimates were little changed by inclusion of age of initiation as a potential mediating variable in the multiple regression models.

Conclusion: Exposure to a lower minimum legal purchase age was associated with a significantly higher risk of a past‐year alcohol or other substance use disorder, even among respondents in their 40s or 50s. However, this association does not seem to be explained by age of initiation of drinking, per se. Instead, it seems plausible that frequency or intensity of drinking in late adolescence may have long‐term effects on adult substance use patterns.
Body weight and serum albumin change after prosthodontic treatment among institutionalized elderly in a long‐term care geriatric hospital
Authors: Kanehisa Yayoi , Yoshida Mitsuyoshi , Taji Tsuyoshi , Akagawa Yasumasa , Nakamura Hideo
Published: September 2009

Abstract –  Objectives:  An important purpose of denture treatment is the improvement of nutritional intake. This is especially important for the dependent elderly who have a high risk of protein‐energy malnutrition. To evaluate the impact of denture treatment on such a population, we compared body weight as an indicator of nutritional status before and 6 months after prosthodontic treatment.

Methods:  This study was conducted in a long‐term care geriatric hospital in Hiroshima, Japan from October 2004 to September 2006. One hundred and four patients received complete or partial denture treatment in both jaws. Nineteen patients were lost to the study because of the development of severe physical conditions or death. Among the remaining 85 patients, 66 used their new prostheses and 19 did not. Body weight and serum albumin levels were examined at prosthesis insertion and 6 months after treatment.

Results:  Six months after prosthodontic treatment body weight changes were significantly different between users and non‐users regardless of denture type and, in addition, serum albumin level were significantly increased among individuals using partial denture in either or both jaws (P < 0.05).

Conclusion:  It can be concluded that prosthodontic treatment may improve the nutritional status of institutionalized elderly.
A ventral prefrontal-amygdala neural system in bipolar disorder: a view from neuroimaging research
Authors: Womer Fay Y. , Kalmar Jessica H. , Wang Fei , Blumberg Hilary P.
Published: September 2009

In the past decade, neuroimaging research has identified key components in the neural system that underlies bipolar disorder (BD). The ventral prefrontal cortex (VPFC) and amygdala are highly interconnected structures that jointly play a central role in emotional regulation. Numerous research groups have reported prominent structural and functional abnormalities within the VPFC and amygdala supporting their essential role in a neural system underlying the emotional dysregulation that is a core feature of BD. Findings in BD also include those in brain regions interconnected with the VPFC and amygdala, including the ventral striatum, hippocampus and the cerebellum. Abnormalities in these regions may contribute to symptoms that reflect disruption in functions sub-served by these structures, including motivational, mnemonic and psychomotor functions.

This article will first review leads from behavioural neurology that implicated these neural system abnormalities in BD. It will then review findings from structural and functional imaging studies to support the presence of abnormalitieswithinthese neural system components in BD. It will also review new findings from studies using diffusion tensor imaging (DTI) that provide increasing evidence of abnormalities in the connectionsbetweenthese neural system components in BD. Emerging data supporting differences in this neural system during adolescence, as well as potential beneficial effects of treatment on structure and function will also be presented. Finally, the article will discuss the implications for future investigations, including those for early identification and treatment of BD.
Different Responses of Plant Growth and Antioxidant System to the Combination of Cadmium and Heat Stress in Transgenic and Non‐transgenic Rice
Authors: Zhao Feng‐Yun , Liu Wen , Zhang Shi‐Yong
Published: September 2009

A comparative study of just cadmium (Cd) or heat and their combination treatments on some physiological parameters and the antioxidant systems in transgenic rice (Oryza sativa L. cv. Zhonghua No.11) carrying glutathione‐S‐transferase (GST, EC. 2.5.1.18) and catalase1 (CAT1, EC. 1.11.1.6) and non‐transgenics was conducted. The results revealed improved resistance in the transgenics to Cd and the combined Cd and heat stress than non‐transgenics. Data showed that the activities of CAT, GST, superoxide dismutase (EC.1.15.1.1) and all components of the ascorbate‐glutathione cycle measured in the stressed transgenics shoots are significantly different from those of non‐transgenics. Results indicated that co‐expression of GST and CAT1 had an important effect on the antioxidant system, in particular, the whole ascorbate‐glutathione cycle. The less oxidative damage induced by Cd and the stress combination in the transgenics resulted not only from the GST and CAT1 transgene but also from the coordination of the whole ascorbate‐glutathione cycle.