bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamic Behavior ofArabidopsiseIF4A-III, Putative Core Protein of Exon Junction Complex: Fast Relocation to Nucleolus and Splicing Speckles under Hypoxia
Authors: Koroleva O.A. , Calder G. , Pendle A.F. , Kim S.H. , Lewandowska D. , Simpson C.G. , Jones I.M. , Brown J.W.S. , Shaw P.J. 
Published: May 2009

AbstractHere, we identify the Arabidopsis thaliana ortholog of the mammalian DEAD box helicase, eIF4A-III, the putative anchor protein of exon junction complex (EJC) on mRNA. Arabidopsis eIF4A-III interacts with an ortholog of the core EJC component, ALY/Ref, and colocalizes with other EJC components, such as Mago, Y14, and RNPS1, suggesting a similar function in EJC assembly to animal eIF4A-III. A green fluorescent protein (GFP)-eIF4A-III fusion protein showed localization to several subnuclear domains: to the nucleoplasm during normal growth and to the nucleolus and splicing speckles in response to hypoxia. Treatment with the respiratory inhibitor sodium azide produced an identical response to the hypoxia stress. Treatment with the proteasome inhibitor MG132 led to accumulation of GFP-eIF4A-III mainly in the nucleolus, suggesting that transition of eIF4A-III between subnuclear domains and/or accumulation in nuclear speckles is controlled by proteolysis-labile factors. As revealed by fluorescence recovery after photobleaching analysis, the nucleoplasmic fraction was highly mobile, while the speckles were the least mobile fractions, and the nucleolar fraction had an intermediate mobility. Sequestration of eIF4A-III into nuclear pools with different mobility is likely to reflect the transcriptional and mRNA processing state of the cell.
Regulatory Features Underlying Pollination-Dependent and -Independent Tomato Fruit Set Revealed by Transcript and Primary Metabolite Profiling
Authors: Wang Hua , Schauer Nicolas , Usadel Bjoern , Frasse Pierre , Zouine Mohamed , Hernould Michel , Latché Alain , Pech Jean-Claude , Fernie Alisdair R. , Bouzayen Mondher 
Published: May 2009

AbstractIndole Acetic Acid 9 (IAA9) is a negative auxin response regulator belonging to the Aux/IAA transcription factor gene family whose downregulation triggers fruit set before pollination, thus giving rise to parthenocarpy. In situ hybridization experiments revealed that a tissue-specific gradient of IAA9 expression is established during flower development, the release of which upon pollination triggers the initiation of fruit development. Comparative transcriptome and targeted metabolome analysis uncovered important features of the molecular events underlying pollination-induced and pollination-independent fruit set. Comprehensive transcriptomic profiling identified a high number of genes common to both types of fruit set, among which only a small subset are dependent on IAA9 regulation. The fine-tuning of Aux/IAA and ARF genes and the downregulation of TAG1 and TAGL6 MADS box genes are instrumental in triggering the fruit set program. Auxin and ethylene emerged as the most active signaling hormones involved in the flower-to-fruit transition. However, while these hormones affected only a small number of transcriptional events, dramatic shifts were observed at the metabolic and developmental levels. The activation of photosynthesis and sucrose metabolism-related genes is an integral regulatory component of fruit set process. The combined results allow a far greater comprehension of the regulatory and metabolic events controlling early fruit development both in the presence and absence of pollination/fertilization.
TheNGATHAGenes Direct Style Development in theArabidopsisGynoecium
Authors: Trigueros Marina , Navarrete-Gómez Marisa , Sato Shusei , Christensen Sioux K. , Pelaz Soraya , Weigel Detlef , Yanofsky Martin F. , Ferrándiz Cristina 
Published: May 2009

AbstractThe gynoecium is the most complex floral organ, designed to protect the ovules and ensure their fertilization. Correct patterning and tissue specification in the developing gynoecium involves the concerted action of a host of genetic factors. In addition, apical-basal patterning into different domains, stigma and style, ovary and gynophore, appears to depend on the establishment and maintenance of asymmetric auxin distribution, with an auxin maximum at the apex. Here, we show that a small subfamily of the B3 transcription factor superfamily, the NGATHA (NGA) genes, act redundantly to specify style development in a dosage-dependent manner. Characterization of the NGA gene family is based on an analysis of the activation-tagged mutant named tower-of-pisa1 (top1), which was found to overexpress NGA3. Quadruple nga mutants completely lack style and stigma development. This mutant phenotype is likely caused by a failure to activate two auxin biosynthetic enzymes, YUCCA2 and YUCCA4, in the apical gynoecium domain. The NGA mutant phenotypes are similar to those caused by multiple combinations of mutations in STYLISH1 (STY1) and additional members of its family. NGA3/TOP1 and STY1 share almost identical patterns of expression, but they do not appear to regulate each other at the transcriptional level. Strong synergistic phenotypes are observed when nga3/top1 and sty1 mutants are combined. Furthermore, constitutive expression of both NGA3/TOP1 and STY1 induces the conversion of the ovary into style tissue. Taken together, these data suggest that the NGA and STY factors act cooperatively to promote style specification, in part by directing YUCCA-mediated auxin synthesis in the apical gynoecium domain.
Invariant natural killer (iNK) T cell deficiency in patients with common variable immunodeficiency
Authors: Fulcher D A , Avery D T , Fewings N L , Berglund L J , Wong S , Riminton D S , Adelstein S , Tangye S G 
Published: May 2009

Summary
Common variable immunodeficiency (CVID) is a B cell immunodeficiency disorder characterized frequently by failure of memory B cell development and antibody secretion. A unifying cellular pathogenesis for CVID has not been forthcoming, but given the immunoregulatory role of invariant NK (iNK) T cells and their absence in several other immunodeficiencies, we quantified these cells in the blood of 58 CVID patients. There was a marked decrease in the proportion of iNK T cells in CVID patients compared with controls. This was particularly notable in those with low isotype-switched memory B cells, but subset analysis demonstrated no difference when stratified by specific clinical features. We propose that the decreased proportion of iNK T cells in CVID might be linked to the failure of memory B cell generation, which may contribute to reduced antibody production in these patients.
Combined measurements of egg fatty acids and stable isotopes as indicators of feeding ecology in lake‐dwelling birds
Authors: RAMÍREZ FRANCISCO , JOVER LLUÍS , SANPERA CAROLINA , RUIZ XAVIER , PIQUÉ ESTER , GUITART RAIMON 
Published: May 2009

Summary1. We examined whether egg fatty acid (FA) profiles and stable isotopes (SIA) could be used in a comparative way to infer the diet of two aquatic bird species with contrasting feeding habits: a surface forager, the pheasant‐tailed jacana (Hydrophasianus chirurgus), and a pursuit‐diving forager, the little cormorant (Phalacrocorax niger), at Haleji Lake (Pakistan).2. The species differed markedly in the overall percentage of saturated and polyunsaturated fatty acids. Moreover, among jacanas, two groups of birds had relatively high or low concentrations of long‐chain essential PUFAs (such as 18:2 n‐6 and 20:4 n‐6), suggesting differing contributions from animal prey and plant material.3. These trophic differences were corroborated by δ15N values which indicated both a higher trophic position in cormorants relative to jacanas, and differences in trophic position for the two groups of jacanas. In this latter species δ13C values in both groups also pointed to differing diets, involving mainly grazing plants or a contribution from animal resources (aquatic invertebrates or insects).4. Both lower values of δ13C and higher percentages of 18:1 n‐7 detected in little cormorants may indicate the influence of the anoxic water, typical of a freshwater system densely covered by macrophytes.5. These results indicate how both biomarkers offer complementary information in studies of feeding ecology, refining interpretations of trophic pathways which are usually based on FA or SIA alone. Comparisons of FA profiles and SIA among species also proved to be a reliable approach for inferring the diet of species for which information is scarce or contradictory, as is the case for the pheasant‐tailed jacana.
A quantitative study of worker reproduction in queenright colonies of the Cape honey bee, Apis mellifera capensis
Authors: BEEKMAN MADELEINE , ALLSOPP MICHAEL H. , JORDAN LYNDON A. , LIM JULIANNE , OLDROYD BENJAMIN P. 
Published: May 2009

AbstractReproduction by workers is rare in honey bee colonies that have an active queen. By not producing their own offspring and preventing other workers from producing theirs, workers are thought to increase their inclusive fitness due to their higher average relatedness towards queen‐produced male offspring compared with worker‐produced male offspring. But there is one exception. Workers of the Cape honey bee, Apis mellifera capensis, are able to produce diploid female offspring via thelytokous parthenogenesis and thus produce clones of themselves. As a result, worker reproduction and tolerance towards worker‐produced offspring is expected to be more permissive than in arrhenotokous (sub)species where worker offspring are male. Here we quantify the extent to which A. m. capensis workers contribute to reproduction in queenright colonies using microsatellite analyses of pre‐emergent brood. We show that workers produced 10.5% of workers and 0.48% of drones. Most of the workers’ contribution towards the production of new workers coincided with the colonies producing new queens during reproductive swarming.
Divergence, hybridization, and recombination in the mitochondrial genome of the human pathogenic yeast Cryptococcus gattii
Authors: XU JIANPING , YAN ZHUN , GUO HONG 
Published: May 2009

AbstractThe inheritance of mitochondrial genes and genomes are uniparental in most sexual eukaryotes. This pattern of inheritance makes mitochondrial genomes in natural populations effectively clonal. Here, we examined the mitochondrial population genetics of the emerging human pathogenic fungus Cryptococcus gattii. The DNA sequences for five mitochondrial DNA fragments were obtained from each of 50 isolates belonging to two evolutionary divergent lineages, VGI and VGII. Our analyses revealed a greater sequence diversity within VGI than that within VGII, consistent with observations of the nuclear genes. The combined analyses of all five gene fragments indicated significant divergence between VGI and VGII. However, the five individual genealogies showed different relationships among the isolates, consistent with recent hybridization and mitochondrial gene transfer between the two lineages. Population genetic analyses of the multilocus data identified evidence for predominantly clonal mitochondrial population structures within both lineages. Interestingly, there were clear signatures of recombination among mitochondrial genes within the VGII lineage. Our analyses suggest historical mitochondrial genome divergence within C. gattii, but there is evidence for recent hybridization and recombination in the mitochondrial genome of this important human yeast pathogen.
Cystic fibrosis: defining a disease under‐diagnosed in Pakistan
Authors: Shah Uzma , Frossard Phillipe , Moatter Tariq 
Published: May 2009

SummaryObjective  Cystic fibrosis is frequently missed in the Pakistani population due to lack of appropriate diagnostic tools. Thus our aim was to define unknown disease‐causing mutations to help create suitable diagnostic tests and improve understanding of what appears to be an aggressive and under‐diagnosed disease in this population.Methods  Patients with elevated sweat chloride values and clinically suspected CF were recruited from Aga Khan University, Pakistan. Mutations DF508, S549R, S549N, Y569D, 296 + 12(T>C), G553X, G551D and G551X were screened for by allele specific polymerase chain reactions. CFTR exons 10, 11 and 12 were sequenced by direct DNA sequencing.Results  Of 150 patients tested by PCR, 26 (17.3%) were positive for ΔF508. One patient was a F508/S549N compound heterozygote. Eighty‐three of 87 patients sequenced for mutations in exon 10 were normal; 42/43 for exon 11 and 29 for exon 12 were normal.Conclusion  This first step in defining mutations involved in Pakistani CF suggests that ΔF508 is uncommon and S549 was the only additional mutation identified in CFTR exons 10, 11 and 12. Identification of the remaining mutations and their frequency is required to design appropriate tests and improve understanding and management of the disease.
Relationship of intentional self‐harm using sharp objects with depressive and dissociative tendencies in pre‐adolescence–adolescence
Authors: Sho Noriko , Oiji Arata , Konno Chizue , Toyohara Koji , Minami Tatsuya , Arai Takashi , Seike Yoji 
Published: May 2009

Aims:  The objectives of the present study were to (i) evaluate the prevalence of children and adolescents who have engaged in intentional self‐harm using a sharp object; and (ii) investigate the relationship between self‐harm with sharp objects and depressive tendencies or dissociative tendencies.Methods:  A total of 1938 students in grades 5–12 in Yokohama, Japan, were enrolled, and they completed anonymous self‐report questionnaires including a question about intentional self‐harm with a sharp object, the Depression Self‐Rating Scale for Children (DSRSC) and the Adolescent Dissociative Experiences Scale (A‐DES).Results:  The prevalence of self‐harm using sharp object was 5.4% among male 5th–6th graders, 4.0% among female 5th–6th graders, 5.3% among male 7th–9th graders, 15.1% among female 7th–9th graders, 6.6% among male 10th–12th graders, and 9.6% among female 10th–12th graders. Categorical regression analysis showed that a small amount of variance in self‐harm by sharp object was explained by DSRSC and A‐DES scores.Conclusions:  Self‐harm with a sharp object was prevalent among pre‐adolescents and adolescents and was associated with depressive and dissociative tendencies.
Smaller amygdala is associated with anxiety in patients with panic disorder
Authors: Hayano Fumi , Nakamura Motoaki , Asami Takeshi , Uehara Kumi , Yoshida Takeshi , Roppongi Tomohide , Otsuka Tatsui , Inoue Tomio , Hirayasu Yoshio 
Published: May 2009

Aims:  Anxiety a core feature of panic disorder, is linked to function of the amygdala. Volume alterations in the brain of patients with panic disorder have previously been reported, but there has been no report of amygdala volume association with anxiety.Methods:  Volumes of hippocampus and amygdala were manually measured using magnetic resonance imaging obtained from 27 patients with panic disorder and 30 healthy comparison subjects. In addition the amygdala was focused on, applying small volume correction to optimized voxel‐based morphometry (VBM). State–Trait Anxiety Inventory and the NEO Personality Inventory Revised were also used to evaluate anxiety.Results:  Amygdala volumes in both hemispheres were significantly smaller in patients with panic disorder compared with control subjects (left: t = −2.248, d.f. = 55, P = 0.029; right: t = −2.892, d.f. = 55, P = 0.005). VBM showed that structural alteration in the panic disorder group occurred on the corticomedial nuclear group within the right amygdala (coordinates [x,y,z (mm)]: [26,−6,−16], Z score = 3.92, family‐wise error‐corrected P = 0.002). The state anxiety was negatively correlated with the left amygdala volume in patients with panic disorder (r = −0.545, P = 0.016).Conclusions:  These findings suggested that the smaller volume of the amygdala may be associated with anxiety in panic disorder. Of note, the smaller subregion in the amygdala estimated on VBM could correspond to the corticomedial nuclear group including the central nucleus, which may play a crucial role in panic attack.
Impact of psychiatric and medical comorbidity on cognitive function in depression
Authors: Baune Bernhard T. , McAfoose Jordan , Leach Geraldine , Quirk Frances , Mitchell David 
Published: May 2009

Aim:  The aim of the present study was to investigate the association between cognitive performance and psychiatric and medical comorbidity in major depression.Methods:  The present study evaluated the cognitive performance of patients (n = 96) diagnosed with a major depressive episode in relation to the presence of medical and/or psychiatric comorbidity. Participants were assessed clinically and cognitively using the Mini International Neuropsychiatric Interview and Repeatable Battery for the Assessment of Neuropsychological Status. Four groups of comorbidity were categorized: (i) no comorbidity, (ii) medical comorbidity; (iii) psychiatric comorbidity; and (iv) both medical and psychiatric comorbidity, and subsequently analyzed for differences across six cognitive domains: immediate memory, visuospatial, language, attention, delayed memory, and total score.Results:  Only 20.8% of the participants did not have a comorbidity of any kind, while psychiatric comorbidities (67.7%) were more frequent than medical comorbidities (39.6%). Education and severity of depressive symptoms negatively influenced cognitive performance. Psychiatric comorbidity alone significantly decreased cognitive performance in the visuospatial/constructional and the language domains and the total score. In addition, increasing numbers of psychiatric comorbidities were related to worse cognitive performance. In contrast, medical illnesses alone had no negative impact on any of the domains of cognitive performance. Evidence was found for additive effects of medical and psychiatric comorbidities in depression on visuospatial/constructional cognitive abilities.Conclusion:  The strongest predictor of poor cognitive performance in depression was psychiatric comorbidity. The assessment and treatment of cognitive dysfunction in depression should consider the relative impact of psychiatric comorbidity.
Medical and psychiatric comorbidity in psychiatric beds in general hospitals: A cross‐sectional study in Tokyo
Authors: Hatta Kotaro , Nakamura Hiroyuki , Usui Chie , Kobayashi Takafumi , Kamijo Yoshito , Hirata Toyoaki , Awata Shuichi , Kishi Yasuhiro , Arai Heii , Kurosawa Hisashi 
Published: May 2009

Aims:  Although somatic diseases in psychiatric patients are increasing with the increase of the aged population, psychiatric wards in general hospitals in Japan have progressively been decreasing. The purpose of this cross‐sectional study was to clarify whether psychiatric beds in general hospitals play sufficient roles in medical comorbidities of psychiatric patients or not.Methods:  This was a cross‐sectional study performed all over Tokyo during the 2‐month period from April to May 2007. The total number of patients who require admission due to both somatic and psychiatric diseases was investigated with their demographic and clinical characteristics.Results:  The total number of patients admitted to psychiatric beds in general hospitals for the above‐mentioned reason was 326, while the number of patients who could not be admitted to them despite the same reason was 88. The rate of surgical diseases in the latter group was higher than that in the former group. In the latter group, diseases requiring orthopedic surgery (22%) and abdominal surgery (22%) were the most frequent, followed by gastrointestinal and hepatic diseases (8%), and gynecological diseases (7%). Patients who had attempted suicide were included more in the latter group than in the former group. Even in the former group, general hospitals could not respond to 34% of requests for emergency admission.Conclusion:  Psychiatric beds in general hospitals do not necessarily function for medical comorbidities in psychiatric patients, especially in severe and emergency cases. Not only the quantity but also the quality of psychiatric wards in general hospitals should be reconsidered.
Proprostate‐specific antigen: Its usefulness in the era of multiple‐core prostate biopsy
Authors: Miyakubo Mai , Ito Kazuto , Yamamoto Takumi , Takechi Hiroyuki , Ohi Masaru , Suzuki Kazuhiro 
Published: May 2009

Objective:  To investigate the clinical significance of prostate‐specific antigen (PSA)‐related markers, including the precursor form of PSA, using the full‐range area under the curve of receiver operating characteristics (AUC‐ROC), partial AUC‐ROC (pAUC‐ROC) and multiple logistic regression analyses.Methods:  Participants consisted of 257 consecutive men (PSA range 4.1–20 ng/mL) undergoing transrectal ultrasonography‐guided age‐adjusted and prostate volume‐adjusted multiple‐core prostate biopsy at Gunma University Hospital between January 2003 and May 2005. Sensitivity, specificity, AUC‐ROC and pAUC‐ROC of the ratio of free PSA to total PSA (free/total PSA), PSA density (PSAD) and PSAD adjusted by transition zone volume, the ratio of [−7/−5] precursor forms of PSA (proPSA) to free PSA (pro/free PSA), the ratio of pro to total PSA and the ratio of pro to free/total PSA (pro/f/t ratio) were investigated. Multiple logistic regression analyses were also carried out to investigate the independency of selected clinical parameters.Results:  According to pAUC‐ROC analyses, pro/free PSA and the pro/f/t ratio were the two best PSA‐related parameters in terms of maintaining high sensitivity and avoiding unnecessary biopsy. Multiple regression analyses revealed that not only pro/free PSA, but also age, findings on digital rectal examination and PSAD were independent parameters for predicting biopsy outcomes.Conclusion:  Pro/free PSA and pro/f/t ratio may be excellent predictive markers for prostate cancer, allowing unnecessary biopsy to be avoided while maintaining high sensitivity at 90% or 95%, in the PSA range 4–20 ng/mL.
The clinical characteristics of renal cell carcinoma in female patients
Authors: Chen Jun , Shi Benkang , Zhang Dongqing , Jiang Xianzhou , Xu Zhishun 
Published: May 2009

Objective:  To investigate the clinical characteristics of renal cell carcinoma (RCC) in female patients.Methods:  The clinical characteristics including sex, age at diagnosis, histological tumor size, histological subtype, Fuhrman nuclear grade and pathological tumor–node–metastasis (TNM) stage of 881 consecutive patients treated with (partial) nephrectomy for RCC from 1998 to 2006 were analyzed. Characteristics of different gender groups and different female age groups were compared. The one‐way anova and t‐test were used to compare means. Pearson's χ2‐test and the likelihood ratio test were used to compare ratios.Results:  Low‐grade tumors accounted for 79.3% of female patients and 64.1% of male patients (P < 0.001). The percentage of stage T1–2 was 76.6% in female patients while it was only 68.5% in male patients (P = 0.011). Also, female patients had more T1–2N0M0 tumors (73.0% vs 64.3%, P = 0.009). Once female patients were classified into three groups according to age diagnosis (≤40, 41–59 and ≥60 years) young female patients seemed to have more tumors with unfavorable histology (8.7% vs 5.1% vs 4.3%), Fuhrman grade 3–4 (23.9% vs 23.1% vs 17.7%) and stage T3–4 (28.3% vs 23.1% vs 22.0%).Conclusion:  Compared with male patients, female patients had lower stage and grade tumors. However, younger female patients had more tumors with unfavorable histology, and higher stage and grade compared to older female patients.