bluuebunny/crossref_metadata_2025_split huggingface dataset:
Shortest path analysis using partial correlations for classifying gene functions from gene expression data
Authors: Fitch A. Marie , Jones M. Beatrix 
Published: November 2008

AbstractMotivation: Gaussian graphical models (GGMs) are a popular tool for representing gene association structures. We propose using estimated partial correlations from these models to attach lengths to the edges of the GGM, where the length of an edge is inversely related to the partial correlation between the gene pair. Graphical lasso is used to fit the GGMs and obtain partial correlations. The shortest paths between pairs of genes are found. Where terminal genes have the same biological function intermediate genes on the path are classified as having the same function. We validate the method using genes of known function using the Rosetta Compendium of yeast (Saccharomyces Cerevisiae) gene expression profiles. We also compare our results with those obtained using a graph constructed using correlations.Results: Using a partial correlation graph, we are able to classify approximately twice as many genes to the same level of accuracy as when using a correlation graph. More importantly when both methods are tuned to classify a similar number of genes, the partial correlation approach can increase the accuracy of the classifications.Contact: m.fitch@massey.ac.nz
A SNARE Complex Unique to Seed Plants Is Required for Protein Storage Vacuole Biogenesis and Seed Development ofArabidopsis thaliana
Authors: Ebine Kazuo , Okatani Yusuke , Uemura Tomohiro , Goh Tatsuaki , Shoda Keiko , Niihama Mitsuru , Morita Miyo Terao , Spitzer Christoph , Otegui Marisa S. , Nakano Akihiko , Ueda Takashi 
Published: November 2008

AbstractThe SNARE complex is a key regulator of vesicular traffic, executing membrane fusion between transport vesicles or organelles and target membranes. A functional SNARE complex consists of four coiled-coil helical bundles, three of which are supplied by Q-SNAREs and another from an R-SNARE. Arabidopsis thaliana VAMP727 is an R-SNARE, with homologs only in seed plants. We have found that VAMP727 colocalizes with SYP22/ VAM3, a Q-SNARE, on a subpopulation of prevacuolar compartments/endosomes closely associated with the vacuolar membrane. Genetic and biochemical analyses, including examination of a synergistic interaction of vamp727 and syp22 mutations, histological examination of protein localization, and coimmunoprecipitation from Arabidopsis lysates indicate that VAMP727 forms a complex with SYP22, VTI11, and SYP51 and that this complex plays a crucial role in vacuolar transport, seed maturation, and vacuole biogenesis. We suggest that the VAMP727 complex mediates the membrane fusion between the prevacuolar compartment and the vacuole and that this process has evolved as an essential step for seed development.
Fostering family resiliency: a review of the key protective factors
Authors: Benzies Karen , Mychasiuk Richelle 
Published: November 2008

ABSTRACTThe aim of this integrative review was to identify the protective factors that contribute to family resiliency. Families are comprised of individuals who interact across levels in a socio‐ecological system. Family resiliency does not develop through evasion of risk, but through successful application of protective factors to engage in adverse situations and emerge from them stronger. In an effort to move away from pathological labelling, this review provides a foundation for strength‐based family interventions. Thirteen peer‐reviewed databases were searched for articles and information regarding family resiliency. Careful review yielded 24 protective factors that foster resiliency across three distinct but interactive levels: individual, family and community. The protective factors identified in this review of the literature offer an excellent starting point for development of clinical interventions to support family resiliency.
Peanut cross‐reacting allergens in seeds and sprouts of a range of legumes
Authors: Jensen L. B. , Pedersen M. H. , Skov P. S. , Poulsen L. K. , Bindslev‐Jensen C. , Andersen S. B. , Torp A. M. 
Published: November 2008

SummaryBackground
Recently, peanut‐allergic patients have reported symptoms upon ingestion of bean sprouts produced from various legumes.Objective
This study was designed to identify immunoreactivity to seeds and sprouts of legumes other than peanut in sera from peanut‐allergic patients.Methods
Crude protein extracts of seeds and sprouts (comprising cotelydons and hypocotyls/epicotyls) of peanut, soybean, green pea, blue lupine, mung bean, alfalfa, broad bean, and azuki bean were prepared. The reactivity of sera from 10 peanut‐allergic patients to these extracts was analysed by indirect histamine release (HR), enzyme‐allergosorbent test (EAST), EAST inhibition, and Western blots. Skin prick tests (SPTs) were performed on the patients with fresh legume seeds as well as four commercial legume sprouts, and food challenges with soybean, pea, and lupine were performed on a subgroup of the patients.Results
All legume seeds and commercial sprouts induced positive SPTs in some of the patients. Indirect HR experiments indicated an extensive co‐reactivity between peanut and the legumes, and cross‐reactivity was observed for soybean, pea, and lupine seeds as well as lupine hypocotyls in EAST inhibition experiments. Of the 16 protein extracts, soybean, pea, and lupine seed extracts produced visible bands in Western blots.Conclusion
The symptoms reported by peanut‐allergic patients after legume sprout intake might be caused by cross‐reactivity of peanut‐specific antibodies. The intake of raw legume sprouts might cause symptoms in peanut‐allergic patients.
Interleukin-18-deficient mice exhibit diminished chronic inflammation and airway remodelling in ovalbumin-induced asthma model
Authors: Yamagata S , Tomita K , Sato R , Niwa A , Higashino H , Tohda Y 
Published: November 2008

Summary
Interleukin (IL)-18, which is produced by activated monocytes/macrophages and airway epithelial cells, is suggested to contribute to the pathophysiology of asthma by modulating airway inflammation. However, the involvement of IL-18 on modulating chronic airway inflammation and airway remodelling, which are characterized in a refractory asthma model exposed to long-term antigen, has not been investigated sufficiently. We examined the role of IL-18 in chronic airway inflammation and airway remodelling by long-term antigen exposure. IL-18-deficient and C57BL/6-wild-type mice were sensitized by ovalbumin (OVA) and were then exposed to aerosolized OVA twice a week for 12 weeks. We assessed airway inflammation by assessing the infiltration of cells into the airspace and lung tissues, and airway remodelling by airway mucus expression, peribronchial fibrosis and smooth muscle thickness. In IL-18-deficient mice, when exposed to OVA, the total cells and neutrophils of the bronchoalveolar lavage fluid (BALF) were diminished, as were the number of infiltrated cells in the lung tissues. IL-18-deficient mice exposed to OVA after 12 weeks showed significantly decreased levels of interferon (IFN)-γ, IL-13 and transforming growth factor (TGF)-β1 in the BALF. The airway hyperresponsiveness to acetyl-β-methacholine chloride was inhibited in IL-18-deficient mice in comparison with wild-type mice. In addition, IL-18-deficient mice exposed to OVA had fewer significant features of airway remodelling. These findings suggest that IL-18 may enhance chronic airway inflammation and airway remodelling through the production of IFN-γ, IL-13 and TGF-β1 in the OVA-induced asthma mouse model.
Clinical relevance of multiple antibody specificity testing in anti-phospholipid syndrome and recurrent pregnancy loss
Authors: Tebo A E , Jaskowski T D , Hill H R , Branch D W 
Published: November 2008

SummaryWe wanted to evaluate whether testing for anti-phosholipid antibodies other than anti-cardiolipin (aCL) and anti-beta-2 glycoprotein I (aβ2GPI) immunoglobulin (Ig)G and IgM identifies patients with recurrent pregnancy loss (RPL) who may be positive for anti-phospholipid syndrome (APS). In a cross-sectional study comprising 62 patients with APS, 66 women with RPL, 50 healthy blood donors and 24 women with a history of successful pregnancies, we tested IgM and IgG antibodies to phosphatidic acid, phosphatidyl choline, phosphatidyl ethanolamine, phosphatidyl glycerol, phosphatidyl inositol and phosphatidyl serine with and without beta-2 glycoprotein I (β2GPI) from a single manufacturer as well as aCL and aβ2GPI antibodies. Diagnostic accuracies of individual and combined anti-phospholipid (aPL) assays were assessed by computing sensitivities, specificities, positive predictive values and negative predictive values together with their 95% confidence intervals. There was a general trend for increased sensitivities in the presence of β2GPI co-factor with significant effect for certain specificities. The overall combined sensitivity of the non-recommended aPL assays was not significantly higher than that of the aCL and aB2GPI tests. Multiple aPL specificities in RPL group is not significantly different from controls and therefore of no clinical significance.
The successful treatment of haemophagocytic syndrome in patients with human immunodeficiency virus-associated multi-centric Castleman's disease
Authors: Stebbing J , Ngan S , Ibrahim H , Charles P , Nelson M , Kelleher P , Naresh K N , Bower M 
Published: November 2008

Summary
Both virus-associated haemophagocytic syndrome (HPS) and human immunodeficiency virus-associated multi-centric Castleman's disease (HIV-MCD) induced by human herpesvirus-8 (HHV-8) are extremely rare. We therefore wished to investigate their occurrence together, and establish the degree of cytokine activation present. From a prospective cohort of individuals with HIV-MCD, we investigated the incidence and outcomes of HPS and measured 15 inflammatory cytokines and the plasma HHV-8 viral loads before and during follow-up. Of 44 patients with HIV-MCD with an incidence of 4·3/10 000 patient years, four individuals (9%) were diagnosed with HPS. All are in remission (range 6–28 months) following splenectomy, etoposide and rituximab-based therapy. Plasma HHV-8 levels were raised markedly at presentation (median 3 840 000 copies/ml). Histological samples from spleen, splenic hilar lymph nodes and bone marrow demonstrated increased phagocytosis by histiocytes and presence of HHV-8-infected plasmablasts outside the follicles. Surprisingly, many known inflammatory plasma cytokines were not elevated, although interleukin (IL)-8 and interferon-γ were increased in all cases and IL-6 levels were raised in three of four patients. HPS in the setting of HIV-MCD is common and treatment can be successful provided the diagnosis is made appropriately. Systemic activation of cytokines was limited, suggesting that immunosuppressive therapy with steroids is not indicated in HHV-8-driven HPS.
Effects ofBifidobacterium animalisadministered during lactation on allergic and autoimmune responses in rodents
Authors: Ezendam J , De Klerk A , Gremmer E R , Van Loveren H 
Published: November 2008

SummaryProbiotics are promoted as being beneficial to health and positive effects on the immune system have been reported. Beneficial immune effects have been attributed to several mechanisms, including stimulating T helper 1 (Th1) immunity. To explore the effects of the probiotic Bifidobacterium animalis on Th1- and Th2-mediated immune responses, two different animal models representing either Th1- or Th2-mediated immune responses were used: a rat model for experimental autoimmune encephalomyelitis (EAE) (Th1) and a mouse model for respiratory allergy induced by ovalbumin (OVA) (Th2). B. animalis administration started when the mice or rats were 2 weeks old. Respiratory allergy or EAE were induced when the animals were 6–7 weeks old. In the allergy model, B. animalis modestly reduced the number of infiltrating eosinophils and lymphocytes in the lungs, but no effects on allergen-specific serum immunoglobulin E levels were found. Cytokine profiles assessed after culturing spleen cells with the mitogen concanvalin A (ConA) showed that B. animalis skewed the Th1/Th2 balance towards Th1 in females. However, allergen-induced cytokine production in females was not affected by B. animalis. In males, B. animalis significantly decreased ConA-induced interleukin-13 and a trend towards lower levels of OVA-induced Th2 cytokines. In the EAE model, B. animalis significantly reduced the duration of clinical symptoms by almost 2 days in males and improved the body weight gain during the experimental period compared with the control group. Our data show that B. animalis reduced several immune parameters in the allergy as well as in the autoimmunity model.
An in vivo rat model for early development of colorectal cancer metastasis to liver
Authors: Robertson John H. P. , Yang Shi Yu , Iga Arthur M. , Seifalian Alexander M. , Winslet Marc C. 
Published: November 2008

SummaryAt diagnosis of colorectal cancer, approximately 25% of the patients have established colorectal liver metastasis. Optimal management of disseminated disease requires therapies targeting multiple stages in hepatic colorectal cancer metastasis development. To facilitate this, biologically accurate in vivo models are required. Early colonic cancer liver metastases development was studied using BDIX and Sprague–Dawley rat strains with human HT29 and rat DHDK12 colonic cancer cell lines. Different cancer cell–host combinations were used. Rat DHDK12 was previously chemically induced in the BDIX rat. Real‐time intra‐vital microscopy was employed to analyse the early development of liver metastases in four groups (n = 6 per group) (HT29–BDIX, DHDK12–BDIX, HT29–SD and DHDK12–SD). Data were compared using one‐way anova with Bonferroni’s multiple comparison test. The total number of tumour cells visualized, adherent cells within the hepatic sinusoids, extravasated tumour cells and migration rates were significantly higher in the DHDK12–BDIX combination. Maximum number of visualized cells and maximum migration rate were also significantly higher in this group. No significant differences were observed in these experimental parameters among the other three groups or in the haemodynamic parameters among all groups. In conclusion, cancer cell line–host selection has a significant effect on early colonic cancer liver metastasis development.
Acute colonic ischaemia in rats results in long‐term structural changes without alterations of colonic sensitivity
Authors: Ravnefjord Anna , Pettersson Madeleine , Rehnström Erika , Martinez Vicente 
Published: November 2008

SummaryColonic ischaemia and mast cells have been involved in the pathophysiology of the functional gastrointestinal disorder irritable bowel syndrome, although the cause–effect relationships remain unknown. We assessed long‐term histopathological and functional changes associated to an acute ischaemic episode (1 h) of the colon, followed by 8‐week recovery, in rats. Functional colonic alterations [sensitivity during colorectal distension (CRD), compliance and propulsive motility] were assessed regularly during the recovery. Colonic histopathology (presence of inflammation, morphometric alterations and variations in neuronal density in the enteric nervous system) 8‐week postischaemia was assessed. Following ischaemia, none of the functional parameters tested (motility, sensitivity and compliance) were affected. At necropsy, the colon presented an overall normal appearance with an increase in weight of the ischaemic area (mg/cm: 99 ± 6;P < 0.05vs. control: 81 ± 4 or sham ischaemia: 81 ± 3). Histopathological evaluations revealed the presence of a local infiltrate of mast cells in the area of ischaemia (nb of mast cells: 142 ± 50;P < 0.05vs. control, 31 ± 14 or sham ischaemia: 40 ± 16), without other significant alterations. Animals subjected to colonic ischaemia and treated 8 weeks later with the mast cell degranulator, compound 48/80, showed no changes in CRD‐related pain responses. These studies show that acute colonic ischaemia is associated with the presence of a long‐term local infiltration of mast cells, located within the serosa and muscle layers, despite the absence of functional changes, including colonic sensitivity. Considering the important pathophysiological functions of mast cells, the observed mast cell infiltration may be involved in ischaemia‐induced functional changes yet to be characterized.
A general practice‐based study of the relationship between indicators of mental illness and challenging behaviour among adults with intellectual disabilities
Authors: Felce D. , Kerr M. , Hastings R. P. 
Published: November 2008

AbstractBackground  Existing studies tend to show a positive association between mental illness and challenging behaviour among adults with intellectual disabilities (ID). However, whether the association is direct or artefactual is less clear. The purpose was to explore the association between psychiatric status and level of challenging behaviour, while controlling for adaptive behaviour and occurrence of autistic spectrum disorders.Methods  Data were collected on the age, gender, adaptive and challenging behaviour, social impairment and psychiatric status of 312 adults with ID. Participants were divided according to psychiatric status, group equivalence in adaptive behaviour and the presence of autistic spectrum disorders achieved, and differences in challenging behaviour explored. In addition, multiple regression was used to examine the association between psychiatric status and challenging behaviour after controlling for other participant characteristics and to test whether the interaction between psychiatric status and adaptive behaviour added significantly to explanation.Results  Challenging behaviour was higher among participants meeting threshold levels on the psychiatric screen. The regression analysis confirmed the association and demonstrated an interaction between total score on the psychiatric screen and level of adaptive behaviour. This moderated effect showed the relationship between psychiatric status and challenging behaviour to be stronger at lower adaptive behaviour.Conclusions  This study reinforces previous findings that psychiatric morbidity among people with ID is associated with higher levels of challenging behaviour and supports predictions that this association is more pronounced for people with severe ID. The precise nature and causal direction of the association requires further clarification. However, the understanding of how psychiatric problems might contribute to challenging behaviour needs to be part of the clinical appreciation of such behaviour.
Cefquinome Concentrations in Endometrium after Intrauterine Treatment of Cobactan 4.5%®in Mares and Inflammatory Response of the Endometrium to this Treatment
Authors: Parlevliet JM , Paccamonti DL , Barker SA 
Published: November 2008

ContentsThis study was conducted to measure the concentration of cefquinome in the endometrium of mares after intrauterine treatment and to evaluate associated inflammation. Mares (n = 14) were randomly assigned to one of the following groups: (i) control (n = 4) were either not treated (n = 2) or received (n = 2) lactated Ringer’s intrauterine for 1 or 3 days; (ii) treated mares (n = 10) received intrauterine cefquinome for 1 or 3 days. After at least 10 days had passed following the last treatment and ovulation, mares were given Prostaglandin F2α (PGF2α) and were randomly assigned to an alternate treatment. Endometrial biopsy samples were taken at 2, 8, 24 and 48 h, or at 4, 12 and 36 h, after the last treatment. Biopsy samples were taken at the same time points from control mares (n = 2) and lactated Ringer‐treated mares (n = 2). Cefquinome concentrations were quantified using a high‐performance liquid chromatography (HPLC) assay and inflammation was assessed using haematoxylin and eosin (H&E)‐stained sections. Concentrations of cefquinome [559 (1 day) and 595 μg/g (3 days) at 2 h, and 403 (1 day) and 370 μg/g (3 days) at 4 h] were similar between treatment groups at 2 and 4 h after treatment (p > 0.05). At 8 h, as well as at 24 and 48 h, concentrations were greater in the 3‐day group (17 vs 301 μg/g, 3 vs 80 μg/g and 0.1 vs 0.2 μg/g, respectively) (p < 0.05). No significant differences (p > 0.05) in the inflammatory response at 2–48 h after treatment were found between groups.
Development of a fall prevention program for elderly Japanese people
Authors: Kato Mayumi , Izumi Kiyoko , Shirai Shizuko , Kondo Kazuko , Kanda Makiko , Watanabe Isao , Ishii Kazuko , Saito Ryoko 
Published: November 2008

AbstractThe purpose of this study was to develop a fall prevention program adapted to the individual risks of elderly patients in a long‐term care facility by increasing the caregiving skills and motivation of the staff members. The fall prevention program was created by synthesizing information based on evidence‐based practice and action research methodology was chosen to complete the development of the program. There were 31 participating patients in the intervention ward and 20 patients in the control ward. The Generalized Self‐efficacy Scale and the Social Support Scale were used to evaluate fall prevention skills the motivation of the staff members. The fall prevention program helped to reduce injuries from 41.9% to 9.7% among the elderly participants and to increase emotional support and self‐efficacy among the staff members. Empowerment was considered to be a driving force. The fall prevention program was shown to be acceptable for use among elderly individuals in a long‐term care facility.
Undesired effects of a combinatorial treatment for spinal cord injury – transplantation of olfactory ensheathing cells and BDNF infusion to the red nucleus
Authors: Bretzner Frederic , Liu Jie , Currie Erin , Roskams A. Jane , Tetzlaff Wolfram 
Published: November 2008

AbstractTransplantations of olfactory ensheathing cells (OECs) have been reported to promote axonal regeneration and functional recovery after spinal cord injury, but have demonstrated limited growth promotion of rat rubrospinal axons after a cervical dorsolateral funiculus crush. Rubrospinal neurons undergo massive atrophy after cervical axotomy and show only transient expression of regeneration‐associated genes. Cell body treatment with brain‐derived neurotrophic factor (BDNF) prevents this atrophy, stimulates regeneration‐associated gene expression and promotes regeneration of rubrospinal axons into peripheral nerve transplants. Here, we hypothesized that the failure of rubrospinal axons to regenerate through a bridge of OEC transplants was due to this weak intrinsic cell body response. Hence, we combined BDNF treatment of rubrospinal neurons with transplantation of highly enriched OECs derived from the nasal mucosa and assessed axonal regeneration as well as behavioral changes after a cervical dorsolateral funiculus crush. Each treatment alone as well as their combination prevented the dieback of the rubrospinal axons, but none of them promoted rubrospinal regeneration beyond the lesion/transplantation site. Motor performance in a food‐pellet reaching test and forelimb usage during vertical exploration (cylinder test) were more impaired after combining transplantation of OECs with BDNF treatment. This impaired motor performance correlated with lowered sensory thresholds in animals receiving the combinatorial therapy – which were not seen with each treatment alone. Only this combinatorial treatment group showed enhanced sprouting of calcitonin gene‐related peptide‐positive axons rostral to the lesion site. Hence, some combinatorial treatments, such as OECs with BDNF, may have undesired effects in the injured spinal cord.