bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ctenophore Whole-Mount Antibody Staining
Authors: Pang Kevin , Martindale Mark Q. 
Published: November 2008

INTRODUCTIONCtenophores, or comb jellies, are a group of marine animals whose unique biological features and phylogenetic placement make them a key taxon for understanding animal evolution. Some characteristics are present in nearly all ctenophores, including biradial symmetry, comb rows composed of linked cilia, an apical sensory organ, and two tentacles bearing specialized adhesive cells. All ctenophores studied thus far have the same stereotyped cleavage program and go through a specific stage of development known as the cydippid larva, after which adult structures develop and diverge greatly among species; this is particularly useful for comparative studies. Because of the ease of embryo collection, their size (up to 1 mm in some species), and their rapid development, ctenophores have been attractive animals for experimental embryologists. This protocol describes how to fix ctenophore embryos and their cydippid larvae for antibody staining. Once the samples have been fixed, tissues are incubated with an antibody to the epitope of interest. A secondary antibody conjugated to a fluorescent molecule then reveals the expression pattern of the epitope. Fluorescent microscopy is used to visualize and document the signal. The protocol also includes methods for staining or counterstaining with a fluorescent derivative of phalloidin, which reveals F-actin in muscles and cell borders. Although the protocol focuses on embryonic and larval samples, the technique can also be applied to adult tissues.
Ctenophore Whole-Mount In Situ Hybridization
Authors: Pang Kevin , Martindale Mark Q. 
Published: November 2008

INTRODUCTIONCtenophores, or comb jellies, are a group of marine animals whose unique biological features and phylogenetic placement make them a key taxon for understanding animal evolution. Some characteristics are present in nearly all ctenophores, including biradial symmetry, comb rows composed of linked cilia, an apical sensory organ, and two tentacles bearing specialized adhesive cells. All ctenophores studied thus far have the same stereotyped cleavage program and go through a specific stage of development known as the cydippid larva, after which adult structures develop and diverge greatly among species; this is particularly useful for comparative studies. In some cases, gene expression patterns appear to be conserved. Of particular interest is the finding that some genes are expressed in regions of the ctenophore body that are not morphologically distinct from the adjacent areas. However, it has proven difficult to determine the orthology of some genes, possibly because of the extreme divergence of ctenophore representatives. This protocol describes how to fix, prepare, and hybridize antisense RNA probes in ctenophore embryos and cydippid larvae, as well as how to detect the probes using an alkaline phosphatase-conjugated antibody and colorimetric substrates. Using these techniques, it is possible to determine which cells or tissues express the gene of interest. Although the protocol focuses on embryonic and larval samples, the technique can also be applied to adult tissues.
Ctenophore Tissue Preparation and Extraction of DNA
Authors: Pang Kevin , Martindale Mark Q. 
Published: November 2008

INTRODUCTIONCtenophores, or comb jellies, are a group of marine animals whose unique biological features and phylogenetic placement make them a key taxon for understanding animal evolution. Some characteristics are present in nearly all ctenophores, including biradial symmetry, comb rows composed of linked cilia, an apical sensory organ, and two tentacles bearing specialized adhesive cells. All ctenophores studied thus far have the same stereotyped cleavage program and go through a specific stage of development known as the cydippid larva, after which adult structures develop and diverge greatly among species; this is particularly useful for comparative studies. In some cases, gene expression patterns appear to be conserved. Of particular interest is the finding that some genes are expressed in regions of the ctenophore body that are not morphologically distinct from the adjacent areas. However, it has proven difficult to determine the orthology of some genes, possibly because of the extreme divergence of ctenophore representatives. This protocol describes how to isolate genomic DNA from ctenophores. The procedure can be applied to adult tissues, but it is best to use embryos and larvae. After washing and concentrating the embryos or larvae, DNA is extracted using DNAzol reagent, a guanidine-detergent lysing solution. The resulting DNA can be used for polymerase chain reaction (PCR) or other applications.
Ctenophore Tissue Preparation and Extraction of RNA
Authors: Pang Kevin , Martindale Mark Q. 
Published: November 2008

INTRODUCTIONCtenophores, or comb jellies, are a group of marine animals whose unique biological features and phylogenetic placement make them a key taxon for understanding animal evolution. Some characteristics are present in nearly all ctenophores, including biradial symmetry, comb rows composed of linked cilia, an apical sensory organ, and two tentacles bearing specialized adhesive cells. All ctenophores studied thus far have the same stereotyped cleavage program and go through a specific stage of development known as the cydippid larva, after which adult structures develop and diverge greatly among species; this is particularly useful for comparative studies. In some cases, gene expression patterns appear to be conserved. Of particular interest is the finding that some genes are expressed in regions of the ctenophore body that are not morphologically distinct from the adjacent areas. However, it has proven difficult to determine the orthology of some genes, possibly because of the extreme divergence of ctenophore representatives. This protocol describes how to isolate total RNA from ctenophore embryos and larvae. After the specimens are sorted, cleaned, and concentrated, they are placed into TRI Reagent, a solution containing phenol and guanidine thiocyanate that allows for the effective isolation of total RNA. The resulting RNA can be used for various applications (e.g., to generate cDNA for reverse transcriptase-polymerase chain reactions). Although the protocol focuses on embryonic and larval samples, the technique can also be applied to adult tissues.
Determining the Sex of Adult Astyanax mexicanus
Authors: Borowsky Richard 
Published: November 2008

INTRODUCTIONThis protocol describes methods for determining the sex of an individual Astyanax mexicanus. Adult males and females differ most obviously in body shape and in form of the anal fin. However, if the sex of an adult cannot be determined by these differences, it can be assessed by testing the anal fin for the presence (or absence) of denticle or hook-like bony elements on the anterior fin rays of the anal fin. These features are observed as an opacity toward the anterior half of the male’s anal fin, detected as described in the method presented here.
Breeding Astyanax mexicanus through Natural Spawning
Authors: Borowsky Richard 
Published: November 2008

INTRODUCTIONMale and female Astyanax mexicanus can be bred successfully in tanks under appropriate conditions. Females should be maintained on a diet high in fats for 10-14 d before breeding. The transfer of a male and female into clean water in a fresh tank and a change (increase) in water temperature are cues for breeding. Newly fertilized eggs may also be obtained through in vitro fertilization. Note that blind fish should never be paired with eyed fish in illuminated aquaria, because the eyed fish are aggressive and will kill even much larger blind fish. Such matings must be carried out in the dark or by using in vitro fertilization.
Prognostic value of kallikrein‐related peptidase 6 protein expression levels in advanced ovarian cancer evaluated by automated quantitative analysis (AQUA)
Authors: Kountourakis Panteleimon , Psyrri Amanda , Scorilas Andreas , Camp Robert , Markakis Sonia , Kowalski Diane , Diamandis Eleftherios P. , Dimopoulos Meletios A. 
Published: November 2008

Kallikrein‐related peptidases, a subgroup of the serine protease enzyme family, are considered important prognostic biomarkers in cancer. In the present study, we sought to determine the prognostic value of kallikrein‐related peptidase 6 (KLK6) in ovarian cancer using a novel method of compartmentalized in situ protein analysis. A tissue array composed of 150 advanced stage ovarian cancers, uniformly treated with surgical debulking followed by platinum‐paclitaxel combination chemotherapy, was constructed. For evaluation of KLK6 protein expression, we used an immunofluorescence‐based method of automated in situ quantitative measurement of protein analysis (AQUA). Mean follow‐up time of the cohort was 34.35 months. One hundred and thirty‐five of 150 cases had sufficient tissue for AQUA analysis. In univariate survival analysis, low tumor KLK6 expression was associated with better outcome for overall survival over 3 years (P = 0.019). There was no association between tumor KLK6 expression and progression‐free survival (P = 0.128). In multivariate survival analysis, adjusting for well‐characterized prognostic variables, low tumor KLK6 expression level was one of the most significant predictor variable for overall survival (95% confidence interval, 1.19–3.50; P = 0.009). High tumor KLK6 protein expression is associated with inferior patient outcome in ovarian cancer. KLK6 may represent a promising disease biomarker and therapeutic target in ovarian cancer. (Cancer Sci 2008; 99: 2224–2229)
Non‐transmissible Sendai virus encoding granulocyte macrophage colony‐stimulating factor is a novel and potent vector system for producing autologous tumor vaccines
Authors: Inoue Hiroyuki , Iga Mutsunori , Nabeta Haruka , Yokoo Tomoko , Suehiro Yoko , Okano Shinji , Inoue Makoto , Kinoh Hiroaki , Katagiri Toyomasa , Takayama Koichi , Yonemitsu Yoshikazu , Hasegawa Mamoru , Nakamura Yusuke , Nakanishi Yoichi , Tani Kenzaburo 
Published: November 2008

The recent clinical application of granulocyte macrophage colony‐stimulating factor (GM‐CSF)‐transduced autologous tumor vaccines revealed substantial antitumor activity and valuable clinical results. However, for these vaccines to be optimally effective, the antitumor efficacies must be improved. Recently, Sendai virus (SeV) vectors, which are cytoplasmic RNA vectors, have emerged as safe vectors with high gene transduction. In the current study, the in vivo therapeutic antitumor efficacies of irradiated GM‐CSF‐transduced mouse renal cell carcinoma (RENCA) vaccine cells mediated by either fusion gene‐deleted non‐transmissible SeV encoding mouse GM‐CSF (SeV/dF/G) or adenovirus (E1, E3 deleted serotype 5 adenovirus) encoding mouse GM‐CSF (AdV/G) (respectively described as irRC/SeV/GM or irRC/AdV/GM) were compared in RENCA‐bearing mice. The results showed that the antitumor effect was equivalent between irRC/SeV/GM and irRC/AdV/GM cells, even though the former produced less GM‐CSF in vitro. The cell numbers of activated (CD80+, CD86+, CD80+CD86+) dendritic cells in lymph nodes from mice treated with irRC/AdV/GM or irRC/SeV/GM cells were increased significantly compared with those of mice treated with the respective controls, at both the earlier and later phases. In an in vitro cytotoxicity assay, splenocytes harvested from mice treated with both irRC/SeV/GM and irRC/AdV/GM cells showed tumor‐specific responses against RENCA cells. The restimulated splenocytes harvested from mice treated with irRC/SeV/GM or irRC/AdV/GM cells produced significantly higher levels of interleukin‐2, interleukin‐4, and interferon‐γ compared with their respective controls (P < 0.05). Furthermore, vaccination with irRC/AdV/GM or irRC/SeV/GM cells induced significantly enhanced recruitment of the cytolytic effectors of CD107a+CD8+ T cells and CD107a+ natural killer cells into tumors compared with those induced by their respective controls (P < 0.05). Taken together, our results suggest that the SeV/dF/G vector is a potential candidate for the production of effective autologous GM‐CSF‐transduced tumor vaccines in clinical cancer immune gene therapy. (Cancer Sci 2008; 99: 2315–2326)
Effectiveness of current treatment approaches for benzodiazepine discontinuation: a meta‐analysis
Authors: Parr Jannette M. , Kavanagh David J. , Cahill Lareina , Mitchell Geoffrey , Young Ross McD. 
Published: November 2008

ABSTRACTAims  To assess the effectiveness of current treatment approaches to assist benzodiazepine discontinuation.Methods  A systematic review of approaches to benzodiazepine discontinuation in general practice and out‐patient settings was undertaken. Routine care was compared with three treatment approaches: brief interventions, gradual dose reduction (GDR) and psychological interventions. GDR was compared with GDR plus psychological interventions or substitutive pharmacotherapies.Results  Inclusion criteria were met by 24 studies, and a further eight were identified by future search. GDR [odds ratio (OR) = 5.96, confidence interval (CI) = 2.08–17.11] and brief interventions (OR = 4.37, CI = 2.28–8.40) provided superior cessation rates at post‐treatment to routine care. Psychological treatment plus GDR were superior to both routine care (OR = 3.38, CI = 1.86–6.12) and GDR alone (OR = 1.82, CI = 1.25–2.67). However, substitutive pharmacotherapies did not add to the impact of GDR (OR = 1.30, CI = 0.97–1.73), and abrupt substitution of benzodiazepines by other pharmacotherapy was less effective than GDR alone (OR = 0.30, CI = 0.14–0.64). Few studies on any technique had significantly greater benzodiazepine discontinuation than controls at follow‐up.Conclusions  Providing an intervention is more effective than routine care. Psychological interventions may improve discontinuation above GDR alone. While some substitutive pharmacotherapies may have promise, current evidence is insufficient to support their use.
Early pubertal maturation in the prediction of early adult substance use: a prospective study
Authors: Hayatbakhsh Mohammad R. , Najman Jake M. , McGee Tara R. , Bor William , O'Callaghan Michael J. 
Published: November 2008

ABSTRACTAims  To examine whether self‐reporting a later stage of pubertal development in early adolescence predicts young adults' use of illicit drugs.Design  Population‐based prospective birth cohort study.Setting  Follow‐up of a cohort of mothers and their children, recruited between 1981 and 1983.Participants  Cohort of 2710 young adults who completed a self‐report questionnaire about their use of cannabis and amphetamines at the 21‐year follow‐up.Measurements  Young adults' use of cannabis and amphetamines were measured at the 21‐year follow‐up. Stage of pubertal development was assessed at the 14‐year follow‐up. Potential confounding and mediating variables were assessed between birth and when the child was 14 years.Findings  Of 2710 young adults, 49.9% (47.3 females and 52.7% males) reported that they had used cannabis and 21.0% (18.9% females and 23.3% males) reported that they had used amphetamines and cannabis by 21 years. In multivariate analyses, adolescents with a later stage of puberty were more likely to use cannabis or amphetamines in young adulthood. This association was not confounded by mother's education or child's gender and age. Part of the relationship was explained by the higher frequency of child externalizing behaviour at 14 years.Conclusions  The findings warrant further attention to puberty as a sensitive period in an individual's development. With regard to prevention, there is a need to understand more about the pathways between pubertal development, child behaviour problems and substance use.
A substrate peptide for the FLT3 receptor tyrosine kinase
Authors: Böhmer Frank‐D. , Uecker Andrea 
Published: November 2008

SummaryFLT3 (fms‐like tyrosine kinase 3) is frequently activated by mutation in acute myeloid leukemia, and is therefore under study as a drug target. Testing and characterization of tyrosine kinase inhibitors is facilitated by the availability of efficient peptide substrates. Searching for FLT3 peptide substrates using phosphorylation experiments on peptide arrays and in solution revealed that the peptide F‐T‐D‐R‐L‐Q‐Q‐Y8‐I‐S‐T‐R‐G‐L‐G is efficiently phosphorylated (apparent Km 10 μmol/l), with Y8 as the phosphorylated site. This peptide presents a novel tool for identifying and characterizing FLT3 kinase inhibitors.
The biocompatible polysaccharide chitosan enhances the oral tolerance to type II collagen
Authors: Porporatto C , Canali M M , Bianco I D , Correa S G 
Published: November 2008

SummaryChitosan is a mucoadhesive polysaccharide that promotes the transmucosal absorption of peptides and proteins. At mucosal sites chitosan exhibits immunomodulatory activities and stimulates the release of regulatory cytokines. Herein we evaluated the effect of the co-administration of chitosan in the tolerance to type II collagen (CII) using an experimental model of arthritis. Rats were fed diluent (acetic acid), 1 mg CII, 1 mg chitosan or 1 mg CII + 1 mg chitosan during 5 days before immunization with CII in Freund's complete adjuvant. Systemic effects were evaluated in draining lymph nodes after antigenic challenge or during the clinical evolution of arthritis. Specific antibodies, proliferation against CII and the production of interferon (IFN)-γ and interleukin-10 were assessed. Clinical signs were observed 13–15 days after primary immunization. The CII : chitosan group presented the lowest incidence and developed moderate arthritis, with reduced levels of immunoglobulin (Ig)G2a anti-CII, a limited proliferation in draining lymph nodes and a lower release of IFN-γ after restimulation with CII. Our results demonstrate that chitosan enhances the tolerance to an articular antigen with a decrease in the inflammatory responses and, as a consequence, an improvement in clinical signs.
Mercury and silver induce B cell activation and anti-nucleolar autoantibody production in outbred mouse stocks: are environmental factors more important than the susceptibility genes in connection with autoimmunity?
Authors: Abedi-Valugerdi M 
Published: November 2008

SummaryEnvironmental and predisposing genetic factors are known to play a crucial role in the development of systemic autoimmune diseases. With respect to the role of environmental factors, it is not known how and to what extent they contribute to the initiation and exacerbation of systemic autoimmunity. In the present study, I considered this issue and asked if environmental factors can induce autoimmunity in the absence of specific susceptible genes. The development of genetically controlled mercury- and silver-induced B cell activation and anti-nucleolar autoantibodies (ANolA) production in genetically heterozygous outbred Institute of Cancer Research (ICR), Naval Medical Research Institute (NMRI) and Black Swiss mouse stocks were analysed. Four weeks of treatment with both mercury and silver induced a strong B cell activation characterized by increased numbers of splenic antibody-secreting cells of at least one or more immunoglobulin (Ig) isotype(s) in all treated stocks. The three stocks also exhibited a marked increase in the serum IgE levels in response to mercury, but not silver. More importantly, in response to mercury a large numbers of ICR (88%), NMRI (96%) and Black Swiss (100%) mice produced different levels of IgG1 and IgG2a ANolA (a characteristic which is linked strictly to the H-2 genes). Similarly, but at lower magnitudes, treatment with silver also induced the production of IgG1 and IgG2a ANolA in 60% of ICR, 75% of NMRI and 100% of Black Swiss mice. Thus, the findings of this study suggest that long-term exposure to certain environmental factors can activate the immune system to produce autoimmunity per se, without requiring specific susceptible genes.
Patients with inflammatory bowel disease may have a transforming growth factor-β-, interleukin (IL)-2- or IL-10-deficient state induced by intrinsic neutralizing antibodies
Authors: Ebert E C , Panja A , Das K M , Praveen R , Geng X , Rezac C , Bajpai M 
Published: November 2008

SummaryUlcerative colitis (UC) and Crohn's disease (CD) are considered to be immunologically mediated disorders that share certain features with murine models of colitis. Whether any of these models are physiologically relevant to the human condition remains controversial. The hypothesis is that increased amounts of antibodies neutralizing transforming growth factor (TGF)-β, interleukin (IL)-2 or IL-10 create a relative immunodeficient state in inflammatory bowel disease (IBD) that predisposes to disease. To evaluate this, serum samples from patients with UC or CD and from normal healthy individuals were studied by enzyme-linked immunosorbent assays. Antibodies recognizing TGF-β were most prevalent in UC (P &lt; 0·01); anti-IL-10 antibodies were elevated in CD (P &lt; 0·05), while anti-IL-2 antibodies were the same for all three groups. Importantly, the percentage of IBD patients with at least one of the antibody levels greater than any control value was 30% for UC and 33% for CD. To verify the presence of these antibodies, immobilized TGF-β was exposed to UC sera and the attached proteins identified by Western blot assay. The proteins proved to be exclusively immunoglobulin (Ig) G. To evaluate the neutralizing activity of these antibodies, cytokine-specific IgG from subjects in each group of patients was incubated with TGF-β, IL-2 or IL-10 before addition to a bioassay with changes in viability determined by a colorimetric analysis. Antibodies from most individuals in all three groups neutralized the action of each cytokine. This study shows that about one-third of IBD patients may have a relative deficiency of TGF-β, IL-2 or IL-10 due to an increase in neutralizing antibodies in their sera.
Transition process of patients with type 1 diabetes (T1DM) from paediatric to the adult health care service: a hospital‐based approach
Authors: Cadario F. , Prodam F. , Bellone S. , Trada M. , Binotti M. , Trada M. , Allochis G. , Baldelli R. , Esposito S. , Bona G. , Aimaretti G. 
Published: November 2008

SummaryIntroduction  The outcomes of different types of transitions of young people with chronic diseases have been poorly investigated.Objective  To evaluate and compare a structured transition from the paediatric diabetes services (PDS) into the adult diabetic services (ADS) with an unstructured one.Design  We retrospectively investigated 62 adolescents and young adults with type 1 diabetes discharged from the PDS from 1 January 1994 to 31 December 2004. Thirty‐two patients (group A) were transferred to the ADS of the same hospital with an unstructured method (letter) and 30 patients after a structured transfer planned with adult physicians (group B). We analysed the date of the first admission in ADS, the glycated haemoglobin (HbA1c), the clinic attendance rate in PDS and in the first year in ADS, and a phone questionnaire on the transition experience.Results  The duration of the transfer was longer in A than in B with a lack of medical assistance during the unstructured transition (P < 0·001). At the first visit in ADS, before any medical intervention, HbA1c was improved in B compared to the last in PDS (P < 0·01), and had a trend in worsening in A. After 1 year in the ADS there was a better clinical attendance, and a lower HbA1c in B than in A (P < 0·05). All the subjects of group B reported a favourable opinion for the structured transition (P < 0·0001).Conclusion  The transition process plays an important role in diabetic care and a structured plan is mandatory to avoid to lose the patients and to get worse their health.