bluuebunny/crossref_metadata_2025_split huggingface dataset:
The adult boar testicular and epididymal transcriptomes
Authors: Guyonnet Benoît , Marot Guillemette , Dacheux Jean-Louis , Mercat Marie-José , Schwob Sandrine , Jaffrézic Florence , Gatti Jean-Luc 
Published: August 2009

AbstractBackgroundMammalians gamete production takes place in the testis but when they exit this organ, although spermatozoa have acquired a specialized and distinct morphology, they are immotile and infertile. It is only after their travel in the epididymis that sperm gain their motility and fertility. Epididymis is a crescent shaped organ adjacent to the testis that can be divided in three gross morphological regions, head (caput), body (corpus) and tail (cauda). It contains a long and unique convoluted tubule connected to the testis via the efferent ducts and finished by joining thevas deferensin its caudal part.ResultsIn this study, the testis, the efferent ducts (vas efferens, VE), nine distinct successive epididymal segments and the deferent duct (vas deferens, VD) of four adult boars of known fertility were isolated and their mRNA extracted. The gene expression of each of these samples was analyzed using a pig generic 9 K nylon microarray (AGENAE program; GEO accession number: GPL3729) spotted with 8931 clones derived from normalized cDNA banks from different pig tissues including testis and epididymis. Differentially expressed transcripts were obtained with moderated t-tests and F-tests and two data clustering algorithms based either on partitioning around medoid (top down PAM) or hierarchical clustering (bottom up HCL) were combined for class discovery and gene expression analysis. Tissue clustering defined seven transcriptomic units: testis,vas efferensand five epididymal transcriptomic units. Meanwhile transcripts formed only four clusters related to the tissues. We have then used a specific statistical method to sort out genes specifically over-expressed (markers) in testis, VE or in each of the five transcriptomic units of the epididymis (including VD). The specific regional expression of some of these genes was further validated by PCR and Q-PCR. We also searched for specific pathways and functions using available gene ontology information.ConclusionThis study described for the first time the complete transcriptomes of the testis, the epididymis, thevas efferensand thevas deferenson the same species. It described new genes or genes not yet reported over-expressed in these boar tissues, as well as new control mechanisms. It emphasizes and fulfilled the gap between studies done in rodents and human, and provides tools that will be useful for further studies on the biochemical processes responsible for the formation and maintain of the epididymal regionalization and the development of a fertile spermatozoa.
The steady-state transcriptome of the four major life-cycle stages of Trypanosoma cruzi
Authors: Minning Todd A , Weatherly D Brent , Atwood James , Orlando Ron , Tarleton Rick L 
Published: August 2009

Abstract

Background
Chronic chagasic cardiomyopathy is a debilitating and frequently fatal outcome of human infection with the protozoan parasite, Trypanosoma cruzi. Microarray analysis of gene expression during the T. cruzi life-cycle could be a valuable means of identifying drug and vaccine targets based on their appropriate expression patterns, but results from previous microarray studies in T. cruzi and related kinetoplastid parasites have suggested that the transcript abundances of most genes in these organisms do not vary significantly between life-cycle stages.

Results
In this study, we used whole genome, oligonucleotide microarrays to globally determine the extent to which T. cruzi regulates mRNA relative abundances over the course of its complete life-cycle. In contrast to previous microarray studies in kinetoplastids, we observed that relative transcript abundances for over 50% of the genes detected on the T. cruzi microarrays were significantly regulated during the T. cruzi life-cycle. The significant regulation of 25 of these genes was confirmed by quantitative reverse-transcriptase PCR (qRT-PCR). The T. cruzi transcriptome also mirrored published protein expression data for several functional groups. Among the differentially regulated genes were members of paralog clusters, nearly 10% of which showed divergent expression patterns between cluster members.

Conclusion
Taken together, these data support the conclusion that transcript abundance is an important level of gene expression regulation in T. cruzi. Thus, microarray analysis is a valuable screening tool for identifying stage-regulated T. cruzi genes and metabolic pathways.
Niche-dependent development of functional neuronal networks from embryonic stem cell-derived neural populations
Authors: Illes Sebastian , Theiss Stephan , Hartung Hans-Peter , Siebler Mario , Dihné Marcel 
Published: August 2009

Abstract

Background
The present work was performed to investigate the ability of two different embryonic stem (ES) cell-derived neural precursor populations to generate functional neuronal networks in vitro. The first ES cell-derived neural precursor population was cultivated as free-floating neural aggregates which are known to form a developmental niche comprising different types of neural cells, including neural precursor cells (NPCs), progenitor cells and even further matured cells. This niche provides by itself a variety of different growth factors and extracellular matrix proteins that influence the proliferation and differentiation of neural precursor and progenitor cells. The second population was cultivated adherently in monolayer cultures to control most stringently the extracellular environment. This population comprises highly homogeneous NPCs which are supposed to represent an attractive way to provide well-defined neuronal progeny. However, the ability of these different ES cell-derived immature neural cell populations to generate functional neuronal networks has not been assessed so far.

Results
While both precursor populations were shown to differentiate into sufficient quantities of mature NeuN+ neurons that also express GABA or vesicular-glutamate-transporter-2 (vGlut2), only aggregate-derived neuronal populations exhibited a synchronously oscillating network activity 2-4 weeks after initiating the differentiation as detected by the microelectrode array technology. Neurons derived from homogeneous NPCs within monolayer cultures did merely show uncorrelated spiking activity even when differentiated for up to 12 weeks. We demonstrated that these neurons exhibited sparsely ramified neurites and an embryonic vGlut2 distribution suggesting an inhibited terminal neuronal maturation. In comparison, neurons derived from heterogeneous populations within neural aggregates appeared as fully mature with a dense neurite network and punctuated vGlut2 expression within presynaptic vesicles. Also those NPCs that had migrated away from adherent neural aggregates maintained their ability to generate a synchronously oscillating neuronal network, even if they were separated from adherent aggregates, dissociated and re-plated.

Conclusion
These findings suggest that the complex environment within niches and aggregates of heterogeneous neural cell populations support the generation of fully mature neurons and functional neuronal networks from ES cell-derived neural cells. In contrast, homogeneous ES cell-derived NPCs within monolayer cultures exhibited an impaired functional neuronal maturation.
Haloperidol changes mRNA expression of a QKI splice variant in human astrocytoma cells
Authors: Jiang Lin , Saetre Peter , Jazin Elena , Carlström Eva Lindholm 
Published: August 2009

Abstract

Background

The quaking homolog, KH domain RNA binding (mouse) (QKI) is a candidate gene for schizophrenia. Disturbed QKI mRNA expression is observed in the prefrontal cortex of patients, and some of these changes correlate to treatment with antipsychotic drugs.
To test if low doses of antipsychotic drugs can modify QKI mRNA expression, human astrocytoma (U343) and oligodendroglioma (HOG) cell lines were treated with five different antipsychotic drugs including Haloperidol, Aripiprazole, Clozapine, Olanzapine and Risperidone. Messenger RNA expression levels of splice variants QKI-5, QKI-6 and QKI-7 were measured by Real-Time PCR.

Results
Haloperidol treatment (0.2 μM) doubled QKI-7 mRNA levels in U343 cells after 6 hours (p-value < 0.02). The effect was dose dependent, and cells treated with ten times higher concentration (2 μM) responded with a five-fold and three-fold increase in QKI-7, 6 and 24 hours after treatment, respectively (p-values < 0.0001).

Conclusion
The results in U343 cells suggest that QKI-7 mRNA expression in human astrocytes is induced by Haloperidol, at concentrations similar to plasma levels relevant to clinical treatment of schizophrenia. The molecular mechanism of action of antipsychotic drugs after binding to receptors is not well known. We hypothesize that QKI regulation is involved in this mechanism.
Systemic acquired resistance in soybean is regulated by two proteins, Orthologous to Arabidopsis NPR1
Authors: Sandhu Devinder , Tasma I Made , Frasch Ryan , Bhattacharyya Madan K 
Published: August 2009

Abstract

Background
Systemic acquired resistance (SAR) is induced in non-inoculated leaves following infection with certain pathogenic strains. SAR is effective against many pathogens. Salicylic acid (SA) is a signaling molecule of the SAR pathway. The development of SAR is associated with the induction of pathogenesis related (PR) genes. Arabidopsis
n

on-expressor of PR1 (NPR1) is a regulatory gene of the SA signal pathway [1–3]. SAR in soybean was first reported following infection with Colletotrichum trancatum that causes anthracnose disease. We investigated if SAR in soybean is regulated by a pathway, similar to the one characterized in Arabidopsis.

Results
Pathogenesis-related gene GmPR1 is induced following treatment of soybean plants with the SAR inducer, 2,6-dichloroisonicotinic acid (INA) or infection with the oomycete pathogen, Phytophthora sojae. In P. sojae-infected plants, SAR was induced against the bacterial pathogen, Pseudomonas syringae pv. glycinea. Soybean GmNPR1-1 and GmNPR1-2 genes showed high identities to Arabidopsis NPR1. They showed similar expression patterns among the organs, studied in this investigation. GmNPR1-1 and GmNPR1-2 are the only soybean homologues of NPR1and are located in homoeologous regions. In GmNPR1-1 and GmNPR1-2 transformed Arabidopsis npr1-1 mutant plants, SAR markers: (i) PR-1 was induced following INA treatment and (ii) BGL2 following infection with Pseudomonas syringae pv. tomato (Pst), and SAR was induced following Pst infection. Of the five cysteine residues, Cys82, Cys150, Cys155, Cys160, and Cys216 involved in oligomer-monomer transition in NPR1, Cys216 in GmNPR1-1 and GmNPR1-2 proteins was substituted to Ser and Leu, respectively.

Conclusion
Complementation analyses in Arabidopsis npr1-1 mutants revealed that homoeologous GmNPR1-1 and GmNPR1-2 genes are orthologous to Arabidopsis NPR1. Therefore, SAR pathway in soybean is most likely regulated by GmNPR1 genes. Substitution of Cys216 residue, essential for oligomer-monomer transition of Arabidopsis NPR1, with Ser and Leu residues in GmNPR1-1 and GmNPR1-2, respectively, suggested that there may be differences between the regulatory mechanisms of GmNPR1 and Arabidopsis NPR proteins.
Immune correlates of CD4 decline in HIV-infected patients experiencing virologic failure before undergoing treatment interruption
Authors: Huang Kenneth H , Loutfy Mona R , Tsoukas Christos M , Bernard Nicole F 
Published: August 2009

Abstract

Background
The advantage of treatment interruptions (TIs) in salvage therapy remains controversial. Regardless, characterizations of the correlates of CD4 count fall during TI are important to identify since patients with virologic failure commonly stop antiretroviral (ARV) therapy. The objective of this study was to determine the predictive value of pre-TI proliferative capacity and cell surface markers for CD4 count change in HIV-infected patients experiencing virologic failure before undergoing TI.

Methods
Peripheral blood mononuclear cells (PBMCs) from 13 HIV-infected patients experiencing virologic failure at baseline time points before the TI were tested for proliferation using the 5,6-carboxyfluorescein diacetate succinimidyl ester (CFSE) dilution assay and a Gag p55 peptide pool, staphylococcus enterotoxin B (SEB), cytomegalovirus (CMV) recall antigen, and anti-CD3 antibody as stimuli. CD28 and CD57 expression on CD4+ and CD8+ T-cells was measured.

Results
The median changes in the CD4+ T-cell count and viral load from baseline to the TI time point corresponding to the CD4 count nadir were -44 cells/mm3 {Interquartile range (IQR) -17, -104} and +85,332 copies/mL (IQR +11,198, +283,327), respectively. CD4+ T-cell proliferation to CMV, pre-TI CD4+ T-cell count, and percent CD4+CD57+ cells correlated negatively with CD4 count change during TI (r = -0.59, p = 0.045, r = -0.61, p = 0.030 and r = -0.69, p = 0.0095, respectively; Spearman correlation). The presence of HIV-specific proliferative responses was not associated with a reduced decline in CD4 count during TI.

Conclusion
The use of pre-TI immune proliferative responses and cell surface markers may have predictive value for CD4 count decline during TI.
Abdominal ultrasonography in HIV/AIDS patients in southwestern Nigeria
Authors: Obajimi Millicent O , Atalabi Mojisola O , Ogbole Godwin I , Adeniji-Sofoluwe Adenike T , Agunloye Atinuke M , Adekanmi Ademola J , Osuagwu Yvonne U , Olarinoye Sefiat A , Olusola-Bello Mojisola A , Ogunseyinde Ayotunde O , Aken'Ova Yetunde A , Adewole Isaac F 
Published: August 2009

Abstract

Background
Though the major target of the HIV-virus is the immune system, the frequency of abdominal disorders in HIV/AIDS patients has been reported to be second only to pulmonary disease. These abdominal manifestations may be on the increase as the use of antiretroviral therapy has increased life expectancy and improved quality of life. Ultrasonography is an easy to perform, non invasive, inexpensive and safe imaging technique that is invaluable in Africa where AIDS is most prevalent and where sophisticated diagnostic tools are not readily available. Purpose: To describe the findings and evaluate the clinical utility of abdominal ultrasonography in HIV/AIDS patients in Ibadan, Nigeria

Methods
A Prospective evaluation of the abdominal ultrasonography of 391 HIV-positive patients as well as 391 age and sex-matched HIV-negative patients were carried out at the University College Hospital, Ibadan.

Results
Of the 391 cases studied, 260 (66.5%) were females; the mean age was 38.02 years, (range 15–66 years). The disease was most prevalent in the 4th decade with an incidence of 40.4%. Compared with the HIV-negative individuals, the HIV+ group of patients had a significantly higher proportion of splenomegaly (13.5% vs. 7.7%; p < 0.01), lymphadenopathy (2.0% vs. 1.3%; p < 0.70), and renal abnormalities (8.4% vs. 3.8%; p < 0.02). There were no differences in hepatic and pancreatic abnormalities between the HIV+ and HIV- groups. There were significantly fewer gallstones in the HIV+ group (1.4% vs. 5.1%; p < 0.01).

Conclusion
AIDS is a multi-systemic disease and its demographic and clinical pattern remains the same globally. Ultrasonography is optimally suited for its clinical management especially in Africa. Its accuracy and sensitivity may be much improved with clinico-pathologic correlation which may not be readily available in developing countries; further studies may provide this much needed diagnostic algorithms.
Highly variable response to cytotoxic chemotherapy in carcinoma-associated fibroblasts (CAFs) from lung and breast
Authors: Sonnenberg Maike , van der Kuip Heiko , Haubeiß Silke , Fritz Peter , Schroth Werner , Friedel Godehard , Simon Wolfgang , Mürdter Thomas E , Aulitzky Walter E 
Published: August 2009

AbstractBackgroundCarcinoma-associated fibroblasts (CAFs) can promote carcinogenesis and tumor progression. Only limited data on the response of CAFs to chemotherapy and their potential impact on therapy outcome are available. This study was undertaken to analyze the influence of chemotherapy on carcinoma-associated fibroblasts (CAFs)in vitroandin vivo.MethodsThein vivoresponse of stromal cells to chemotherapy was investigated in 22 neoadjuvant treated breast tumors on tissue sections before and after chemotherapy. Response to chemotherapy was analyzedin vitroin primary cultures of isolated CAFs from 28 human lung and 9 breast cancer tissues. The response was correlated toMdm2,ERCC1andTP53polymorphisms andTP53mutation status. Additionally, the cytotoxic effects were evaluated in anex vivoexperiment using cultured tissue slices from 16 lung and 17 breast cancer specimens.ResultsNine of 22 tumors showed a therapy-dependent reduction of stromal activity. Pathological response of tumor or stroma cells did not correlate with clinical response. Isolated CAFs showed little sensitivity to paclitaxel. In contrast, sensitivity of CAFs to cisplatinum was highly variable with a GI50 ranging from 2.8 to 29.0 μM which is comparable to the range observed in tumor cell lines. No somaticTP53mutation was detected in any of the 28 CAFs from lung cancer tissue. In addition, response to cisplatinum was not significantly associated with the genotype ofTP53norMdm2andERCC1polymorphisms. However, we observed a non-significant trend towards decreased sensitivity in the presence ofTP53variant genotype. In contrast to the results obtained in isolated cell culture, in tissue slice culture breast cancer CAFs responded to paclitaxel within their microenvironment in the majority of cases (9/14). The opposite was observed in lung cancer tissues: only few CAFs were sensitive to cisplatinum within their microenvironment (2/15) whereas a higher proportion responded to cisplatinum in isolated culture.ConclusionSimilar to cancer cells, CAF response to chemotherapy is highly variable. Beside significant individual/intrinsic differences the sensitivity of CAFs seems to depend also on the cancer type as well as the microenvironment.
Selecting short-statured children needing growth hormone testing: Derivation and validation of a clinical decision rule
Authors: Duché Laëtitia , Trivin Christine , Chemaitilly Wassim , Souberbielle Jean Claude , Bréart Gérard , Brauner Raja , Chalumeau Martin 
Published: August 2009

AbstractBackgroundNumerous short-statured children are evaluated for growth hormone (GH) deficiency (GHD). In most patients, GH provocative tests are normal and are thus in retrospect unnecessary.MethodsA retrospective cohort study was conducted to identify predictors of growth hormone (GH) deficiency (GHD) in children seen for short stature, and to construct a very sensitive and fairly specific predictive tool to avoid unnecessary GH provocative tests. GHD was defined by the presence of 2 GH concentration peaks < 10 ng/ml. Certain GHD was defined as GHD and viewing pituitary stalk interruption syndrome on magnetic resonance imaging. Independent predictors were identified with uni- and multi-variate analyses and then combined in a decision rule that was validated in another population.ResultsThe initial study included 167 patients, 36 (22%) of whom had GHD, including 5 (3%) with certain GHD. Independent predictors of GHD were: growth rate < -1 DS (adjusted odds ratio: 3.2; 95% confidence interval [1.3–7.9]), IGF-I concentration < -2 DS (2.8 [1.1–7.3]) and BMI z-score ≥ 0 (2.8 [1.2–6.5]). A clinical decision rule suggesting that patients be tested only if they had a growth rate < -1 DS and a IGF-I concentration < -2 DS achieved 100% sensitivity [48–100] for certain GHD and 63% [47–79] for GHD, and a specificity of 68% [60–76]. Applying this rule to the validation population (n = 40, including 13 patients with certain GHD), the sensitivity for certain GHD was 92% [76–100] and the specificity 70% [53–88].ConclusionWe have derived and performed an internal validation of a highly sensitive decision rule that could safely help to avoid more than 2/3 of the unnecessary GH tests. External validation of this rule is needed before any application.
Is it worth investing in mental health promotion and prevention of mental illness? A systematic review of the evidence from economic evaluations
Authors: Zechmeister Ingrid , Kilian Reinhold , McDaid David ,   the MHEEN group
Published: August 2009

AbstractBackgroundWhile evidence on the cost of mental illness is growing, little is known about the cost-effectiveness of programmes in the areas of mental health promotion (MHP) and mental disorder prevention (MDP). The paper aims at identifying and assessing economic evaluations in both these areas to support evidence based prioritisation of resource allocation.MethodsA systematic review of health and non health related bibliographic databases, complemented by a hand search of key journals and analysis of grey literature has been carried out. Study characteristics and results were qualitatively summarised. Economic evaluations of programmes that address mental health outcome parameters directly, those that address relevant risk factors of mental illness, as well as suicide prevention interventions were included, while evaluations of drug therapies were excluded.Results14 studies fulfilled the inclusion criteria. They varied in terms of topic addressed, intervention used and study quality. Robust evidence on cost-effectiveness is still limited to a very small number of interventions with restricted scope for generalisability and transferability. The most favourable results are related to early childhood development programmes.ConclusionPrioritisation between MHP and MDP interventions requires more country and population-specific economic evaluations. There is also scope to retrospectively add economic analyses to existing effectiveness studies. The nature of promotion and prevention suggests that innovative approaches to economic evaluation that augment this with information on the challenges of implementation and uptake of interventions need further development.
THR Simulator – the software for generating radiographs of THR prosthesis
Authors: Wu Tai-Yin , Yang Rong-Sen , Fuh Chiou-Shann , Hou Sheng-Mou , Liaw Chen-Kun 
Published: August 2009

Abstract

Background
Measuring the orientation of acetabular cup after total hip arthroplasty is important for prognosis. The verification of these measurement methods will be easier and more feasible if we can synthesize prosthesis radiographs in each simulated condition. One reported method used an expensive mechanical device with an indeterminable precision. We thus develop a program, THR Simulator, to directly synthesize digital radiographs of prostheses for further analysis.
Under Windows platform and using Borland C++ Builder programming tool, we developed the THR Simulator. We first built a mathematical model of acetabulum and femoral head. The data of the real dimension of prosthesis was adopted to generate the radiograph of hip prosthesis. Then with the ray tracing algorithm, we calculated the thickness each X-ray beam passed, and then transformed to grey scale by mapping function which was derived by fitting the exponential function from the phantom image. Finally we could generate a simulated radiograph for further analysis.

Results
Using THR Simulator, the users can incorporate many parameters together for radiograph synthesis. These parameters include thickness, film size, tube distance, film distance, anteversion, abduction, upper wear, medial wear, and posterior wear. These parameters are adequate for any radiographic measurement research. This THR Simulator has been used in two studies, and the errors are within 2° for anteversion and 0.2 mm for wearing measurement.

Conclusion
We design a program, THR Simulator that can synthesize prosthesis radiographs. Such a program can be applied in future studies for further analysis and validation of measurement of various parameters of pelvis after total hip arthroplasty.