bluuebunny/crossref_metadata_2025_split huggingface dataset:
Steroidogenic factor-1 (SF-1) gene mutation as a frequent cause of primary amenorrhea in 46,XY female adolescents with low testosterone concentration
Authors: Philibert Pascal , Leprieur Elodie , Zenaty Delphine , Thibaud Elisabeth , Polak Michel , Frances Anne-Marie , Lespinasse James , Raingeard Isabelle , Servant Nadège , Audran Françoise , Paris Françoise , Sultan Charles 
Published: April 2010

AbstractBackgroundPrimary amenorrhea due to 46,XY disorders of sex differentiation (DSD) is a frequent reason for consultation in endocrine and gynecology clinics. Among the genetic causes of low-testosterone primary amenorrhea due to 46,XY DSD, SRY gene is reported to be frequently involved, but other genes, such as SF1 and WT1, have never been studied for their prevalence.MethodsWe directly sequenced SRY, SF1 and WT1 genes in 15 adolescent girls with primary amenorrhea, low testosterone concentration, and XY karyotype, to determine the prevalence of mutations. We also analyzed the LH receptor gene in patients with high LH and normal FSH concentrations.ResultsAmong the 15 adolescents with primary amenorrhea and low testosterone concentration, we identified two new SRY mutations, five new SF1 mutations and one new LH receptor gene mutation. Our study confirms the 10-15% prevalence of SRY mutations and shows the high prevalence (33%) of SF1 abnormalities in primary amenorrhea due to 46,XY DSD with low plasma testosterone concentration.ConclusionsThe genetic analysis of low-testosterone primary amenorrhea is complex as several factors may be involved. This work underlines the need to systematically analyze the SF1 sequence in girls with primary amenorrhea due to 46,XY DSD and low testosterone, as well as in newborns with 46,XY DSD.
Discriminating between rival biochemical network models: three approaches to optimal experiment design
Authors: Mélykúti Bence , August Elias , Papachristodoulou Antonis , El-Samad Hana 
Published: April 2010

Abstract

Background
The success of molecular systems biology hinges on the ability to use computational models to design predictive experiments, and ultimately unravel underlying biological mechanisms. A problem commonly encountered in the computational modelling of biological networks is that alternative, structurally different models of similar complexity fit a set of experimental data equally well. In this case, more than one molecular mechanism can explain available data. In order to rule out the incorrect mechanisms, one needs to invalidate incorrect models. At this point, new experiments maximizing the difference between the measured values of alternative models should be proposed and conducted. Such experiments should be optimally designed to produce data that are most likely to invalidate incorrect model structures.

Results
In this paper we develop methodologies for the optimal design of experiments with the aim of discriminating between different mathematical models of the same biological system. The first approach determines the 'best' initial condition that maximizes the L
2 (energy) distance between the outputs of the rival models. In the second approach, we maximize the L
2-distance of the outputs by designing the optimal external stimulus (input) profile of unit L
2-norm. Our third method uses optimized structural changes (corresponding, for example, to parameter value changes reflecting gene knock-outs) to achieve the same goal. The numerical implementation of each method is considered in an example, signal processing in starving Dictyostelium amœbæ.

Conclusions
Model-based design of experiments improves both the reliability and the efficiency of biochemical network model discrimination. This opens the way to model invalidation, which can be used to perfect our understanding of biochemical networks. Our general problem formulation together with the three proposed experiment design methods give the practitioner new tools for a systems biology approach to experiment design.
Control of disseminated intravascular coagulation in Klippel-Trenaunay-Weber syndrome using enoxaparin and recombinant activated factor VIIa: a case report
Authors: Beier Ulf H , Schmidt Mary Lou , Hast Howard , Kecskes Susan , Valentino Leonard A 
Published: April 2010

Abstract

Introduction
Vascular malformation is associated with coagulopathies, especially when hemostasis is challenged.

Case presentation
We present the case of an 11-year-old Hispanic girl with Klippel-Trenaunay-Weber syndrome that developed disseminated intravascular coagulation after minor surgery, which was controlled by blood product transfusions and enoxaparin to address an ongoing consumptive coagulopathy. The patient, however, developed bacteremia and liver trauma that resulted in severe bleeding. To the best of our knowledge, we report here the first known instance of administering recombinant coagulation factor VIIa to control acute bleeding in a patient with Klippel-Trenaunay-Weber syndrome.

Conclusions
This case illustrates the concept of enoxaparin maintenance to suppress an ongoing consumptive coagulopathy and the use of recombinant coagulation factor VIIa to control its potentially fatal severe bleeding episodes.
Olf1/EBF associated zinc finger protein interfered with antinuclear antibody production in patients with systemic lupus erythematosus
Authors: Feng Xuebing , Li Rongliang , Huang Jing , Zhang Huayong , Zhu Lina , Hua Bingzhu , Tsao Betty P , Sun Lingyun 
Published: April 2010

Abstract
Introduction
The aim of the study was to determine whether Olf1/EBF associated zinc finger protein (OAZ), a transcription factor encoded by a positional systemic lupus erythematosus (SLE) candidate gene, plays a functional role in the pathogenesis in SLE.

Methods
Gene expression levels in peripheral blood cells (PBLs) measured using quantitative real-time polymerase chain reaction (qPCR) were assessed for association with disease activity and the presence of specific autoantibodies. Peripheral blood mononuclear cells (PBMCs) were incubated with specific siRNAs for three days, then cells were harvested for measuring mRNA levels using qPCR, and supernatants for levels of total immunoglobulin (Ig)G and IgM as well as secreted cytokines, chemokine and antinuclear antibodies (ANA) using ELISA. Indirect immunofluorescence was also applied for ANA detection.

Results
OAZ gene expressions in PBLs from 40 ANA-positive SLE patients were significantly increased than those from 30 normal controls (P < 0.0001) and 18 patients with rheumatoid arthritis (P < 0.01). In SLE patients, OAZ transcripts were positively correlated with SLE disease activity index (SLEDAI) score (r = 0.72, P < 0.0001) and higher in those positive for anti-dsDNA or anti-Sm antibodies (both P < 0.05). Co-culturing with OAZ siRNAs reduced mRNA levels of OAZ by 74.6 ± 6.4% as compared to those co-cultured with non-targeting siRNA and OAZ silencing resulted in reduced total IgG, ANA, interferon (IFN)-γ, interleukin (IL)-10, IL-12 and IL-21, but elevated CCL2 levels in culture supernatants (P < 0.05). The declined ANA levels correlated with inhibited OAZ expression (r = 0.88, P = 0.05), reduced IL-21 levels (r = 0.99, P < 0.01), and elevated chemokine (C-C motif) ligand 2 levels (r = -0.98, P < 0.01). Expressions of ID1-3 were significantly down-regulated by 68.7%, 70.2% and 67.7% respectively after OAZ silence, while ID3 was also highly expressed in SLE PBLs (P < 0.0001) and associated with disease activity (r = 0.76, P < 0.0001) as well as anti-dsDNA or anti-Sm antibodies (both P < 0.05).

Conclusions
Elevated expression of OAZ transcripts in SLE PBLs were strongly correlated with disease activity. Suppression of OAZ expression inhibited downstream ID levels, and secretion of ANA and IL-21, implicating a role of OAZ pathway in the pathogenesis of SLE.
Attenuation of fibrosis in vitro and in vivo with SPARC siRNA
Authors: Wang Jiu-Cun , Lai Syeling , Guo Xinjian , Zhang Xuefeng , de Crombrugghe Benoit , Sonnylal Sonali , Arnett Frank C , Zhou Xiaodong 
Published: April 2010

Abstract
Introduction
SPARC is a matricellular protein, which, along with other extracellular matrix components including collagens, is commonly over-expressed in fibrotic diseases. The purpose of this study was to examine whether inhibition of SPARC can regulate collagen expression in vitro and in vivo, and subsequently attenuate fibrotic stimulation by bleomycin in mouse skin and lungs.

Methods
In in vitro studies, skin fibroblasts obtained from a Tgfbr1 knock-in mouse (TBR1CA; Cre-ER) were transfected with SPARC siRNA. Gene and protein expressions of the Col1a2 and the Ctgf were examined by real-time RT-PCR and Western blotting, respectively. In in vivo studies, C57BL/6 mice were induced for skin and lung fibrosis by bleomycin and followed by SPARC siRNA treatment through subcutaneous injection and intratracheal instillation, respectively. The pathological changes of skin and lungs were assessed by hematoxylin and eosin and Masson's trichrome stains. The expression changes of collagen in the tissues were assessed by real-time RT-PCR and non-crosslinked fibrillar collagen content assays.

Results
SPARC siRNA significantly reduced gene and protein expression of collagen type 1 in fibroblasts obtained from the TBR1CA; Cre-ER mouse that was induced for constitutively active TGF-β receptor I. Skin and lung fibrosis induced by bleomycin was markedly reduced by treatment with SPARC siRNA. The anti-fibrotic effect of SPARC siRNA in vivo was accompanied by an inhibition of Ctgf expression in these same tissues.

Conclusions
Specific inhibition of SPARC effectively reduced fibrotic changes in vitro and in vivo. SPARC inhibition may represent a potential therapeutic approach to fibrotic diseases.
Selection and reliability of internal reference genes for quantitative PCR verification of transcriptomics during the differentiation process of porcine adult mesenchymal stem cells
Authors: Monaco Elisa , Bionaz Massimo , de Lima Alecsandra Sobreira , Hurley Walter L , Loor Juan J , Wheeler Matthew B 
Published: April 2010

Abstract
Introduction
The objective of this study was to find highly reliable internal-control genes (ICGs) for normalization of qPCR data from porcine adult mesenchymal stem cells induced to differentiate toward adipogenic and osteogenic lineages.

Methods
Stem cells were acquired from subcutaneous back fat and bone marrow of three castrated Yorkshire crossbred male pigs. Adipose and bone marrow-derived stem cells (ADSCs and BMSCs) were cultured in vitro with specific osteogenic or adipogenic differentiation medium for 4 weeks. Total RNA was extract for microarray (13,000 oligonucleotides) and qPCR analyses. Microarray data were used to uncover the most stably expressed genes (that is, potential ICGs). Co-regulation among potential ICGs was evaluated with Ingenuity Pathway Analysis. qPCR was performed on the non-coregulated ICGs candidates and on specific osteogenic (COL1A1) and adipogenic (DBI) genes. geNorm was used to uncover the most reliable ICGs by using qPCR data and the optimal number of ICGs to be used to calculate the normalization factor.

Results
Microarray data analysis revealed 27 potential ICGs. Among those, 10 genes without known co-regulation were selected to perform qPCR. geNorm performed on qPCR data uncovered high stability in expression ratio among the selected ICGs. However, especially reliable normalization was obtained by geometric mean of NSUN5, TIMM17B, and VPS4A. The effect of normalization, assessed on specific osteogenic (COL1A1) and adipogenic (DBI) genes, was apparent for the adipogenic and less apparent for the osteogenic differentiation.

Conclusions
The combination of microarray data and pairwise gene analysis allowed identification of novel and highly reliable ICGs for qPCR data normalization of adult porcine stem cells induced to differentiate to adipogenic and osteogenic lineages.
Age in Men Does Not Determine Gonadotropin-Releasing Hormone’s Dose-Dependent Stimulation of Luteinizing Hormone Secretion under an Exogenous Testosterone Clamp
Authors: Iranmanesh Ali , Mulligan Thomas , Veldhuis Johannes D. 
Published: April 2010

AbstractBackground: Aging is associated with a decline in incremental LH pulse amplitude, which could be due to decreased GnRH secretion or impaired GnRH action.Hypothesis: Inconsistent published studies of GnRH action in older men may be due to disparate sex-steroid milieus.Facility: This study was conducted at a clinical translational-research unit.Subjects: We studied 16 healthy men (8 young men and 8 older men).Methods: An overnight transdermal testosterone (T) clamp was implemented before randomly ordered injections of 0, 2.5, 10, 25, 250, and 750 ng GnRH on separate days (96 study sessions).Outcomes: LH responses were quantified by variable-waveform deconvolution analysis.Results: The T clamp maintained age-invariant mean concentrations of total, bioavailable, and free T, SHBG, LH, FSH, and prolactin. By two-way analysis of covariance, GnRH dose (P &lt; 0.001) but not age (0.15 ≤ P ≤ 0.83) determined mean, peak, incremental, and pulsatile LH responses. Statistical power (median) was 95, 98, 90, and 99% to detect a 30% or greater age contrast at P ≤ 0.05 in mean, peak, incremental, and pulsatile LH responses, and greater than 99% to detect a 30% or greater age contrast in bioavailable or total T concentrations. Higher GnRH doses (P &lt; 0.001) abbreviated LH secretory bursts in both age groups.Conclusion: In the face of eugonadal concentrations of total, bioavailable, and free T, young and older men exhibit remarkably similar LH responses to a 300-fold dose range of exogenous GnRH. Accordingly, previously reported disparate effects of age on GnRH action may reflect in part age-discrepant sex-steroid milieus.
Stoneley Type Flexure Waves in Thin Elastic Plates
Authors: Andronov Ivan V. 
Published: April 2010

The Stoneley type waves are known to propagate along free edges of fluid loaded elastic plates [1], [2], [3]. In the case of a plate cut by a straight line two edge waves can be possible. One is symmetric and the other is anti-symmetric in the cross-section orthogonal to the cut. It is shown in [4] that the symmetric wave exists at any frequency and for any parameters of the plate and fluid. The anti-symmetric edge wave on the contrary exists only in some frequency range. In this paper the effects that regulate the existence or nonexistence of the anti-symmetric edge wave are analyzed and the energy characteristics of edge waves are studied.
High-Accuracy PVT Relationships for Compressed Fluids and Their Application to BET-like Modelling of CO2 and CH4 Adsorption
Authors: Milewska-Duda Janina , Duda Jan Tadeusz 
Published: April 2010

This paper presents a set of high-accuracy formulae enabling the evaluation of the compression factor, activity and cohesion energy of fluids at near-critical and super-critical temperatures, with reduced molar volumes ranging from 0.4. Such data are necessary in BET-like theoretical modelling of adsorption process. The proposed fluid state equation (PVT relationship) combines a theoretical description of the fluid entropy (based on a hard-sphere model) with cohesion energy relationships obtained via high-accuracy approximations of universal compression factor data and vapour-liquid equilibria. The resultant relationships are incorporated into a BET-like description of adsorption in materials of irregular microporous structure (LBET model). The set of formulae gathered together in this paper allows the possible effective calculation of adsorption isotherms at near- and super-critical temperatures relative to the pore structures. A multi-variant fitting of the LBET model to the empirical data is proposed to detect active constraints for multilayer adsorption and, hence, to obtain information on the structure of the pores. Application of the formulae to the analysis of methane and carbon dioxide adsorption onto an active carbon is discussed.
The Peculiar Nodal Generator: A Speculation
Authors: Vollen Jason , Clifford Dale 
Published: April 2010

Economically abandoned cities as well as urban cores depopulated because of catastrophic events have spawned urban renewal projects of all varieties. Often these projects promote civic programs such as arenas, theaters, museums, and aquariums as replacements for what was once an interactive public realm. Unfortunately the realization of these large programs promotes a disconnected series of sequestered activities rather than the prospect of a lively and potentially frenetic urban center governed by chance interactions. As an intervening strategy, this paper considers the possibility of implementing Nodal Generators, responsive systems that sense and adapt to environmental fluctuations to create localized microclimates capable of providing unscripted public space in the discarded and interstitial regions of the modern city. Inspired biotically and explored digitally, the Nodal Generators provide a linkage between community and technology using smart materials and adaptive assemblies. This paper details several speculations on the nature and form of these nodes and proposes their implementation into urban arid situations. We can postulate that while the nodal generators speculated upon in this paper might at first draw attention to themselves through spectacle, they will ultimately create a shared community experience through eventual inhabitation of that public space.
Single-Tube Analysis of DNA Methylation with Silica Superparamagnetic Beads
Authors: Bailey Vasudev J , Zhang Yi , Keeley Brian P , Yin Chao , Pelosky Kristen L , Brock Malcolm , Baylin Stephen B , Herman James G , Wang Tza-Huei 
Published: April 2010

Abstract
Background: DNA promoter methylation is a signature for the silencing of tumor suppressor genes. Most widely used methods to detect DNA methylation involve 3 separate, independent processes: DNA extraction, bisulfite conversion, and methylation detection via a PCR method, such as methylation-specific PCR (MSP). This method includes many disconnected steps with associated losses of material, potentially reducing the analytical sensitivity required for analysis of challenging clinical samples.
Methods: Methylation on beads (MOB) is a new technique that integrates DNA extraction, bisulfite conversion, and PCR in a single tube via the use of silica superparamagnetic beads (SSBs) as a common DNA carrier for facilitating cell debris removal and buffer exchange throughout the entire process. In addition, PCR buffer is used to directly elute bisulfite-treated DNA from SSBs for subsequent target amplifications. The diagnostic sensitivity of MOB was evaluated by methylation analysis of the CDKN2A [cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4); also known as p16INK4a] promoter in serum DNA of lung cancer patients and compared with that of conventional methods.
Results: Methylation analysis consisting of DNA extraction followed by bisulfite conversion and MSP was successfully carried out within 9 h in a single tube. The median pre-PCR DNA yield was 6.61-fold higher with the MOB technique than with conventional techniques. Furthermore, MOB increased the diagnostic sensitivity in our analysis of the CDKN2A promoter in patient serum by successfully detecting methylation in 74% of cancer patients, vs the 45% detection rate obtained with conventional techniques.
Conclusions: The MOB technique successfully combined 3 processes into a single tube, thereby allowing ease in handling and an increased detection throughput. The increased pre-PCR yield in MOB allowed efficient, diagnostically sensitive methylation detection.
Validation of an Enzyme Immunoassay for Detection and Semiquantification of Cannabinoids in Oral Fluid
Authors: Schwope David M , Milman Garry , Huestis Marilyn A 
Published: April 2010

Abstract
Background: Oral fluid (OF) is gaining prominence as an alternative matrix for monitoring drugs of abuse in the workplace, criminal justice, and driving under the influence of drugs programs. It is important to characterize assay performance and limitations of screening techniques for Δ9-tetrahydrocannabinol (THC) in OF.
Methods: We collected OF specimens by use of the Quantisal™ OF collection device from 13 daily cannabis users after controlled oral cannabinoid administration. All specimens were tested with the Immunalysis Sweat/OF THC Direct ELISA and confirmed by 2-dimensional GC-MS.
Results: The limit of detection was &lt;1 μg/L THC equivalent, and the assay demonstrated linearity from 1 to 50 μg/L, with semiquantification to 200 μg/L. Intraplate imprecision (n = 7) ranged from 2.9% to 7.7% CV, and interplate imprecision (n = 20) was 3.0%–9.1%. Cross-reactivities at 4 μg/L were as follows: 11-hydroxy-THC, 198%; Δ8-tetrahydrocannabinol (Δ8-THC), 128%; 11-nor-9-carboxy-THC (THCCOOH), 121%; THC (target), 98%; cannabinol, 87%; THCCOOH-glucuronide, 11%; THC-glucuronide, 10%; and cannabidiol, 2.4%. Of 499 tested OF specimens, 52 confirmed positive (THC 2.0–290 μg/L), with 100% diagnostic sensitivity at the proposed Substance Abuse and Mental Health Services Administration screening cutoff of 4 μg/L cannabinoids and GC-MS cutoff of 2 μg/L THC. Forty-seven specimens screened positive but were not confirmed by 2D-GC-MS, yielding 89.5% diagnostic specificity and 90.6% diagnostic efficiency. Thirty-one of 47 unconfirmed immunoassay positive specimens were from 1 individual and contained &gt;400 ng/L THCCOOH, potentially contributing to cross-reactivity.
Conclusions: The Immunalysis Sweat/OF THC Direct ELISA is an effective screening procedure for detecting cannabinoids in OF.
The kidney in acromegaly: renal structure and function in patients with acromegaly during active disease and 1 year after disease remission
Authors: Auriemma Renata S , Galdiero Mariano , De Martino Maria C , De Leo Monica , Grasso Ludovica F S , Vitale Pasquale , Cozzolino Alessia , Lombardi Gaetano , Colao Annamaria , Pivonello Rosario 
Published: April 2010

BackgroundThe GH/insulin-like growth factor 1 axis is physiologically involved in the regulation of electrolytes and water homeostasis by kidneys, and influences glomerular filtration and tubular re-absorption processes. The aim of the study was to investigate renal structure and function in acromegalic patients during active disease and disease remission.PatientsThirty acromegalic patients (15 males and 15 females), aged 32–70 years, were enrolled for the study. Tende novopatients had active disease, whereas 20 patients showed disease remission 1 year after medical treatment with somatostatin analogs (SA) (ten patients) or surgery (ten patients). Thirty healthy subjects matched for age, gender, and body surface area were enrolled as controls.ResultsIn both active (A) and controlled (C) patients, creatinine clearance (P<0.001) and citrate (P<0.05) and oxalate levels (P<0.001) were higher, whereas filtered Na (P<0.001) and K (P<0.001) fractional excretions were lower than those in the controls. Urinary Ca (P<0.001) and Ph (P<0.05) levels were significantly increased compared with the controls, and in patients with disease control, urinary Ca (P<0.001) levels were significantly reduced compared with active patients. Microalbuminuria was significantly increased in active patients (P<0.05) compared with controlled patients and healthy control subjects. The longitudinal (P<0.05) and transverse (P<0.05) diameters of kidneys were significantly higher than those in the controls. In all patients, the prevalence of micronephrolithiasis was higher than that in the controls (P<0.001), and was significantly correlated to disease duration (r=0.871,P<0.001) and hydroxyproline values (r=0.639,P<0.001).ConclusionsThe results of the current study demonstrated that acromegaly affects both renal structure and function. The observed changes are not completely reversible after disease remission.