bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diffusion and association processes in biological systems: theory, computation and experiment
Authors: Mereghetti Paolo , Kokh Daria , McCammon J Andrew , Wade Rebecca C 
Published: March 2011

Abstract
Macromolecular diffusion plays a fundamental role in biological processes. Here, we give an overview of recent methodological advances and some of the challenges for understanding how molecular diffusional properties influence biological function that were highlighted at a recent workshop, BDBDB2, the second Biological Diffusion and Brownian Dynamics Brainstorm.
Brownian dynamics simulation of analytical ultracentrifugation experiments
Authors: Díez AI , Ortega A , Garcia de la Tore J 
Published: March 2011

Abstract

Background
We have devised a protocol for the Brownian dynamics simulation of an analytical ultracentrifugation experiment that allows for an accurate and efficient prediction of the time-dependent concentration profiles, c(r, t) in the ultracentrifuge cell. The procedure accounts for the back-diffusion, described as a Brownian motion that superimposes to the centrifugal drift, and considers the sector-shaped geometry of the cell and the boundaries imposed by the meniscus and bottom.

Results
Simulations are carried out for four molecules covering a wide range of the ratio of sedimentation and diffusion coefficients. The evaluation is done by extracting the molecular parameters that were initially employed in the simulation by analyzing the profiles with an independent tool, the well-proved SEDFIT software. The code of simulation algorithm has been parallelized in order to take advantage of current multi-core computers.

Conclusions
Our Brownian dynamics simulation procedure may be considered as an alternative to other predictors based in numerical solutions of the Lamm equation, and its efficiency could make it useful in the most relevant, inverse problem, which is that of extracting the molecular parameters from experimentally determined concentration profiles.
Human β-defensin-2 enhances IFN-γ and IL-10 production and suppresses IL-17 production in T cells
Authors: Kanda Naoko , Kamata Masahiro , Tada Yayoi , Ishikawa Takeko , Sato Shinichi , Watanabe Shinichi 
Published: March 2011

ABSTRACTPsoriasis is an inflammatory dermatosis with enhanced expression of hBD-2 in keratinocytes and infiltration of cytokine-producing T cells, which in turn, up- or down-regulate hBD-2 expression. We determined the serum levels of hBD-2 and cytokines in psoriasis patients and analyzed the effects of hBD-2 on cytokine production in human peripheral blood T cells. Serum hBD-2 levels in patients were higher than those in controls and correlated with PASI, serum IFN-γ, and IL-10 levels and correlated inversely with serum IL-17 levels. IFN-γ, IL-17, IL-22, TNF-α, IL-1β, and IL-6 enhanced, and IL-10, IL-4, and IL-13 suppressed hBD-2 secretion from keratinocytes. hBD-2 enhanced secretion and mRNA levels of IFN-γ, TNF-α, IL-10, IL-1β, IL-6, and IL-22 and reduced those of IL-17 in CD3/28-stimulated T cells. These effects of hBD-2 were counteracted by PTX. hBD-2 induced phosphorylation of JNK, ERK, and Akt in T cells. Inhibitors of these signals attenuated hBD-2-induced production of IFN-γ, TNF-α, IL-10, IL-1β, IL-6, and IL-22. hBD-2 suppressed phosphorylation of STAT3 and enhanced expression of SOCS3 in CD3/28-stimulated T cells. siRNA against SOCS3 reversed hBD-2-induced suppression of IL-17 production and STAT3 phosphorylation. JNK and MEK inhibitors suppressed hBD-2-induced expression of SOCS3. In conclusion, hBD-2 may bind PTX-sensitive GPCR(s) on T cells and act as a stimulator by enhancing IFN-γ, TNF-α, IL-1β, IL-6, and IL-22 production via JNK, MEK/ERK, and PI3K/Akt and as a regulator by suppressing IL-17 production via SOCS3 or by stimulating IL-10 production.
Complementary and contrasting roles of NK cells and T cells in pediatric umbilical cord blood transplantation
Authors: Merindol Natacha , Charrier Emily , Duval Michel , Soudeyns Hugo 
Published: March 2011

ABSTRACTUCBT has been used for almost 25 years to treat a variety of malignant and nonmalignant childhood diseases. The biological properties of NK cells and T cells and their implication in engraftment, immune reconstitution, OIs, leukemic relapse, and GvHD have been explored in the context of UCBT. These studies have established that lymphocytes have a major impact on the outcome of UCBT and that NK cells and T cells play complementary and contrasting roles in immune reconstitution and the GvL effect. Therefore, novel strategies to improve the outcome of UCBT recipients, including immunotherapeutic regimens, should be based on key immunologic features of UCB T lymphocytes and NK cells.
The CD40/CD40 ligand interactions exert pleiotropic effects on bone marrow granulopoiesis
Authors: Mavroudi Irene , Papadaki Vassiliki , Pyrovolaki Katerina , Katonis Pavlos , Eliopoulos Aristides G , Papadaki Helen A 
Published: March 2011

ABSTRACTCD40 is a member of the TNFR family and upon interaction with its cognate ligand (CD40L), induces diverse biologic responses related to cell survival/growth. As altered CD40/CD40L interactions have been associated with neutropenia, we investigated the role of CD40/CD40L on human granulopoiesis using immunomagnetically sorted CD34+, CD34–/CD33+, and CD34–/CD33–/CD15+ BM cells, which represent sequential stages of the granulocytic development, the KG-1 cells that constantly express CD34 and CD33, and LTBMCs that mimic the BM microenvironment. CD40 and CD40L were minimally expressed on CD34+, CD34–/CD33+, and CD34–/CD33–/CD15+ cells, but CD40 was substantially induced in the presence of TNF-α. Cross-linking of CD40 in the above cell populations resulted in induction of apoptosis that was enhanced further in the presence of FasL. CD40 activation in primary as wells as in KG-1 cells resulted in Fas up-regulation, providing a mechanism for the CD40-mediated apoptosis. Addition of CD40L in clonogenic assays resulted in a significant decrease in the colony-forming capacity of BMMCs from patients with chronic neutropenia, presumably expressing high levels of CD40 in the progenitor cells, and this effect was reversed upon CD40 blockade. CD40 was constitutively expressed on LTBMC stromal cells and upon activation, resulted in an increase in G-CSF and GM-CSF production. These data show that CD40/CD40L interactions may promote granulopoiesis under steady-state conditions by inducing the stromal release of granulopoiesis-supporting cytokines, whereas under inflammatory conditions, they may affect the granulocytic progenitor/precursor cell survival by accelerating the Fas-mediated apoptosis.
Unreplaced Sex Steroid Deficiency, Corticotropin Deficiency, and Lower IGF-I Are Associated with Lower Bone Mineral Density in Adults with Growth Hormone Deficiency: A KIMS Database Analysis
Authors: Tritos Nicholas A. , Greenspan Susan L. , King Donna , Hamrahian Amir , Cook David M. , Jönsson Peter J. , Wajnrajch Michael P. , Koltowska-Häggstrom Maria , Biller Beverly M. K. 
Published: March 2011

Context:
GH deficiency (GHD) is associated with low bone mineral density (BMD). Risk factors for lower BMD in this GHD population have not been fully elucidated. In particular, there are limited published data in GH-naïve subjects.

Objective:
The objective of the study was to identify endocrine correlates of low BMD in treatment-naïve adult GHD subjects.

Design:
This was a retrospective analysis of data extracted from the (Pfizer International Metabolic Study) KIMS database.

Setting:
The study was an international epidemiological survey of more than 15,000 adult GHD patients from 31 countries.

Patients:
A total of 1218 subjects with stringently defined GHD of adult onset (641 women and 577 men) who were GH naïve and had BMD measured in the posterior anterior lumbar spine and femoral neck by dual-energy X-ray absorptiometry.

Main Outcome Measures:
Variables associated with standardized BMD (sBMD) in adult-onset GHD were examined.

Results:
In the LS, body mass index (r = 0.13, P &lt; 0.01), unreplaced sex steroid deficiency (r = −0.17, P &lt; 0.0001), and corticotropin deficiency (r = −0.11, P &lt; 0.01) were independently associated with sBMD. In the FN, age (r = −0.19, P &lt; 0.0001), female gender (r = −0.18, P &lt; 0.0001), body mass index (r = 0.21, P &lt; 0.0001), and decreased IGF-I sd scores (r = 0.10, P &lt; 0.001) were independently associated with sBMD.

Conclusions:
Hormone variables associated with lower sBMD in patients with adult-onset GHD include unreplaced sex steroid deficiency and corticotropin deficiency in the LS and lower IGF-I SDS in the FN.
Diagnosis and Treatment of Subclinical Hypercortisolism
Authors: Chiodini Iacopo 
Published: March 2011

Context:Subclinical hypercortisolism (SH) is a condition of biochemical cortisol excess without the classical signs or symptoms of overt hypercortisolism. It is thought to be present in the 5–30% of patients with incidentally discovered adrenal mass (adrenal incidentalomas), which in turn are found in 4–7% of the adult population. Therefore, SH has been suggested to be present in 0.2–2.0% of the adult population. Some studies suggested that this condition is present in 1–10% of patients with diabetes or established osteoporosis. The present manuscript reviews the literature on diagnostic procedures and the metabolic effect of the recovery from SH.Evidence Acquisition:A PubMed search was used to identify the available studies. The most relevant studies from 1992 to November 2010 have been included in the review.Evidence Synthesis:The available data suggest that SH may be associated with chronic complications, such as hypertension, diabetes mellitus, overweight/obesity, and osteoporosis. The available intervention studies suggest that the recovery from SH may lead to the improvement of hypertension and diabetes mellitus. A retrospective study suggests that this beneficial effect could be predicted before surgery.Conclusions:SH is suggested to be associated with some chronic complications of overt cortisol excess. Recovery from this condition seems to improve these complications. However, a large, prospective, randomized study is needed to confirm this hypothesis and to establish the best diagnostic approach to identify patients with adrenal incidentalomas who can benefit from surgery.
Effects of an oral supplementation of germinated barley foodstuff on serum tumour necrosis factor-α, interleukin-6 and -8 in patients with ulcerative colitis
Authors: Faghfoori Zeinab , Navai Lida , Shakerhosseini Rahebeh , Somi Mohammad Hossein , Nikniaz Zeinab , Norouzi Mohammad Fahmideh 
Published: March 2011

Background The efficacy of germinated barley foodstuff (GBF) on tumour necrosis factor-alpha (TNF- α), interleukin-6 (IL-6) and -8 (IL-8) in patients with ulcerative colitis (UC) has not yet been examined. The aim of the present study was to determine the effect of administration of GBF on serum TNF- α, IL-6 and -8 levels in UC patients in remission. Methods Forty-one patients with UC were divided into two groups, namely control and GBF group. Twenty-one patients in the control group received standard treatment while 20 patients in the GBF group received 30 g of GBF daily by oral administration during two months of the study along with standard drug therapy. Results Levels of TNF- α, IL-6 and -8 all decreased in the GBF group compared with baseline during the two-month study, while in the control group all values rose. For IL-6 and -8 this effect was significant, P = 0.034 and 0.013, respectively. Conclusions The results of the present study showed that the consumption of GBF may reduce the level of serum TNF- α, IL-6 and -8 in patients with UC. This investigation was designed as a pilot study and the results may provide a basis for more future clinical trials.
Measurement of serum lanthanum in patients treated with lanthanum carbonate by inductively coupled plasma-mass spectrometry
Authors: Handley S A , Raja K B , Sharpe C , Flanagan R J 
Published: March 2011

Background Lanthanum carbonate is used as a phosphate binder in patients with stage V chronic kidney disease (CKD). While well tolerated in clinical trials, with no toxicity reported as regards bone and liver metabolism, and cognitive function, concerns remain over possible toxicity. Published methods for the measurement of lanthanum ion in biological samples include aggressive and complicated sample preparation steps that are unsuitable for routine use. A simple method has been developed and validated for the measurement of serum lanthanum. Method A ThermoFisher Scientific XSERIES-II inductively coupled plasma-mass spectrometer was used to monitor 139La. Validation was undertaken using internal quality control solutions containing lanthanum ion (0.20, 0.70 and 4.00 μg/L). Lanthanum was measured in patients (number = 20) with CKD prescribed lanthanum carbonate (500–1500 mg/d) and patients undergoing haemodialysis not prescribed lanthanum carbonate (number = 20). Results Accuracy and imprecision were >95% and <5%, respectively. Calibration was linear (range 0.1–5 μg/L, R2 = 0.99). The lower limit of quantification (LLoQ) was 0.1 μg/L lanthanum ion. In patients with CKD not prescribed lanthanum carbonate, serum lanthanum was below the LLoQ. Out of 20 CKD patients prescribed lanthanum carbonate, serum lanthanum was measurable in only 12 (range 0.11–0.60 μg/L lanthanum ion). There was no apparent relationship between dose and serum lanthanum in these patients. Conclusions A lack of relationship between the dose of lanthanum carbonate and the serum lanthanum concentration may have been due to poor adherence to the treatment regimen. However the concentrations measured were close to the LLoQ.
Clinical quality indicators in laboratory medicine: a survey of current practice in the UK
Authors: Barth Julian H 
Published: March 2011

Background Clinical outcomes are the current paradigm for assessing the performance of health institutions. In contrast, clinical laboratories are assessed on largely operational criteria. Methods An invitation to an online questionnaire was sent to all members of the Association for Clinical Biochemistry in the UK and Eire. All data were normalized to the total number of respondents irrespective of how many respondents answered each question. Results A total of 335 individuals responded to the survey. A further six responses were discarded as the respondents worked outside clinical laboratories. Overall responses showed that of the selected quality indicators, responses ranged from 7% to 84%. In general, although most laboratories provided an advisory and interpretative service, there was little evaluation and audit of this component of the service. The majority of respondents reported a written critical (alert) list and a hospital point-of-care committee. Conclusion This survey has explored clinical quality indicators in the preanalytical, analytical and postanalytical phases of laboratory practice. This should act as a template for laboratory assessment and clinical quality improvement.
Measuring carbonic anhydrase IX as a hypoxia biomarker: differences in concentrations in serum and plasma using a commercial enzyme-linked immunosorbent assay due to influences of metal ions
Authors: Wind Tobias C , Messenger Michael P , Thompson Douglas , Selby Peter J , Banks Rosamonde E 
Published: March 2011

Background There is increasing interest in measuring the soluble forms of carbonic anhydrase IX (CA IX) in blood as a marker of hypoxia for prognostic purposes or for predictive use in therapeutic trials in various cancers. Following our initial observations of marked differences in the measured concentrations of CA IX in EDTA plasma versus serum, we sought to investigate these further in order to determine their effects on results in published studies and to ensure accurate measurement in future studies. Methods Serum and EDTA plasma samples from healthy controls and patients with renal cancer were used in the validation of two commercially available enzyme-linked immunosorbent assays (ELISAs) for CA IX with examination of recovery, parallelism and specificity and comparison of paired plasma and serum. Results Successful validation of one of the ELISAs was not achieved with particular problems with parallelism and marked differences in measured CA IX concentrations between EDTA plasma and serum. This appeared to be due to a metal ion-dependent epitope on CA IX recognized by the detection antibody in this assay. The other commercially available ELISA examined was successfully validated and showed no difference in CA IX between EDTA plasma and serum. Conclusions These results have important consequences for published studies using this assay where the conclusions drawn from the measurements made may be invalid. This study highlights the need for stringent validation of commercially available assays, including examination of various sample types, before use in research studies.
Beryllium Measurement in Commercially Available Wet Wipes
Authors: Youmans-McDonald Linda D. , Brisson Mike , Bernard Maureen , Agrawal Anoop , Cronin John P. , Adams Lori 
Published: March 2011

Abstract
Analysis for beryllium by fluorescence is now an established method which is used in many government run laboratories and commercial facilities. This study investigates the use of this technique using commercially available wet wipes. The fluorescence method is widely documented [1,2] and has been approved as a standard test method by the ASTM International and the National Institute for Occupational Safety and Health. The procedure involves dissolution of samples in an aqueous ammonium bifluoride solution and then adding a small aliquot to a basic hydroxybenzoquinoline sulfonate fluorescent dye, (Berylliant™, Inc., Detection Solution Part #CH-2) and measuring the fluorescence. This method is specific to beryllium. This work will explore the use of three different commercial wipes spiked with beryllium as beryllium acetate or as beryllium oxide and subsequent analysis by optical fluorescence. The effect of possible interfering metals such as Fe, Ti, and Pu in the wipe medium is also examined.
(S)-1-[N-(Benzylidene)hydrazinylcarbonyl]-2-hydroxyethylcarbamate esters: layered structures created from X—H···O (X = N,O) hydrogen-bonds
Authors: Howie R. Alan , de Souza Marcos V. N. , Pinheiro Alessandra , Kaiser Carlos R. , Wardell James L. , Wardell Solange M. S. V. 
Published: March 2011

Abstract
The molecular structures of tert-butyl (S)-2-hydroxy-[N-(substituted-benzylidene)hydrazinyl-carbonyl]-ethylcarbamates, C15H20N3O4X (3: X = H, o-OH, o-NO2, m-NO2 and p-CN), derived from L-serine, are formally rather similar. Despite the variation in substituent, X, tricälinic (3: X = H), (3: X = o-OH), (3: X = m-NO2)and(3: X = p-CN) are isostructural and exhibit, with minor variations, the same fundamental intermolecular O—H···O and N—H···O hydrogen-bond connectivity in two-dimensions in layers of molecules. In monoclinic(3: X = o-NO2), however, the oxygen atoms of the nitro group function as additional O—H···O and N—H···O hydrogen-bond acceptors resulting in a more complex form of two-dimensional connectivity.
Combining halogen and hydrogen bonding in the 1 : 1 molecular salt (hexamethylenetetraminium) · (p-iodobenzoate) to form 1-D zig-zag chains
Authors: Lemmerer Andreas 
Published: March 2011

Abstract
The crystal structure of the molecular salt (hexamethylenetetraminium) · (p-iodobenzoate) is the first example of a complex using the hexamethylene (HMTA) molecule that has both halogen and hydrogen bonding. The desired supramolecular packing arrangement of 1-D zig-zag chains was observed. A detailed breakdown of related HMTA complexes in the literature was used to show that zig-zag chains are a common packing feature of HMTA complexes with bifunctional molecules. The crystal structure determination of the molecular salt shows that the two intermolecular interactions N—H+···OOC– and N···I are positionally disordered around a centre of inversion.
Identification of Novel Ras-Cooperating Oncogenes in Drosophila melanogaster: A RhoGEF/Rho-Family/JNK Pathway Is a Central Driver of Tumorigenesis
Authors: Brumby Anthony M , Goulding Karen R , Schlosser Tanja , Loi Sherene , Galea Ryan , Khoo Peytee , Bolden Jessica E , Aigaki Toshiro , Humbert Patrick O , Richardson Helena E 
Published: March 2011

Abstract
We have shown previously that mutations in the apico-basal cell polarity regulators cooperate with oncogenic Ras (RasACT) to promote tumorigenesis in Drosophila melanogaster and mammalian cells. To identify novel genes that cooperate with RasACT in tumorigenesis, we carried out a genome-wide screen for genes that when overexpressed throughout the developing Drosophila eye enhance RasACT-driven hyperplasia. RasACT-cooperating genes identified were Rac1 Rho1, RhoGEF2, pbl, rib, and east, which encode cell morphology regulators. In a clonal setting, which reveals genes conferring a competitive advantage over wild-type cells, only Rac1, an activated allele of Rho1 (Rho1ACT), RhoGEF2, and pbl cooperated with RasACT, resulting in reduced differentiation and large invasive tumors. Expression of RhoGEF2 or Rac1 with RasACT upregulated Jun kinase (JNK) activity, and JNK upregulation was essential for cooperation. However, in the whole-tissue system, upregulation of JNK alone was not sufficient for cooperation with RasACT, while in the clonal setting, JNK upregulation was sufficient for RasACT-mediated tumorigenesis. JNK upregulation was also sufficient to confer invasive growth of RasV12-expressing mammalian MCF10A breast epithelial cells. Consistent with this, HER2+ human breast cancers (where human epidermal growth factor 2 is overexpressed and Ras signaling upregulated) show a significant correlation with a signature representing JNK pathway activation. Moreover, our genetic analysis in Drosophila revealed that Rho1 and Rac are important for the cooperation of RhoGEF2 or Pbl overexpression and of mutants in polarity regulators, Dlg and aPKC, with RasACT in the whole-tissue context. Collectively our analysis reveals the importance of the RhoGEF/Rho-family/JNK pathway in cooperative tumorigenesis with RasACT.
A Leed Investigation of (111) Oriented Si, Ge and GaAs Surfaces Following Pulsed Laser Irradiation
Authors: Zehner D. M. , Noonan J. R. , Davis H. L. , White C. W. , Ownby G. W. 
Published: March 2011

ABSTRACTThe low energy electron diffraction (LEED) patterns obtained from clean (111) oriented Si, Ge and GaAs single crystals subsequent to their irradiation with the output of a pulsed ruby laser in an ultra-high vacuum (UHV) environment suggest that metastable (1×1) surface structures are produced in the regrowth process. Conventional LEED analyses of the Si and Ge surfaces suggest that they terminate in registry with the bulk but that the two outermost interlayer spacings differ from those of the bulk. For the case of Si these changes are a contraction of 25.5 ± 2.5% and an expansion of 3.2 ± 1.5% between the first and second and second and third layers respectively.
Direct Measurement of Cw Laser-Induced Crystal Growth Dynamics by Time-Resolved Optical Reflectivity
Authors: Olson G.L. , Kokorowski S.A. , Roth J.A. , Hess L.D. 
Published: March 2011

ABSTRACTWe report the use of time-resolved optical reflectivity to directly monitor the dynamics of cw laser-induced solid phase epitaxy (SPE) of thin films. This in situ measurement technique utilizes optical interference effects between light reflected from the surface of a sample and from an advancing interface to provide continuous temporal and spatial resolution of crystal growth processes. SPE growth rates of ionimplanted films which are five orders of magnitude faster than previously observed can be induced and accurately measured with the laser method. Arsenic enhances the SPE rate, and spatially resolved measurements show that the growth rate for arsenic implanted films varies in accordance with the ionimplantation profile. Results are reported for silicon selfimplanted samples with and without subsequent arsenic ion implantation, and for silicon samples directly implanted with arsenic.