Performance of the distributed central analysis in BaBar

The total dataset produced by the BaBar experiment at the Stanford Linear Accelerator Center (SLAC) currently comprises roughly$3times 10^9$data events and an equal amount of simulated events, corresponding to 23 Tbytes of real data and 51 Tbytes simulated events. Since individual analyses typically select a very small fraction of all events, it would be extremely inefficient if each analysis had to process the full dataset. A first, centrally managed analysis step is therefore a common pre-selection (‘skimming’) of all data according to very loose, inclusive criteria to facilitate data access for later analysis. Usually, there are common selection criteria for several analysis. However, they may change over time, e.g., when new analyses are developed. Currently,$cal

Rating of Sweetness by Molar Refractivity and Ionization Potential: QSAR Study of Sucrose and Guanidine Derivatives

A quantitative structure activity relationship study of 31 sucrose derivatives and 30 guanidine derivatives has been undertaken. Their sweetness values, relative to sucrose (RS), have been taken from literature.  The study has been made with the help of CAChe Pro software by using eight descriptors, viz. electron  affinity, ionization potential, electrophilicity index, total energy, heat of formation, steric energy, molar refractivity and solvent accessible surface area. Multi-linear regression (MLR) analysis has been  performed with different combinations of descriptors and the quality of regression has been adjudged by the correlation coefficient, cross-validation coefficient and other statistical parameters like the standard error, standard error of the estimate, degrees of freedom, etc. The study indicates that ionization potential appears an important descriptor for sucrose derivatives, whereas molar refractivity appears an important descriptor for guanidine derivatives. The ionization potential alone and in combination with the electrophilicity index, molar refractivity and solvent accessibility surface area provide dependable QSARmodels for sucrose derivatives. Molar refractivity alone and in combination with solvent  accessibility surface area, ionization potential and heat of formation provide dependable QSAR models for guanidine derivatives. The predicted sweetness values obtained by these QSAR models are close to observed sweetness.KEYWORDS: Sweetness, sucrose, guanidine, DFT, PM3

Development of an HPLC method for determination of pentachloronitrobenzene, hexachlorobenzene and their possible metabolites

<p>Abstract</p> <p>Background</p> <p>Pentachloronitrobenzene (PCNB) and hexachlorobenzene (HCB) are highly toxic and widespread in every environmental compartment. Some of metabolic products such as amino/nitro containing chlorinated aromatic compounds can be determined by gas chromatography coupled with electron capture detector (GC-ECD). However, it is difficult to identify some of chlorophenolic and chloroquinolic intermediates produced from PCNB and HCB by the above mentioned technique. Therefore, for analysis of these compounds and their metabolites, we have developed a high performance liquid chromatography (HPLC) based method.</p> <p>Results</p> <p>The extraction of PCNB and HCB from soil and minimal salt medium was carried out with ethyl acetate and hexane respectively with good recoveries (98% for PCNB and 97% for HCB). The validation of the proposed extraction and HPLC method was done by analysis of PCNB and HCB biodegradation and their metabolites identification from anaerobic enriched soil samples.</p> <p>Conclusion</p> <p>A rapid, sensitive and simple HPLC based analytical method was developed for the analysis of PCNB, HCB and their possible intermediates.</p

Smokeless tobacco - a substantial risk for oral potentially malignant disorders in South Asia

Data sources: Medline, the Science Citation Index (SCI) via Web of Science, Scopus, CINAHL, Global Index Medicus, Google Scholar and SLT-related reports of the International Agency for Research on Cancer and the National Cancer Institute of the United States. Study selection: Observational studies on the use of SLT and the risk of developing OPMDs in South Asian Populations. Data extraction and synthesis: Duplicate selection of studies was undertaken with two reviewers undertaking data abstraction and quality assessment independently. Risk and odds ratios were extracted or calculated for studies where possible. Meta odds ratios (mOR) were calculated using a random effects analysis. Results: Fifteen papers reporting 18 studies were included. The majority (12) were from India. All the studies were case-control designs. MOR for any OPMD with the use of any SLT product was 15.5 (95% CI; 9.9–24.2). Risk was higher in women; mOR = 22.2 (95% CI, 9.1–54.1) than men; mOR = 8.7 (95% CI, 2.1–34.8). Betel quid with tobacco carried the highest risk for OPMD, mOR = 16.1 (95% CI, 7.8–33.5). Conclusions: The findings of our study point towards a strong association between some forms of OPMDs and SLT use in South Asia. The risk estimates are high, irrespective of controlling for confounders such as smoking and alcohol or stratification by sex, country or source of controls. There is also an exposure-response relationship between OPMDs and SLT use

Formulation and Permeation Kinetic Studies of Flurbiprofen Gel

Purpose: To investigate the in vitro permeation and drug release kinetics of flurbiprofen gel.Methods: Thirteen batches (G1, G2 … G13) of flurbiprofen gels were prepared using different ratios ofpermeation enhancers, i.e., propylene glycol (PG) and polyethylene glycol (PEG), by response surface methodology (RSM). Viscosity, pH, spreadability, consistency and drug content of the flurbiprofen gels were measured. Permeation experiments were conducted using silicone membrane in a modified Franz diffusion cell. Permeation parameters determined include diffusion coefficient (D), Flux (J), lag time (tLag), permeation coefficient (Kp), input rate (IR) and enhancement ratio (ER). Primary skin irritation test was performed for the optimized gel, G3, using 11 human volunteers.Results: Maximum solubility (72.15 ± 0.02 mg/mL) of flurbiprofen was observed in a mixture (2:1) of methanol and water. Partition coefficient (Ko/w) was determined as logP = 3.68 ± 0.11. The gels were stable under various storage conditions, and were homogenous, crystalline and transparent. Viscosity, pH, spreadability, consistency and drug content were in the range of 150 – 178 × 102 cps, 5.42 - 5.75, 5.0 - 7.0 g.cm/s, 3.0 - 9.0 mm, and 97.99 - 99.86 %, respectively. No irritation or lesions (erythma, redness and ulceration) occurred in human volunteers over a 30-day period. The optimized formulation, G3, showed maximum flux through silicone membrane.Conclusion: PG and PEG are effective enhancers of flurbiprofen from  various formulations when used in various ratios.Keywords: Flurbiprofen, Gel, Diffusion, Permeation enhancers, Skin irritation, Silicone membran

Normal Hematopoietic Progenitor Subsets Have Distinct Reactive Oxygen Species, BCL2 and Cell-Cycle Profiles That Are Decoupled from Maturation in Acute Myeloid Leukemia

In acute myeloid leukemia (AML) quiescence and low oxidative state, linked to BCL2 mitochondrial regulation, endow leukemic stem cells (LSC) with treatment-resistance. LSC in CD34+ and more mature CD34− AML have heterogeneous immunophenotypes overlapping with normal stem/progenitor cells (SPC) but may be differentiated by functional markers. We therefore investigated the oxidative/reactive oxygen species (ROS) profile, its relationship with cell-cycle/BCL2 for normal SPC, and whether altered in AML and myelodysplasia (MDS). In control BM (n = 24), ROS levels were highest in granulocyte-macrophage progenitors (GMP) and CD34− myeloid precursors but megakaryocyte-erythroid progenitors had equivalent levels to CD34+CD38low immature-SPC although they were ki67high. BCL2 upregulation was specific to GMPs. This profile was also observed for CD34+SPC in MDS-without-excess-blasts (MDS-noEB, n = 12). Erythroid CD34− precursors were, however, abnormally ROS-high in MDS-noEB, potentially linking oxidative stress to cell loss. In pre-treatment AML (n = 93) and MDS-with-excess-blasts (MDS-RAEB) (n = 14), immunophenotypic mature-SPC had similar ROS levels to co-existing immature-SPC. However ROS levels varied between AMLs; Flt3ITD+/NPM1wild-type CD34+SPC had higher ROS than NPM1mutated CD34+ or CD34− SPC. An aberrant ki67lowBCL2high immunophenotype was observed in CD34+AML (most prominent in Flt3ITD AMLs) but also in CD34− AMLs and MDS-RAEB, suggesting a shared redox/pro-survival adaptation. Some patients had BCL2 overexpression in CD34+ ROS-high as well as ROS-low fractions which may be indicative of poor early response to standard chemotherapy. Thus normal SPC subsets have distinct ROS, cell-cycle, BCL2 profiles that in AML /MDS-RAEB are decoupled from maturation. The combined profile of these functional properties in AML subpopulations may be relevant to differential treatment resistance

Bone marrow mesenchymal stem cells do not enhance intra-synovial tendon healing despite engraftment and homing to niches within the synovium

Intra-synovial tendon injuries display poor healing, which often results in reduced functionality and pain. A lack of effective therapeutic options has led to experimental approaches to augment natural tendon repair with autologous mesenchymal stem cells (MSCs) although the effects of the intra-synovial environment on the distribution, engraftment and functionality of implanted MSCs is not known. This study utilised a novel sheep model which, although in an anatomically different location, more accurately mimics the mechanical and synovial environment of the human rotator cuff, to determine the effects of intra-synovial implantation of MSCs

The quality of reporting of primary test accuracy studies in obstetrics and gynaecology: application of the STARD criteria

<p>Abstract</p> <p>Background</p> <p>In obstetrics and gynaecology there has been a rapid growth in the development of new tests and primary studies of their accuracy. It is imperative that such studies are reported with transparency allowing the detection of any potential bias that may invalidate the results. The objective of this study was to determine the quality of reporting in diagnostic test accuracy studies in obstetrics and gynaecology using the Standards for Reporting of Diagnostic Accuracy - STARD checklist.</p> <p>Methods</p> <p>The included studies of ten systematic reviews were assessed for compliance with each of the reporting criteria. Using appropriate statistical tests we investigated whether there was an improvement in reporting quality since the introduction of the STARD checklist, whether a correlation existed between study sample size, country of origin of study and reporting quality.</p> <p>Results</p> <p>A total of 300 studies were included (195 for obstetrics, 105 for gynaecology). The overall reporting quality of included studies to the STARD criteria was poor. Obstetric studies reported adequately > 50% of the time for 62.1% (18/29) of the items while gynaecologic studies did the same 51.7% (15/29). There was a greater mean compliance with STARD criteria in the included obstetric studies than the gynaecological (p < 0.0001). There was a positive correlation, in both obstetrics (p < 0.0001) and gynaecology (p = 0.0123), between study sample size and reporting quality. No correlation between geographical area of publication and compliance with the reporting criteria could be demonstrated.</p> <p>Conclusions</p> <p>The reporting quality of papers in obstetrics and gynaecology is improving. This may be due to initiatives such as the STARD checklist as well as historical progress in awareness among authors of the need to accurately report studies. There is however considerable scope for further improvement.</p

Top down tandem mass spectrometric analysis of a chemically modified rough-type lipopolysaccharide vaccine candidate

Recent advances in lipopolysaccharide (LPS) biology have led to its use in drug discovery pipelines, including vaccine and vaccine adjuvant discovery. Desirable characteristics for LPS vaccine candidates include both the ability to produce a specific antibody titer in patients and a minimal host inflammatory response directed by the innate immune system. However, in-depth chemical characterization of most LPS extracts has not been performed; hence, biological activities of these extracts are unpredictable. Additionally, the most widely adopted workflow for LPS structure elucidation includes nonspecific chemical decomposition steps before analyses, making structures inferred and not necessarily biologically relevant. In this work, several different mass spectrometry workflows that have not been previously explored were employed to show proof-of-principle for top down LPS primary structure elucidation, specifically for a rough-type mutant(J5) E.coli-derived LPS component of a vaccine candidate. First, ion mobility filtered precursor ions were subjected to collision induced dissociation (CID) to define differences in native J5 LPS v. chemically detoxified J5 LPS (dLPS). Next, ultra-high mass resolving power, accurate mass spectrometry was employed for unequivocal precursor and product ion empirical formulae generation. Finally, MS 3 analyses in an ion trap instrument showed that previous knowledge about dissociation of LPS components can be used to reconstruct and sequence LPS in a top down fashion. A structural rationale is also explained for differential inflammatory dose-response curves, in vitro, when HEK-Blue hTLR4 cells were administered increasing concentrations of native J5 LPS v. dLPS, which will be useful in future drug discovery efforts