136 research outputs found
FT-IR and Raman vibrational analysis, B3LYP and M06-2X simulations of 4-bromomethyl-6-tert-butyl-2H-chromen-2-one
In this study, the experimental and theoretical vibrational frequencies of a newly synthesized bacteriostatic and anti-tumor molecule namely, 4-bromomethyl-6-tert-butyl-2H-chromen-2-one have been investigated. The experimental FT-IR (4000-400 cm- 1) and Raman spectra (4000-100 cm- 1) of the compound in solid phase have been recorded. The theoretical vibrational frequencies and optimized geometric parameters have been calculated using density functional theory (DFT/B3LYP: Becke, 3-parameter, Lee-Yang-Parr and DFT/M06-2X: highly parametrized, empirical exchange correlation function) with 6-311++G(d, p) basis set by Gaussian 03 software, for the first time. The assignments of the vibrational frequencies have been done by potential energy distribution (PED) analysis using VEDA 4 software. The theoretical optimized geometric parameters and vibrational frequencies have been found to be in good agreement with the corresponding experimental data and results in the literature. In addition, the highest occupied molecular orbital (HOMO) energy, the lowest unoccupied molecular orbital (LUMO) energy and the other related molecular energy values of the compound have been investigated using the same theoretical calculations. © 2014 Elsevier B.V. All rights reserved
Parallel Mapper
The construction of Mapper has emerged in the last decade as a powerful and
effective topological data analysis tool that approximates and generalizes
other topological summaries, such as the Reeb graph, the contour tree, split,
and joint trees. In this paper, we study the parallel analysis of the
construction of Mapper. We give a provably correct parallel algorithm to
execute Mapper on multiple processors and discuss the performance results that
compare our approach to a reference sequential Mapper implementation. We report
the performance experiments that demonstrate the efficiency of our method
Multivariate biophysical markers predictive of mesenchymal stromal cell multipotency
The capacity to produce therapeutically relevant quantities of multipotent mesenchymal stromal cells (MSCs) via in vitro culture is a common prerequisite for stem cell-based therapies. Although culture expanded MSCs are widely studied and considered for therapeutic applications, it has remained challenging to identify a unique set of characteristics that enables robust identification and isolation of the multipotent stem cells. New means to describe and separate this rare cell type and its downstream progenitor cells within heterogeneous cell populations will contribute significantly to basic biological understanding and can potentially improve efficacy of stem and progenitor cell-based therapies. Here, we use multivariate biophysical analysis of culture-expanded, bone marrow-derived MSCs, correlating these quantitative measures with biomolecular markers and in vitro and in vivo functionality. We find that, although no single biophysical property robustly predicts stem cell multipotency, there exists a unique and minimal set of three biophysical markers that together are predictive of multipotent subpopulations, in vitro and in vivo. Subpopulations of culture-expanded stromal cells from both adult and fetal bone marrow that exhibit sufficiently small cell diameter, low cell stiffness, and high nuclear membrane fluctuations are highly clonogenic and also exhibit gene, protein, and functional signatures of multipotency. Further, we show that high-throughput inertial microfluidics enables efficient sorting of committed osteoprogenitor cells, as distinct from these mesenchymal stem cells, in adult bone marrow. Together, these results demonstrate novel methods and markers of stemness that facilitate physical isolation, study, and therapeutic use of culture-expanded, stromal cell subpopulations.National University of Singapore (Graduate School for Integrative Sciences and Engineering Program)Singapore-MIT Alliance (Singapore-MIT Alliance-3 graduate fellowship program)Singapore. National Research FoundationSingapore-MIT Alliance for Research and Technology (BioSystems and Micromechanics Interdisciplinary Research Group)Singapore. National Medical Research Council (NMRC/Clinician Scientist Award/012/2009
Magnetic correlations and quantum criticality in the insulating antiferromagnetic, insulating spin liquid, renormalized Fermi liquid, and metallic antiferromagnetic phases of the Mott system V_2O_3
Magnetic correlations in all four phases of pure and doped vanadium
sesquioxide V_2O_3 have been examined by magnetic thermal neutron scattering.
While the antiferromagnetic insulator can be accounted for by a Heisenberg
localized spin model, the long range order in the antiferromagnetic metal is an
incommensurate spin-density-wave, resulting from a Fermi surface nesting
instability. Spin dynamics in the strongly correlated metal are dominated by
spin fluctuations in the Stoner electron-hole continuum. Furthermore, our
results in metallic V_2O_3 represent an unprecedentedly complete
characterization of the spin fluctuations near a metallic quantum critical
point, and provide quantitative support for the SCR theory for itinerant
antiferromagnets in the small moment limit. Dynamic magnetic correlations for
energy smaller than k_BT in the paramagnetic insulator carry substantial
magnetic spectral weight. However, the correlation length extends only to the
nearest neighbor distance. The phase transition to the antiferromagnetic
insulator introduces a sudden switching of magnetic correlations to a different
spatial periodicity which indicates a sudden change in the underlying spin
Hamiltonian. To describe this phase transition and also the unusual short range
order in the paramagnetic state, it seems necessary to take into account the
orbital degrees of freedom associated with the degenerate d-orbitals at the
Fermi level in V_2O_3.Comment: Postscript file, 24 pages, 26 figures, 2 tables, accepted by Phys.
Rev.
Binding of molecules to DNA and other semiflexible polymers
A theory is presented for the binding of small molecules such as surfactants
to semiflexible polymers. The persistence length is assumed to be large
compared to the monomer size but much smaller than the total chain length. Such
polymers (e.g. DNA) represent an intermediate case between flexible polymers
and stiff, rod-like ones, whose association with small molecules was previously
studied. The chains are not flexible enough to actively participate in the
self-assembly, yet their fluctuations induce long-range attractive interactions
between bound molecules. In cases where the binding significantly affects the
local chain stiffness, those interactions lead to a very sharp, cooperative
association. This scenario is of relevance to the association of DNA with
surfactants and compact proteins such as RecA. External tension exerted on the
chain is found to significantly modify the binding by suppressing the
fluctuation-induced interaction.Comment: 15 pages, 7 figures, RevTex, the published versio
Predictors of uptake of eye examination in people living with diabetes mellitus in three counties of Kenya
Curation of viral genomes: challenges, applications and the way forward
BACKGROUND: Whole genome sequence data is a step towards generating the 'parts list' of life to understand the underlying principles of Biocomplexity. Genome sequencing initiatives of human and model organisms are targeted efforts towards understanding principles of evolution with an application envisaged to improve human health. These efforts culminated in the development of dedicated resources. Whereas a large number of viral genomes have been sequenced by groups or individuals with an interest to study antigenic variation amongst strains and species. These independent efforts enabled viruses to attain the status of 'best-represented taxa' with the highest number of genomes. However, due to lack of concerted efforts, viral genomic sequences merely remained as entries in the public repositories until recently. RESULTS: VirGen is a curated resource of viral genomes and their analyses. Since its first release, it has grown both in terms of coverage of viral families and development of new modules for annotation and analysis. The current release (2.0) includes data for twenty-five families with broad host range as against eight in the first release. The taxonomic description of viruses in VirGen is in accordance with the ICTV nomenclature. A well-characterised strain is identified as a 'representative entry' for every viral species. This non-redundant dataset is used for subsequent annotation and analyses using sequenced-based Bioinformatics approaches. VirGen archives precomputed data on genome and proteome comparisons. A new data module that provides structures of viral proteins available in PDB has been incorporated recently. One of the unique features of VirGen is predicted conformational and sequential epitopes of known antigenic proteins using in-house developed algorithms, a step towards reverse vaccinology. CONCLUSION: Structured organization of genomic data facilitates use of data mining tools, which provides opportunities for knowledge discovery. One of the approaches to achieve this goal is to carry out functional annotations using comparative genomics. VirGen, a comprehensive viral genome resource that serves as an annotation and analysis pipeline has been developed for the curation of public domain viral genome data . Various steps in the curation and annotation of the genomic data and applications of the value-added derived data are substantiated with case studies
Impact of primary kidney disease on the effects of empagliflozin in patients with chronic kidney disease: secondary analyses of the EMPA-KIDNEY trial
Background: The EMPA KIDNEY trial showed that empagliflozin reduced the risk of the primary composite outcome of kidney disease progression or cardiovascular death in patients with chronic kidney disease mainly through slowing progression. We aimed to assess how effects of empagliflozin might differ by primary kidney disease across its broad population. Methods: EMPA-KIDNEY, a randomised, controlled, phase 3 trial, was conducted at 241 centres in eight countries (Canada, China, Germany, Italy, Japan, Malaysia, the UK, and the USA). Patients were eligible if their estimated glomerular filtration rate (eGFR) was 20 to less than 45 mL/min per 1·73 m2, or 45 to less than 90 mL/min per 1·73 m2 with a urinary albumin-to-creatinine ratio (uACR) of 200 mg/g or higher at screening. They were randomly assigned (1:1) to 10 mg oral empagliflozin once daily or matching placebo. Effects on kidney disease progression (defined as a sustained ≥40% eGFR decline from randomisation, end-stage kidney disease, a sustained eGFR below 10 mL/min per 1·73 m2, or death from kidney failure) were assessed using prespecified Cox models, and eGFR slope analyses used shared parameter models. Subgroup comparisons were performed by including relevant interaction terms in models. EMPA-KIDNEY is registered with ClinicalTrials.gov, NCT03594110. Findings: Between May 15, 2019, and April 16, 2021, 6609 participants were randomly assigned and followed up for a median of 2·0 years (IQR 1·5–2·4). Prespecified subgroupings by primary kidney disease included 2057 (31·1%) participants with diabetic kidney disease, 1669 (25·3%) with glomerular disease, 1445 (21·9%) with hypertensive or renovascular disease, and 1438 (21·8%) with other or unknown causes. Kidney disease progression occurred in 384 (11·6%) of 3304 patients in the empagliflozin group and 504 (15·2%) of 3305 patients in the placebo group (hazard ratio 0·71 [95% CI 0·62–0·81]), with no evidence that the relative effect size varied significantly by primary kidney disease (pheterogeneity=0·62). The between-group difference in chronic eGFR slopes (ie, from 2 months to final follow-up) was 1·37 mL/min per 1·73 m2 per year (95% CI 1·16–1·59), representing a 50% (42–58) reduction in the rate of chronic eGFR decline. This relative effect of empagliflozin on chronic eGFR slope was similar in analyses by different primary kidney diseases, including in explorations by type of glomerular disease and diabetes (p values for heterogeneity all >0·1). Interpretation: In a broad range of patients with chronic kidney disease at risk of progression, including a wide range of non-diabetic causes of chronic kidney disease, empagliflozin reduced risk of kidney disease progression. Relative effect sizes were broadly similar irrespective of the cause of primary kidney disease, suggesting that SGLT2 inhibitors should be part of a standard of care to minimise risk of kidney failure in chronic kidney disease. Funding: Boehringer Ingelheim, Eli Lilly, and UK Medical Research Council
Effects of hospital facilities on patient outcomes after cancer surgery: an international, prospective, observational study
Background Early death after cancer surgery is higher in low-income and middle-income countries (LMICs) compared with in high-income countries, yet the impact of facility characteristics on early postoperative outcomes is unknown. The aim of this study was to examine the association between hospital infrastructure, resource availability, and processes on early outcomes after cancer surgery worldwide.Methods A multimethods analysis was performed as part of the GlobalSurg 3 study-a multicentre, international, prospective cohort study of patients who had surgery for breast, colorectal, or gastric cancer. The primary outcomes were 30-day mortality and 30-day major complication rates. Potentially beneficial hospital facilities were identified by variable selection to select those associated with 30-day mortality. Adjusted outcomes were determined using generalised estimating equations to account for patient characteristics and country-income group, with population stratification by hospital.Findings Between April 1, 2018, and April 23, 2019, facility-level data were collected for 9685 patients across 238 hospitals in 66 countries (91 hospitals in 20 high-income countries; 57 hospitals in 19 upper-middle-income countries; and 90 hospitals in 27 low-income to lower-middle-income countries). The availability of five hospital facilities was inversely associated with mortality: ultrasound, CT scanner, critical care unit, opioid analgesia, and oncologist. After adjustment for case-mix and country income group, hospitals with three or fewer of these facilities (62 hospitals, 1294 patients) had higher mortality compared with those with four or five (adjusted odds ratio [OR] 3.85 [95% CI 2.58-5.75]; p<0.0001), with excess mortality predominantly explained by a limited capacity to rescue following the development of major complications (63.0% vs 82.7%; OR 0.35 [0.23-0.53]; p<0.0001). Across LMICs, improvements in hospital facilities would prevent one to three deaths for every 100 patients undergoing surgery for cancer.Interpretation Hospitals with higher levels of infrastructure and resources have better outcomes after cancer surgery, independent of country income. Without urgent strengthening of hospital infrastructure and resources, the reductions in cancer-associated mortality associated with improved access will not be realised
Hyaluronic acid hydrogels incorporating platelet lysate enhance human pulp cell proliferation and differentiation
The restoration of dentine-pulp complex remains a challenge for dentists; nonetheless, it has been poorly addressed. An ideal system should modulate the host response, as well as enable the recruitment, proliferation and differentiation of relevant progenitor cells. Herein was proposed a photocrosslinkable hydrogel system based on hyaluronic acid (HA) and platelet lysate (PL). PL is a cocktail of growth factors (GFs) and cytokines involved in wound healing orchestration, obtained by the cryogenic processing of platelet concentrates, and was expected to provide the HA hydrogels specific biochemical cues to enhance pulp cellsâ recruitment, proliferation and differentiation. Stable HA hydrogels incorporating PL (HAPL) were prepared after photocrosslinking of methacrylated HA (Met-HA) previously dissolved in PL, triggered by the Ultra Violet activated photoinitiator Irgacure 2959. Both the HAPL and plain HA hydrogels were shown to be able to recruit cells from a cell monolayer of human dental pulp stem cells (hDPSCs) isolated from permanent teeth. The hDPCs were also seeded directly over the hydrogels (5 Ã 104 cells/hydrogel) and cultured in osteogenic conditions. Cell metabolism and DNA quantification were higher, in all time-points, for PL supplemented hydrogels (p < 0,05). Alkaline phosphatase (ALPL) activity and calcium quantification peaks were observed for the HAPL group at 21 days (p < 0,05). The gene expression for ALPL and COLIA1 was up-regulated at 21 days to HAPL, compared with HA group (p < 0,05). Within the same time point, the gene expression for RUNX2 did not differ between the groups. Overall, data demonstrated that the HA hydrogels incorporating PL increased the cellular metabolism and stimulate the mineralized matrix deposition by hDPSCs, providing clear evidence of the potential of the proposed system for the repair of damaged pulp/dentin tissue and endodontics regeneration.LFDA acknowledges Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) for the grant 2014/12017-8. Portuguese Foundation for Science and Technology (FCT) for PSB PhD grant SFRH/BD/73403/2010, MTR post-doctoral grant (SFRH/BPD/111729/2015), MEG grant (IF/00685/2012), and RECOGNIZE project (UTAP-ICDT/CTM-BIO/0023/2014), RL3-TECT - NORTE-07-0124-FEDER-000020 project co-financed by ON.2 (NSRF) through ERD. This study also received financial support from FCT/Ministério da Ciência, Tecnologia, e Ensino Superior (FCT/MCTES) and Fundo Social Europeu through Programa Operacional do Capital Humano (FSE/POCH) PD/59/2013 for the LA ICVS-3Bs (UID/Multi/50026/2013). The authors would like to thank Maurizio Gulino, for its support in the in vitro experiments and Maló Clinic, Porto, Dra Ana Ferro and Dr Bruno Queridinha for the donation of permanent teethinfo:eu-repo/semantics/publishedVersio
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