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Finding informative low-dimensional descriptions of high-dimensional simulation data (like the ones arising in molecular dynamics or kinetic Monte Carlo simulations of physical and chemical processes) is crucial to understanding physical phenomena, and can also dramatically assist in accelerating the simulations themselves. In this paper, we discuss and illustrate the use of nonlinear intrinsic variables (NIV) in the mining of high-dimensional multiscale simulation data. In particular, we focus on the way NIV allows us to functionally merge different simulation ensembles, and different partial observations of these ensembles, as well as to infer variables not explicitly measured. The approach relies on certain simple features of the underlying process variability to filter out measurement noise and systematically recover a unique reference coordinate frame. We illustrate the approach through two distinct sets of atomistic simulations: a stochastic simulation of an enzyme reaction network exhibiting both fast and slow time scales, and a molecular dynamics simulation of alanine dipeptide in explicit water.

The primary quorum sensing system in the opportunistic pathogen Pseudomonas aeruginosa is regulated through the synthesis and secretion of N-3-oxo-dodecanoyl-L-homoserine lactone (C12) which binds the transcriptional activator LasR. In this study we report the design, synthesis and biological evaluation of new analogs of C12. Analysis of the autoinducer binding site cavity of LasR revealed a positively charged cavity near the center of bound C12. Accordingly, we synthesized two piperidine-C12 diastereoisomers and tested their biological activity. Both analogs proved to be strong LasR agonists that showed a synergistic effect when presented together with the natural ligand. Moreover, binding of the analogs resulted in phenotypic changes characteristic of QS controlled receptor activation.

Objective: To report on a collective pectineal ligament suspension experience acquired over 12 years in India with 119 women who presented with prolapsed vaginal vault. The feasibility and effectiveness of the procedure was assessed for the open and laparoscopic routes., Methods: The prolapsed vaginal vault was suspended unilaterally to the pectineal ligament using polyester tape at 3 urban and 3 rural hospitals. The procedure was done through a Cherney incision in 104 women. In the remaining 15 women, it was done laparoscopically at a single urban center., Results: There were no intraoperative complications. The mean follow-up was 5.5 years (range, 0.5-12 years). Only 2 women had vaginal prolapse recurrence, at 3 and 5 years. Two had asymptomatic tape erosion, at 2 and 5 years, and a mild cystocele appeared in 5 women and a low rectocele in 4. However, none of these women required further vaginal surgery during their follow-up period., Conclusion: The present study demonstrates the long-term safety and effectiveness of pectineal ligament suspension for vaginal vault prolapse by the open and the laparoscopic routes. As it was done by surgeons of varying experience at centers with varying resources, the procedure can be readily mastered by any gynecologic surgeon., (© 2013.)

Researchers generating new genome-wide data in an exploratory sequencing study can gain biological insights by comparing their data with well-annotated data sets possessing similar genomic patterns. Data compression techniques are needed for efficient comparisons of a new genomic experiment with large repositories of publicly available profiles. Furthermore, data representations that allow comparisons of genomic signals from different platforms and across species enhance our ability to leverage these large repositories. Here, we present a signal processing approach that characterizes protein-chromatin interaction patterns at length scales of several kilobases. This allows us to efficiently compare numerous chromatin-immunoprecipitation sequencing (ChIP-seq) data sets consisting of many types of DNA-binding proteins collected from a variety of cells, conditions and organisms. Importantly, these interaction patterns broadly reflect the biological properties of the binding events. To generate these profiles, termed Arpeggio profiles, we applied harmonic deconvolution techniques to the autocorrelation profiles of the ChIP-seq signals. We used 806 publicly available ChIP-seq experiments and showed that Arpeggio profiles with similar spectral densities shared biological properties. Arpeggio profiles of ChIP-seq data sets revealed characteristics that are not easily detected by standard peak finders. They also allowed us to relate sequencing data sets from different genomes, experimental platforms and protocols. Arpeggio is freely available at http://sourceforge.net/p/arpeggio/wiki/Home/.

Objectives: Bortezomib is an effective antimyeloma therapy, but clinical benefits can be limited by neurotoxicity. In newly diagnosed, older patients, modification of the biweekly dosing schedule to weekly regimens improves tolerability whilst maintaining efficacy. There is less information on the efficacy and tolerability of weekly bortezomib regimens in the relapsed/refractory setting. Here, we report our experience of weekly intravenous bortezomib in clinical practice in relapsed/refractory patients., Methods: We analysed fifty-two patients who received weekly bortezomib for relapsed/refractory MM., Results: Thirty-one per cent of patients received bortezomib beyond first relapse. Almost all (94%) also received steroids and 48% also received an alkylator. The median cumulative dose was 22.6 mg/m(2) , and median length of treatment was 164 d. Three patients reported grade 2 sensory neuropathy, and one reported grade 3 motor neuropathy. There were no grade 4 neurotoxicities. Eighty-three per cent achieved a PR or greater, and the median PFS for the whole group was 13 months. One-year PFS and OS were 53% (95% CI 39-66.6%) and 78% (95% CI 66.7-89.6%), respectively., Conclusions: Weekly intravenous bortezomib when used in combination with steroids ± alkylator is effective in relapsed/refractory MM, producing outcomes comparable with biweekly regimens and with lower rates of peripheral neuropathy., (© 2013 John Wiley & Sons A/S.)

The use of consolidation or maintenance to improve disease response, and hence clinical outcome, following autologous stem cell transplantation (ASCT) remains the subject of intense clinical research. We carried out a single-arm study to assess the toxicity and efficacy of a short block of consolidation therapy with cyclophosphamide, low dose thalidomide and dexamethasone (CTD) in patients within 6 months following ASCT, as part of frontline therapy for symptomatic multiple myeloma. Forty-five patients who had not progressed were enrolled on the study, and 43 completed treatment on protocol. This regimen was well tolerated soon after ASCT, with only grade 1/2 toxicity apart from neutropenia, and no long-term sequelae. Importantly, CTD consolidation improved the depth of response in treated patients, increasing the complete/very good partial response rate from 44% at 3 months, to 72% at 12 months, which was significantly higher compared with a historical group of control patients (P = 0·002). There was a trend to longer progression-free survival that favoured the study group. Consolidation therapy did not adversely affect subsequent disease response to salvage therapies at relapse. We conclude that CTD consolidation may be a useful, non-toxic and cost-effective strategy to deepen disease response following ASCT, and deserves further study in a randomized trial., (© 2012 Blackwell Publishing Ltd.)

Patients with multiple myeloma commonly develop focal osteolytic bone disease, as well as generalised osteoporosis. The mechanisms underlying the development of osteoporosis in patients with myeloma are poorly understood. Although disruption of the RANKL/OPG pathway has been shown to underlie formation of focal osteolytic lesions, its role in the development of osteoporosis in myeloma remains unclear. Increased soluble RANKL in serum from patients with myeloma raises the possibility that this molecule plays a key role. The aim of the present study was to establish whether sRANKL produced by myeloma cells contributes directly to osteoporosis. C57BL/KaLwRij mice were injected with either 5T2MM or 5T33MM murine myeloma cells. 5T2MM-bearing mice developed osteolytic bone lesions (p<0.05) with increased osteoclast surface (p<0.01) and reduced trabecular bone volume (p<0.05). Bone volume was also reduced at sites where 5T2MM cells were not present (p<0.05). In 5T2MM-bearing mice soluble mRANKL was increased (p<0.05), whereas OPG was not altered. In contrast, 5T33MM-bearing mice had no changes in osteoclast surface or trabecular bone volume and did not develop osteolytic lesions. Soluble mRANKL was undetectable in serum from 5T33MM-bearing mice. In separate experiments, RPMI-8226 human myeloma cells were transduced with an human RANKL/eGFP construct, or eGFP alone. RPMI-8226/hRANKL/eGFP cells, but not RPMI-8226/eGFP cells, stimulated osteoclastic bone resorption (p<0.05) in vitro. Sub-cutaneous injection of NOD/SCID mice with RPMI-8226/hRANKL/eGFP or RPMI-8226/eGFP cells resulted in tumour development in all mice. RPMI-8226/hRANKL/eGFP-bearing mice exhibited increased serum soluble hRANKL (p<0.05) and a three-fold increase in osteoclast number (p<0.05) compared to RPMI-8226/eGFP-bearing mice. This was associated with reduced trabecular bone volume (27%, p<0.05), decreased trabecular number (29%, p<0.05) and increased trabecular thickness (8%, p<0.05). Our findings demonstrate that soluble RANKL produced by myeloma cells causes generalised bone loss, suggesting that targeting RANKL may prevent osteoporosis in patients with myeloma.

A 76-year-old Afro-Caribbean man presenting with heart failure was diagnosed with isolated cardiac amyloid. He had evidence of myeloma on bone marrow biopsy suggesting AL amyloid, the commonest type of systemic amyloidosis, as the underlying cause. He had no other myeloma-related organ damage. However, endocardial biopsy revealed amyloid fibrils composed of transthyretin and genetic typing established heterozygozity for the valine to isoleucine mutation at position 122 (Val122Ile). The diagnosis was therefore hereditary systemic amyloidosis as a result of a genetic transthyretin variant (ATTR) causing cardiac amyloidosis and coexistent asymptomatic myeloma. This requires symptomatic treatment of heart failure only. This article discusses a rare cause of heart failure and uses this case to illustrate that histological confirmation of the amyloid-causing protein is essential. Mistaken assumption of AL amyloid could have resulted in inappropriate cytotoxic therapy targeting the plasma cell clone.

POEMS (polyneuropathy, organomegaly, endocrinopathy, monoclonal gammopathy, skin changes) syndrome is a rare haematological condition with a constellation of clinical features that can present to the clinician in a variety of ways. This case highlights how a seemingly uncomplicated myocardial infarction can herald the development of this rare haematological disorder. While knowledge of the pathophysiological mechanisms that underpin POEMS syndrome is developing, so too are the diagnostic and treatment strategies available to the clinician.

Background: Human mesenchymal stem cells are potential agents for tissue regeneration, enhancing hematopoietic stem cell transplantation and delivering genes of therapeutic interest. To implement any of these strategies successfully, we need a better understanding of factors that influence the tissue distribution of systemically administered mesenchymal stem cells., Design and Methods: The present study was designed to investigate the short-term tissue homing of mesenchymal stem cells in immunodeficient mouse models, exploring the effects of animal age, duration of ex vivo expansion of mesenchymal stem cells, lentiviral transduction and CXCR4 over-expression. Dye-labeled mesenchymal stem cells (1.5-2.0 x 10(6)/animal) were injected via the tail vein into unconditioned beta2m/NOD/SCID animals. Animals were sacrificed 20-24 hours later and cell suspensions from tissues were examined by flow cytometry for the presence of PKH-positive cells., Results: PKH-positive cells were readily detected in the bone marrow, spleen, liver and lungs at 20-24 hours after infusion. The homing of systemically infused mesenchymal stem cells to the bone marrow and spleen of unconditioned beta2m/NOD/SCID animals was significantly (>2-fold, p<0.001) higher in younger (<10 weeks) animals, and was reduced with increasing passage number. Despite low surface CXCR4 expression, human mesenchymal stem cells migrated to SDF-1 in vitro, and this was enhanced by over-expression of CXCR4 using lentiviral transduction. Over-expression of CXCR4 by lentiviral transduction (>80%) did not alter the bone marrow homing of mesenchymal stem cells in unconditioned animals, but caused a significant (p<0.05) increase in homing to bone marrow and spleen of animals that had received prior irradiation., Conclusions: Tissue homing of systemically administered mesenchymal stem cells is influenced by host factors such as age, is diminished by prolonged in vitro culture, and can be increased by enforced expression of CXCR4, at least in irradiated hosts.

D-type cyclin genes are universally dysregulated in multiple myeloma (MM), but the functional consequences are unclear as D-type cyclin gene expression does not correlate with proliferation or disease progression. We examined the protein expression and regulation of D-type cyclins and other cell cycle regulators in human myeloma cell lines and primary CD138(+) plasma cells (PCs). Cyclin D1, cyclin D2, cyclin dependent kinase (CDK) 4, CDK6, p27(Kip1) p18(INK4C) and retinoblastoma protein (pRb) were absent in normal PCs, heterogeneously expressed in primary MM cells and positively correlated with disease activity/progression. Cyclins D1 and D2 complexed with both CDK4 and CDK6, suggesting that both phosphorylate pRb in MM. Furthermore, cyclin D2 expressed via either t(14;16) or t(4;14) IgH translocations was functionally upregulated by fetal calf serum or insulin-like growth factor-I, leading to pRb phosphorylation and cell cycle entry/progression, and in some cases inversely correlated with p27(Kip1). However, pRb phosphorylation and cell cycle progression mediated by cyclin D1 expressed via t(11;14) was less dependent on exogenous stimuli. These data suggest that the presence or absence of specific IgH translocations underlying aberrant D-type cyclin expression may influence their response to mitogens in the bone marrow microenvironment. We showed for the first time that D-type cyclins are functionally regulated in MM, differentially responsive to exogenous growth factors and upregulated with disease progression.

We describe a new model of myeloma bone disease in which beta2m NOD/SCID mice injected with KMS-12-BM cells develop medullary disease after tail vein administration. Micro-computed tomography analysis demonstrated significant bone loss in the tibiae and vertebrae of diseased animals compared to controls, with loss of cortical bone (P<0.01), as well as trabecular bone volume, thickness and number (P<0.05 for all). Bone marrow of diseased animals demonstrated an increase in osteoclasts (P<0.01) and reduction in osteoblasts (P<0.01) compared to control animals. Both bone loss and osteoclast increase correlated with the degree of disease involvement. Mesenchymal stem cells (MSCs) were lentivirally transduced to express human osteoprotegerin (hOPG). Systemic administration of OPG expressing MSC reduced osteoclast activation (P<0.01) and trabecular bone loss in the vertebrae (P<0.05) and tibiae of diseased animals, to levels comparable to non-diseased controls. Because of its predominantly medullary involvement and quantifiable parameters of bone disease, the KMS-12-BM xenogeneic model provides unique opportunities to test therapies targeted at the bone marrow microenvironment.

We present a method to enhance, by postprocessing, the performance of gradient-based edge detectors. It improves the performance of the edge detector by adding terms which are similar to the artificial dissipation that appear in the numerical solution of hyperbolic PDEs. This term is added to the output of the edge detector. The edges that are missed or blurred by the edge detector are reconstructed through the addition of the artificial dissipation terms. Edges that are detected correctly by the edge detector are preserved. We present the theory of the artificial dissipation and its improvement of the quality of the detected edges. We demonstrate the performance of the algorithm on diverse images.

We report the case of a 46-year-old male who developed dermatomyositis and a sarcoid-like reaction in association with testicular relapse of multiple myeloma. The myositis progressed despite chemotherapy directed at the underlying malignant disorder and immunosuppressive treatment. There was, however, a dramatic and sustained response to high-dose chemotherapy and autologous peripheral blood stem cell transplantation which resulted in resolution of the myopathy and partial resolution of the sarcoid-like reaction. This case report highlights the potential of autologous stem cell transplantation as treatment for para-neoplastic disorders associated with haematological malignancies.

Being attentive to the educational needs of chronically ill children is a relatively recent development in American education. Advances in medical sciences that have improved survival rates for some conditions and increased public acceptance of people who are different or disabled and legislation that has established education as an entitlement for all children have allowed for the entrance of many chronically ill children into mainstream education. Successful school reentry is essential if the child is to develop normally, in terms of intellect, social skills, and peer relationships. Caregivers must not lose sight of the fact that school provides opportunities for social, emotional, and cognitive development. Thus the pediatric nurse practitioner can promote the benefits gained from schooling in numerous ways and provide the child, family, and school personnel with the support and information needed for a smooth transition back into the school system.