The new versatile general purpose surface-muon instrument (GPS) based on silicon photomultipliers for µSR measurements on a continuous-wave beam.

We report on the design and commissioning of a new spectrometer for muon-spin relaxation/rotation studies installed at the Swiss Muon Source (SµS) of the Paul Scherrer Institute (PSI, Switzerland). This new instrument is essentially a new design and replaces the old general-purpose surface-muon (GPS) instrument that has been for long the workhorse of the µSR user facility at PSI. By making use of muon and positron detectors made of plastic scintillators read out by silicon photomultipliers, a time resolution of the complete instrument of about 160 ps (standard deviation) could be achieved. In addition, the absence of light guides, which are needed in traditionally built µSR instrument to deliver the scintillation light to photomultiplier tubes located outside magnetic fields applied, allowed us to design a compact instrument with a detector set covering an increased solid angle compared with the old GPS.

A mathematical framework for virtual IMRT QA using machine learning.

PURPOSE: It is common practice to perform patient-specific pretreatment verifications to the clinical delivery of IMRT. This process can be time-consuming and not altogether instructive due to the myriad sources that may produce a failing result. The purpose of this study was to develop an algorithm capable of predicting IMRT QA passing rates a priori. METHODS: From all treatment, 498 IMRT plans sites were planned in eclipse version 11 and delivered using a dynamic sliding window technique on Clinac iX or TrueBeam Linacs. 3%/3 mm local dose/distance-to-agreement (DTA) was recorded using a commercial 2D diode array. Each plan was characterized by 78 metrics that describe different aspects of their complexity that could lead to disagreements between the calculated and measured dose. A Poisson regression with Lasso regularization was trained to learn the relation between the plan characteristics and each passing rate. RESULTS: Passing rates 3%/3 mm local dose/DTA can be predicted with an error smaller than 3% for all plans analyzed. The most important metrics to describe the passing rates were determined to be the MU factor (MU per Gy), small aperture score, irregularity factor, and fraction of the plan delivered at the corners of a 40 × 40 cm field. The higher the value of these metrics, the worse the passing rates. CONCLUSIONS: The Virtual QA process predicts IMRT passing rates with a high likelihood, allows the detection of failures due to setup errors, and it is sensitive enough to detect small differences between matched Linacs.

Molecular Profile of Mitochondrial Dysfunction in Kidney Transplant Biopsies Is Associated With Poor Allograft Outcome.

BACKGROUND: In kidney transplantation (KT), progression of chronic histological damage with subclinical inflammation is associated with poor long-term allograft survival. The role of nonimmunological pathways in chronic allograft injury has not been fully assessed. METHODS: We analyzed a public microarray dataset that used 1-year protocol kidney transplant biopsy specimens to investigate whether nonimmunological genes and pathways might influence long-term allograft outcome. The selected microarray dataset included 3 patient/sample groups based on their histological findings: normal histology (n = 25), interstitial fibrosis alone (IF alone, n = 24), and interstitial fibrosis with inflammation (IF+i, n = 16). The IF+i group had lower death-censored graft survival and renal function in patients with a mean follow-up of 4 years. We performed statistical analysis comparing gene expression patterns in the 3 group samples. RESULTS: Gene cluster enrichment and group-specific expression patterns demonstrated a divergent pattern between mitochondrial and immune response genes, with downregulation of mitochondrial genes in the IF+i group. Gene ontological analysis of the downregulated mitochondrial genes identified generation of precursor metabolite and energy, and response to oxidative stress as the most significant biological processes. The transcription regulation pathway analysis of downregulated gene cluster demonstrated transcription factors involved in mitochondrial biogenesis. CONCLUSIONS: The molecular signature of mitochondrial dysfunction reflects mitochondrial energetic insufficiency, and inadequate antioxidant response involved in mitochondria biogenesis pathways is associated with IF+i and worse long-term allograft survival. Thus, mitochondria function impairment appears to be an important nonimmune factor involved in chronic allograft injury.

Direct spectroscopic observation of a shallow hydrogenlike donor state in insulating SrTiO3.

We present a direct spectroscopic observation of a shallow hydrogenlike muonium state in SrTiO(3) which confirms the theoretical prediction that interstitial hydrogen may act as a shallow donor in this material. The formation of this muonium state is temperature dependent and appears below ∼ 70K. From the temperature dependence we estimate an activation energy of ∼ 50 meV in the bulk and ∼ 23 meV near the free surface. The field and directional dependence of the muonium precession frequencies further supports the shallow impurity state with a rare example of a fully anisotropic hyperfine tensor. From these measurements we determine the strength of the hyperfine interaction and propose that the muon occupies an interstitial site near the face of the oxygen octahedron in SrTiO(3). The observed shallow donor state provides new insight for tailoring the electronic and optical properties of SrTiO(3)-based oxide interface systems.

Metadata-driven comparative analysis tool for sequences (meta-CATS): an automated process for identifying significant sequence variations that correlate with virus attributes.

The Virus Pathogen Resource (ViPR; www.viprbrc.org) and Influenza Research Database (IRD; www.fludb.org) have developed a metadata-driven Comparative Analysis Tool for Sequences (meta-CATS), which performs statistical comparative analyses of nucleotide and amino acid sequence data to identify correlations between sequence variations and virus attributes (metadata). Meta-CATS guides users through: selecting a set of nucleotide or protein sequences; dividing them into multiple groups based on any associated metadata attribute (e.g. isolation location, host species); performing a statistical test at each aligned position; and identifying all residues that significantly differ between the groups. As proofs of concept, we have used meta-CATS to identify sequence biomarkers associated with dengue viruses isolated from different hemispheres, and to identify variations in the NS1 protein that are unique to each of the 4 dengue serotypes. Meta-CATS is made freely available to virology researchers to identify genotype-phenotype correlations for development of improved vaccines, diagnostics, and therapeutics.

Photo-induced persistent inversion of germanium in a 200-nm-deep surface region.

The controlled manipulation of the charge carrier concentration in nanometer thin layers is the basis of current semiconductor technology and of fundamental importance for device applications. Here we show that it is possible to induce a persistent inversion from n- to p-type in a 200-nm-thick surface layer of a germanium wafer by illumination with white and blue light. We induce the inversion with a half-life of ~12 hours at a temperature of 220 K which disappears above 280 K. The photo-induced inversion is absent for a sample with a 20-nm-thick gold capping layer providing a Schottky barrier at the interface. This indicates that charge accumulation at the surface is essential to explain the observed inversion. The contactless change of carrier concentration is potentially interesting for device applications in opto-electronics where the gate electrode and gate oxide could be replaced by the semiconductor surface.

Design and commissioning of a high magnetic field muon spin relaxation spectrometer at the ISIS pulsed neutron and muon source.

The high magnetic field (HiFi) muon instrument at the ISIS pulsed neutron and muon source is a state-of-the-art spectrometer designed to provide applied magnetic fields up to 5 T for muon studies of condensed matter and molecular systems. The spectrometer is optimised for time-differential muon spin relaxation studies at a pulsed muon source. We describe the challenges involved in its design and construction, detailing, in particular, the magnet and detector performance. Commissioning experiments have been conducted and the results are presented to demonstrate the scientific capabilities of the new instrument.

A unique antibody gene signature is prevalent in the central nervous system of patients with multiple sclerosis.

B cells isolated from the CSF of patients with multiple sclerosis (MS) have a unique accumulation of somatic hypermutation within the B cell receptor, termed the antibody gene signature (AGS). The focus of this study was to investigate whether the AGS could also be detected in MS brain tissue. Genetic analysis of B cells isolated from post-mortem CNS tissue samples from four MS brains demonstrated that signature enriched B cells are present at the site of tissue injury as well as in the circulating CSF.

Direct measurement of the electronic spin diffusion length in a fully functional organic spin valve by low-energy muon spin rotation.

Electronic devices that use the spin degree of freedom hold unique prospects for future technology. The performance of these 'spintronic' devices relies heavily on the efficient transfer of spin polarization across different layers and interfaces. This complex transfer process depends on individual material properties and also, most importantly, on the structural and electronic properties of the interfaces between the different materials and defects that are common to real devices. Knowledge of these factors is especially important for the relatively new field of organic spintronics, where there is a severe lack of suitable experimental techniques that can yield depth-resolved information about the spin polarization of charge carriers within buried layers of real devices. Here, we present a new depth-resolved technique for measuring the spin polarization of current-injected electrons in an organic spin valve and find the temperature dependence of the measured spin diffusion length is correlated with the device magnetoresistance.

Intrinsic mobility limit for anisotropic electron transport in Alq3.

Muon spin relaxation has been used to probe the charge carrier motion in the molecular conductor Alq3 (tris[8-hydroxy-quinoline] aluminum). At 290 K, the magnetic field dependence of the muon spin relaxation corresponds to that expected for highly anisotropic intermolecular electron hopping. Intermolecular mobility in the fast hopping direction has been found to be 0.23+/-0.03 cm2 V-1 s(-1) in the absence of an electric- field gradient, increasing to 0.32+/-0.06 cm2 V-1 s(-1) in an electric field gradient of 1 MV m(-1). These intrinsic mobility values provide an estimate of the upper limit for mobility achievable in bulk material.

Using spin polarised positive muons for studying guest molecule partitioning in soft matter structures.

Fully polarised positive muons substituted for protons in organic free radicals can be used as spin labels which reveal information about the structure, dynamics and environment of these radicals. In applications via the technique of avoided-level-crossing muon spin resonance (ALC-microSR), the positive muon has been used to study the partitioning of phenyl alcohols in lamellar phase colloidal dispersions of a cationic dichain surfactant. Here we describe the experimental technique which permits highly sensitive spectroscopy as previously demonstrated for surfactant mixtures. We also demonstrate its capability in the study of partitioning of cosurfactant molecules in surfactant bilayers in order to elucidate the main factors which contribute to cosurfactant ordering at interfaces. The technique takes advantage of the positive muon combining with an electron to a hydrogen-like atom that is called muonium. This atom attaches to a phenyl group, forming a cyclohexadienyl-type radical that contains the muon as a polarised spin label, providing an excellent probe even for very low phenyl alcohol concentrations. The position of one type of resonance, which on the basis of spectroscopic selection rules is denoted as Delta(0), is related to the solvent polarity of the radicals' environment. The results derived from Delta(0) measurements reveal a systematic trend where the increasing chain length of the phenyl alcohol results in a deeper immersion of the phenyl ring of the alcohol into the surfactant bilayer with the OH group anchored at the interface. In addition, the data suggest partial penetration of water molecules into the bilayer. Furthermore, data ensuing from a second resonance (called Delta(1), which is dependent upon the degree of confinement of the radical within the surfactant aggregate structure) indicates not only that the phenyl alcohol resides in an anisotropic environment, (i.e. that the host molecule is unable to undergo full 3-D reorientation on a timescale of 50 ns), but the resonance line widths indicate that the radicals are undergoing fast rotation about a particular axis, in this instance about the first C-C substituent bond at the phenyl ring. Detailed analysis of these Delta(1) line shapes suggests that other types of motion involving reorientation of the above rotation axis are also present. At room temperature, the hydrocarbon chains of the double layers form an aggregate state commonly referred to as the L(beta) phase, where the motions of surfactant alkyl chains are effectively frozen out. These chains melt on heating over a temperature range which is solution composition dependent (ca. 51 to 67 degrees C), but in all cases leading to a liquid-like disordered hydrocarbon regime whilst retaining the overall lamellar structure (and in this state is termed L(alpha)). Above the L(alpha)/L(beta) chain ordering phase transition the tracer molecules reside within the bilayer, but below this transition (and depending on their water-oil solubility) they are completely or partly expelled. This interpretation is further supported by Heisenberg spin exchange experiments. The water-bilayer partitioning reflects both typical classical and nonclassical hydrophobic solvation depending on temperature and chain length of phenyl alcohols.

Lymphoid apoptosis and myeloid hyperplasia in CCAAT displacement protein mutant mice.

CCAAT displacement protein (cux/CDP) is an atypical homeodomain protein that represses expression of several developmentally regulated lymphoid and myeloid genes in vitro, including gp91-phox, immunoglobulin heavy chain, the T-cell receptor beta and gamma chains, and CD8. To determine how this activity affects cell development in vivo, a hypomorphic allele of cux/CDP was created by gene targeting. Homozygous mutant mice (cux/CDP(Delta HD/Delta HD)) demonstrated a partial neonatal lethality phenotype. Surviving animals suffered from a wasting disease, which usually resulted in death between 2 and 3 weeks of age. Analysis of T lymphopoiesis demonstrated that cux/CDP(Delta HD/Delta HD) mice had dramatically reduced thymic cellularity due to enhanced apoptosis, with a preferential loss of CD4(+)CD8(+) thymocytes. Ectopic CD25 expression was also observed in maturing thymocytes. B lymphopoiesis was also perturbed, with a 2- to 3-fold reduction in total bone marrow B-lineage cells and a preferential loss of cells in transition from pro-B/pre-BI to pre-BII stages due to enhanced apoptosis. These lymphoid abnormalities were independent of effects related to antigen receptor rearrangement. In contrast to the lymphoid demise, cux/CDP(Delta HD/Delta HD) mice demonstrated myeloid hyperplasia. Bone marrow reconstitution experiments identified that many of the hematopoietic defects were linked to microenvironmental effects, suggesting that underexpression of survival factors or overexpression of death-inducing factors accounted for the phenotypes observed. Tumor necrosis factor (TNF) levels were elevated in several tissues, especially thymus, suggesting that TNF may be a target gene for cux/CDP-mediated repression. These data suggest that cux/CDP regulates normal hematopoiesis, in part, by modulating the levels of survival and/or apoptosis factors expressed by the microenvironment.

Prevalence and cellular reservoir of latent human herpesvirus 6 in tonsillar lymphoid tissue.

There are few studies that examine prevalence, quantity, and cellular proclivity of latent human herpesvirus 6 (HHV-6) in healthy populations. We examined 69 tonsils with paired blood specimens from children without evidence of acute infection. By polymerase chain reaction (PCR), HHV-6 was detected at low levels in 100% of tonsils and 39% of blood samples (n = 27), suggesting that prevalence of latent HHV-6 infection is high in children and may be underestimated by PCR analysis of blood. Although HHV-6A and HHV-6B were detected, HHV-6B predominated, being found in 97% of samples (n = 67). Tonsil sections from 7 cases were examined by in situ hybridization using 2 HHV-6 probes and immunohistochemical analysis. Using both in situ hybridization and immunohistochemical analysis, all tissues revealed marked HHV-6-specific staining in the squamous epithelium of the tonsillar crypts and rare positive lymphocytes. We conclude that HHV-6 is present universally in tonsils of children, and tonsillar epithelium may be an important viral reservoir in latent infection.

Connection between B lymphocyte and osteoclast differentiation pathways.

Osteoclasts differentiate from the hemopoietic monocyte/macrophage cell lineage in bone marrow through cell-cell interactions between osteoclast progenitors and stromal/osteoblastic cells. Here we show another osteoclast differentiation pathway closely connected with B lymphocyte differentiation. Recently the TNF family molecule osteoclast differentiation factor/receptor activator of NF-kappaB ligand (ODF/RANKL) was identified as a key membrane-associated factor regulating osteoclast differentiation. We demonstrate that B-lymphoid lineage cells are a major source of endogenous ODF/RANKL in bone marrow and support osteoclast differentiation in vitro. In addition, B-lymphoid lineage cells in earlier developmental stages may hold a potential to differentiate into osteoclasts when stimulated with M-CSF and soluble ODF/RANKL in vitro. B-lymphoid lineage cells may participate in osteoclastogenesis in two ways: they 1) express ODF/RANKL to support osteoclast differentiation, and 2) serve themselves as osteoclast progenitors. Consistent with these observations in vitro, a decrease in osteoclasts is associated with a decrease in B-lymphoid cells in klotho mutant mice (KL(-/-)), a mouse model for human aging that exhibits reduced turnover during bone metabolism, rather than a decrease in the differentiation potential of osteoclast progenitors. Taken together, B-lymphoid lineage cells may affect the pathophysiology of bone disorders through regulating osteoclastogenesis.

Transcriptional activation by a matrix associating region-binding protein. contextual requirements for the function of bright.

Bright (B cell regulator of IgH transcription) is a B cell-specific, matrix associating region-binding protein that transactivates gene expression from the IgH intronic enhancer (E mu). We show here that Bright has multiple contextual requirements to function as a transcriptional activator. Bright cannot transactivate via out of context, concatenated binding sites. Transactivation is maximal on integrated substrates. Two of the three previously identified binding sites in E mu are required for full Bright transactivation. The Bright DNA binding domain defined a new family, which includes SWI1, a component of the SWI.SNF complex shown to have high mobility group-like DNA binding characteristics. Similar to one group of high mobility group box proteins, Bright distorts E mu binding site-containing DNA on binding, supporting the concept that it mediates E mu remodeling. Transfection studies further implicate Bright in facilitating spatially separated promoter-enhancer interactions in both transient and stable assays. Finally, we show that overexpression of Bright leads to enhanced DNase I sensitivity of the endogenous E mu matrix associating regions. These data further suggest that Bright may contribute to increased gene expression by remodeling the immunoglobulin locus during B cell development.

Diagnostic applications of quantitative polymerase chain reaction for cytomegalovirus.

Eight viruses in the herpes family have been identified that infect humans: herpes simplex viruses 1 and 2, varicella-zoster virus, Epstein-Barr virus, cytomegalovirus (CMV), human herpesviruses 6 and 7 and the Kaposi sarcomaassociated herpesvirus (1). In immunocompetent individuals, primary infections are usually handled effectively by the host immune system without therapeutic intervention. However, these viruses are never completely eradicated by the immune response, probably because these viruses have the capacity to enter a latent state in a subset of infected cells. However, this does not normally pose a problem since the host immune system has been primed to handle any subsequent reactivation. Thus, human herpesviruses rarely cause serious problems in immunocompetent individuals.

Tyrosine kinase activation in the decision between growth, differentiation, and death responses initiated from the B cell antigen receptor.

Immunoglobulin-containing receptors expressed on B lineage lymphocytes play critical roles in the development and function of the humoral arm of the immune system. The preB cell antigen receptor (preBCR) contains the immunoglobulin mu heavy chain (Ig mu) and signals to the preB cell that heavy chain rearrangement has been successful, a process termed heavy chain selection. The B cell antigen receptor (BCR) contains both Ig heavy and light chains and is expressed on immature and mature B cells before and after antigen encounter. Both receptor types from a complex with the Ig alpha and Ig beta proteins that link the predominantly extracellular Ig with intracellular signal transduction pathways. Signaling through the BCR induces different cellular responses depending on the nature of the signaling agent and the development stage of the target cell. These responses include clonal anergy and apoptotic deletion in immature B cells and survival, proliferation, and differentiation in mature B and preB cells. Several protein tyrosine kinases are activated rapidly following engagement of the BCR/preBCR complexes, including members of the Src family (Lyn and Blk), the Syk/ZAP70 family (Syk), and the Tec family (Btk). In this review, we discuss possible mechanisms by which engagement of these similar receptor complexes can give rise to different cellular responses and the role that these kinases play in this process.

Kinetics of early therapeutic response as measured by quantitative PCR predicts survival in a murine xenograft model of human T cell acute lymphoblastic leukemia.

The identification of prognostic parameters and surrogate markers for defining patient risk has been beneficial in effectively guiding therapy and increasing the survival of leukemia patients. It has been hypothesized that the therapeutic response, as measured by a change in tumor burden during therapy, might serve as a new surrogate marker of survival. Here we describe the development of a murine SCID xenograft model of human T cell acute lymphoblastic leukemia (T-ALL), and the use of a sensitive, quantitative PCR assay for the measurement of tumor levels to investigate the relationships between tumor burden quantification, therapeutic response and survival. Animals engrafted with the CCRF-CEM (CEM) human T-ALL cell line develop leukemia that closely resembles the human disease. Quantitative PCR detects the expanding tumor mass in the peripheral blood of the animals several weeks before death. In response to induction therapy with chemotherapeutic agents, both the level of minimal residual disease (MRD) in peripheral blood at the end of therapy and the rate of tumor reduction in peripheral blood during therapy strongly correlated with animal survival. Thus, these surrogate markers, which can be measured during the early stages of therapy, may help improve patient survival through dynamic risk stratification.

Predictive value of quantitative PCR-based viral burden analysis for eight human herpesviruses in pediatric solid organ transplant patients.

Human herpesviruses can cause significant morbidity and mortality in pediatric solid organ transplant recipients. It was hypothesized that viral burden quantification by polymerase chain reaction using an internal calibration standard could aid in distinguishing between viral disease and latency. Here we report the results of a 2-year prospective study of 27 pediatric solid organ (liver, kidney, or heart) transplant recipients in which multiple samples were analyzed for levels of all eight human herpesviruses by internal calibration standard-polymerase chain reaction. Herpes simplex viruses 1 and 2, varicella-zoster virus, and Kaposi's sarcoma-associated herpesvirus were not detected in any of these samples. Human herpesvirus types 6 and 7 were detected in half of the patients, but were present at low levels, similar to those found in reference populations. Epstein-Barr virus (EBV) and cytomegalovirus (CMV) were detected in 89% and 56% of the patients, respectively. Viral burden analysis suggested distinct patient populations for CMV, with a natural cutoff of 10,000 viral targets/ml blood strongly associated with disease. In some cases, a dramatic increase in CMV levels preceded clinical evidence of disease by several weeks. EBV viral burden was relatively high in the only patient presenting with an EBV syndrome. However, two other patients without evidence of EBV disease had single samples with high EBV burden. Rapid reduction in both EBV and CMV burden occurred with antiviral treatment. These data suggest that viral burden analysis using internal calibration standard-polymerase chain reaction for CMV, and possibly other herpesviruses, is an effective method for monitoring pediatric transplant patients for significant herpesvirus infection and response to therapy.