BACKGROUND: Primary central nervous system lymphoma (PCNSL) is an aggressive non-Hodgkin lymphoma (NHL) confined to the CNS. Whether there is a PCNSL-specific genomic signature and, if so, how it differs from systemic DLBCL is uncertain. To address this gap in critical knowledge we performed a comprehensive genomic study in a cohort of 19 immunocompetent PCNSL patients by combining aCGH, whole exome sequencing and mate-pair whole genome sequencing. METHODS: 1) Tumor samples from 19 immunocompetent (HIV-, EBV-) PCNSL. 2) DNA from frozen tissue or from formalin-fixed paraffin embedded (FFPE) tissues. 3) All samples analyzed using a combination of aCGH, whole exome sequencing, mate-pair whole genome sequencing, targeted sequencing and FISH. 4) Overall survival estimated using Kaplan Meier method. RESULTS: We found a complex karyotype with a median of 21 copy-number abnormalities, 6 structural abnormalities and 3.3 non-synonymous mutations per Mb. We found a remarkably high prevalence of MYD88 activating mutations (79%) and CDKN2A biallelic loss (60%). Biallelic losses of TOX (a regulator of T-cell development), PRKCD (protein kinase C delta) and chromosomal breakpoints in DLGAP1 (discs large-associated protein 1) were recurrently found in PCNSL but not in systemic DLBCL, suggesting a specific role in PCNSL pathogenesis. Several other genes recurrently affected in PCNSL are common with systemic DLBCL of the ABC-type, such as loss of TNFAIP3, PRDM1, GNA13, TMEM30A, TBL1XR1, B2M and CD58, activating mutations of CD79B, CARD11, BRAF3 and translocations of IgH-BCL6. Overall, components of the NF-□B signaling pathway were altered in >90% of PNCSL, highlighting the potential value of this pathway for targeted therapeutic approaches. Furthermore, integrated analysis also showed an enrichment of networks associated with immune response, proliferation, regulation of apoptosis, and lymphocyte differentiation. CONCLUSIONS: We report a PCNSL genomic landscape closely related to ABC-DLBCL but with critical elements that support the existence of a subset of PCNSL-specific abnormalities, helping to genetically differentiate PCNSL from systemic DLBCL and related lymphomas. SECONDARY CATEGORY: Immunobiology & Immunotherapy.
Despite its ubiquitous presence in the built environment, concrete’s molecular-level properties are only recently being explored using experimental and simulation studies. Increasing societal concerns about concrete’s environmental footprint have provided strong motivation to develop new concrete with greater specific stiffness or strength (for structures with less material). Herein, a combinatorial approach is described to optimize properties of cement hydrates. The method entails screening a computationally generated database of atomic structures of calcium-silicate-hydrate, the binding phase of concrete, against a set of three defect attributes: calcium-to-silicon ratio as compositional index and two correlation distances describing medium-range silicon-oxygen and calcium-oxygen environments. Although structural and mechanical properties correlate well with calcium-to-silicon ratio, the cross-correlation between all three defect attributes reveals an indentation modulus-to-hardness ratio extremum, analogous to identifying optimum network connectivity in glass rheology. We also comment on implications of the present findings for a novel route to optimize the nanoscale mechanical properties of cement hydrate.
Concrete is a vital material in meeting present day construction demands. Here, the authors report a computational combinatorial approach to understand how molecular level characteristics influence the mechanical properties of cement hydrates, via screening against distinct defect types.
To evaluate the relationship of diet to incident diabetes among non-Black and Black participants in the Adventist Health Study-2.
Methods and Results
Participants were 15,200 men and 26,187 women (17.3% Blacks) across the U.S. and Canada who were free of diabetes and who provided demographic, anthropometric, lifestyle and dietary data. Participants were grouped as vegan, lacto ovo vegetarian, pesco vegetarian, semi-vegetarian or non-vegetarian (reference group). A follow-up questionnaire after two years elicited information on the development of diabetes. Cases of diabetes developed in 0.54% of vegans, 1.08% of lacto ovo vegetarians, 1.29% of pesco vegetarians, 0.92% of semi-vegetarians and 2.12% of non-vegetarians. Blacks had an increased risk compared to non-Blacks (odds ratio [OR] 1.364; 95% confidence interval [CI], 1.093–1.702). In multiple logistic regression analysis controlling for age, gender, education, income, television watching, physical activity, sleep, alcohol use, smoking and BMI, vegans (OR 0.381; 95% CI 0.236–0.617), lacto ovo vegetarians (OR 0.618; 95% CI 0.503–0.760) and semi-vegetarians (OR 0.486, 95% CI 0.312–0.755) had a lower risk of diabetes than non-vegetarians. In non-Blacks vegan, lacto ovo and semi-vegetarian diets were protective against diabetes (OR 0.429, 95% CI 0.249–0.740; OR 0.684, 95% CI 0.542–0.862; OR 0.501, 95% CI 0.303–0.827); among Blacks vegan and lacto ovo vegetarian diets were protective (OR 0.304, 95% CI 0.110–0.842; OR 0.472, 95% CI 0.270–0.825). These associations were strengthened when BMI was removed from the analyses.
Vegetarian diets (vegan, lacto ovo, semi-) were associated with a substantial and independent reduction in diabetes incidence. In Blacks the dimension of the protection associated with vegetarian diets was as great as the excess risk associated with Black ethnicity.
Vegetarianism; Black; African American; Diabetes; Ethnicity; Diet
We tested the accuracy of immunocytochemistry (ICC) for minichromosome maintenance protein-2 (MCM-2) in diagnosing bladder cancer, using cells retrieved from urine.
Adequate samples were obtained from 497 patients, the majority presenting with gross haematuria (GH) or undergoing cystoscopic surveillance (CS) following previous bladder cancer. We performed an initial study of 313 patients, followed by a validation study of 184 patients. In all cases, presence/absence of bladder cancer was established by cystoscopy/biopsy.
In the initial study, receiver operator characteristic analysis showed an area under the curve of 0.820 (P<0.0005) for the GH group and 0.821 (P<0.01) for the CS group. Optimal sensitivity/specificity were provided by threshold values of 50+ MCM-2-positive cells in GH samples and 200+ cells in CS samples, based on a minimum total cell number of 5000. Applying these thresholds to the validation data set gave 81.3% sensitivity, 76.0% specificity and 92.7% negative predictive value (NPV) in GH and 63.2% sensitivity, 89.9% specificity and 89.9% NPV in CS. Minichromosome maintenance protein-2 ICC provided clinically relevant improvements over urine cytology, with greater sensitivity in GH and greater specificity in CS (P=0.05).
Minichromosome maintenance protein-2 ICC is a reproducible and accurate test that is suitable for both GH and CS patient groups.
bladder cancer; urothelial carcinoma; MCM-2; cytology; immunocytochemistry; biomarker
Next-generation sequencing has led to a revolution in the study of hematological malignancies with a substantial number of publications and discoveries in the last few years. Significant discoveries associated with disease diagnosis, risk stratification, clonal evolution and therapeutic intervention have been generated by this powerful technology. As part of the post-genomic era, sequencing analysis will likely become part of routine clinical testing and the challenge will ultimately be successfully transitioning from gene discovery to preventive and therapeutic intervention as part of individualized medicine strategies. In this report, we review recent advances in the understanding of hematological malignancies derived through genome-wide sequence analysis.
hematological malignancy; genome sequencing; RNA sequencing; clonal architecture
Smokeless tobacco products have been associated with increased risks of oro-pharyngeal cancers, due in part to the presence of tobacco-specific nitrosamines (TSNAs) such as 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK). These potent carcinogens are formed during tobacco curing and as a result of direct nitrosation reactions that occur in the oral cavity. In the current work we describe the isolation and characterization of a hybridoma secreting a high-affinity, NNK-specific monoclonal antibody. A structurally-related benzoyl derivative was synthesized to facilitate coupling to NNK-carrier proteins, which were characterized for the presence of the N-nitroso group using the Griess reaction, and used to immunize BALB/c mice. Splenocytes from mice bearing NNK-specific antibodies were used to create hybridomas. Out of four, one was selected for subcloning and characterization. Approximately 99% of the monoclonal antibodies from this clone were competitively displaced from plate-bound NNKB conjugates in the presence of free NNK. The affinity of the monoclonal antibody to the NNKB conjugates was Kd = 2.93 nM as determined by surface plasmon resonance. Free nicotine was a poor competitor for the NNKB binding site. The heavy and light chain antibody F(ab) fragments were cloned, sequenced and inserted in tandem into an expression vector, with an FMDV Furin 2A cleavage site between them. Expression in HEK 293 cells revealed a functional F(ab) with similar binding features to that of the parent hybridoma. This study lays the groundwork for synthesizing transgenic tobacco that expresses carcinogen-sequestration properties, thereby rendering it less harmful to consumers.
TSNAs; F(ab); NNK; monoclonal antibody; 2A cleavage
Natural Killer T (NKT) cells respond to a variety of CD1d-restricted antigens (Ags), although the basis for Ag discrimination by the NKT cell receptor (TCR) is unclear. Here we describe NKT TCR fine specificity against several closely related Ags, termed altered glycolipid ligands (AGLs), which differentially stimulate NKT cells. The structures of five ternary complexes all revealed similar docking. Acyl chain modifications did not affect the interaction, but reduced NKT cell proliferation, indicating an affect on Ag processing or presentation. Conversely, truncation of the phytosphingosine chain caused an induced fit mode of TCR binding that affected TCR affinity. Modifications in the glycosyl head group had a direct impact on the TCR interaction and associated cellular response, with ligand potency reflecting the t1/2 life of the interaction. Accordingly, we have provided a molecular basis for understanding how modifications in AGLs can result in striking alterations in the cellular response of NKT cells.
Lisch nodules associated with Neurofibromatosis Type 1 (NF1) are usually multiple and bilateral in nature. Here, we report a 21-year-old healthy, Caucasian female who was diagnosed with multiple, unilateral Lisch nodules during routine eye examination. A thorough history and physical examination revealed no other signs of NF1. We diagnosed the rare occurrence of numerous, unilateral Lisch nodules in the absence of additional features of NF1 in our patient and provide a discussion concerning the differential diagnosis of Lisch nodules as well as the potential genetic explanation of this finding.
There is ample evidence in the international literature for pharmacist involvement in the prevention and management of cardiovascular disease (CVD) conditions in primary care. Systematic reviews and meta-analyses have confirmed the significant clinical benefits of pharmacist interventions for a range of CVD conditions and risk factors. Evidence generated in research studies of Australian community pharmacist involvement in CVD prevention and management is summarised in this article.
Commonwealth funding through the Community Pharmacy Agreements has facilitated research to establish the feasibility and effectiveness of new models of primary care involving community pharmacists. Australian community pharmacists have been shown to effect positive clinical, humanistic and economic outcomes in patients with CVD conditions. Improvements in blood pressure, lipid levels, medication adherence and CVD risk have been demonstrated using different study designs. Satisfaction for GPs, pharmacists and consumers has also been reported. Perceived ‘turf‘ encroachment, expertise of the pharmacist, space, time and remuneration are challenges to the implementation of disease management services involving community pharmacists.
Cardiovascular; community pharmacy; outcomes; pharmacist; primary care
The stress response—increases in circulating glucocorticoids following a stressor—is typically considered adaptive, but few studies address the fitness consequences of individual variation in stress response. Generally, due to negative consequences of prolonged elevation of glucocorticoids, animals should have a transient stress response just sufficient to cope with the stressor. In rodents, stress responsiveness is affected by early developmental experience, and hyper-responsiveness to stress is linked to morbidity and mortality. We assessed individual variation in stress responses in free-living song sparrows, Melospiza melodia, in relation to fitness-related measures including song and overwinter survival. Birds with greater increases in corticosterone 30 min following restraint stress were less likely to return to breed the following year. Stress responsiveness was also correlated with song complexity: males with fewer syllables in their song repertoires had greater stress reactivity. Our findings support the hypothesis that developmental stressors both impair song development and affect the adult stress response. Thus, individual variation in the stress response may relate to variation in fitness.
birdsong; stress response; survival
Mouse iNKT cell receptors (iNKT TCRs) use a single Vα14-Jα18 sequence and Vβs that are almost always Vβ8.2, Vβ7 or Vβ2, although the basis of this differential usage is unclear. We show that the Vβ bias occurs as a consequence of the CDR2β loops determining the affinity of the iNKT TCR for CD1d/glycolipids, thus controlling positive selection. Within a conserved iNKT-TCR-CD1d docking framework, these inherent Vβ-CD1d affinities are further modulated by the hypervariable CDR3β loop, thereby defining a functional interplay between the two iNKT TCR CDRβ loops. These Vβ biases reveal a broadly hierarchical response in which Vβ8.2 > Vβ7 > Vβ2 in the recognition of diverse CD1d ligands. This restriction of the iNKT TCR Vβ repertoire during thymic selection paradoxically ensures that each peripheral iNKT cell recognizes a similar spectrum of antigens.
Four 3”- and 4”-deoxy and -fluorogalactosyl ceramides were synthesized, and their ability to stimulate iNKT cells, based on levels of IL-2 production, was assessed in three NKT cell receptor hybridomas. In two of the hybridomas, 1.2 and 2H4, all of the analogs were immunostimulatory, while in the 1.4 hybridoma only the 4”-fluoro analog led to the production of significant levels of IL-2.
Children enter elementary school with widely different skill levels in core subjects. Whether because of differences in aptitude or in preparedness, these initial skill differences often translate into systematic disparities in achievement over time. How can teachers reduce these disparities? Three possibilities are to offer basic skills training, to expose students to higher order instruction, or to provide socioemotional support. Repeated measures analyses of longitudinal data from the Eunice Kennedy Shriver National Institute of Child Health and Human Development Study of Early Child Care and Youth Development revealed that children with low, average, or high math skills prior to elementary school followed different but parallel trajectories of math achievement up through fifth grade. When enrolled in classes with inference-based instruction, however, the initially least skilled children narrowed the achievement gap as long as they did not have conflictual relations with their teachers. They did not make this kind of progress if they were in classes focused exclusively on basic skills instruction or if they were in inference-focused classes but had conflictual relations with teachers.
elementary school; instruction; teacher–student relations; math
To assess the feasibility of using magnetic resonance imaging (MRI) measurements as a surrogate end point for disease progression in a therapeutic trial for Alzheimer's disease (AD).
Three-hundred-sixty-two patients with probable AD from 38 different centers participated in the MRI portion of a 52 week randomized placebo controlled trial of milameline, a muscarinic receptor agonist. The therapeutic trial itself was not completed due to projected lack of efficacy on interim analysis; however, the MRI arm of the study was continued. Of the 362 subjects who underwent a baseline MRI study, 192 subjects underwent a second MRI one-year later. Hippocampal volume and temporal horn volume were measured from the MRI scans.
The annualized percent change in hippocampal volume (−4.9%) and temporal horn volume (16.1%) in the study patients were consistent with data from prior single site studies. Correlations between the rate of MRI volumetric change and change in behavioral/cognitive measures were greater for the temporal horn than for the hippocampus. Decline over time was more consistently seen with imaging measures, 99% of the time for the hippocampus, than behavioral/cognitive measures (p<0.001). Greater consistency in MRI than behavioral/clinical measures resulted in markedly lower estimated sample size requirements for clinical trials. The estimated number of subjects per arm required to detect a 50% reduction in the rate of decline over one year are: ADAS-Cog 320; MMSE 241; hippocampal volume 21; temporal horn volume fifty-four.
The consistency of MRI measurements obtained across sites, and the consistency between the multi-site milameline data and that obtained in prior single site studies, demonstrate the technical feasibility of using structural MRI measures as a surrogate end point of disease progression in therapeutic trials. However, validation of imaging as a biomarker of therapeutic efficacy in AD still awaits a positive trial.
To determine exercise training effects on cardiac size and left ventricular (LV) diastolic function and relationships of exercise induced changes in physiological and body composition parameters with cardiac parameters.
Prospective, randomised controlled trial.
Men and women (63.6 (5.7) years, body mass index 29.5 (4.4) kg/m2) with untreated hypertension (systolic blood pressure (BP) 130–159 or diastolic BP 85–99 mm Hg).
Main outcome measures
Cardiac size and LV diastolic function, peak oxygen uptake (Vo2), muscle strength, general and abdominal fatness, and insulin resistance.
6 months of exercise training versus usual care.
When analysed by group at six months, cardiac size and LV diastolic function did not differ between exercisers (n = 51) and controls (n = 53), whereas exercisers had significantly higher peak Vo2 (28 v 24 ml/kg/min) and strength (383 v 329 kg), and lower fatness (34% v 37%), diastolic BP (73 v 75 mm Hg) and insulin resistance (quantitative insulin sensitivity check index 0.35 v 0.34) versus controls (all p ⩽ 0.05). By regression analysis, among six month changes, increased peak Vo2 and reduced abdominal fat were associated with increased cardiac size. Increased peak Vo2 and reduced abdominal fat, BP and insulin resistance were associated with improved LV diastolic function. r Values ranged from 0.20 to 0.32 (p ⩽ 0.05).
When examined by group assignment, exercise had no effect on cardiac size or LV diastolic function. When individual variations in six month changes were examined, participants attaining the greatest increases in fitness and reductions in abdominal fatness, insulin resistance and BP showed a modest trend towards physiological hypertrophy characterised by increased cardiac size and improved LV diastolic function. These results suggest that decreased abdominal fatness may have a role in improving cardiovascular health.
exercise; blood pressure; obesity; diastole; cardiac structure
Mouse natural killer T (NKT) cells expressing an invariant T cell antigen receptor (TCR) recognize glycosphingolipids (GSLs) from Sphingomonas bacteria. The synthetic antigens previously tested, however, were designed to closely resemble the potent synthetic agonist α-galactosyl ceramide (αGalCer), which contains a monosaccharide and a C18:0 sphingosine lipid. Some Sphingomonas bacteria, however, also have oligosaccharide containing GSLs, and they normally synthesize several GSLs with different sphingosine chains, including one with a cyclopropyl ring containing C21:0 (C21cycl) sphingosine. Here we studied the stimulation of NKT cells with synthetic GSL antigens containing natural tetrasaccharide sugars, or the C21cyclo sphingosine. Our results indicate that there is great degree of variability of the antigenic potency of different natural Sphingomonas glycolipids, with the (C21cycl) sphingosine having intermediate potency, and the oligosaccharide-containing antigens exhibiting limited or no stimulatory capacity.
This series highlights a previously unreported hazard for children within the home, hair straightening irons. Thermal injury is a common reason for presentation at the emergency department. Contact burns from domestic irons and hair curling tongs are well documented in the literature. We have become aware of this new hazard in the home, which has resulted in several presentations to our department with deep partial thickness or full thickness burns.
burns; hair straighteners; children
Although it has been established how CD1 binds a variety of lipid antigens (Ag), data are only now emerging that show how αβ T cell receptors (TCRs) interact with CD1-Ag. Using the structure of the human semiinvariant NKT TCR–CD1d–α-galactosylceramide (α-GalCer) complex as a guide, we undertook an alanine scanning mutagenesis approach to define the energetic basis of this interaction between the NKT TCR and CD1d. Moreover, we explored how analogues of α-GalCer affected this interaction. The data revealed that an identical energetic footprint underpinned the human and mouse NKT TCR–CD1d–α-GalCer cross-reactivity. Some, but not all, of the contact residues within the Jα18-encoded invariant CDR3α loop and Vβ11-encoded CDR2β loop were critical for recognizing CD1d. The residues within the Vα24-encoded CDR1α and CDR3α loops that contacted the glycolipid Ag played a smaller energetic role compared with the NKT TCR residues that contacted CD1d. Collectively, our data reveal that the region distant to the protruding Ag and directly above the F′ pocket of CD1d was the principal factor in the interaction with the NKT TCR. Accordingly, although the structural footprint at the NKT TCR–CD1d–α-GalCer is small, the energetic footprint is smaller still, and reveals the minimal requirements for CD1d restriction.
Given the tolerance of the right heart circulation to mild regurgitation and gradient, we study the potential of using motionless devices to regulate the pulmonary circulation. In addition, we document the flow performance of two mechanical valves. A motionless diode, a nozzle, a mechanical bileaflet valve, and a tilting disk valve were tested in a pulmonary mock circulatory system over the normal human range of pulmonary vascular resistance (PVR). For the mechanical valves, regurgitant fractions (RFs) and transvalvular pressure gradients were found to be weak functions of PVR. On the low end of normal PVR, the bileaflet and tilting disk valves fluttered and would not fully close. Despite this anomaly, the regurgitant fraction of either valve did not change significantly. The values for RF and transvalvular gradient measured varied from 4 to 7% and 4 to 7 mm Hg, respectively, at 5 lpm for all tests. The diode valve was able to regulate flow with mild regurgitant fraction and trivial gradient but with values higher than either mechanical valve tested. Regurgitant fraction ranged from 2 to 17% in tests extending from PVR values of 1 to 4.5 mm Hg/lpm at 5 lpm and with concomitant increases in gradient up to 17 mm Hg. The regurgitant fraction for the nozzle increased from 2 to 23% over the range of PVR with gradients increasing to 18 mm Hg. The significant findings were: (1) the mechanical valves controlled regurgitation at normal physiological cardiac output and PVR even though they failed to close at some normal values of PVR and showed leaflet flutter; and (2) it may be possible to regulate the pulmonary circulation to tolerable levels using a motionless pulmonary valve device.
mechanical heart valve; pulmonary vascular resistance; diode; regurgitant fraction
BACKGROUND—Anecdotal evidence suggests that people from non-Anglo-Celtic backgrounds are under-represented at familial cancer clinics in the UK, the USA, and Australia. This article discusses cultural beliefs as a potential key barrier to access, reviews previous empirical research on cultural aspects of cancer genetics, draws implications from findings, and sets a research agenda on the inter-relationships between culture, cancer genetics, and kinship.
METHODS—The CD-ROM databases MEDLINE, PsychLIT, CINAHL, and Sociological Abstracts were searched from 1980 onwards.
RESULTS—Cultural aspects of cancer genetics is the focus of an emerging body of publications. Almost all studies assessed African-American women with a family history of breast cancer and few studies included more diverse samples, such as Americans of Ashkenazi Jewish background or Hawaiian- and Japanese-Americans. Our analysis of published reports suggests several directions for future research. First, an increased focus on various Asian societies appears warranted. Research outside North America could explore the extent to which findings can be replicated in other multicultural settings. In addition, control group designs are likely to benefit from systematically assessing culture based beliefs and cultural identity in the "majority culture" group used for comparative purposes.
CONCLUSION—More data on which to base the provision of culturally appropriate familial cancer clinic services to ethnically diverse societies are needed. Empirical data will assist with culturally appropriate categorisation of people from other cultures into risk groups based on their family histories and provide the basis for the development of culturally appropriate patient education strategies and materials.
Keywords: hereditary cancer; kinship; culture; family history; cultural competence
Habitat quality and metapopulation effects are the main hypotheses that currently explain the disproportionate decline of insects in cultivated Holarctic landscapes. The former assumes a degradation in habitat quality for insects within surviving ecosystems, the latter that too few, small or isolated islands of ecosystem remain in landscapes for populations to persist. These hypotheses are often treated as alternatives, and this can lead to serious conflict in the interpretations of conservationists. We present the first empirical demonstration that habitat quality and site isolation are both important determinants of where populations persist in modern landscapes. We described the precise habitat requirements of Melitaea cinxia, Polyommatus bellargus and Thymelicus acteon, and quantified the variation in carrying capacity within each butterfly's niche. We then made detailed surveys to compare the distribution and density of every population of each species with the size, distance apart and quality of their specific habitats in all their potential habitat patches in three UK landscapes. In each case, within-site variation in habitat quality explained which patches supported a species' population two to three times better than site isolation. Site area and occupancy were not correlated in any species. Instead of representing alternative paradigms, habitat quality and spatial effects operate at different hierarchical levels within the same process: habitat quality is the missing third parameter in metapopulation dynamics, contributing more to species persistence, on the basis of these results, than site area or isolation. A reorientation in conservation priorities is recommended.