Executive summary of AAPM Report Task Group 113: Guidance for the physics aspects of clinical trials

The charge of AAPM Task Group 113 is to provide guidance for the physics aspects of clinical trials to minimize variability in planning and dose delivery for external beam trials involving photons and electrons. Several studies have demonstrated the importance of protocol compliance on patient outcome. Minimizing variability for treatments at different centers improves the quality and efficiency of clinical trials. Attention is focused on areas where variability can be minimized through standardization of protocols and processes through all aspects of clinical trials. Recommendations are presented for clinical trial designers, physicists supporting clinical trials at their individual clinics, quality assurance centers, and manufacturers.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/146453/1/acm212384_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146453/2/acm212384.pd

A chirped-pulse Fourier-transform microwave/pulsed uniform flow spectrometer. I. The low-temperature flow system

We report the development of a new instrument that combines chirped-pulse microwave spectroscopy with a pulsed uniform supersonic flow. This combination promises a nearly universal detection method that can deliver isomer and conformer specific, quantitative detection and spectroscopic characterization of unstable reaction products and intermediates, product vibrational distributions, and molecular excited states. This first paper in a series of two presents a new pulsed-flow design, at the heart of which is a fast, high-throughput pulsed valve driven by a piezoelectric stack actuator. Uniform flows at temperatures as low as 20 K were readily achieved with only modest pumping requirements, as demonstrated by impact pressure measurements and pure rotational spectroscopy. The proposed technique will be suitable for application in diverse fields including fundamental studies in spectroscopy, kinetics, and reaction dynamics.National Science Foundation (U.S.) (Award MRI-ID 1126380

Immunologic monitoring and immunotherapy in Ewing's sarcoma

Serial immunological monitoring was performed on 31 patients with Ewing's sarcoma who were on a randomized immunotherapy trial with BCG administered by dermal scarification with a Heaf gun. Patients were skin-tested for delayed hypersensitivity reactions (DCHR) to recall antigens and extracts of tumor cells, and with keyhole limpet hemocyanin (KLH). In vitro testing consisted of lymphocyte counts, percentages of cells forming rosettes with sheep erythrocytes at 29° C and at 4° C, and leukocyte migration inhibition to tuberculin (PPD) and to 3 M KCl extracts of tumor cells. At the time of diagnosis, nearly all patients had positive DCHR to mumps and streptococcal antigens and were negative to PPD. Neither the skin tests nor the lymphocyte counts at this time gave useful prognostic information. In tests during and after therapy, the patients who responded and remained free of detectable disease had a higher incidence of DCHR to KLH and of rosette values in the normal range than did the patients who developed recurrent disease. The BCG immunotherapy had no apparent effect on immunologic parameters except for conversion of reactions to PPD.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/46861/1/262_2004_Article_BF00200108.pd

Task workflow design and its impact on performance and volunteers' subjective preference in virtual citizen science

Virtual citizen science platforms allow non-scientists to take part in scientific research across a range of disciplines. What they ask of volunteers varies considerably in terms of task type, variety, user judgement required and user freedom, which has received little direct investigation. A study was performed with the Planet Four: Craters project to investigate the effect of task workflow design on both volunteer experience and the scientific results they produce. Participants' feedback through questionnaire responses indicated a preference for interfaces providing greater autonomy and variety, with free-text responses suggesting that autonomy was the more important. This did not translate into improved performance however, with the most autonomous interface not resulting in significantly better performance in data volume, agreement or accuracy compared to other less autonomous interfaces. The interface with the least number of task types, variety and autonomy resulted in the greatest data coverage. Agreement, both between participants and with the expert equivalent, was significantly improved when the interface most directly afforded tasks that captured the required underlying data (i.e. crater position or diameter). The implications for the designers of virtual citizen science platforms is that they have a balancing act to perform, weighing up the importance of user satisfaction, the data needs of the science case and the resources that can be committed both in terms of time and data reduction

Defective recognition of ATG8/LC3B by mutant SQSTM1/p62 implicates impairment of autophagy as a pathogenic mechanism in ALS-FTLD

Growing evidence implicates impairment of autophagy as a candidate pathogenic mechanism in the spectrum of neurodegenerative disorders which includes amyotrophic lateral sclerosis and frontotemporal lobar degeneration (ALS-FTLD). SQSTM1, which encodes the autophagy receptor SQSTM1/p62, is genetically associated with ALS-FTLD, although to date autophagy-relevant functional defects in disease-associated variants have not been described. A key protein-protein interaction in autophagy is the recognition of lipid-anchored ATG8/LC3 within the phagophore membrane by SQSTM1, mediated through its LC3-interacting region (LIR), and notably some ALS-FTLD mutations map to this region. Here we show that although representing a conservative substitution and predicted to be benign, the ALS-associated L341V mutation of SQSTM1 is defective in recognition of LC3B. We place our observations on a firm quantitative footing by showing the L341V-mutant LIR is associated with a ~3-fold reduction in LC3B binding affinity and using protein NMR we rationalise the structural basis for the effect. This functional deficit is realised in motor neurone-like cells, with L341V mutant EGFP-mCherry-SQSTM1 less readily incorporated into acidic autophagic vesicles than wild-type. Our data supports a model in which the L341V mutation limits the critical step of SQSTM1 recruitment to the phagophore. The oligomeric nature of SQSTM1 which presents multiple LIRs to template growth of the phagophore potentially gives rise to avidity effects which amplify the relatively modest impact of any single mutation on LC3B binding. Over the lifetime of a neurone impaired autophagy could expose a vulnerability which ultimately tips the balance from cell survival towards cell death

The Delphi Delirium Management Algorithms. A practical tool for clinicians, the result of a modified Delphi expert consensus approach

Delirium is common in hospitalised patients, and there is currently no specific treatment. Identifying and treating underlying somatic causes of delirium is the first priority once delirium is diagnosed. Several international guidelines provide clinicians with an evidence-based approach to screening, diagnosis and symptomatic treatment. However, current guidelines do not offer a structured approach to identification of underlying causes. A panel of 37 internationally recognised delirium experts from diverse medical backgrounds worked together in a modified Delphi approach via an online platform. Consensus was reached after five voting rounds. The final product of this project is a set of three delirium management algorithms (the Delirium Delphi Algorithms), one for ward patients, one for patients after cardiac surgery and one for patients in the intensive care unit.</p

A novel Alzheimer disease locus located near the gene encoding tau protein

This is the author accepted manuscript. The final version is available from the publisher via the DOI in this recordAPOE ε4, the most significant genetic risk factor for Alzheimer disease (AD), may mask effects of other loci. We re-analyzed genome-wide association study (GWAS) data from the International Genomics of Alzheimer's Project (IGAP) Consortium in APOE ε4+ (10 352 cases and 9207 controls) and APOE ε4- (7184 cases and 26 968 controls) subgroups as well as in the total sample testing for interaction between a single-nucleotide polymorphism (SNP) and APOE ε4 status. Suggestive associations (P<1 × 10-4) in stage 1 were evaluated in an independent sample (stage 2) containing 4203 subjects (APOE ε4+: 1250 cases and 536 controls; APOE ε4-: 718 cases and 1699 controls). Among APOE ε4- subjects, novel genome-wide significant (GWS) association was observed with 17 SNPs (all between KANSL1 and LRRC37A on chromosome 17 near MAPT) in a meta-analysis of the stage 1 and stage 2 data sets (best SNP, rs2732703, P=5·8 × 10-9). Conditional analysis revealed that rs2732703 accounted for association signals in the entire 100-kilobase region that includes MAPT. Except for previously identified AD loci showing stronger association in APOE ε4+ subjects (CR1 and CLU) or APOE ε4- subjects (MS4A6A/MS4A4A/MS4A6E), no other SNPs were significantly associated with AD in a specific APOE genotype subgroup. In addition, the finding in the stage 1 sample that AD risk is significantly influenced by the interaction of APOE with rs1595014 in TMEM106B (P=1·6 × 10-7) is noteworthy, because TMEM106B variants have previously been associated with risk of frontotemporal dementia. Expression quantitative trait locus analysis revealed that rs113986870, one of the GWS SNPs near rs2732703, is significantly associated with four KANSL1 probes that target transcription of the first translated exon and an untranslated exon in hippocampus (P≤1.3 × 10-8), frontal cortex (P≤1.3 × 10-9) and temporal cortex (P≤1.2 × 10-11). Rs113986870 is also strongly associated with a MAPT probe that targets transcription of alternatively spliced exon 3 in frontal cortex (P=9.2 × 10-6) and temporal cortex (P=2.6 × 10-6). Our APOE-stratified GWAS is the first to show GWS association for AD with SNPs in the chromosome 17q21.31 region. Replication of this finding in independent samples is needed to verify that SNPs in this region have significantly stronger effects on AD risk in persons lacking APOE ε4 compared with persons carrying this allele, and if this is found to hold, further examination of this region and studies aimed at deciphering the mechanism(s) are warranted

The role of Fc gamma receptors in the activity of therapeutic monoclonal antibodies

Fc gamma receptors (FcγRs) are the major family of receptors responsible for interacting with immunoglobulin G (IgG). They are known to be required for the anti-tumour activity of direct targeting mAbs through expression on NK cells and macrophages. Furthermore, recent work has suggested that cross-linking via FcγRs is required for the activity of agonistic, immune modulatory mAb. This thesis sought to investigate the requirement for these receptors for different aspects of mAb activity; from T cell activation to tumour depletion, using a combination of in vitro and in vivo systems.A panel of CHO-K1 cells were generated and transfected to express the polymorphic variants of human FcγRs. These were characterised for their ability to bind IgG before being used as feeder cells in T cell proliferation assays. The assays found that cross-linking of the anti-CD28 mAb, TGN1412 by FcγRIIb (CD32b) or FcγRIIa (CD32a) but not FcγRIIIa (CD16a) transfected cells induced T cell proliferation. Furthermore, this was accompanied by the release of pro-inflammatory cytokines including TNF-α, IFN-γ and IL-2. With the importance of cross-linking via CD32b demonstrated, experiments probed the mechanism of expression using Ramos and Raji cells. These experiments investigated the gene and promoter sequences as well as the effect of epigenetic inhibitors, however further investigation is required.Next a novel mouse model was developed to investigate the efficacy of anti-human (h)CD20 mAbs. The type II mAb obinutuzumab was found to give prolonged tumour clearance compared to the type I rituximab in a fully syngeneic model with the target antigen expressed on malignant and normal B cells. The use of immune compromised mice confirmed that activatory FcγRs were required for efficient anti-CD20 mediated tumour clearance. Further experiments demonstrated that anti-CD20 mAbs could be combined with the PI3Kδ inhibitor, GS9820, to prolong tumour clearance. These experiments unexpectedly revealed that hIgG1 had an abnormally short half-life in NOD SCID mice, causing the basis for this to be examined as NOD SCID mice are widely used for immunotherapy experiments, particularly patient derived xenografts. Further investigations found that half-life could be restored through genetic deletion of mouse CD32 or by reconstitution with IgG. The polymorphic variant of CD32 found in NOD SCID mice had a higher affinity for hIgG1 which could explain the short half-life.Overall the results presented here demonstrate the multiple roles played by FcγRs in the many aspects of mAb immunotherapy, from effector cell activation to cross-linking and altering mAb half-life. This knowledge will help guide the next generation of therapeutic mAbs

Chirped-pulse Fourier-transformation microwave/pulsed uniform flow spectrometer: the low-temperature, pulsed uniform supersonic flow system

Traditional techniques (e.g. REMPI, imaging, etc.) that are used to study reaction dynamics are able to provide a great deal of fundamental information about systems containing atoms and smaller molecules. However, as larger molecules and more complex systems are targeted, it becomes more of a challenge to determine isomer- and vibrational level-specific information and accurate branching ratios. In order to complement existing methods and obtain information about larger systems, a Ka-band (26-40 GHz) chirped-pulse Fourier transform microwave (CP-FTMW) spectrometer has been has been constructed. The system integrates a pulsed uniform supersonic flow (PUSF) source to ensure that experimental conditions, such as temperature and density, are well-known and constant. This PUSF system is based around a high-throughput piezoelectric stack valve, a Laval nozzle, and simple pumping scheme. This system is able to produce cold, uniform flows with densities on the order of 10$^{16}$ cm$^{-3}$ that persist for up to 20 cm from the nozzle exit. A description of this system and its characterization will be presented.Ope

Fc-engineering for modulated effector functions—improving antibodies for cancer treatment

The majority of monoclonal antibody (mAb) therapeutics possess the ability to engage innate immune effectors through interactions mediated by their fragment crystallizable (Fc) domain. By delivering Fc-Fc gamma receptor (FcγR) and Fc-C1q interactions, mAb are able to link exquisite specificity to powerful cellular and complement-mediated effector functions. Fc interactions can also facilitate enhanced target clustering to evoke potent receptor signaling. These observations have driven decades-long research to delineate the properties within the Fc that elicit these various activities, identifying key amino acid residues and elucidating the important role of glycosylation. They have also fostered a growing interest in Fc-engineering whereby this knowledge is exploited to modulate Fc effector function to suit specific mechanisms of action and therapeutic purposes. In this review, we document the insight that has been generated through the study of the Fc domain; revealing the underpinning structure-function relationships and how the Fc has been engineered to produce an increasing number of antibodies that are appearing in the clinic with augmented abilities to treat cancer