Tissue informative cell-free DNA methylation sites in amyotrophic lateral sclerosis

Cell-free DNA (cfDNA) is increasingly recognized as a promising biomarker candidate for disease monitoring. However, its utility in neurodegenerative diseases, like amyotrophic lateral sclerosis (ALS), remains underexplored. Existing biomarker discovery approaches are tailored to a specific disease context or are too expensive to be clinically practical. Here, we address these challenges through a new approach combining advances in molecular and computational technologies. First, we develop statistical tools to select tissue-informative DNA methylation sites relevant to a disease process of interest. We then employ a capture protocol to select these sites and perform targeted methylation sequencing. Multi-modal information about the DNA methylation patterns are then utilized in machine learning algorithms trained to predict disease status and disease progression. We applied our method to two independent cohorts of ALS patients and controls (n=192). Overall, we found that the targeted sites accurately predicted ALS status and replicated between cohorts. Additionally, we identified epigenetic features associated with ALS phenotypes, including disease severity. These findings highlight the potential of cfDNA as a non-invasive biomarker for ALS.

8 Unexpected retinopathy in a patient presenting with bilateral optic disc swelling

A 12-year-old boy presented with 5 day history of blurry vision, 'wobbly eyes', tinnitus and difficulty seeing at night. Local ophthalmology noted bilateral optic disc swelling and referred him urgently for neurological investigations.Clinical Findings: At presentation VA was RE 0.00 and LE 0.2 with normal Ishihara colour vision. His extraocular movements were full without manifest strabismus. Fundoscopy showed bilateral optic disc swelling. Electrophysiology unexpectedly revealed a functionally cone isolated retina with markedly abnormal rod function. Pattern VEPs indicated bilateral macular pathway dysfunction affecting left eye more than right eye. Wide field imaging showed bilateral diffusely scattered yellow-white flecks in the midperiphery of each eye. His kinetic visual fields were moderately restricted bilaterally. MRI showed a Chiari 1 malformation with cerebellar tonsil herniation, but LP opening pressure was normal.Differential diagnosis included RDH5 retinopathy or vitamin A deficiency. On questioning he reported a diet restricted to only meat and biscuits. His vitamin A levels were subnormal at 0.14 umol/L (reference range 0.9-2.5umol/l) and he was started on high-dose Vitamin A supplements.Four months after supplementation retinal appearances had normalised, the rod ERGs recovered, nyctalopia and visual field restriction resolved. PVEPs had improved but an element of LE macular pathway dysfunction remained. Optic disc swelling settled leaving mild temporal pallor, particularly of the LE with some RNFL loss.It is important to recognise nutritional Vitamin A deficiency in children as prompt recognition and treatment can improve symptoms, reverse retinal pathology which we have demonstrated with electrophysiological findings.

MRC2020: improvements to Ximdisp and the MRC image-processing programs

The great success of single-particle electron cryo-microscopy (cryoEM) during the last decade has involved the development of powerful new computer programs and packages that guide the user along a recommended processing workflow, in which the wisdom and choices made by the developers help everyone, especially new users, to obtain excellent results. The ability to carry out novel, non-standard or unusual combinations of image-processing steps is sometimes compromised by the convenience of a standard procedure. Some of the older programs were written with great flexibility and are still very valuable. Among these, the original MRC image-processing programs for structure determination by 2D crystal and helical processing alongside general-purpose utility programs such as Ximdisp, label, imedit and twofile are still available. This work describes an updated version of the MRC software package (MRC2020) that is freely available from CCP-EM. It includes new features and improvements such as extensions to the MRC format that retain the versatility of the package and make it particularly useful for testing novel computational procedures in cryoEM.

Rationale and design of a multisite randomized clinical trial examining an integrated behavioral treatment for veterans with co-occurring chronic pain and opioid use disorder: The pain and opioids integrated treatment in veterans (POSITIVE) trial

BACKGROUND

Chronic pain and opioid use disorder (OUD) individually represent a risk to health and well-being. Concerningly, there is evidence that they are frequently co-morbid. While few treatments exist that simultaneously target both conditions, preliminary work has supported the feasibility of an integrated behavioral treatment targeting pain interference and opioid misuse. This treatment combined Acceptance and Commitment Therapy (ACT) and Mindfulness-Based Relapse Prevention (ACT+MBRP). This paper describes the protocol for the adequately powered efficacy study of this integrated treatment.

METHODS

A multisite randomized controlled trial will examine the efficacy of ACT+MBRP in comparison to a parallel education control condition, focusing on opioid safety and pain education. Participants include veterans (n = 160; 21-75 years old) recruited from three Veterans Administration (VA) Healthcare Systems with chronic pain who are on a stable dose of buprenorphine. Both conditions include twelve weekly 90 min group sessions delivered via telehealth. Primary outcomes include pain interference (Patient Reported Outcome Measurement Information System - Pain Interference) and hazardous opioid use (Current Opioid Misuse Measure), which will be examined at the end of the active treatment phase and through 12 months post-intervention. Secondary analyses will evaluate outcomes including pain intensity, depression, pain-related fear, and substance use, as well as treatment mechanisms.

CONCLUSION

This study will determine the efficacy of an integrated behavioral treatment program for pain interference and hazardous opioid use among veterans with chronic pain and OUD who are prescribed buprenorphine, addressing a critical need for more integrated treatments for chronic pain and OUD.

TRIAL REGISTRATION

ClinicalTrials.gov Identifier: NCT04648228.

CyBorD-DARA in Newly Diagnosed Transplant-Eligible Multiple Myeloma: Results from the 16-BCNI-001/CTRIAL-IE 16-02 Study Show High Rates of MRD Negativity at End of Treatment

The phase 1b 16-BCNI-001/CTRIAL-IE 16-02 CyBorD-DARA trial investigated the combination of Daratumumab with cyclophosphamide, bortezomib and dexamethasone in patients with newly diagnosed multiple myeloma (NDMM), followed by autologous stem cell transplantation and Daratumumab maintenance. CR/sCR rates were 50% after transplant and 62.5% at end of treatment. The overall percentage of patients achieving complete response or better was 77.8%. Progression-free survival rate at end of maintenance was 81.3% and estimated 2-year overall survival was 88.9%. 37.5% of patients demonstrated sustained MRD negativity to a level of 10^-5 from transplant to analysis at EOT. In this phase 1b study, we have shown CyBorD-DARA to be an effective and well-tolerated immunomodulatory agent-free regiment in transplant-eligible NDMM.

Evaluation of prognostic risk models for postoperative pulmonary complications in adult patients undergoing major abdominal surgery: a systematic review and international external validation cohort study

BACKGROUND

Stratifying risk of postoperative pulmonary complications after major abdominal surgery allows clinicians to modify risk through targeted interventions and enhanced monitoring. In this study, we aimed to identify and validate prognostic models against a new consensus definition of postoperative pulmonary complications.

METHODS

We did a systematic review and international external validation cohort study. The systematic review was done in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. We searched MEDLINE and Embase on March 1, 2020, for articles published in English that reported on risk prediction models for postoperative pulmonary complications following abdominal surgery. External validation of existing models was done within a prospective international cohort study of adult patients (≥18 years) undergoing major abdominal surgery. Data were collected between Jan 1, 2019, and April 30, 2019, in the UK, Ireland, and Australia. Discriminative ability and prognostic accuracy summary statistics were compared between models for the 30-day postoperative pulmonary complication rate as defined by the Standardised Endpoints in Perioperative Medicine Core Outcome Measures in Perioperative and Anaesthetic Care (StEP-COMPAC). Model performance was compared using the area under the receiver operating characteristic curve (AUROCC).

FINDINGS

In total, we identified 2903 records from our literature search; of which, 2514 (86·6%) unique records were screened, 121 (4·8%) of 2514 full texts were assessed for eligibility, and 29 unique prognostic models were identified. Nine (31·0%) of 29 models had score development reported only, 19 (65·5%) had undergone internal validation, and only four (13·8%) had been externally validated. Data to validate six eligible models were collected in the international external validation cohort study. Data from 11 591 patients were available, with an overall postoperative pulmonary complication rate of 7·8% (n=903). None of the six models showed good discrimination (defined as AUROCC ≥0·70) for identifying postoperative pulmonary complications, with the Assess Respiratory Risk in Surgical Patients in Catalonia score showing the best discrimination (AUROCC 0·700 [95% CI 0·683-0·717]).

INTERPRETATION

In the pre-COVID-19 pandemic data, variability in the risk of pulmonary complications (StEP-COMPAC definition) following major abdominal surgery was poorly described by existing prognostication tools. To improve surgical safety during the COVID-19 pandemic recovery and beyond, novel risk stratification tools are required.

FUNDING

British Journal of Surgery Society.

OP0281 PHARMACODYNAMIC EFFECT OF SEQUENTIAL BELIMUMAB (BEL) AND RITUXIMAB (RTX) THERAPY IN PATIENTS (PTS) WITH SYSTEMIC LUPUS ERYTHEMATOSUS (SLE): THE PHASE 3, RANDOMISED, PLACEBO-CONTROLLED BLISS-BELIEVE STUDY

Background

BEL is approved for active SLE and lupus nephritis (adults only). Despite failed trials,1 RTX remains in the SLE treatment armamentarium. Sequential BEL and RTX therapy offers a promising strategy to target B cells by distinct but complementary mechanisms.

Objectives

To assess the pharmacodynamic effects of BEL and a single RTX cycle on immunologic biomarkers in adults with SLE.

Methods

In this 104-week (wk) study (NCT03312907), all pts with active SLE received subcutaneous BEL 200 mg/wk for 52 wks. Pts were randomised to receive intravenous (IV) RTX 1000 mg at Wks 4 + 6 (BEL/RTX), IV PBO at Wks 4 + 6 (BEL/PBO), or continued treatment with standard therapy (BEL/ST). For BEL/RTX and BEL/PBO pts, a 52-wk treatment-free observational phase followed the 52-wk treatment phase; BEL/ST pts continued to receive BEL for 104 wks. Changes from baseline (BL) in anti-dsDNA and C3/C4 levels, and counts of total B cells (CD19+) and B-cell subsets (CD20+; naïve; memory; activated B-cells), were analysed.

Results

292 pts received ≥1 study treatment dose (BEL/PBO n=72; BEL/RTX n=144; BEL/ST n=76). For pts assessed at Wk 52, reductions from BL in anti-dsDNA levels were seen in all 3 groups with a significant difference between BEL/RTX and BEL/PBO (p=0.0495). C3/C4 levels increased from BL to Wks 52 and 104 in all groups, with trends for greater increases with BEL/RTX versus BEL/PBO (Table 1). At Wk 52, total B cells and most B-cell subsets decreased in all 3 groups (Table 1), with significant differences between BEL/RTX and BEL/PBO (p<0.0001 for all). During the observation period, repopulation of total CD19+ B cells (comprising mostly of naïve CD20+CD27-) towards BL levels by Wk 104 was most evident with BEL/RTX, while low circulating CD20+CD27+ memory B cell levels remained relatively unchanged (Table 1).

Table 1.

Absolute changes in biomarkers for treatment phase completers*

Median (25th, 75thpercentile)Change from BLAt Wk 52At Wk 104BEL/PBOBEL/RTXBEL/STBEL/PBOBEL/RTXBEL/STn=54n=102n=58n=24n=44n=50Anti-dsDNA (IU/ml)-9 (-83, 1)-51 (-155, -3)-5 (-61, 0)-9.5 (-197, 2)-55 (-329, -2)-6.5 (-57, -1)C3 (md/dl)8.5 (-8, 21)15† (0, 30)1‡ (-6, 11)6 (-5.5, 19.5)11 (-7, 27)7.5 (-5, 23)C4 (md/dl)2 (0, 5)4† (2, 9)2‡ (-1, 4)1.5 (-1.5, 4.5)3 (0, 8)3 (1, 5)B cells and B-cell subsets (cells/ml)n=48n=93n=55n=20n=40n=47CD19+-57,570 (-120,810, -5861)-95,313 (-193,946, -44,240)-57,399 (-152,403, -12,562)-41,343 (-105,789, 23,819)-11,932 (-77,822, 45,773)-48,783 (-151,528, -15,603)CD20+-58,112 (-110,681, -3126)-93,482 (-189,567, -42,636)-57,428 (-147,094, -3590)-40,773 (-95,658, 25,547)-3986 (-75,942, 49,021)-45,110 (-143,321, -15,063)Naïve CD20+CD27--60,929 (-112,623, -15,316)-61,405 (-152,261, -28,496)-62,477 (-142,009, -16,191)-22,210 (-72,131, 28,335)6941 (-62,669, 67,355)-51,254 (-142,712, -14,736)Activated CD95+-5012 (-12,701, 278)-9991 (-17,900, -5560)-3895 (-10,068, -1347)-3834 (-13,274, 1490)-5821 (-11,216, -233)-5641 (-14,810, -3341)Memory CD20+CD27+9,586 (1500, 30,983)-15,076 (-42,880, -6376)5532 (-146, 14,393)-13,927 (-24,816, -3064)-11,534 (-25,646, -2958)-1229 (-8466, 7300)

*Excluded from analysis: all pts who discontinued the investigational product before Wk 52 and BEL/ST pts if discontinued before Wk 104, and BEL/PBO and BEL/RTX pts who re-started BEL after Wk 53; †n=101; ‡n=57.

Conclusion

An improvement in anti-dsDNA and C3/C4 levels was generally observed across all 3 treatment groups with greater reductions in anti-dsDNA antibodies following BEL/RTX versus BEL/PBO and BEL/ST. We believe that BEL induced a pharmacodynamic window for subsequent RTX treatment for a marked reduction in circulating memory B cells and other B-cell subsets. Our findings underscore the need for better understanding of the bridge from pharmacodynamic to clinical outcomes, given that BEL/RTX did not show an improvement in disease control over BEL/PBO.1

References

[1]Aranow C, et al. Arthritis Rheumatol 2021;73 (suppl 10).

Acknowledgements

This analysis of the GSK Study 205646 was funded by GlaxoSmithKline (GSK). Medical writing support was provided by Nicholas Thomas, PhD, Fishawack Indicia Ltd. UK, part of Fishawack Health, and was funded by GSK.

Disclosure of Interests

Y.K. Onno Teng Consultant of: GSK, Aurinia Pharmaceuticals, Novartis, KezarBio, Otsuka, Vifor Pharma, Grant/research support from: GSK, Vifor Pharma, Aurinia Pharmaceuticals, Andre van Maurik Shareholder of: GSK, Employee of: GSK, Kenneth L Clark Shareholder of: GSK, Employee of: GSK, Norma Lynn Fox Shareholder of: GSK, Employee of: GSK, Yun Irene Gregan Shareholder of: GSK, Employee of: GSK, James Groark Shareholder of: GSK, Employee of: GSK, Robert Henderson Shareholder of: GSK, Employee of: GSK, Josephine Ocran-Appiah Shareholder of: GSK, Employee of: GSK, David Roth Shareholder of: GSK, Employee of: GSK, Don Shanahan Shareholder of: GSK, Employee of: GSK, Paul-Peter Tak Shareholder of: GSK, Employee of: GSK, Cynthia Aranow Consultant of: BMS, Kezar, GSK, Grant/research support from: GSK

ChemInformatics Model Explorer (CIME): exploratory analysis of chemical model explanations

The introduction of machine learning to small molecule research- an inherently multidisciplinary field in which chemists and data scientists combine their expertise and collaborate - has been vital to making screening processes more efficient. In recent years, numerous models that predict pharmacokinetic properties or bioactivity have been published, and these are used on a daily basis by chemists to make decisions and prioritize ideas. The emerging field of explainable artificial intelligence is opening up new possibilities for understanding the reasoning that underlies a model. In small molecule research, this means relating contributions of substructures of compounds to their predicted properties, which in turn also allows the areas of the compounds that have the greatest influence on the outcome to be identified. However, there is no interactive visualization tool that facilitates such interdisciplinary collaborations towards interpretability of machine learning models for small molecules. To fill this gap, we present CIME (ChemInformatics Model Explorer), an interactive web-based system that allows users to inspect chemical data sets, visualize model explanations, compare interpretability techniques, and explore subgroups of compounds. The tool is model-agnostic and can be run on a server or a workstation.

Event history and topological data analysis

Persistent homology is used to track the appearance and disappearance of features as we move through a nested sequence of topological spaces. Equating the nested sequence to a filtration and the appearance and disappearance of features to events, we show that simple event history methods can be used for the analysis of topological data. We propose a version of the well-known Nelson–Aalen cumulative hazard estimator for the comparison of topological features of random fields and for testing parametric assumptions. We suggest a Cox proportional hazards approach for the analysis of embedded metric trees. The Nelson–Aalen method is illustrated on globally distributed climate data and on neutral hydrogen distribution in the Milky Way. The Cox method is used to compare vascular patterns in fundus images of the eyes of healthy and diabetic retinopathy patients.

New onset left bundle branch block after transcatheter aortic valve implantation and the effect on long-term survival – a UK wide experience

Introduction

New onset left bundle branch block (LBBB) is the most common conduction disturbance associated with transcatheter aortic valve implantation (TAVI). It has been shown to adversely affect cardiac function and increase re-hospitalisation, although its impact on mortality remains contentious.

Methods

We conducted an observational cohort analysis of all TAVI procedures performed by 13 heart teams in the United Kingdom from inception of their structural programmes until 31st July 2013. The primary outcome was 1-year all-cause mortality. Secondary outcomes included left ventricular ejection fraction (LVEF) at 30 days and need for a post-TAVI permanent pacemaker (PPM).

Results

1785 patients were eligible for inclusion to the study. The primary analysis cohort was composed of 1409 patients with complete electrocardiographic (ECG) data pre- and post-TAVI. Pre-existing LBBB was present in 200 (14.2%) patients. New LBBB occurred in 323 (22.9%) patients post TAVI, which resolved in 99 (7%) patients prior to discharge. A balloon-expandable device was implanted in 968 (69%) patients, whilst 421 (30%) patients received a self-expandable valve. New LBBB was observed in 120 (12.4%) and 192 (45.6%) patients receiving a balloon- or self-expandable prosthesis respectively.

Overall 1-year all-cause mortality post TAVI was 18.7%. New onset LBBB was not associated with an increase in 1-year all-cause mortality (p=0.416). Factors that were associated with mortality included an increasing logistic EuroScore (p=0.05), history of previous balloon aortic valvuloplasty (p=0.001), renal impairment (p=0.003), previous myocardial infarction with pre-existing LBBB (p=0.028) and atrial fibrillation (p=0.039). Lower baseline peak and mean AV gradients were also associated with greater mortality at 1 year (p=0.001), likely reflecting underlying left ventricular dysfunction.

In the majority of patients, LVEF remained unchanged following TAVI. Interestingly, the presence or absence of new onset LBBB did not affect LVEF improvement at 30 days. 10% of patients required a PPM post TAVI. Predictors of PPM included new LBBB (OR 2.6, p&lt;0.001), pre-TAVI left ventricular systolic impairment (OR 1.2, p=0.037), a self-expandable device (p&lt;0.001), and pre-existing RBBB (OR 4.0, p&lt;0.001).

Conclusions

These findings suggest that new onset LBBB post TAVI does not increase mortality at 1 year or adversely affect LVEF at 30 days.

Funding Acknowledgement

Type of funding source: None

Abstract MP44: Proteolytic Activation Of ENaC Mediates Fructose-Induced Salt-Sensitive Hypertension

In nephrotic syndrome, glomerular injury leads to filtration of plasma proteases. Once in the urine, these enzymes cleave and activate the epithelial Na channel (ENaC) causing inappropriate Na retention and hypertension. Dietary fructose causes inappropriate Na retention and salt-sensitive hypertension but whether proteolytic activation of ENaC is involved, and the source of the proteases, is unknown. We hypothesized that dietary fructose increases expression and release of proteases from the proximal nephron, and that these enzymes activate ENaC thereby causing Na retention and salt-sensitive hypertension. To test this hypothesis we first measured proximal nephron protease expression and urinary protease excretion in rats on either a high-salt diet without fructose (high salt) or one containing 4% NaCl plus 20% fructose in the drinking water (high salt/fructose) for 7 days. High salt/fructose treatment increased proximal nephron expression of trypsin I, an enzyme known to cleave and activate ENaC, by 68±7% (p < 0.01). Urinary excretion of trypsin I was 8.4±1.3 arbitrary units/μg protein in rats fed high salt while it was 20.3±4.6 arbitrary units/μg protein in those on the high salt/fructose diet, 142% greater (p < 0.02). There was no difference in total urinary protein excretion between groups. Finally, we examined the effect of high salt/fructose and high salt plus 20% glucose) high salt/glucose) on blood pressure before and after oral amiloride. After 7 days the systolic blood pressure of rats on high salt/fructose was 148±6 mm Hg while it was only 124±5 in those on high salt/glucose (p < 0.02). Amiloride reduced systolic blood pressure in rats on the high salt/fructose diet from 148±6 to 134±5 mm Hg but had no significant effect on the high salt/glucose group. We conclude that proteolytic cleavage of ENaC contributes to fructose-induced salt-sensitive hypertension and that the source of the protease(s) is likely the proximal tubule rather than glomerular filtration.

Adaptive treatment and robust control

A control theory perspective on determination of optimal dynamic treatment regimes is considered. The aim is to adapt statistical methodology that has been developed for medical or other biostatistical applications to incorporate powerful control techniques that have been designed for engineering or other technological problems. Data tend to be sparse and noisy in the biostatistical area and interest has tended to be in statistical inference for treatment effects. In engineering fields, experimental data can be more easily obtained and reproduced and interest is more often in performance and stability of proposed controllers rather than modeling and inference per se. We propose that modeling and estimation should be based on standard statistical techniques but subsequent treatment policy should be obtained from robust control. To bring focus, we concentrate on A-learning methodology as developed in the biostatistical literature and H ∞ -synthesis from control theory. Simulations and two applications demonstrate robustness of the H ∞ strategy compared to standard A-learning in the presence of model misspecification or measurement error.

Weak Acid Permeation in Synthetic Lipid Vesicles and Across the Yeast Plasma Membrane

We present a fluorescence-based approach for determination of the permeability of small molecules across the membranes of lipid vesicles and living cells. With properly designed experiments, the method allows us to assess the membrane physical properties both in vitro and in vivo. We find that the permeability of weak acids increases in the order of benzoic > acetic > formic > lactic, both in synthetic lipid vesicles and the plasma membrane of Saccharomyces cerevisiae, but the permeability is much lower in yeast (one to two orders of magnitude). We observe a relation between the molecule permeability and the saturation of the lipid acyl chain (i.e., lipid packing) in the synthetic lipid vesicles. By analyzing wild-type yeast and a manifold knockout strain lacking all putative lactic acid transporters, we conclude that the yeast plasma membrane is impermeable to lactic acid on timescales up to ∼2.5 h.

CryoEM at 100 keV: a demonstration and prospects

100 kV is investigated as the operating voltage for single-particle electron cryomicroscopy (cryoEM). Reducing the electron energy from the current standard of 300 or 200 keV offers both cost savings and potentially improved imaging. The latter follows from recent measurements of radiation damage to biological specimens by high-energy electrons, which show that at lower energies there is an increased amount of information available per unit damage. For frozen hydrated specimens around 300 Å in thickness, the predicted optimal electron energy for imaging is 100 keV. Currently available electron cryomicroscopes in the 100-120 keV range are not optimized for cryoEM as they lack both the spatially coherent illumination needed for the high defocus used in cryoEM and imaging detectors optimized for 100 keV electrons. To demonstrate the potential of imaging at 100 kV, the voltage of a standard, commercial 200 kV field-emission gun (FEG) microscope was reduced to 100 kV and a side-entry cryoholder was used. As high-efficiency, large-area cameras are not currently available for 100 keV electrons, a commercial hybrid pixel camera designed for X-ray detection was attached to the camera chamber and was used for low-dose data collection. Using this configuration, five single-particle specimens were imaged: hepatitis B virus capsid, bacterial 70S ribosome, catalase, DNA protection during starvation protein and haemoglobin, ranging in size from 4.5 MDa to 64 kDa with corresponding diameters from 320 to 72 Å. These five data sets were used to reconstruct 3D structures with resolutions between 8.4 and 3.4 Å. Based on this work, the practical advantages and current technological limitations to single-particle cryoEM at 100 keV are considered. These results are also discussed in the context of future microscope development towards the goal of rapid, simple and widely available structure determination of any purified biological specimen.

Preequilibrium Asymmetries in the ^{239}Pu(n,f) Prompt Fission Neutron Spectrum

The physical properties of neutrons emitted from neutron-induced fission are fundamental to our understanding of nuclear fission. However, while state-of-the-art fission models still incorporate isotropic fission neutron spectra, it is believed that the preequilibrium prefission component of these spectra is strongly anisotropic. The lack of experimental guidance on this feature has not motivated incorporation of anisotropic neutron spectra in fission models, though any significant anisotropy would impact descriptions of a fissioning system. In the present work, an excess of counts at high energies in the fission neutron spectrum of ^{239}Pu is clearly observed and identified as an excess of the preequilibrium prefission distribution above the postfission neutron spectrum. This excess is separated from the underlying postfission neutron spectrum, and its angular distribution is determined as a function in incident neutron energy and outgoing neutron detection angle. Comparison with neutron scattering models provides the first experimental evidence that the preequilibrium angular distribution is uncorrelated with the fission axis. The results presented here also impact the interpretation of several influential prompt fission neutron spectrum measurements.

A Note on Testing for Intervention Effects on Binary Responses

Objectives: In some circumstances controlled trials are not feasible and treatments can only be evaluated using clinical databases. Here we consider the situation where treatment is introduced at a particular calendar time and can only be evaluated by comparison with historical controls. In these circumstances Heuer and Abel recommended using change-point methods to search for change in characteristics over the whole study period rather than simply comparing treated and untreated patients. Their recommendation is to only conclude that the intervention had an effect if a change-point could be demonstrated close in time to the introduction of the new treatment. This reduces the risk of false positives caused by confounding changes in population characteristics or changes in patient management. For binary data we develop a method that follows their philosophy and apply it to an observational study in the treatment of pin sites after orthopaedic surgery.

Methods: Tests for change in binomial probabilities based on Brownian bridge and Hansen’s approximation for maximally selected X 2 statistics are compared to an exact test by Worsley. The approximate method is generalized to logistic regression models allowing for covariates.

Results: The agreement of the exact and approximate method is good for sample sizes of 100 or more. The actual test size of the Hansen approximate test allowing for covariates is close to the nominal level, whereas the Brownian bridge approximation is slightly conservative. The change in pin site treatment significantly reduces the risk of infection for both adults and children.

Conclusions: We consider the Hansen approximation to provide a very good and very simple method for obtaining the p-value when testing for a change in binary data event probabilities, with or without covariates.

Accredited accommodation: an alternative to in-patient care in rural north Powys

Various alternatives to psychiatric in-patient care have recently been reviewed (Boardman & Hodgson, 2000). The Accredited Accommodation Scheme in north Powys represents a novel, local alternative to in-patient care, for a targeted group of patients with enduring forms of mental illness.

Proton-solute coupling mechanism of the maltose transporter from Saccharomyces cerevisiae

Mal11 catalyzes proton-coupled maltose transport across the plasma membrane of Saccharomyces cerevisiae. We used structure-based design of mutants and a kinetic analysis of maltose transport to determine the energy coupling mechanism of transport. We find that wildtype Mal11 is extremely well coupled and allows yeast to rapidly accumulate maltose to dangerous levels, resulting under some conditions in self-lysis. Three protonatable residues lining the central membrane-embedded cavity of Mal11 were identified as having potential roles in proton translocation. We probed the mechanistic basis for proton coupling with uphill and downhill transport assays and found that single mutants can still accumulate maltose but with a lower coupling efficiency than the wildtype. Next, we combined the individual mutations and created double and triple mutants. We found some redundancy in the functions of the acidic residues in proton coupling and that no single residue is most critical for proton coupling to maltose uptake, unlike what is usually observed in related transporters. Importantly, the triple mutants were completely uncoupled but still fully active in downhill efflux and equilibrium exchange. Together, these results depict a concerted mechanism of proton transport in Mal11 involving multiple charged residues.

Second malignancies in the context of lenalidomide treatment: an analysis of 2732 myeloma patients enrolled to the Myeloma XI trial

We have carried out the largest randomised trial to date of newly diagnosed myeloma patients, in which lenalidomide has been used as an induction and maintenance treatment option and here report its impact on second primary malignancy (SPM) incidence and pathology. After review, 104 SPMs were confirmed in 96 of 2732 trial patients. The cumulative incidence of SPM was 0.7% (95% confidence interval (CI) 0.4–1.0%), 2.3% (95% CI 1.6–2.7%) and 3.8% (95% CI 2.9–4.6%) at 1, 2 and 3 years, respectively. Patients receiving maintenance lenalidomide had a significantly higher SPM incidence overall (P=0.011). Age is a risk factor with the highest SPM incidence observed in transplant non-eligible patients aged >74 years receiving lenalidomide maintenance. The 3-year cumulative incidence in this group was 17.3% (95% CI 8.2–26.4%), compared with 6.5% (95% CI 0.2–12.9%) in observation only patients (P=0.049). There was a low overall incidence of haematological SPM (0.5%). The higher SPM incidence in patients receiving lenalidomide maintenance therapy, especially in advanced age, warrants ongoing monitoring although the benefit on survival is likely to outweigh risk.

Direct Electron Detectors

Direct electron detectors have played a key role in the recent increase in the power of single-particle electron cryomicroscopy (cryoEM). In this chapter, we summarize the background to these recent developments, give a practical guide to their optimal use, and discuss future directions.

Penalised logistic regression and dynamic prediction for discrete-time recurrent event data

We consider methods for the analysis of discrete-time recurrent event data, when interest is mainly in prediction. The Aalen additive model provides an extremely simple and effective method for the determination of covariate effects for this type of data, especially in the presence of time-varying effects and time varying covariates, including dynamic summaries of prior event history. The method is weakened for predictive purposes by the presence of negative estimates. The obvious alternative of a standard logistic regression analysis at each time point can have problems of stability when event frequency is low and maximum likelihood estimation is used. The Firth penalised likelihood approach is stable but in removing bias in regression coefficients it introduces bias into predicted event probabilities. We propose an alterative modified penalised likelihood, intermediate between Firth and no penalty, as a pragmatic compromise between stability and bias. Illustration on two data sets is provided.

Thon rings from amorphous ice and implications of beam-induced Brownian motion in single particle electron cryo-microscopy

We have recorded dose-fractionated electron cryo-microscope images of thin films of pure flash-frozen amorphous ice and pre-irradiated amorphous carbon on a Falcon II direct electron detector using 300 keV electrons. We observe Thon rings [1] in both the power spectrum of the summed frames and the sum of power spectra from the individual frames. The Thon rings from amorphous carbon images are always more visible in the power spectrum of the summed frames whereas those of amorphous ice are more visible in the sum of power spectra from the individual frames. This difference indicates that while pre-irradiated carbon behaves like a solid during the exposure, amorphous ice behaves like a fluid with the individual water molecules undergoing beam-induced motion. Using the measured variation in the power spectra amplitude with number of electrons per image we deduce that water molecules are randomly displaced by a mean squared distance of ∼1.1 Å² for every incident 300 keV e⁻/Ų. The induced motion leads to an optimal exposure with 300 keV electrons of 4.0 e⁻/Ų per image with which to observe Thon rings centred around the strong 3.7 Å scattering peak from amorphous ice. The beam-induced movement of the water molecules generates pseudo-Brownian motion of embedded macromolecules. The resulting blurring of single particle images contributes an additional term, on top of that from radiation damage, to the minimum achievable B-factor for macromolecular structure determination.

•

Thon rings can be seen from amorphous ice.

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Radiation damage to amorphous ice randomly displaces water molecules.

•

Each incident 300 keV e⁻/Ų displaces water molecules on average by ∼1 Å.

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Macromolecules embedded in amorphous ice undergo beam induced Brownian motion.

Novel integrative genomic tool for interrogating lithium response in bipolar disorder

We developed a novel integrative genomic tool called GRANITE (Genetic Regulatory Analysis of Networks Investigational Tool Environment) that can effectively analyze large complex data sets to generate interactive networks. GRANITE is an open-source tool and invaluable resource for a variety of genomic fields. Although our analysis is confined to static expression data, GRANITE has the capability of evaluating time-course data and generating interactive networks that may shed light on acute versus chronic treatment, as well as evaluating dose response and providing insight into mechanisms that underlie therapeutic versus sub-therapeutic doses or toxic doses. As a proof-of-concept study, we investigated lithium (Li) response in bipolar disorder (BD). BD is a severe mood disorder marked by cycles of mania and depression. Li is one of the most commonly prescribed and decidedly effective treatments for many patients (responders), although its mode of action is not yet fully understood, nor is it effective in every patient (non-responders). In an in vitro study, we compared vehicle versus chronic Li treatment in patient-derived lymphoblastoid cells (LCLs) (derived from either responders or non-responders) using both microRNA (miRNA) and messenger RNA gene expression profiling. We present both Li responder and non-responder network visualizations created by our GRANITE analysis in BD. We identified by network visualization that the Let-7 family is consistently downregulated by Li in both groups where this miRNA family has been implicated in neurodegeneration, cell survival and synaptic development. We discuss the potential of this analysis for investigating treatment response and even providing clinicians with a tool for predicting treatment response in their patients, as well as for providing the industry with a tool for identifying network nodes as targets for novel drug discovery.

Comparison of optimal performance at 300keV of three direct electron detectors for use in low dose electron microscopy

Low dose electron imaging applications such as electron cryo-microscopy are now benefitting from the improved performance and flexibility of recently introduced electron imaging detectors in which electrons are directly incident on backthinned CMOS sensors. There are currently three commercially available detectors of this type: the Direct Electron DE-20, the FEI Falcon II and the Gatan K2 Summit. These have different characteristics and so it is important to compare their imaging properties carefully with a view to optimise how each is used. Results at 300 keV for both the modulation transfer function (MTF) and the detective quantum efficiency (DQE) are presented. Of these, the DQE is the most important in the study of radiation sensitive samples where detector performance is crucial. We find that all three detectors have a better DQE than film. The K2 Summit has the best DQE at low spatial frequencies but with increasing spatial frequency its DQE falls below that of the Falcon II.

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Three direct electron detectors offer better DQE than film at 300 keV.

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Recorded 300 keV electron events on the detectors have very similar Landau distributions.

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The Gatan K2 Summit detector has the highest DQE at low spatial frequency.

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The FEI Falcon II detector has the highest DQE beyond one half the Nyquist frequency.

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The Direct Electron DE-20 detector has the fastest data acquisition rate.

Molecular analysis of intragenic recombination at the tryptophan synthetase locus in Neurospora crassa

Fifteen different classically generated and mapped mutations at the tryptophan synthetase locus in Neurospora crassa have been characterized to the level of the primary sequence of the gene. This sequence analysis has demonstrated that intragenic recombination is accurate to order mutations within one open reading frame. While classic genetic analysis correctly ordered the mutations, the position of mutations characterized by gene sequence analysis was more accurate. A leaky mutation was found to have a wild-type primary sequence. The presence of unique polymorphisms in the primary sequence of the trp-3 gene from strain 861 confirms that it has a unique history relative to the other strains studied. Most strains that were previously shown to be immunologically nonreactive with antibody preparations raised against tryptophan synthetase protein were shown to have nonsense mutations. This work defines 14 alleles of the N. crassa trp-3 gene.

CD4(+) T-cell inhibitory ligands: a tool for characterizing dysfunctional CD4(+) T cells during chronic infection

Activation of CD4(+) T cells helps to establish and maintain immune responses. During infection with lymphocytic choriomeningitis virus (LCMV) clone 13, the CD4(+) T-cell responses are lost. In this study, we were interested in the nature of the CD4(+) T-cell responses following infection with LCMV clone 13. To pursue this question, we infected C57BL/6 mice with LCMV clone 13. We used a GP66-80 MHC Class II tetramer to determine whether the CD4(+) T cells were present following infection with LCMV clone 13. We determined that the cells were present and antigen specific, but not functional. We attributed their dysfunction to the presence of CD4(+) T-cell inhibitory ligands. We further stained for the presence of CD4(+) T-cell inhibitory ligands. We found that the during chronic infection the number of CD4(+) T cells expressing programmed death-1 and CD160 were greater over the time-course study than the other CD4(+) T-cell inhibitory ligands. These data show that using CD4(+) T-cell inhibitory ligands as a reagent for characterization can help in understanding the complex immune responses associated with persistent infections.

Note: multi-confocal fluorescence correlation spectroscopy in living cells using a complementary metal oxide semiconductor-single photon avalanche diode array

Living cells are heterogeneous and rapidly changing biological samples. It is thus desirable to measure molecular concentration and dynamics in many locations at the same time. In this note, we present a multi-confocal setup capable of performing simultaneous fluorescence correlation spectroscopy measurements, by focusing the spots with a spatial light modulator and acquiring data with a monolithic 32 × 32 single-photon avalanche photodiode array. A post-processing method is proposed to correct cross-talk effects between neighboring spots. We demonstrate the applicability of our system by simultaneously measuring the diffusion of free enhanced Green Fluorescent Protein (eGFP) molecules at nine different points in living cells.

Memory T cells in latent Mycobacterium tuberculosis infection are directed against three antigenic islands and largely contained in a CXCR3+CCR6+ Th1 subset

An understanding of the immunological footprint of Mycobacterium tuberculosis (MTB) CD4 T cell recognition is still incomplete. Here we report that human Th1 cells specific for MTB are largely contained in a CXCR3⁺CCR6⁺ memory subset and highly focused on three broadly immunodominant antigenic islands, all related to bacterial secretion systems. Our results refute the notion that secreted antigens act as a decoy, since both secreted proteins and proteins comprising the secretion system itself are targeted by a fully functional T cell response. In addition, several novel T cell antigens were identified which can be of potential diagnostic use, or as vaccine antigens. These results underline the power of a truly unbiased, genome-wide, analysis of CD4 MTB recognition based on the combined use of epitope predictions, high throughput ELISPOT, and T cell libraries using PBMCs from individuals latently infected with MTB.

Mycobacterium tuberculosis is one of the most life-threatening pathogens of all time, having infected one-third of the present human population. There is an urgent need for both novel vaccines and diagnostic strategies. Here, we were able to identify the targets most dominantly recognized by latently infected individual that successfully contain infection. These targets are contained in three broadly genomic antigenic islands, all related to bacterial secretion systems and composed by several distinct ORFs. Thus, our results suggest that vaccination with one or few defined antigens will fail to replicate the response associated with natural immunity. Our analysis also pinpoints that the Th1 cells dominating the response are associated with novel and well-defined phenotypic markers, suggesting that the response is molded by unique MTB associated factors. This study demonstrates further that the approach combining peptide binding predictions with modern high throughput techniques is generally applicable to the study of immunity to other complex pathogens. Together, our data provide a new angle in the worldwide fight against M. tuberculosis and could be used for diagnostic or vaccine developments.

Anoxia-induced release of colloid- and nanoparticle-bound phosphorus in grassland soils

Particle-facilitated transport is a key mechanism of phosphorus (P) loss in agroecosystems. We assessed contributions of colloid- and nanoparticle-bound P (nPP; 1-415 nm) to total P released from grassland soils receiving biannual poultry litter applications since 1995. In laboratory incubations, soils were subjected to 7 days of anoxic conditions or equilibrated at pH 6 and 8 under oxic conditions and then the extract was size fractionated by differential centrifugation/ultrafiltration for analysis of P, Al, Fe, Si, Ti, and Ca. Selected samples were characterized by transmission electron microscopy-energy dispersive spectroscopy (TEM-EDS) and field flow fractionation (FFF-ICP-MS). Particles released were present as nanoaggregates with a mean diameter of 200-250 nm, composed of ~50-nm aluminosilicate flakes studded with Fe and Ti-rich clusters (<10 nm) that contained most of the P detected by EDS. Anoxic incubation of stimulated nPP release with seasonally saturated soils released more nPP and Fe(2+)(aq) than well-drained soils; whereas, nonreductive particle dispersion, accomplished by raising the pH, yielded no increase in nPP release. This suggests Fe acts as a cementing agent, binding to the bulk soil P-bearing colloids that can be released during reducing conditions. Furthermore, it suggests prior periodic exposure to anoxic conditions increases susceptibility to redox-induced P mobilization.