Examination of the Feasibility of Transferred Electron Devices for Optoelectronic Interaction: Theory and Experiment

The engineering feasibility of Transferred Electron Devices (TEDs), configured as modulators, was explored. Vertical and planar implementations of the same device were pursued concurrently. An existing "side-wall bonding pad" vertical device was replaced by a revised structure, incorporating dual anode contacts and dielectric isolation. Natural self-resonant frequency inhibition with device capacitance was assessed for both of these vertical devices. The reappraisal was shown to provide benefits of reduced capacitance, reduced current capacity and greater symmetry of the electric field distribution in the active region. Modelling of the optical confinement attributes of rib waveguides for device designs was performed using the FWAVE III and LWAVE application programs. Confinement afforded by the rib-substrate interface and 33% AlGaAs layers, in vertical and planar devices respectively, was determined for multi-moded propagation. Efficiently confmed propagation at infrared wavelengths was observed. Theoretical predictions for modulation depths were calculated for rib waveguide devices. The modulation potential of mechanisms such as Pockels effect, Franz-Keldysh electro-absorption and free carrier influences were analysed. These evaluations were made employing very idealised conditions, leading to consistent over-estimates of modulation indices. The requirements for deep modulation were identified in the context of the engineering designs of real devices. The prospect for voltage-controlled frequency modulation in planar devices, required the development of analytical theory for tapered (graded area) devices. The functional variation of the pre threshold electric field distribution was obtained. This permitted the derivation of a predictive current-voltage function for a general transferred electron device with defined semiconductor and physical parameters. The time constant governing growth / decay of nucleated disturbances in tapered devices was sought, verifying the possibility of transit mode operation, A fully calculable function, encapsulating the influences of inter-valley transfer and dipole formation, was developed and quoted. Both vertical and planar devices were fabricated and assessed experimentally. The theoretical current voltage function was used as a fulcrum for the analysis of the influence of the cathode boundary conditions in planar devices. The behaviour of graded and non-graded elements was modified by varying the annealing conditions in a standard contact metal recipe. A mechanism was conjectured to explain these variations in the context of the Kroemer hypothesis. The resulting empirical functions were used to assess the inhibition of injected electrons at the cathode. Endfire analysis was performed on waveguide devices, with electrical biassing applied in-situ. In response to theoretical thermal modelling, in conjunction with practical observations of real devices, a circular mesa form of waveguide device was proposed and fabricated. Estimates of maximum permissible pulse width were made, assisted by Laplace transform analysis of a thermal - electrical analogue circuit. A simple formula for rib-substrate thermal resistance was derived for this analysis. Permissible pulse widths were demonstrated to be incompatible with the notion of a viable modulator operating near to CW

Species and genus level resolution analysis of gut microbiota in Clostridium difficile patients following fecal microbiota transplantation

BACKGROUND: Clostridium difficile is an opportunistic human intestinal pathogen, and C. difficile infection (CDI) is one of the main causes of antibiotic-induced diarrhea and colitis. One successful approach to combat CDI, particularly recurrent form of CDI, is through transplantation of fecal microbiota from a healthy donor to the infected patient. In this study we investigated the distal gut microbial communities of three CDI patients before and after fecal microbiota transplantation, and we compared these communities to the composition of the donor’s fecal microbiota. We utilized phylogenetic Microbiota Array, high-throughput Illumina sequencing, and fluorescent in situ hybridization to profile microbiota composition down to the genus and species level resolution. RESULTS: The original patients’ microbiota had low diversity, was dominated by members of Gammaproteobacteria and Bacilli, and had low numbers of Clostridia and Bacteroidia. At the genus level, fecal samples of CDI patients were rich in members of the Lactobacillus, Streptococcus, and Enterobacter genera. In comparison, the donor community was dominated by Clostridia and had significantly higher diversity and evenness. The patients’ distal gut communities were completely transformed within 3 days following fecal transplantation, and these communities remained stable in each patient for at least 4 months. Despite compositional differences among recipients’ pre-treatment gut microbiota, the transplanted gut communities were highly similar among recipients post-transplantation, were indistinguishable from that of the donor, and were rich in members of Blautia, Coprococcus, and Faecalibacterium. In each case, the gut microbiota restoration led to a complete patient recovery and symptom alleviation. CONCLUSION: We conclude that C. difficile infection can be successfully treated by fecal microbiota transplantation and that this leads to stable transformation of the distal gut microbial community from the one abundant in aerotolerant species to that dominated by members of the Clostridia

An investigation of the relation between the number of children and education in Italy

In this paper we have investigated the impact of the level of education on the number of children in Italy. We have selected 1,490 families from the 1997- 2005 Longitudinal Investigation on Italian Families (ILFI) dataset. Our dependent variable is represented by the number of children ever born to each respondent (and to his partner). Since the number of children ever born (CEB) is a count variable, we have implemented three empirical models: Poisson, Zero-Truncated Poisson and an Instrumental Variable Poisson, where grandparents’ education is exerted as an instrument of parents’ education. In particular, we have considered two stages for each model: in the first stage, we have estimated the impact of female’s education on her number of children, and in the second one, we have used also partner’s education to identify the previous effect. From the empirical results, we may observe a significant negative effect of the level of education on the number of children

Genomic profile of advanced breast cancer in circulating tumour DNA.

The genomics of advanced breast cancer (ABC) has been described through tumour tissue biopsy sequencing, although these approaches are limited by geographical and temporal heterogeneity. Here we use plasma circulating tumour DNA sequencing to interrogate the genomic profile of ABC in 800 patients in the plasmaMATCH trial. We demonstrate diverse subclonal resistance mutations, including enrichment of HER2 mutations in HER2 positive disease, co-occurring ESR1 and MAP kinase pathway mutations in HR + HER2- disease that associate with poor overall survival (p = 0.0092), and multiple PIK3CA mutations in HR + disease that associate with short progression free survival on fulvestrant (p = 0.0036). The fraction of cancer with a mutation, the clonal dominance of a mutation, varied between genes, and within hotspot mutations of ESR1 and PIK3CA. In ER-positive breast cancer subclonal mutations were enriched in an APOBEC mutational signature, with second hit PIK3CA mutations acquired subclonally and at sites characteristic of APOBEC mutagenesis. This study utilises circulating tumour DNA analysis in a large clinical trial to demonstrate the subclonal diversification of pre-treated advanced breast cancer, identifying distinct mutational processes in advanced ER-positive breast cancer, and novel therapeutic opportunities

Circulating tumour DNA analysis to direct therapy in advanced breast cancer (plasmaMATCH): a multicentre, multicohort, phase 2a, platform trial.

BACKGROUND: Circulating tumour DNA (ctDNA) testing might provide a current assessment of the genomic profile of advanced cancer, without the need to repeat tumour biopsy. We aimed to assess the accuracy of ctDNA testing in advanced breast cancer and the ability of ctDNA testing to select patients for mutation-directed therapy. METHODS: We did an open-label, multicohort, phase 2a, platform trial of ctDNA testing in 18 UK hospitals. Participants were women (aged ≥18 years) with histologically confirmed advanced breast cancer and an Eastern Cooperative Oncology Group performance status 0-2. Patients had completed at least one previous line of treatment for advanced breast cancer or relapsed within 12 months of neoadjuvant or adjuvant chemotherapy. Patients were recruited into four parallel treatment cohorts matched to mutations identified in ctDNA: cohort A comprised patients with ESR1 mutations (treated with intramuscular extended-dose fulvestrant 500 mg); cohort B comprised patients with HER2 mutations (treated with oral neratinib 240 mg, and if oestrogen receptor-positive with intramuscular standard-dose fulvestrant); cohort C comprised patients with AKT1 mutations and oestrogen receptor-positive cancer (treated with oral capivasertib 400 mg plus intramuscular standard-dose fulvestrant); and cohort D comprised patients with AKT1 mutations and oestrogen receptor-negative cancer or PTEN mutation (treated with oral capivasertib 480 mg). Each cohort had a primary endpoint of confirmed objective response rate. For cohort A, 13 or more responses among 78 evaluable patients were required to infer activity and three or more among 16 were required for cohorts B, C, and D. Recruitment to all cohorts is complete and long-term follow-up is ongoing. This trial is registered with ClinicalTrials.gov, NCT03182634; the European Clinical Trials database, EudraCT2015-003735-36; and the ISRCTN registry, ISRCTN16945804. FINDINGS: Between Dec 21, 2016, and April 26, 2019, 1051 patients registered for the study, with ctDNA results available for 1034 patients. Agreement between ctDNA digital PCR and targeted sequencing was 96-99% (n=800, kappa 0·89-0·93). Sensitivity of digital PCR ctDNA testing for mutations identified in tissue sequencing was 93% (95% CI 83-98) overall and 98% (87-100) with contemporaneous biopsies. In all cohorts, combined median follow-up was 14·4 months (IQR 7·0-23·7). Cohorts B and C met or exceeded the target number of responses, with five (25% [95% CI 9-49]) of 20 patients in cohort B and four (22% [6-48]) of 18 patients in cohort C having a response. Cohorts A and D did not reach the target number of responses, with six (8% [95% CI 3-17]) of 74 in cohort A and two (11% [1-33]) of 19 patients in cohort D having a response. The most common grade 3-4 adverse events were raised gamma-glutamyltransferase (13 [16%] of 80 patients; cohort A); diarrhoea (four [25%] of 20; cohort B); fatigue (four [22%] of 18; cohort C); and rash (five [26%] of 19; cohort D). 17 serious adverse reactions occurred in 11 patients, and there was one treatment-related death caused by grade 4 dyspnoea (in cohort C). INTERPRETATION: ctDNA testing offers accurate, rapid genotyping that enables the selection of mutation-directed therapies for patients with breast cancer, with sufficient clinical validity for adoption into routine clinical practice. Our results demonstrate clinically relevant activity of targeted therapies against rare HER2 and AKT1 mutations, confirming these mutations could be targetable for breast cancer treatment. FUNDING: Cancer Research UK, AstraZeneca, and Puma Biotechnology

Results of the c-TRAK TN trial: a clinical trial utilising ctDNA mutation tracking to detect molecular residual disease and trigger intervention in patients with moderate and high-risk early stage triple negative breast cancer

Background: Post-treatment detection of circulating tumour DNA (ctDNA) in early-stage triple negative breast cancer (TNBC) patients predicts high risk of relapse. c-TRAK-TN assessed the utility of prospective ctDNA surveillance in TNBC and the activity of pembrolizumab in patients with ctDNA detected (ctDNA+). Patients and methods: c-TRAK-TN, a multi-centre phase II trial, with integrated prospective ctDNA surveillance by digital PCR, enrolled patients with early-stage TNBC and residual disease following neoadjuvant chemotherapy, or, stage II/III with adjuvant chemotherapy. ctDNA surveillance comprised three monthly blood sampling to 12 months (18 months if samples were missed due to COVID), and ctDNA+ patients were randomised 2:1; intervention:observation. ctDNA results were blinded unless patients were allocated to intervention, when staging scans were done and those free of recurrence were offered pembrolizumab. A protocol amendment (16/09/2020) closed the observation group; all subsequent ctDNA+ patients were allocated to intervention. Co-primary endpoints were i) ctDNA detection rate ii) sustained ctDNA clearance rate on pembrolizumab (NCT03145961). Results: 208 patients registered between 30/01/18 - 06/12/19, 185 had tumour sequenced, 171 (92·4%) had trackable mutations, and 161 entered ctDNA surveillance. Rate of ctDNA detection by 12 months was 27·3% (44/161,95%CI:20·6-34·9). Seven patients relapsed without prior ctDNA detection. 45 patients entered the therapeutic component (intervention n=31; observation n=14; 1 observation patient was re-allocated to intervention following protocol amendment). Of patients allocated intervention, 72% (23/32) had metastases on staging at time of ctDNA+, and 4 patients declined pembrolizumab. Of the five patients who commenced pembrolizumab, none achieved sustained ctDNA clearance. Conclusion: c-TRAK-TN is the first prospective study to assess whether ctDNA assays have clinical utility in guiding therapy in TNBC. Patients had a high rate of metastatic disease on ctDNA detection. Findings have implications for future trial design, emphasising the importance of commencing ctDNA testing early, with more sensitive and/or frequent ctDNA testing regimes

In situ multiple sulfur isotope analysis by SIMS of pyrite, chalcopyrite, pyrrhotite, and pentlandite to refine magmatic ore genetic models

With growing interest in the application of in situ multiple sulfur isotope analysis to a variety of mineral systems, we report here the development of a suite of sulfur isotope standards for distribution relevant to magmatic, magmatic-hydrothermal, and hydrothermal ore systems. These materials include Sierra pyrite (FeS2), Nifty-b chalcopyrite (CuFeS2), Alexo pyrrhotite (Fe(1 −x)S), and VMSO pentlandite ((Fe,Ni)9S8) that have been chemically characterized by electron microprobe analysis, isotopically characterized for δ33S, δ34S, and δ36S by fluorination gas-source mass spectrometry, and tested for homogeneity at the micro-scale by secondary ion mass spectrometry. Beam-sample interaction as a function of crystallographic orientation is determined to have no effect on δ34S and Δ33S isotopic measurements of pentlandite. These new findings provided the basis for a case study on the genesis of the Long-Victor nickel-sulfide deposit located in the world class Kambalda nickel camp in the southern Kalgoorlie Terrane of Western Australia. Results demonstrate that precise multiple sulfur isotope analyses from magmatic pentlandite, pyrrhotite and chalcopyrite can better constrain genetic models related to ore-forming processes. Data indicate that pentlandite, pyrrhotite and chalcopyrite are in isotopic equilibrium and display similar Δ33S values + 0.2‰.This isotopic equilibrium unequivocally fingerprints the isotopic signature of the magmatic assemblage. The three sulfide phases show slightly variable δ34S values (δ34Schalcopyrite = 2.9 ± 0.3‰, δ34Spentlandite = 3.1 ± 0.2‰, and δ34Spyrrhotite = 3.9 ± 0.5‰), which are indicative of natural fractionation. Careful in situ multiple sulfur isotope analysis of multiple sulfide phases is able to capture the subtle isotopic variability of the magmatic sulfide assemblage, which may help resolve the nature of the ore-forming process. Hence, this SIMS-based approach discriminates the magmatic sulfur isotope signature from that recorded in metamorphic- and alteration-related sulfides, which may not be resolved during bulk rock fluorination analysis. The results indicate that, unlike the giant dunite-hosted komatiite systems that thermo-mechanically assimilated volcanogenic massive sulfides proximal to vents and display negative Δ33S values, the Kambalda ores formed in relatively distal environments assimilating abyssal sulfidic shales

Comparison of circulating tumor DNA assays for Molecular Residual Disease detection in early-stage triple negative breast cancer

Purpose: Detection of circulating tumor DNA (ctDNA) in patients who have completed treatment for early-stage breast cancer is associated with a high risk of relapse, yet the optimal assay for ctDNA detection is unknown. Experimental design: The cTRAK-TN clinical trial prospectively used tumor informed digital PCR (dPCR) assays for ctDNA molecular residual disease (MRD) detection in early-stage triple negative breast cancer. We compared tumor informed dPCR assays with tumor informed personalized multi-mutation sequencing assays in 141 patients from cTRAK-TN. Results: MRD was first detected by personalized sequencing in 47.9% of patients, 0% first detected by dPCR, and 52.1% with both assays simultaneously (p<0.001, Fisher’s exact test). The median lead time from ctDNA detection to relapse was 6.1 months with personalized sequencing and 3.9 months with dPCR (p=0.004, mixed effects Cox model). Detection of MRD at the first timepoint was associated with a shorter time to relapse compared with detection at subsequent timepoints (median lead time 4.2 vs 7.1 months, p=0.02). Conclusions: Personalized multi-mutation sequencing assays have potential clinically important improvements in clinical outcome in the early detection of MRD

Olaparib and celarasertib (AZD6738) in patients with triple negative advanced breast cancer: results from Cohort E of the plasmaMATCH trial (CRUK/15/010)

Background Approximately 10-15% of triple negative breast cancers (TNBCs) have deleterious mutations in BRCA1 and BRCA2 and may benefit from polyadenosine 5’diphosphoribose polymerase (PARP) inhibitor treatment. PARP inhibitors may also increase exogenous replication stress and thereby increase sensitivity to inhibitors of ataxia telangiectasia and Rad3-related protein (ATR). This phase II study examined the activity of the combination of PARP inhibitor, Olaparib, and ATR inhibitor, celerasertib (AZD6738), in patients with advanced TNBC. Patients and methods Patients with TNBC on most recent biopsy who had received 1 or 2 lines of chemotherapy for advanced disease or had relapsed within 12 months of (neo)adjuvant chemotherapy were eligible. Treatment was olaparib 300mg twice a day continuously and celarasertib 160mg on days 1–7 on a 28 day cycle until disease progression. The primary endpoint was confirmed objective response rate (ORR). Tissue and plasma biomarker analyses were pre-planned to identify predictors of response. Results 70 evaluable patients were enrolled. Germline BRCA1/2 mutations were present in 10 (14%) patients and 3 (4%) patients had somatic BRCA mutations. The confirmed ORR was 12/70; 17.1% (95%CI: 10.4-25.5). Responses were observed in patients without germline or somatic BRCA1/2 mutations, including patients with mutations in other homologous recombination repair genes and tumours with functional homologous recombination deficiency by RAD51 foci. Conclusion The response rate to olaparib and ceralasertib did not meet pre-specified criteria for activity in the overall evaluable population, but responses were observed in patients who would not be expected to respond to Olaparib monotherapy

HER2-enriched subtype and novel molecular subgroups drive aromatase inhibitor resistance and an increased risk of relapse in early ER+/HER2+ breast cancer

BACKGROUND: Oestrogen receptor positive/ human epidermal growth factor receptor positive (ER+/HER2+) breast cancers (BCs) are less responsive to endocrine therapy than ER+/HER2- tumours. Mechanisms underpinning the differential behaviour of ER+HER2+ tumours are poorly characterised. Our aim was to identify biomarkers of response to 2 weeks’ presurgical AI treatment in ER+/HER2+ BCs. METHODS: All available ER+/HER2+ BC baseline tumours (n=342) in the POETIC trial were gene expression profiled using BC360™ (NanoString) covering intrinsic subtypes and 46 key biological signatures. Early response to AI was assessed by changes in Ki67 expression and residual Ki67 at 2 weeks (Ki672wk). Time-To-Recurrence (TTR) was estimated using Kaplan-Meier methods and Cox models adjusted for standard clinicopathological variables. New molecular subgroups (MS) were identified using consensus clustering. FINDINGS: HER2-enriched (HER2-E) subtype BCs (44.7% of the total) showed poorer Ki67 response and higher Ki672wk (p<0.0001) than non-HER2-E BCs. High expression of ERBB2 expression, homologous recombination deficiency (HRD) and TP53 mutational score were associated with poor response and immune-related signatures with High Ki672wk. Five new MS that were associated with differential response to AI were identified. HER2-E had significantly poorer TTR compared to Luminal BCs (HR 2.55, 95% CI 1.14–5.69; p=0.0222). The new MS were independent predictors of TTR, adding significant value beyond intrinsic subtypes. INTERPRETATION: Our results show HER2-E as a standardised biomarker associated with poor response to AI and worse outcome in ER+/HER2+. HRD, TP53 mutational score and immune-tumour tolerance are predictive biomarkers for poor response to AI. Lastly, novel MS identify additional non-HER2-E tumours not responding to AI with an increased risk of relapse