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1.
Phys Rev Lett ; 129(20): 207201, 2022 Nov 11.
Article in English | MEDLINE | ID: mdl-36461990

ABSTRACT

Spinons are well known as the elementary excitations of one-dimensional antiferromagnetic chains, but means to realize spinons in higher dimensions is the subject of intense research. Here, we use resonant x-ray scattering to study the layered trimer iridate Ba_{4}Ir_{3}O_{10}, which shows no magnetic order down to 0.2 K. An emergent one-dimensional spinon continuum is observed that can be well described by XXZ spin-1/2 chains with a magnetic exchange of ∼55 meV and a small Ising-like anisotropy. With 2% isovalent Sr doping, magnetic order appears below T_{N}=130 K along with sharper excitations in (Ba_{1-x}Sr_{x})_{4}Ir_{3}O_{10}. Combining our data with exact diagonalization calculations, we find that the frustrated intratrimer interactions effectively reduce the system into decoupled spin chains, the subtle balance of which can be easily tipped by perturbations such as chemical doping. Our results put Ba_{4}Ir_{3}O_{10} between the one-dimensional chain and two-dimensional quantum spin liquid scenarios, illustrating a new way to suppress magnetic order and realize fractional spinons.

2.
BMC Cancer ; 22(1): 276, 2022 Mar 15.
Article in English | MEDLINE | ID: mdl-35291965

ABSTRACT

BACKGROUND: AGITG DOCTOR was a randomised phase 2 trial of pre-operative cisplatin, 5 fluorouracil (CF) followed by docetaxel (D) with or without radiotherapy (RT) based on poor early response to CF, detected via PET, for resectable oesophageal adenocarcinoma. This study describes PROs over 2 years. METHODS: Participants (N = 116) completed the EORTC QLQ-C30 and oesophageal module (QLQ-OES18) before chemotherapy (baseline), before surgery, six and 12 weeks post-surgery and three-monthly until 2 years. We plotted PROs over time and calculated the percentage of participants per treatment group whose post-surgery score was within 10 points (threshold for clinically relevant change) of their baseline score, for each PRO scale. We examined the relationship between Grade 3+ adverse events (AEs) and PROs. This analysis included four groups: CF responders, non-responders randomised to DCF, non-responders randomised to DCF + RT, and "others" who were not randomised. RESULTS: Global QOL was clinically similar between groups from 6 weeks post-surgery. All groups had poorer functional and higher symptom scores during active treatment and shortly after surgery, particularly the DCF and DCF + RT groups. DCF + RT reported a clinically significant difference (-13points) in mean overall health/QOL between baseline and pre-surgery. Similar proportions of patients across groups scored +/- 10 points of baseline scores within 2 years for most PRO domains. Instance of grade 3+ AEs were not related to PROs at baseline or 2 years. CONCLUSIONS: By 2 years, similar proportions of patients scored within 10 points of baseline for most PRO domains, with the exception of pain and insomnia for the DCF + RT group. Non-responders randomised to DCF or DCF + RT experienced additional short-term burden compared to CF responders, reflecting the longer duration of neoadjuvant treatment and additional toxicity. This should be weighed against clinical benefits reported in AGITG DOCTOR. This data will inform communication of the trajectory of treatment options for early CF non-responders. TRIAL REGISTRATION: Australia New Zealand Clinical Trials Registry (ANZCTR), ACTRN12609000665235 . Registered 31 July 2009.


Subject(s)
Adenocarcinoma , Neoadjuvant Therapy , Adenocarcinoma/drug therapy , Antineoplastic Combined Chemotherapy Protocols/adverse effects , Humans , Neoadjuvant Therapy/methods , Patient Reported Outcome Measures , Quality of Life
3.
Phys Rev Lett ; 126(17): 177601, 2021 Apr 30.
Article in English | MEDLINE | ID: mdl-33988428

ABSTRACT

Revealing the predominant driving force behind symmetry breaking in correlated materials is sometimes a formidable task due to the intertwined nature of different degrees of freedom. This is the case for La_{2-x}Sr_{x}NiO_{4+δ}, in which coupled incommensurate charge and spin stripes form at low temperatures. Here, we use resonant x-ray photon correlation spectroscopy to study the temporal stability and domain memory of the charge and spin stripes in La_{2-x}Sr_{x}NiO_{4+δ}. Although spin stripes are more spatially correlated, charge stripes maintain a better temporal stability against temperature change. More intriguingly, charge order shows robust domain memory with thermal cycling up to 250 K, far above the ordering temperature. These results demonstrate the pinning of charge stripes to the lattice and that charge condensation is the predominant factor in the formation of stripe orders in nickelates.

4.
Ann Oncol ; 31(2): 236-245, 2020 02.
Article in English | MEDLINE | ID: mdl-31959340

ABSTRACT

BACKGROUND: Patients with oesophageal/gastro-oesophageal junction adenocarcinoma (EAC) not showing early metabolic response (EMR) to chemotherapy have poorer survival and histological response rates <5%. We investigated whether tailoring neoadjuvant therapy can improve outcomes in these patients. PATIENTS AND METHODS: Patients with resectable EAC were enrolled and randomised into two single-arm, multicentre phase II trials. After induction cisplatin and 5-fluorouracil (CF), all were assessed by day 15 positron emission tomography (PET). Patients with an EMR [maximum standardised uptake values (SUVmax) ≥35% reduction from baseline to day 15 PET] received a second CF cycle then oesophagectomy. Non-responders were randomised 1 : 1 to two cycles of CF and docetaxel (DCF, n = 31) or DCF + 45 Gy radiotherapy (DCFRT, n = 35) then oesophagectomy. The primary end point was major histological response (<10% residual tumour) in the oesophagectomy specimen; secondary end points were overall survival (OS), progression-free survival (PFS), and locoregional recurrence (LR). RESULTS: Of 124 patients recruited, major histological response was achieved in 3/45 (7%) with EMR, 6/30 (20%) DCF, and 22/35 (63%) DCFRT patients. Grade 3/4 toxicities occurred in 12/45 (27%) EMR (CF), 13/31 (42%) DCF, and 25/35 (71%) DCFRT patients. No treatment-related deaths occurred. LR by 3 years was seen in 5/45 (11%) EMR, 10/31 (32%) DCF, and 4/35 (11%) DCFRT patients. PFS [95% confidence interval (CI)] at 36 months was 47% (31% to 61%) for EMR, 29% (15% to 45%) for DCF, and 46% (29% to 61%) for DCFRT patients. OS (95% CI) at 60 months was 53% (37% to 67%) for EMR, 31% (16% to 48%) for DCF, and 46% (29% to 61%) for DCFRT patients. CONCLUSIONS: EMR is associated with favourable OS, PFS, and low LR. For non-responders, the addition of docetaxel augmented histological response rates, but OS, PFS, and LR remained inferior compared with responders. DCFRT improved histological response and PFS/LR outcomes, matching the EMR group. Early PET/CT has the potential to tailor therapy for patients not showing an early response to chemotherapy. TRIAL REGISTRATION: ACTRN12609000665235.


Subject(s)
Adenocarcinoma , Esophageal Neoplasms , Adenocarcinoma/drug therapy , Adenocarcinoma/radiotherapy , Antineoplastic Combined Chemotherapy Protocols/therapeutic use , Cisplatin/therapeutic use , Docetaxel/therapeutic use , Esophageal Neoplasms/drug therapy , Fluorouracil/therapeutic use , Humans , Neoplasm Recurrence, Local , Positron Emission Tomography Computed Tomography , Treatment Outcome
5.
Phys Rev Lett ; 125(9): 097002, 2020 Aug 28.
Article in English | MEDLINE | ID: mdl-32915627

ABSTRACT

Charge density wave (CDW) correlations are prevalent in all copper-oxide superconductors. While CDWs in conventional metals are driven by coupling between lattice vibrations and electrons, the role of the electron-phonon coupling (EPC) in cuprate CDWs is strongly debated. Using Cu L_{3} edge resonant inelastic x-ray scattering, we study the CDW and Cu-O bond-stretching phonons in the stripe-ordered cuprate La_{1.8-x}Eu_{0.2}Sr_{x}CuO_{4+δ}. We investigate the interplay between charge order and EPC as a function of doping and temperature and find that the EPC is enhanced in a narrow momentum region around the CDW ordering vector. By detuning the incident photon energy from the absorption resonance, we extract an EPC matrix element at the CDW ordering vector of M≃0.36 eV, which decreases to M≃0.30 eV at high temperature in the absence of the CDW. Our results suggest a feedback mechanism in which the CDW enhances the EPC which, in turn, further stabilizes the CDW.

6.
Phys Rev Lett ; 124(20): 207005, 2020 May 22.
Article in English | MEDLINE | ID: mdl-32501068

ABSTRACT

The discovery of charge-density-wave-related effects in the resonant inelastic x-ray scattering spectra of cuprates holds the tantalizing promise of clarifying the interactions that stabilize the electronic order. Here, we report a comprehensive resonant inelastic x-ray scattering study of La_{2-x}Sr_{x}CuO_{4} finding that charge-density wave effects persist up to a remarkably high doping level of x=0.21 before disappearing at x=0.25. The inelastic excitation spectra remain essentially unchanged with doping despite crossing a topological transition in the Fermi surface. This indicates that the spectra contain little or no direct coupling to electronic excitations near the Fermi surface, rather they are dominated by the resonant cross section for phonons and charge-density-wave-induced phonon softening. We interpret our results in terms of a charge-density wave that is generated by strong correlations and a phonon response that is driven by the charge-density-wave-induced modification of the lattice.

7.
Dis Esophagus ; 33(6)2020 Jun 15.
Article in English | MEDLINE | ID: mdl-31676907

ABSTRACT

BACKGROUND: Several studies have reported that neutrophil-lymphocyte ratio (NLR) can predict survival in esophageal and gastroesophageal junction adenocarcinoma, as it reflects systemic inflammation. Hence, we aimed to determine whether baseline NLR holds prognostic value for esophageal adenocarcinoma patients treated with neoadjuvant chemotherapy (nCT) followed by surgery. METHODS: We studied the data of 139 patients that received nCT before undergoing esophagectomy with curative intent, all identified from a prospectively maintained database (1998-2016). Pretreatment hematology reports were used to calculate the baseline NLR. A receiver operating characteristic curve (ROC-curve) was plotted to determine an optimal cutoff value. NLR quartiles were used to display possible differences between groups in relation to overall survival (OS) and disease-free survival (DFS) using the method of Kaplan-Meier. Cox regression analysis was performed to assess the prognostic value of NLR. RESULTS: The median OS and DFS times were 46 months (interquartile range [IQR]: 19-166) and 30 months (IQR: 13-166], respectively, for the entire cohort. The ROC-curve showed that NLR has no discriminating power for survival status (area under the curve = 0.462) and therefore no optimal cutoff value could be determined. There were no statistically significant differences in median OS times for NLR quartiles: 65 (Q1), 32 (Q2), 45 (Q3), and 46 months (Q4) (P = 0.926). Similarly, DFS showed no difference between quartile groups, with median survival times of 27 (Q1), 19 (Q2), 36 (Q3), and 20 months (Q4) (P = 0.973). Age, pN, pM, and resection margin were independent prognostic factors for both OS and DFS. On the contrary, NLR was not associated with OS or DFS in univariable and multivariable analyses. CONCLUSION: Baseline NLR holds no prognostic value for esophageal and gastroesophageal junction adenocarcinoma patients treated with nCT in this study, in contrast to other recently published papers. This result questions the validity of NLR as a reliable prognostic indicator and its clinical usefulness in these patients.


Subject(s)
Adenocarcinoma , Esophageal Neoplasms , Lymphocytes , Neutrophils , Adenocarcinoma/drug therapy , Esophageal Neoplasms/drug therapy , Humans , Neoadjuvant Therapy , Prognosis , Retrospective Studies
8.
Theor Popul Biol ; 122: 5-11, 2018 07.
Article in English | MEDLINE | ID: mdl-29432792

ABSTRACT

This article describes and compares methods for simulating the component counts of random logarithmic combinatorial structures such as permutations and mappings. We exploit the Feller coupling for simulating permutations to provide a very fast method for simulating logarithmic assemblies more generally. For logarithmic multisets and selections, this approach is replaced by an acceptance/rejection method based on a particular conditioning relationship that represents the distribution of the combinatorial structure as that of independent random variables conditioned on a weighted sum. We show how to improve its acceptance rate. We illustrate the method by estimating the probability that a random mapping has no repeated component sizes, and establish the asymptotic distribution of the difference between the number of components and the number of distinct component sizes for a very general class of logarithmic structures.


Subject(s)
Computer Simulation , Models, Statistical , Probability , Algorithms , Logistic Models , Poisson Distribution
9.
J Math Biol ; 77(3): 765-793, 2018 09.
Article in English | MEDLINE | ID: mdl-29671043

ABSTRACT

We consider the approximation of the equilibrium of a metapopulation model, in which a finite number of patches are randomly distributed over a bounded subset [Formula: see text] of Euclidean space. The approximation is good when a large number of patches contribute to the colonization pressure on any given unoccupied patch, and when the quality of the patches varies little over the length scale determined by the colonization radius. If this is the case, the equilibrium probability of a patch at z being occupied is shown to be close to [Formula: see text], the equilibrium occupation probability in Levins's model, at any point [Formula: see text] not too close to the boundary, if the local colonization pressure and extinction rates appropriate to z are assumed. The approximation is justified by giving explicit upper and lower bounds for the occupation probabilities, expressed in terms of the model parameters. Since the patches are distributed randomly, the occupation probabilities are also random, and we complement our bounds with explicit bounds on the probability that they are satisfied at all patches simultaneously.


Subject(s)
Models, Biological , Population Dynamics/statistics & numerical data , Animals , Linear Models , Mathematical Concepts , Probability , Spatio-Temporal Analysis
10.
HIV Med ; 17(1): 28-35, 2016 Jan.
Article in English | MEDLINE | ID: mdl-26200570

ABSTRACT

OBJECTIVES: The aim of the study was to identify differences in infant outcomes, virological efficacy, and preterm delivery (PTD) outcome between women exposed to lopinavir/ritonavir (LPV/r) and those exposed to atazanavir/ritonavir (ATV/r). METHODS: A retrospective case note review was carried out. The case notes of 493 women who conceived while on LPV/r or ATV/r or initiated LPV/r or ATV/r during pregnancy and who delivered between 1 September 2007 and 30 August 2012 were reviewed. Data collected included demographics, antiretroviral use, HIV markers, and pregnancy and infant outcomes. Infant outcomes, virological efficacies and PTD rates for LPV/r and ATV/r were compared. RESULTS: A total of 306 women received LPV/r (82 conceiving while on the drug and 224 commencing it post-conception) and 187 received ATV/r (96 conceiving while on the drug and 91 commencing it post-conception). Comparing the two protease inhibitors (PIs), viral suppression rates were similar and, in women starting antiretroviral therapy (ART) post-conception, the median times to first undetectable HIV viral load were not significantly different (P = 0.64). PTD rates did not differ by therapy overall (ATV/r, 13%; LPV/r, 14%) or when considering the timing of first exposure (conceiving on ART, P = 0.81; commencing ART in pregnancy, P = 0.08). Poor fetal outcomes were very uncommon. There were two transmissions, giving a mother-to-child transmission (MTCT) rate of 0.4% (95% confidence interval 0.05-1.5%). CONCLUSIONS: Both ART regimens were well tolerated and successful in preventing MTCT. No significant differences in tolerability or in pregnancy or infant outcomes were observed, which supports the provision of a choice of PI in pregnancy.


Subject(s)
Atazanavir Sulfate/administration & dosage , HIV Infections/drug therapy , HIV Protease Inhibitors/administration & dosage , Lopinavir/administration & dosage , Premature Birth/epidemiology , Ritonavir/administration & dosage , Viral Load/drug effects , Adolescent , Adult , Atazanavir Sulfate/pharmacology , Drug Combinations , Drug Therapy, Combination , Female , HIV Protease Inhibitors/pharmacology , Humans , Infant , Infant, Newborn , Lopinavir/pharmacology , Middle Aged , Pregnancy , Pregnancy Outcome/epidemiology , Premature Birth/etiology , Retrospective Studies , Ritonavir/pharmacology , Treatment Outcome , Young Adult
11.
Phys Rev Lett ; 117(16): 167001, 2016 Oct 14.
Article in English | MEDLINE | ID: mdl-27792368

ABSTRACT

The occurrence of charge-density-wave (CDW) order in underdoped cuprates is now well established, although the precise nature of the CDW and its relationship with superconductivity is not. Theoretical proposals include contrasting ideas such as that pairing may be driven by CDW fluctuations or that static CDWs may intertwine with a spatially modulated superconducting wave function. We test the dynamics of CDW order in La_{1.825}Ba_{0.125}CuO_{4} by using x-ray photon correlation spectroscopy at the CDW wave vector, detected resonantly at the Cu L_{3} edge. We find that the CDW domains are strikingly static, with no evidence of significant fluctuations up to 2 ¾ h. We discuss the implications of these results for some of the competing theories.

12.
Br J Surg ; 102(12): 1459-72, 2015 Nov.
Article in English | MEDLINE | ID: mdl-26350029

ABSTRACT

BACKGROUND: R0 resection rates (complete tumour removal with negative resection margins) in pancreatic cancer are 70-80 per cent when a 0-mm margin is used, declining to 15-24 per cent with a 1-mm margin. This review evaluated the R0 resection rates according to different margin definitions and techniques. METHODS: Three databases (MEDLINE from 1946, PubMed from 1946 and Embase from 1949) were searched to mid-October 2014. The search terms included 'pancreatectomy OR pancreaticoduodenectomy' and 'margin'. A meta-analysis was performed with studies in three groups: group 1, axial slicing technique (minimum 1-mm margin); group 2, other slicing techniques (minimum 1-mm margin); and group 3, studies with minimum 0-mm margin. RESULTS: The R0 rates were 29 (95 per cent c.i. 26 to 32) per cent in group 1 (8 studies; 882 patients) and 49 (47 to 52) per cent in group 2 (6 studies; 1568 patients). The combined R0 rate (groups 1 and 2) was 41 (40 to 43) per cent. The R0 rate in group 3 (7 studies; 1926 patients) with a 0-mm margin was 72 (70 to 74) per cent The survival hazard ratios (R1 resection/R0 resection) revealed a reduction in the risk of death of at least 22 per cent in group 1, 12 per cent in group 2 and 23 per cent in group 3 with an R0 compared with an R1 resection. Local recurrence occurred more frequently with an R1 resection in most studies. CONCLUSION: Margin clearance definitions affect R0 resection rates in pancreatic cancer surgery. This review collates individual studies providing an estimate of achievable R0 rates, creating a benchmark for future trials.


Subject(s)
Neoplasm Recurrence, Local/epidemiology , Pancreatectomy/methods , Pancreatic Neoplasms/surgery , Global Health , Humans , Incidence , Prognosis
13.
J Math Biol ; 71(3): 713-33, 2015 Sep.
Article in English | MEDLINE | ID: mdl-25266056

ABSTRACT

Density dependent Markov population processes with countably many types can often be well approximated over finite time intervals by the solution of the differential equations that describe their average drift, provided that the total population size is large. They also exhibit diffusive stochastic fluctuations on a smaller scale about this deterministic path. Here, it is shown that the individuals in such processes experience an almost deterministic environment. Small groups of individuals behave almost independently of one another, evolving as Markov jump processes, whose transition rates are prescribed functions of time. In the context of metapopulation models, we show that 'individuals' can represent either patches or the individuals that migrate among the patches; in host-parasite systems, they can represent both hosts and parasites.


Subject(s)
Models, Biological , Population Density , Animals , Computer Simulation , Host-Pathogen Interactions , Humans , Markov Chains , Mathematical Concepts , Population Dynamics , Stochastic Processes
14.
J Math Biol ; 71(6-7): 1481-504, 2015 Dec.
Article in English | MEDLINE | ID: mdl-25735440

ABSTRACT

In this paper, we study the relationship between certain stochastic and deterministic versions of Hanski's incidence function model and the spatially realistic Levins model. We show that the stochastic version can be well approximated in a certain sense by the deterministic version when the number of habitat patches is large, provided that the presence or absence of individuals in a given patch is influenced by a large number of other patches. Explicit bounds on the deviation between the stochastic and deterministic models are given.


Subject(s)
Ecosystem , Models, Biological , Animals , Markov Chains , Mathematical Concepts , Population Dynamics/statistics & numerical data , Stochastic Processes , Time Factors
15.
Pharmacogenomics J ; 14(3): 223-8, 2014 Jun.
Article in English | MEDLINE | ID: mdl-24018621

ABSTRACT

Using a derivation cohort (N=349), we developed the first warfarin dosing algorithm that includes recently discovered polymorphisms in VKORC1 and CYP2C9 associated with warfarin dose requirement in African Americans (AAs). We tested our novel algorithm in an independent cohort of 129 AAs and compared the dose prediction to the International Warfarin Pharmacogenetics Consortium (IWPC) dosing algorithms. Our algorithm explains more of the phenotypic variation (R(2)=0.27) than the IWPC pharmacogenomics (R(2)=0.15) or clinical (R(2)=0.16) algorithms. Among high-dose patients, our algorithm predicted a higher proportion of patients within 20% of stable warfarin dose (45% vs 29% and 2% in the IWPC pharmacogenomics and clinical algorithms, respectively). In contrast to our novel algorithm, a significant inverse correlation between predicted dose and percent West African ancestry was observed for the IWPC pharmacogenomics algorithm among patients requiring ⩾60 mg per week (ß=-2.04, P=0.02).


Subject(s)
Anticoagulants/therapeutic use , Pharmacogenetics , Warfarin/therapeutic use , Anticoagulants/pharmacokinetics , Cohort Studies , Cytochrome P-450 CYP2C9/genetics , Female , Humans , Male , Vitamin K Epoxide Reductases/genetics , Warfarin/pharmacokinetics
16.
Br J Surg ; 100(1): 95-104, 2013 Jan.
Article in English | MEDLINE | ID: mdl-23148025

ABSTRACT

BACKGROUND: Oesophageal malignancy is a disease with a poor prognosis. Oesophagectomy is the mainstay of curative treatment but associated with substantial morbidity and mortality. Although mortality rates have improved, the incidence of perioperative morbidity remains high. This study assessed the impact of postoperative morbidity on long-term outcomes. METHODS: A prospective database was designed for patients undergoing oesophagectomy for malignancy from 1998 to 2011. An observational cohort study was performed with these data, assessing intraoperative technical complications, postoperative morbidity and effects on overall survival. RESULTS: Some 618 patients were included, with a median follow-up of 51 months for survivors. The overall complication rate was 64·6 per cent (399 of 618), with technical complications in 124 patients (20·1 per cent) and medical complications in 339 (54·9 per cent). Technical complications were associated with longer duration of surgery (308 min versus 293 min in those with no technical complications; P = 0·017), greater operative blood loss (448 versus 389 ml respectively; P = 0·035) and longer length of stay (22 versus 13 days; P < 0·001). Medical complications were associated with greater intraoperative blood loss (418 ml versus 380 ml in those with no medical complications; P = 0·013) and greater length of stay (16 versus 12 days respectively; P < 0·001). Median overall and disease-free survival were 41 and 43 months. After controlling for age, tumour stage, resection margin, length of tumour, adjuvant therapy, procedure type and co-morbidities, there was no effect of postoperative complications on disease-specific survival. CONCLUSION: Technical and medical complications following oesophagectomy were associated with greater intraoperative blood loss and a longer duration of inpatient stay, but did not predict disease-specific survival.


Subject(s)
Adenocarcinoma/surgery , Esophageal Neoplasms/surgery , Esophagectomy/mortality , Intraoperative Complications/epidemiology , Neoplasms, Squamous Cell/surgery , Postoperative Complications/epidemiology , Adenocarcinoma/mortality , Adenocarcinoma/pathology , Adolescent , Adult , Aged , Aged, 80 and over , Anastomotic Leak/epidemiology , Chemoradiotherapy, Adjuvant , Cohort Studies , Comorbidity , Diabetes Mellitus/epidemiology , Esophageal Neoplasms/mortality , Esophageal Neoplasms/pathology , Esophagectomy/adverse effects , Female , Hospital Mortality , Humans , Length of Stay , Male , Middle Aged , Myocardial Ischemia/epidemiology , Neoplasm Grading , Neoplasm Transplantation , Neoplasms, Squamous Cell/mortality , Neoplasms, Squamous Cell/pathology , Prospective Studies , Surgical Wound Infection/epidemiology , Survival Analysis , Survival Rate , Urinary Retention/epidemiology , Young Adult
17.
J Math Biol ; 66(1-2): 95-114, 2013 Jan.
Article in English | MEDLINE | ID: mdl-22252506

ABSTRACT

Since its discovery, mobile DNA has fascinated researchers. In particular, many researchers have debated why insertion sequences persist in prokaryote genomes and populations. While some authors think that insertion sequences persist only because of occasional beneficial effects they have on their hosts, others argue that horizontal gene transfer is strong enough to overcome their generally detrimental effects. In this study, we model the long-term fate of a prokaryote cell population, of which a small proportion of cells has been infected with one insertion sequence per cell. Based on our model and the distribution of IS5, an insertion sequence for which sufficient data is available in 525 fully sequenced proteobacterial genomes, we show that the fitness cost of insertion sequences is so small that they are effectively neutral or only slightly detrimental. We also show that an insertion sequence infection can persist and reach the empirically observed distribution if the rate of horizontal gene transfer is at least as large as the fitness cost, and that this rate is well within the rates of horizontal gene transfer observed in nature. In addition, we show that the time needed to reach the observed prevalence of IS5 is unrealistically long for the fitness cost and horizontal gene transfer rate that we computed. Occasional beneficial effects may thus have played an important role in the fast spreading of insertion sequences like IS5.


Subject(s)
DNA Transposable Elements , Genetic Fitness , Models, Genetic , DNA, Bacterial/genetics , Gene Transfer, Horizontal , Genome, Bacterial , Interspersed Repetitive Sequences , Likelihood Functions , Mathematical Concepts , Proteobacteria/genetics
18.
ESMO Open ; 7(3): 100452, 2022 06.
Article in English | MEDLINE | ID: mdl-35798469

ABSTRACT

BACKGROUND: The incidence of oesophageal adenocarcinoma (OAC) is rapidly increasing and despite improvements in treatment, the 5-year survival rate remains poor. Prognostic biomarkers that address the genomic heterogeneity in this highly complex disease will aid the development of precision therapeutics and improve patient survival. The aim of this study was to determine whether circulating tumour DNA (ctDNA) has prognostic significance as a biomarker in OAC patients. PATIENTS AND METHODS: We profiled 209 blood and tumour samples from 57 OAC patients. Using a panel of 77 cancer genes, we sequenced ctDNA in plasma samples (n = 127) which were taken at multiple time points before and after therapy. In parallel, we sequenced matched tumour samples from 39 patients using the same gene panel. To assess whether the ctDNA profile reflected the tumour heterogeneity, we sequenced additional multi-region primary tumour samples in 17 patients. In addition, we analysed whole-genome and whole-exome sequencing data from primary tumours for a subset of 18 patients. RESULTS: Using a tumour-agnostic approach, we found that detectable ctDNA variants in post-treatment plasma samples were associated with worse disease-specific survival. To evaluate whether the ctDNA originated from the primary tumour, we carried out a tumour-informed analysis which confirmed post-treatment ctDNA variants were associated with worse survival. To determine whether ctDNA could be used as a clinical follow-up test, we assessed blood samples from multiple time points before and after treatment, in a subset of patients. Results showed that the variant allele frequency of ctDNA variants increased with disease recurrence. CONCLUSION: This study demonstrates that ctDNA variants can be detected in patients with OAC and this has potential clinical utility as a prognostic biomarker for survival.


Subject(s)
Adenocarcinoma , Circulating Tumor DNA , Esophageal Neoplasms , Adenocarcinoma/diagnosis , Adenocarcinoma/genetics , Biomarkers, Tumor/genetics , Circulating Tumor DNA/genetics , Esophageal Neoplasms/diagnosis , Esophageal Neoplasms/genetics , Humans , Mutation
19.
ESMO Open ; 7(4): 100540, 2022 08.
Article in English | MEDLINE | ID: mdl-35849877

ABSTRACT

BACKGROUND: Next-generation sequencing is used in cancer research to identify somatic and germline mutations, which can predict sensitivity or resistance to therapies, and may be a useful tool to reveal drug repurposing opportunities between tumour types. Multigene panels are used in clinical practice for detecting targetable mutations. However, the value of clinical whole-exome sequencing (WES) and whole-genome sequencing (WGS) for cancer care is less defined, specifically as the majority of variants found using these technologies are of uncertain significance. PATIENTS AND METHODS: We used the Cancer Genome Interpreter and WGS in 726 tumours spanning 10 cancer types to identify drug repurposing opportunities. We compare the ability of WGS to detect actionable variants, tumour mutation burden (TMB) and microsatellite instability (MSI) by using in silico down-sampled data to mimic WES, a comprehensive sequencing panel and a hotspot mutation panel. RESULTS: We reveal drug repurposing opportunities as numerous biomarkers are shared across many solid tumour types. Comprehensive panels identify the majority of approved actionable mutations, with WGS detecting more candidate actionable mutations for biomarkers currently in clinical trials. Moreover, estimated values for TMB and MSI vary when calculated from WGS, WES and panel data, and are dependent on whether all mutations or only non-synonymous mutations were used. Our results suggest that TMB and MSI thresholds should not only be tumour-dependent, but also be sequencing platform-dependent. CONCLUSIONS: There is a large opportunity to repurpose cancer drugs, and these data suggest that comprehensive sequencing is an invaluable source of information to guide clinical decisions by facilitating precision medicine and may provide a wealth of information for future studies. Furthermore, the sequencing and analysis approach used to estimate TMB may have clinical implications if a hard threshold is used to indicate which patients may respond to immunotherapy.


Subject(s)
Exome , Neoplasms , Biomarkers, Tumor , High-Throughput Nucleotide Sequencing , Humans , Microsatellite Instability , Mutation , Exome Sequencing
20.
J Dent Res ; 100(3): 318-325, 2021 03.
Article in English | MEDLINE | ID: mdl-33078669

ABSTRACT

The presence of periodontal diseases (PDs) often strongly correlates with other severe chronic inflammatory conditions, including cardiovascular disease, diabetes, and arthritis. However, the mechanisms through which these diseases interact are unclear. In PD, tissue and bone destruction in the mouth is driven by elevated recruitment of polymorphonuclear neutrophils (PMNs), which are primed and recruited from the circulation to sites of inflammation. We predicted that systemic effects on PMN mobilization or priming could account for the interaction between PD and other inflammatory conditions. We tested this using a mouse model of ligature-induced PD and found elevated PMN counts specifically in bone marrow, supporting a systemic effect of periodontal tissue inflammation on PMN production. In contrast, mice with induced peritonitis had elevated PMN counts in the blood, peritoneum, and colon. These elevated counts were further significantly increased when acute peritonitis was induced after ligature-induced PD in mice, revealing a synergistic effect of multiple inflammatory events on PMN levels. Flow cytometric analysis of CD marker expression revealed enhanced priming of PMNs from mice with both PD and peritonitis compared to mice with peritonitis alone. Thus, systemic factors associated with PD produce hyperinflammatory PMN responses during a secondary infection. To analyze this systemic effect in humans, we induced gingival inflammation in volunteers and also found significantly increased activation of blood PMNs in response to ex vivo stimulation, which reverted to normal following resolution of gingivitis. Together, these results demonstrate that periodontal tissue inflammation has systemic effects that predispose toward an exacerbated innate immune response. This indicates that peripheral PMNs can respond synergistically to simultaneous and remote inflammatory triggers and therefore contribute to the interaction between PD and other inflammatory conditions. This suggests larger implications of PD beyond oral health and reveals potential new approaches for treating systemic inflammatory diseases that interact with PD.


Subject(s)
Gingivitis , Peritonitis , Animals , Immunity, Innate , Inflammation , Neutrophils
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