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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.
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
3.
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
4.
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
5.
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.

6.
BJS Open ; 5(1)2021 01 08.
Article in English | MEDLINE | ID: mdl-33609389

ABSTRACT

BACKGROUND: Minimally invasive oesophagectomy (MIO) is reported to produce fewer respiratory complications than open oesophagectomy. This study assessed differences in postoperative complications between MIO and hybrid MIO (HMIO) employing thoracoscopy and laparotomy, along with the influence of co-morbidities on postoperative outcomes. METHODS: Patients with oesophageal cancer undergoing three-stage MIO or three-stage HMIO between 1999 and 2018 were identified from a prospectively developed database, which included patient demographics, co-morbidities, preoperative therapies, and cancer stage. The primary outcome was postoperative complications in the two groups. Secondary outcomes included duration of operation, blood transfusion requirement, duration of hospital stay, and overall survival. RESULTS: There were 828 patients, of whom 722 had HMIO and 106 MIO, without significant baseline differences. Median duration of operation was longer for MIO (325 versus 289 min; P < 0.001), but with less blood loss (median 250 versus 300 ml; P < 0.001) and a shorter hospital stay (median 12 versus 13 days; P = 0.006). Respiratory complications were not associated with operative approach (31.1 versus 35.2 per cent for MIO and HMIO respectively; P = 0.426). Anastomotic leak rates (10.4 versus 10.2 per cent) and 90-day mortality (1.0 versus 1.7 per cent) did not differ. Cardiac co-morbidity was associated with more medical and surgical complications. Overall survival was associated with AJCC stage and co-morbidities, but not operative approach. CONCLUSION: MIO had a small benefit in terms of blood loss and hospital stay, but not in operating time. Oncological outcomes were similar in the two groups. Postoperative complications were associated with pre-existing cardiorespiratory co-morbidities rather than operative approach.


Subject(s)
Esophageal Neoplasms/mortality , Esophagectomy/mortality , Esophagectomy/methods , Minimally Invasive Surgical Procedures/methods , Postoperative Complications/etiology , Aged , Anastomotic Leak/etiology , Esophageal Neoplasms/surgery , Female , Humans , Laparoscopy/adverse effects , Length of Stay/statistics & numerical data , Male , Middle Aged , Prospective Studies , Survival Analysis , Treatment Outcome
7.
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
8.
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.

9.
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.

11.
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
12.
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
13.
Nat Commun ; 10(1): 1435, 2019 03 29.
Article in English | MEDLINE | ID: mdl-30926816

ABSTRACT

Although CDW correlations are a ubiquitous feature of the superconducting cuprates, their disparate properties suggest a crucial role for pinning the CDW to the lattice. Here, we report coherent resonant X-ray speckle correlation analysis, which directly determines the reproducibility of CDW domain patterns in La1.875Ba0.125CuO4 (LBCO 1/8) with thermal cycling. While CDW order is only observed below 54 K, where a structural phase transition creates inequivalent Cu-O bonds, we discover remarkably reproducible CDW domain memory upon repeated cycling to far higher temperatures. That memory is only lost on cycling to 240(3) K, which recovers the four-fold symmetry of the CuO2 planes. We infer that the structural features that develop below 240 K determine the CDW pinning landscape below 54 K. This opens a view into the complex coupling between charge and lattice degrees of freedom in superconducting cuprates.

14.
Nat Commun ; 9(1): 5013, 2018 11 27.
Article in English | MEDLINE | ID: mdl-30479333

ABSTRACT

Manipulating magnetic domains is essential for many technological applications. Recent breakthroughs in Antiferromagnetic Spintronics brought up novel concepts for electronic device development. Imaging antiferromagnetic domains is of key importance to this field. Unfortunately, some of the basic domain types, such as antiphase domains, cannot be imaged by conventional techniques. Herein, we present a new domain projection imaging technique based on the localization of domain boundaries by resonant magnetic diffraction of coherent X rays. Contrast arises from reduction of the scattered intensity at the domain boundaries due to destructive interference effects. We demonstrate this approach by imaging antiphase domains in a collinear antiferromagnet Fe2Mo3O8, and observe evidence of domain wall interaction with a structural defect. This technique does not involve any numerical algorithms. It is fast, sensitive, produces large-scale images in a single-exposure measurement, and is applicable to a variety of magnetic domain types.

15.
Clin Oncol (R Coll Radiol) ; 30(10): 642-649, 2018 10.
Article in English | MEDLINE | ID: mdl-30017206

ABSTRACT

AIMS: To analyse outcomes and patterns of failure following dose-escalated definitive chemoradiotherapy (CRT) for oesophageal squamous cell carcinoma using fluorodeoxyglucose positron emission tomography for staging and treatment planning. MATERIALS AND METHODS: A retrospective review of patients with oesophageal squamous cell carcinoma receiving definitive CRT to a dose of ≥56 Gy was conducted. Patient and tumour characteristics, treatment received and first sites of relapse were analysed. RESULTS: Between 2003 and 2014, 72 patients were treated with CRT to a median dose of 60 Gy (range 56-66 Gy). The median age was 63 years; most (61%) were stage III/IVa. The median follow-up was 57 months. Three year in-field control, relapse-free survival and overall survival was 64% (95% confidence interval 50-75%), 38% (95% confidence interval 27-50%) and 42% (95% confidence interval 30-53%), respectively. Of the 41 failures prior to death or at last follow-up date, isolated locoregional relapse occurred in 16 patients (22%) with isolated in-field recurrence in 11 patients (15%). Distant failure as first site of relapse was present in 25 patients (35%). No in-field failures occurred in the 11 patients with cT1-2, N0-1 tumours. The median survival for cT4 tumours was 8 months, with five of eight patients developing local progression within the first 6 months. CONCLUSIONS: Dose-escalated radiotherapy was associated with promising rates of in-field local control, with the exception of cT4 tumours. Distant failure remains a significant competing risk. Our data supports the need for current trials re-examining the role of dose escalation in the modern era.


Subject(s)
Chemoradiotherapy/methods , Esophageal Neoplasms/diagnostic imaging , Esophageal Neoplasms/therapy , Esophageal Squamous Cell Carcinoma/diagnostic imaging , Esophageal Squamous Cell Carcinoma/therapy , Neoplasm Recurrence, Local , Adult , Aged , Disease Progression , Disease-Free Survival , Esophageal Neoplasms/pathology , Esophageal Squamous Cell Carcinoma/secondary , Female , Fluorodeoxyglucose F18 , Humans , Male , Middle Aged , Neoplasm Recurrence, Local/pathology , Neoplasm Staging , Positron-Emission Tomography , Radiopharmaceuticals , Radiotherapy Dosage , Retrospective Studies , Survival Rate , Treatment Failure
16.
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
17.
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
18.
J Thromb Haemost ; 15(4): 735-743, 2017 04.
Article in English | MEDLINE | ID: mdl-28135054

ABSTRACT

Essentials Genetic variants controlling gene regulation have not been explored in pharmacogenomics. We tested liver expression quantitative trait loci for association with warfarin dose response. A novel predictor for increased warfarin dose response in African Americans was identified. Precision medicine must take into account population-specific variation in gene regulation. SUMMARY: Background Warfarin is commonly used to control and prevent thromboembolic disorders. However, because of warfarin's complex dose-requirement relationship, safe and effective use is challenging. Pharmacogenomics-guided warfarin dosing algorithms that include the well-established VKORC1 and CYP2C9 polymorphisms explain only a small proportion of inter-individual variability in African Americans (AAs). Objectives We aimed to assess whether transcriptomic analyses could be used to identify regulatory variants associated with warfarin dose response in AAs. Patients/Methods We identified a total of 56 expression quantitative trait loci (eQTLs) for CYP2C9, VKORC1 and CALU derived from human livers and evaluated their association with warfarin dose response in two independent AA warfarin patient cohorts. Results We found that rs4889606, a strong cis-eQTL for VKORC1 (log10 Bayes Factor = 12.02), is significantly associated with increased warfarin daily dose requirement (ß = 1.1; 95% confidence interval [CI] 0.46 to 1.8) in the discovery cohort (n = 305) and in the replication cohort (ß = 1.04; 95% CI 0.33 -1.7; n = 141) after conditioning on relevant covariates and the VKORC1 -1639G>A (rs9923231) variant. Inclusion of rs4889606 genotypes, along with CYP2C9 alleles, rs9923231 genotypes and clinical variables, explained 31% of the inter-patient variability in warfarin dose requirement. We demonstrate different linkage disequilibrium patterns in the region encompassing rs4889606 and rs9923231 between AAs and European Americans, which may explain the increased dose requirement found in AAs. Conclusion Our approach of interrogating eQTLs identified in liver has revealed a novel predictor of warfarin dose response in AAs. Our work highlights the utility of leveraging information from regulatory variants mapped in the liver to uncover novel variants associated with drug response and the importance of population-specific research.


Subject(s)
Genetic Variation , Thromboembolism/ethnology , Thromboembolism/genetics , Warfarin/administration & dosage , Adult , Black or African American , Aged , Algorithms , Calcium-Binding Proteins/genetics , Cohort Studies , Cytochrome P-450 CYP2C9/genetics , Female , Gene Expression Profiling , Gene Expression Regulation , Genotype , Humans , Linkage Disequilibrium , Liver/drug effects , Liver/metabolism , Male , Middle Aged , Pharmacogenetics , Precision Medicine , Quantitative Trait Loci , Thromboembolism/drug therapy , Vitamin K Epoxide Reductases/genetics
19.
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.

20.
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
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