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Implementation of 2D DomainDecomposition in the UCAN Gyrokinetic Particle-in-Cell Code and Resulting Performance of UCAN2

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Communications in Computational Physics 2016年第1期19卷 205-225页

作者： Jean-noel G.Leboeuf Viktor K.Decyk David E.Newman Raul Sanchez Department of Physics University of AlaskaFairbanksAK 99775-5920USA Department of Physics and Astronomy and Institute for Digital Research and Education(IDRE)University of CaliforniaLos AngelesCA 90095-1547USA Departamento de Fsica Universidad Carlos IIILeganes 28911MadridSpain

The massively parallel,nonlinear,three-dimensional(3D),toroidal,electrostatic,gyrokinetic,particle-in-cell(PIC),Cartesian geometry UCANcode,with particle ions and adiabatic electrons,has been successfully exercised to identify non-diffusive transport characteristics in present day tokamak *** limitation in applying UCAN to larger scale discharges is the 1D domain decomposition in the toroidal(or z-)direction for massively parallel implementation using MPI which has restricted the calculations to a few hundred ion Larmor radii or gyroradii per plasma minor *** exceed these sizes,we have implemented 2D domain decomposition in UCANwith the addition of the y-direction to the processor *** has been facilitated by use of relevant components in the P2LIB library of field and particle management routines developed for UCLA’s UPIC Framework of conventional PIC *** gyroaveraging specific to gyrokinetic codes is simplified by the use of replicated arrays for efficient charge accumulation and force *** 2D domain-decomposed UCAN2 code reproduces the original 1D domain nonlinear results within *** of UCAN2 on the Cray XC30 Edison at NERSC demonstrate ideal scaling when problem size is increased along with processor number up to the largest power of 2 available,namely 131,072 *** particle weak scaling benchmarks also indicate that the 1 nanosecond per particle per time step and 1 TFlops barriers are easily broken by UCAN2 with 1 billion particles or more and 2000 or more processors.

关键词： Gyrokinetic simulation particle-in-cell method massive parall

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Potential of damage associated molecular patterns in synergising radiation and the immune response in oesophageal cancer

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World Journal of Gastrointestinal Oncology 2023年第8期15卷 1349-1365页

作者： noel E Donlon Maria Davern Andrew Sheppard Fiona O'Connell Brendan Moran Timothy S Nugent Aisling Heeran James J Phelan Anshul Bhardwaj Christine Butler Narayanasamy Ravi Claire L Donohoe Niamh Lynam-Lennon Stephen Maher John V Reynolds Joanne Lysaght Cancer Immunology and Immunotherapy Group Department of SurgeryTrinity Translational Medicine Institute and Trinity St James’s Cancer InstituteTrinity College DublinSt James’s HospitalDublin D08Ireland

BACKGROUND There is an intimate crosstalk between cancer formation,dissemination,treatment response and the host immune system,with inducing tumour cell death the ultimate therapeutic goal for most anti-cancer ***,inducing a purposeful synergistic response between conventional therapies and the immune system remains *** release of damage associated molecular patterns(DAMPs)is indicative of immunogenic cell death and propagation of established immune ***,there is a gap in the literature regarding the importance of DAMP expression in oesophageal adenocarcinoma(OAC)or by immune cells *** To investigate the effects of conventional therapies on DAMP expression and to determine whether OAC is an immunogenic *** We investigated the levels of immunogenic cell death-associated DAMPs,calreticulin(CRT)and HMGB1 using an OAC isogenic model of *** expression was also assessed directly using ex vivo cancer patient T cells(n=10)and within tumour biopsies(n=9)both pre and post-treatment with clinically relevant chemo(radio)*** Hypoxia in combination with nutrient deprivation significantly reduces DAMP expression by OAC cells in *** increased frequencies of T cell DAMP expression in OAC patients were observed following chemo-(radio)therapy,which was significantly higher in tumour tissue compared with peripheral *** with high expression of HMGB1 had a significantly better tumour regression grade(TRG 1-2)compared to low *** In conclusion,OAC expresses an immunogenic phenotype with two distinct subgroups of high and low DAMP expressors,which correlated with tumour regression grade and lymphatic *** also identifies DAMPs namely CRT and HMGB1 as potential promising biomarkers in predicting good pathological responses to conventional chemo(radio)therapies currently used in the multimodal management of locally advanced disease.

关键词： Damage associated molecular patterns HMGB1 Calreticulin Oesophageal adenocarcinoma T cells Radiation

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Hypoxia and its impact on the tumour microenvironment of gastroesophageal cancers

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World Journal of Gastrointestinal Oncology 2021年第5期13卷 312-331页

作者： Ross King Conall Hayes Claire L Donohoe Margaret R Dunne Maria Davern noel E Donlon Department of Surgery St.James’s Hospital CampusTrinity Translational Medicine InstituteDublin D8Ireland

The malfeasant role of the hypoxic tumour microenvironment(TME)in cancer progression was recognized decades ago but the exact mechanisms that augment the hallmarks of cancer and promote treatment resistance continue to be *** cancers(GOCs)represent a major burden of worldwide disease,responsible for the deaths of over 1 million people *** the impact of hypoxia in GOCs enables a better overall understanding of the disease pathogenesis while shining a light on novel therapeutic strategies and facilitating precision treatment approaches with the ultimate goal of improving outcomes for patients with these *** review discusses the underlying principles and processes of the hypoxic response and the effect of hypoxia in promoting the hallmarks of cancer in the context of *** focus on its bidirectional influence on inflammation and how it drives angiogenesis,innate and adaptive immune evasion,metastasis,and the reprogramming of cellular *** contribution of the hypoxic GOC TME to treatment resistance is examined and a brief overview of the pharmacodynamics of hypoxiatargeted therapeutics is *** principal methods that are used in measuring hypoxia and how they may enhance prognostication or provide rationale for individually tailored management in the case of tumours with significant hypoxic regions are also discussed.

关键词： Esophageal cancer Gastric cancer Tumor hypoxia Tumour microenvironment Gastroesophageal cancer

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Objective and subjective scar aesthetics with topical Manuka honey post-thyroidectomy:A randomized control study

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World Journal of Otorhinolaryngology-Head and Neck Surgery 2016年第4期2卷 -页

作者： Andrew Thamboo Graeme Mulholland Kathleen Matthews noel Ayoub Donald Anderson Department of 0tolaryngology e Head and Neck Surgery Stanford University School of Medicine 801 Welch Road Stanford CA 94305 USA

UNASSIGNED:Honey (Manuka honey) has proven to be effective in improving acute and chronic wound healing presumably due to its antibacterial and anti-inflammatory properties. The aim is to determine if Manuka honey decreases scar formation and results in a cosmetically appealing scar.;UNASSIGNED:A prospective single-blinded randomized control trial was performed. All patients received an 8 cm incision. Patients randomized to honey treatment were instructed to apply Manuka honey paste topically to the incision site once per day post surgery for 4 weeks. The patients' scar was then analyzed objectively by a blinded observer and subjectively at 4 and 8 weeks postoperatively. The primary outcome measure used was the Patient and Observer Scar Assessment Scale (POSAS).;UNASSIGNED:A total of 21 patients completed the entire scar analysis (honey treatment = 9, standard treatment = 12). There was no statistically significant difference between patient scar assessment scale and observer scar assessment scale at 4 and 8 weeks postoperatively.;UNASSIGNED:Despite Honey's reported anti-inflammatory and antibacterial properties, this study did not show a difference in scar appearance when applied.

关键词： Aesthetics Honey Naturopathic Scar Thyroid Thyroidectomy Topical Wound healing

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Impact of radiotherapy on the immune landscape in oesophageal adenocarcinoma

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World Journal of Gastroenterology 2022年第21期28卷 2302-2319页

作者： noel E Donlon Maria Davern Fiona O'Connell Andrew Sheppard Aisling Heeran Anshul Bhardwaj Christine Butler Ravi Narayanasamy Claire Donohoe James J Phelan Niamh Lynam-Lennon Margaret R Dunne Stephen Maher Jacintha O'Sullivan John V Reynolds Joanne Lysaght Department of Surgery Trinity Translational Medicine InstituteSt James HospitalDublin D08Ireland

BACKGROUND In the contemporary era of cancer immunotherapy,an abundance of clinical and translational studies have reported radiotherapy(RT)and immunotherapies as a viable option for immunomodulation of many cancer subtypes,with many related clinical trials *** locally advanced disease,chemotherapy or chemoradiotherapy followed by surgical excision of the tumour remain the principal treatment strategy in oesophageal adenocarcinoma(OAC),however,the use of the host immune system to improve anti-tumour immunity is rapidly garnering increased support in the curative *** To immunophenotype OAC patients’immune checkpoint(IC)expression with and without radiation and evaluate the effects of checkpoint blockade on cell *** In the contemporary era of cancer immunotherapy,an abundance of studies have demonstrated that combination RT and IC inhibitors(ICIs)are effective in the immunomodulation of many cancer subtypes,with many related clinical trials *** surgical excision and elimination of tumour cells by chemotherapy or chemoradiotherapy remains the gold standard approach in OAC,the propagation of anti-tumour immune responses is rapidly garnering increased support in the curative *** aim of this body of work was to immunophenotype OAC patients’IC expression with and without radiation and to establish the impact of checkpoint blockade on cell *** study was a hybrid combination of in vitro and ex vivo *** of serum immune proteins was performed by enzyme-linked immunosorbent *** cytometry staining was performed to evaluate IC expression for in vitro OAC cell lines and ex vivo OAC *** viability in the presence of radiation with and without IC blockade was assessed by a cell counting kit-8 *** We identified that conventional dosing and hypofractionated approaches resulted in increased IC expression(PD-1,PD-L1,TIM3,TIGIT)in vitro and ex vivo in *** were two distinct subco

关键词： Oesophageal Cancer Radiotherapy Immunotherapy Immunology Surgery Oncology

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Absence of high amplitude propagating contractions in subjects with chronic spinal cord injury

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World Journal of Gastroenterology 2010年第43期16卷 5435-5439页

作者： Hanumantha R Ancha noel R Fajardo William A Bauman Alan S Rosman Marinella Galea Graham Creasey Mark A Korsten Rehabilitation Research and Development Center of Excellence for Medical Consequences of Spinal Cord Injury James J. Peters VA Medical Center Medical Service James J. Peters VA Medical Center Department of Medicine Mount Sinai School of Medicine Department of Rehabilitation Medicine Mount Sinai School of Medicine Spinal Cord Injury Service James J. Peters VA Medical Center Spinal Cord Injury Service VA Medical Center

AIM: To investigate the presence or absence of high amplitude propagating contractions (HAPC), as well as the other measures of colonic motility, in persons with spinal cord injury (SCI). METHODS: Prolonged colonic ambulatory manometric studies were performed on 14 male volunteers: 8 with SCI (mean age, 59 ± 13 years; mean duration of injury, 13 ± 4 years) and 6 healthy able-bodied controls (mean age, 57 ± 10 years). A solid-state manometry catheter was endoscopically clipped to the splenic flexure. Recording was performed for > 24 h after manometric catheter placement. RESULTS: HAPC were absent in individuals with SCI during pre-sleep, sleep, and post-sleep phases. HAPC were significantly increased after awakening in non-SCI controls (0.8 ± 0.2 HAPC/h vs 10.5 ± 2.0 HAPC/h, P < 0.005). The motility index was lower in those with SCI than in controls preand post-sleep (SCI vs non-SCI: Pre-sleep, 2.4 ± 0.4 vs 8.8 ± 1.9, P < 0.01; Post-sleep, 4.3 ± 0.8 vs 16.5 ± 4.5, P < 0.05). However, a sleepinduced depression of colonic motility was observed in both the SCI and non-SCI groups (Pre-sleep vs Sleep, non-SCI: 8.8 ± 1.9 vs 2.1 ± 0.9, P < 0.002; SCI: 2.4 ± 0.4 vs 0.2 ± 0.03, P < 0.001), with the motility index of those with SCI during sleep not significantly different than that of the controls. CONCLUSION: HAPC were not observed in individuals with SCI preor post-sleep. A sleep-induced depression in general colonic motility was evident in SCI and control subjects.

关键词： Spinal cord injury Neurogenic bowel Bowel motility High amplitude propagating contractions Motility index

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Physico-Mechanical Properties of Bio-Based Bricks

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Journal of Materials Science and Chemical Engineering 2022年第4期10卷 16-29页

作者： Valentin Makomra Lionel Karga Tapsia Benoit Ndiwe Maxime Dawoua Kaoutoing noel Konai Abel Njom Tawe Laynde Danwe Raidandi National Advanced School of Publics Works University of Yaounde1 BP 510 Yaoundé Cameroon Department of Mechanical Petroleum and Gas Engineering National Advanced School of Mines and Petroleum Industries of the University of Maroua PO BOX 08 Kaélé Cameroon Higher Technical Teacher Training College of the University of Douala BP 1872 Douala Cameroon Laboratory of Civil Engineering and Mechanical National Advanced School of Engineering University of Yaoundé 1 BP 8390 Yaoundé Cameroon Laboratory of Materials Architecture and Civil Engineering National Advanced School of Engineering University of Maroua BP 46 Maroua Cameroon

The aim of this work is to improve the high performance of mud bricks. The latter was reinforced with rice straws as stabiliser leading to an improvement of the physico-mechanical properties. Thus, the physical characteristics of the clay such as natural water content, density, atterberg limit, plasticity limit (Wp) and plasticity index (Ip) were determined. Their values are respectively 8.39%, 2025.73 Kg/m3, 47.66%, 29.75% and 17.91%. The clay used is a low plastic organic silt. The normal proctocol provided an optimum dry density (ɣOP) of 1.28 Kg/m3 at an optimum moisture content of 12.42%. The actual density of the straw is 464 Kg/m3, its absorption rate reached 206% in 5 mins and stabilised at 385% at 480 mins of immersion. The maximum bending and compression strengths are respectively 1.52 and 0.164 MPa. The mud brick absorption coefficients obtained are between 4.875 at 0% straw and 20.573% at 3% straw.

关键词： Mud Bricks Physico-Mechanical Characteristics Clay Rice Straw

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Predictors of dehydration and acute renal failure in patients with diverting loop ileostomy creation after colorectal surgery

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World Journal of Clinical Cases 2019年第14期7卷 1805-1813页

作者： Omar Vergara-Fernández Mario Trejo-Avila Oscar Santes Danilo Solórzano-Vicu?a noel Salgado-Nesme Department of Colorectal Surgery Instituto Nacional de Ciencias Médicas y Nutrición "Salvador Zubirán"

BACKGROUND Despite the potential benefits of fecal diversion after low pelvic anastomosis in colorectal surgery, diverting loop ileostomy construction is related to significant rates of complications. AIM To determine potential predictors of high output related complications in patients with diverting loop ileostomy creation after colorectal surgery. METHODS Patients who underwent open and laparoscopic colorectal surgery requiring a diverting loop ileostomy from January 2010 to March 2018 were retrospectively analyzed. We included patients older than 18 years, who underwent colorectal surgery with primary low pelvic anastomosis, and with the creation of a diverting loop ileostomy, at elective or emergency settings for the treatment of benign or malignant conditions. Univariate and multivariate logistic regression analysis was used to determine the effect of the potential predictors on the rate of high output related complications. The high output related complications were dehydration and acute renal failure that required visits to the emergency department and hospitalizations. RESULTS Of the 102 patients included in the study, 23.5%(n = 24) suffered high output related complications. In this group of patients at least one visit to the emergency department (mean 1.6), and at least one readmission to the hospital was needed. The factors associated with high-output ileostomy, in the univariate analysis, were: urgent surgical intervention (OR = 2.6;P = 0.047), the development of postoperative complications (OR = 3;P = 0.024), have ulcerative colitis (OR = 4.8;P = 0.017), use of steroids (OR = 4.3;P = 0.010), mean output at discharge greater than 1000 mL/24 h (OR = 3.2;P = 0.016), and use of loperamide at discharge (OR = 2.8;P = 0.032). Multivariate logistic regression analysis identified two independent risk factors for high output related complications: ulcerative colitis [OR = 7.6 (95%CI: 1.81-31.95);P = 0.006], and ileostomy output at discharge ≥ 1000 mL/24 h [OR =

关键词： Loop ileostomy High-output ileostomy Loop ileostomy complications Dehydration Colorectal surgery

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Computing Reachable Sets as Capture-Viability Kernels in Reverse Time

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Applied Mathematics 2012年第11期3卷 1593-1597页

作者： noel Bonneuil National Institute of Demographic Studies ParisFrance Advanced Studies in Social Sciences ParisFrance

The set SF(x0;T) of states y reachable from a given state x0 at time T under a set-valued dynamic x’(t)∈F(x (t)) and under constraints x(t)∈K where K is a closed set, is also the capture-viability kernel of x0 at T in reverse time of the target {x0} while remaining in K. In dimension up to three, Saint-Pierre’s viability algorithm is well-adapted;for higher dimensions, Bonneuil’s viability algorithm is better suited. It is used on a large-dimensional example.

关键词： Set-Valued Analysis Reachable Set

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Atomic-scale structural signature of dynamic heterogeneities in metallic liquids

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npj Computational Materials 2017年第1期3卷 179-188页

作者： Alain Pasturel noel Jakse University Grenoble Alpes CNRSGrenoble INPSIMaPF-38000 GrenobleFrance

With sufficiently high cooling rates,liquids will cross their equilibrium melting temperatures and can be maintained in a metastable undercooled state before *** of undercooled liquids reveal several intriguing dynamic phenomena and because explicit connections between liquid structure and liquids dynamics are difficult to identify,it remains a major challenge to capture the underlying structural link to these *** initio molecular dynamics(AIMD)simulations are yet especially powerful in providing atomic-scale details otherwise not accessible in *** the AIMD-based study of Cr additions in Al-based liquids,we evidence for the first time a close relationship between the decoupling of component diffusion and the emergence of dynamic heterogeneities in the undercooling *** addition,we demonstrate that the origin of both phenomena is related to a structural heterogeneity caused by a strong interplay between chemical short-range order(CSRO)and local fivefold topology(ISRO)at the short-range scale in the liquid phase that develops into an icosahedral-based medium-range order(IMRO)upon ***,our findings reveal that this structural signature is also captured in the temperature dependence of partial pair-distribution functions which opens up the route to more elaborated experimental studies.

关键词： structural dynamic signature

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