ATLAS and CMS applications on the WorldGrid testbed

WorldGrid is an intercontinental testbed spanning Europe and the US integrating architecturally different Grid implementations based on the Globus toolkit. It has been developed in the context of the DataTAG and iVDGL projects, and successfully demonstrated during the WorldGrid demos at IST2002 (Copenhagen) and SC2002 (Baltimore). Two HEP experiments, ATLAS and CMS, successful exploited the WorldGrid testbed for executing jobs simulating the response of their detectors to physics eve nts produced by real collisions expected at the LHC accelerator starting from 2007. This data intensive activity has been run since many years on local dedicated computing farms consisting of hundreds of nodes and Terabytes of disk and tape storage. Within the WorldGrid testbed, for the first time HEP simulation jobs were submitted and run indifferently on US and European resources, despite of their underlying different Grid implementations, and produced data which could be retrieved and further analysed on the submitting machine, or simply stored on the remote resources and registered on a Replica Catalogue which made them available to the Grid for further processing. In this contribution we describe the job submission from Europe for both ATLAS and CMS applications, performed through the GENIUS portal operating on top of an EDG User Interface submitting to an EDG Resource Broker, pointing out the chosen interoperability solutions which made US and European resources equivalent from the applications point of view, the data management in the WorldGrid environment, and the CMS specific production tools which were interfaced to the GENIUS portal.Comment: Poster paper from the 2003 Computing in High Energy and Nuclear Physics (CHEP03), La Jolla, Ca, USA, March 2003, 10 pages, PDF. PSN TUCP004; added credit to funding agenc

Chromatin Protamination and Catsper Expression in Spermatozoa Predict Clinical Outcomes after Assisted Reproduction Programs

Abstract Identification of parameters predicting assisted reproductive technologies (ARTs) success is a major goal of research in reproduction. Quality of gametes is essential to achieve good quality embryos and increase the success of ARTs. We evaluated two sperm parameters, chromatin maturity and expression of the sperm specific calcium channel CATSPER, in relation to ART outcomes in 206 couples undergoing ARTs. Chromatin maturity was evaluated by Chromomycin A3 (CMA3) for protamination and Aniline Blue (AB) for histone persistence and CATSPER expression by a flow cytometric method. CMA3 positivity and CATSPER expression significantly predicted the attainment of good quality embryos with an OR of 6.6 and 14.3 respectively, whereas AB staining was correlated with fertilization rate. In the subgroup of couples with women ≤35 years, CATSPER also predicted achievement of clinical pregnancy (OR = 4.4). Including CMA3, CATSPER and other parameters affecting ART outcomes (female age, female factor and number of MII oocytes), a model that resulted able to predict good embryo quality with high accuracy was developed. CMA3 staining and CATSPER expression may be considered two applicable tools to predict ART success and useful for couple counseling. This is the first study demonstrating a role of CATSPER expression in embryo development after ARTs programs

Arsenic in mining environments: evidences from Sardinia (Italy)

In Sardinia, the dispersion of arsenic in the environment appears strictly linked with mineralised bodies and mining activities. Currently, the areas of main concern are the active gold mine at Furtei, and the abandoned Pb- As mine at Baccu Locci. At Furtei, the main sources of arsenic are enargite, and arsenian pyrite; an ongoing monitoring program of water quality in the area around the mine documented so far no major changes with respect to pre-mine conditions, except for the formation of extremely acid, As-rich pit lakes. At Baccu Locci, the main primary source is arsenopyrite; arsenic dispersion is essentially due to the past unwise practice of discarding mine tailings into the nearby creek. Arsenic is slowly released from residual arsenopyrite and temporary secondary mineral traps such as Fe-oxyhydroxides, causing contamination of soils and waters as far as 10 km downstream of the mine

Distributed Computing Grid Experiences in CMS

The CMS experiment is currently developing a computing system capable of serving, processing and archiving the large number of events that will be generated when the CMS detector starts taking data. During 2004 CMS undertook a large scale data challenge to demonstrate the ability of the CMS computing system to cope with a sustained data-taking rate equivalent to 25% of startup rate. Its goals were: to run CMS event reconstruction at CERN for a sustained period at 25 Hz input rate; to distribute the data to several regional centers; and enable data access at those centers for analysis. Grid middleware was utilized to help complete all aspects of the challenge. To continue to provide scalable access from anywhere in the world to the data, CMS is developing a layer of software that uses Grid tools to gain access to data and resources, and that aims to provide physicists with a user friendly interface for submitting their analysis jobs. This paper describes the data challenge experience with Grid infrastructure and the current development of the CMS analysis system

Substantial lymph-vascular space invasion (Lvsi) as predictor of distant relapse and poor prognosis in low-risk early-stage endometrial cancer

Objective: The aim of this study is to analyze the prognostic role of lymph-vascular space invasion (LVSI), evaluated in a semi-quantitative fashion on prognosis of early stage, low risk endometrial cancer (EC). Methods: We enrolled patients who underwent surgery for endometrial cancer between 2003 and 2018 in two referral cancer center. All patients had endometrioid EC, G1–G2, with myometrial invasion <50%, and no lymph-node involvement. LVSI was analyzed in a semi-quantitative way, according to a 3-tiered scoring system in absent, focal and substantial. Results: Among 524 patients, any positive LVSI was found in 57 patients (10.9%) with focal LVSI (n=35, 6.7%) and substantial LVSI (n=22, 4.2%). Substantial LVSI was associated to higher rate of G2 (p<0.001), myometrial infiltration (p=0.002) and greater tumor dimensions (p=0.014). Patients with substantial LVSI were more likely to receive adjuvant treatment (6.6% vs. 52.6%, p<0.001). The 5-year OS was 99.5% in patients with absent LVSI and 70.6% in those with substantial LVSI (p<0.001). The 5-year disease free survival (DFS) was 93.6% in patients with absent LVSI and 56.5% in those with substantial LVSI (p<0.001). The rate of distant failures increased from 1.8% for absent LVSI to 22.7% for substantial LVSI (p=0.002). In univariate analysis substantial LVSI was the strongest predictor of poor overall survival (hazard ratio [HR]=11.9, p=0.001). Multivariate analysis showed that substantial LVSI was an independent predictive factor of both recurrence (HR=5.88, p=0.001) and distant failure (HR=10.6, p=0.006). Conclusions: Substantial LVSI represents the strongest independent risk factor for decreased survival and distant relapse, indicating a role for potential hematogenous dissemination

HEP Applications Evaluation of the EDG Testbed and Middleware

Workpackage 8 of the European Datagrid project was formed in January 2001 with representatives from the four LHC experiments, and with experiment independent people from five of the six main EDG partners. In September 2002 WP8 was strengthened by the addition of effort from BaBar and D0. The original mandate of WP8 was, following the definition of short- and long-term requirements, to port experiment software to the EDG middleware and testbed environment. A major additional activity has been testing the basic functionality and performance of this environment. This paper reviews experiences and evaluations in the areas of job submission, data management, mass storage handling, information systems and monitoring. It also comments on the problems of remote debugging, the portability of code, and scaling problems with increasing numbers of jobs, sites and nodes. Reference is made to the pioneeering work of Atlas and CMS in integrating the use of the EDG Testbed into their data challenges. A forward look is made to essential software developments within EDG and to the necessary cooperation between EDG and LCG for the LCG prototype due in mid 2003.Comment: Talk from the 2003 Computing in High Energy and Nuclear Physics Conference (CHEP03), La Jolla, CA, USA, March 2003, 7 pages. PSN THCT00

Fertility-sparing treatment for endometrial cancer and atypical endometrial hyperplasia in patients with Lynch Syndrome: Molecular diagnosis after immunohistochemistry of MMR proteins

Introduction: Lynch Syndrome (LS) represents the hereditary condition that is most frequently associated with endometrial cancer (EC). The aim of this study is to assess the presence of Lynch Syndrome (LS) in young women with mismatch repair (MMR)-deficient atypical endometrial hyperplasia (AEH) and non-myoinvasive FIGO G1 endometrioid EC and its possible impact on the outcome of conservative treatment. Methods: Six MMR-deficient cases identified from a previous cohort of 69 conservatively treated patients were selected to be screened for germline mutations in MMR genes. In each patient, the outcomes of conservative treatment for AEH and EEC, including response, relapse, progression, and pregnancy, were assessed. Results: Five out of 6 patients underwent genetic test for LS. Three out of these 5 patients showed a positive genetic test. Patient 1 showed the c.942 + 2 T>A heterozygous variant of MSH2 mutation; after 12 months of complete response, she had relapse and progression of disease. Patient 4 showed the c.2459-1G>C variant of MSH2 mutation; after complete response, she failed to achieve pregnancy; she had relapse after 24 months and underwent hysterectomy. Patient 6 showed the c.803 + 1 heterozygous variant of PMS2 mutation; she had relapse of disease after 18 months from the first complete response and then underwent hysterectomy. Conclusions: In this series, 3 out of 6 women with MMR-deficiency had LS. None of the patients achieved pregnancy, and those who responded to treatment had subsequent relapse of disease. Patients undergoing fertility-sparing treatment for atypical endometrial hyperplasia and endometrial cancer should perform MMR immunohistochemical analysis in order to screen LS

Risk factors for abnormally invasive placenta: a systematic review and meta-analysis.

Purpose of the article. To explore the strength of association between different maternal and pregnancy characteristics and the occurrence of abnormally invasive placenta (AIP). MATERIALS AND METHODS: Pubmed, Embase, CINAHL databases were searched. The risk factors for AIP explored were: obesity, age > 35 years, smoking before or during pregnancy, placenta previa, prior cesarean section (CS), placenta previa and prior CS, prior uterine surgery, abortion and uterine curettage, in vitro fertilization (IVF) pregnancy and interval between a previous CS and a subsequent pregnancy. Random-effect head-to-head meta-analyses were used to analyze the data. RESULTS: Forty-six were included in the systematic review. Maternal obesity (Odd ratio, OR: 1.4, 95% CI 1.0-1.8), advanced maternal age (OR: 3.1, 95% CI 1.4-7.0) and parity (OR: 2.5, 95% CI 1.7-3.6), but not smoking were associated with a higher risk of AIP. The presence of placenta previa in women with at least a prior CS was associated with a higher risk of AIP compared to controls, with an OR of 12.0, 95% CI 1.6-88.0. Furthermore, the risk of AIP increased with the number of prior CS (OR of 2.6, 95% CI 1.6-4.4 and 5.4, 95% CI 1.7-17.4 for two and three prior CS respectively). Finally, IVF pregnancies were associated with a high risk of AIP, with an OR of 2.8 (95% CI 1.2-6.8). CONCLUSION: A prior CS and placenta previa are among the strongest risk factors for the occurrence of AIP

A Multicentric Randomized Trial to Evaluate the ROle of Uterine MANipulator on Laparoscopic/Robotic HYsterectomy for the Treatment of Early-Stage Endometrial Cancer: The ROMANHY Trial

Objective: This prospective randomized trial aimed to assess the impact of the uterine manipulator in terms of lymph vascular space invasion (LVSI) in patients undergoing minimally invasive staging for early-stage endometrial cancer. Methods: In this multicentric randomized trial, enrolled patients were randomly allocated in two groups according to the no use (arm A) or the use (arm B) of the uterine manipulator. Inclusion criteria were G1-G2 early-stage endometrial cancer at preoperative evaluation. The variables collected included baseline demographic characteristics, perioperative data, final pathology report, adjuvant treatment, and follow-up. Results: In the study, 154 patients (76 in arm A and 78 in arm B) were finally included. No significant differences were recorded regarding the baseline characteristics. A statistically significant difference was found in operative time for the laparoscopic staging (p=0.005), while no differences were reported for the robotic procedures (p=0.419). The estimated blood loss was significantly lower in arm A (p=0.030). No statistically significant differences were recorded between the two study groups in terms of peritoneal cytology, LVSI (p=0.501), and pattern of LVSI (p=0.790). No differences were detected in terms of overall survival and disease-free survival (p=0.996 and p=0.480, respectively). Similarly, no differences were recorded in the number of recurrences, 6 (7.9%) in arm A and 4 (5.2%) in arm B (p=0.486). The use of the uterine manipulator had no impact on DFS both at univariable and multivariable analyses. Conclusions: The intrauterine manipulator does not affect the LVSI in early-stage endometrial cancer patients undergoing laparoscopic/robotic staging. Clinical Trial Registration: https://clinicaltrials.gov, identifier (NCT: 02762214