Progress towards an improved particle flow algorithm at CMS with machine learning

The particle-flow (PF) algorithm, which infers particles based on tracks and calorimeter clusters, is of central importance to event reconstruction in the CMS experiment at the CERN LHC, and has been a focus of development in light of planned Phase-2 running conditions with an increased pileup and detector granularity. In recent years, the machine learned particle-flow (MLPF) algorithm, a graph neural network that performs PF reconstruction, has been explored in CMS, with the possible advantages of directly optimizing for the physical quantities of interest, being highly reconfigurable to new conditions, and being a natural fit for deployment to heterogeneous accelerators. We discuss progress in CMS towards an improved implementation of the MLPF reconstruction, now optimized using generator/simulation-level particle information as the target for the first time. This paves the way to potentially improving the detector response in terms of physical quantities of interest. We describe the simulation-based training target, progress and studies on event-based loss terms, details on the model hyperparameter tuning, as well as physics validation with respect to the current PF algorithm in terms of high-level physical quantities such as the jet and missing transverse momentum resolutions. We find that the MLPF algorithm, trained on a generator/simulator level particle information for the first time, results in broadly compatible particle and jet reconstruction performance with the baseline PF, setting the stage for improving the physics performance by additional training statistics and model tuning.Comment: 7 pages, 4 Figures, 1 Tabl

Razlika u infestaciji krpeljima: Hyalomma dromedarii i Rhipicephalus sanguineus sensu lato na jugu Alžira

The aim of this study was to identify the species and parasitic indices of ticks. A flock of 57 individuals (sheep, goats, cattle and dogs) in southern Algeria was studied from March 2019 to February 2020 during monthly visits. A total of 2544 ticks were collected by examining the entire body of the animal. Two tick species were identified: Hyalomma dromedarii (2430 ticks) and Rhipicephalus sanguineus sensu lato (114 ticks). The first species had annual activity and consisted only of adults, while the second species had spring and summer activity and contained both adults and nymphs. At the annual level, the prevalence of infestation, abundance, and intensity were 38.60%, 44.63 and 115.64 ticks per animal, respectively. At the monthly level there were species specific fluctuations, with a peak in activity in September.Ova je studija provedena na jugu Alžira u svrhu identifikacije vrste i parazitskih indeksa krpelja, a proučavano je stado u vremenskom razdoblju od ožujka 2019. do veljače 2020. uz učestalu posjetu jednom mjesečno. Ispitivanjem cijelog tijela životinje prikupljena su ukupno 2544 krpelja ispitivanjem cijelog tijela životinje. Identificirane su dvije vrste krpelja: Hyalomma dromedarii (2430 krpelja) i Rhipicephalus sanguineus sensu lato (114 krpelja). Prva vrsta bila je aktivna cijelu godinu i sadržavala je samo odrasle jedinke, dok je druga vrsta bila aktivna u proljeće i jesen i sadržala je i odrasle i nimfe. Pojavnost infestacije, brojnost i intenzitet bili su 38,60 %, 44,63, odnosno 115,64 krpelja godišnje po životinji. Na mjesečnoj razini te ovisno o vrsti životinje, bilo je fluktuacija, s vrhuncem aktivnosti u rujnu

Scalable neural network models and terascale datasets for particle-flow reconstruction

We study scalable machine learning models for full event reconstruction in high-energy electron-positron collisions based on a highly granular detector simulation. Particle-flow (PF) reconstruction can be formulated as a supervised learning task using tracks and calorimeter clusters or hits. We compare a graph neural network and kernel-based transformer and demonstrate that both avoid quadratic memory allocation and computational cost while achieving realistic PF reconstruction. We show that hyperparameter tuning on a supercomputer significantly improves the physics performance of the models. We also demonstrate that the resulting model is highly portable across hardware processors, supporting Nvidia, AMD, and Intel Habana cards. Finally, we demonstrate that the model can be trained on highly granular inputs consisting of tracks and calorimeter hits, resulting in a competitive physics performance with the baseline. Datasets and software to reproduce the studies are published following the findable, accessible, interoperable, and reusable (FAIR) principles.Comment: 19 pages, 7 figure

M (M: Cu, Co, Cr or Fe) nanoparticles-loaded metal-organic framework MIL-101(Cr) material by sonication process: Catalytic activity and antibacterial properties

The current study deals with the preparation and development of nanomaterials based on iron, copper, chromium or cobalt to study their antibacterial and catalytic properties. To achieve this, the different metals were dispersed in the material MIL-101(Cr) by an ultrasonic-assisted method and then treated by chemical reduction in order to produce corresponding metal nanoparticles (MNPs). The obtained nanocatalysts MIL-101(Cr)/MNPs were characterized by various techniques such as XRD, XPS, SEM, TEM, FTIR; TGA, XRF, Adsorption-desoprtion of nitrogen at 77 K and UV–vis DR. The results showed that the nanocatalysts consist of a mixture of metal phases and oxides. All the prepared nanocatalysts were evaluated based on their performance in reducing the methylene blue (MB) dye in the presence of NaBH4 as reducing agent, for selection of the optimal catalyst. The best catalytic activity was obtained by the MIL-101 (Cr)/CuNPs nanocatalyst in which 6 min was sufficient to reduce the MB dye and the recorded rate constant kapp was 0.503 min−1. The performance of this catalyst was evaluated by varying the effects of three important parameters such as catalyst loading and the concentration of NaBH4 and MB dye. The study of the effects of these three parameters on the reduction process reveals that more than 99% of MB dye was reduced using 0.6 mM of MB dye, 6.8 mM of NaBH4 and 3 mg of nanocatalyst. The kinetic study shows that the reduction of MB dye by the MOF-101(Cr)/CuNPs nanocatalyst follows pseudo-first order kinetics. In addition, the MIL-101(Cr)/CoNPs and MIL-101(Cr)/CuNPs samples demonstrated efficacy at inhibiting bacterial and fungal growth. Hence, it is concluded through this work that the nature, size and concentration of nanoparticles present in the MOF matrix are the key parameters that can influence the catalytic and antibacterial properties of these MNP-loaded MIL-101(Cr) systems

Fluorogenic derivatization of aryl halides based on the formation of biphenyl by Suzuki coupling reaction with phenylboronic acid.

The fluorogenic derivatization method for aryl halide was developed for the first time. This method was based on the formation of fluorescent biphenyl structure by Suzuki coupling reaction between aryl halides and non-fluorescent phenylboronic acid (PBA). We measured the fluorescence spectra of the products obtained by the reaction of p-substituted aryl bromides (i.e., 4-bromobenzonitrile, 4-bromoanisole, 4-bromobenzoic acid ethyl ester and 4-bromotoluene) with PBA in the presence of palladium (II) acetate as a catalyst. The significant fluorescence at excitation maximum wavelength of 275-290 nm and emission maximum wavelength of 315-350 nm was detected in all the tested aryl bromides. This result demonstrated that non-fluorescent aryl bromides could be converted to the fluorescent biphenyl derivatives by the coupling reaction with non-fluorescent PBA. We tried to determine these aryl bromides by HPLC-fluorescence detection with pre-column derivatization. The aryl bromide derivatives were detected on the chromatogram within 30 min without any interfering peak derived from the reagent blank. The detection limits (S/N=3) for aryl bromides were 13-157 fmol/injection

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London

Surgical site infection after gastrointestinal surgery in high-income, middle-income, and low-income countries: a prospective, international, multicentre cohort study

Background: Surgical site infection (SSI) is one of the most common infections associated with health care, but its importance as a global health priority is not fully understood. We quantified the burden of SSI after gastrointestinal surgery in countries in all parts of the world. Methods: This international, prospective, multicentre cohort study included consecutive patients undergoing elective or emergency gastrointestinal resection within 2-week time periods at any health-care facility in any country. Countries with participating centres were stratified into high-income, middle-income, and low-income groups according to the UN's Human Development Index (HDI). Data variables from the GlobalSurg 1 study and other studies that have been found to affect the likelihood of SSI were entered into risk adjustment models. The primary outcome measure was the 30-day SSI incidence (defined by US Centers for Disease Control and Prevention criteria for superficial and deep incisional SSI). Relationships with explanatory variables were examined using Bayesian multilevel logistic regression models. This trial is registered with ClinicalTrials.gov, number NCT02662231. Findings: Between Jan 4, 2016, and July 31, 2016, 13 265 records were submitted for analysis. 12 539 patients from 343 hospitals in 66 countries were included. 7339 (58·5%) patient were from high-HDI countries (193 hospitals in 30 countries), 3918 (31·2%) patients were from middle-HDI countries (82 hospitals in 18 countries), and 1282 (10·2%) patients were from low-HDI countries (68 hospitals in 18 countries). In total, 1538 (12·3%) patients had SSI within 30 days of surgery. The incidence of SSI varied between countries with high (691 [9·4%] of 7339 patients), middle (549 [14·0%] of 3918 patients), and low (298 [23·2%] of 1282) HDI (p < 0·001). The highest SSI incidence in each HDI group was after dirty surgery (102 [17·8%] of 574 patients in high-HDI countries; 74 [31·4%] of 236 patients in middle-HDI countries; 72 [39·8%] of 181 patients in low-HDI countries). Following risk factor adjustment, patients in low-HDI countries were at greatest risk of SSI (adjusted odds ratio 1·60, 95% credible interval 1·05–2·37; p=0·030). 132 (21·6%) of 610 patients with an SSI and a microbiology culture result had an infection that was resistant to the prophylactic antibiotic used. Resistant infections were detected in 49 (16·6%) of 295 patients in high-HDI countries, in 37 (19·8%) of 187 patients in middle-HDI countries, and in 46 (35·9%) of 128 patients in low-HDI countries (p < 0·001). Interpretation: Countries with a low HDI carry a disproportionately greater burden of SSI than countries with a middle or high HDI and might have higher rates of antibiotic resistance. In view of WHO recommendations on SSI prevention that highlight the absence of high-quality interventional research, urgent, pragmatic, randomised trials based in LMICs are needed to assess measures aiming to reduce this preventable complication

Global economic burden of unmet surgical need for appendicitis

Background: There is a substantial gap in provision of adequate surgical care in many low-and middle-income countries. This study aimed to identify the economic burden of unmet surgical need for the common condition of appendicitis. Methods: Data on the incidence of appendicitis from 170 countries and two different approaches were used to estimate numbers of patients who do not receive surgery: as a fixed proportion of the total unmet surgical need per country (approach 1); and based on country income status (approach 2). Indirect costs with current levels of access and local quality, and those if quality were at the standards of high-income countries, were estimated. A human capital approach was applied, focusing on the economic burden resulting from premature death and absenteeism. Results: Excess mortality was 4185 per 100 000 cases of appendicitis using approach 1 and 3448 per 100 000 using approach 2. The economic burden of continuing current levels of access and local quality was US $92 492 million using approach 1 and$73 141 million using approach 2. The economic burden of not providing surgical care to the standards of high-income countries was $95 004 million using approach 1 and$75 666 million using approach 2. The largest share of these costs resulted from premature death (97.7 per cent) and lack of access (97.0 per cent) in contrast to lack of quality. Conclusion: For a comparatively non-complex emergency condition such as appendicitis, increasing access to care should be prioritized. Although improving quality of care should not be neglected, increasing provision of care at current standards could reduce societal costs substantially

Pooled analysis of WHO Surgical Safety Checklist use and mortality after emergency laparotomy

Background The World Health Organization (WHO) Surgical Safety Checklist has fostered safe practice for 10 years, yet its place in emergency surgery has not been assessed on a global scale. The aim of this study was to evaluate reported checklist use in emergency settings and examine the relationship with perioperative mortality in patients who had emergency laparotomy. Methods In two multinational cohort studies, adults undergoing emergency laparotomy were compared with those having elective gastrointestinal surgery. Relationships between reported checklist use and mortality were determined using multivariable logistic regression and bootstrapped simulation. Results Of 12 296 patients included from 76 countries, 4843 underwent emergency laparotomy. After adjusting for patient and disease factors, checklist use before emergency laparotomy was more common in countries with a high Human Development Index (HDI) (2455 of 2741, 89.6 per cent) compared with that in countries with a middle (753 of 1242, 60.6 per cent; odds ratio (OR) 0.17, 95 per cent c.i. 0.14 to 0.21, P <0001) or low (363 of 860, 422 per cent; OR 008, 007 to 010, P <0.001) HDI. Checklist use was less common in elective surgery than for emergency laparotomy in high-HDI countries (risk difference -94 (95 per cent c.i. -11.9 to -6.9) per cent; P <0001), but the relationship was reversed in low-HDI countries (+121 (+7.0 to +173) per cent; P <0001). In multivariable models, checklist use was associated with a lower 30-day perioperative mortality (OR 0.60, 0.50 to 073; P <0.001). The greatest absolute benefit was seen for emergency surgery in low- and middle-HDI countries. Conclusion Checklist use in emergency laparotomy was associated with a significantly lower perioperative mortality rate. Checklist use in low-HDI countries was half that in high-HDI countries.Peer reviewe

Global variation in anastomosis and end colostomy formation following left-sided colorectal resection

Background End colostomy rates following colorectal resection vary across institutions in high-income settings, being influenced by patient, disease, surgeon and system factors. This study aimed to assess global variation in end colostomy rates after left-sided colorectal resection. Methods This study comprised an analysis of GlobalSurg-1 and -2 international, prospective, observational cohort studies (2014, 2016), including consecutive adult patients undergoing elective or emergency left-sided colorectal resection within discrete 2-week windows. Countries were grouped into high-, middle- and low-income tertiles according to the United Nations Human Development Index (HDI). Factors associated with colostomy formation versus primary anastomosis were explored using a multilevel, multivariable logistic regression model. Results In total, 1635 patients from 242 hospitals in 57 countries undergoing left-sided colorectal resection were included: 113 (6·9 per cent) from low-HDI, 254 (15·5 per cent) from middle-HDI and 1268 (77·6 per cent) from high-HDI countries. There was a higher proportion of patients with perforated disease (57·5, 40·9 and 35·4 per cent; P < 0·001) and subsequent use of end colostomy (52·2, 24·8 and 18·9 per cent; P < 0·001) in low- compared with middle- and high-HDI settings. The association with colostomy use in low-HDI settings persisted (odds ratio (OR) 3·20, 95 per cent c.i. 1·35 to 7·57; P = 0·008) after risk adjustment for malignant disease (OR 2·34, 1·65 to 3·32; P < 0·001), emergency surgery (OR 4·08, 2·73 to 6·10; P < 0·001), time to operation at least 48 h (OR 1·99, 1·28 to 3·09; P = 0·002) and disease perforation (OR 4·00, 2·81 to 5·69; P < 0·001). Conclusion Global differences existed in the proportion of patients receiving end stomas after left-sided colorectal resection based on income, which went beyond case mix alone