Measuring Change Over Time: A Systematic Review of Evaluative Measures of Cognitive Functioning in Traumatic Brain Injury

Objectives: The purpose of evaluative instruments is to measure the magnitude of change in a construct of interest over time. The measurement properties of these instruments, as they relate to the instrument's ability to fulfill its purpose, determine the degree of certainty with which the results yielded can be viewed. This work systematically reviews all instruments that have been used to evaluate cognitive functioning in persons with traumatic brain injury (TBI), and critically assesses their evaluative measurement properties: construct validity, test-retest reliability, and responsiveness.Data Sources: MEDLINE, Central, EMBASE, Scopus, PsycINFO were searched from inception to December 2016 to identify longitudinal studies focused on cognitive evaluation of persons with TBI, from which instruments used for measuring cognitive functioning were abstracted. MEDLINE, instrument manuals, and citations of articles identified in the primary search were then screened for studies on measurement properties of instruments utilized at least twice within the longitudinal studies.Study Selection: All English-language, peer-reviewed studies of longitudinal design that measured cognition in adults with a TBI diagnosis over any period of time, identified in the primary search, were used to identify instruments. A secondary search was carried out to identify all studies that assessed the evaluative measurement properties of the instruments abstracted in the primary search.Data Extraction: Data on psychometric properties, cognitive domains covered and clinical utility were extracted for all instruments.Results: In total, 38 longitudinal studies from the primary search, utilizing 15 instruments, met inclusion and quality criteria. Following review of studies identified in the secondary search, it was determined that none of the instruments utilized had been assessed for all the relevant measurement properties in the TBI population. The most frequently assessed property was construct validity.Conclusions: There is insufficient evidence for the validity and reliability of instruments measuring cognitive functioning, longitudinally, in persons with TBI. Several instruments with well-defined construct validity in TBI samples warrant further assessment for test-retest reliability and responsiveness.Registration Number:www.crd.york.ac.uk/PROSPERO/, identifier CRD42017055309

Pythia: AI-assisted Code Completion System

In this paper, we propose a novel end-to-end approach for AI-assisted code completion called Pythia. It generates ranked lists of method and API recommendations which can be used by software developers at edit time. The system is currently deployed as part of Intellicode extension in Visual Studio Code IDE. Pythia exploits state-of-the-art large-scale deep learning models trained on code contexts extracted from abstract syntax trees. It is designed to work at a high throughput predicting the best matching code completions on the order of 100 $ms$. We describe the architecture of the system, perform comparisons to frequency-based approach and invocation-based Markov Chain language model, and discuss challenges serving Pythia models on lightweight client devices. The offline evaluation results obtained on 2700 Python open source software GitHub repositories show a top-5 accuracy of 92\%, surpassing the baseline models by 20\% averaged over classes, for both intra and cross-project settings.Comment: Published in Proceedings of the 25th ACM SIGKDD International Conference on Knowledge Discovery & Data Mining (KDD '19

MaxCorrMGNN: A Multi-Graph Neural Network Framework for Generalized Multimodal Fusion of Medical Data for Outcome Prediction

With the emergence of multimodal electronic health records, the evidence for an outcome may be captured across multiple modalities ranging from clinical to imaging and genomic data. Predicting outcomes effectively requires fusion frameworks capable of modeling fine-grained and multi-faceted complex interactions between modality features within and across patients. We develop an innovative fusion approach called MaxCorr MGNN that models non-linear modality correlations within and across patients through Hirschfeld-Gebelein-Renyi maximal correlation (MaxCorr) embeddings, resulting in a multi-layered graph that preserves the identities of the modalities and patients. We then design, for the first time, a generalized multi-layered graph neural network (MGNN) for task-informed reasoning in multi-layered graphs, that learns the parameters defining patient-modality graph connectivity and message passing in an end-to-end fashion. We evaluate our model an outcome prediction task on a Tuberculosis (TB) dataset consistently outperforming several state-of-the-art neural, graph-based and traditional fusion techniques.Comment: To appear in ML4MHD workshop at ICML 202

Application of nanosatellites for lunar missions

Two major themes for the space sector in recent years have been the resurgence of missions to the Moon, facilitating the expansion of human presence into the Solar System, and the rapid growth in CubeSat launches. Lunar missions will play an important role in sustainable space exploration, as discussed in the Global Exploration Roadmap. The Roadmap outlines the next steps for the current and next generation of explorers and reaffirms the interest of 14 space agencies to return to the Moon. Over the past decade, a more daring approach to space innovation and the proliferation of low-cost small satellites have invited commercialization and, subsequently, have accelerated the development of miniaturized technologies and substantially reduced the costs associated with CubeSats. In this context, CubeSats are increasingly being considered as platforms for pioneering missions beyond low-Earth orbit. This paper describes a 3U nanosatellite mission to the Moon, designed as part of the UKSEDS Satellite Design Competition, capable of capturing and analysing details of the lunar environment. To achieve the primary mission objectives, a camera and an infrared spectrometer have been included to relay information about historic lunar landmarks to Earth. The design was developed to be integrated with Open Cosmos' OpenKit and reviewed by experts in the field from SSPI. The paper includes a detailed assessment of the current state of miniaturized instruments and the quality of scientific return which can be achieved by a lunar CubeSat mission. This concludes in an overall feasibility study of lunar CubeSats, a discussion of the current limitations and challenges associated with CubeSat technologies and a framework for future missions

Anal and oral human papillomavirus (HPV) infection in HIV-infected subjects in northern Italy: a longitudinal cohort study among men who have sex with men

<p>Abstract</p> <p>Background</p> <p>A study including 166 subjects was performed to investigate the frequency and persistence over a 6-month interval of concurrent oral and anal Human Papillomavirus (HPV) infections in Human Immunodeficiency Virus (HIV)-infected men who have sex with men (MSM).</p> <p>Methods</p> <p>Patients with no previously documented HPV-related anogenital lesion/disease were recruited to participate in a longitudinal study. Polymerase chain reaction (PCR) was performed to detect HPV from oral and anal swabs and to detect Human Herpes Virus 8 (HHV-8) DNA in saliva on 2 separate specimen series, one collected at baseline and the other collected 6 months later. A multivariate logistic analysis was performed using anal HPV infection as the dependent variable versus a set of covariates: age, HIV plasma viral load, CD4+ count, hepatitis B virus (HBV) serology, hepatitis C virus (HCV) serology, syphilis serology and HHV-8 viral shedding. A stepwise elimination of covariates with a p-value > 0.1 was performed.</p> <p>Results</p> <p>The overall prevalence of HPV did not vary significantly between the baseline and the follow-up, either in the oral (20.1 and 21.3%, respectively) or the anal specimens (88.6 and 86.3%). The prevalence of high-risk (HR) genotypes among the HPV-positive specimens was similar in the oral and anal infections (mean values 24.3% and 20.9%). Among 68 patients with either a HR, low-risk (LR) or undetermined genotype at baseline, 75% had persistent HPV and the persistence rates were 71.4% in HR infections and 76.7% in LR infections. There was a lack of genotype concordance between oral and anal HPV samples. The prevalence of HR HPV in anus appeared to be higher in the younger patients, peaking (> 25%) in the 43-50 years age group. A decrease of the high level of anal prevalence of all genotypes of HPV in the patients > 50 years was evident. HHV-8 oral shedding was positively related to HPV anal infection (p = 0.0046). A significant correlation was found between the persistence of HHV-8 shedding and HIV viral load by logistic bivariate analysis (Odds Ratio of HHV-8 persistence for 1-log increase of HIV viral load = 1.725 ± 0.397, p = 0.018).</p> <p>Conclusions</p> <p>A high prevalence of HPV infection was found in our cohort of HIV-infected MSM, with a negative correlation between anal HPV infection and CD4 cell count.</p

Occupation and motor neuron disease: a New Zealand case-control study.

OBJECTIVES: To assess associations between occupation and motor neuron disease (MND). METHODS: We conducted a population-based case-control study with cases (n=321) recruited through the New Zealand Motor Neurone Disease Association and hospital discharge data. Controls (n=605) were recruited from the Electoral Roll. Information on personal and demographic details, lifestyle factors and a full occupational history was collected using questionnaires and interviews. Associations with ever/never employed and employment duration were estimated using logistic regression stratified by sex and adjusted for age, ethnicity, socioeconomic deprivation, education and smoking. RESULTS: Elevated risks were observed for field crop and vegetable growers (OR 2.93, 95% CI 1.10 to 7.77); fruit growers (OR 2.03, 95% CI 1.09 to 3.78); gardeners and nursery growers (OR 1.96, 95% CI 1.01 to 3.82); crop and livestock producers (OR 3.61, 95% CI 1.44 to 9.02); fishery workers, hunters and trappers (OR 5.62, 95% CI 1.27 to 24.97); builders (OR 2.90, 95% CI 1.41 to 5.96); electricians (OR 3.61, 95% CI 1.34 to 9.74); caregivers (OR 2.65, 95% CI 1.04 to 6.79); forecourt attendants (OR 8.31, 95% CI 1.79 to 38.54); plant and machine operators and assemblers (OR 1.42, 95% CI 1.01 to 2.01); telecommunications technicians (OR 4.2, 95% CI 1.20 to 14.64); and draughting technicians (OR 3.02, 95% CI 1.07 to 8.53). Industries with increased risks were agriculture (particularly horticulture and fruit growing), construction, non-residential care services, motor vehicle retailing, and sport and recreation. Positive associations between employment duration and MND were shown for the occupations fruit growers, gardeners and nursery growers, and crop and livestock producers, and for the horticulture and fruit growing industry. CONCLUSIONS: This study suggests associations between MND and occupations in agriculture and several other occupations

COVID-19 Risk Factors for Cancer Patients: A First Report with Comparator Data from COVID-19 Negative Cancer Patients

none32siSimple SummaryThe COVID-19 pandemic has had a detrimental impact on cancer patients globally. Whilst there are several studies looking at the potential risk factors for COVID-19 disease and related death, most of these include non-cancerous patients as the COVID-19 negative comparator group, meaning it is difficult to draw hard conclusions as to the implications for cancer patients. In our study, we utilized data from over 2000 cancer patients from a large tertiary Cancer Centre in London. In summary, our study found that patients who are male, of Black or Asian ethnicity, or with a hematological malignancy are at an increased risk of COVID-19. The use of cancer patients as the COVID-19 negative comparator group is a major advantage to the study as it means we can better understand the true impact of COVID-19 on cancer patients and identify which factors pose the biggest risk to their likelihood of infection with SARS-CoV2.Very few studies investigating COVID-19 in cancer patients have included cancer patients as controls. We aimed to identify factors associated with the risk of testing positive for SARS CoV2 infection in a cohort of cancer patients. We analyzed data from all cancer patients swabbed for COVID-19 between 1(st) March and 31(st) July 2020 at Guy's Cancer Centre. We conducted logistic regression analyses to identify which factors were associated with a positive COVID-19 test. Results: Of the 2152 patients tested for COVID-19, 190 (9%) tested positive. Male sex, black ethnicity, and hematological cancer type were positively associated with risk of COVID-19 (OR = 1.85, 95%CI:1.37-2.51; OR = 1.93, 95%CI:1.31-2.84; OR = 2.29, 95%CI:1.45-3.62, respectively) as compared to females, white ethnicity, or solid cancer type, respectively. Male, Asian ethnicity, and hematological cancer type were associated with an increased risk of severe COVID-19 (OR = 3.12, 95%CI:1.58-6.14; OR = 2.97, 95%CI:1.00-8.93; OR = 2.43, 95%CI:1.00-5.90, respectively). This study is one of the first to compare the risk of COVID-19 incidence and severity in cancer patients when including cancer patients as controls. Results from this study have echoed those of previous reports, that patients who are male, of black or Asian ethnicity, or with a hematological malignancy are at an increased risk of COVID-19.openRussell, Beth; Moss, Charlotte L; Palmer, Kieran; Sylva, Rushan; D'Souza, Andrea; Wylie, Harriet; Haire, Anna; Cahill, Fidelma; Steel, Renee; Hoyes, Angela; Wilson, Isabelle; Macneil, Alyson; Shifa, Belul; Monroy-Iglesias, Maria J; Papa, Sophie; Irshad, Sheeba; Ross, Paul; Spicer, James; Kordasti, Shahram; Crawley, Danielle; Zaki, Kamarul; Sita-Lumsden, Ailsa; Josephs, Debra; Enting, Deborah; Swampillai, Angela; Sawyer, Elinor; Fields, Paul; Wrench, David; Rigg, Anne; Sullivan, Richard; Van Hemelrijck, Mieke; Dolly, SaoirseRussell, Beth; Moss, Charlotte L; Palmer, Kieran; Sylva, Rushan; D'Souza, Andrea; Wylie, Harriet; Haire, Anna; Cahill, Fidelma; Steel, Renee; Hoyes, Angela; Wilson, Isabelle; Macneil, Alyson; Shifa, Belul; Monroy-Iglesias, Maria J; Papa, Sophie; Irshad, Sheeba; Ross, Paul; Spicer, James; Kordasti, Shahram; Crawley, Danielle; Zaki, Kamarul; Sita-Lumsden, Ailsa; Josephs, Debra; Enting, Deborah; Swampillai, Angela; Sawyer, Elinor; Fields, Paul; Wrench, David; Rigg, Anne; Sullivan, Richard; Van Hemelrijck, Mieke; Dolly, Saoirs

rAAV-compatible MiniPromoters for restricted expression in the brain and eye

Abstract Background Small promoters that recapitulate endogenous gene expression patterns are important for basic, preclinical, and now clinical research. Recently, there has been a promising revival of gene therapy for diseases with unmet therapeutic needs. To date, most gene therapies have used viral-based ubiquitous promoters–however, promoters that restrict expression to target cells will minimize off-target side effects, broaden the palette of deliverable therapeutics, and thereby improve safety and efficacy. Here, we take steps towards filling the need for such promoters by developing a high-throughput pipeline that goes from genome-based bioinformatic design to rapid testing in vivo. Methods For much of this work, therapeutically interesting Pleiades MiniPromoters (MiniPs; ~4 kb human DNA regulatory elements), previously tested in knock-in mice, were “cut down” to ~2.5 kb and tested in recombinant adeno-associated virus (rAAV), the virus of choice for gene therapy of the central nervous system. To evaluate our methods, we generated 29 experimental rAAV2/9 viruses carrying 19 different MiniPs, which were injected intravenously into neonatal mice to allow broad unbiased distribution, and characterized in neural tissues by X-gal immunohistochemistry for icre, or immunofluorescent detection of GFP. Results The data showed that 16 of the 19 (84 %) MiniPs recapitulated the expression pattern of their design source. This included expression of: Ple67 in brain raphe nuclei; Ple155 in Purkinje cells of the cerebellum, and retinal bipolar ON cells; Ple261 in endothelial cells of brain blood vessels; and Ple264 in retinal Müller glia. Conclusions Overall, the methodology and MiniPs presented here represent important advances for basic and preclinical research, and may enable a paradigm shift in gene therapy

Immune activation apoptosis and Treg activity are associated with persistently reduced CD4+ T-cell counts during antiretroviral therapy

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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