Exploring Model-Based Engineering Concepts for Additive Manufacturing

Robust geometry and tolerance representations are needed in additive manufacturing for precise part specification and interoperability with downstream activities such as manufacturing, inspection, and long-term archiving. A disconnection exists between process-independent part geometry and tolerances, and process-dependent information requirements for additive manufacturing. Existing and emerging standards for part geometry (ASTM AMF, 3MF, ISO 10303 STEP) and tolerances (ASME Y14) contain information related to the additive manufacturing process. Details of the standards will be discussed, how their use and improvement can benefit the additive manufacturing process, and their integration into the model-based engineering paradigm.Mechanical Engineerin

Introduction to derived categories of coherent sheaves

In these notes, an introduction to derived categories and derived functors is given. The main focus is the bounded derived category of coherent sheaves on a smooth projective variety.Comment: 24 pages, minor changes, same content as published versio

Respiratory symptoms in people living with HIV and the effect of antiretroviral therapy: a systematic review and meta-analysis

BACKGROUND: Antiretroviral therapy (ART) has significantly altered the pattern of acute and chronic HIV-related disease. However, it is not clear what this means in terms of respiratory symptoms. We sought to investigate the association between HIV status and respiratory symptoms and how these have changed with the availability of ART. METHODS: We searched Cochrane, Medline and Embase databases for studies published between 1946 and August 2015 comparing the prevalence of respiratory symptoms in populations with and without HIV infection. We undertook random effects meta-analysis of the main symptoms reported. We studied heterogeneity and completed sensitivity analyses and funnel plots. RESULTS: From 5788 unique references identified, 24 papers provided relevant data: 18 documented the prevalence of cough and 11 examined the prevalence of breathlessness among other symptoms reported. Compared with the HIV negative, people living with HIV (PLWH) were more likely to have respiratory symptoms with pooled ORs for the prevalence of cough of 3.05 (95% CI 2.24 to 4.16) in resource-limited populations without access to ART; 2.18 (1.56 to 3.18) in resource-rich populations without access to ART and 1.11 (0.99 to 1.24) in resource-rich populations with access to ART. In resource-rich settings, although the availability of ART was associated with a reduction in the difference between HIV-positive and HIV-negative individuals, PLWH were more likely to report breathlessness, OR 1.39 (95% CI 1.11 to 1.73). CONCLUSIONS: Respiratory symptoms are more common in PLWH than controls. This association persists although at a reduced level in populations with access to ART

Efficient chaining of seeds in ordered trees

We consider here the problem of chaining seeds in ordered trees. Seeds are mappings between two trees Q and T and a chain is a subset of non overlapping seeds that is consistent with respect to postfix order and ancestrality. This problem is a natural extension of a similar problem for sequences, and has applications in computational biology, such as mining a database of RNA secondary structures. For the chaining problem with a set of m constant size seeds, we describe an algorithm with complexity O(m2 log(m)) in time and O(m2) in space

Helping education undergraduates to use appropriate criteria for evaluating accounts of motivation

The aim of the study was to compare students in a control group with those in a treatment group with respect to evaluative comments on psychological accounts of motivation. The treatment group systematically scrutinized the nature and interpretation of evidence that supported different accounts, and the assumptions, logic, coherence and clarity of accounts. Content analysis of 74 scripts (using three categories) showed that the control group students made more assertions than either evidential or evaluative points, whereas the treatment group used evaluative statements as often as they used assertion. The findings provide support for privileging activities that develop understanding of how knowledge might be contested, and suggest a need for further research on pedagogies to serve this end. The idea is considered that such understanding has a pivotal role in the development of critical thinking

Detailed assessment of benefits and risks of retrievable inferior vena cava filters on patients with complicated injuries: the da Vinci multicentre randomised controlled trial study protocol

Introduction Retrievable inferior vena cava (IVC) filters have been increasingly used in patients with major trauma who have contraindications to anticoagulant prophylaxis as a primary prophylactic measure against venous thromboembolism (VTE). The benefits, risks and cost-effectiveness of such strategy are uncertain. Methods and analysis Patients with major trauma, defined by an estimated Injury Severity Score >15, who have contraindications to anticoagulant VTE prophylaxis within 72 hours of hospitalisation to the study centre will be eligible for this randomised multicentre controlled trial. After obtaining consent from patients, or the persons responsible for the patients, study patients are randomly allocated to either control or IVC filter, within 72 hours of trauma admission, in a 1:1 ratio by permuted blocks stratified by study centre. The primary outcomes are (1) the composite endpoint of (A) pulmonary embolism (PE) as demonstrated by CT pulmonary angiography, high probability ventilation/perfusion scan, transoesophageal echocardiography (by showing clots within pulmonary arterial trunk), pulmonary angiography or postmortem examination during the same hospitalisation or 90-day after trauma whichever is earlier and (B) hospital mortality; and (2) the total cost of treatment including the costs of an IVC filter, total number of CT and ultrasound scans required, length of intensive care unit and hospital stay, procedures and drugs required to treat PE or complications related to the IVC filters. The study started in June 2015 and the final enrolment target is 240 patients. No interim analysis is planned; incidence of fatal PE is used as safety stopping rule for the trial. Ethics and dissemination Ethics approval was obtained in all four participating centres in Australia. Results of the main trial and each of the secondary endpoints will be submitted for publication in a peer-reviewed journal. Trial registration number ACTRN12614000963628; Pre-results

Spot sputum samples are at least as good as early morning samples for identifying Mycobacterium tuberculosis

Background The use of early morning sputum samples (EMS) to diagnose tuberculosis (TB) can result in treatment delay given the need for the patient to return to the clinic with the EMS, increasing the chance of patients being lost during their diagnostic workup. However, there is little evidence to support the superiority of EMS over spot sputum samples. In this new analysis of the REMoxTB study, we compare the diagnostic accuracy of EMS with spot samples for identifying Mycobacterium tuberculosis pre- and post-treatment. Methods Patients who were smear positive at screening were enrolled into the study. Paired sputum samples (one EMS and one spot) were collected at each trial visit pre- and post-treatment. Microscopy and culture on solid LJ and liquid MGIT media were performed on all samples; those missing corresponding paired results were excluded from the analyses. Results Data from 1115 pre- and 2995 post-treatment paired samples from 1931 patients enrolled in the REMoxTB study were analysed. Patients were recruited from South Africa (47%), East Africa (21%), India (20%), Asia (11%), and North America (1%); 70% were male, median age 31 years (IQR 24–41), 139 (7%) co-infected with HIV with a median CD4 cell count of 399 cells/μL (IQR 318–535). Pre-treatment spot samples had a higher yield of positive Ziehl–Neelsen smears (98% vs. 97%, P = 0.02) and LJ cultures (87% vs. 82%, P = 0.006) than EMS, but there was no difference for positivity by MGIT (93% vs. 95%, P = 0.18). Contaminated and false-positive MGIT were found more often with EMS rather than spot samples. Surprisingly, pre-treatment EMS had a higher smear grading and shorter time-to-positivity, by 1 day, than spot samples in MGIT culture (4.5 vs. 5.5 days, P < 0.001). There were no differences in time to positivity in pre-treatment LJ culture, or in post-treatment MGIT or LJ cultures. Comparing EMS and spot samples in those with unfavourable outcomes, there were no differences in smear or culture results, and positive results were not detected earlier in Kaplan–Meier analyses in either EMS or spot samples. Conclusions Our data do not support the hypothesis that EMS samples are superior to spot sputum samples in a clinical trial of patients with smear positive pulmonary TB. Observed small differences in mycobacterial burden are of uncertain significance and EMS samples do not detect post-treatment positives any sooner than spot samples

Estimating the risk of mortality attributable to recent late HIV diagnosis following admission to the intensive care unit: A single-centre observational cohort study

OBJECTIVES: Despite improvements in survival of people with HIV admitted to the intensive care unit (ICU), late diagnosis continues to contribute to in-ICU mortality. We quantify the population attributable fraction (PAF) of in-ICU mortality for recent late diagnosis among people with HIV admitted to a London ICU. METHODS: Index ICU admissions among people with HIV were considered from 2000 to 2019. Recent late diagnosis was a CD4 T-cell count < 350 cells/μL and/or AIDS-defining illness at/within 6 months prior to ICU admission. Univariate comparisons were conducted using Wilcoxon rank-sum/Cochran-Armitage/χ2 /Fisher's exact tests. We used Poisson regression (robust standard errors) to estimate unadjusted/adjusted (age, sex, calendar year of ICU admission) risk ratios (RRs) and regression standardization to estimate the PAF. RESULTS: In all, 207 index admissions were included [median (interquartile range) age: 46 (38-53) years; 72% male]; 58 (28%) had a recent late diagnosis, all of whom had a CD4 count < 350 cells/μL, and 95% had advanced HIV (CD4 count < 200 cells/μL and/or AIDS at admission) as compared with 57% of those who did not have a recent late diagnosis (p < 0.001). In-ICU mortality was 27% (55/207); 38% versus 22% in those who did and did not have a recent late diagnosis, respectively (p = 0.02). Recent late diagnosis was independently associated with increased in-ICU mortality risk (adjusted RR = 1.75) (95% confidence interval: 1.05-2.91), with 17.08% (16.04-18.12%) of deaths being attributable to this. CONCLUSIONS: There is a need for improved public health efforts focused on HIV testing and reporting of late diagnosis to better understand potentially missed opportunities for earlier HIV diagnosis in healthcare services

IsoRankN: spectral methods for global alignment of multiple protein networks

Motivation: With the increasing availability of large protein–protein interaction networks, the question of protein network alignment is becoming central to systems biology. Network alignment is further delineated into two sub-problems: local alignment, to find small conserved motifs across networks, and global alignment, which attempts to find a best mapping between all nodes of the two networks. In this article, our aim is to improve upon existing global alignment results. Better network alignment will enable, among other things, more accurate identification of functional orthologs across species. Results: We introduce IsoRankN (IsoRank-Nibble) a global multiple-network alignment tool based on spectral clustering on the induced graph of pairwise alignment scores. IsoRankN outperforms existing algorithms for global network alignment in coverage and consistency on multiple alignments of the five available eukaryotic networks. Being based on spectral methods, IsoRankN is both error tolerant and computationally efficient.National Science Council of Taiwan (NSC-096-2917-I- 002-114)National Science Council of Taiwan (NSC-095-2221-E-001-016-MY3)Fannie and John Hertz Foundatio