Miracle-dz/UniFAR-FTUs huggingface dataset:
OC-061 A prospective multi-national study of the colorectal cancer mucosal microbiome reveals specific taxonomic changes indicative of disease stage and prognosis

Introduction The colorectal cancer (CRC) microbiome is niche specific and individualised. Several putative driver organisms enriched on CRCs have been identified from human studies, but few data exist which properly account for important clinical variables in CRC. In this study, we used a meta-taxonomic approach to demonstrate how the CRC microbiome varies with disease stage, histological markers of prognosis and host molecular phenotypes. Method A prospective study was performed on patients undergoing colonoscopy and elective surgery for CRC at three hospitals in UK and Czech Republic. Tissue was sampled from tumours, adenomas, adjacent normal mucosa and mucosa from healthy colon controls. The V1-2 regions of the 16S rRNA gene were sequenced (Illumina MiSeq); data were processed in Mothur and analysed in Stamp and R. Species assignment was performed with NCBI BLAST for microbial genomes. False discovery rate p value correction accounted for multiple testing. Histological analysis and tumour molecular phenotyping were performed according to Royal College of Pathology guidelines. Results One hundred and ninety six patients were recruited: 158 CRC patients, 24 adenoma patients and 14 normal colon controls (median age 70; range 35–90). Tumours were staged as 6 T0, 4 T1, 23 T2, 97 T3, 27 T4; 99 N0, 40 N1, 27 N2; 6 M1. No significant differences were seen in diversity or taxonomy between the UK and Czech cohorts. Adenoma and healthy colon control samples were taxonomically indistinct. However, CRCs were characterised by reduced Shannon diversity (p<0.01), with enrichment of organisms including Bacteroides fragilis,Fusobacterium nucleatum and under-representation of Bacteroides vulgatus,Bacteroides uniformisandFaecalibacterium prausnitzii (all q<0.01). Furthermore, we found a significant progressive reduction in the expression of Bacteroides vulgatus with advancing T stage and a corresponding increase in Fusobacterium nucleatum expression (figure). Additionaly, samples from patients with T4 tumours and cancers expressing histological and molecular markers of poor prognosis were characterised by enrichment of certain low abundance oral pathobionts: Parvimonas micra,Porphyromonas gingivalis and Prevotella spp. Conclusion This large prospective analysis demonstrates that the CRC microbiome is stage-specific and appears to evolve with disease progression. We conclude that oral pathobionts which colonise advanced stage disease relate to markers of tumour prognosis, raising the possibility that they may be directly influencing tumour invasion. Disclosure of Interest None Declared Abstract OC-061 Figure 1 Progressive change in relative abundance of Bacteroides Vulgatus (left) and Fusobacterium Nucleatum (right) against T stage (A: Adenoma).
Higher risk of abdominal obesity , elevated LDL cholesterol and hypertriglyceridemia , but not of hypertension , in people living with HIV : results from the Copenhagen Comorbidity in HIV infection ( COCOMO ) Study

Viro-immunology Research Unit, Department of Infectious Diseases 8632, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark; The Copenhagen General Population Study, Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark; CHIP, Department of Infectious Diseases 8632, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark; HIV Epidemiology and Biostatistics Unit, Department of Infection and Population Health, UCL, London, UK; Center for inflammation and Metabolism, Rigshospitalet; Department of Cardiology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark; Faculty of Health and Medical Scienses, University of Copenhagen, Denmark
WORKPLACE STRESS AND MUSCULOSKELETAL DISORDER: THE RELATIVE ROLES OF PSYCHOSOCIAL AND PHYSICAL RISK FACTORS MUHAMMAD AFDHALUDDIN BIN MUHAMMAD ADIB KGJ 150043 RESEARCH PROJECT SUBMITTED IN PARTIAL FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF ENGINEERING

iii Abstrak.iv Acknowledgement.v List of Figures.vii List of Tables.viii List of Symbols and Abbreviations.ix List of Appendices.x CHAPTER 1: INTRODUCTION.1 1.0 Background Research.1 1.1 Problem Statement.3 1.2 Aim, Purpose and Objectives of Study.5 1.3 Scope & Limitation of Study.5 1.4 Report Outline.6 CHAPTER 2: LITERATURE RIVIEW.7 2.0 Introduction.7 2.1 Work Related Musculoskeletal Disorders (WRMSD). 7 2.2 Psychosocial Stress Factors at Workplace.9 2.3 Models Linking Psychosocial Work Stress to Work-related Musculoskeletal Disorders (WRMSD). 12 2.3. 1 The Balance Theory of Job Design and Stress.12 2.3. 2 The Biopsychosocial Model of Psychosocial Work Stress Factor.14 2.3. 3 Ecological Model.14 2.3. 4 Workstyle Model.15 2.3. 5 Summary of Models.17 2.4 Shared Service Company.17 2.5 Psychosocial Stress Factors Workplace Control Measures.18 2.5. 1 Communication and Feedback.18 Un ive rsi ty of Ma lay a
The PaTagonian TooThfish ( Dissostichus eleginoiDes ) fishery in The Kerguelen islands ( indian oCean seCTor of The souThern oCean )

Patagonian toothfish (Dissostichus eleginoides) have been fished in the Kerguelen Islands zone for 20 years, firstly with trawlers and more recently with longliners. This is the oldest fishery targeting D. eleginoides in the Indian Ocean sector of the Southern Ocean. However illegal, unreported and unregulated (IUU) fishing has occurred in the area since 1997. A generalised linear model (GLM) analysis was performed using statistical data from the legal fishery to assess the trends in and the factors affecting catch-per-unit-effort (CPUE) in both the trawl and the longline fisheries. The most recent trends show a decrease in CPUE, indicating probable local overfishing. The expansion of the bathymetric range of the fishery to increasingly deeper waters seems to have partially masked this situation. In addition, some biological data (such as depth distribution, timing and area of spawning, and movements between geographical sectors) on the adult section of the exploited population have been obtained from scientific observation programs conducted by fishery observers on board fishing vessels.
Precession phasing offset between Indian summer monsoon and Arabian Sea productivity linked to changes in Atlantic overturning circulation

Results from transient climate modeling experiments indicate an in-phase relationship between insolation forcing and Indian summer monsoonal precipitation. This is in contrast to high-resolution radioisotopically dated speleothem oxygen isotope (δ18O) records of China, which showed that East Asian Monsoon maxima lag Northern Hemisphere peak summer insolation by ∼2,700 years, while an approximately 8,000-year time lag was derived from late Pleistocene records of Arabian Sea sediments. Here, we evaluate the precession phase of the Arabian Sea signal by comparing a new high-resolution productivity and oxygen minimum zone (OMZ) intensity record from the Arabian Sea over the past 450,000 years with the results of a transient climate modeling experiment that includes glacial-bound ice volume variations. The well established tuning technique between radioisotopically dated North Atlantic cold events and the occurrence of deep-dwelling planktonic foraminifera in the Arabian Sea for the last glacial cycle was used to extend the Arabian Sea chronology, independent of orbital tuning. Cross-spectral analysis over the last 224,000 years reveals that Arabian Sea productivity maxima lag precession minima by ∼6,900 ± 200 years, i.e., in close agreement with previous reconstructions. Also our climate modeling simulations are in accord with previous studies indicating an in-phase relationship between precession minima and maximum summer monsoon intensity. We argue that the summer monsoon is most likely not the main driver of changes in Arabian Sea biological productivity and OMZ intensity at the precession frequency band, but that changes in the intensity of the Atlantic meridional overturning circulation (AMOC) have played the prominent role in controlling the nutrient delivery into the euphotic layer of the northern Indian Ocean, and hence the amount of primary productivity and intensity of the oxygen minimum zone in the Arabian Sea. Such a mechanism explains the large precession-related time lag between minimum precession and maximum productivity and OMZ conditions in the Arabian Sea, since intensified AMOC occurred during precession maxima.
Title Identification of possible hypoxia sensor for behavioralresponses in a marine annelid , Capitella teleta

Hypoxia often occurs in summer and causes deleterious effects on marine benthic animals. A marine annelid, Capitella teleta, is tolerant to hypoxia, as shown by the fact that it inhabits organically polluted areas, where severe hypoxia is often observed. To understand how this species adapts to the environment, we focused on its hypoxia sensor, and we showed that TRPAbasal was a possible contributor to hypoxia detection inC. teleta. To examine the involvement of TRPA1 in the response of C. teleta to hypoxia, we exposed C. teleta to hypoxic water with or without a TRPA1-specific inhibitor, A-967079. Hypoxic stimulation induced escape behavior in C. teleta from the sediment, and this behavior was suppressed by the inhibitor. The cloned TRPA gene from C. teletawas phylogenetically categorized into TRPAbasal, and contains an oxygen-dependent degradation domain, which is important for the detection of hypoxia. Whole-mount in situ hybridization analysis showed that the gene was transcribed in the prostomium, where sensing functions are localized. These results suggested that the worm has a hypoxia-sensing system possibly utilizing CtTRPAbasal, and this system contributes to expanding the organism’s niches in hypoxic environments by detecting whether hypoxia exceeds a level that would imperil its survival.
Build your own entrepreneur

Disclaimer This document contains a student thesis (bachelor's or master's), as authored by a student at Eindhoven University of Technology. Student theses are made available in the TU/e repository upon obtaining the required degree. The grade received is not published on the document as presented in the repository. The required complexity or quality of research of student theses may vary by program, and the required minimum study period may vary in duration.
Revisiting The Sri Performance Debate: A Heterogeneity-Consistent Approach Abstract version

Short abstract —In earlier research, socially responsible investment (SRI) funds were found to have either a slight underperformance or a statistically indistinguishable performance vis-à-vis conventional funds. However, the approach to testing for this performance differential has mostly been based on a dichotomous distinction between both types of funds. In our paper, we revisit earlier SRI mutual fund performance research by introducing heterogeneity in both the extent to which mutual funds can be socially responsible and the effect of covariates on estimated fund returns. To do so, we implement a robust process-oriented social responsibility sorting tool and a quantile regression estimation approach
3 D PRINTED-POLY ( LACTIC ACID ) SCAFFOLDS WITH IMPROVED BIOACTIVITY FOR BONE TISSUE ENGINEERING

in conferences:  TEIXEIRA, B. N. ; APRILE, P.; THIRÉ, R.M.S.M. ; KELLY, D. J. . Stem cell response to 3D printed PLA scaffolds functionalised with polydopamine and collagen. In: 22nd Bioengineering in Ireland BINI, 2016, Galway. Book of Abstract. Galway: NUI Galway, 2016. p. 79.
An Exploratory Account of Incentives for Underexploitation in an Open Innovation Environment

This paper presents an empirical account of incentives for underexploiting intellectual property in an open innovation setting. In this exploratory empirical account the phenomenon is observed in a research, development and innovation program where participants are required to share intellectual property rights within the consortium. In sum, our argument is that the observed underexploitation is induced by negative incentives for commercialization that follow from setting a coercive open innovation regime that will constrain appropriability of IPR. This phenomenon is named so graphically, because such an event is not only costly in terms of time and resources, but can in fact render IPR effectively worthless in terms of commercial exploitation and block innovation. This finding is pertinent to policy makers designing research, development and innovation instruments, as well as for managers who need to make choices how to implement open practices in innovation. Abstract: This paper presents an empirical account of incentives for underexploiting intellectual property in an open innovation setting. In this exploratory empirical account the phenomenon is observed in a research, development and innovation program where participants are required to share intellectual property rights within the consortium. In sum, our argument is that the observed underexploitation is induced by negative incentives for commercialization that follow from setting a coercive open innovation regime that will constrain appropriability of IPR. This phenomenon is named so graphically, because such an event is not only costly in terms of time and resources, but can in fact render IPR effectively worthless in terms of commercial exploitation and block innovation. This finding is pertinent to policy makers designing research, development and innovation instruments, as well as for managers who need to make choices how to implement open practices in innovation.
University of Dundee The Application of a Performance-Based Self-Administered Intra-procedural Checklist on Surgical Trainees During Laparoscopic Cholecystectomy

Introduction Surgical checklists are in use to reduce errors for safer surgery. We aimed to study the effect of a previously designed performance-based self-administered intra-procedural checklist on the performance of trainees during elective laparoscopic cholecystectomy. Methods Twenty-four laparoscopic cholecystectomies were enrolled into the study. Six surgical trainees each performed four procedures, two without the checklist and directly followed by two procedures with the checklist. A soft beeping sound reminded each trainee to apply the checklist every 4 min during the procedures. The unedited videos were analysed using the human reliability analysis technique for the number of consequential errors, number of interventions by the trainer, number of instrument movements and time execution. The trainees’ satisfaction was assessed on a 5-point Likert scale questionnaire. Nonparametric test was used for data analysis. p value was defined as significant when p\ 0.05. Results Participants performed statistically better with the application of the checklist compared to when no checklist was used, respectively: Median [IQR] total number of errors 1.51 [0.80] versus 3.84 [1.42] (p = 0.002) and consequential errors 0.20 [0.12] versus 0.45 [0.42] (p = 0.005), and the number of instrument movements per time decreased from 11.90 [5.34] to 10.38 [5.16] (p = 0.04). With the introduction of the checklist, the number of interventions by the trainer per time decreased from 2.79 [1.85] to 0.43 [1.208] (p = 0.003). The trainees satisfaction score was 4.5 [1] for the first question, 4 [1] for the second question and 4 [2] for the third question. Conclusion The self-administered intra-procedural checklist improved the performance of surgical trainees and decreased the number of interventions by the trainer during laparoscopic cholecystectomy. The trainees were generally satisfied using the checklist during the procedures.
Resonant triads in the two layer rotating shallow water equations

Analysis of triad resonances of the rotating shallow water equations is examined for the case when there are two free interfaces, with a focus on the parameter regime with small Rossby and Froude numbers. The nonlinear interaction coefficients in the triad equations are derived using a multiple scales analysis, and confirmed using energy and enstrophy conservation. Separate equations controlling the slow geostrophic and fast gravity wave modes are found to first order in the Rossby number (the relevant amplitude parameter), and compared with the two layer quasigeostrophic equations. Important differences between this two layer case and the well-known one layer rotating shallow water equations are found. Unlike the latter case, there are triad interactions in certain parameter ranges between the gravity wave modes due to the presence of two branches of fast gravity waves, an external (barotropic) mode and an internal (baroclinic) mode. Similarly there are two branches of the slow geostrophic mode with a repeated branch of the dispersion relation, and the consequences of this are explored.
DEVELOPING THE INFORMATION SEARCH SYSTEM FOR SELECTING THE MOULDS FORMING ELEMENTS

Today the information environment is highly developed, it enables collecting, processing, storing, distributing, searching and transferring of information. The need for automation of information activities and information resources management at all levels stipulates the demand for the development of information search systems. The subject matter of this research is the information search system for selecting the moulds forming elements. The aim of this work is to reduce the time for searching and determining the main parameters of the matrices, punches and characters by means of creating the information search system for selecting the moulds forming elements. To achieve this goal the following tasks should be solved: to review the main moulds forming elements and their technical parameters; to develop a search algorithm; to develop the database structure for selecting the moulds forming elements; to design the interface of the information search system. While solving the set tasks, the methodology of the systems analysis and modelling was used. The review the main objectives and characteristics of information search systems resulted in the development of the database logical structure which consists of 6 tables. The interface of the information search system was developed. It provides the “easy” and self-explanatory selection of moulds forming elements. Thus, the developed system includes information about the unique number of the forming elements; their type, name and properties; material and features of the quality of a workpiece surface; a workpiece kind and form to determine the nominal dimensions of forming elements. The use of the system enables reducing the time of searching and identifying forming the key technical parameters of forming elements as well as storing and manipulating the data about these elements.
University of Dundee Fully Connected Crf With Data-driven Prior for Multi-class Brain Tumor Segmentation

Grid conditional random fields (CRFs) are widely applied in both natural and medical image segmentation tasks. However, they only consider the label coherence in neighborhood pixels or regions, which limits their ability to model long-range connections within the image and generally results in excessive smoothing of tumor boundaries. In this paper, we present a novel method for brain tumor segmentation in MR images based on fully-connected CRF (FC-CRF) model that establishes pairwise potentials on all pairs of pixels in the images. We employ a hierarchical approach to differentiate different structures of tumor and further formulate a FC-CRF model with learned data-driven prior knowledge of tumor core. The methods were evaluated on the testing and leaderboard set of Brain Tumor Image Segmentation Benchmark (BRATS) 2013 challenge. The precision of segmented tumor boundaries is improved significantly and the results are competitive compared to the start-of-the-arts.
The Surprisingly Broad Range of Professional Skills Required for Engineers

Ensuring engineering program graduates possess the skillset sought by employers is critical to the success of colleges and universities offering these degrees. Accrediting bodies are demanding that engineering programs better integrate professional skills in their curriculum. The IET Accreditation of Higher Education Programmes (AHEP) requires academic programs to include non-technical competencies such as working with information ambiguity, communication, innovation, project management, teamwork, and ethics (AHEP, 2014). The American Society of Engineering Education (ASEE), the American Society of Mechanical Engineers (ASME) and the National Academy of Engineering (NAE) want graduates from engineering programs to possess both technical and non-technical skills (Dukhan and Rayess, 2014). A study of engineering graduates’ perspectives on the importance of various ABET technical and non-technical competencies, found the non-technical skills of working in teams, data analysis, problem solving, and communication were critical to graduates’ professional success (Passow, 2012). Missing from extant literature is a comprehensive understanding of which competencies make up the broad classification generically known as “professional” or “non-technical skills. ” To address this gap, the authors undertake a rigorous literature review to develop a complete list of the competencies that comprise professional skills (e.g. Ahn et al., 2014; Borrego et al., 2013; Colby & Sullivan, 2008; Johnson et al., 2015; Ling, 2002). The 51 competencies identified from the literature are then validated using a database of online employment advertisements seeking engineers. The dataset of job advertisements includes professional opportunities across engineering disciplines. The rigorous methodology of Software-Assisted Content Analysis is used to identify professional skills required of engineering job applicants. Results affirm that employers want engineering graduates to possess a portfolio of professional skills. Job advertisements predominantly required multiple professional skills. Furthermore, results show a positive relationship between the years of experience and number of professional skills required. Results also validate the literature-based list of professional skills, with 65% of those professional skills found in the job advertisements. This study supports that employers seeking to fill engineering positions are requiring a wide range of professional skills, suggesting that the breadth of professional skills needed by engineering program graduates is much greater than what is currently required by accrediting bodies and addressed in most engineering curriculum.