Miracle-dz/UniFAR-FTUs huggingface dataset:
A Novel Prioritization Method in Identifying Recurrent Venous Thromboembolism-Related Genes

Identifying the genes involved in venous thromboembolism (VTE) recurrence is important not only for understanding the pathogenesis but also for discovering the therapeutic targets. We proposed a novel prioritization method called Function-Interaction-Pearson (FIP) by creating gene-disease similarity scores to prioritize candidate genes underling VTE. The scores were calculated by integrating and optimizing three types of resources including gene expression, gene ontology and protein-protein interaction. As a result, 124 out of top 200 prioritized candidate genes had been confirmed in literature, among which there were 34 antithrombotic drug targets. Compared with two well-known gene prioritization tools Endeavour and ToppNet, FIP was shown to have better performance. The approach provides a valuable alternative for drug targets discovery and disease therapy.
GENERALIZATION BASED ON LEAST SQUARES ADJUSTMENT

The paper presents solutions for generalization problems using least squares adjustment theory. This concept allows for the introduction of several observations in terms of constraints and for a holistic solution of all these - possibly contrary and competing - constraints. Two examples are used to demonstrate the validity of this approach: the simplification of building ground plans and the displacement of arbitrary cartographic objects. Each approach is verified with several examples; furthermore, the integration of these different approaches is presented, in terms of the fusion of cadastral and topographic data. Least Squares Adjustment theory (LSA) is a well known general framework to determine unknown parameters based on given observations. This optimization technique is well founded in mathematics, operations research, and in geodesy. This general concept allows for the integration of different constraints in order to solve an overall, complex problem. This paper proposes to use adjustment theory for generalization. One problem is the set-up of the constraints for the various generalization tasks. The generalization of building ground plans is formulated in terms of a model-based approach, the problem being the determination of the model. In this case it is derived by the application of some rules. The second generalization operation treated with LSA is displacement: different objects have to be displayed on a map - for reasons of legibility certain constraints have to be satisfied, e.g. minimal object sizes and minimal object distances have to be enforced. LSA offers a straightforward framework to introduce different kinds of these constraints. In one step, all these constraints are solved simultaneously, resulting in one optimized solution with the feature that all residuals are distributed evenly among all the observations. Besides this result, quality parameters indicate how well the initial constraints have been satisfied. The paper is organized as follows: after a review of related work, the simplification of building ground plans using a model-based approach is presented, together with some examples showing the possibilities and the deficiencies. Then the approach for displacement based on least squares adjustment is shown, giving both the theoretical background, and explanatory examples. The integration of the two approaches is demonstrated with the example of the fusion of cadastral information with topographic information. Finally, a summary concludes the paper.
Assessing representations of South African Indian English in writing: An application of variation theory

This article examines three representations of South African Indian English in print: The Adventures of Applesammy and Naidoo (1946) by Ray Rich; The Lahnee's Pleasure (c. 1972) by Ronnie Govender; and The Wedding (2001) by Imraan Coovadia. The use of dialect is a defining feature of all three texts. I show that the tools provided by variation theory are particularly useful in the analysis of literature that uses direct speech to portray characters and types. In particular, the principles of variation theory can be used to: (a) reveal the nature of stereotyping in the first text (a parody), which relies on the suppression of variation, and the generalization of linguistic and social characteristics; (b) evaluate the fidelity of a “realist” dialect representation of the community in the second text (a play); and (c) help characterize the nonrealist, nonstereotyping, imaginative use of language in the third text (a post-modern novel). An early version of the research for this article was presented at the IAWE (International Association of World Englishes) Conference, Potchefstroom University, 2001; at seminars at the University of Cape Town and University of Pennsylvania in 2002; and at NWAVE (New Ways of Analysing Variation in English and Other Languages), Stanford University, 2002. A revised and expanded version was presented at ASNEL (Association for the Study of New English Literatures), Magdeburg, 2003. I thank participants at these conferences and three anonymous LVC referees for feedback and comments, Malcah Yaeger-Dror for discussions of her related research, and Sarah and Clare Johnson for the graphics. I am especially grateful to the University of Cape Town's Research Committee for a grant that supported this research.
Cohesin controls planar cell polarity by regulating the level of the seven‐pass transmembrane cadherin Flamingo

Planar cell polarity (PCP) refers to the coordination of global organ axes and individual cell polarity in vertebrate and invertebrate epithelia. Mechanisms of PCP have been best studied in the Drosophila wing, in which each epidermal cell produces a single wing hair at the distal cell edge, and this spatial specification is mediated by redistribution of the core group proteins, including the seven‐pass transmembrane cadherin Flamingo/Starry night (Fmi/Stan), to selective plasma membrane domains. Through genetic screening, we found that a mutation of the SMC3 gene caused dramatic misspecification of wing hair positions. SMC3 protein is one subunit of the cohesin complex, which regulates sister chromatid cohesion and also plays a role in transcriptional control of gene expression. In the SMC3 mutant cells, Fmi appeared to be upregulated by a posttranscriptional mechanism(s), and this elevation of Fmi was at least one cause of the PCP defect. In addition to the PCP phenotype, the loss of the cohesin function affected wing morphogenesis at multiple levels: one malformation was loss of the wing margin, and this was most likely a result of downregulation of the homeodomain protein Cut. At the cellular level, apical cell size and hexagonal packing were affected in the mutant wing. Dysfunction of cohesin in humans results in Cornelia de Lange syndrome (CdLS), which is characterized by various developmental abnormalities and mental retardation. Our analysis of cohesin in epithelia may provide new insight into cellular and molecular mechanisms of CdLS.
Culture-Independent Investigation of the Microbiome Associated with the Nematode Acrobeloides maximus

Background Symbioses between metazoans and microbes are widespread and vital to many ecosystems. Recent work with several nematode species has suggested that strong associations with microbial symbionts may also be common among members of this phylu. In this work we explore possible symbiosis between bacteria and the free living soil bacteriovorous nematode Acrobeloides maximus. Methodology We used a soil microcosm approach to expose A. maximus populations grown monoxenically on RFP labeled Escherichia coli in a soil slurry. Worms were recovered by density gradient separation and examined using both culture-independent and isolation methods. A 16S rRNA gene survey of the worm-associated bacteria was compared to the soil and to a similar analysis using Caenorhabditis elegans N2. Recovered A. maximus populations were maintained on cholesterol agar and sampled to examine the population dynamics of the microbiome. Results A consistent core microbiome was extracted from A. maximus that differed from those in the bulk soil or the C. elegans associated set. Three genera, Ochrobactrum, Pedobacter, and Chitinophaga, were identified at high levels only in the A. maximus populations, which were less diverse than the assemblage associated with C. elegans. Putative symbiont populations were maintained for at least 4 months post inoculation, although the levels decreased as the culture aged. Fluorescence in situ hybridization (FISH) using probes specific for Ochrobactrum and Pedobacter stained bacterial cells in formaldehyde fixed nematode guts. Conclusions Three microorganisms were repeatedly observed in association with Acrobeloides maximus when recovered from soil microcosms. We isolated several Ochrobactrum sp. and Pedobacter sp. , and demonstrated that they inhabit the nematode gut by FISH. Although their role in A. maximus is not resolved, we propose possible mutualistic roles for these bacteria in protection of the host against pathogens and facilitating enzymatic digestion of other ingested bacteria.
Play to win: How competitive modes of play have influenced cultural practice in digital games

The aim of this thesis is to explore the function of emergence and spectatorship as cultural practices within the competitive arena of Blizzard's World of Warcraft (WoW). The game and its peripheral web spaces and paratexts will be subject to both qualitative and quantitative research approaches, including content analysis and autoethnography. Grounded theory content analysis was used to explore emergence in the context of player gameplay tactics (emergent play). It is argued that players who succeed in the game's competitive arena do so on the privilege of effective tactics and a thorough understanding of the game mechanics. Additional insight into the phenomenon of emergence was gained from a study of paratexts and the ways in which emergence conflicts with authorial intent. The ecology of competitive gaming is comprised not only of players but also spectators. Grounded theory content analysis and quantitative analysis were used to examine the cultural practice of spectatorship. Broadcasting platforms (Twitch.tv and YouTube) facilitate indirect player interaction with games. It is my contention that viewers utilise these broadcasts of highend play as a form of paratext to guide their individual playstyle. Analyses suggest that the spectatorship of live and recorded emergent gameplay is directly linked to the formulation of gameplay tactics. Data also indicated tension between authorial intent and emergent practices. In some instances players worked with developers as co-authors to highlight malfunctioning gameplay mechanics (exposed via emergent play patterns). Other scenarios involved the conveyance of absolute authorial power by Blizzard. As a result of these differing relationships with players, Blizzard appear to have struggled with the implementation of a linear, single-authored experience. Although my own gameplay experiences guided the exploration of emergence and spectatorship, my expertise with the game facilitated a sophisticated mechanical analysis and allowed me to provide novel cultural insights into competitive play. The outcomes of this research inform both theory and practice. New typologies for understanding games are established. This inquiry introduces the term emergent paratext in order to best understand the function of paratexts within competitive play. In terms of practical implications, this study will help develop a more complete consumption model for digital
Travelling neo-tribes: conceptualising recreational vehicle users

Neo-tribes have been defined as including people from different walks of life who come together in fluid groupings, bound by common interests, similar lifestyles, rituals and language. This concept is popular in sociological literature, but has rarely been applied to travellers or tourism literature. This study sought to understand whether neo-tribalism could add insights into our existing knowledge of recreational vehicle (RV) users in Canada. Using a grounded theory approach including focus groups and in-depth interviews, the research found RV users exhibit neo-tribal characteristics which can be characterised as symbolic and behavioural. The behavioural aspects of this neo-tribe are evident in campsites, where rituals such as happy hours exist. Symbolic aspects included fluidity of membership and commitment to the RVing lifestyle. The findings suggest that the neo-tribal concept is a highly useful tool for understanding the motivations, behaviour and needs of travellers and adds new insights into our understanding of the RVing experience.
RETRIEVAL OF SOIL MOISTURE DATA AT GLOBAL SCALES WITH AMSR-E

An algorithm for the estimate of the soil moisture content on a global scale from dual-frequency (Cand Xbands) microwave data of the Advanced Microwave Scanning Radiometer (AMSR-E) is presented in this paper. The algorithm is based on the brightness temperature at C-band and uses the Polarization Index at X-band to correct for vegetation effects. The retrieval is obtained by inverting a simplified Radiative Transfer model by using the NelderMead iterative minimization method. The algorithm was validated with microwave data collected on two sites, located in Italy and in Iowa (US), during the MASMEx02 (Microwave Alpine Soil Moisture Experiment) and the SMEX02 (Soil Moisture Experiment) experiments, respectively.
Relation between hospital orthopaedic specialisation and outcomes in patients aged 65 and older: retrospective analysis of US Medicare data

Objective To explore the relation between hospital orthopaedic specialisation and postoperative outcomes after total hip or knee replacement surgery. Design Retrospective analysis of US Medicare data, 2001-5. Setting 3818 US hospitals carrying out total joint replacement. Population 1 273 081 Medicare beneficiaries age 65 and older who underwent primary or revision hip or knee replacement. Main outcome measures Hospitals were stratified into fifths on the basis of their degree of orthopaedic specialisation (lowest fifth, least specialised; highest fifth, most specialised). The primary outcome was defined as a composite representing the occurrence of one or more of pulmonary embolism, deep vein thrombosis, haemorrhage, infection, myocardial infarction, or death within 90 days of the index surgery. Results As hospital orthopaedic specialisation increased from the lowest fifth to highest fifth, the proportion of people admitted who were women or black, or who had diabetes or heart failure progressively decreased (P<0.001), whereas procedural volume increased. Compared with the most specialised hospitals (highest fifth), after adjustment for patient characteristics and hospital volume, the odds of adverse outcomes increased progressively with decreased hospital specialisation: lowest fifth (odds ratio 1.59, 95% confidence interval 1.53 to 1.65), second fifth (1.32, 1.28 to 1.36), third fifth (1.24, 1.21 to 1.28), and fourth fifth (1.10, 1.07 to 1.13). Conclusions Increased hospital orthopaedic specialisation is associated with improved patient outcomes after adjusting for both patient characteristics and hospital procedural volume. These results should be interpreted with caution because the possibility that other unmeasured confounders related to socioeconomic status or different factors are responsible for the improved patient outcomes rather than hospital specialisation can not be excluded. The findings suggest that hospital specialisation may capture different components of hospital quality than the components captured by hospital volume.
Obedience in Modern Society: The Utrecht Studies

The Utrecht Studies on Obedience, a series of 19 experiments, demonstrated that obedience is extremely high when the violence to be exerted is a contemporary form of mediated violence, and remains high even when the subjects receive detailed information about the task in advance. Observation of the subjects and analysis of data from questionnaires and the debriefing show that the subject's attitude to the experimenter's commands is critical to very critical, and that they found it unpleasant and stressful to carry out the task. This stress was not, however, sufficient to make the subjects disobedient. They attempted to hide their stress from the victim and to act as if nothing was wrong, displaying the behavior of an official. The explanation for the high level of obedience should not be sought in the inability of the subjects to resist the scientific authority (see the results of the condition of Legal Liability), but in their attitude to social institutions and their distant relationship with fellow citizens. Active role playing offers an attractive opportunity for ethically acceptable obedience research.
Early Cosmic Chemical Evolution: Relating the Origin of a Diffuse Intergalactic Medium and the First Long-Lived Stars

Nucleosynthetic signatures in common are found between the gas responsible for the high-redshift Lyα forest and a subsample of extremely metal-poor stars. A simple mass-loss model of chemical evolution with physically motivated parameters provides a consistent picture in which the gas is identified with that lost by supernova-driven winds during the first generation of star formation. Substantial mass loss occurs, which can account for a diffuse IGM with up to 80% of the total baryon content and a peak [C-O/H] abundance of ~-2.9. This mass-loss component differs from one produced later, during galaxy formation and evolution, which contributes to a circumgalactic medium (CGM). The CGM has earlier been shown to have a mass of ~10% of all baryons and peak [Fe/H] ~ -1.
Investigating interruptions in the context of computerised cognitive testing for older adults

Interruptions in the home pose a threat to the validity of self-administered computerised cognitive testing. We report the findings of a laboratory experiment investigating the effects of increased interruption workload demand on older adults' computerised cognitive test performance. Related work has reported interruptions having a range of inhibitory and facilitatory effects on primary task performance. Cognitive ageing literature suggests that increased interruption workload demand should have greater detrimental effects on older adults' performance, when compared to younger adults. With 36 participants from 3 age groups (20-54, 55-69, 70+), we found divergent effects of increased interruption demand on two primary tasks. Results suggest that older and younger adults experience interruptions differently, but at no age is test performance compromised by demanding interruptions. This finding is reassuring with respect to the success of a self-administered computerised cognitive assessment test, and is likely to be useful for other applications used by older adults.
Structure of human procathepsin L reveals the molecular basis of inhibition by the prosegment.

Cathepsin L is a member of the papain superfamily of cysteine proteases and, like many other proteases, it is synthesized as an inactive proenzyme. Its prosegment shows little homology to that of procathepsin B, whose structure, the first for a cysteine protease proenzyme, has been determined recently. We report here the 3‐D structure of a mutant of human procathepsin L determined at 2.2 A resolution, describe the mode of binding employed by the prosegment and discuss the molecular basis for other possible roles of the prosegment. The N‐terminal part of the prosegment is globular and contains three alpha‐helices with a small hydrophobic core built around aromatic side chains. This domain packs against a loop on the enzyme's surface, with the aromatic side chain from the prosegment being located in the center of this loop and providing a large contact area. The C‐terminal portion of the prosegment assumes an extended conformation and follows along the substrate binding cleft toward the N‐terminus of the mature enzyme. The direction of the prosegment in the substrate binding cleft is opposite to that of substrates. The previously described role of the prosegment in the interactions with membranes is supported by the structure of its N‐terminal domain. The fold of the prosegment and the mechanism by which it inhibits the enzymatic activity of procathepsin L is similar to that observed in procathepsin B despite differences in length and sequence, suggesting that this mode of inhibition is common to all enzymes from the papain superfamily.
Teste de Bender com disléxicos: comparação de dois sistemas de pontuação

The present study aimed to evaluate maturity and dysfunctional aspects referred to visualmotor perception of dyslexics using for this, the Bender Test analyzed under two correction systems, being the gradual scoring system (B-SPG) and Lacks system. Twenty dyslexics have taken part in the research with ages from 9 to 16 years (average=12), being 16 males and 4 females. The data showed the average of mistakes committed by the dyslexics was above the expected for children from nine to ten years who compose the B-SPG normative sample. According to the Lacks scoring system the factors more affected in the sample of dyslexics were referred to changes on the gestalt form and distortions, factors which are equivalent to the form distortions on the B-SPG. The correlation index between these two systems was significant (r = 0.76).
Crystal structure of 2-(2,4-dichlorophenyl)-4-hydroxy-9-phenylsulfonyl-9H-carbazole-3-carbaldehyde

The hydroxy group in this carbazole derivative is involved in an intramolecular O—H⋯O hydrogen bond, which generates an S(6) graph-set motif. In the crystal, pairs of C—H⋯Cl hydrogen bonds link molecules into inversion dimers with an R 2 2(26) motif. Weak C—H⋯O interactions further link these dimers into ribbons propagating in [100].
Invisible Marker Tracking System Using Image Watermarking for Augmented Reality

In this paper, we propose a new tracking system based on invisible markers using the image watermarking technique for augmented reality. Markers are invisibly embedded into image or video contents and then it is extracted from the scene image acquired by a general camera. Our method has the advantages of the marker-based methods and the marker-less methods at the same time without additional hardware.
Hierarchical Control or Individuals' Moral Autonomy? Addressing a Fundamental Tension in the Management of Business Ethics

There is a fundamental tension in business ethics between the apparent need to ensure ethical conduct through hierarchical control, and the encouragement of individuals' potential for autonomous moral judgement. In philosophical terms, these positions are consequentialist and Kantian, respectively. This paper assumes the former to be the dominant position in practice, and probably in theory also, but regards it as a misplaced extension of the more general managerial tendency to seek and maintain control over employees. While the functions of such control are recognized, the arguments in favour of individuals' moral autonomy are pursued from both a Kantian and a socialtheoretic perspective. Reference is made to Kohlberg's research on moral development that provides an insight into how individuals, through participation in debate with colleagues, might become more effective moral agents within organizational settings. This is contrasted with a managerial perspective, which pays lip service to individuals' right to such genuine involvement. The paper considers psychological manipulation and the legitimacy of managerial authority on matters of ethics, as opposed to in the purely technical context. The wider societal significance of such hierarchical power in organizations constitutes an important background to the paper. It is concluded that genuine, non-manipulative, participation by employees (and others) is the way forward for the ethical management of business ethics.