Miracle-dz/UniFAR-FTUs huggingface dataset:
Novel Aberrations Uncovered in Barrett's Esophagus and Esophageal Adenocarcinoma Using Whole Transcriptome Sequencing

Esophageal adenocarcinoma (EAC) has one of the fastest increases in incidence of any cancer, along with poor five-year survival rates. Barrett's esophagus (BE) is the main risk factor for EAC; however, the mechanisms driving EAC development remain poorly understood. Here, transcriptomic profiling was performed using RNA-sequencing (RNA-seq) on premalignant and malignant Barrett's tissues to better understand this disease. Machine-learning and network analysis methods were applied to discover novel driver genes for EAC development. Identified gene expression signatures for the distinction of EAC from BE were validated in separate datasets. An extensive analysis of the noncoding RNA (ncRNA) landscape was performed to determine the involvement of novel transcriptomic elements in Barrett's disease and EAC. Finally, transcriptomic mutational investigation of genes that are recurrently mutated in EAC was performed. Through these approaches, novel driver genes were discovered for EAC, which involved key cell cycle and DNA repair genes, such as BRCA1 and PRKDC. A novel 4-gene signature (CTSL, COL17A1, KLF4, and E2F3) was identified, externally validated, and shown to provide excellent distinction of EAC from BE. Furthermore, expression changes were observed in 685 long noncoding RNAs (lncRNA) and a systematic dysregulation of repeat elements across different stages of Barrett's disease, with wide-ranging downregulation of Alu elements in EAC. Mutational investigation revealed distinct pathways activated between EAC tissues with or without TP53 mutations compared with Barrett's disease. In summary, transcriptome sequencing revealed altered expression of numerous novel elements, processes, and networks in EAC and premalignant BE. Implications: This study identified opportunities to improve early detection and treatment of patients with BE and esophageal adenocarcinoma. Mol Cancer Res; 15(11); 1558–69. ©2017 AACR.
Analysis of business process maturity and organisational performance relations

The paper aims to present results of the study on business process maturity in relation to organisational performance. A two-phase methodology, based on literature review and survey was used. The literature is a source of knowledge about business process maturity and organisational performance, whereas the research on process maturity vs organisational performance in Polish Enterprises provides findings based on 84 surveyed companies. The main areas of the research covered: identification and analysis of maturity related variables and identification of organisational performance perspectives and its relation to process maturity. The study shows that there is a significant positive relation between process maturity and organisational performance. Although there are research on such relation available, they are scarce and have some significant limitations in terms of research sample or the scope of maturity or organisational performance covered. This publication is part of a project funded by the National Science Centre awarded by decision number DEC-2011/01/D/HS4/04070.
Rethinking the relations between identity and foreign policy: analysing Russia’s foreign policy discourse towards China

This master’s thesis aims to reconstruct Russian identity discourse related to its foreign policy towards China. Taking the timeline surrounding the crisis in Ukraine and Crimea (2010-2016), this thesis was based on the background of the rising concept of “pivot to Asia/East”. Using China as the main actor in Russia’s Asian policy, this thesis tries to answer the questions regarding the construction of Russia’s identity discourse towards China and whether the changing Russian policy after Crimea initiate any changing identity. Based on the poststructuralist approach in foreign policy analysis and the methods of discourse analysis as offered by Campbell (1990), Waever (2002), and Hansen (2006), this thesis offers an alternative understanding of the (re)construction of the identity structure and the intricate relationship between identity and foreign policy. In using the Hansen’s methods of discourse analysis, this thesis analyses official speeches and interviews as part of the 1st model of poststructuralist discourse analysis, and both academic articles and opinions as part of the 2nd model. This thesis finds several patterns of discursive identity structure. Firstly, concurring with Waever’s argument, this thesis finds that existing discursive structure created limitations to the possibility of any changes in Russia’s identity/policy before Crimea. The crisis in Ukraine did provide some concrete policy changes, but these changes at the outmost layer of discursive structure were unable to drastically change the identity discourse in Russia related to China in the post-Crimean timeframe. The effect of this limitation was the stagnation of concrete policy switch towards China. From those findings, two important theoretical contributions could be noted. These findings show that there was the aspect of timeframe which poststructuralist theory of identity/foreign policy change should take into considerations when analyzing the probability of change or nonchange. However, this issue did not diminish the usefulness of poststructuralist approach in deepening the understanding of identity construction and its relations with foreign policy.
The Dynamics of Exporting and Innovation: Evidence from the Tunisian Manufacturing Sector

We analyse the dynamics of internationalisation and innovation decisions using firm-level data on Tunisian manufacturing firms from 2004 to 2006. We examine whether there are complementarities between exporting and innovation investments, and whether and how these complementarities affect the firm's performance. The analysis has been conducted on two clusters of firms. The first cluster distinguishes exporters from non-exporters, and the second distinguishes fully exporting firms from others. The results are consistent with complementarities between the exporting and innovation. The results also indicate that these complementarities positively affect the firm's performance for fully exporting firms.
Evidence for the Absence of Stimulus Quality Differences in Tests of the Accuracy of Sexual Orientation Judgments: A Reply to Cox, Devine, Bischmann, and Hyde (2016)

An article recently published in this journal (Cox, Devine, Bischmann, & Hyde, 2016) questioned the validity of existing research on the accurate judgment of sexual orientation from photographs of faces. Specifically, those authors reported a confound in their stimuli whereby the photos of sexual minorities (gay men and lesbians) were of higher quality than the photos of heterosexuals. Based on this finding, they concluded that the accuracy in judging sexual orientation from faces demonstrated in the broader literature is an artifact of stimulus quality differences. Here, we addressed this claim by systematically testing the numerous photo sets that we have used in 61 studies documenting accurate judgments of sexual orientation from facial cues published since 2007. Contrary to their claim, the overwhelming majority of studies (93%) showed no significant differences in photo quality according to sexual orientation. Of those that did show differences, most revealed that heterosexual targets’ photos were actually of higher quality than sexual minority targets’ photos – opposite of what Cox et al. found. In addition, we highlight additional research using stimuli equated for quality differences overlooked in the recent article by Cox et al., lending further support to the conclusion that sexual orientation is legible from multiple sensory cues.
Crime and Punishment (Scotland) Act 1997: A Survey of Sentencers’ Views concerning the Scottish ‘Hybrid Order’

The Crime and Punishment (Scotland) Act 1997 introduced the hospital direction (HD), often termed the ‘hybrid order’ because it allows courts to simultaneously send a mentally disordered offender to hospital and impose a prison sentence, to be completed after hospital discharge. It is the first measure that explicitly allows the imposition of a prison sentence for an offender meeting criteria for detention under the Mental Health (Scotland) Act 1984. A previous survey showed that psychiatrists in Scotland favoured the principle of a hybrid order (Darjee et al., 2000). In this study all Scottish Sheriffs (n=110) and High Court Judges (n=26) were surveyed for their views on the HD. Of the 56 respondents 19 felt unable to participate largely due to lack of experience in sentencing mentally disordered offenders. Respondents felt the HD was a useful measure, but, in contrast to Scottish Office guidance, indicated that psychiatrists should recommend it directly if they considered that it was an appropriate disposal. Respondents viewed the HD as primarily an incapacitating measure and most respondents hoped that it would encourage psychiatrists to admit ‘psychopaths’ although Scottish psychiatrists do not favour the hospitalisation of offenders with primary personality disorders. It is concluded that in its current form and with current guidance the HD is difficult to use, as there are no criteria to differentiate it from a hospital order (HO) and psychiatrists cannot recommend it. Further, recent legislation that makes public safety the primary concern when deciding on the discharge of restricted patients in Scotland, erodes the utility of the HD as an incapacitating measure. However following the Reports of the Millan and MacLean Committees in Scotland, the role of the HD may be strengthened and clarified.
Effects of trade and FDI on economic growth in Africa: an empirical investigation

Abstract The Bhagwati hypothesis predicts a growth enhancing effects of trade (exports) and foreign direct investment (FDI) interaction. This paper tests the validity of the Bhagwati hypothesis by investigating the extent to which the interaction of trade (exports) and FDI has had an impact on economic growth for a sample of 45 African countries over the period 1990–2014. To do so, we estimate an augmented endogenous growth model with the aid of a dynamic system generalised method of moment (GMM) estimation technique, which adequately cope with potential endogeneity issues. The findings reveal support for the Bhagwati hypothesis and provide vital information for policy formulation aimed at promoting more credible export-promotion strategies and channelling of FDI into export-oriented sectors in long-term development strategies in African countries.
Countries Lending Infrastructure and Capital Structure Determination: The case of European SMEs

We test in a European context the impact of countries' lending infrastructure on SMEs (small and medium sized enterprises) capital structure. Devised from Berger and Udell (2006), this infrastructure is comprised of the information, legal, judicial, bankruptcy, social, tax and regulatory environments. We find that SME debt is higher in countries with more efficient bankruptcy environments in terms of debt recovery and in countries with less stringent regulatory environments by way of lower capital regulatory requirements for banks. Components of the lending infrastructure are found to differ with debt maturity. Long-term debt is synonymous with efficient bankruptcy environments, whilst the information and legal environments matter more for short-term debt. The regulatory environment is important for both long-term and short-term debt. Our results also lend support for the Pecking-Order, Trade-Off and Agency theories of capital structure.
Bug Characteristics in Blockchain Systems: A Large-Scale Empirical Study

Bugs severely hurt blockchain system dependability. A thorough understanding of blockchain bug characteristics is required to design effective tools for preventing, detecting and mitigating bugs. We perform an empirical study on bug characteristics in eight representative open source blockchain systems. First, we manually examine 1,108 bug reports to understand the nature of the reported bugs. Second, we leverage card sorting to label the bug reports, and obtain ten bug categories in blockchain systems. We further investigate the frequency distribution of bug categories across projects and programming languages. Finally, we study the relationship between bug categories and bug fixing time. The findings include: (1) semantic bugs are the dominant runtime bug category, (2) frequency distributions of bug types show similar trends across different projects and programming languages, (3) security bugs take the longest median time to be fixed, (4) 35.71% performance bugs are fixed in more than one year, performance bugs take the longest average time to be fixed.
Signal tracking approach for phase estimation in digital holographic interferometry.

In this research work, we introduce a novel approach for phase estimation from noisy reconstructed interference fields in digital holographic interferometry using an unscented Kalman filter. Unlike conventionally used unwrapping algorithms and piecewise polynomial approximation approaches, this paper proposes, for the first time to the best of our knowledge, a signal tracking approach for phase estimation. The state space model derived in this approach is inspired from the Taylor series expansion of the phase function as the process model, and polar to Cartesian conversion as the measurement model. We have characterized our approach by simulations and validated the performance on experimental data (holograms) recorded under various practical conditions. Our study reveals that the proposed approach, when compared with various phase estimation methods available in the literature, outperforms at lower SNR values (i.e., especially in the range 0-20 dB). It is demonstrated with experimental data as well that the proposed approach is a better choice for estimating rapidly varying phase with high dynamic range and noise.
Diversification of sympatric broadcast‐spawning limpets (Cellana spp.) within the Hawaiian archipelago

Speciation remains a central enigma in biology, and nowhere is this more apparent than in shallow tropical seas where biodiversity rivals that of tropical rainforests. Obvious barriers to gene flow are few and most marine species have a highly dispersive larval stage, which should greatly decrease opportunities for speciation via geographic isolation. The disparity in the level of geographic isolation for terrestrial and marine species is exemplified in Hawai‘i where opportunities for allopatric speciation abound in the terrestrial realm. In contrast, marine colonizers of Hawai‘i are believed to produce only a single endemic species or population, due to the lack of isolating barriers. To test the assertion that marine species do not diversify within Hawai‘i, we examine the evolutionary origin of three endemic limpets (Cellana exarata, C. sandwicensis and C. talcosa) that are vertically segregated across a steep ecocline on rocky shores. Analyses of three mtDNA loci (12S, 16S, COI; 1565 bp) and two nDNA loci (ATPSβ, H3; 709 bp) in 26 Indo‐Pacific Cellana species (N = 414) indicates that Hawai‘i was colonized once ∼3.4–7.2 Ma from the vicinity of Japan. Trait mapping demonstrates that high‐shore residence is the ancestral character state, such that mid‐ and low‐shore species are the product of subsequent diversification. The Hawaiian Cellana are the first broadcast‐spawners demonstrated to have speciated within any archipelago. The habitat stratification, extensive sympatry, and evolutionary history of these limpets collectively indicate a strong ecological component to speciation and support the growing body of evidence for non‐allopatric speciation in the ocean.
Measuring low-vision rehabilitation outcomes with the NEI VFQ-25.

PURPOSE To evaluate the sensitivity of the National Eye Institute Visual Functioning Questionnaire-25 (NEI VFQ-25) to change in visual abilities after low-vision rehabilitation in two different Veterans Administration (VA) low-vision programs METHODS Seventy-seven legally blind veterans from the Blind Rehabilitation Center (BRC) at Hines VA Hospital and 51 partially sighted veterans from the Visual Impairment Center to Optimize Remaining Sight (VICTORS) program at the Chicago Health Care Network, West Side Division, were administered the NEI VFQ-25 plus supplement in interview format at admission and discharge. Instructions for administration were modified to have study participants answer all the questions as if they were wearing glasses or contact lenses or were using low-vision devices. Interval measures of person ability and item difficulty were estimated from the patients' responses to 34 of the 39 items on the VFQ-25 plus supplement before and after rehabilitation, by the polytomous rating scale measurement model of Wright and Masters. RESULTS In VICTORS patients, item order by difficulty before rehabilitation agreed with item order for BRC patients. Visual ability scales are used similarly by different patients with different degrees of low vision. Based on prerehabilitation person measure distributions, VICTORS patients were less disabled, as would be predicted by visual acuity, than were BRC patients. After rehabilitation, estimated item difficulty for 4 of the 34 items decreased significantly in both BRC and VICTORS patients. CONCLUSIONS The present study demonstrates that the NEI VFQ-25 plus supplement can be used to measure the effects of low-vision rehabilitation; however, only 7 of the 34 items tested are sensitive to change after rehabilitation. Targeted activities, such as reading ordinary print, small print, and street signs are easier to perform for graduates of both programs after rehabilitation. The patients' visual ability also shows improvement in both BRC and VICTORS. Improvement in visual ability is independent of change in difficulty of targeted items. Although this was not a controlled clinical trial, the decrease in difficulty of targeted items may reflect the use of low-vision aids and training to make tasks easier. The change in visual ability may reflect positive outcomes of rehabilitation or may be the consequence of patients' overestimates of their functional ability at the time of discharge.
Global Path Planning for Autonomous Mobile Robot Using Genetic Algorithm

Mobile robots work in different kinds of environment, and it is necessary for them to move and maneuver in places with objects and obstacles. In order to navigate the robot in a collision free path, path planning algorithms have been presented. The main goal of path planning is to determine the optimal possible path between the initial point and the defined goal position in the minimal possible time. In this work, a path planning method by utilizing genetic algorithm (GA) is presented. The optimized path in terms of length and cost is generated by GA optimization. The proposed method is a global path planning method with hexagonal grid map modelling. It reads the map of the environment and plans the optimized path by using GA method simulated in MATLAB R2012b software. The simulation results are presented and analyzed.
Successful Reduction of Immunosuppression in Older Renal Transplant Recipients Who Exhibit Donor-Specific Regulation

Background. We hypothesized that T-regulatory cells specific for donor alloantigens would protect a renal transplant during partial withdrawal of immunosuppression. Methods. To test this hypothesis, 32 renal transplant recipients aged 55 years and older with excellent renal function were tested for donor-specific regulation (DSR) by trans-vivo delayed type hypersensitivity assay at the time of enrollment (T=0) and 6 months later (T=6). Twenty-two patients had prednisone withdrawn during a 3-month period, whereas 10 controls were maintained on triple therapy (prednisone, cyclosporine, and mycophenolate). Results. Of 22 patients in the steroid withdrawal group, 10 were DSR+ and 12 were DSR− at the time of enrollment (T=0). None of the DSR+ patients experienced acute rejection, nor did any have donor-specific human leukocyte antigen (HLA) antibody during or after withdrawal. Of 12 DSR− patients, three developed acute rejection, which were reversed with bolus steroid treatment, and four were donor-specific antibody+ at T=0 or T=6. Two years later, 80% (8 of 10) of DSR+ patients in the withdrawal group remain steroid free while maintaining excellent renal function, as compared with only 58% (7 of 12) DSR− patients. Patient survival at 4 years was similar for DSR+ (9 of 10) and DSR− (11 of 12) patients in the withdrawal group. Patients maintained on triple therapy remained rejection free during the 4-year follow-up regardless of initial DSR status, with patient survival rate of 70% (7 of 10). Conclusions. DSR before steroid withdrawal may identify a subset of transplant patients who could benefit from reduction of immunosuppression without elevated risk of rejection or deteriorating renal function.
Towards a new framework for SMEs success: a literature review

SMEs have long been established as an effective mechanism to generate employment and promote economic growth. Even though there has been significant empirical research on the determinants of small business success, there is still no agreed-upon definition of SMEs and business success, no unifying theory and with success factors varying with the business environment (country and industry). Knowledge remains more fragmented than cumulative. This paper reviews and synthesises empirical contributions in the small business success literature from the early 1990s with a view to consolidate knowledge. This is done in the form of a conceptual framework that categorises success factors into entrepreneurial, enterprise and business environment. The paper concludes that more empirical research is needed to develop a more unified approach to SMEs success factors and informs thinking on this critical to policy makers and business owners area.
Multidimensional pain assessment in premature neonates: a pilot study.

OBJECTIVE To describe the physiologic and behavioral responses of premature neonates to a painful stimulus. DESIGN Descriptive. SETTING Secondary-level neonatal unit in a large metropolitan university teaching hospital. PARTICIPANTS Forty neonates between 32 and 34 weeks' postconceptual age and less than 5 days' postnatal age. MAIN OUTCOME MEASURES Physiologic (heart rate, oxygen saturation, and intracranial pressure) and behavioral (facial expression and cry) outcomes observed during a routine heel stick. RESULTS Physiologic responses were significant, but were not specific to pain. Behavioral responses were more promising and indicated that premature neonates were capable of responding in a manner similar to full-term neonates. CONCLUSIONS Premature neonates are capable of expressing their pain in a manner similar to healthy, full-term neonates. Factors that alter this response were not clearly delineated. Further research is needed to determine more precise patterns of response in this age group.