Miracle-dz/UniFAR-FTUs huggingface dataset:
Survival analysis of bank loans in the presence of longterm survivors

In this paper we model competing risks, default and early settlement events, in the presence of long term survivors and compare survival and logistic methodologies. Cause specific Cox regression models were fitted and adjustments were made to accommodate a proportion of long term survivors. Methodologies were compared using ROC curves and area under the curves. The results show that survival methods perform better than logistic regression methods when modelling lifetime data in the presence of competing risks and in the presence of long term survivors.
Machine learning for medical applications

Machine learning has been well applied and recognized as an eﬀective tool to handle a wide range of real situations, including medical applications. In this scenario, it can help to alleviate problems typically suﬀered by researchers in this ﬁeld, such as saving time for practitioners and providing unbiased results. This tutorial is concerned with the use of machine learning techniques to solve diﬀerent medical problems. We provide a survey of recent methods developed or applied to this context, together with a review of novel contributions to the ESANN 2016 special session on Machine learning for medical applications.
A comparative modeling and molecular docking study on Mycobacterium tuberculosis targets involved in peptidoglycan biosynthesis

An alarming rise of multidrug-resistant Mycobacterium tuberculosis strains and the continuous high global morbidity of tuberculosis have reinvigorated the need to identify novel targets to combat the disease. The enzymes that catalyze the biosynthesis of peptidoglycan in M. tuberculosis are essential and noteworthy therapeutic targets. In this study, the biochemical function and homology modeling of MurI, MurG, MraY, DapE, DapA, Alr, and Ddl enzymes of the CDC1551 M. tuberculosis strain involved in the biosynthesis of peptidoglycan cell wall are reported. Generation of the 3D structures was achieved with Modeller 9.13. To assess the structural quality of the obtained homology modeled targets, the models were validated using PROCHECK, PDBsum, QMEAN, and ERRAT scores. Molecular dynamics simulations were performed to calculate root mean square deviation (RMSD) and radius of gyration (Rg) of MurI and MurG target proteins and their corresponding templates. For further model validation, RMSD and Rg for selected targets/templates were investigated to compare the close proximity of their dynamic behavior in terms of protein stability and average distances. To identify the potential binding mode required for molecular docking, binding site information of all modeled targets was obtained using two prediction algorithms. A docking study was performed for MurI to determine the potential mode of interaction between the inhibitor and the active site residues. This study presents the first accounts of the 3D structural information for the selected M. tuberculosis targets involved in peptidoglycan biosynthesis.
Purine Salvage Pathways among Borrelia Species

ABSTRACT Genome sequencing projects on two relapsing fever spirochetes, Borrelia hermsii and Borrelia turicatae, revealed differences in genes involved in purine metabolism and salvage compared to those in the Lyme disease spirochete Borrelia burgdorferi. The relapsing fever spirochetes contained six open reading frames that are absent from the B. burgdorferi genome. These genes included those for hypoxanthine-guanine phosphoribosyltransferase (hpt), adenylosuccinate synthase (purA), adenylosuccinate lyase (purB), auxiliary protein (nrdI), the ribonucleotide-diphosphate reductase alpha subunit (nrdE), and the ribonucleotide-diphosphate reductase beta subunit (nrdF). Southern blot assays with multiple Borrelia species and isolates confirmed the presence of these genes in the relapsing fever group of spirochetes but not in B. burgdorferi and related species. TaqMan real-time reverse transcription-PCR demonstrated that the chromosomal genes (hpt, purA, and purB) were transcribed in vitro and in mice. Phosphoribosyltransferase assays revealed that, in general, B. hermsii exhibited significantly higher activity than did the B. burgdorferi cell lysate, and enzymatic activity was observed with adenine, hypoxanthine, and guanine as substrates. B. burgdorferi showed low but detectable phosphoribosyltransferase activity with hypoxanthine even though the genome lacks a discernible ortholog to the hpt gene in the relapsing fever spirochetes. B. hermsii incorporated radiolabeled hypoxanthine into RNA and DNA to a much greater extent than did B. burgdorferi. This complete pathway for purine salvage in the relapsing fever spirochetes may contribute, in part, to these spirochetes achieving high cell densities in blood.
Simple, Inexpensive, Reliable Method for Differentiation of Candida dubliniensis fromCandida albicans

ABSTRACT Candida dubliniensis is a recently described pathogenic species which shares many phenotypic features with Candida albicans, including the ability to form germ tubes and chlamydospores. These similarities have caused significant problems in the identification of C. dubliniensis by the average clinical mycology laboratory. To facilitate the differentiation of these species, we investigated the growth of 120 isolates of C. dubliniensis and 98 C. albicans isolates at 42 and 45°C on Emmons’ modified Sabouraud glucose agar (SGA) and 10 isolates of each species in yeast-peptone-dextrose broth. None of theC. dubliniensis isolates grew on the agar or in the broth medium at 45°C, while 11 isolates were capable of growing on SGA at 42°C. In contrast, all of the C. albicans isolates but one grew at 45°C on or in either medium. These reproducible results clearly demonstrate that the incubation of isolates suspected to beC. dubliniensis or C. albicans at 45°C provides a simple, reliable, and inexpensive method for the differentiation of the two species.
Unravelling the dynamics of HRM implementation: a process perspective

This dissertation is focused on three research problems. Firstly, the concept of HRM-as-a-process is incomplete. In most studies, the HRM implementation process seems to finish after employees have perceived HRM practices. As such, little is known about what happens to HRM practices during the HRM implementation process and the way in which they evolve. Secondly, in its current state, HRM implementation seems to be a one-directional, mechanistic process which logically leads from point a to b. This suggests that HRM implementation is a plannable process which involves ticking boxes. Herewith, the dynamics of this complex process are overlooked. Thirdly, in HRM implementation literature a strict separation exists between roles of organisational actors in HRM implementation. In this, policymakers design HRM practices, line managers implementation, and employees perceive. However, this clear separation of ‘who does what’ seems to provide an overly simplistic division of tasks. In this dissertation, a process perspective is used to study the dynamics that take place during the HRM implementation process, as well as the roles that organisational actors play in this process. The theoretical insights and empirical findings which are discussed in this dissertation demonstrate that during their implementation process, HRM practices continue to develop. At the moment of taking the decision to adopt a new HRM practice, it is rather an anticipated one, instead of an end product. During the dynamic HRM implementation process, HRM practices evolve into an orchestrated version which is in line with the ideas, interests and routines of organisational stakeholders. Rather than seeing this process as an unwanted effect of the involvement of a large number of stakeholders in HRM implementation, I argue it is a necessary element which can contribute to the creation of a supported, fitting and sustainable HRM practice.
Overview of Live‐Cell Imaging: Requirements and Methods Used

Live-cell imaging is an important analytical tool in laboratories studying biomedical research disciplines, such as cell biology, neurobiology, pharmacology, and developmental biology. Imaging of fixed cells and tissues (for which photobleaching is the major issue) usually requires a high illumination intensity and long exposure time; however, these must be avoided when imaging living cells. Live-cell microscopy usually involves a compromise between obtaining image quality and maintaining healthy cells. Therefore, to avoid a high illumination intensity and long exposure time, spatial and temporal resolutions are often limited in an experiment. Imaging live cells involves a wide range of contrast-enhanced imaging methods for optical microscopy. Most investigations use one of the many types of fluorescence microscopy, and this is often combined with transmitted light techniques, which will be discussed below. Continual advances in imaging techniques and design of fluorescent probes improve the power of this approach, ensuring that live-cell imaging will continue to be an important tool in biology.
Purposeful Normalization When Caring for Husbands Recovering From Prostate Cancer

Despite a growing awareness that prostate cancer is a “couple’s disease,” the coping strategies, subjective distress, and emotional needs of partners are not adequately addressed. To better understand wives’ experiences and processes they enact, we recruited 28 low-income Latinas caring for husbands recovering from prostatectomies to participate in interviews at three time points. Their narratives destabilize a common focus on physical side effects and an implicit bias toward men’s reactions. We critically examine an overarching process of normalization, with underlying themes working both toward and against normality. We identified dissonance between detailed accounts of major lifestyle changes and professed normalization. We detail the women’s purposeful methods to counteract negative impacts on their lives while seeking support externally. A better understanding of women’s strategies and coping is critical to design interventions and education to both capitalize on partners’ role in recovery while also addressing hidden causes of increased subjective distress.
Peer-to-Peer Crowdshipping as an Omnichannel Retail Strategy

Crowdshipping is an emerging operations model proposed to tackle the last-mile delivery problem for online and omnichannel retailers in urban markets. Major retailers such as Amazon and Walmart, as well as start-ups such as Instacart and Deliv, have adopted or experimented with variants of crowdshipping models. Peer-to-peer crowdshipping, i.e., using in-store customers as a resource to deliver online orders), carries important implications on the marketing-operations interface for omnichannel retailers: on the one hand, it offers the opportunity to improve last-mile delivery efficiency (the efficiency effect); on the other hand, it provides an additional tool for the retailer to price discriminate between the online and in-store channels (the pricing effect). We model an omnichannel retail network's pricing decision for its online and in-store channels, and consumers' decisions on purchase, channel choice and participation in crowdshipping. Contrasting two reimbursement modes for crowdshipping, i.e., reimbursing shopper-deliverers their incurred delivery costs or providing an additional premium as a (cross-channel) subsidy, against a store-operated delivery model, our analysis reveals that the potential benefits of crowdshipping to the retailer and consumers depend upon the interactions between the aforementioned efficiency and pricing effects. In particular, whether the efficiency effect benefits the firm depends on the availability of shoppers with low value of time; whereas the pricing effect benefits firms selling high-end products. The impact on consumer surplus of the two effects, however, depend on spatial store density. All in all, peer-to-peer crowdshipping can lead to significant win-win outcomes in dense urban markets for high-end items.
Mobile technologies for the world's children

In this panel, academic, non-profit, and industry professionals will discuss their global perspectives on mobile technologies for the world's children. Panelists will explore such issues concerning children's access to mobile devices, the decreasing age that children have access to these technologies, mobile innovations for learning, and challenges/opportunities in diverse countries. This interactive session will begin with each panelist giving a short summary of their work-to-date with children and various mobile applications. Then the panelists will be asked questions by children from different countries via pre-recorded video. Audience members will be invited to offer their thoughts and comments as well as the panelists during the video question period. Audience members will also be able to ask further questions throughout the panel discussion.
Current Advancements of and Future Developments for Fourth Party Logistics in a Digital Future

This paper aims to analyze the potential future of the 4PL concept based on expert opinions withspecial regard to the influence of digitalization coming with a disruptive trans-formation of supply chains.Service arrangements, provider capabilities and benefits resulting from a 4PL partnership are compared incurrent and future configurations. The research follows an explorative mixed methods approach with semistructuredinterviews followed by an expert panel. This builds a basis for an online survey questionnaire toinquire on important future aspects for the 4PL concept by a sample of respondents from multinationalcompanies. Our results show a clear trend away from simply organizing transportation and logisticsactivities towards the provision of an IT platform as well as further value-added service activities such asplanning, analytics and monitoring. Along with this, IT capabilities appear to be an important differentiatorfor 4PL providers in the future. Moreover, relationships between 4PL providers and their clients becomecloser and more strategic, which leads to a customer valuing not only direct cost reductions but ratherimprovements resulting from optimized operations through superior analysis and planning functions.
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine 928 Transcriptional and Epigenetic Regulation of Epithelial-Mesenchymal Transition

Tan, E. -J. 2013. Transcriptional and Epigenetic Regulation of Epithelial-Mesenchymal Transition. Acta Universitatis Upsaliensis. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine 928. 51 pp. Uppsala. ISBN 978-91-554-8734-8. The transforming growth factor beta (TGFβ) is a cytokine that regulates a plethora of cellular processes such as cell proliferation, differentiation, migration and apoptosis. TGFβ signals via serine/threonine kinase receptors and activates the Smads to regulate gene expression. Enigmatically, TGFβ has a dichotomous role as a tumor suppressor and a tumor promoter in cancer. At early stages of tumorigenesis, TGFβ acts as a tumor suppressor by exerting growth inhibitory effects and inducing apoptosis. However, at advanced stages, TGFβ contributes to tumor malignancy by promoting invasion and metastasis. The pro-tumorigenic TGFβ potently triggers an embryonic program known as epithelialmesenchymal transition (EMT). EMT is a dynamic process whereby polarized epithelial cells adapt a mesenchymal morphology, thereby facilitating migration and invasion. Downregulation of cell-cell adhesion molecules, such as E-cadherin and ZO-1, is an eminent feature of EMT. TGFβ induces EMT by upregulating a non-histone chromatin factor, high mobility group A2 (HMGA2). This thesis focuses on elucidating the molecular mechanisms by which HMGA2 elicits EMT. We found that HMGA2 regulates a network of EMT transcription factors (EMT-TFs), such as members of the Snail, ZEB and Twist families, during TGFβ-induced EMT. HMGA2 can interact with Smad complexes to synergistically induce Snail expression. HMGA2 also directly binds and activates the Twist promoter. We used mouse mammary epithelial cells overexpressing HMGA2, which are mesenchymal in morphology and highly invasive, as a constitutive EMT model. Snail and Twist have complementary roles in HMGA2-mesenchymal cells during EMT, and tight junctions were restored upon silencing of both Snail and Twist in these cells. Finally, we also demonstrate that HMGA2 can epigenetically silence the E-cadherin gene. In summary, HMGA2 modulates multiple reprogramming events to promote EMT and invasion.
Origin of aortic cell clusters in the chicken embryo

In 3‐day‐old embryos the aortic cell clusters formed two parallel ridges in the ventrolateral part of the aorta. The border of the somato‐ and splanch‐nopleures close to the aorta showed a very intensive cell proliferation and a cell emigration up to the aorta. This cell flow and the bilateral appearance of the intraaortic ridges suggested that the aortic cell clusters originated from the coelomic epithelium. This intraembryonic hemopoietic stem cell formation from the splanchnopleure was comparable to that of the blood island formation in the yolk sac from extraembryonic splancnopleure. The appearance of the white blood cells and definitive erythrocytes with adult‐type hemoglobin was preceded by the aortic cell clusters. We concluded that the stem cells of the adult‐type blood developed from the aortic cell clusters whereas the blood islands of the yold sac may contribute only the primitive red blood cells.
Electronic circuit for stand-alone wind energy conversion system

This paper presents an electronic circuit for stand-alone systems application. The converters architecture is composed by a battery charge controller, a step-up converter based on three-state switching cell, and a voltage source inverter (VSI). All of them operate with pulse width modulation (PWM) technique. The battery charge controller is a classic boost converter that operates in continuous conduction mode (CCM) and it is used to regulate the battery bank voltage, and also to reach the maximum power point from wind turbine. The second converter is a step-up, where a secondary winding is coupled to the transformer to raise the battery voltage up to 400VDC. It also operates in CCM applying two overlapping gate signals. In order to perform the DC-AC conversion, a classical voltage source inverter operating with unipolar voltage switching technique is used. Principles of operation, as well as, experimental results of the assembled prototype are presented.
Experimental studies on the axons intrinsic to the glomerular layer of the olfactory bulb.

Lesions have been made in the superficial layers of the dorsal surface of the rat olfactory bulb; the resulting axonal degeneration has been studied with light and electron microscopy, in order to determine the mode and extent of interconnexion of the intrinsic interneurons of the glomerular layer. Although the lesions necessarily involve extrinsic pathways, the axonal distribution of each of the intrinsic neurons may be deduced from this evidence and a knowledge of normal and experimental material. Tufted cell collaterals extend for 6-12 glomeruli, periglomerular cell axons for 4-5 glomeruli and superficial short-axon cell axons for 2-3 glomeruli; these figures correspond well with observations of Golgi-impregnated material. The experimental approach to the study of intrinsic connexions and its applicability to other sites is considered, and the results are discussed from the point of view of neural coding and odour specificity.
Study on Wave Propagation and Boundary Absorption Performance using a Body-of-Revolution Finite-Difference Time-Domain (BOR-FDTD) Method

This paper presents some studies on electromagnetic wave propagation and absorption performance at boundary through an in-house developed solver based on a body-of-revolution finite-difference time-domain (BOR-FDTD) method. A generalized unsplit perfectly matched layer (U-PML) technique is incorporated with the solver. Time domain results on wave propagation through various structures, including parallel-plate disk, coaxial cable and general free-space, and frequency spectrum of the U-PML performance are presented. The U-PML shows a good absorption performance through flexibility in adjusting the layer thickness. The BOR-FDTD method offers tremendous savings in both computational memory and time when rotationally symmetric structures are analyzed
Network-based models of transmission of infectious diseases: a brief overview

The main purpose of this document is to give a brief but mathematically rigorous description of the network-based models of transmission of infectious diseases that are studied on this web site1. Readers will be able to find a much more detailed development of this material in our book chapters [5, 6]. We also briefly describe how the network-based models that are defined here are related to compartment-level models that are used in most on the literature on mathematical epidemiology.
SHIP1 Negatively Regulates Proliferation of Osteoclast Precursors via Akt-Dependent Alterations in D-Type Cyclins and p271

Osteoclasts arise from macrophage progenitors in bone marrow (BMMs) as a consequence of signaling events elicited by M-CSF and receptor activator of NF-κB ligand, acting on their unique receptors, via c-Fms and receptor activator of NF-κB. Both receptors activate the PI3K and MAPK pathways, which promote cell proliferation and survival. SHIP1 is essential for normal bone homeostasis, as mice lacking the protein exhibit osteoporosis resulting from increased numbers of hyper-resorptive osteoclasts. In this study, we show that BMMs from SHIP1 null mice respond to M-CSF, but not receptor activator of NF-κB ligand, by increasing Akt activation. In consequence, there are up-regulation of D-type cyclins, down-regulation of the cyclin-dependent kinase inhibitor p27, and, therefore, increased phosphorylation of the retinoblastoma protein and cell proliferation. Surprisingly, cell survival of wild-type and knockout BMMs is unaltered. Finally, osteoclastogenesis and periarticular bone erosions are markedly increased in SHIP1−/− mice with inflammatory arthritis, a condition characterized by increased M-CSF expression. The SHIP1/Akt pathway therefore suppresses bone loss in pathological states associated with an excess of the cytokine.
Socialising the Losses and Privatising the Gains (The Case of Cyprus Five Years After the Bail-in of Bank Deposits)

Private sector indebtedness in Cyprus remains extremely high. Yet the Government and the banks in Cyprus continue to define the problem as being the non-performing loans (NPLs) and the proposed solution as being any tools and legislation which will improve repayment but also enable the banks to take these off their balance sheets. It is argued that reducing the NPLs in this manner is treating a symptom of the disease. Such sale of loans will not reduce the private debt which is the real problem of the Cyprus economy. On the contrary, it is likely to make private indebtedness a lot worse as the allowed provisions that the banks have been making will be used as discounts to entice the funds and other “investors” to buy them. This is likely to throw the country into a balance sheet recession. This means that because of the excessive and quite unprecedented levels of private debt (3 to 4 times the size of the country’s GDP) weighing on households and corporations alike, it is practically impossible for the country to overcome the recessionary effects of the austerity and forced repayment conditions that would be imposed through the adoption of such myopic and one sided Government policy. The article concludes that the government should not create a bad bank for the NPLs of the banks but rather should establish a reconstruction and development financing institution that will be able to provide solutions and spin back into the economy economically viable projects.