Miracle-dz/UniFAR-FTUs huggingface dataset:
The zoonotic pathogen Borrelia afzelii in its natural hosts : Bacterial dissemination and immuno-transcriptomics

Most pathogens can infect a number of different host species, but host species often differ considerably in susceptibility to a given pathogen. In the case of zoonotic pathogens, natural hosts typically present little or no disease symptoms, while humans and other “spill-over” hosts often present severe symptoms. Differences in susceptibility do not only occur between natural and non-natural hosts, though, but also among natural hosts.The natural hosts of the tick-transmitted bacterium Borrelia afzelii, which is one of three causative agents of Lyme borreliosis in humans, include a variety of small mammals like voles and mice. Studies of Borrelia infection in laboratory mice and humans have revealed mechanisms behind susceptibility to disease. However, less is known about colonization, pathology, and host immune responses to Lyme borreliosis spirochetes in their natural hosts.In this thesis, I used B. afzelii and its natural hosts (primarily yellow-necked mouse, Apodemus flavicollis; and bank vole, Myodes glareolus) as study system to investigate the colonization of a zoonotic pathogen in different natural host species, and the possible factors that cause inter- and intra-specific variation in susceptibility.In papers I-III, I focused on interspecific variation in susceptibility to B. afzelii. In Paper I, I found that B. afzelii disseminates from the site of infection (skin) to internal tissues in natural hosts, like spirochetes do in non-natural hosts, but levels of colonization vary between both species and tissues. Significantly higher bacterial loads were seen in bank voles than in yellow-necked mice. However, none of the natural hosts showed signs of pathological effects of B. afzelii infection. In Paper II, species-specific regulation of immune responses (IFNα response, IL6 signaling and the complement pathway) associated with B. afzelii resistance was demonstrated by using RNA-sequencing to quantify gene expression in the spleen of voles and mice. Further analyses of the RNA-seq data set indicated that interspecific divergence in expression of pattern recognition receptors (PRRs), and cyto- and chemokines contribute disproportionately to interspecific variation in immune function in general (Paper III). In Paper IV, I focused on intra- specific variation in resistance in the bank vole, and showed that the previously demonstrated effect of variation in the PRR TLR2 on resistance to B. afzelii could be a result of polymorphisms in the coding sequence, and/or polymorphisms in non-coding sequences affecting expression of TLR2.In summary, the findings in this study have provided new insights to understand the causes of inter- and intraspecific variation in susceptibility to a zoonotic pathogen in its natural host species. (Less)
DockAnalyse: An Algorithm for Protein-Protein Interaction Analysis

Is it possible to know what the best solution is of the output of a docking program? The apparent obvious answer to this question is the highest-score solution, but the interaction between proteins seems to be a dynamic mechanism where the interaction region has to be wide enough to allow protein-protein interactions coming from different orientations, and sometimes, as in a multimeric complex, several interacting regions are possible. Consequently, in all these cases, there is not a single solution. To extract the significant solutions from the docking-output data, we have developed an unsupervised and automatic cluster computational program supported on a mathematical algorithm. This algorithm is based on the DBscan clustering method, which searches for continuities among clusters generated by the outputdocking data representation. The DBscan clustering method solves some of the inconsistency problems of the classical clustering methods like k-means: a) it allows the easy treatment of outliers (isolated points) taking into account only those clusters that are large enough to be an interaction region, b) it allows the finding of all cluster members independently of the cluster shape and, c) it is not dependent on the previously defined number of clusters. A pre-processing step finds the radius, which is necessary to run the DBscan method, without requiring any tuning parameter by the user. We used this approach to postulate complex interaction mechanisms that involve surface displacements among proteins that interact together to carry out a specific function. Another useful application for the mathematical model presented here could be the prediction of the putative structure of protein complexes. The algorithm and the application (implemented in the R package) are accessible on: http://wwweio.upc. es/~delicado/Rfiles/DockAnalyse.zip.
Revisiting Telemetry in Pakistan’s Indus Basin Irrigation System

The Indus Basin Irrigation System (IBIS) lacks a system for measuring canal inflows, storages, and outflows that is trusted by all parties, transparent, and accessible. An earlier attempt for telemetering flows in the IBIS did not deliver. There is now renewed interest in revisiting telemetry in Pakistan’s IBIS at both national and provincial scales. These investments are typically approached with an emphasis on hardware procurement contracts. This paper describes the experience from field installations of flow measurement instruments and communication technology to make the case that canal flows can be measured at high frequency and displayed remotely to the stakeholders with minimal loss of data and lag time between measurement and display. The authors advocate rolling out the telemetry system across IBIS as a data as a service (DaaS) contract rather than as a hardware procurement contract. This research addresses a key issue of how such a DaaS contract can assure data quality, which is often a concern with such contracts. The research findings inform future telemetry investment decisions in large-scale irrigation systems, particularly the IBIS.
Validation testing of an integrated process and structural health monitoring system based on piezoelectric sensors on a PAX door edgemember made by RTM

Recently the authors developed a novel integrated process and structural health monitoring concept based on piezo sensors. The basic idea is to place a number of piezo sensors on predefined positions over the RTM mold. In a first step the piezo sensors are operated as pressure sensors to monitor the flow front propagation in the mold. Once the whole pre-form was impregnated by the resin and curing starts, the impedance of the piezo sensors are measured over the time and the change in the impedance spectrum is used to determine the degree of cure. Finally, when the curing process is finished, all piezo sensors are co-cured on the surface of the part and remain on the part to be used for structural health monitoring either in passive mode as acoustic emission sensors or in active mode using guided ultrasonic waves. Within this paper the authors will present detailed validation results of the developed system during the production and damage assessment of a PAX door edge-member made by Resin Transfer Molding. The results showed that the developed system is very well suited to monitor the flow front propagation, the curing status and simulated impact damages.
Effects of media stereotypes of older workers on the aggregate level

Information distributed via the news media is acknowledged as a potential source of negative beliefs about, and biased behaviors towards, olderworkers. Focusingon theNetherlands, the current study explains age discrimination claims filed by older workers by investigating the impact of visibility and media stereotypes of older workers in the news media, while controlling for real-world events and older workers’ expectations of unemployment (2004 – 2014). The results, based on time-series analysis, reveal that the visibility of older workers in the newsmedia is associated with higher levels of age discrimination claims. This effect can be partly explained with the visibility of the negative media stereotype that older workers experience health problems in the content of news coverage. Furthermore, unemployment expectations decreased the number of age discrimination claims. These results offer support for the notion that the news environment is a source of variation in the experience of age discrimination at the workplace.
Raman Spectroscopy and Single ‐ Crystal High ‐ Temperature Investigations of Bentorite , Ca 6 Cr 2 ( SO 4 ) 3 ( OH ) 12 ∙ 26 H 2 O

The crystal structure of bentorite, ideally Ca6Cr2(SO4)3(OH)12·26H2O, a Cr3+ analogue of ettringite, is for the first time investigated using X‐ray single crystal diffraction. Bentorite crystals of suitable quality were found in the Arad Stone Quarry within the pyrometamorphic rock of the Hatrurim Complex (Mottled Zone). The preliminary semi‐quantitative data on the bentorite composition obtained by SEM‐EDS show that the average Cr/(Cr + Al) ratio of this sample is >0.8. Bentorite crystallizes in space group P31c, with a = b = 11.1927(5) Å, c =21.7121(10) Å, V = 2355.60(18) Å3, and Z = 2. The crystal structure is refined, including the hydrogen atom positions, to an agreement index R1 = 3.88%. The bentorite crystal chemical formula is Ca6(Cr1.613Al0.387)Σ2[(SO4)2.750(CO3)0.499]Σ3. 249(OH)11.502∙~25.75H2O. The Raman spectra of bentorite from two different localities exhibit the presence of the main stretching and bending vibrations related to the sulfate group at 983 cm−1 (ν1), 1109 cm−1 (ν3), 442 cm−1 (ν2), and 601 cm−1 (ν4). Moreover, the presence of bands assigned to the symmetric Cr(OH)63− stretching mode and hydroxyl deformation vibrations of Cr–OH units at ~540 cm−1 and ~757 cm−1, respectively, may be used to distinguish between ettringite and bentorite. In situ high temperature single crystal XRD experiments show that the decomposition of bentorite starts at ca. 45 °C and that a dehydroxylation product similar to metaettringite is formed.
Running head: TASK SWITCHING HURTS MEMORY ENCODING Task Switching hurts Memory Encoding

Research consistently shows that task switching slows down performance on switch compared to repeat trials, but the consequences on memory are less clear. In the present study, we investigated the impact of task switching on subsequent memory performance. Participants had to switch between two semantic classification tasks. In Experiment 1 the stimuli were univalent, in Experiment 2 the stimuli were bivalent (relevant for both tasks). The aim was to disentangle the conflicts triggered by task switching and bivalency. In both experiments, recognition memory for switch and repeat stimuli was tested subsequently. During encoding, task switching produced switch costs. Critically, subsequent memory was lower for switch compared to repeat stimuli in both experiments, and this effect was increased in Experiment 2 with bivalent material. We suggest that the requirement to switch tasks hurts the encoding of task-relevant information and thus impairs subsequent memory performance.
COMIBINATORIAL EFFICACY OF GTF ON ALTERED HEMATOLOGICAL AND LIPID PROFILE IN TYPE-2 DIABETIC WISTAR RATS

Objective To investigate the combinatorial effect of polyherbal formulation of GTF on altered haematological indices in high fat diet and high fructose fed Type-2 diabetic rats. Methods A total of 24 rats, 18 diabetic and 6 normal rats were used for this study. Diabetes was induced in male Wistar rats by high fat diet and high fructose feeding. After being confirmed diabetic, animals were orally treated with GTF polyherbal formulation in the ratio of 2:3:1 (100 mg, 150mg and 50mg/kg body weight) daily for 30 days. The haematological parameters including red blood and white blood cells and their functional indices were evaluated in diabetic, diabetic treated groups compared with the controls. Results GTF significantly reduced the blood glucose and lipid levels except HDL in HFD and HF fed diabetic rats. Similarly, the levels of red blood, white blood cells and their functional indices were significantly restored after GTF administration. Conclusions It can be concluded that the GTF possesses antihyperglycemic and anti-hyperlipidemic properties. In addition, the extract can prevent various complications of diabetes and improve some haematological parameters. Further experimental investigation is needed to exploit its relevant therapeutic effect to substantiate its ethnomedicinal usage.
The Role of Autophagy in Pancreatic Cancer—Recent Advances

Pancreatic ductal adenocarcinoma (PDAC) remains one of the deadliest cancers with a 5-year survival rate of only 9%, despite ongoing efforts to improve treatment. This dismal prognosis is due to the difficulty of early stage diagnosis, drug resistance, and likelihood of metastasis development. It is therefore of great importance to identify appropriate therapeutic targets and gain a greater understanding of PDAC biology. Autophagy is a membrane-mediated degradation and recycling mechanism, which is crucial for cell homeostasis. There is evidence for both a tumor-suppressive and a tumor-promoting role of autophagy in cancer, and this is likely context dependent. Within PDAC, a large body of evidence points towards autophagy being required for tumor survival and metabolism. In this review, we describe the recent advances in the understanding of the role and regulation of autophagy in PDAC.
Empirical characterization of faults in complex software systems, and strategies to mitigate them

With software systems becoming increasingly large and complex, coping with software defects (“bugs”) is more and more difficult. Despite good development practices, thorough testing, and proper maintenance policies, software is still shipped with a significant number of bugs, which represent a severe threat for the reliability and security of critical infrastructures. The practice of defect analysis is recognized as an essential task for software process and product improvement. Understanding the type of residual bugs is fundamental for adopting proper countermeasures in current and future software releases. Researchers, across years, have analysed bugs from different viewpoints in order to improve the knowledge about their characteristics. Regardless of the semantics of the error committed by a developer, a fundamental aspect in bug comprehension is related to the process by which a bug manifests itself as a failure. In fact, while static properties of a bug (e.g., its type, or origin) are related to how a bug is introduced in the code, there are different causes for a bug provoking a failure. Expectedly, many bugs systematically cause the same failure on a given (sequence of) input(s). On the other hand, there is a non-negligible set of bugs that cause a failure depending on the state of the execution environment, and hence may appear as non-deterministic or transient failure, as the failure does not occur unless the environment is in a certain state. The latter category contains bugs that have likely escaped testing, since their exposure may be a rare event. Specific strategies are required to cope with these bugs. Examples are fault tolerance strategies that mask faults, for instance by reinitializing the software state and retrying the failed operation, and verification techniques that do not need to actually reproduce the fault trigger during execution, such as code reviews and model checking. Instead, faults that can easily be triggered require more thorough testing in order to improve reliability. Therefore, knowing how bugs manifest themselves (namely, the fault triggering conditions that make the bug to surface as a failure, and to impact on the rest of the infrastructure) is strictly tied to the effectiveness of in-process fault detection/correction activities, and of runtime mechanisms against resid-
THE CREATIVITY OF READING FICTION: AN EXPLORATION OF THE CREATIVE PROCESSES AND RESPONSES OF FICTION READERS

Fiction reading is a valuable leisure activity with the potential to confer a wide range of positive benefits upon readers. The indication is that reading can powerfully impact upon an individuals’ quality of life, and this has led to increased efforts to promote fiction reading in recent years. Reader-centred approaches (known collectively as reader development) are key to this promotional effort. They aim to develop confident readers capable of maximising the quality of each reading encounter through an increased understanding of their own reading experience. Integral to this approach is the concept of ‘creative reading’, which is intended as a means of raising the status of the reader as an active, creative force. Little is known about the creative processes that take place within fiction reading; this study aimed to provide an increased understanding of the way in which readers ‘create’ their own reading experience. In order to provide a basis for the recognition of the interaction between reader and text, reader-response theory was used as the theoretical framework for this study. The detailed, nuanced nature of the information required indicated the need to apply qualitative research methods. In accordance with best practice in this field, focus groups were the primary research tool in this study. Focus group composition was a purposive sample of enthusiastic readers who could provide rich, high quality data. In addition, a comprehensive literature review was undertaken. Findings indicated that readers played an important creative role in the reading experience, with the majority of readers identifying the existence of a creative partnership between the reader and the writer. Highly creative processes and outcomes were very much in evidence across all groups, and evidence suggested that textual quality was of only limited importance in this area. However, it was clear that despite the strong evidence in support of reader creativity, reading continued to be viewed as non-creative by many. There was a distinct indication that earlier reading interventions through formal education were key to the formation of this view, through the emphasis that such teaching placed on
Evaluation of Sleep Quality in Patients with Breast Cancer

Evaluation of Sleep Quality in Patients with Breast Cancer This study aimed to characterize the socio-demographic and clinical profile of patients with breast cancer and to evaluate their quality of sleep. It is an exploratory-descriptive research with quantitative approach, developed in the Rio Grande do Norte League against Cancer, a reference center in the city of Natal-RN, in the period from January to March of 2011. The data collection instruments were: clinical and socio-demographic score sheet, The Pittsburgh Sleep Quality Index, and Intervenient Factors Affecting Sleep Quality. The study included 52 women with a clinical diagnosis of breast cancer. They were between 51-60 years old (30.8%); married or in consensual union (46.2%); with household income of 1-2 minimum wages (84.6%); 57.8% had incomplete primary education; 73% were Catholic and 67.3% from the interior of the state. Clinically it was observed that the patients had diagnostic time not under 6 months (46.1%) and the treatment chosen was surgery (78.8%) or chemotherapy (44.2%). In addition, 59.6% presented changes in sleep quality. The chemotherapy or radiotherapy proved to be an intervenerto an unpleasant sleep (63%) due to pain symptoms (33.3%). Health professionals should understand the importance of sleep in the promotion of the quality of life for patients with breast cancer and act so as to track possible changes and look for interventionist measures.
Evaluation of Efficacy of Walnut (Juglans Nigra) On Blood Pressure, Haematological and Biochemical Profile of Hypertensive Subjects.

The potential anti-hypertensive effects associated with the administration of walnut was investigated using 130 hypertensive subjects. Result showed that Juglans nigra normalizes high blood pressure if short term meal of walnut is taken; other parameters that walnut normalises are high cholesterol and serum electrolytes. Walnut meal has no effect on haemoglobin concentration, white blood cell count, Packed cell volume and platelet counts compared with their corresponding controls. It could be deduced from this study that walnut contains some principle elements that is anti-hypertensive.
A Collaboration System Model for Planning and Evaluating Participatory Design Projects

Understanding the complexity of collaboration is vital to planning and evaluating participatory design (PD) projects. PD has become more popular over the past decade due to its effectiveness in generating appropriate solutions and socially and creatively empowering involved participants. As it has spread into more varied fields of application, the number of documented challenges has also increased. For example, the use of PD with participants with low-education levels in developing contexts has resulted in challenges focused on a lack of experience with formal activities, lack of tenacity, and lack of creative ability (Mazzurco, 2016; Molapo & Marsden, 2013; Winschiers, 2006). Similarly, challenges focused on the technical expert’s ability to equalize power relations, use appropriate activities, and work within the relevant socio-cultural context have also been noted (Godjo, Boujut, Marouzé, & Giroux, 2015; Kam et al., 2006; Winschiers-Theophilus, Chivuno-Kuria, Kapuire, Bidwell, & Blake, 2010). In an attempt to understand the causes of these challenges, an increasing number of researchers have investigated PD collaboration, focusing on participation (Brandt, 2006; Druin, 2002), evaluation of participation (Frauenberger, Good, Fitzpatrick, & Iversen, 2015; Gerrard & Sosa, 2014), and participant empowerment (Drain, Shekar, & Grigg, 2017; Hussain, 2010). However, there is a need for a holistic conceptual model to describe the influential components of PD collaboration explicitly, as well as their interaction. Such a model would allow for more detailed planning of PD projects and evaluation of their effectiveness and help to address criticisms that PD lacks “empirically demonstrable benefits in outcomes” (Wang & Oygur, 2010, p. 357). This article presents the PD Collaboration System Model, a new conceptual model for planning and evaluating collaboration during PD projects. The article begins by examining extant literature in the areas of PD and PD collaboration. It then presents six first-hand case studies that were undertaken by the first author, designing assistive technology with people with disability in rural Cambodia. Finally, the Collaboration System Model is presented and discussed in relation to both extant literature and case study findings. This article adds to the field of PD through providing a new conceptual model with which to explicitly understand the components that influence collaboration and how these components interact with each other. With this new understanding, we argue PD practitioners can better plan their collaborative activities, by explicitly optimizing each component ORIGINAL ARTICLE