Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of gene expression patterns in wild eelpout from the Baltic Sea - Identification of expression patterns for differentially expressed genes connected to pollution

In a world where the human makes large toxic footprints the anthropogenic pollution of the aquatic environment is evident. It is therefore of great importance to understand what and how pollution adversely affect organisms in the environmental ecosystems. The aim of this study is to understand microarray gene expression patterns in the fish eelpout and how they change in connection to pollution. The analysed dataset is unique due to its extensive set-up with 158 wild fish from 16 sites located in four large geographical regions in the Baltic Sea. The expression profiles were found to be highly varying. Clustering analysis showed that fish from the same region and site had a high tendency to group together. Comparison between fish from reference and polluted sites showed significant differences in gene expression but the effects were in general small. This is likely an indication that there are few shared effects between the polluted sites. Similarly, there were small effects on the gene expression between fish with a high and low reproduction success. Large and significant effects were however seen when comparing fish with low and high values of the known biomarker EROD. We also observed strong correlations between measured gene expression for the CYP1A gene and EROD. The strength of the correlation varied between regions and the highest correlation was found at the Swedish west coast. Finally, we assessed the independence between sampled fish and found that several genes had a high within-site correlation (median correlation over all genes were 0.18). Our results suggest that there are small effects on gene expression connected to pollution and reproduction success. We could, however, identify large effects connected to region and site which may indicate that ecological factors and population parameters had a substantial impact on the observed gene expression profiles. Acknowledgements First of all I want to express my gratitude to my supervisor Erik Kristiansson for his excellent guidance into the world of applied statistics and for his never-ending time for questions. Then I would like to thank my collaborators at the University of Gothenburg who not only made this thesis possible but also much more interesting by giving a biological view of the statistical results. It wouldn’t have been as fun without you. Lastly, I want to turn my gratitude to everyone who not contributed directly to the thesis but indirectly by creating a warm atmosphere in which to spend the breaks. Emma Wijkmark, Gothenburg ,July 2014
Steroid Receptors in Renal Cell Carcinoma

Renal cell carcinomas (RCCs) are the most common epithelial neoplasms of adult kidney. It has been estimated that there will be about 60,920 new cases of kidney cancer in the United States in 2011 and about 13,120 people will die from this disease (Siegel et al. 2011). Currently, surgery remains the only effective treatment for RCC, since metastatic disease is highly resistant to radiotherapy and chemotherapy. Approximately 20 to 30% of patients with RCCs present with non-resectable metastatic disease and 20 to 40% of patients undergoing nephrectomy for clinically localized RCC will develop metastatic disease. In the past two decades significant advances in the diagnosis and treatment of patients with RCC have resulted in improved survival of a select group of patients. Prior to the availability of targeted therapies, Interferon-(IFN) was the standard of care but was associated with a low response rate and significant toxicity (Interferon-alpha and survival in metastatic renal carcinoma: early results of a randomized controlled trial. Medical Research Council Renal Cancer Collaborators 1999). High dose interleukin-2 (IL-2) has a similar response rate as IFN, but can cure approximately 3-5% of patients (Yang, Sherry, et al. 2003). Targeted molecular therapies include inhibitors of angiogenesis (Yang, Haworth, et al. 2003), inhibitors of receptor tyrosine kinases with promiscuous targets including VEGFR1 and VEGFR2, PDGFR, C-Kit, Raf kinase, mammalian target of rapamycin (mTOR) (Atkins et al. 2004; Motzer et al. 2006; Porta et al. 2011) and combination treatment modalities (Escudier et al. 2007; Hudes et al. 2007; Motzer et al. 2007). These novel therapies have demonstrated improved outcomes and have become the first line of therapy in patients with advanced metastatic disease or second line of therapy in patients who have failed prior cytokine immunotherapy (Leveridge & Jewett 2011). As new treatment modalities become standard of care, clinical practices in diagnosis and treatment of the primary tumor will undergo revision. For instance, the role of cytoreductive surgery in patients selected for targeted therapy has not yet been established. This could increase the number of cases diagnosed and treated based on core needle biopsies alone, presenting new challenges to surgical pathologists who will likely have to use smaller amounts of tissue to accurately classify the tumor and provide molecular information aimed to personalize clinical care.
The role of the pufX gene product of Rhodobacter capsulatus

The 2.7 kilobase transcript of the puf operon of the photosynthetic bacterium Rhodobacter capsulatus has five open reading frames. The gene products of four of these open reading frames (pufB, A, L,and M) are well characterized as structural polypeptides of the reaction center ipufL and M) and the B870 light-harvesting antenna complex (pufB and A), The role of the pufX gene product has been unknown. By deleting the pufX gene from a plasmid carrying the puf operon and using this plasmid to reconstitute a strain of R. capsulatus which had the puf operon deleted, it was possible to characterize the pufX gene product. It was found that the pufX' mutant was unable to grow photosynthetically until a secondary suppressor mutation had occurred. It appeared that either more than one type of suppressor mutation could occur or that one suppressor mutation could be accompanied by further mutations. To determine the nature of the lesion caused by the deletion of pufX, the structure of the photosynthetic unit and the ability of the subunits of the photosynthetic unit to accomplish energy and electron transfer of the mutant were compared to a pseudo-wild type. Spectrophotometric techniques, including fluorescence detection, reduced minus oxidized spectra, flash-induced absorbance change spectra, and ground state absorption spectra were used for these comparisons as well as biochemical assays. The biochemical assays measured the ability of chromatophores to transfer electrons from a quinone analog to horse-heart cytochrome c and to pump protons in response to light irradiation. The results of these comparisons indicated that the individual components of the photosynthetic unit functioned normally but that electron transfer between these components, specifically between the reaction center and the cytochrome blcx complex, was impaired. It thus seemed likely that there was some structural defect in the photosynthetic unit. The structure of the photosynthetic units of pseudo-wild type and mutant strains was probed using sodium dodecyl sulfate-
Global maps of climate change impacts on the favourability for human habitation and economic activity

This paper analyzes the statistical relationship between climatic factors and the global distribution of population and economic activity. Building on this analysis, a new method is developed for assessing geographically explicit impacts of climate change on the suitability of regions for human habitation and economic activity. This method combines information about differences in the conditional distributions of population density and economic activity across climate categories with climate change projections from an ensemble of general circulation models. In contrast to other cross-sectional analyses of the economic impacts of climate change, the method applied here does not require specific assumptions about the functional form of the relationship between climatic and non-climatic factors on the one hand, and population density and economic activity on the other. The results indicate that climate change will improve the habitability of some scarcely populated regions, in particular in Canada, Scandinavia, Russia, Mongolia, northern China, Tibet, and parts of Central Asia, but it will impair the habitability of many densely populated regions in the eastern USA, southern Europe, northern and southern Africa, eastern China, and parts of Australia. Most parts of India, South-East Asia and Oceania, Central America and northern South America, the Sahara and the Sahel are projected to experience climatic conditions during this century that have no geographical analogue in the present climate. Hence, a large majority of the world’s population is living in regions whose habitability is either projected to decrease or that are projected to experience globally unprecedented climate conditions within this century under a business-as-usual emissions scenario.
Tuning across Universalities with a Driven Open Condensate

Driven-dissipative systems in two dimensions can differ substantially from their equilibrium counterparts. In particular, a dramatic loss of off-diagonal algebraic order and superfluidity has been predicted to occur due to the interplay between coherent dynamics and external drive and dissipation in the thermodynamic limit. We show here that the order adopted by the system can be substantially altered by a simple, experimentally viable, tuning of the driving process. More precisely, by considering the long-wavelength phase dynamics of a polariton quantum fluid in the optical parametric oscillator regime, we demonstrate that simply changing the strength of the pumping mechanism in an appropriate parameter range can substantially alter the level of effective spatial anisotropy induced by the driving laser, and move the system into distinct scaling regimes. These include: (i) the classic algebraically ordered superfluid below the Berezinskii-Kosterlitz-Thouless (BKT) transition, as in equilibrium; (ii) the non-equilibrium, long-wave-length fluctuation dominated Kardar-Parisi-Zhang (KPZ) phase; and the two associated topological defect dominated disordered phases caused by proliferation of (iii) entropic BKT vortex-antivortex pairs or (iv) repelling vortices in the KPZ phase. Further, by analysing the renormalization group flow in a finite system, we examine the length scales associated with these phases, and assess their observability in current experimental conditions.
Using Willingness-to-Pay Surveys When Assessing Dam Removal: A New Hampshire Case Study

As dams in the United States age and become obsolete and river restoration emerges as a new priority, dam removals have increased . Feasibility studies serve to detail the costs and benefits of such proposed dam removals; however, most do not consider intangibles such as the benefits derived from reconnect ing seasonal fish habitat or improving the biological diversity within a river . In this research, a willingness-to-pay survey was used to assign a monetary value to intangible goods associated with the proposed removal of an historic dam on the Ashuelot River in southwestern New Hampshire . Within the town where the dam is located, we administered an intercept survey in order to document environmental, historic, and existence values associated with the dam . Results indicated that the environmental benefits of removing the dam, such as improving water quality and restoring fish populations, were highly valued by surrounding community members, while historic and existence values associated with keeping the dam were significantly lower . The results from this analysis provide further support for removal of this dam .
Bioefficacy of fungicides, bio-control agents and botanicals against leaf spot of turmeric incited by Colletortricum capsici

Efficacy of ten fungicides with three different concentrations, that is, 500, 1000 and 1500 ppm were studied in vitro against Colletortricum capsici by poisoned food technique. Results revealed that Propiconazole was significantly superior to all other fungicides by inhibiting (100%) growth followed by Hexaconazole (96.55%) and Chlorothalonil (86.78%) over control after 10 days of incubation. Biocontrol agent namely, Trichoderma viride,Gliocladium spp. , Trichoderma harzianum, Trichoderma koningii and Pseudomonas fluorescens were evaluated for their efficacy against C. capsici in vitro. Percent inhibition of the test pathogen ranged from 41.18 to 53.33%. T. harzianum, was found to be the most effective antagonist which caused growth inhibition of 53.33%. It showed the possibility of the most ecofriendly and inexpensive method of control of the leaf spot disease. A total of eleven plant extracts which were locally available were evaluated in vitro against C. capsici and were tested applying poisoned food technique. Overall percent inhibition of growth of the fungus ranged from 7.30 to 76.15%. Polyalthia longifoliarecorded maximum inhibition of 76.15% at 15% concentration followed by rhizome extractCurcuma longa with 66.88% and Allium cepa 63.96%. Whereas, Aegale marmelos andParthenium hysterophorus showed minimum mean inhibition of 20.86 and 28.66%, respectively. The results from pot culture experiment revealed that Propiconazole (0.05%) was found to be significantly superior among all the treatments. The next best fungicide was Hexaconazole (0.10%) and Chlorothalonil (0.15%). Among plant extracts, P. longifolia(15%) was superior over all other plant extracts. In the case of biocontrol agents, T. viridewas superior over T. harzianum in pot culture experiment. Key words: Turmeric, efficacy, fungicides, bioagents, botanicals, Colletotrichum capsici.
Professors’ Training in Cardiopulmonary Resuscitation Using Realistic Simulation Evaluation of the Effectiveness*

ABSTRACT Objective: To evaluate the effectiveness of training in cardiopulmonary resuscitation using realistic simulation as a subsidy to plan an emergency training program for healthcare professors. Methods: Quasi-experimental research, whose intervention was the theoretical and practical training and the outcome was the level of knowledge about the guidelines for cardiopulmonary resuscitation, involving 22 professors of health courses from two universities in Sao Paulo, Brazil. The tests were applied in different periods to identify changes after training, both in assessing the quality of training method used, the absorption and relevance of the strategy. Results: There was statistical significance of the success rate between the first and the second test only in the theoretical training, and this result remained after the practical training and realistic simulation, regardless of the professor’s area of ​​expertise. Forty-nine percent (49%) of correct answers were found in a pretest before training, 88% after the theoretical stage and 80% after the third and final period. Conclusion: the number of correct answers between the first and second test increased more significantly and remained in the third test, demonstrating that the strategy of teaching with demonstrative lecture and especially the practicing stage by using realistic simulations were effective, as the practical stage was carried out after 15 days of theoretical training. Keywords: Cardiac Arrest; Cardiopulmonary Resuscitation; Simulated Training.
Segmentation of retinal blood vessels for detection of diabetic retinopathy: A review

Diabetic detinopathy (DR) is effect of diabetes mellitus to the human vision that is the major cause of blindness. Early diagnosis of DR is an important requirement in diabetes treatment. Retinal fundus image is commonly used to observe the diabetic retinopathy symptoms. It can present retinal features such as blood vessel and also capture the pathologies which may lead to DR. Blood vessel is one of retinal features which can show the retina pathologies. It can be extracted from retinal image by image processing with following stages: pre-processing, segmentation, and post-processing. This paper contains a review of public retinal image dataset and several methods from various conducted researches. All discussed methods are applicable to each researcher cases. There is no further analysis to conclude the best method which can be used for general cases. However, we suggest morphological and multiscale method that gives the best accuracy in segmentation.
Factors influencing Manx Shearwater grounding on the west coast of Scotland

Grounding of thousands of newly fledged petrels and shearwaters (family Procellariidae) in built-up areas due to artificial light is a global problem. Due to their anatomy these grounded birds find it difficult to take off from built-up areas and many fall victim to predation, cars, dehydration or starvation. This research investigated a combination of several factors that may influence the number of Manx Shearwater Puffinus puffinus groundings in a coastal village of Scotland located close to a nesting site for this species. A model was developed that used meteorological variables and moon cycle to predict the daily quantity of birds that were recovered on the ground. The model, explaining 46.32% of the variance of the data, revealed how new moon and strong onshore winds influence grounding. To a lesser extent, visibility conditions can also have an effect on grounding probabilities. The analysis presented in this study can improve rescue campaigns of not only Manx Shearwaters but also other species attracted to the light pollution by predicting conditions leading to an increase in the number of groundings. It could also inform local authorities when artificial light intensity needs to be reduced.
E-business Ecosystem and its Evolutionary Path: The Case of the Alibaba Group in China

The rapid growth of online consumers and e-business websites in China has attracted a large number of organizations to participate in the e-business industry; many of them have gone through several stages of evolution and aggregations. The purpose of this study is to apply the business ecosystem theory as the theoretical lens to explore the phenomenon of e-business growth in China. The Alibaba Group was chosen as a case to demonstrate the process by which a typical e-business ecosystem got shaped, developed, and matured. Four stages in the evolution path of Alibaba’s ecosystem and their respective characteristics are identified. The findings are useful for understanding the development of e-business in china. Implications for researchers and practitioners are discussed.
Social risk and ambiguity in the trust game

Despite intensive research there is no clear evidence for a link between lottery risk preferences and risk involved in trusting others. We argue that this is partially due to a misalignment of the underlying sources of risk. Trusting is giving up control to a human source of risk while lottery risk has a mechanistic source. We propose a risky trust game that experimentally elicits social risk preferences that pertain to the same underlying human source. Our results show that transfers in the classic trust game are indeed best explained by social risk preferences and not by lottery risk preferences with an underlying mechanistic source. In addition, we argue that the type of uncertainty also plays a role. In the absence of objectively known probabilities of trustworthiness, trust also has an ambiguous component. We therefore decompose uncertainty in the trust game into social risk and an ambiguous component. Our results provide evidence that, when accounting for social risk, subjects who score high on ambiguity tolerance explain some of the remainder of trusting behavior.
ANTI-EPILEPTIC ACTIVITY OF VANDA TESSELLATA ROXB. ON MAXIMAL ELECTROSHOCK INDUCED SEIZURE IN ALBINO WISTAR RATS

ABSTRACT Vanda tessellata Roxb. (Family: Orchidaceae) plants have been used in the indigenous medicine such as Ayurveda and local traditional medical practices. The petroleum ether extract of Vanda tessellata Roxb. (PVT) was subjected to acute toxicity and then screened for anticonvulsant activity on Maximal Electroshock (MES) induced seizures model in albino wistar rats. Acute toxicity of extract was non toxic up to the recommended dose 2000 mg/kg. p.o. Animals were treated with PVT at doses of 250 and 500 mg/kg body weight. Study results showed, the mean duration of extensor phase of treated groups reduced significant level than compared to control group. PVT showed anti-epileptic activity against MES animal models. However, further studies still needed to be carried on exposure of the extract to humans
PRP Injections in Orthopaedic Surgery: Why, When and How to Use PRP Dynamic Liquid Scaffold Injections in Orthopaedic Surgery

Platelet-rich plasma (PRP) products can be described as any autologous blood platelet concentrate within a plasma suspension. PRP products include plasma and twofold or greater increases in platelet concentrations above baseline levels. The injection of acti- vated PRP in its liquid formulation delivers growth factors locally and simultaneously mimics and amplifies the spontaneous healing response in injured areas and in special cell niches, which would otherwise be inaccessible. This in situ generated transient three-dimensional scaffold will gradually release growth factors and maintain their concentra - tion at the site of the scaffold formation. The combination of liquid PRP with surgical techniques in orthopaedic surgery allows a wide range of therapeutic strategies in the management of injuries in the field of orthopaedics and sports medicine. The use of dif ferent therapeutic elements, including PRP as biological stimuli and rehabilitation and physiotherapy treatments as mechanical stimuli, provides extremely favourable syner-gies that will help fulfil the physician’s objective, to stop the progression of disease and to improve function in the shortest period of time
Australian Home Care Workers’ Learning of Safe Manual Handling

How home care workers adapt what they learn in manual handling classroom training sessions to their workplaces (i.e., their clients’ homes) is central to their own safety, as their musculoskeletal injuries continue to occur at unacceptably high rates. For this inquiry, new workers were directly observed in their workplaces following classroom training. Findings from these observations propose three environmental considerations for supporting new workers to learn safe manual handling techniques: (1) The physical setting for manual handling is important, (2) clients and their significant others may offer a valuable form of learning support, and (c) when initially learning the requirements for their roles, new workers should be encouraged to focus only on the manual handling tasks at hand.