Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection and typing of TT virus DNA genotype by the PCR-RFLP method.

TT virus (TTV) is a novel single-stranded DNA virus that was identified in patients with post-transfusion-hepatitis of non-A-G type in Japan in 1997. We developed a new detection and typing method for TTV DNA strains, by combining polymerase chain reaction (PCR) and restriction fragment length polymorphism (PCR-RFLP) techniques. TTV DNA was amplified by nested-PCR with TTV-specific mixed primers derived from the conserved open reading frame 1 (ORF1) region of the published TTV DNA sequences. Using the enzymes Hae III, Dra I, Eco RI and Pst I, we were able to distinguish between the four TTV genotypes. In 200 serum samples obtained from healthy pregnant women at an outpatient clinic, the positive rate of TTV detection was 27.0%, almost identical to the positive rate of the detection of ORF1-PCR in Japanese healthy individuals. The strains detected in the positive serum samples were genotype 1a (9.3%), genotype 1b (11.1%), genotype 2 (51.9%), genotype 3 (7.4%) and other genotypes (1.9%). This results indicate that genotype 1 and genotype 2 were the two major strains in the Japanese population. Moreover, 10 serum samples (18.5%) presented RFLP patterns in which some genotypes were mixed.
Folate receptor type β is a neutrophilic lineage marker and is differentially expressed in myeloid leukemia

The membrane‐associated folate receptor (FR) type β is elevated in the spleen in patients with chronic myeloid leukemia (CML) and acute myeloid leukemia (AML). In this study, the authors investigated possible cell type and differentiation stage specificity of expression of FR‐β in normal and leukemic hematopoietic cells.
Human snRNA genes use polyadenylation factors to promote efficient transcription termination

RNA polymerase II transcribes both protein coding and non-coding RNA genes and, in yeast, different mechanisms terminate transcription of the two gene types. Transcription termination of mRNA genes is intricately coupled to cleavage and polyadenylation, whereas transcription of small nucleolar (sno)/small nuclear (sn)RNA genes is terminated by the RNA-binding proteins Nrd1, Nab3 and Sen1. The existence of an Nrd1-like pathway in humans has not yet been demonstrated. Using the U1 and U2 genes as models, we show that human snRNA genes are more similar to mRNA genes than yeast snRNA genes with respect to termination. The Integrator complex substitutes for the mRNA cleavage and polyadenylation specificity factor complex to promote cleavage and couple snRNA 3'-end processing with termination. Moreover, members of the associated with Pta1 (APT) and cleavage factor I/II complexes function as transcription terminators for human snRNA genes with little, if any, role in snRNA 3'-end processing. The gene-specific factor, proximal sequence element-binding transcription factor (PTF), helps clear the U1 and U2 genes of nucleosomes, which provides an easy passage for pol II, and the negative elongation factor facilitates termination at the end of the genes where nucleosome levels increase. Thus, human snRNA genes may use chromatin structure as an additional mechanism to promote efficient transcription termination in vivo.
The Link between Health Condition Costs and Standard of Living: A Structural Equation Modelling

This study employs a Structural Equation Modelling (SEM) to explore the health related costs using the Standard of Livings (SoL) approach in Turkey, employing data from the crosssectional Household Budget Survey (HBS) over the period 2002-2013. The SEM allows us to investigate all these concerns simultaneously. A health condition index is created regarding questions related to the mental and physical limitations (disability) of people. The study extends the previous research by the following ways. First, a SEM framework is introduced, which accounts for the measurement error in both SoL and health-condition indices and it allows for the simultaneous estimation of the link between health condition costs and SoL using structural equations. The underlying theory of the SoL approach is that a household’s SoL is a function of needs and income and the additional costs of disability can be estimated by comparing the standard of livings of household with and without disabled members and controlling for other source of variation. The results show that disability has a significant and negative impact on SoL. Second, exploiting the health reform of 2008, a quasi-experiment approach using difference-in-difference (DID) regression within a SEM framework between the disabled and non-disabled households takes place. The disability related costs consist of the 23 per cent of the household income corresponding to 4,000 Turkish Liras (TL).
Coherent Change Detection for Multi-Polarization SAR

This paper presents a solution to the coherent change detection (CCD) problem using multi-polarization synthetic aperture radar (SAR) imagery. The multi-polarization SAR imagery (i.e., the day-1 reference and day-2 test images) are modeled as jointly correlated complex Gaussian vectors with unknown correlation, rho = gammaejPhi . Maximum likelihood estimates of the unknown phase and coherence parameters (Phi,gamma) are derived. Accuracy of the MLE estimates is evaluated; and the benefit of using multi-polarization data versus single-polarization data is quantified
Gene expression profiling of yeasts overexpressing wild type or misfolded Pma1 variants reveals activation of the Hog1 MAPK pathway

Dominant negative PMA1 mutants render misfolded proteins that are retained in the endoplasmic reticulum (ER) and slowly degraded by ER‐associated degradation. Accumulation of misfolded proteins in the ER activates an ER‐to‐nucleus signalling pathway termed the unfolded protein response (UPR). We have used a PMA1‐D378T dominant negative mutant to analyse its impact on UPR induction. Our results show that overexpression of the misfolded mutant Pma1 does not lead to activation of the UPR. In addition, in mutants with a constitutively activated UPR the turnover rate of the mutant ATPase is not altered. To determine if the expression of the misfolded mutant protein induces some other kind of response we performed global gene expression analysis experiments in yeasts overexpressing either wild type or dominant lethal PMA1 alleles. The results suggest that the high osmolarity glycerol (Hog1) mitogen‐activated protein kinase (MAPK) pathway is activated by both wild type and mutant ATPases. We show that expression of the PMA1 alleles induces phosphorylation of Hog1 and activation of the Hog1 MAPK cascade. This activation is mediated by the Sln1 branch of the stress‐dependent Hog1 MAPK network. Finally, we show that at least two other plasma membrane proteins are also able to activate the Hog1 MAPK system.
Essential role of caspase‐11 in activation‐induced cell death of rat astrocytes

We have previously shown that rat astrocytes undergo apoptosis upon inflammatory activation. Nitric oxide (NO) produced by activated astrocytes was the major cytotoxic mediator in this type of autoregulatory apoptosis. However, an inhibitor of nitric oxide synthase did not completely block the apoptosis of activated astrocytes, suggesting the presence of other apoptotic pathways. Here, we present evidence that caspase‐11 is an essential molecule in NO‐independent apoptotic pathway of activated astrocytes. Inflammatory activation (lipopolysaccharide, interferon‐γ, and tumor necrosis factor‐α treatment) of rat astrocyte cultures and C6 glioma cells led to the induction of caspase‐11 followed by activation of caspases‐11, ‐1, and ‐3. In contrast, NO donors induced activation of caspase‐3 only. Inactivation of caspase‐11 by the transfection of dominant negative mutant or treatment with the caspase inhibitors rendered the astrocytes partially resistant to the apoptosis following inflammatory activation, but not NO donor exposure. These results indicate that inflammatory stimuli not only induce the production of cytotoxic NO, but also␣initiate NO‐independent apoptotic pathway through the induction of caspase‐11 expression.
CO2-Emissionszertifikate - Preismodellierung und Derivatebewertung

EU-Unternehmen mussen seit 2005 entsprechend ihrem CO2-Ausstos genugend Emissionszertifikate einreichen. Da die Zertifikate frei handelbar sind, stellt sich ihnen CO2 als ein zusatzlicher Produktionsfaktor mit unsicherem Preis dar. Derivative Finanzinstrumente helfen beim Management der damit verbundenen Risiken. Die Arbeit analysiert und beantwortet grundlegende Fragestellungen zur Modellierung und Bewertung solcher Finanzinstrumente im Emissionshandel.
Multistate Comparison of Attractants for Monitoring Drosophila suzukii (Diptera: Drosophilidae) in Blueberries and Caneberries

ABSTRACT Drosophila suzukii Matsumara, also referred to as the spotted wing drosophila, has recently expanded its global range with significant consequences for its primary host crops: blueberries, blackberries, raspberries, cherries, and strawberries. D. suzukii populations can increase quickly, and their infestation is difficult to predict and prevent. The development of effective tools to detect D. suzukii presence in new areas, to time the beginning of activity within a crop, to track seasonal activity patterns, and to gauge the effectiveness of management efforts has been a key research goal. We compared the efficiency, selectivity, and relationship to fruit infestation of a range of commonly used homemade baits and a synthetic formulated lure across a wide range of environments in 10 locations throughout the United States. Several homemade baits were more efficient than apple cider vinegar, a commonly used standard, and a commercially formulated lure was, in some configurations and environments, comparable with the most effective homemade attractant as well as potentially more selective. All alternative attractants also captured flies between 1 and 2 wk earlier than apple cider vinegar, and detected the presence of D. suzukii prior to the development of fruit infestation. Over half the Drosophila spp. flies captured in traps baited with any of the attractants were not D. suzukii, which may complicate their adoption by nonexpert users. The alternative D. suzukii attractants tested are improvement on apple cider vinegar and may be useful in the development of future synthetic lures.
Current evidence of peripheral vestibular symptoms secondary to otitis media

Abstract Background: The association between otitis media and vestibular symptoms has been hypothesized in the past. Thus, in this study, we aimed to critically analyze (based in a systematic review of the literature) whether patients who have otitis media are at greater risk of developing vestibular impairment or not. Methods: We performed a systematic review of the literature and identified potentially relevant articles reporting vestibular symptoms and results of vestibular function tests in patients with otitis media through searches of the PubMED, Web of Science, Scopus, and Google Scholar databases. The quality of the final set of records was assessed using the “Newcaste–Ottawa Scale”. Results: Of the 2334 records searched, 43 met our inclusion and exclusion criteria, and those included 2250 patients. The records comprised 20 longitudinal studies, 21 cross-sectional studies, and 2 case reports. Regarding the type of otitis media studied, 25 examined vestibular impairment in otitis media with effusion, 6 acute otitis media, and 12 chronic otitis media. Results of anamnesis, clinical exams, and several vestibular function tests are reported and critically discussed. Conclusion: Most studies evaluating the association between otitis media and vestibular symptoms have potential methodological flaws. Clinical evidence suggests that patients with otitis media have increased chances for having vestibular symptoms, delayed acquisition of developmental milestones, and abnormalities in several vestibular function tests as compared with controls. Future studies with rigorous methodology aiming to assess the clinical significance (and prognostic factors) of the association between otitis media and vestibular impairment are warranted. Key message Several studies demonstrated long-term sequelae secondary to otitis media. However, the evidence supporting those assumptions are based in low-quality evidence. Thus, better structured studies are warranted to better understand the clinical relevance of such association.
Functional MRI Detection of Deception After Committing a Mock Sabotage Crime *

Abstract: Using Blood Oxygen Level Dependent (BOLD) functional MRI (fMRI) to detect deception is feasible in simple laboratory paradigms. A mock sabotage scenario was used to test whether this technology would also be effective in a scenario closer to a real‐world situation. Healthy, nonmedicated adults were recruited from the community, screened, and randomized to either a Mock‐crime group or a No‐crime group. The Mock‐crime group damaged and stole compact discs (CDs), which contained incriminating video footage, while the No‐crime group did not perform a task. The Mock‐crime group also picked up an envelope from a researcher, while the No‐crime group did not perform this task. Both groups were instructed to report that they picked up an envelope, but did not sabotage any video evidence. Participants later went to the imaging center and were scanned while being asked questions regarding the mock crime. Participants also performed a simple laboratory based fMRI deception testing (Ring‐Watch testing). The Ring‐Watch testing consisted of “stealing” either a watch or a ring. The participants were instructed to report that they stole neither object. We correctly identified deception during the Ring‐Watch testing in 25 of 36 participants (Validated Group). In this Validated Group for whom a determination was made, computer‐based scoring correctly identified nine of nine Mock‐crime participants (100% sensitivity) and five of 15 No‐crime participants (33% specificity). BOLD fMRI presently can be used to detect deception concerning past events with high sensitivity, but low specificity.
Predicting noncompliant levels of ochratoxin A in cereal grain from Penicillium verrucosum counts

Aims: To model the probability of exceeding the European legislative limit of 5 μg ochratoxin A (OTA) per kilogram grain in relation to Penicillium verrucosum levels and storage conditions, and to evaluate the possibilities of using P. verrucosum colony counts for predicting noncompliant OTA levels.
The impact of hard and soft policy measures on new technology-based firms

ABSTRACT The impact of hard and soft policy measures on new technology-based firms. Regional Studies. Entrepreneurship policies in support of new technology-based firms fall into two main categories of intervention: hard measures (financial-type support such as loans and grants) and soft measures (counselling and business advice services). This study investigates the association between hard and soft support measures delivered to entrepreneurs, and the performance of the subsequently constituted new technology-based firms. The empirical framework analyses the outcomes of the Spinner Programme – a regional policy measure implemented in the Italian region of Emilia-Romagna during 2000–06. The analysis finds that soft measures are positively related to a higher probability of exiting the market and to higher sales growth. The results also show that the magnitude of the effect of soft measures on growth is greater than the effect of hard measures.
Texture Slab Projection and BSP Tree for GPU Accelerated Volume Rendering

An improved method using graphics processing unit (GPU) is proposed for ray casting algorithm because of large volume data and slow speed in volume rendering. The algorithm combines texture slices to form texture slabs, and codes texture slabs with BSP tree, then, projects the slabs and renders non-empty slabs from front to back. Because of texture slab projection includes information of empty region, full region and early ray terminated region of volume data, so accelerated volume rendering can be achieved through texture slab projection along the ray direction. Texture slab projection is created on the fly by GPU without any pre-processing time, and the creation time of BSP tree is still small in relation to the whole volume rendering. The experiment results show that this method can speed up average 3.41 times of volume rendering on GPU and achieve good rendering effects.
Exploring Italy's Growth Challenge: A Model-Based Exercise

Since the mid-1990s, Italy’s economic growth faltered, primarily due to sluggish productivity growth. This article investigates the root causes of the slow growth. Firstly, it benchmarks Italy over time visa-vis euro area and OECD countries in the area of human capital, product market regulation, taxation structure and innovation. The analysis shows that Italy's gaps in these areas have grown over the last 15 years and are particularly large for human capital. Secondly, it uses a set of stylized simulations in QUEST R&D model of the European Commission to assess the potential impact of a package of growth-enhancing reforms in these areas. The simulations show that structural reforms could boost productivity and GDP growth significantly. Important reforms are ongoing. Given the very nature and the size of the gaps, it is important that the reform momentum is maintained.
"Health in All Policies": taking stock of emerging practices to incorporate health in decision making in the United States.

OBJECTIVE Policies affecting the determinants of health lie largely outside the control of the health care and public health sectors. Ensuring health considerations in the formation and implementation of policies, programs, projects, and plans from all sectors, though lofty, is the overall aim of Health in All Policies. The purpose of this article was to identify categories of strategies that illustrate how Health in All Policies had been implemented in the United States. DESIGN We used a 3-phased process: (1) review of the published and gray literature; (2) analysis of case examples to identify a draft framework, which included tactics and strategies for implementing Health in All Policies; and (3) vetting the draft framework through individual and group consultation. RESULTS We identify 7 interrelated strategies for incorporating health considerations into decisions and systems: (1) developing and structuring cross-sector relationships; (2) incorporating health into decision-making processes; (3) enhancing workforce capacity; (4) coordinating funding and investments; (5) integrating research, evaluation and data systems; (6) synchronizing communications and messaging; and (7) implementing accountability structures. For each strategy, we provide illustrative examples from the United States to help public health leaders identify effective tactics for Health in All Policies implementation. CONCLUSIONS Through our review, we offer a starting point for categorizing and describing the emerging practices used to work across sectors and address the determinants of health. By delineating the different types of strategies and tactics to achieve Health in All Policies, we provide public health practitioners with a "menu" of options for incorporating Health in All Policies into their work.
Mechanistic aspects of HIV‐1 reverse transcription initiation

During reverse transcription, the positive‐strand HIV‐1 RNA genome is converted into a double‐stranded DNA copy which can be permanently integrated into the host cell genome. Recent analyses show that HIV‐1 reverse transcription is a highly regulated process. The initiation reaction can be distinguished from a subsequent elongation reaction carried out by a reverse transcription complex composed of (at least) heterodimeric reverse transcriptase, cellular tRNAlys3 and HIV‐1 genomic RNA sequences. In addition, viral factors including Tat, Nef, Vif, Vpr, IN and NCp7, cellular proteins, and TAR RNA and other RNA stem‐loop structures appear to influence this complex and contribute to the efficiency of the initiation reaction. As viral resistance to many antiretroviral compounds is a continuing problem, understanding the ways in which these factors influence the reverse transcription complex will likely lead to novel antiretroviral strategies. Copyright © 2001 John Wiley & Sons, Ltd.
Stories becoming sticky : how civic initiatives strive for connection to governmental spatial planning agendas

This thesis aims to understand the phenomenon of self-organizing civic initiatives, how they engage in and connect to planning practices aimed at the improvement of the quality of places and why these connections lead to alteration or transformation of governmental planning agendas or not. By providing greater understanding about these processes the thesis aims to contribute to debates about how planners can improve connections with civil society initiatives and how a more responsive and adaptive attitude towards a dynamically changing society can be achieved. Conclusions were drawn from two in-depth case-studies of civic initiatives in two Dutch regions: 1) initiatives of business entrepreneurs and experts to develop New Markets which support the cultural landscape of the region Heuvelland, and 2) initiatives of citizens for the protection and development of landscape values in the urban-rural fringe Gouda-Krimpenerwaard. Building on agenda-setting and framing theory the analysis focused on how initiatives self-organized and connected to other stakeholders and how outcomes of their efforts in terms of their ambitions and government agendas could be understood. The research results point to the crucial role of storytelling and the day-to-day interactions in which stories emerge and become ‘sticky’. Sticky stories are strong ‘attractors’ that mobilize attention and support. The stickiness of a story was enhanced through discursive processes in which the story was connected to the self-referential frames of targeted supporters. Thus, sticky stories could not emerge without empathic listening, timing and patience. Three interplaying conditions were critical in the process of a story becoming sticky or fading away: 1) formal and informal ‘catalytic’ conversations as the medium of storytelling; 2) storytelling by people who perform as connectors and enable the travelling of stories through a wider network, and 3) signalling and incorporating focusing events into evolving stories in ways considered meaningful and relevant by targeted supporters. This results in a model that offers a way to understand dynamical change of policy and planning agendas by focusing on the interactive construction, connection, and subtle alteration of stories in day-to-day conversations, by the right people, at the right moments.
Three-dimensional organ modeling based on deformable surfaces applied to radio-oncology

This paper describes a method based on an energy minimizing deformable model applied to the 3D biomechanical modeling of a set of organs considered as regions of interest (ROI) for radiotherapy. The initial model consists of a quadratic surface that is deformed to the exact contour of the ROI by means of the physical properties of a mass-spring system. The exact contour of each ROI is first obtained using a geodesic active contour model. The ROI is then parameterized by the vibration modes resulting from the deformation process. Once each structure has been defined, the method provides a 3D global model including the whole set of ROIs. This model allows one to describe statistically the most significant variations among its structures. Statistical ROI variations among a set of patients or through time can be analyzed. Experimental results are presented using the pelvic zone to simulate anatomical variations among structures and its application in radiotherapy treatment planning.