Miracle-dz/UniFAR-FTUs huggingface dataset:
Knockout of Drosophila RNase ZL impairs mitochondrial transcript processing, respiration and cell cycle progression

RNase ZL is a highly conserved tRNA 3′-end processing endoribonuclease. Similar to its mammalian counterpart, Drosophila RNase ZL (dRNaseZ) has a mitochondria targeting signal (MTS) flanked by two methionines at the N-terminus. Alternative translation initiation yields two protein forms: the long one is mitochondrial, and the short one may localize in the nucleus or cytosol. Here, we have generated a mitochondria specific knockout of the dRNaseZ gene. In this in vivo model, cells deprived of dRNaseZ activity display impaired mitochondrial polycistronic transcript processing, increased reactive oxygen species (ROS) and a switch to aerobic glycolysis compensating for cellular ATP. Damaged mitochondria impose a cell cycle delay at the G2 phase disrupting cell proliferation without affecting cell viability. Antioxidants attenuate genotoxic stress and rescue cell proliferation, implying a critical role for ROS. We suggest that under a low-stress condition, ROS activate tumor suppressor p53, which modulates cell cycle progression and promotes cell survival. Transcriptional profiling of p53 targets confirms upregulation of antioxidant and cycB-Cdk1 inhibitor genes without induction of apoptotic genes. This study implicates Drosophila RNase ZL in a novel retrograde signaling pathway initiated by the damage in mitochondria and manifested in a cell cycle delay before the mitotic entry.
Test Case Generation for Temporal Properties

1 The goal of testing is to make statements about the relation between the traces of an implementation and a temporal property. This is not possible for all temporal properties. Within this paper safety and guarantee properties are identi ed to be testable temporal properties and for these testable properties a test case de nition is given. This is done by representing a safety property as a labeled transition system and by representing the guarantee property as a nite automaton. The test case de nition is applied to practical testing by using SDL descriptions to specify safety properties and by using Message Sequence Charts (MSCs) to specify guarantee properties. CR
Neutralization Profiles of Primary Human Immunodeficiency Virus Type 1 Isolates in the Context of Coreceptor Usage

ABSTRACT Most strains of human immunodeficiency virus type 1 (HIV-1) which have only been carried in vitro in peripheral blood mononuclear cells (primary isolates) can be neutralized by antibodies, but their sensitivity to neutralization varies considerably. To study the parameters that contribute to the differential neutralization sensitivity of primary HIV-1 isolates, we developed a neutralization assay with a panel of genetically engineered cell lines (GHOST cells) that express CD4, one of eight chemokine receptors which function as HIV-1 coreceptors, and a Tat-dependent green fluorescent protein reporter cassette which permits the evaluation and quantitation of HIV-1 infection by flow cytometry. All 21 primary isolates from several clades could grow in the various GHOST cell lines, and their use of one or more coreceptors could easily be defined by flow cytometric analysis. Ten of these primary isolates, three that were CXCR4 (X4)-tropic, three that were CCR5 (R5)-tropic, and four that were dual- or polytropic were chosen for study of their sensitivity to neutralization by human monoclonal and polyclonal antibodies. Viruses from the X4-tropic category of viruses were first tested since they have generally been considered to be particularly neutralization sensitive. It was found that the X4-tropic virus group contained both neutralization-sensitive and neutralization-resistant viruses. Similar results were obtained with R5-tropic viruses and with dual- or polytropic viruses. Within each category of viruses, neutralization sensitivity and resistance could be observed. Therefore, sensitivity to neutralization appears to be the consequence of factors that influence the antibody-virus interaction and its sequelae rather than coreceptor usage. Neutralization of various viruses by the V3-specific monoclonal antibody, 447-52D, was shown to be dependent not only on the presence of the relevant epitope but also on its presentation. An epitope within the envelope of a particular virus is not sufficient to render a virus sensitive to neutralization by an antibody that recognizes that epitope. Moreover, conformation-dependent factors may overcome the need for absolute fidelity in the match between an antibody and its core epitope, permitting sufficient affinity between the viral envelope protein and the antibody to neutralize the virus. The studies indicate that the neutralization sensitivity of HIV-1 primary isolates is a consequence of the complex interaction between virus, antibody, and target cell.
Optimizing Binary MRFs via Extended Roof Duality

Many computer vision applications rely on the efficient optimization of challenging, so-called non-submodular, binary pairwise MRFs. A promising graph cut based approach for optimizing such MRFs known as "roof duality" was recently introduced into computer vision. We study two methods which extend this approach. First, we discuss an efficient implementation of the "probing" technique introduced recently by Bows et al. (2006). It simplifies the MRF while preserving the global optimum. Our code is 400-700 faster on some graphs than the implementation of the work of Bows et al. (2006). Second, we present a new technique which takes an arbitrary input labeling and tries to improve its energy. We give theoretical characterizations of local minima of this procedure. We applied both techniques to many applications, including image segmentation, new view synthesis, super-resolution, diagram recognition, parameter learning, texture restoration, and image deconvolution. For several applications we see that we are able to find the global minimum very efficiently, and considerably outperform the original roof duality approach. In comparison to existing techniques, such as graph cut, TRW, BP, ICM, and simulated annealing, we nearly always find a lower energy.
Association of single nucleotide polymorphisms of MD-1 gene with pediatric and adult asthma in the Taiwanese population.

BACKGROUND AND PURPOSE MD-1 (myeloid differentiation 1; also known as Ly86, lymphocyte antigen 86), interacting with radioprotective 105, plays an important role in the Toll-like receptor 4 signaling pathway. It has been suggested that MD-1 is involved in the development of inflammation and atopic diseases. The purpose of this study was to investigate the genetic association of single nucleotide polymorphisms (SNPs) of MD-1 and asthma in the Taiwanese population. METHODS Genotyping 34 SNPs in the MD-1 gene region was performed in a case-control study involving 281 children with asthma and 237 controls. A further 309 children and adults were genotyped for the SNP rs7740529 only, for validation of an identified association. RESULTS In intron 1, we identified an SNP, rs7740529, which is associated with asthma in Taiwanese children (p=0.0358). Inclusion of a further 309 subjects increased the significance of the association (p=0.0093), and also demonstrated that rs7740529 is associated with adult asthma. The TT genotype confers risk of both pediatric and adult asthma. CONCLUSION These results suggest that MD-1 could be a susceptible gene for asthma in the Taiwanese population.
Fusion of Multiple Features for Chinese Organization Names Recognition Based on SVM

In this paper, a hybrid pattern for Chinese organization names based on Support Vector Machine(SVM) is proposed, which fuses multiple features. With consideration of the features of Chinese organization names, local features and global features are abstracted, and feature-vectors are expressed in binary, the training collection is established. From the experimental results on testing set for 1998 peoples’ daily corpus, it can be concluded that the established hybrid model is effective on recognition for Chinese Organization Names. And the experiments on another different testing set also confirm the above conclusion, which shows that this algorithm has consistence on different testing data sources.
Dietary Iron and Heme Iron Intake and Risk of Breast Cancer: A Prospective Cohort Study

Recent studies suggest that elevated body iron levels may contribute to breast carcinogenesis; however, epidemiologic evidence is lacking. We used data from a large cohort study of Canadian women to assess breast cancer in association with total iron and heme iron intake. Among 49,654 women ages 40 to 59 followed for an average of 16.4 years, we identified 2,545 incident breast cancer cases. Data from a food frequency questionnaire administered at baseline were used to calculate total dietary iron and heme iron intake. Using Cox proportional hazards models, we found no association of iron or heme iron intake with risk of breast cancer overall, in women consuming 30+ g of alcohol per day, or in women who had ever used hormone replacement therapy. The present study offers no support for an association of iron or heme iron intake with breast cancer risk or for a modification by iron of the effect of alcohol or estrogen. However, further cohort studies with repeated measurement of iron intake are warranted. (Cancer Epidemiol Biomarkers Prev 2007;16(6):1306–8)
Political Legitimacy and Normative Disorientation in European Liberal Democracies

Legitimacy is one of the fundamental topics of the social and political sciences, as well as a valid issue in contemporary Western societies. Legitimacy is based on the existence of a common standard for evaluating social and political systems. If such a standard is absent, legitimacy is impossible by definition (Beetham 1991). The research question of this article is: to what extent is the level of a political system’s legitimacy explained by the effect of normative disorientation? Data from round 5 of the European Social Survey is analyzed by multilevel linear regression models in order to verify hypotheses about the strength and direction of the correlation between political legitimacy and normative disorientation. Analysis showed that normative disorientation is negatively correlated with the level of political legitimacy.
Affecting Racial Bias via Perspective-Taking in a Virtual Environment

ii Acknowledgments. iii Vita . iv List of Tables . viii Chapter 1: Introduction . 1 Chapter 2: Literature Review . 3 Virtual Environments . 3 Avatars, Proteus Effect, and Embodiment . 4 Presence . 7 Identification . 9 Perspective-Taking . 12 Stereotyping and VEs . 13 Chapter 3: The Current Experiment . 16 Chapter 4: Method . 23 Participants . 23 Sample . 23
Subdiffusive dynamics in washboard potentials: two different approaches and different universality classes

We consider and compare two different approaches to the fractional subdiffusion and transport in washboard potentials. One is based on the concept of random fractal time and is associated with the fractional Fokker-Planck equation. Another approach is based on the fractional generalized Langevin dynamics and is associated with anti-persistent fractional Brownian motion and its generalizations. Profound differences between these two different approaches sharing the common adjective "fractional" are explained in spite of some similarities they share in the absence of a nonlinear force. In particular, we show that the asymptotic dynamics in tilted washboard potentials obey two different universality classes independently of the form of potential.
Rate adaptation in cognitive radio links with time-varying channels

In this work we address the optimal rate adaptation problem of a cognitive radio (CR) link in time-variant channels. A secondary user (SU) link detects an idle channel and starts the transmission with the goal of transmitting a given amount of data packets. During the transmission the transmitter dynamically adapts the frames rate, from a finite number of available rates, according to the channel state. If a frame is decoded with error, the corresponding data must be retransmitted in further frames. If a primary user (PU) access the channel during the process, the CR link immediately stops the transmission. The rate adaptation problem is formulated as an infinite-horizon Markov decision process (MDP). We split the problem in a finite number of much simpler MDP problems that can be efficiently solved by conventional MDP solving algorithms. So, the optimal policy and the corresponding maximum probability of successful transmission can be easily obtained.
Investigation of the main Design Parameters Affecting the Performance of a PCCC Turbo Code

In this paper we undertake a comprehensive study of the characteristics that affect the bit error probability performance of a Parallel Concatenated Convolutional Code (PCCC) for an OFDM based system. This knowledge enables us to choose proper design parameters in accordance to specific performance requirements. Curves for BER vs. Eb/No are plotted to show the influence of various parameters, including the number of iterations, the frame size, the code rate, and the code generator. Key Words: Turbo Codes, Parallel Concatenated Convolutional Code (PCCC).
Evaluating and Extending the Coverage of HPSG Grammars: A Case Study for German

In this work, we examine and attempt to extend the coverage of a German HPSG grammar. We use the grammar to parse a corpus of newspaper text and evaluate the proportion of sentences which have a correct attested parse, and analyse the cause of errors in terms of lexical or constructional gaps which prevent parsing. Then, using a maximum entropy model, we evaluate prediction of lexical types in the HPSG type hierarchy for unseen lexemes. By automatically adding entries to the lexicon, we observe that we can increase coverage without substantially decreasing precision.
Measuring the Balmer Jump and the Effective Gravity in FGK Stars

It is difficult to accurately measure the effective gravity (log g) in late‐type stars using broadband (e.g., UBV or SDSS) or intermediate‐band (uvby) photometric systems, especially when the stars can cover a range of metallicities and reddenings. However, simple spectroscopic observational and data reduction techniques can yield accurate values for log g through comparison of the Balmer jumps of low‐resolution spectra with recent grids of synthetic flux spectra.
System Architecture and Mobility Management for Mobile Immersive Communications

We propose a system design for delivery of immersive communications to mobile wireless devices based on a distributed proxy model. It is demonstrated that this architecture addresses key technical challenges for the delivery of these services, that is, constraints on link capacity and power consumption in mobile devices. However, additional complexity is introduced with respect to application layer mobility management. The paper proposes three possible methods for updating proxy assignments in response to mobility management and compares the performance of these methods.
Generating Succinct Test Cases Using Don't Care Analysis

We study the problem of reducing test cases generated by bit vector based symbolic execution test generators. In particular, we first consider a guileless test case generation approach that generates assignment statements for each symbolic scalars, array and structure elements and object fields. We show that test cases generated by this approach can be significantly verbose. We then propose a method for making the generated test cases more succinct using a novel analysis entitled don't care analysis. Don't care analysis identifies assignment statements that can be safely removed from the test cases without affecting the overall code coverage. Our algorithm is based on binary and delta-debugging search. Because it exploits the knowledge of the internal SAT solver, it is effective and efficient in practice. To our knowledge, this is the first fully automatic approach that reduces the sizes of test cases generated using symbolic execution. We implement our test case reduction technique for the KLEE test generation tool and evaluate on 295 programs and functions. Our results are encouraging: in average, the reduced test cases are 50 times smaller than the test cases generated by the guileless test case generator. In addition, since our don't care analysis is tightly integrated into the test case generation tool, its overhead to the overall test generation process is negligible.
The -844 G>A PAI-1 Polymorphism Is Associated with Acute Coronary Syndrome in Mexican Population

Background. Acute coronary syndrome (ACS) has an important impact in public health with high morbidity and mortality. Prothrombotic and proinflammatory states are involved in the pathogenesis of the disease. Plasminogen activator inhibitor-1 (PAI-1) is the major inhibitor of the fibrinolysis and also is part of immune response. The -844 G>A gene polymorphism is related to increased PAI-1 protein levels. The aim of the study is to evaluate the association of -844 G>A PAI-1 polymorphism with ACS. Methods. A total of 646 individuals were recruited from Western Mexico: 350 unrelated healthy subjects and 296 patients with diagnosis of ACS. Results. The most important risk factor in our population was hypertension, followed by smoking. The genetic distribution showed an association of the A allele (OR = 1.27, P = 0.04) and AA genotype (OR = 1.86, P = 0.02) with ACS. The recessive model displayed similar results (OR = 1.76, P = 0.02). As additional finding, we observed significant differences in the genetic distribution of ACS dyslipidemic patients (OR = 1.99, P = 0.04). The A allele and AA genotype of -844 polymorphism of PAI-1 gene are risk factors for ACS. The AA genotype might be associated with the development of dyslipidemia in ACS patients.
Investigation of interactions between two monoclonal antibodies and SARS virus with a Label-free Protein Array

The investigation of interactions between two kinds of monoclonal antibodies and SARS virus with a label-free protein array technique were presented in this paper. The performance consists of three parts: a surface modification for ligand immobilization/surface, a protein array fabrication with an integrated microfluidic system for patterning, packaging and liquid handling, and a protein array reader of imaging ellipsometer. This revealed the technique could be used as an immunoassay for qualitative and quantitative detection as well as kinetic analysis of biomolecule interaction
Evidence of injury caused by gas bubbles in a live marine mammal: barotrauma in a California sea lion Zalophus californianus.

A yearling male California sea lion Zalophus californianus with hypermetric ataxia and bilateral negative menace reflexes was brought to The Marine Mammal Center, Sausalito, California, U.S.A. , in late 2009 for medical assessment and treatment. The clinical signs were due to multiple gas bubbles within the cerebellum. These lesions were intraparenchymal, multifocal to coalescing, spherical to ovoid, and varied from 0.5 to 2.4 cm diameter. The gas composed 21.3% of the total cerebellum volume. Three rib fractures were also noted during diagnostic evaluation and were presumed to be associated with the gas bubbles in the brain. The progression of clinical signs and lesion appearance were monitored with magnetic resonance imaging, cognitive function testing and computed tomography. Gas filled voids in the cerebellum were filled with fluid on follow up images. Clinical signs resolved and the sea lion was released with a satellite tag attached. Post release the animal travelled approximately 75 km north and 80 km south of the release site and the tag recorded dives of over 150 m depth. The animal re-stranded 25 d following release and died of a subacute bronchopneumonia and pleuritis. This is the first instance of clinical injury due to gas bubble formation described in a living pinniped and the first sea lion with quantifiable cerebellar damage to take part in spatial learning and memory testing.
Honest Image Thumbnails : Algorithm and Subjective Evaluation

Image thumbnails are commonly used for selecting images for display, sharing or printing. Current, standard thumbnails do not distinguish between high and low quality originals. Both sharp and blurry originals appear sharp in the thumbnails, and both clean and noisy originals appear clean in the thumbnails. This leads to errors and inefficiencies during image selection. In this paper, thumbnails generated using image analysis better represent the local blur and the noise of the originals. The new thumbnails provide a quick, natural way for users to identify images of good quality, while allowing the viewer’s knowledge to select desired subject matter. A subjective evaluation using twenty subjects shows the new thumbnails are more representative of their originals for blurry images. In addition, there are no significant differences between the results of the new thumbnails and the standard thumbnails for clean images. The noise component improves the results for noisy images, but degrades the results for textured images. The blur component of the new thumbnails may always be used. The decision to use the noise component of the new thumbnails should be based on testing with the particular image mix expected for the application.
Rapid classification of mixed hyperspectral data by ROAA SVM

Capturing of high resolution hyperspectral images is one of the most expensive tasks in imaging industry. The main problem of low resolution hyperspectral data is the classification of pixels where more than one land cover type lie in one pixel, called a mixed pixel. To resolve this issue, methods composed of hard and soft classification techniques have shown good results. For rapid classification of these mixed hyperspectral images, we propose to use Reduced OAA SVM combined with spectral mixture analysis at sub-pixel level and a fast post processing step to eliminate unwanted solitary mappings. Experiments conducted over a common hyperspectral image show great improvements in terms of overall classification accuracy and computation time.
Heritability and Genome-Wide Linkage Scan of Subjective Happiness

Abstract Causes of individual differences in happiness, as assessed with the Subjective Happiness Scale, are investigated in a large of sample twins and siblings from the Netherlands Twin Register. Over 12,000 twins and siblings, average age 24.7 years (range 12 to 88), took part in the study. A genetic model with an age by sex design was fitted to the data with structural equation modeling in Mx. The heritability of happiness was estimated at 22% for males and 41% in females. No effect of age was observed. To identify the genomic regions contributing to this heritability, a genome-wide linkage study for happiness was conducted in sibling pairs. A subsample of 1157 offspring from 441 families was genotyped with an average of 371 micro-satellite markers per individual. Phenotype and genotype data were analyzed in MERLIN with multipoint variance component linkage analysis and age and sex as covariates. A linkage signal (logarithm of odds score 2.73, empirical p value 0.095) was obtained at the end of the long arm of chromosome 19 for marker D19S254 at 110 cM. A second suggestive linkage peak was found at the short arm of chromosome 1 (LOD of 2.37) at 153 cM, marker D1S534 (empirical p value of .209). These two regions of interest are not overlapping with the regions found for contrasting phenotypes (such as depression, which is negatively associated with happiness). Further linkage and future association studies are warranted.