Miracle-dz/UniFAR-FTUs huggingface dataset:
Epigenetic regulation of serotype expression antagonizes transcriptome dynamics in Paramecium tetraurelia

Phenotypic variation of a single genotype is achieved by alterations in gene expression patterns. Regulation of such alterations depends on their time scale, where short-time adaptations differ from permanently established gene expression patterns maintained by epigenetic mechanisms. In the ciliate Paramecium, serotypes were described for an epigenetically controlled gene expression pattern of an individual multigene family. Paradoxically, individual serotypes can be triggered in Paramecium by alternating environments but are then stabilized by epigenetic mechanisms, thus raising the question to which extend their expression follows environmental stimuli. To characterize environmental adaptation in the context of epigenetically controlled serotype expression, we used RNA-seq to characterize transcriptomes of serotype pure cultures. The resulting vegetative transcriptome resource is first analysed for genes involved in the adaptive response to the altered environment. Secondly, we identified groups of genes that do not follow the adaptive response but show co-regulation with the epigenetically controlled serotype system, suggesting that their gene expression pattern becomes manifested by similar mechanisms. In our experimental set-up, serotype expression and the entire group of co-regulated genes were stable among environmental changes and only heat-shock genes altered expression of these gene groups. The data suggest that the maintenance of these gene expression patterns in a lineage represents epigenetically controlled robustness counteracting short-time adaptation processes.
Narrowband UVB Phototherapy for Clinically Isolated Syndrome: A Trial to Deliver the Benefits of Vitamin D and Other UVB-Induced Molecules

Low vitamin D and insufficient sun exposure are additive independent risk factors for the development of multiple sclerosis (MS). The usual measure of vitamin D status, serum 25-hydroxy vitamin D [25(OH)D], is also a marker of recent exposure to the UVB rays of sunshine. The main evidence for a protective effect for MS development of higher 25(OH)D comes from observational studies, but this study design cannot separate out whether 25(OH)D is acting as a marker of vitamin D status, sun exposure, or both. In light of a lack of definitive outcomes in MS patients after trials of vitamin D supplementation and the ability of narrowband UVB to induce vitamin D, as well as other immune-regulatory molecules in skin, the Phototherapy for Clinically Isolated Syndrome (PhoCIS) trial was established to investigate the benefits of narrowband UVB, in addition to supplemented vitamin D, on MS development in individuals with Clinically Isolated Syndrome. We propose that the PhoCIS trial provides a fresh approach to re-defining the reported associations of 25(OH)D levels with MS development and progression.
Major Evolutionary Trends in Hydrogen Isotope Fractionation of Vascular Plant Leaf Waxes

Hydrogen isotopic ratios of terrestrial plant leaf waxes (δD) have been widely used for paleoclimate reconstructions. However, underlying controls for the observed large variations in leaf wax δD values in different terrestrial vascular plants are still poorly understood, hampering quantitative paleoclimate interpretation. Here we report plant leaf wax and source water δD values from 102 plant species grown in a common environment (New York Botanic Garden), chosen to represent all the major lineages of terrestrial vascular plants and multiple origins of common plant growth forms. We found that leaf wax hydrogen isotope fractionation relative to plant source water is best explained by membership in particular lineages, rather than by growth forms as previously suggested. Monocots, and in particular one clade of grasses, display consistently greater hydrogen isotopic fractionation than all other vascular plants, whereas lycopods, representing the earlier-diverging vascular plant lineage, display the smallest fractionation. Data from greenhouse experiments and field samples suggest that the changing leaf wax hydrogen isotopic fractionation in different terrestrial vascular plants may be related to different strategies in allocating photosynthetic substrates for metabolic and biosynthetic functions, and potential leaf water isotopic differences.
Clinical implications of Brief Psychiatric Rating Scale scores.

BACKGROUND Despite the widespread use of the Brief Psychiatric Rating Scale (BPRS), the clinical meaning of its total score and cut-off values used to define treatment response are unclear. AIMS To link the BPRS to Clinical Global Impression (CGI) ratings. METHOD Equipercentile linking of BPRS and CGI ratings from seven drug trials in acutely ill patients with schizophrenia (n=1979). RESULTS 'Mildly ill' according to the CGI approximately corresponded to a BPRS total score of 31, 'moderately ill'to a BPRS score of 41 and'markedly ill'to a BPRS score of 53. 'Minimally improved'according to the CGI score was associated with percentage BPRS reductions of 24, 27 and 30% at weeks 1, 2 and 4, respectively. The corresponding numbers for a CGI rating of 'much improved' were 44, 53 and 58%. CONCLUSIONS The results provide a clearer understanding of how to interpret BPRS total and percentage reduction scores in clinical trials with patients acutely ill with schizophrenia who are experiencing positive symptoms.
Structure of Adeno-Associated Virus Serotype 8, a Gene Therapy Vector

ABSTRACT Adeno-associated viruses (AAVs) are being developed as gene therapy vectors, and their efficacy could be improved by a detailed understanding of their viral capsid structures. AAV serotype 8 (AAV8) shows a significantly greater liver transduction efficiency than those of other serotypes, which has resulted in efforts to develop this virus as a gene therapy vector for hemophilia A and familial hypercholesterolemia. Pseudotyping studies show that the differential tissue tropism and transduction efficiencies exhibited by the AAVs result from differences in their capsid viral protein (VP) amino acids. Towards identifying the structural features underpinning these disparities, we report the crystal structure of the AAV8 viral capsid determined to 2.6-Å resolution. The overall topology of its common overlapping VP is similar to that previously reported for the crystal structures of AAV2 and AAV4, with an eight-stranded β-barrel and long loops between the β-strands. The most significant structural differences between AAV8 and AAV2 (the best-characterized serotype) are located on the capsid surface at protrusions surrounding the two-, three-, and fivefold axes at residues reported to control transduction efficiency and antibody recognition for AAV2. In addition, a comparison of the AAV8 and AAV2 capsid surface amino acids showed a reduced distribution of basic charge for AAV8 at the mapped AAV2 heparin sulfate receptor binding region, consistent with an observed non-heparin-binding phenotype for AAV8. Thus, this AAV8 structure provides an additional platform for mutagenesis efforts to characterize AAV capsid regions responsible for differential cellular tropism, transduction, and antigenicity for these promising gene therapy vectors.
The Impact of Different Support Vectors on GOSAT-2 CAI-2 L2 Cloud Discrimination

Greenhouse gases Observing SATellite-2 (GOSAT-2) will be launched in fiscal year 2018. GOSAT-2 will be equipped with two sensors: the Thermal and Near-infrared Sensor for Carbon Observation (TANSO)-Fourier Transform Spectrometer 2 (FTS-2) and the TANSO-Cloud and Aerosol Imager 2 (CAI-2). CAI-2 is a push-broom imaging sensor that has forward- and backward-looking bands to observe the optical properties of aerosols and clouds and to monitor the status of urban air pollution and transboundary air pollution over oceans, such as PM2.5 (particles less than 2.5 micrometers in diameter). CAI-2 has important applications for cloud discrimination in each direction. The Cloud and Aerosol Unbiased Decision Intellectual Algorithm (CLAUDIA1), which applies sequential threshold tests to features is used for GOSAT CAI L2 cloud flag processing. If CLAUDIA1 is used with CAI-2, it is necessary to optimize the thresholds in accordance with CAI-2. However, CLAUDIA3 with support vector machines (SVM), a supervised pattern recognition method, was developed, and then we applied CLAUDIA3 for GOSAT-2 CAI-2 L2 cloud discrimination processing. Thus, CLAUDIA3 can automatically find the optimized boundary between clear and cloudy areas. Improvements in CLAUDIA3 using CAI (CLAUDIA3-CAI) continue to be made. In this study, we examined the impact of various support vectors (SV) on GOSAT-2 CAI-2 L2 cloud discrimination by analyzing (1) the impact of the choice of different time periods for the training data and (2) the impact of different generation procedures for SV on the cloud discrimination efficiency. To generate SV for CLAUDIA3-CAI from MODIS data, there are two times at which features are extracted, corresponding to CAI bands. One procedure is equivalent to generating SV using CAI data. Another procedure generates SV for MODIS cloud discrimination at the beginning, and then extracts decision function, thresholds, and SV corresponding to CAI bands. Our results indicated the following. (1) For the period from November to May, it is more effective to use SV generated from training data from February while for the period from June to October it is more effective to use training data from August; (2) In the preparation of SV, features obtained using MODIS bands are more effective than those obtained using the corresponding GOSAT CAI bands to automatically extract cloud training samples.
More taxa are not necessarily better for the reconstruction of ancestral character states.

Ancestral state reconstruction is an important approach to understanding the origins and evolution of key features of different living organisms (Liberles, 2007). For example, ancestral proteins and genomic sequences have been reconstructed for investigating the origins of genes and proteins (Hillis et al., 1994; Jermann et al., 1995; Zhang and Rosenberg, 2002; Gaucher et al., 2003; Thornton et al., 2003; Blanchette et al., 2004; Cai et al., 2004; Felsenstein, 2004; Taubenberger et al., 2005). A variety of reconstruction methods, including parsimony and maximum likelihood, exist for biomolecular sequencing (Yang et al., 1995; Koshi and Goldstein, 1996; Elias and Tuller, 2007), multistate discrete data (Schultz et al., 1996; Mooers and Schluter, 1999; Pagel, 1999), and continuous data (Martins, 1999). These different reconstruction methods have been assessed by both theoretical analyses (Maddison, 1995; Yang et al., 1995) and computer simulation (Schultz et al., 1996; Zhang and Nei, 1997; Salisbury and Kim, 2001; Blanchette et al., 2004; Mooers, 2004; Williams et al., 2006). One important observation in these investigations is that the topology of the phylogenetic tree relating the extant taxa to the target ancestor has a significant influence on reconstruction accuracy. For instance, a star-like phylogeny allows the ancestral character states to be inferred more accurately than other topologies given the same number of terminal taxa under the two-state symmetric model (Schultz et al., 1996; Evans et al., 2000). For more complex models (e.g., on four-states such as DNA), the influence of topology on reconstruction accuracy is more complicated (Lucena and Haussler, 2005).
Multi-Fractal Nature of HS 300 Index and its Traded Volume

A study of the multi-fractal nature of three time series related to the Hushen300 index, HS300, including daily closing prices, daily yield rates and daily traded volumes time series is presented. Multi-fractal Detrended Fluctuation Analysis (MFDFA) is used in the study. The results show that the three related time series are with strong persistence characters. By multi-fractal spectrum analysis, the width of the multi-fractal Spectra of traded volume series is to be found the biggest among the three. It means that the traded volumes series are most irregular.
Frequency analysis of sleep spindles by Extended Prony model: Validation by signal reconstruction

In order to classify sleep spindles from human EEG the advantages of the Extended Prony Method in spectral estimation are presented. This method assumes that the original signal is a sum of damped complex exponential sinusoids. The method has the best frequency resolution compared to the other parametric methods. Given the parameters of the Prony model, a synthetic spindle can be generated. Since these parameters are used both in spectral estimation and in the reconstructi on process, the associated Power Spectral Density (PSD) is more especially estimated as the error function between the reconstructed and the raw signal is minimized. Limitations of the method are also discussed.
Speaker Recognition and Speaker Characterization over Landline, VoIP and Wireless Channels

The automatic detection of people's identity and characteristics such as age, gender, emotion and personality from their voices generally requires the transmission of the speech to remote servers that perform the recognition task. This transmission may introduce severe distortions and channel mismatch that degrade the system performance or vary the detection of the actual emotions and speaker traits. Concurrently, humans also cope with the difficulty of reliably identifying and characterizing talkers from speech transmitted over telephone channels, particularly detecting emotions on a call to a friend or relative. The present research addresses the evaluation of human and automatic performances under different channel distortions caused by bandwidth limitation, codecs, and electro-acoustic user interfaces, among other impairments. Special attention is paid to the creation of robust automatic systems that can handle channel variations, and thus enhance voice-based human-computer interaction in applications where the speech is transmitted. This paper outlines the work completed to date and the potential future work plans to be finalized within the next 1.5 years.
Analysis of pesticide residues in strawberries and soils by GC-MS/MS, LC-MS/MS and two-dimensional GC-time-of-flight MS comparing organic and integrated pest management farming

This study analysed 22 strawberry and soil samples after their collection over the course of 2 years to compare the residue profiles from organic farming with integrated pest management practices in Portugal. For sample preparation, we used the citrate-buffered version of the quick, easy, cheap, effective, rugged, and safe (QuEChERS) method. We applied three different methods for analysis: (1) 27 pesticides were targeted using LC-MS/MS; (2) 143 were targeted using low pressure GC-tandem mass spectrometry (LP-GC-MS/MS); and (3) more than 600 pesticides were screened in a targeted and untargeted approach using comprehensive, two-dimensional gas chromatography time-of-flight mass spectrometry (GC × GC-TOF-MS). Comparison was made of the analyses using the different methods for the shared samples. The results were similar, thereby providing satisfactory confirmation of both similarly positive and negative findings. No pesticides were found in the organic-farmed samples. In samples from integrated pest management practices, nine pesticides were determined and confirmed to be present, ranging from 2 µg kg−1 for fluazifop-p-butyl to 50 µg kg−1 for fenpropathrin. Concentrations of residues in strawberries were less than European maximum residue limits. Graphical Abstract
Accepted for Publication in Ieee Transactions on Information Theory. Iterative Decoding Threshold Analysis for Ldpc Convolutional Codes

—An iterative decoding threshold analysis for terminated regular LDPC convolutional (LDPCC) codes is presented. Using density evolution techniques, the convergence behavior of an iterative belief propagation decoder is analyzed for the binary erasure channel and the AWGN channel with binary inputs. It is shown that for a terminated LDPCC code ensemble, the thresholds are better than for corresponding regular and irregular LDPC block codes.
Efficient Scalable Serial Multiplier Over GF( $\textbf {2}^{\boldsymbol {m}}$ ) Based on Trinomial

This brief presents a novel low-complexity scalable serial architecture for finite field multiplication over GF(2m) based on irreducible trinomial. This architecture was explored by applying nonlinear technique that allows the designer, using progressive product reduction technique, to control the workload per processor and also allows the communication overhead between processors to be reduced. By comparing the ASIC implementation of the proposed structure to some of the previously published structures, the proposed structure have at least 71.7% lower area and at least 89.9% lower power compared with most of them. This makes the proposed design more suitable for constrained implementations of cryptographic primitives in resource constrained applications, such as smart cards, handheld devices, and implantable medical devices.
Eliciting Risk and Time Preferences

We design experiments to jointly elicit risk and time preferences for the adult Danish population. Since subjects are generally risk averse, we find that joint elicitation provides estimates of discount rates that are significantly lower than those found in previous studies and more in line with what would be considered as a priori reasonable rates. The statistical specification relies on a theoretical framework that involves a latent trade-off between long-run optimization and short-run temptation. Estimation of this specification is undertaken using structural, maximum likelihood methods. Our main results based on exponential discounting are robust to alternative specifications such as hyperbolic discounting. These results have direct implications for attempts to elicit time preferences, as well as debates over the appropriate domain of the utility function when characterizing risk aversion and time consistency.
Overview of the Fifth Text REtrieval Conference (TREC-5)

Presentation des objectifs, des methodes (la routing task, la tâche adhoc, la comparaison des differents systemes, les concepts de confusion, de filtrage, de multilinguisme, de traitement du langage naturel, evaluation de la pertinence), et des resultats issus des traitements manuels et automatiques des differentes equipes presentes a TREC-5
Unbiasedness of the likelihood ratio test for lattice conditional independence models

The lattice conditional independence (LCI) model N() is defined to be the set of all normal distributions N(0, [Sigma]) on I such that for every pair L, M [set membership, variant] , xL and xM are conditionally independent given xL [intersection] M. Here is a ring of subsets (hence a distributive lattice) of the finite index set I such that [empty set][combining character] I [set membership, variant] , while for K [set membership, variant] , xK is the coordinate projection of x [set membership, variant] I onto K. Andersson and Perlman in the preceding paper derived the likelihood ratio (LR) statistic [lambda] for testing one LCI model against another, i.e., for testing N() vs N() based on a random sample from N(0, [Sigma]), where is a subring of . In the present paper the strict unbiasedness of the LR test is established, and related results regarding the distribution of the maximum likelihood estimator of [Sigma] under the LCI model N() are presented.
Which interconnects for which 3D applications? Status and perspectives

Some 3D interconnects technologies are reviewed and discussed in this paper with respect to emerging 3D applications. While 2.5D Si interposer and 3D packaging seem to rely to cu pillars for the coming years, the very fine pitch below 10μm will be mandatory for 3DIC and many options like cu-cu bonding or μ-tubes are in the race. Specific interconnects for RF/mm-waves and low volume electronics devices are also discussed with relevant examples.
Attitude Control Mechanism for Underwater Robot with Flexible Plastic Film Body

This paper describes an attitude control mechanism for an underwater robot with a flexible plastic film body. Insulating fluid was poured into a packaging resin film, the outer layer of the robot, to improve its pressure resistance under water. The attitude control mechanism consisted of an arrangement of the insulating fluid and floating blocks inside the robot. The attitude control mechanism will allow threedimensional non-holonomical movements of the robot under water.
Surgical approach and outcomes for treatment of pulmonary metastases

AIMS: To investigate the surgical approach and outcomes, as well as prognostic factors for pulmonary metastasectomy. METHODS: Clinical data of 201 patients treated by pulmonary metastasectomy between January 1990 and December 2009 were retrospectively reviewed. One hundred thirty three patients were received an approach of thoracotomy while 68 with video-assisted thoracoscopic surgery (VATS). There were 54 lobectomies, 139 wedge resections and 8 pneumonectomies. Hilar or mediastinal lymph nodes dissection or sampling was carried out in 38 patients with lobectomy. The Kaplan-Meier method was used for the survival analysis. Cox proportional hazards model was used for multivariate analysis. RESULTS: The 5 years survival rate of patients after metastasectomy was 50.5%, and the median survival time was 65.9 months. The median survival time of patients with hilar or mediastinal lymph nodes metastasis was 23 months. By univariate analysis, significant prognostic factors included disease-free interval (DFI), number of metastases, number of affected lobe, surgical approach (open vs. VATS) and pathology types. DFI, number of metastases, and pathology types were revealed by Cox multivariate analysis as independent prognostic factors. CONCLUSION: Surgical resection of pulmonary metastases is safe and effective. Palpation of the lung is still seen as necessary to detect the occult nodule. More accurate and sensitive pre-operative mediastinal staging are required.
Expression of peropsin in human skin is related to phototransduction of violet light in keratinocytes

Opsins are photosensitive receptor proteins mediating phototransduction, whereby photons absorbed are translated to cellular response. [1] Members of the opsin family belong to the G proteincoupled receptors (GPCRs) superfamily. While many opsin members were originally discovered in the eye, several visual and nonvisual opsins, including rhodopsin, shortwavelength opsin, melanopsin and neuropsin are also expressed in nonvisual tissues such as the skin. [2,3] Previous study has suggested rhodopsin to contribute to UVA phototransduction in human epidermal melanocytes. [4] However, the role of these opsins in keratinocytes, the outermost skin layer constantly exposed to light, remains unclear. Peropsin, a new opsin member initially detected in human ocular tissue,[5] has never been described in the skin. Here, we examined the presence of peropsin in human skin and its potential role in keratinocytes.
Classification of driver fatigue in an electroencephalography-based countermeasure system with source separation module

An electroencephalography (EEG)-based counter measure device could be used for fatigue detection during driving. This paper explores the classification of fatigue and alert states using power spectral density (PSD) as a feature extractor and fuzzy swarm based-artificial neural network (ANN) as a classifier. An independent component analysis of entropy rate bound minimization (ICA-ERBM) is investigated as a novel source separation technique for fatigue classification using EEG analysis. A comparison of the classification accuracy of source separator versus no source separator is presented. Classification performance based on 43 participants without the inclusion of the source separator resulted in an overall sensitivity of 71.67%, a specificity of 75.63% and an accuracy of 73.65%. However, these results were improved after the inclusion of a source separator module, resulting in an overall sensitivity of 78.16%, a specificity of 79.60% and an accuracy of 78.88% (p <; 0.05).