Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogeography of the Marsh Fritillary Euphydryas aurinia (Lepidoptera: Nymphalidae) in the UK

Abstract We sampled extant (and extinct) populations of Euphydryas aurinia to examine the phylogeography of the species in the UK. We were interested in whether the genetic structuring of populations reflects anything other than a single recent post-glacial colonization event. Four hundred base pairs of the mitochondrial Cytochrome b gene were sequenced from individuals from populations throughout the UK, as well as populations in France and Portugal and seven polymorphic allozyme loci resolved. The mean number of allozyme alleles per locus was 4 and isolation by distance was shown not to be a factor in the geographic structuring of genetic diversity either with or without the inclusion of the French data (Mantel statistic Z=0.015 and 0.112 respectively, P >0.5). Cytochrome b nucleotide diversity (average number of nucleotide differences per site between two sequences) was low overall (0.003, n =63) but mean cytochrome b gene diversity over all populations was 0.77. The presence of the Portuguese and French haplotype in Scottish populations indicates that the Iberian peninsula was likely to be one glacial refugium for E. aurinia populations. The pattern of mitochondrial DNA found in the UK could be interpreted in one of two ways: (1) two separate colonization events or (2) a single slow colonization event. Allele frequency distributions followed a similar geographical pattern as mitochondrial DNA haplotypes. An AMOVA assigned just 2.68% of allozyme genetic variation to the grouping tested, providing more support for the single colonization event theory.
An Interactive 3-D Visualization Tool for Accurate Estimation of Miss Rates

Making use of information on cache performance requires a quick way to comprehend how the miss rate for an application changes as cache and input size varies. In 1970, Mattson et al. showed how to measure miss rates for all cache sizes. Recently, Zhong et al. showed how to predict miss rates for all program input data sizes. This paper builds on the previous results and shows the miss rate of a program as a function over the domain with cache and data input size as two orthogonal dimensions. This paper makes three contributions. First, it presents an interactive tool that visualizes the miss rates in threedimensional plots. It measures the compounded error of prediction for different cache sizes for program inputs that are never ran let along simulated on a cache simulator. Second, it applies predictions to a new set of benchmark programs with dynamic data structures. Finally, it discusses possible uses of the new tool. Experiments show that the compounded prediction error for the hit rate is within 6.5% for caches of all sizes and with a small amount of associativity. The visualization tool can run on any machine with Java 3D. It can be downloaded from http://www.cs. rochester.edu/research/locality.
Biochemistry and genetics of inherited disorders of peroxisomal fatty acid metabolism

In humans, peroxisomes harbor a complex set of enzymes acting on various lipophilic carboxylic acids, organized in two basic pathways, α-oxidation and β-oxidation; the latter pathway can also handle ω-oxidized compounds. Some oxidation products are crucial to human health (primary bile acids and polyunsaturated FAs), whereas other substrates have to be degraded in order to avoid neuropathology at a later age (very long-chain FAs and xenobiotic phytanic acid and pristanic acid). Whereas total absence of peroxisomes is lethal, single peroxisomal protein deficiencies can present with a mild or severe phenotype and are more informative to understand the pathogenic factors. The currently known single protein deficiencies equal about one-fourth of the number of proteins involved in peroxisomal FA metabolism. The biochemical properties of these proteins are highlighted, followed by an overview of the known diseases.
POPULATION STUDIES ON LEAD‐TOLERANT AGROSTIS TENUIS

Populations of A. tenuis growing on disused lead mines are shown to be generally lead tolerant when compared with populations from normal habitats. There is variation in the degree of tolerance possessed by genotypes on particular mines. Plants of the lead mine populations are smaller for a range of morphological characters, lower yielding than normal populations, and earlier flowering. The adaptive significance of these characters is discussed. Comparison of a mine and normal population in sand culture shows that the mine population is adapted to the low levels of calcium and phosphate found in lead mine soils. Sites only 50 yards across are quite capable of supporting distinct populations adapted to the site characteristics. It is suggested that such adapted populations have risen during the last two or three hundred years at the most.
Faster upper body pose recognition and estimation using compute unified device architecture

The SASL project is in the process of developing a machine translation system that can translate fully-fledged phrases between SASL and English in real-time. To-date, several systems have been developed by the project focusing on facial expression, hand shape, hand motion, hand orientation and hand location recognition and estimation. Achmed developed a highly accurate upper body pose recognition and estimation system. The system is capable of recognizing and estimating the location of the arms from a twodimensional video captured from a monocular view at an accuracy of 88%. The system operates at well below real-time speeds. This research aims to investigate the use of optimizations and parallel processing techniques using the CUDA framework on Achmed’s algorithm to achieve real-time upper body pose recognition and estimation. A detailed analysis of Achmed’s algorithm identified potential improvements to the algorithm. A reimplementation of Achmed’s algorithm on the CUDA framework, coupled with these improvements culminated in an enhanced upper body pose recognition and estimation system that operates in real-time with an increased accuracy.
Nuclear Reprogramming in Mouse Primordial Germ Cells: Epigenetic Contribution

The unique capability of germ cells to give rise to a new organism, allowing the transmission of primary genetic information from generation to generation, depends on their epigenetic reprogramming ability and underlying genomic totipotency. Recent studies have shown that genome-wide epigenetic modifications, referred to as “epigenetic reprogramming”, occur during the development of the gamete precursors termed primordial germ cells (PGCs) in the embryo. This reprogramming is likely to be critical for the germ line development itself and necessary to erase the parental imprinting and setting the base for totipotency intrinsic to this cell lineage. The status of genome acquired during reprogramming and the associated expression of key pluripotency genes render PGCs susceptible to transform into pluripotent stem cells. This may occur in vivo under still undefined condition, and it is likely at the origin of the formation of germ cell tumors. The phenomenon appears to be reproduced under partly defined in vitro culture conditions, when PGCs are transformed into embryonic germ (EG) cells. In the present paper, I will try to summarize the contribution that epigenetic modifications give to nuclear reprogramming in mouse PGCs.
Estimation of regional evapotranspiration over Northwest China by using remotely sensed data

A transpiration estimation model for complete vegetation and an evaporation estimation model for bare soil are presented, based on information of surface parameters. Combined with vegetation coverage data, a model for regional evapotranspiration (ET) estimation over the heterogeneous landscape is derived. This approach provided a reliable estimate of ET over Northwest China, the semiarid and arid region of China. The accuracy of the model for regional ET estimation is checked, which shows a high accuracy result. The features of ET over Northwest China are also discussed with the model.
Mapeamento dos sítios de latência e reativação pelo herpesvírus bovino tipo 5 (BoHV-5) e por mutante deletado no gene da timidina quinase em ovinos

ABSTRACT. - Cadore G.C. , Marcon G. , Brum M.C. S. , Weiblen R. & Flores E.F. 2013. Mapping the sites of latency and reactivation by bovine herpesvirus 5 (BoHV-5) and a thymi-dine kinase-deleted BoHV-5 in lambs. Pesquisa Veterinaria Brasileira 33(12):1409-1415. Departamento de Medicina Veterinaria Preventiva, Universidade Federal de Santa Maria, Camobi, Santa Maria, RS 97105-900, Brazil. E-mail: eduardofurtadoflores@gmail.comA thymidine kinase ( tk )-deleted bovine herpesvirus 5 (BoHV-5 tk Δ) was previously shown to establish latent infection and reactivate - even poorly - in a sheep model (Cadore et al. 2013). As TK-negative alphaherpesviruses are unlike to reactivate in neural tissue, this study investigated the sites of latency and reactivation by this recombinant in lambs. For this, groups of lambs were inoculated intranasally with the parental BoHV-5 strain (SV-507/99) or with the recombinant BoHV-5 tk Δ. During latent infection (40 days post-inoculation, pi), the distribution of recombinant virus DNA in neural and non-neural tissues was similar to that of the parental virus. Parental and recombinant virus DNA was consistently detected by PCR in trigeminal ganglia (TGs); frequently in palatine and pharyngeal tonsils and, less frequently in the retropharyngeal lymph nodes. In addition, latent DNA of both viruses was detected in several areas of the brain. After dexamethasone (Dx) administration (day 40pi), the recombinant virus was barely detected in nasal secretions contrasting with marked shedding of the parental virus. In tissues of lambs euthanized at day 3 post-Dx treatment (pDx), reverse-transcription-PCR (RT-PCR) for a late viral mRNA (glycoprotein D gene) dem-onstrated reactivation of parental virus in neural (TGs) and lymphoid tissues (tonsils, lymph node). In contrast, recombinant virus mRNA was detected only in lymphoid tissues. These results demonstrate that BoHV-5 and the recombinant BoHV-5
Variation in reading literacy : a cross-national approach

In 2001, the International Association for the Evaluation of Educational Achievement (IEA) conducted a comparative study of reading literacy (PIRLS 2001). A reading comprehension assessment instrument was developed and translated into the languages of 35 participating countries for this purpose. After field testing of the instrument, the final version of the Reading Literacy Test (henceforth RLT) was established. An important question is nevertheless whether the linguistic characteristics of a particular version of the test may influence the difficulty of the test or not. The procedures followed for finalization of the test can also be questioned. In two studies, the validity of the Dutch version of the RLT was therefore examined. In the first study, comparison of the linguistic characteristics of the Dutch and English versions of the test showed the Dutch passages and items to contain both a greater number of words and longer words than the English passages and items. However, the use of more and longer words did not produce a higher level of complexity with respect to content, sentence structure, text structure, or test items as judged by a panel of bilingual experts. While the Dutch children had to read more and longer words than the English children, moreover, they had no problems finishing the test within the allocated amount of time. Nevertheless, the reading of a greater number of words and longer words may have placed the Dutch children at a disadvantage because it takes more cognitive effort that might otherwise have been devoted to the processing of the text and the actual answering of the test items. In the second study, the possible impact of the changes made after the field testing of the RLT was examined. The omission of passages and the modification or omission of test items were found to have no negative or positive consequences for the psychometric properties of the Dutch version of the test when the internal consistency; inter-scorer agreement; item-country interactions; and percentages of correct responding were
From population structure to individual behaviour: genetic analysis of social structure in the European wild rabbit (Oryctolagus cuniculus)

Abstract The European wild rabbit ( Oryctolagus cuniculus ) lives in stable, territorial breeding groups, with male-biased natal dispersal, female philopatry, and a polygynous mating system. It was introduced into Britain in the 11th century and kept in captive warrens as a food and fur resource. Populations expanded in the wild in the 18th century. Microsatellite markers were employed to examine the genetic structure of wild rabbit populations on three spatial scales: macrogeographic structure of 17 populations in East Anglia, microgeographic structure of a tagged population in the grounds of the University of East Anglia over four consecutive years, and pairwise kinships and individual movement within this tagged population. Populations across East Anglia were found to be genetically distinct, and heterozygote deficits were observed at all loci indicating sub-division within sampled populations. Analysis of the tagged population confirmed that rabbit populations are genetically sub-divided among social groups. Studying this population over four consecutive years revealed that as the population size increased, the number of social groups increased. Analysis of individual pairwise relatedness of females indicated that individuals did not necessarily group with kin, and behavioural data indicate that an optimum group size may exist which maximizes reproductive success.
THE ROLE OF PROBIOTICS IN THE POULTRY INDUSTRY

The increase of productivity in the poultry industry has been accompanied by various impacts, including emergence of a large variety of pathogens and bacterial resistance. These impacts are in part due to the indiscriminate use of chemotherapeutic agents as a result of management practices in rearing cycles. This review provides a summary of the use of probiotics for prevention of bacterial diseases in poultry, as well as demonstrating the potential role of probiotics in the growth performance and immune response of poultry, safety and wholesomeness of dressed poultry meat evidencing consumer’s protection, with a critical evaluation of results obtained to date.
Structure and function of the strophiolar plug in seeds of Albizia lophantha.

Entry of water into the testa of hard seeds of Albizia lophantha (WilId.) Benth. is controlled by a small strophiolar plug (0.3 x 0.25 mm), adjacent to the hilum, which is lost by eruption after heating. Movement of water through the testa is facilitated by the vascular bundle which arches close to the strophiole. Each seed imbibes 90 to 110 p] of water. This water enters the testa with an average flux of 165 pl/mm2/hr. Development of the testa is described with particular relevance to the strophiolar plug and associated tissues.
ON TRAFFIC ANALYSIS ATTACKS TO ENCRYPTED VOIP CALLS

The increasing popularity of VoIP telephony has brought a lot of attention and concern over security and privacy issues of VoIP communication. This thesis proposes a new class of traffic analysis attacks to encrypted VoIP calls. The goal of these attacks is to detect speaker or speech of encrypted VoIP calls. The proposed traffic analysis attacks exploit silent suppression, an essential feature of VoIP telephony. These attacks are based on application-level features so that the attacks can detect the same speech or the same speaker of different VoIP calls made with different VoIP codecs. We evaluate the proposed attacks by extensive experiments over different type of networks including commercialized anonymity networks and campus networks. The experiments show that the proposed traffic analysis attacks can detect speaker and speech of encrypted VoIP calls with a high detection rate which is a great improvement comparing with random guess. With the help of intersection attacks, the detection rate for speaker detection can be increased. In order to shield the detrimental effect of this proposed attacks, a countermeasure is proposed to mitigate the proposed traffic analysis attacks.
A digital-serial silicon compiler

A novel silicon compiler is described, called PARSIFAL. It constructs chips with a data-flow architecture in which data is passed in a digit-wide pipeline form one computational element to the next. The size of a digit can be specified by the user to be any value between one and the full word size of the chip. A digit size of one gives bit-serial chips, whereas a digit-size equal to the word-size gives fully parallel computation. It is shown that an intermediate value of the digit-size usually gives the most efficient chips in terms of throughput per unit area. <<ETX>>
Multi-agent collaboration: an e-commerce example

Summary form only given. E-commerce represents a model of modern commerce in which autonomous software agents represent the roles of different trading entities. Applications of e-commerce are characterized as consisting of a number of distributed heterogeneous entities operating in dynamic environments. Building on top of an open framework for multiagent collaboration, we study collaboration between trade entities performing a trade purchase transaction.
Pilot-aided channel estimation for OFDM/OQAM

OFDM/offsetQAM is an interesting alternative to classical OFDM modulation, as it does not require the use of guard interval. This characteristic makes its spectral efficiency optimal. On the other hand, this modulation is less robust to Rayleigh fading channel. Indeed, when classical channel estimation used for OFDM modulation is applied straightforwardly to OFDM/OQAM modulation, an intrinsic inter-symbol-interference is observed. This deeply degrades its performances. In this paper, we theoretically explain this phenomenon and propose a reliable method to significantly reduce it. Results of different methods of pilot-aided channel estimation over delay-Doppler channels are shown in this paper.
Determination of the primary structures of 16 asialo-carbohydrate units derived from human plasma α1-acid glycoprotein by 360-MHz 1H NMR spectroscopy and permethylation analysis

The present study was initiated in order to determine the primary structures of the carbohydrate units of desialyzed human plasma al-acid glycoprotein. In an earlier investigation I6 glycopeptides which originated from four of the five glycosylation sites of this protein were prepared in the homogeneous state. Since the elucidation of the structures of such a large number of carbohydrate units by the conventional chemical and enzymatic procedures would require a very long period of time and considerable amounts of material, a new method-360-MHz H NMR spectroscopy-in combination with methylation analysis and partial acetolysis was introduced i n the present study. This highly sensitive method allowed the elucidation of the structures of the carbohydrate units of the mentioned glycopeptides to be carried out in a very short period of time. The present investigation revealed that the structures of the 16 heteroglycans can be grouped into five classes, and, except for those of two classes, the structures are new. Two classes designated A and B possess the known bi- and trimtennary structures, respectively. A third class designated C proved to be tetraantennary in its structure, whereas the other classes designated BF and CF are, in comparison with the structures of classes B and C, characterized by an additional fucose residue in a hitherto unknown position and linkage. The latter monosaccharide residue is attached in an a( 1-3) bond, vicinal to Gal@(1 +4), to the GlcNAc residue 7. The present study also revealed that each glycosylation site of pooled a]-acid glycoprotein possesses carbohydrate units with different structures.
Combining Multi-User Diversity with Eigenbeamforming in Correlated Channels

In a time varying point-to-multi-point link such as the downlink of a network with a base station and several users, there exists an inherent form of diversity called multi-user diversity. This diversity is harnessed by the use of a proper scheduler such as the proportional fair scheduler. Among other factors, the multi-user diversity gain is determined by the dynamic range of the channel fluctuations. For several scenarios including correlated fading channels, this range can be increased by deploying multiple antennas at the transmitter and using opportunistic beamforming. However, point-to-point link transmitting techniques such as eigenbeamforming exist that have proven to be useful in correlated channels. We present the concept of exploiting multi-user diversity in correlated channels with eigenbeamforming. We show how combining eigenbeamforming with the proportional fair scheduler results in a larger multi-user diversity gain than the one achieved through opportunistic beamforming.
Fuzzy Logic for Personalized Healthcare and Diagnostics : FuzzyApp — A Fuzzy Logic Based Allergen-Protein Predictor

The path to personalized medicine demands the use of new and customized biopharmaceutical products containing modified proteins. Hence, assessment of these products for allergenicity becomes mandatory before they are introduced as therapeutics. Despite the availability of different tools to predict the allergenicity of proteins, it remains challenging to predict the allergens and nonallergens, when they share significant sequence similarity with known nonallergens and allergens, respectively. Hence, we propose ‘‘FuzzyApp,’’ a novel fuzzy rule based system to evaluate the quality of the query protein to be an allergen. It measures the allergenicity of the protein based on the fuzzy IF-THEN rules derived from five different modules. On various datasets, FuzzyApp outperformed other existing methods and retained balance between sensitivity and specificity, with positive Mathew’s correlation coefficient. The high specificity of allergen-like putative nonallergens (APN) revealed the FuzzyApp’s capability in distinguishing the APN from allergens. In addition, the error analysis and whole proteome dataset analysis suggest the efficiency and consistency of the proposed method. Further, FuzzyApp predicted the Tropomyosin from various allergenic and nonallergenic sources accurately. The web service created allows batch sequence submission, and outputs the result as readable sentences rather than values alone, which assists the user in understanding why and what features are responsible for the prediction. FuzzyApp is implemented using PERL CGI and is freely accessible at http://fuzzyapp.bicpu. edu.in/predict.php. We suggest the use of Fuzzy logic has much potential in biomarker and personalized medicine research to enhance predictive capabilities of post-genomics diagnostics.
'Most' meanings are superlative.

Probing for native speaker intuitions regarding entailment patterns associated with most may not be a feasible approach to detecting the ambiguity. This chapter reviews the debate between the approach that views most as a lexical primitive and the approach which views most as a complex superlative construction. It presents novel data from three different experiments which support the view that most is uniformly a superlative construction. The chapter shows that under certain circumstances speakers can access a latent superlative interpretation of most in subject position, in addition to the expected proportional meaning. It compares the authors' results with the findings of a related study in Lidz et al. and argues that the seemingly conflicting results of that study are a result of quite different task demands. The chapter develops an account of the ambiguity within a decompositional analysis of most which exploits the mechanism of association with focus. Keywords: decompositional analysis of most ; entailment patterns; native speaker intuitions; subject position; superlative construction