Miracle-dz/UniFAR-FTUs huggingface dataset:
High mutational rates of large-scale duplication and deletion in Daphnia pulex

Knowledge of the genome-wide rate and spectrum of mutations is necessary to understand the origin of disease and the genetic variation driving all evolutionary processes. Here, we provide a genome-wide analysis of the rate and spectrum of mutations obtained in two Daphnia pulex genotypes via separate mutation-accumulation (MA) experiments. Unlike most MA studies that utilize haploid, homozygous, or self-fertilizing lines, D. pulex can be propagated ameiotically while maintaining a naturally heterozygous, diploid genome, allowing the capture of the full spectrum of genomic changes that arise in a heterozygous state. While base-substitution mutation rates are similar to those in other multicellular eukaryotes (about 4 × 10−9 per site per generation), we find that the rates of large-scale (>100 kb) de novo copy-number variants (CNVs) are significantly elevated relative to those seen in previous MA studies. The heterozygosity maintained in this experiment allowed for estimates of gene-conversion processes. While most of the conversion tract lengths we report are similar to those generated by meiotic processes, we also find larger tract lengths that are indicative of mitotic processes. Comparison of MA lines to natural isolates reveals that a majority of large-scale CNVs in natural populations are removed by purifying selection. The mutations observed here share similarities with disease-causing, complex, large-scale CNVs, thereby demonstrating that MA studies in D. pulex serve as a system for studying the processes leading to such alterations.
To Effective Search Of Outsourced Data In Cloud By Using RKS

Cloud computing economically enables the paradigm of data service outsourcing. However, to protect data privacy, sensitive cloud data have to be encrypted before outsourced to the commercial public cloud, which makes effective data utilization service a very challenging task. Although traditional searchable encryption techniques allow users to securely search over encrypted data through keywords, they support only Boolean search and are not yet sufficient to meet the effective data utilization need that is inherently demanded by large number of users and huge amount of data files in cloud. In this paper, we define and solve the problem of secure ranked keyword search over encrypted cloud data. Ranked search greatly enhances system usability by enabling search result relevance ranking instead of sending undifferentiated results, and further ensures the file retrieval accuracy. Specifically, we explore the statistical measure approach, i.e., relevance score, from information retrieval to build a secure searchable index, and develop a one-to-many order-preserving mapping technique to properly protect those sensitive score information. The resulting design is able to facilitate efficient server-side ranking without losing keyword privacy. Thorough analysis shows that our proposed solution enjoys “as strong-as-possible” security guarantee compared to previous searchable encryption schemes, while correctly realizing the goal of ranked keyword search. Extensive experimental results demonstrate the efficiency of the proposed solution.
Global Genetic Architecture of an Erythroid Quantitative Trait Locus, HMIP-2

HMIP‐2 is a human quantitative trait locus affecting peripheral numbers, size and hemoglobin composition of red blood cells, with a marked effect on the persistence of the fetal form of hemoglobin, HbF, in adults. The locus consists of multiple common variants in an enhancer region for MYB (chr 6q23.3), which encodes the hematopoietic transcription factor cMYB. Studying a European population cohort and four African‐descended groups of patients with sickle cell anemia, we found that all share a set of two spatially separate HbF‐promoting alleles at HMIP‐2, termed “A” and “B. ” These typically occurred together (“A–B”) on European chromosomes, but existed on separate homologous chromosomes in Africans. Using haplotype signatures for “A” and “B,” we interrogated public population datasets. Haplotypes carrying only “A” or “B” were typical for populations in Sub‐Saharan Africa. The “A–B” combination was frequent in European, Asian, and Amerindian populations. Both alleles were infrequent in tropical regions, possibly undergoing negative selection by geographical factors, as has been reported for malaria with other hematological traits. We propose that the ascertainment of worldwide distribution patterns for common, HbF‐promoting alleles can aid their further genetic characterization, including the investigation of gene–environment interaction during human migration and adaptation.
Is There a Potential for Increases in FDI for Central and Eastern European Countries Following EU Accession?

The speed of the collapse of central planning in central and eastern Europe and the former Soviet Union was one of the most startling political events of the second half of the twentieth century. No-one really knew how long the process of stabilisation and adjustment would take. What was clear, however, was that the international community would not just sit back and let it happen. Substantial resource transfers took place as well as extensive policy advice. The European Union was in the vanguard of this post-Communist reconstruction effort with both financial aid through programmes such as PHARE and policy initiatives such as the Europe Agreements. The latter not only elevated the central and east European countries (CEECs) to the apex of the Union’s ‘pyramid of privilege’ but laid the foundations for progress towards eventual accession. By the middle of 1996, ten CEECs had applied for membership of the Union; in 1998 serious negotiations over entry began; and in December 2000 a formal Treaty commitment was made at the Nice Summit. The most recent Commission report on readiness for accession (in October 2002), concluded that eight of the ten CEECs will be ready to join the EU in 2004.
The zinc finger transcriptional repressor Blimp1/Prdm1 is dispensable for early axis formation but is required for specification of primordial germ cells in the mouse

Blimp1, a zinc-finger containing DNA-binding transcriptional repressor, functions as a master regulator of B cell terminal differentiation. Considerable evidence suggests that Blimp1 is required for the establishment of anteroposterior axis formation and the formation of head structures during early vertebrate development. In mouse embryos, Blimp1 is strongly expressed in axial mesendoderm, the tissue known to provide anterior patterning signals during gastrulation. Here, we describe for the first time the defects caused by loss of Blimp1 function in the mouse. Blimp1 deficient embryos die at mid-gestation, but surprisingly early axis formation, anterior patterning and neural crest formation proceed normally. Rather, loss of Blimp1 expression disrupts morphogenesis of the caudal branchial arches and leads to a failure to correctly elaborate the labyrinthine layer of the placenta. Blimp1 mutant embryos also show widespread blood leakage and tissue apoptosis, and, strikingly, Blimp1 homozygous mutants entirely lack PGCs. At the time of PGC allocation around 7.25 days post coitum, Blimp1 heterozygous embryos exhibit decreased numbers of PCGs. Thus Blimp1 probably acts to turn off the default pathway that allows epiblast cells to adopt a somatic cell fate, and shifts the transcriptional program so that they become exclusively allocated into the germ cell lineage.
Atherosclerosis and Thrombosis: Identification of Targets for Magnetic Resonance Imaging

Imaging techniques are needed that will allow earlier and more refined diagnosis, guide targeted treatment in individual patients and monitor response to that treatment. Magnetic resonance imaging is well-suited to these tasks as it can provide anatomical, structural, and functional data on the arterial wall. Its capabilities are further enhanced by the use of a range of increasingly sophisticated contrast agents that target specific molecules, cells, and biological processes. This article will consider the pathogenesis of atherosclerosis and systematically identify biologically relevant targets for imaging at different stages of disease process.
Novel Associations of Multiple Genetic Loci With Plasma Levels of Factor VII, Factor VIII, and von Willebrand Factor: The CHARGE (Cohorts for Heart and Aging Research in Genome Epidemiology) Consortium

Background— Plasma levels of coagulation factors VII (FVII), VIII (FVIII), and von Willebrand factor (vWF) influence risk of hemorrhage and thrombosis. We conducted genome-wide association studies to identify new loci associated with plasma levels. Methods and Results— The setting of the study included 5 community-based studies for discovery comprising 23 608 European-ancestry participants: Atherosclerosis Risk In Communities Study, Cardiovascular Health Study, British 1958 Birth Cohort, Framingham Heart Study, and Rotterdam Study. All subjects had genome-wide single-nucleotide polymorphism (SNP) scans and at least 1 phenotype measured: FVII activity/antigen, FVIII activity, and vWF antigen. Each study used its genotype data to impute to HapMap SNPs and independently conducted association analyses of hemostasis measures using an additive genetic model. Study findings were combined by meta-analysis. Replication was conducted in 7604 participants not in the discovery cohort. For FVII, 305 SNPs exceeded the genome-wide significance threshold of 5.0×10−8 and comprised 5 loci on 5 chromosomes: 2p23 (smallest P value 6.2×10−24), 4q25 (3.6×10−12), 11q12 (2.0×10−10), 13q34 (9.0×10−259), and 20q11.2 (5.7×10−37). Loci were within or near genes, including 4 new candidate genes and F7 (13q34). For vWF, 400 SNPs exceeded the threshold and marked 8 loci on 6 chromosomes: 6q24 (1.2×10−22), 8p21 (1.3×10−16), 9q34 (<5.0×10−324), 12p13 (1.7×10−32), 12q23 (7.3×10−10), 12q24.3 (3.8×10−11), 14q32 (2.3×10−10), and 19p13.2 (1.3×10−9). All loci were within genes, including 6 new candidate genes, as well as ABO (9q34) and VWF (12p13). For FVIII, 5 loci were identified and overlapped vWF findings. Nine of the 10 new findings were replicated. Conclusions— New genetic associations were discovered outside previously known biological pathways and may point to novel prevention and treatment targets of hemostasis disorders.
B-type supergiants in the Small Magellanic Cloud: rotational velocities and implications for evolutionary models

High-resolution spectra for 24 SMC and Galactic B-type supergiants have been analysed to estimate the contributions of both macroturbulence and rotation to the broadening of their metal lines. Two different methodologies are considered, viz. goodness-of-fit comparisons between observed and theoretical line profiles and identifying zeros in the Fourier transforms of the observed profiles. The advantages and limitations of the two methods are briefly discussed with the latter techniques being adopted for estimating projected rotational velocities (v sini )b ut the former being used to estimate macroturbulent velocities. The projected rotational velocity estimates range from approximately 20 to 60 km s −1 , apart from one SMC supergiant, Sk 191, with a v sini � 90 km s −1 . Apart from Sk 191, the distribution of projected rotational velocities as a function of spectral type are similar in both our Galactic and SMC samples with larger values being found at earlier spectral types. There is marginal evidence for the projected rotational velocities in the SMC being higher than those in the Galactic targets but any differences are only of the order of 5–10 km s −1 , whilst evolutionary models predict differences in this effective temperature range of typically 20 to 70 km s −1 . The combined sample is consistent with a linear variation of projected rotational velocity with effective temperature, which would imply rotational velocities for supergiants of 70 km s −1 at an effective temperature of 28 000 K (approximately B0 spectral type) decreasing to 32 km s −1 at 12 000 K (B8 spectral type). For all targets, the macroturbulent broadening would appear to be consistent with a Gaussian distribution (although other distributions cannot be discounted) with an 1 half-width varying from approximately 20 km s −1 at B8 to 60 km s −1 at B0 spectral types.
Application classification in cellular backhaul networks

Cellular backhaul networks carry user's traffic within encrypted tunnels. With tunneled traffic, the application classifier cannot identify the underline TCP/UDP connections and cannot use any IP packet header information. Yet, some statistical properties can be considered in this case too, such as: volume per tunnel, tunnel durations, inter-packets delays (however, sequential packets might belong to different TCP connections), packet sizes, and packet direction. This research deals with blind classification of the dominated application of user tunneled traffic into 4 classes: (1) Control, VoIP and IM; (2) Video streaming; (3) Web browsing; and (4) file download/sharing. Our experimental results show that such a blind on-line classifier can classify the dominated application of a user tunnel into these four classes with more than 80% accuracy.
Revisiting Stein's paradox: multi-task averaging

We present a multi-task learning approach to jointly estimate the means of multiple independent distributions from samples. The proposed multi-task averaging (MTA) algorithm results in a convex combination of the individual task's sample averages. We derive the optimal amount of regularization for the two task case for the minimum risk estimator and a minimax estimator, and show that the optimal amount of regularization can be practically estimated without cross-validation. We extend the practical estimators to an arbitrary number of tasks. Simulations and real data experiments demonstrate the advantage of the proposed MTA estimators over standard averaging and James-Stein estimation.
Realizable parasitic reduction using generalized Y-/spl Delta/ transformation

We propose a realizable RCLK-in-RCLK-out parasitic reduction technique. The method employs generalized Y-/spl Delta/ transformation. In our method, admittances are kept in their original rational forms of s, and their orders are reduced by truncating high-order terms. Therefore reduced admittances match the low-order terms in exact admittances. First-order realization of admittances is guaranteed, and higher-order realization is achieved by template optimization using geometric programming. The algorithm uniquely uses common-factor identification and cancellation operations to make Y-/spl Delta/ transformation numerically stable. The experiment shows that our method can achieve higher reduction ratio than TICER and comparable simulation results with PRIMA.
Psychopathy and Aggression.

Psychopathy is a personality disorder charaeterized by a major affective deficit accompanied by a disregard for the rights of others and for societal rules in generaI (e.g., Hare, 1996). As defined by the well-validated Psychopathy Checklist-Revised (PCL-R; Hare, 1991), psychopaths are manipulative, callous, remorseless, impulsive, irresponsible individuals (e.g., Hare, 1996, 1998). In this chapter, we begin by outlining the contribution of psychopathy to the prediction of whether and the degree to which a person will engage in aggressive behavior. Our attention then turns to a much newer focus of research-the characteristics of violent actions by psychopaths. We review studies investigating the nature of their violence, examine the possible link between psychopathy and sadistic behavior, and consider how this work informs our understanding of their criminal motivations.
The Polyploid Series of the Achillea millefolium Aggregate in the Iberian Peninsula Investigated Using Microsatellites

The Achillea millefolium aggregate is one of the most diverse polyploid complexes of the Northern hemisphere and has its western Eurasian boundary in the Iberian Peninsula. Four ploidy levels have been detected in A. millefolium, three of which have already been found in Iberia (diploid, hexaploid and octoploid), and a fourth (tetraploid) reported during the preparation of this paper. We collected a sample from 26 Iberian populations comprising all ploidy levels, and we used microsatellite markers analyzed as dominant in view of the high ploidy levels. Our goals were to quantify the genetic diversity of A. millefolium in the Iberian Peninsula, to elucidate its genetic structure, to investigate the differences in ploidy levels, and to analyse the dispersal of the species. The lack of spatial genetic structure recovered is linked to both high levels of gene flow between populations and to the fact that most genetic variability occurs within populations. This in turn suggests the existence of a huge panmictic yarrow population in the Iberian Peninsula. This is consistent with the assumption that recent colonization and rapid expansion occurred throughout this area. Likewise, the low levels of genetic variability recovered suggest that bottlenecks and/or founder events may have been involved in this process, and clonal reproduction may have played an important role in maintaining this genetic impoverishment. Indeed, the ecological and phenologic uniformity present in the A. millefolium agg. in Iberia compared to Eurasia and North America may be responsible for the low number of representatives of this complex of species present in the Iberian Peninsula. The low levels of genetic differentiation between ploidy levels recovered in our work suggest the absence of barriers between them.
Influence of menstrual phase and arid vs. humid heat stress on autonomic and behavioural thermoregulation during exercise in trained but unacclimated women

Despite an attenuated fluctuation in ovarian hormone concentrations in well‐trained women, one in two of such women believe their menstrual cycle negatively impacts training and performance. Forthcoming large international events will expose female athletes to hot environments, and studies evaluating aerobic exercise performance in such environments across the menstrual cycle are sparse, with mixed findings. We have identified that autonomic heat loss responses at rest and during fixed‐intensity exercise in well‐trained women are not affected by menstrual cycle phase, but differ between dry and humid heat. Furthermore, exercise performance is not different across the menstrual cycle, yet is lower in humid heat, in conjunction with reduced evaporative cooling. Menstrual cycle phase does not appear to affect exercise performance in the heat in well‐trained women, but humidity impairs performance, probably due to reduced evaporative power.
Cytotoxic Compounds Derived from Marine Sponges. A Review (2010–2012)

This extensive review covers research published between 2010 and 2012 regarding new compounds derived from marine sponges, including 62 species from 60 genera belonging to 33 families and 13 orders of the Demospongia class (Porifera). The emphasis is on the cytotoxic activity that bioactive metabolites from sponges may have on cancer cell lines. At least 197 novel chemical structures from 337 compounds isolated have been found to support this work. Details on the source and taxonomy of the sponges, their geographical occurrence, and a range of chemical structures are presented. The compounds discovered from the reviewed marine sponges fall into mainly four chemical classes: terpenoids (41.9%), alkaloids (26.2%), macrolides (8.9%) and peptides (6.3%) which, along with polyketides, sterols, and others show a range of biological activities. The key sponge orders studied in the reviewed research were Dictyoceratida, Haplosclerida, Tetractinellida, Poecilosclerida, and Agelasida. Petrosia, Haliclona (Haplosclerida), Rhabdastrella (Tetractinellida), Coscinoderma and Hyppospongia (Dictyioceratida), were found to be the most promising genera because of their capacity for producing new bioactive compounds. Several of the new compounds and their synthetic analogues have shown in vitro cytotoxic and pro-apoptotic activities against various tumor/cancer cell lines, and some of them will undergo further in vivo evaluation.
BSP Sorting: An experimental Study

The Bulk-Synchronous Parallel model of computation has been used for the architecture independent design and analysis of parallel algorithms whose performance is expressed not only in terms of problem size n but also in terms of parallel machine properties. In this paper the performance of implementations of deterministic and randomized BSP sorting algorithms is examined. The deterministic algorithm uses deterministic regular oversampling and parallel sample sorting and is augmented to handle duplicate keys transparently with optimal asymptotic efficiency. The randomized algorithm is sample-sort based and uses oversampling and the ideas introduced with the deterministic algorithm. The resulting randomized design, however, works differently from traditional parallel sample-sort based algorithms and is also augmented to transparently handle duplicate keys with optimal asymptotic efficiency thus eliminating the need to tag all input keys and to double communication/computation time. Both algorithms are shown to balance the work-load evenly among the processors and the use and precise tuning of oversampling that the BSP analysis allows combined with the transparent duplicate-key handling insures regular and balanced communication.
Discovering Trends in Text Databases

We address the problem of discovering trends in text databases. Trends can be used, for example, to discover that a company is shifting interests from one domain to another. We are given a database V of documents. Each document consists of one or more text fields and a timestamp. The unit of text is a word and a phrase is a list of words. (We defer the discussion of more complex structures till the “Methodology” secl-inn \ Ao.aw.;,tc.rl .r;th r.rh nhrano ;a s h;rtmw nf the YAVU., ~uu”~Icu”n,L& ““lull \.uIUIA yuLCll”U I” Lo ,YYUY”~ y “I Yll” frequency of occurrence of the phrase, obtained by partitioning the documents based upon their timestamps. The frequency of occurrence in a particular time period is the number of documents that contain the phrase. (Other measures of frequency are possible, e.g. counting each occurrence of the phrase in a document.) A trend is a specific subsequence of the history of a phrase that satisfies the users’ query over the histories. For example, the user may specify a “spike” query to finds those phrases whose frequency of occurrence increased and then decreased.
Towards a generic adaptive hypermedia platform: a conversion case study

This paper reports about the recent advances towards establishing a common platform for adaptive educational hypermedia (AEH) authoring. We present the conversion from MOT, a dedicated authoring system, to AHA! used in this context as delivery system for AEH. Moreover, we describe two new representation languages that emerged in the process: a common format for defining the static material, CAF, and an extended adaptation language for the description of the dynamic behaviour, LAG. Finally, some evaluations are shown and conclusions are drawn.
Empirical estimators for semi-Markov processes

A semi-Markov process stays in state x for a time s and then jumps to state y according to a transition distribution Q(x; dy; ds). A statistical model is described by a family of such transition distributions. We give conditions for a nonparametric version of local asymptotic normality as the observation time tends to innnity. Then we introducèempirical' estimators for linear functionals of the distribution (dx)Q(x; dy; ds), with denoting the invariant distribution of the embedded Markov chain, and characterize the empirical estimators which are eecient for a given model. We discuss eeciency of several classical estimators, in particular the jump frequency, the proportion of visits to a given set, the proportion of time spent in a set, and an estimator for Q (x; fyg 0; t]) suggested by Moore and Pyke (1968) for countable state space.