Miracle-dz/UniFAR-FTUs huggingface dataset:
Factors affecting phasing quality in a commercial layer population

The step from genotyping results to phased haplotypes represents a quality improvement in the genetic information that has many applications, e.g. imputation of low frequency variants or inferring points of recombination (Browning & Browning, 2012). Length and distribution of haplotype blocks and the number of independent chromosome segments are population specific and key parameters to assess genetic diversity and expected accuracy in genomic selection programs (Daetwyler et al., 2013). The haplotype phases can be obtained by experimental methods (laboratory-based) or by computational approaches with phasing software. The cost of laboratory methods is still too high to be routinely applied in genetic programs. Due to this condition, many computational methods have been developed. A review of different computational methods was done by Browning & Browning (2012), pointing out that factors affecting phasing accuracy are sample size, marker density, genotype accuracy, relatedness in the sample and the degree of ethnic stratification. The results evidenced that there is not a single solution in phasing methods, and phasing accuracy is a multifactorial variable. This study aims at assessing haplotype phasing quality for a highly-related laying hen population using two different phasing programs, FImpute and Beagle. Beagle (Browning and Browning, 2007) creates local cluster of haplotypes in a way that haplotypes in the same cluster have similar probabilities for further allele markers. FImpute is a phasing and imputation software (Sargolzaei et al., 2014) specially developed for livestock scenarios, which relies in IBD haplotypes to reconstruct the phase.
Extrapolations of Standing-Stocks of Big Bacteria in Humboldt Eastern Boundary Current Ecosystem (HEBCE)

The sublittoral seafloor of the Humboldt Eastern Boundary Current ecosystem (HEBCE) is characterized by sediments rich in sulfur compounds and extensive and sometimes massive benthic bacterial mats. This sulfur-based sublittoral ecosystem is maintained by the very high input of organic matter from the productive surface waters and the concurrence of subsurface hypoxic to anoxic waters of the Peru-Chile Undercurrent (PCU). Generically here named the “Humboldt Sulfuretum” (HS), this benthic habitat extends latitudinally along the continental margins off Peru and Chile for over 3,500 km potentially covering around 100,000 km2 thus making it one of the largest reduced soft sediment regions in the world. Since its first recognition in 1962 the HS has consistently been found the home of massive bacterial mats which can attain standing-stocks in the order of 1,000 gm-2 (wet weight). Although hosting a complex and diverse community of prokaryotes, microbial eukaryotes, and meio- and occasional macrobenthic fauna, the dominant components, both in weight and volume, are large vacuolated species of megabacteria of the Beggiatoaceae family (Gammaproteobacteria). These mat-forming autotrophic/mixotrophic species singularly link the C, S, and N cycles (possibly also the P cycle) and constitute one of the largest macroscopic bacterial populations living in today’s naturally reduced world oceans, i.e., eastern boundary current systems, in fact the HS with its microbial communities could be considered modern analogs of Proterozoic benthic systems. This work intends to highlight the extensive geographic distribution, the huge, although variable, massiveness, and thus the potential biogeochemical significance of the giant mat-forming prokaryotes and their accompanying microbial community, as a contribution to a better understanding HEBCE’s functioning one of the most productive eastern boundary current systems of the world.
Student’s Engagement in School: Conceptualization and relations with Personal Variables and Academic Performance

This article reviews the literature regarding Student’s Engagement in School (SES), its relationship with personal variables, as well as with academic performance. Although SES’ conceptualization may vary across studies, there is general agreement concerning the multidimensional nature of this construct, encompassing three dimensions – cognitive, affective and behavioural. It is seen as an antecedent of several required outcomes, at academic level, but also as a valorous construct itself, both as mediator and product. More particularly, this concept has been the focus of debate concerning academic success and school dropout. There can also be found a significant number of studies which suggest that personal (self-efficacy, self-concept), as well as contextual (peers, school, family) factors are related with school engagement; additionally, the lack of engagement is linked with low academic performance, behavioural problems and school dropout. Thus, Student’s Engagement in School is perceived as a potentially effective response to the problems affecting schools and their students, and an aspect to be considered in preventing problematic patterns related to scholary contexts.
Spectro-Temporal Analysis of Auscultatory Sounds

Auscultation is a useful procedure for diagnostics of pulmonary or cardiovascular disorders. The effectiveness of auscultation depends on the skills and experience of the clinician. Further issues may arise due to the fact that heart sounds, for example, have dominant frequencies near the human threshold of hearing, hence can often go undetected (1). Computer-aided sound analysis, on the other hand, allows for rapid, accurate, and reproducible quantification of pathologic conditions, hence has been the focus of more recent research (e.g., (1–5)). During computer-aided auscultation, however, lung sounds are often corrupted by intrusive quasiperiodic heart sounds, which alter the temporal and spectral characteristics of the recording. Separation of heart and lung sound components is a difficult task as both signals have overlapping frequency spectra, in particular at frequencies below 100 Hz (6). For lung sound analysis, signal processing strategies based on conventional time, frequency, or time-frequency signal representations have been proposed for heart sound cancelation. Representative strategies include entropy calculation (7) and recurrence time statistics (8) for heart sound detection-and-removal followed by lung sound prediction, adaptive filtering (e.g., (9; 10)), time-frequency spectrogram filtering (11), and time-frequency wavelet filtering (e.g., (12–14)). Subjective assessment, however, has suggested that due to the temporal and spectral overlap between heart and lung sounds, heart sound removal may result in noisy or possibly “non-recognizable" lung sounds (15). Alternately, for heart sound analysis, blind source extraction based on periodicity detection has recently been proposed for heart sound extraction from breath sound recordings (16); subjective listening tests, however, suggest that the extracted heart sounds are noisy and often unintelligible (17). In order to benefit fully from computer-aided auscultation, both heart and lung sounds should be extracted or blindly separated from breath sound recordings. In order to achieve such a difficult task, a few methods have been reported in the literature, namely, wavelet filtering (18), independent component analysis (19; 20), and more recently, modulation domain filtering (21). The motivation with wavelet filtering lies in the fact that heart sounds contain large components over several wavelet scales, while coefficients associated with lung sounds quickly decrease with increasing scale. Heart and lung sounds are iteratively separated based on an adaptive hard thresholding paradigm. As such, wavelet coefficients at each scale with amplitudes above the threshold are assumed to correspond to heart sounds and the remaining coefficients are associated with lung sounds. Independent component analysis, in turn, makes use
A contribution to the knowledge of Arctic zooplankton diurnal variability (Kongsfjorden, Svalbard)

Zooplankton was investigated at fixed site in 24 hours in Kongsfjorden, a glacial fjord situated on the west coast of Spitsbergen (Svalbard) (79N, 12E), in order to unveil the level of diurnal variability in community composition and abundance. Parallel to zoo− plankton study water temperature and salinity were measured while information on local tides and winds was obtained from external sources. Observed changes did not exceed the range of variability regarded intrinsic, resulting from the nature of plankton. Because of this low variability we are of the opinion that the data presented can be regarded a valid measure of the natural heterogeneity of zooplankton communities in hydrologically dynamic Arctic coastal waters in summer. The observed changes in zooplankton were primarily induced by the complex dynamics of the fjord's water masses. In spite of importance of tidal forcing, the variability in zooplankton did not demonstrate similar temporal fluctuations due to modification of the water movement by other irregular forces (local wind). Also, we have not found any indication of diel vertical migration in coastal water in the Arctic under the condition of midnight sun.
Adapting Threat Modeling Methods for the Automotive Industry

We live in a world that is getting more interconnected by each day and we are witnessing a global change where all the devices in our surroundings are becoming “smart” and connected to the Internet. The automotive industry is also a part of this change. Today's vehicles have more than 150 small computers, embedded control units (ECUs), and multiple connection points to the Internet which makes them vulnerable to various on-line threats. Recent attacks on connected vehicles have all been results of security vulnerabilities that could have been avoided if appropriate risk assessment methods were in place during software development. In this paper we demonstrate how the threat modeling process, common for the computer industry, can be adapted and applied in the automotive industry. The overall contribution is achieved by providing two threat modeling methods that are specifically adapted for the concept of the connected car and can further be used by automotive experts. The methods were chosen after an extensive literature survey and with support of domain experts from the vehicle industry. The two methods were then successfully applied to the connected car and the underlying software architecture based on the AUTOSAR standard. We have empirically validated our results with domain experts as well as tested the found vulnerabilities in a simulated vehicle environment.
A search for thermal X‐ray signatures in gamma‐ray bursts – II. The Swift sample

In several gamma-ray bursts (GRBs) excess emission, in addition to the standard synchrotron afterglow spectrum, has been discovered in the early-time X-ray observations. It has been proposed that this excess comes from blackbody emission, which may be related to the shock breakout of a supernova in the GRBs progenitor star. This hypothesis is supported by the discovery of excess emission in several GRBs with an associated supernova. Using mock spectra we show that it is only likely to detect such a component, similar to the one proposed in GRB 101219B, at low redshift and in low absorption environments. We also perform a systematic search for blackbody components in all the GRBs observed with the Swift satellite and find six bursts (GRBs 061021, 061110A, 081109, 090814A, 100621A and 110715A) with possible blackbody components. Under the assumption that their excess emission is due to a blackbody component we present radii, temperatures and luminosities of the emitting components. We also show that detection of blackbody components only is possible in a fraction of the Swift bursts.
On the Determination of the Gas Temperature From the Velocity of the Muzzle Rarefaction Wave

Abstract : The temperature of the propellant gas as it flows out of the muzzle of a gun is a principal factor in respect to the strength of the air blast which accompanies the discharge of the projectile. The temperature also plays a dominant role in respect to the occurrence of secondary combustion of flash. We discuss the fundamental basis for a method of determining the temperature from measurements of the velocity of the unloading wave or rarefaction created by the discharge of the projectile. The method is, of course, restricted to cases in which the projectile velocity is less than the speed of sound in the gas directly behind it. For charges which are completely burnt and in which the products of combustion at the muzzle are purely gaseous, three sources of error are identified. First, the measurement time may be approximately equal to the relaxation time for changes in chemical composition. This will result in dispersion and since the unloading wave contains components of all frequencies, part of the wave will move with the frozen wave speed and part move with the equilibrium speed. Due to dissipation the faster frozen components will be less detectable at increasing distances from the muzzle. Second, the unloading wave is not one-dimensional and the radial relaxation time is of the same order as the measurement time. Significant geometrical dispersion will result and will be superimposed on the chemical relaxation. Third, the temperature of the gas in the measurement zone may differ significantly from the space-mean value as a consequence of a non-uniform release of chemical energy by the propellant and the deviation may be to higher or to lower values.
New directional assembly for optical code division multiple access systems including a single reflective element

In this paper we present an encoding/decoding device for OCDMA communications. The device uses a single reflecting element to perform both the encoding of outgoing signal and the decoding of incoming signal. A directional optical assembly allows differentiating the origin of the signals to forward the outgoing signals after encoding to the network and the incoming signals after decoding to a receiver.
Understanding the Other Side: The Traits of Partners of Individuals with Neurotic Traits in Committed Premarital Relationships

UNDERSTANDING THE OTHER SIDE: THE TRAITS OF PARTNERS OF INDIVIDUALS WITH NEUROTIC TRAITS IN COMMITTED PREMARITAL RELATIONSHIPS Ryan W. Blick Marriage and Family Therapy Program School of Family Life Master of Science The purpose of this study was to identify the partners’ traits and skills that predict relationship satisfaction in committed, premarital relationships in which one person has neurotic traits, as well as to examine the degree of consensus about neuroticism for both individuals. Data from 198 never-married, young adult, premarital couples who had completed the RELATionship Evaluation (RELATE) questionnaire were used in the analyses. Measures of perceived partner traits and skills included levels of empathic communication, clear sending, flooding, kindness, flexibility, criticism, and contempt and defensiveness. Relationship satisfaction as measured by RELATE was the criterion variable. Results showed little agreement between self and partner perceptions of the specific neurotic traits manifested by neurotic individuals; that is, levels of anxiety, depression, anger, and low self-esteem. A negative relationship between partner-rated neurosis and each person’s relationship satisfaction, however, was present for both genders. The significant positive predictors of the neurotic female actor’s relationship satisfaction were her perceptions of her partner’s: 1) empathic communication, 2) flexibility, and 3) clear sending, as well as 4) the length of the relationship. The only significant predictor of the non-neurotic male partner’s relationship satisfaction was the neurotic female actor’s perception of his empathic communication. The significant predictors of the neurotic male actor’s relationship satisfaction were his perceptions of his partner’s: 1) criticism (a negative relationship), 2) kindness, 3) flooding (a negative relationship), and 4) empathic communication. The significant predictors of the healthy female partner’s relationship satisfaction were the neurotic male actor’s perceptions of her: 1) kindness, 2) flexibility, 3) criticism, 4) flooding, and 5) empathic communication, as well as 6) the length of the relationship. These results suggest that certain partner traits and skills may help to increase the relationship satisfaction for both partners in relationships in which one partner possesses neurotic traits. Implications of these results for therapists working with premarital couples in which one partner has neurotic traits are outlined.
Regional and chronological patterns in lithic raw material behaviour during the late glacial and some implications for the British Later Upper Palaeolithic

This paper considers lithic raw material procurement strategies of hunter-gatherers in the Late Glacial Interstadial in Britain. It compares the Creswellian (13–12,000 radiocarbon years ago) with the Federmesser (12–11,000 radiocarbon years ago) and suggests on present evidence that the movement of prepared blades and cores by people, sometimes over long distance, was more prevalent in the earlier period. In contrast, to the Creswellian, more variable behaviour is observed in the Federmesser which might partly be a consequence of changes in the landscape, although other contributory factors are considered also. Full reference: Barton, R.N. E. 2010. Regional and chronological patterns in lithic raw material behaviour during the late glacial and some implications for the British Later Upper Palaeolithic. Lithics: the Journal of the Lithic Studies Society 31: 33–43. Keywords: Creswellian, Federmesser, raw material procurement, Late Glacial, hunter-gatherers.
Seasonal variations in available N and N-mineralization in relation to fine roots in landslide damaged sites in the sal forest ecosystem of Nepal Himalaya

Seasonal dynamics of available nitrogen and N-mineralization in relation to fine root biomass was studied in five landslide damaged (1 to 58 years old) sites in the moist tropical sal ( Shorea robusta ) forest ecosystem of Nepal Himalaya. Comparisons were made with an undisturbed mature sal forest site located in the same region. Concentrations of soil available-N (NH 4 + and NO 3 - ) increased with the age of site till 40-year old sites and then declined. However, the proportion of NH 4 + in total available N increased distinctly with increase in the age of sites. The NH 4 + : NO 3 - ratio increased considerably from 1.15 in 1-year site to 2.4 in mature sal forest. On the other hand, the net N-mineralization rate increased consistently until 58 years of age but the proportion of nitrification rate relative to ammonification rate distinctly decreased beyond 40 years indicating the dominance of ammonification over nitrification in the older sites. Fine root biomass and N- mineralization rate both increased but available-N decreased during rainy season. On the other hand fine root biomass and N-mineralization rate both decreased and available N increased during summer season. During the summer season, fine root biomass decreased by 57 - 68% indicating a rapid turnover. High turnover of fine root at the younger sites (1 to 15 yrs old) add more organic matter for the developing vegetation. Fine root biomass was positively correlated with the concentration of available-N and N-mineralization rate. It is concluded that fine root development was facilitated by higher amounts of available-N. DOI: http://dx.doi. org/10.3126/njbs.v1i0. 7478 Nepalese Journal of Biosciences 1: 114-124 (2011)
The Effects of Roads on Trade and Migration: Evidence from a Planned Capital City

A large body of literature studies how infrastructure facilitates trade. We ask whether infrastructure also facilitates migration. Using a general equilibrium trade model and rich spatial data, we study the impact of a large, plausibly exogenous shock to highways in Brazil on both goods and labor markets. We find the highway system increased welfare by 2.8 percent, of which 76 percent was due to reduced trade costs and 24 percent to reduced migration costs. An implication of costly migration is spatial heterogeneity in benefits: the range of welfare improvement is 1 to 15 percent, as opposed to uniform gains with perfect mobility. (JEL H54, H76, O18, R23, R42, R53)
Does the increase in house prices influence the creation of business startups? The case of Sweden

Entrepreneurs are at the core of economic development in that they start new businesses or make existing ﬁrms grow. To fulﬁll this important role, entrepreneurs need access to ﬁnancing. Owing to information asymmetry and the relatively high risk associated with business startups, many ﬁnanciers shy away from engaging in relationships with ﬁrms during the early stages of their development. Based on the existing body of knowledge on the ﬁnancing of entrepreneurship, we know that insider ﬁnance is of paramount importance in the early stages of ﬁrms’ development. We expand this knowledge base by analyzing the inﬂuence of house prices on business startups across municipalities in Sweden. In our analysis, we include data from all municipalities in Sweden. Our data on house prices and control variables are collected in period one, and our data on the frequency of startups are collected in period two. We ﬁnd that rising house prices in a municipality lead to a higher frequency of startups. In our spatial Durbin model, we ﬁnd that a 1% increase in house prices leads to around 0.15% increase in startups. Our ﬁndings are in line with the limited international research that has been previously conducted, and therefore, our study might make a small but vital addition to this growing body of knowledge within the area of entrepreneurship and regional development.
DISCUSSION PAPER SERIES EFFICIENCY GAIN FROM OWNERSHIP DEREGULATION : ESTIMATES FOR THE RADIO

Reducing xed cost duplication a common justi cation for concentrated market structure motivated the US government to relax the number of radio stations a rm could operate in any local market. After deregulation the number of rms per market decreased. The implied cost saving depends on the per market xed costs incurred by each rm. Using data from 140 markets we estimate upper and lower bounds to xed costs using (i) an empirical model of gross pro t and (ii) the assumption that the observed post-deregulation market structure is a Nash equilibrium. The estimates suggest that the e¢ ciency savings were signi cant. JEL Numbers L10, L40, L82 This paper is developed from joint work in Section 2 with Catherine OGorman. I would also like to thank Keble College for nancial assistance in obtaining the Arbitron data, James Duncan Jr. for industry advice, and Yuwi Manachotphong for excellent research assistance. I am also grateful for helpful comments from Elena Argentesi, Estelle Cantillon, Stijn Ferrari, Gauthier Lanot, Frank Verboven and seminar/conference participants at the Network of Industrial Economists at Warwick University (December 2005), ECARES, Brussels (December 2005), the CEPR IO Conference in Funchal (May 2006), Keele University (November 2007) and the RNIC Workshop in Mannheim (January 2008). yDepartment of Economics, Oxford University, Manor Road, Oxford, OX1 3UQ.