Miracle-dz/UniFAR-FTUs huggingface dataset:
Run of Homozygosity a Procedure to Detecting Inbreeding in Farm Animals

Inbreeding depression is a harmful phenomenon in livestock which is outcome of inbreeding. Inbreeding is consequence mating between two individuals who are more related to each other than average relatedness in population, which results in reducing in fitness of progenies and genetic variability in populations. Development of high-density genome-wide single nucleotide polymorphism (SNP) array facilitated inbreeding measurement as molecular data through calculating autozygosity region in individual genome. Autozygosity refer to chromosomal fragments that are identical-by-descent (IBD) and can be measured using runs of homozygosity (ROH). ROH is therefore defined as contiguous homozygous regions of the genome where two haplotypes inherited from the parents are IBD. The length and frequency of ROH may describe the history and recent bottlenecks in population and also revealed signatures of positive selection in population. Inbreeding coefficient can be derived from ROH (FROH), which is defined as total lengths of all ROH divided by the total autosomal genome length. A lot of studies calculated inbreeding level as FROH in human, cattle, pig, sheep, chicken and other farm animals through SNP array. In most of them, accuracy and preciseness of FROH were confirmed in comparing to FPED, Some of them calculated inbreeding depression by using FROH and some other evaluated the relationship between ROH location with gene and quantitative trait locus (QTL) position on genome. These studies indicated that inbreeding levels in bovine and porcine populations are much higher than those in human populations. Even though most of researches concluded that FROHcan precisely calculated Inbreeding and it can be useful for estimating inbreeding coefficient in absent of pedigree, but some concern were exist in about of panel density, genotyping errors and undetected heterozygosity within continuous ROH which complicated identifying and quantifying ROH. In this review, run of homozygosity is defined and discussed in detail in human and livestock.
PE ] 2 4 M ay 2 01 8 Impact of the infectious period on epidemics

The duration of the infectious period is a crucial determinant of the ability of an infectious disease to spread. We consider an epidemic model that is network-based and non-Markovian, containing classic Kermack-McKendrick, pairwise, message passing and spatial models as special cases. For this model, we prove a monotonic relationship between the variability of the infectious period (with fixed mean) and the probability that the infection will reach any given subset of the population by any given time. For certain families of distributions, this result implies that epidemic severity is decreasing with respect to the variance of the infectious period. The striking importance of this relationship is demonstrated numerically. We then prove, with a fixed basic reproductive ratio (R0), a monotonic relationship between the variability of the posterior transmission probability (which is a function of the infectious period) and the probability that the infection will reach any given subset of the population by any given time. Thus again, even when R0 is fixed, variability of the infectious period tends to dampen the epidemic. Numerical results illustrate this but indicate the relationship is weaker. We then show how our results apply to message passing, pairwise, and Kermack-McKendrick epidemic models, even when they are not exactly consistent with the stochastic dynamics. For Poisson contact processes, and arbitrarily distributed infectious periods, we demonstrate how systems of delay differential equations (DDEs) and ordinary differential equations (ODEs) can provide upper and lower bounds respectively for the probability that any given individual has been infected by any given time.
Endogenous and Exogenous Components of Economic Growth

The aim of the article is to explain the role of the main factors determining the level of economic growth in both the short and long term. The analysis concerns an open economy that is initially balanced inside and outside. It is assumed that capital investments are in balance with investments in innovation and that investments in new capital are in balance with investment replacing old capital. Unlike endogenous factors, which impact economic growth in a way similar – though not identical – to that described in the neoclassical model, exogenous factors to a large extent bear the features of multiplier interventions, which can be described with the help of a deeply modified IS-LM-BP model. In addition to long-term economic inertia and short-term multiplier impacts, there is also an immediate stimulation that needs to be considered in the model. In the article, a fundamental model is presented that, on the demand side, is based on a debt function developed according to the author’s own idea. The model also relies on a consumption function that to an extent is inspired by the rational expectations theory. As far as the supply side is concerned, the model is based on cost, revenue and profit functions inspired by R. Vernon’s theory of product life cycles. These functions are synchronized and combined into a single model, which also incorporates the formally modified IS-LM-BP model. The main conclusion from the analysis is that the contemporary economy is a heterogeneous entity. At the same time, it is market driven in the sense that it is possible not to differentiate among the different kinds of investments in the model. But the contemporary economy is also subject to impacts that are not seen as market driven under the neoclassical view.
Independence for Sets of Full Conditional Probabilities, Sets of Lexicographic Probabilities, and Sets of Desirable Gambles

In this paper we examine concepts of independence for sets of full conditional probabilities; that is, for sets of set-functions where conditional probability is the primitive concept, and where conditioning can be considered on events of probability zero. We also discuss the related issue of independence for (sets of) lexicographic probabilities and for sets of desirable gambles.
J ul 2 01 7 Journeys from Quantum Optics to Quantum Technology

Stephen M. Barnett1, Almut Beige2, Artur Ekert3, Barry M. Garraway4, Christoph H. Keitel5, Viv Kendon6, Manfred Lein7, Gerard J. Milburn8, Héctor M. Moya-Cessa9, Mio Murao10, Jiannis K. Pachos2, G. Massimo Palma11, Emmanuel Paspalakis12, Simon J. D. Phoenix13, Bernard Piraux14, Martin B. Plenio15, Barry C. Sanders16,17,18,19, Jason Twamley20, A. Vidiella-Barranco21, and M. S. Kim22 1 School of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ, UK 2 The School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK 3 Mathematical Institute, University of Oxford & Centre for Quantum Technologies, National University of Singapore. 4 Department of Physics and Astronomy, University of Sussex, Falmer, Brighton, BN1 9QH, UK 5 Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany 6 Department of Physics, Durham University, South Road, Durham DH1 3LE, UK 7 Institute for Theoretical Physics, Leibniz Universität Hannover, 30167 Hannover, Germany 8Centre for Engineered Quantum Systems, School of Mathematics and Physics, The University of Queensland, Australia, 4072. 9 Instituto Nacional de Astrofı́sica, Óptica y Electrónica, Calle Luis Enrique Erro No. 1, Sta. Ma. Tonantzintla, Pue. CP 72840, Mexico 10 Department of Physics, Graduate School of Science, The University of Tokyo, Japan 11 NEST, Istituto Nanoscienze-CNR and Dipartimento di Fisica e Chimica, Università degli Studi di Palermo, via Archirafi 36, I-90123 Palermo, Italy 12 Materials Science Department, School of Natural Sciences, University of Patras, Patras 265 04, Greece 13 Department of Applied Mathematics and Sciences, Khalifa University, P.O. Box: 127788, Abu Dhabi, UAE 14 Laboratoire de Physique Atomique, Moleculaire et Optique (unite PAMO), Universite Catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium 15 Institute of Theoretical Physics and Center for Integrated Quantum Science and Technology (IQST), Albert-Einstein-Allee 11, Universität Ulm, 89069 Ulm, Germany 16 Institute for Quantum Science and Technology, University of Calgary, Alberta T2N 1N4, Canada 17 Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui 230026, China 18 Shanghai Branch, CAS Center for Excellence and Synergetic Innovation Center in Quantum Information and Quantum Physics, University of Science and Technology of China, Shanghai 201315, China 19 Program in Quantum Information Science, Canadian Institute for Advanced Research, Toronto, Ontario M5G 1Z8, Canada 20 Centre for Engineered Quantum Systems, Department of Physics and Astronomy, Macquarie University, Sydney, NSW 2109, Australia 21 QOLS, Blackett Laboratory, Imperial College London, SW7 2AZ, UK and 222 Instituto de Fı́sica “Gleb Wataghin”, Universidade Estadual de Campinas UNICAMP, 13083-859, Campinas, SP, Brazil (Dated: September 15, 2018)
VORTEX SPUN YARN VS. AIR-JET SPUN YARN

Abstract Vortex spinning can be viewed as a refinement of jet spinning, or a natural development in fasciated yarn technology. As in all other fasciated yarns, the structure of vortex yarn consists of a core of parallel fibres held together by wrapper fibres. This has been revealed by examining an untwisted vortex yarn sample under the Scanning Electron Microscope. Subsequently, the physical properties of vortex and air-jet yarns produced from different polyester cotton blends were compared. Results indicated that vortex yarns have tenacity advantages over air jet yarns, particularly at high cotton contents.
A joint stock assessment for the anchovy stock of the northern and central Adriatic Sea: comparison of two catch-at-age models

Anchovy ( Engraulis encrasicolus , L.) is one of the most important commercial species of the northern and central Adriatic Sea, as well as one of the most productive fisheries in the whole Mediterranean. In the Adriatic Sea the stock of anchovy is shared between Italy, Croatia and Slovenia. A joint stock assessment was carried out using catch data from all the fleets for the time interval 1975-2009. Analyses were performed using estimates of natural mortality at age obtained by means of two different methods and two population dynamics methods based on the analysis of catch-at-age data: Laurec-Sheperd virtual population analysis (VPA) and integrated catch-at-age (ICA), both tuned to acoustic estimates of abundance. Gislason’s estimates for natural mortality appeared to be more realistic and were thus preferred for short-lived species. The general trend of biomass and fishing mortality is similar for the two models, highlighting the major collapse of the stock in 1987. Nevertheless, ICA has enough flexibility to combine all the data available without adding too much complexity in comparison with a VPA approach and seems to perform better in terms of the spawning stock biomass/recruitment relationship and diagnostics (i.e. the retrospective pattern). For the stock status, the exploitation rate from ICA is higher than the suggested threshold of 0.4 proposed by Patterson for small pelagic species.
Bernstein type inequalities for self-normalized martingales with applications

ABSTRACT For self-normalized martingales with conditionally symmetric differences, de la Peña [A general class of exponential inequalities for martingales and ratios. Ann Probab. 1999;27(1):537–564] established the Gaussian type exponential inequalities. Bercu and Touati [Exponential inequalities for self-normalized martingales with applications. Ann Appl Probab. 2008;18:1848–1869] extended de la Peña's inequalities to martingales with differences heavy on left. In this paper, we establish Bernstein type exponential inequalities for self-normalized martingales with differences bounded from below. Moreover, applications to t-statistics and autoregressive processes are discussed.
Northwest Africa 1500: Plagioclase‐bearing monomict ureilite or ungrouped achondrite?

Abstract— Northwest Africa (NWA) 1500 is an ultramafic meteorite dominated by coarse (˜100–500 μm) olivine (95–96%), augite (2–3%), and chromite (0.6–1.6%) in an equilibrated texture. Plagioclase (0.7–1.8%) occurs as poikilitic grains (up to ˜3 mm) in vein‐like areas that have concentrations of augite and minor orthopyroxene. Other phases are Cl‐apatite, metal, sulfide, and graphite. Olivine ranges from Fo 65–73, with a strong peak at Fo 68–69. Most grains are reversezoned, and also have ˜10–30 μm reduction rims.
Video Game Play and Consciousness Development: A Replication and Extension

Cognitive skill improvement associated with video game play has been well documented showing a range of improved abilities from spatial skills to problem solving and general intelligence. The implications for consciousness and it’s development have not been as widely examined. Recent research into the emergence of consciousness in sleep as related to video game play has suggested one consciousness development outcome, lucid dreaming. Other related consciousness experiences have been examined with less clear results. In the present study previous results are replicated and extended with an examination of flow. Specificially high-end gamers, as defined by a several variables, evidenced more lucid dreaming, consciousness during sleep, as well as other sleep and waking consciousness development outcomes than low-end gamers. Flow loaded positively with these consciousness experiences on a factor analysis for high-end gamers but negatively for low-end gamers. The implications for the impact of gaming on various consciousness growth indicates is discussed.
Are aerobic fitness and repeated sprint ability linked to fatigue in professional soccer match-play? A pilot study

Are Aerobic Fitness and Repeated Sprint Ability Linked to Fatigue in Professional Soccer Match-Play? A Pilot Study In professional soccer, a strong relationship has been observed between measures of physical fitness derived from tests of repeated sprint ability, intermittent endurance and aerobic capacity and running performance in competition determined from time motion analyses data. Unfortunately, these studies have generally only examined associations with ‘overall’ time motion measures of running performance such as the total distance run or that covered in sprinting. The potential relationship between fitness scores and declines in competitive physical performance in professional soccer players has up to now not received any attention despite the comprehensive body of research from time motion analyses that has indirectly demonstrated the existence of fatigue during matchplay. To our knowledge, only two studies, both conducted in elite youth soccer players, have addressed this gap in the literature. In the former for example, despite a significant association between intermittent-endurance fitness (Yo-Yo IR1 test) and overall distance covered in high-intensity activity, no relationship was observed between fitness measures and first- vs. second-half decrements in running distance.
Clinical Presentation, Treatment Outcome and Predictors of Severity in Autoimmune Hepatitis: A Retrospective, Multicenter Experience

AIM: Autoimmune Hepatitis (AIH) is a chronic hepatitis of unknown etiology. It affects adults and children and can progress to cirrhosis. We aim to investigate the mode of presentation, predictors of severity and treatment outcome of AIH in Saudi patients. METHODS: This is a multicenter retrospective study that involved patients diagnosed with AIH from 3 tertiary hospitals. Clinical, biochemical, radiological and histopathological data were collected and treatment outcomes were reported. RESULTS: A total of 212 patients were included. Female: male ratio was 3:2 and the mean age was 36.2 ± 16.8 years while 50 patients (23.6%) were above age of 50. Abnormal liver function tests (LFTs) were found in (45%). Presentation was chronic in 37.7%, acute in 30.7%, with evidence of liver cirrhosis in 28.8% and with a fulminant disease in 2.8%. Antinuclear antibody (ANA) and Anti-smooth muscle antibody (ASMA) were negative in 65 (30.6%) and 74 (35%) patients respectively. Pre-treatment liver biopsies in 166 patients showed advanced fibrosis (stage 3 and 4) in 63.3%. On multivariate analysis, platelets, alanine transaminase (ALT) level and immunoglobulin G (IgG) level were predictors of fibrosis. Complete response was achieved in 74.5% while 9% had partial response and 16.5% had no response to treatment. CONCLUSION: The majority of AIH patients had advanced fibrosis at the time of diagnosis and liver cirrhosis was found in nearly one-third of cases. IgG, ALT, and platelet were predictors of advanced fibrosis. Complete response to treatment was achieved in two-third of patients. Relying on autoimmune markers for diagnosis can be misleading.
Physical growth in children with transfusion-dependent thalassemia

correspondence: Harish K Pemde Department of Pediatrics, Lady Hardinge Medical college, Kalawati saran children’s Hospital, Bangla sahib Marg, new Delhi 110001, india Tel +91 11 23363432 Fax +91 11 23365792 email harishpemde@gmail.com Objective: To describe physical growth and related factors in transfusion-dependent thalassemia patients. Methods: This is a cross-sectional analysis of the records of the patients registered at and being followed up by the Thalassemia Day Care Center (TDCC) at Kalawati Saran Children’s Hospital, New Delhi, India. Clinical and laboratory parameters were recorded on a spreadsheet for analysis. Clinical parameters included weight, height, sexual maturity ratings, and general and systemic physical examination. Laboratory parameters included pretransfusion hemoglobin (Hb), periodic serum ferritin, and tests for viral markers of human immunodeficiency virus (HIV) and hepatitis B and C. Z-scores for weight, height, and body mass index (BMI) were calculated using World Health Organization reference data. Statistical analysis was carried out using Microsoft Excel and Stata software. Results: Out of 214 patients registered at the TDCC since 2001, 154 were included in this study. The mean age of patients was 9.19 years (range 0.5–20 years). Pretransfusion Hb was well maintained (mean 9.21 g/dL; 95% confidence interval [CI]: 9.06–9.36), but the mean serum ferritin levels were approximately three times (3112 ng/mL) the desired value despite the patients being on deferiprone (72%) or deferasirox (25%). One-third (33.11%) of the patients had short stature, 13% were thin, and 10.82% were very thin (BMI z-score ,-3). No patient was overweight or obese. Linear regression coefficient showed that for every 1-year increase in age, the mean ferritin value increased by 186.21 pg/mL (95% CI: 143.31–228.27). Height z-scores had significant correlation with mean ferritin levels, whereas correlation with mean pretransfusion Hb was not significant statistically. Mean ferritin levels were significantly higher in patients with short stature than in the patients with normal height. Regression analysis showed that an increase of 3571 units of serum ferritin was associated with a decrease of one point in height z-scores. One-fifth (19.40%) of adolescent patients had delayed puberty. Conclusion: Approximately one-third (33.11%) of patients with transfusion-dependent thalassemia major were of short stature. In this group of patients with pretransfusion Hb levels maintained at desired levels, physical growth was correlated with status of iron overload.
Leukemia Inhibitory Factor ( LIF ) and is aberrant 1 in Lif-/-mouse uterus 1 2

15 This study addresses the regulation of the Interleukin 1 (IL1) system in the murine uterine 16 luminal epithelium (LE) and stroma by leukemia inhibitory factor (LIF). Using RT-PCR we 17 compared expression of Il1a, Il1b, Il1rn, Il1r1 and Il1r2 during the preand peri-implantation 18 periods of pregnancy in wild type (wt) and LIF null LE and stroma. In wt LE, Il1a transcripts 19 were down-regulated on day (D) 4am with renewed expression by D4pm. In Lif -/LE there was 20 a gradual decrease in expression from D2 which became undetectable by D6. Il1b and Il1r1 21 expression were similar in wt and null mice, but Il1rn expression was almost completely lost 22 during the peri-implantation period in Lif -/LE. In the stroma Il1a was sharply down-regulated 23 on D4 am reappearing on D4 pm, but in the null mice was only expressed on D3 and D5. 24 Stromal Il1r1 and Il1r2 were also misregulated. Il1rn showed constitutive expression in null 25 stroma in contrast to the loss of expression on D4am in the wt mouse. In Lif deficient mice, 26 immunostaining indicated a reduction of endometrial IL1A at the time of implantation and of 27 Il1B in stroma. LE-stromal co-culture revealed that LIF stimulated apical secretion of both IL1A 28 and PTGES2 by LE cells without affecting basal secretion of IL1A and with only a small effect 29 on basal PTGES2 secretion. We conclude that Il1a and Il1rn in LE and Il1a, Il1rn and Il1r1 in 30 stroma are regulated by LIF which stimulates apical secretion of IL1A by LE. 3
Demersal fish assemblages of the Gulf of Salamanca, Colombia (southern Caribbean Sea)

The structure of the demersal fish assemblages of the Gulf of Salamanca, Colombian Caribbean Sea, was studied based on 4 trawl surveys carried out in December 1995, April and August 1996, and February 1997. Multivariate analysis revealed the presence of 2 distinct assemblages, one belonging to the continental shelf (150 m depth) and the other belonging to the upper slope (>50 m depth). The continental shelf assen~blage showed significantly more biomass per tow but not more individuals or species It is typified by specles of interest for the artisanal fishery, like Lutjanus analis and Calamuspenna. Lutjanus synagris, however, also of interest for the fishery, typlfies the upper slope assemblage. No temporal change was detected in the assemblage structure, at least for the samphng dates in this study, but many species in the assemblages were scarce and rare, Indicating high spatial and temporal patchiness. The assemblages found do not fully adjust to existing zonation schemes or assemblages defined in neighboring areas, probably due to the effect of the spatial scale of the studies and the width of the shelf in the Gulf of Salamanca.
Subcontracting Filial Piety

Based on in-depth interviews with middle-class Taiwanese and Hong Kong immigrant families in California, the author examines how the cultural meaning and social practice of filial care for aging parents have been transformed in the U.S. context. The author analyzes the commodification of elder care from three dimensions—where care takes places, who gives care, and who pays for care—and examines its impacts on Chinese family relations. Although three-generational cohabitation may have declined on foreign soil, the family remains the nexus of care networks and economic ties among Chinese immigrants. Through recruiting home care workers as fictive kin, immigrant adult children are able to maintain the cultural ideal of filial care. The receipt of public care among immigrant elders does not necessarily indicate the diminishment of family bonds, but it reinforces kin connections as channels for circulating economic resources.