bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation and comparison of methods for recapitulation of 3D spatial chromatin structures
Authors: Park Jincheol , Lin Shili 
Published: September 2017

Abstract
How chromosomes fold and how distal genomic elements interact with one another at a genomic scale have been actively pursued in the past decade following the seminal work describing the Chromosome Conformation Capture (3C) assay. Essentially, 3C-based technologies produce two-dimensional (2D) contact maps that capture interactions between genomic fragments. Accordingly, a plethora of analytical methods have been proposed to take a 2D contact map as input to recapitulate the underlying whole genome three-dimensional (3D) structure of the chromatin. However, their performance in terms of several factors, including data resolution and ability to handle contact map features, have not been sufficiently evaluated. This task is taken up in this article, in which we consider several recent and/or well-regarded methods, both optimization-based and model-based, for their aptness of producing 3D structures using contact maps generated based on a population of cells. These methods are evaluated and compared using both simulated and real data. Several criteria have been used. For simulated data sets, the focus is on accurate recapitulation of the entire structure given the existence of the gold standard. For real data sets, comparison with distances measured by Florescence in situ Hybridization and consistency with several genomic features of known biological functions are examined.
A Bayesian framework for the inference of gene regulatory networks from time and pseudo-time series data
Authors: Sanchez-Castillo M , Blanco D , Tienda-Luna I M , Carrion M C , Huang Yufei 
Published: September 2017

Abstract

Motivation
Molecular profiling techniques have evolved to single-cell assays, where dense molecular profiles are screened simultaneously for each cell in a population. High-throughput single-cell experiments from a heterogeneous population of cells can be experimentally and computationally sorted as a sequence of samples pseudo-temporally ordered samples. The analysis of these datasets, comprising a large number of samples, has the potential to uncover the dynamics of the underlying regulatory programmes.

Results
We present a novel approach for modelling and inferring gene regulatory networks from high-throughput time series and pseudo-temporally sorted single-cell data. Our method is based on a first-order autoregressive moving-average model and it infers the gene regulatory network within a variational Bayesian framework. We validate our method with synthetic data and we apply it to single cell qPCR and RNA-Seq data for mouse embryonic cells and hematopoietic cells in zebra fish.

Availability and implementation
The method presented in this article is available at https://github.com/mscastillo/GRNVBEM.
Modeling the Environmental Suitability for Aedes (Stegomyia) aegypti and Aedes (Stegomyia) albopictus (Diptera: Culicidae) in the Contiguous United States
Authors: Johnson Tammi L , Haque Ubydul , Monaghan Andrew J , Eisen Lars , Hahn Micah B , Hayden Mary H , Savage Harry M , McAllister Janet , Mutebi John-Paul , Eisen Rebecca J 
Published: September 2017

Abstract
The mosquitoes Aedes (Stegomyia) aegypti (L.)(Diptera:Culicidae) and Ae. (Stegomyia) albopictus (Skuse) (Diptera:Culicidae) transmit dengue, chikungunya, and Zika viruses and represent a growing public health threat in parts of the United States where they are established. To complement existing mosquito presence records based on discontinuous, non-systematic surveillance efforts, we developed county-scale environmental suitability maps for both species using maximum entropy modeling to fit climatic variables to county presence records from 1960–2016 in the contiguous United States. The predictive models for Ae. aegypti and Ae. albopictus had an overall accuracy of 0.84 and 0.85, respectively. Cumulative growing degree days (GDDs) during the winter months, an indicator of overall warmth, was the most important predictive variable for both species and was positively associated with environmental suitability. The number (percentage) of counties classified as environmentally suitable, based on models with 90 or 99% sensitivity, ranged from 1,443 (46%) to 2,209 (71%) for Ae. aegypti and from 1,726 (55%) to 2,329 (75%) for Ae. albopictus. Increasing model sensitivity results in more counties classified as suitable, at least for summer survival, from which there are no mosquito records. We anticipate that Ae. aegypti and Ae. albopictus will be found more commonly in counties classified as suitable based on the lower 90% sensitivity threshold compared with the higher 99% threshold. Counties predicted suitable with 90% sensitivity should therefore be a top priority for expanded mosquito surveillance efforts while still keeping in mind that Ae. aegypti and Ae. albopictus may be introduced, via accidental transport of eggs or immatures, and potentially proliferate during the warmest part of the year anywhere within the geographic areas delineated by the 99% sensitivity model.
Forming clusters within clusters: how 30 Doradus recollapsed and gave birth again
Authors: Rahner Daniel , Pellegrini Eric W , Glover Simon C O , Klessen Ralf S 
Published: September 2017

Abstract
The 30 Doradus nebula in the Large Magellanic Cloud (LMC) contains the massive starburst cluster NGC 2070 with a massive and probably younger stellar sub clump at its centre: R136. It is not clear how such a massive inner cluster could form several million years after the older stars in NGC 2070, given that stellar feedback is usually thought to expel gas and inhibit further star formation. Using the recently developed 1D feedback scheme warpfield to scan a large range of cloud and cluster properties, we show that an age offset of several million years between the stellar populations is in fact to be expected given the interplay between feedback and gravity in a giant molecular cloud with a density ≳500 cm−3 due to re-accretion of gas on to the older stellar population. Neither capture of field stars nor gas retention inside the cluster have to be invoked in order to explain the observed age offset in NGC 2070 as well as the structure of the interstellar medium around it.
Internal dark matter structure of the most massive galaxy clusters
Authors: Le Brun A M C , Arnaud M , Pratt G W , Teyssier R 
Published: September 2017

Abstract
We investigate the evolution of the dark matter density profiles of the most massive galaxy clusters in the Universe. Using a ‘zoom-in’ procedure on a large suite of cosmological simulations of total comoving volume of 3 (h − 1 Gpc)3, we study the 25 most massive clusters in four redshift slices from z ∼ 1 to the present. The minimum mass is M500 &gt; 5.5 × 1014 M⊙ at z = 1. Each system has more than two million particles within r500. Once scaled to the critical density at each redshift, the dark matter profiles within r500 are strikingly similar from z ∼ 1 to the present day, exhibiting a low dispersion of 0.15 dex, and showing little evolution with redshift in the radial logarithmic slope and scatter. They have the running power-law shape typical of the Navarro–Frenk–White type profiles, and their inner structure, resolved to 3.8 h−1 comoving kpc at z = 1, shows no signs of converging to an asymptotic slope. Our results suggest that this type of profile is already in place at z &gt; 1 in the highest-mass haloes in the Universe, and that it remains exceptionally robust to merging activity.
Public Liturgy
Authors: Glixon Jonathan E. 
Published: September 2017

Abstract
Unlike those in many other cities, Venetian nuns acted primarily as patrons, rather than performers. This chapter examines the employment of musicians, both singers and instrumentalists, for a wide range of religious occasions, from weekly sung Masses involving primarily clergy, to annual public expositions of the Holy Sacrament, to spectacular celebrations of the annual patronal feast of each nunnery, with the participation of some of the most important musicians of the city. These events were witnessed and described by both Venetians and foreign visitors, and were publicized in visitors’ guidebooks by such people as Vincenzo Coronelli. Both civic and ecclesiastical authorities attempted, with varying degrees of success, to limit expenditures for these events and what was sometimes seen as excessive display, more appropriate for the theater than the church. Authorities also worked to restrict contact between the nuns and the men whom they paid to perform.
The Porous Grate
Authors: Glixon Jonathan E. 
Published: September 2017

Abstract
There were several reasons why the nunneries found it necessary to hire male music teachers. While in most cases new nuns learned plainchant from the older members of the choir, in certain situations outside expertise was required. Novices also required training in singing their portions of the rituals of clothing and profession, a role often carried out by secular professionals. The nunneries also housed young women resident students, whose studies, in addition to languages and comportment, sometimes included vocal or instrumental music. Teachers for these various purposes included G. B. Volpe, Giovanni Rovetta, Bartolomeo Barbarino, and Francesco Cavalli. All of these activities involved potentially dangerous interactions between the nuns and unrelated men, so the civil and ecclesiastical authorities attempted to maintain close control, if necessary arresting and trying men, including the organist Giovanni Pichi, who violated procedures.
A Virtuous Recreation? Musical and Theatrical Entertainments for and by the Nuns
Authors: Glixon Jonathan E. 
Published: September 2017

Abstract
Church authorities recognized that the nuns needed some opportunity for appropriate recreation, so allowed them to perform sacred or moral theatrical works for themselves. This chapter also refutes, however, hypotheses put forth by other scholars that printed plays dedicated to nuns can be seen as a repertoire of works they performed. The nuns often violated the rules, performing secular plays and even operas, not only for themselves, but also for an audience of the public in the parlor. Similarly, rules entirely forbade the performance of theatrical or concerts in the parlors of nunneries by outsiders, but such events, including balls, happened often, sometimes apparently with the tacit approval of the authorities. Musicians known to have performed in the parlors include the composer Antonio Sartorio and the prima donna Marietta Barbieri. The Provveditori sopra Monasteri also prosecuted musicians and their patrons for performances of musical serenades outside the walls of convents but within the hearing of the nuns.
Introduction
Authors: Cheng Russell 
Published: September 2017

AbstractThis chapter provides an overview of the book. The book investigates non-standard parametric, mainly continuous univariate estimation problems. The basic difference between standard and non-standard problems is explained in this chapter. The book considers different non-standard problems that can arise. Though some of the problems are advanced, a strong emphasis is placed on providing statistical methods to analyse them that are simple to understand and implement. Maximum likelihood (ML) estimation is the main method used to estimate parameters when fitting parametric models. This chapter outlines the method, emphasizing how it can be implemented numerically. Parametric bootstrapping is used throughout the book to analyse the statistical behaviour of estimators. This chapter gives the rationale of the approach, explaining its simplicity and wide applicability. Also explained is the underlying model building theme of the book.
Non-Standard Problems: Some Examples
Authors: Cheng Russell 
Published: September 2017

AbstractThis chapter provides motivation for the rest of the book by giving a selection of simple examples showing how non-standard behaviour can occur. The well-known maximum likelihood estimator is used throughout this book to estimate an unknown vector of parameters. Its behaviour is standard if the log-likelihood is a concave quadratic function with the maximum in the neighbourhood of the true parameter value, but is otherwise non-standard. Examples of non-standard situations given in this chapter include the true parameter value not being an internal point of the parameter space, but being on a fixed boundary that may not even be finite, or where the mathematical form of the log-likelihood is different with non-estimable indeterminate parameters, or where the true model is an embedded model. Other examples given include where the log-likelihood is unbounded at a finite parameter point, is discontinuous, or is no longer quadratic.
Infinite Likelihood
Authors: Cheng Russell 
Published: September 2017

AbstractThis chapter examines methods that overcome a difficulty with infinite likelihoods. In shifted threshold distributions where the PDF has the form f(y) ∼ k(b,c)(y−a)c−1, if y tends to the threshold parameter a, then the log-likelihood tends to infinity if c &lt; 1 and a also tends to y(1) the smallest observation. The maximum likelihood (ML) method fails in this case, yielding parameter estimates that are not consistent. A method is described overcoming this problem, called the maximum product of spacings method. This yields parameter estimates with the same consistency and asymptotic normality properties as ML estimators when these exist, and which yield, when c &lt; 1 where ML fails, consistent estimates with that for a hyper-efficient. Confidence intervals for a are difficult to obtain theoretically when c &lt; 2. A method is given using percentiles of the stable law distribution and this is numerically compared with bootstrap confidence intervals.
The Pearson and Johnson Systems
Authors: Cheng Russell 
Published: September 2017

AbstractThis chapter re-examines two of the best-known systems of parametric distributions: the Pearson and the Johnson. It is shown that, in the Pearson system, Pearson Types III and V are boundary embedded models of the main Types I, IV, and VI. A comprehensive way of finding the best type to fit is given using appropriate score statistics to guide a systematic search of all model types, including symmetric boundary models. Maximum likelihood estimation is used and details of its numerical implementation are given. Type IV can be a difficult model to fit. A method is discussed for this model that is reasonably robust, subject to certain restrictions on the parameter values. The same examination is made of the Johnson system where the lognormal, SL family is shown to be an embedded subsystem of both the main subsystems SB and SU. Two real data examples are given.
Change-Point Models
Authors: Cheng Russell 
Published: September 2017

AbstractThis chapter investigates change-point (hazard rate) probability models for the random survival time in some population of interest. A parametric probability distribution is assumed with parameters to be estimated from a sample of observed survival times. If a change-point parameter, denoted by τ, is included to represent the time at which there is a discrete change in hazard rate, then the model is non-standard. The profile log-likelihood, with τ as profiling parameter, has a discontinuous jump at every τ equal to a sampled value, becoming unbounded as τ tends to the largest observation. It is known that maximum likelihood estimation can still be used provided the range of τ is restricted. It is shown that the alternative maximum product of spacings method is consistent without restriction on τ. Censored observations which commonly occur in survival-time data can be accounted for using Kaplan-Meier estimation. A real data numerical example is given.
Randomized-Parameter Models
Authors: Cheng Russell 
Published: September 2017

AbstractThis chapter does not involve non-standard behaviour but is included as a contribution to the broader book theme on model building. The basic idea is to obtain greater flexibility in fitting a standard two-parameter base distribution by multiplying one of its parameters by a one-parameter mixing random variable with mean unity. Absorbing the random effect by integration yields what will be called a randomized parameter (also called compound) distribution depending on all three parameters involved. This chapter collects together a large number of examples where there is a gamma mixing distribution. Their tail behaviour is compared. For the cases where the base distribution is the Pearson Type III or V, the randomized three-parameter model is the Pearson Type VI, providing a different view of the relationship between these distributions previously examined via embeddedness. Fits obtained using some of these models in a real-data example are given.
Indeterminacy
Authors: Cheng Russell 
Published: September 2017

AbstractThis chapter discusses models like the exponential regression model y = a[1− exp(− bx)] where if a = 0 then b is an indeterminate, non-identifiable parameter, as it vanishes from the model. The hypothesis test that H0 : a = 0 versus H1 : a ≠ 0 is then non-standard. The well-known Davies test is explained. This uses a portmanteau test statistic T that is a functional of Sn(b), L&lt; b&lt; U, where Sn(b) is a regular test statistic of the null hypothesis a = 0 versus the alternative a ≠ 0 with b fixed. The null distribution of T is not usually easy to obtain. One can instead just test if a = 0 using a GoF test or a lack-of-fit test with an alternative hypothesis not specified. In the exponential regression example, this means simply testing if the observations are solely pure error. This elementary approach is compared with the Davies approach.
Nested Nonlinear Regression Models
Authors: Cheng Russell 
Published: September 2017

AbstractStepwise fitting of nonlinear nested regression models is considered in this chapter. The forward stepwise method of linear model building is used as far as possible. With linear models this is straightforward as there is in principle a free choice of the order that individual terms or factors are selected for inclusion. The only real issue is that sufficient submodels are examined to ensure that those finally selected really are amongst the best. The nonlinear case is not so straightforward, as embeddedness and parameter indeterminacy issues impose restrictions on the order in which steps can be taken to build a valid model, as certain parameters can only be meaningfully included if other specific parameters are definitely present. A systematic way of building valid nonlinear models of increasing complexity is described and illustrated by two examples using real data. A brief review of non-nested model building is also given.
Bootstrapping Linear Models
Authors: Cheng Russell 
Published: September 2017

AbstractBootstrap model selection is proposed for the difficult problem of selecting important factors in non-orthogonal linear models when the number of factors, P, is large. In the method, the full model is first fitted to the original data. Then B parametric bootstrap samples are drawn from the fitted model, and the full model fitted to each. A submodel is obtained from each fitted full model by rejecting those factors found unimportant in the fit. Each distinct selected submodel is then fitted to the original data and its Mallows Cp statistic calculated. A subset of good submodels based on the Cp values is then obtained. A reliability check can be made by fitting this subset to the BS samples also, to see how often each submodel is found to be a good fit. Use of the method is illustrated using a real-data sample.
Finite Mixture Examples; MAPIS Details
Authors: Cheng Russell 
Published: September 2017

AbstractTwo detailed numerical examples are given in this chapter illustrating and comparing mainly the reversible jump Markov chain Monte Carlo (RJMCMC) and the maximum a posteriori/importance sampling (MAPIS) methods. The numerical examples are the well-known galaxy data set with sample size 82, and the Hidalgo stamp issues thickness data with sample size 485. A comparison is made of the estimates obtained by the RJMCMC and MAPIS methods for (i) the posterior k-distribution of the number of components, k, (ii) the predictive finite mixture distribution itself, and (iii) the posterior distributions of the component parameters and weights. The estimates obtained by MAPIS are shown to be more satisfactory and meaningful. Details are given of the practical implementation of MAPIS for five non-normal mixture models, namely: the extreme value, gamma, inverse Gaussian, lognormal, and Weibull. Mathematical details are also given of the acceptance-rejection importance sampling used in MAPIS.
Inbreeding reduces reproductive fitness
Authors: Frankham Richard , Ballou Jonathan D. , Ralls Katherine , Eldridge Mark D. B. , Dudash Michele R. , Fenster Charles B. , Lacy Robert C. , Sunnucks Paul 
Published: September 2017

AbstractThe harmful impacts of inbreeding are generally greater in species that naturally outbreed compared to those in inbreeding species, greater in stressful than benign environments, greater for fitness than peripheral traits, and greater for total fitness compared to its individual components. Inbreeding reduces survival and reproduction (i.e., it causes inbreeding depression), and thereby increases the risk of extinction. Inbreeding depression is due to increased homozygosity for harmful alleles and at loci exhibiting heterozygote advantage. Natural selection may remove (purge) the alleles that cause inbreeding depression, especially following inbreeding or population bottlenecks, but it has limited effects in small populations and usually does not completely eliminate inbreeding depression. Inbreeding depression is nearly universal in sexually reproducing organisms that are diploid or have higher ploidies.
Genetic rescue by augmenting gene flow
Authors: Frankham Richard , Ballou Jonathan D. , Ralls Katherine , Eldridge Mark D. B. , Dudash Michele R. , Fenster Charles B. , Lacy Robert C. , Sunnucks Paul 
Published: September 2017

AbstractInbreeding is reduced and genetic diversity enhanced when a small isolated inbred population is crossed to another unrelated population. Crossing can have beneficial or harmful effects on fitness, but beneficial effects predominate, and the risks of harmful ones (outbreeding depression) can be predicted and avoided. For crosses with a low risk of outbreeding depression, there are large and consistent benefits on fitness that persist across generations in outbreeding species. Benefits are greater in species that naturally outbreed than those that inbreed, and increase with the difference in inbreeding coefficient between crossed and inbred populations in mothers and zygotes. However, benefits are similar across invertebrates, vertebrates and plants. There are also important benefits for evolutionary potential of crossing between populations.
Modified rescue and risk expectations for species with diverse mating systems and modes of inheritance
Authors: Frankham Richard , Ballou Jonathan D. , Ralls Katherine , Eldridge Mark D. B. , Dudash Michele R. , Fenster Charles B. , Lacy Robert C. , Sunnucks Paul 
Published: September 2017

AbstractThe risks of inbreeding and outbreeding depression, and the prospects for genetic rescue are often different in species with alternative mating systems and mode of inheritance (compared to outbreeding diploids), such as self-incompatible, self-fertilizing, mixed mating, non-diploid (haploid, haplodiploid and polyploid) and asexual.