bluuebunny/crossref_metadata_2025_split huggingface dataset:
Outcomes for the superior cavopulmonary connection in children with hypoplastic left heart syndrome: a 30-year experience
Authors: Hunt Mallory L , Ittenbach Richard F , Kaplinski Michelle , Ravishankar Chitra , Rychik Jack , Steven James M , Fuller Stephanie M , Nicolson Susan C , Spray Thomas L , Gaynor J William , Mascio Christopher E 
Published: March 2020

Abstract

OBJECTIVES
The objective of this study was to estimate hospital mortality and length of stay (LOS) for children with hypoplastic left heart syndrome undergoing superior cavopulmonary connection (SCPC).

METHODS
All hypoplastic left heart syndrome interstage survivors who underwent SCPC between 1 January 1988 and 31 December 2017 were included. The study period was divided into 4 eras based on changes in operative or medical management. Mortality rates were estimated using standard binomial proportions. Adjusted and unadjusted logistic regression models were used to identify risk factors for mortality and LOS.

RESULTS
The most common procedures for the cohort (n = 958) were Hemi-Fontan (57.3%) or Bidrectional Glenn shunt (35.7%). The mortality was 4.1% overall and decreased in all 3 later eras compared to era 1. Factors associated with mortality in a multiple covariate model included longer total support time, earlier gestational age, longer LOS at the Norwood Procedure and need for additional procedures. Overall, the median LOS was 7.0 days with a decrease from eras 1 to 2 and plateaued in eras 3 and 4. Predictors of longer LOS included genetic anomaly, longer Norwood LOS, additional procedures, lower weight at surgery and longer total support time. The type of SCPC was not associated with mortality or LOS.

CONCLUSIONS
In this large cohort of patients with hypoplastic left heart syndrome undergoing SCPC, hospital mortality has decreased significantly. LOS initially declined but plateaued in recent eras. The risk factors for mortality and longer LOS are related to patient and procedural complexity, especially the need for additional procedures at the time of SCPC.
Specialized microbiome of the cave-dwelling sponge Plakina kanaky (Porifera, Homoscleromorpha)
Authors: Ruiz César , Villegas-Plazas Marcela , Thomas Olivier P , Junca Howard , Pérez Thierry 
Published: March 2020

ABSTRACTThe recent description of the polychromatic sponge Plakina kanaky revealed original microsymbionts, with some morphotypes recorded for the first time in Homoscleromorpha and others never before observed in other sponge groups. Illumina 16S amplicon sequencing was used to characterize this microbial community by comparing contents of seven specimens of this Plakinidae with five other sponge species: one Homoscleromopha of the Oscarellidae family and four Demospongiae. A total of 256 458 sequences of the hypervariable V5-V6 region of the 16S rRNA gene were clustered into 2,829 OTUs at 97% similarity, with Proteobacteria, Poribacteria and Chloroflexi being the most abundant phyla. The Plakina kanaky specific community appeared to be mainly composed by five OTUs representing about 10% of the total microbiome. Among these, the filamentous bacterium Candidatus Entotheonella, which was among the dominant morphotypes previously observed in the mesohyl and the larvae of P. kanaky, was detected in all studied specimens. However, other original and dominant morphotypes could not be assigned to a known prokaryotic taxon. This cave dwelling sponge species harbors a distinctive microbiome composition of potential taxonomic and metabolic novelties that may be linked to its ecological success in such extreme environments.
Complex Evolutionary History of the Y Chromosome in Flies of the Drosophila obscura Species Group
Authors: Bracewell Ryan , Bachtrog Doris 
Published: March 2020

AbstractThe Drosophila obscura species group shows dramatic variation in karyotype, including transitions among sex chromosomes. Members of the affinis and pseudoobscura subgroups contain a neo-X chromosome (a fusion of the X with an autosome), and ancestral Y genes have become autosomal in species harboring the neo-X. Detailed analysis of species in the pseudoobscura subgroup revealed that ancestral Y genes became autosomal through a translocation to the small dot chromosome. Here, we show that the Y-dot translocation is restricted to the pseudoobscura subgroup, and translocation of ancestral Y genes in the affinis subgroup likely followed a different route. We find that most ancestral Y genes have translocated to unique autosomal or X-linked locations in different taxa of the affinis subgroup, and we propose a dynamic model of sex chromosome formation and turnover in the obscura species group. Our results suggest that Y genes can find unique paths to escape unfavorable genomic environments that form after sex chromosome–autosome fusions.
A statistical representation and frequency-domain window-rejection algorithm for single-station HVSR measurements
Authors: Cox Brady R , Cheng Tianjian , Vantassel Joseph P , Manuel Lance 
Published: March 2020

SUMMARYThe horizontal-to-vertical spectral ratio (HVSR) of ambient noise measurement is commonly used to estimate a site's resonance frequency (${f_0}$). For sites with a strong impedance contrast, the HVSR peak frequency (${f_{0,\mathrm{ HVSR}}}$) has been shown to be a good estimate of ${f_0}$. However, the random nature of ambient noise (both in time and space), in conjunction with variable environmental conditions and sensor coupling issues, can lead to uncertainty in ${f_{0,\mathrm{ HVSR}}}$ estimates. Hence, it is important to report ${f_{0,\mathrm{ HVSR}}}$ in a statistical manner (e.g. as a mean or median value with standard deviation). In this paper, we first discuss widely accepted procedures to process HVSR data and estimate the variance in ${f_{0,\mathrm{ HVSR}}}$. Then, we propose modifications to improve these procedures in two specific ways. First, we propose using a lognormal distribution to describe ${f_{0,\mathrm{ HVSR}}}$ rather than the more commonly used normal distribution. The use of a lognormal distribution for ${f_{0,\mathrm{ HVSR}}}$ has several advantages, including consistency with earthquake ground motion processing and allowing for a seamless transition between HVSR statistics in terms of both frequency and its reciprocal, period. Second, we introduce a new frequency-domain window-rejection algorithm to decrease variance and enhance data quality. Finally, we use examples of 114 high-variance HVSR measurements and 77 low-variance HVSR measurements collected at two case study sites to demonstrate the effectiveness of the new rejection algorithm and the proposed statistical approach. To encourage their adoption, and promote standardization, the rejection algorithm and lognormal statistics presented in this paper have been incorporated into hvsrpy, an open-source Python package for HVSR processing.
An inverse semi-oriented radial data envelopment analysis measure for dealing with negative data
Authors: Ghiyasi Mojtaba , Zhu Ning 
Published: March 2020

Abstract
The conventional inverse data envelopment analysis (DEA) model is only applicable to positive data, while negative data are commonly present in most real-world applications. This paper proposes a novel inverse DEA model that can handle negative data. The conventional inverse DEA model is a special case of our model as our model is more general in terms of returns-to-scale properties. The proposed model is used to evaluate the efficiency of the Chinese commercial banks after the global financial crisis, where negative outputs existed. We show that our model is feasible in the presence of negative data and generates empirical findings that are consistent with reality.
On critical points of quadratic low-rank matrix optimization problems
Authors: Uschmajew André , Vandereycken Bart 
Published: March 2020

AbstractThe absence of spurious local minima in certain nonconvex low-rank matrix recovery problems has been of recent interest in computer science, machine learning and compressed sensing since it explains the convergence of some low-rank optimization methods to global optima. One such example is low-rank matrix sensing under restricted isometry properties (RIPs). It can be formulated as a minimization problem for a quadratic function on the Riemannian manifold of low-rank matrices, with a positive semidefinite Riemannian Hessian that acts almost like an identity on low-rank matrices. In this work new estimates for singular values of local minima for such problems are given, which lead to improved bounds on RIP constants to ensure absence of nonoptimal local minima and sufficiently negative curvature at all other critical points. A geometric viewpoint is taken, which is inspired by the fact that the Euclidean distance function to a rank-$k$ matrix possesses no critical points on the corresponding embedded submanifold of rank-$k$ matrices except for the single global minimum.
Eremenko’s Conjecture for Functions with Real Zeros: The Role of the Minimum Modulus
Authors: Nicks D A , Rippon P J , Stallard G M 
Published: March 2020

Abstract
We consider the class of real transcendental entire functions $f$ of finite order with only real zeros and show that if the iterated minimum modulus tends to $\infty $, then the escaping set $I(\,f)$ of $f$ has the structure of a spider’s web, in which case Eremenko’s conjecture holds. This minimum modulus condition is much weaker than that used in previous work on Eremenko’s conjecture. For functions in this class, we analyse the possible behaviours of the iterated minimum modulus in relation to the order of the function $f$.
Translation efficiency affects the sequence-independent +1 ribosomal frameshifting by polyamines
Authors: Oguro Akihiro , Shigeta Tomoaki , Machida Kodai , Suzuki Tomoaki , Iwamoto Takeo , Matsufuji Senya , Imataka Hiroaki 
Published: March 2020

AbstractAntizyme (AZ) interacts with ornithine decarboxylase, which catalyzes the first step of polyamine biosynthesis and recruits it to the proteasome for degradation. Synthesizing the functional AZ protein requires transition of the reading frame at the termination codon. This programmed +1 ribosomal frameshifting is induced by polyamines, but the molecular mechanism is still unknown. In this study, we explored the mechanism of polyamine-dependent +1 frameshifting using a human cell-free translation system. Unexpectedly, spermidine induced +1 frameshifting in the mutants replacing the termination codon at the shift site with a sense codon. Truncation experiments showed that +1 frameshifting occurred promiscuously in various positions of the AZ sequence. The probability of this sequence-independent +1 frameshifting increased in proportion to the length of the open reading frame. Furthermore, the +1 frameshifting was induced in some sequences other than the AZ gene in a polyamine-dependent manner. These findings suggest that polyamines have the potential to shift the reading frame in the +1 direction in any sequence. Finally, we showed that the probability of the sequence-independent +1 frameshifting by polyamines is likely inversely correlated with translation efficiency. Based on these results, we propose a model of the molecular mechanism for AZ +1 frameshifting.
Parental Behaviors, Emotions at Bedtime, and Sleep Disturbances in Children with Cancer
Authors: Kim Hyun , Zhou Eric S , Chevalier Lydia , Lun Phyllis , Davidson Ryan D , Pariseau Emily M , Long Kristin A 
Published: March 2020

AbstractBackgroundPoor sleep is common for children during cancer treatment, but there is limited understanding of the nature of children’s sleep throughout the treatment trajectory. The current exploratory study used an explanatory sequential mixed method approach to examine quantitative associations among sleep problems in children with cancer, parental behavior, and children’s sleep hygiene, with follow-up qualitative characterizations of children’s sleep across cancer treatment stages.ProcedureEighty parents of children with cancer (aged 2–10 years; in active treatment, maintenance treatment, or off treatment) completed an online survey querying the child’s sleep quality (Sleep Disturbance Scale for Children—Disorders of Initiating and Maintaining Sleep subscale) and behaviors (Child Sleep Hygiene Scale) and sleep-related parenting behaviors (Parental Sleep Strategies). A subsample (n = 17 parents) participated in qualitative interviews to better characterize the processes of children’s sleep and parents’ sleep-related behaviors.ResultsChildren’s sleep quality, sleep hygiene, or parental sleep strategies were not significantly different by cancer treatment groups. Greater sleep disturbance in children was associated with their parents’ tendency to accommodate the child’s bedtime requests. Qualitatively, cancer treatment-related anxiety in both children and parents influence the onset of these disruptive sleep behaviors.ConclusionParents’ sleep-related behaviors affect children’s sleep during cancer treatment. Parents’ accommodation may start during active treatment to alleviate cancer-related challenges, and these behaviors may continue into maintenance therapy and off treatment to reinforce sleep disturbance. Behavioral interventions targeting unhelpful parental behaviors may improve sleep in children with cancer during and after cancer treatment.
Double-edged risk: unaccompanied minor refugees (UMRs) in Sweden and their search for safety
Authors: Horning Amber , Jordenö Sara V , Savoie Nicole 
Published: March 2020

Abstract
Many unaccompanied minor refugees (UMRs) arrived in Sweden with the mass exodus of refugees who fled to the EU in 2015. UMRs are individuals who are under 18 years of age, outside their country of origin and separated from legal care-givers (Separated Children in Europe Programme 2004). In 2016, Swedish public opinion of asylum seekers began to shift from sympathy to fear (Kärrman 2015; Herz 2018) and Sweden implemented policies restricting UMRs’ rights. It was at this pivotal moment that we interviewed UMRs in two youth asylum-centres in rural Sweden. We contextualized this analysis through our concept of ‘double-edged risk’—that is, being at risk despite being viewed as risky. Portrayals of risky refugees depict them as manipulative, and even predatory (Banks 2012). Many of these minors lacked agency from the inception of their journey to the EU to their waiting for their asylum decision. For instance, all of the UMRs in this study were forced by parents to leave and stated they would not have taken the journey had they known the dangers. Initially, we sought to understand how UMRs garnered agency in light of their ‘double-edged’ risk; however, the most salient theme that emerged was their search for safety. In order to attain safety, many of these UMRs resiliently relinquished agency. These findings demystify ideas of the ‘dangerous’ refugee and are useful for understanding UMRs’ plight for refuge in the EU and to improving policies that thwart UMRs’ development.
Large inguinoscrotal hernia containing ureter: reminder to General Surgeons
Authors: Beh Han N , Ongso Yuni F 
Published: March 2020

Abstract
Inguinal hernia is a common general surgery presentation. Large inguinoscrotal hernias can contain large bowel, omentum, small bowel, Meckel’s diverticulum but rarely ureter and bladder. Ultrasound can further clarify contents of inguinal hernia, and for this patient, it showed a cystic structure in the hernia contents. This was further investigated and found to be the left ureter with moderate to severe hydronephrosis. The patient underwent left inguinal hernia repair without any complication because of the anticipated anatomical anomaly. This case is to raise awareness that a simple inguinoscrotal hernia repair could be complicated by ureteric injury if not investigated thoroughly in the preoperative stage.
Penetrating thoracic injury from a bean bag round complicated by development of post-operative empyema
Authors: Guenther Timothy M , Gustafson Joshua D , Wozniak Curtis J , Zakaluzny Scott A , Utter Garth H 
Published: March 2020

Abstract
Bean bag guns were developed as a nonlethal means for law enforcement personnel to subdue individuals. The large surface area and lower velocities of the bean bag round theoretically result in transfer of most of the energy to the skin/subcutaneous tissue and minimize the likelihood of dermal penetration, thereby ‘stunning’ intended victims without causing injury to deeper structures. However, this technology has been associated with significant intra-abdominal and intrathoracic injuries, skin penetration and death. We present a 59-year-old man who sustained a penetrating thoracic injury from a bean bag gun. Although the bean bag was successfully removed, the patient developed a postoperative empyema requiring operative management. We discuss the unique aspects of thoracic trauma from bean bag ballistics as well as considerations in management of patients with this uncommon mechanism of injury.
On the FRB luminosity function – – II. Event rate density
Authors: Luo Rui , Men Yunpeng , Lee Kejia , Wang Weiyang , Lorimer D R , Zhang Bing 
Published: March 2020

ABSTRACT
The luminosity function of Fast Radio Bursts (FRBs), defined as the event rate per unit cosmic co-moving volume per unit luminosity, may help to reveal the possible origins of FRBs and design the optimal searching strategy. With the Bayesian modelling, we measure the FRB luminosity function using 46 known FRBs. Our Bayesian framework self-consistently models the selection effects, including the survey sensitivity, the telescope beam response, and the electron distributions from Milky Way/ the host galaxy/ local environment of FRBs. Different from the previous companion paper, we pay attention to the FRB event rate density and model the event counts of FRB surveys based on the Poisson statistics. Assuming a Schechter luminosity function form, we infer (at the 95 per cent confidence level) that the characteristic FRB event rate density at the upper cut-off luminosity $L^*=2.9_{-1.7}^{+11.9}\times 10^{44}\, \mathrm{erg}\, \mathrm{s}^{-1}$ is $\phi ^*=339_{-313}^{+1074}\, \mathrm{Gpc}^{-3}\, \mathrm{yr}^{-1}$, the power-law index is $\alpha =-1.79_{-0.35}^{+0.31}$, and the lower cut-off luminosity is $L_0\le 9.1\times 10^{41}\, \mathrm{erg}\, \mathrm{s}^{-1}$. The event rate density of FRBs is found to be $3.5_{-2.4}^{+5.7}\times 10^4\, \mathrm{Gpc}^{-3}\, \mathrm{yr}^{-1}$ above $10^{42}\, \mathrm{erg}\, \mathrm{s}^{-1}$, $5.0_{-2.3}^{+3.2}\times 10^3\, \mathrm{Gpc}^{-3}\, \mathrm{yr}^{-1}$ above $10^{43}\, \mathrm{erg}\, \mathrm{s}^{-1}$ , and $3.7_{-2.0}^{+3.5}\times 10^2\, \mathrm{Gpc}^{-3}\, \mathrm{yr}^{-1}$ above $10^{44}\, \mathrm{erg}\, \mathrm{s}^{-1}$. As a result, we find that, for searches conducted at 1.4 GHz, the optimal diameter of single-dish radio telescopes to detect FRBs is 30–40 m. The possible astrophysical implications of the measured event rate density are also discussed in the current paper.
Newton versus the machine: solving the chaotic three-body problem using deep neural networks
Authors: Breen Philip G , Foley Christopher N , Boekholt Tjarda , Zwart Simon Portegies 
Published: March 2020

ABSTRACT
Since its formulation by Sir Isaac Newton, the problem of solving the equations of motion for three bodies under their own gravitational force has remained practically unsolved. Currently, the solution for a given initialization can only be found by performing laborious iterative calculations that have unpredictable and potentially infinite computational cost, due to the system’s chaotic nature. We show that an ensemble of converged solutions for the planar chaotic three-body problem obtained using an arbitrarily precise numerical integrator can be used to train a deep artificial neural network (ANN) that, over a bounded time interval, provides accurate solutions at a fixed computational cost and up to 100 million times faster than the numerical integrator. In addition, we demonstrate the importance of training an ANN using converged solutions from an arbitrary precise integrator, relative to solutions computed by a conventional fixed precision integrator, which can introduce errors in the training data, due to numerical round-off and time discretization, that are learned by the ANN. Our results provide evidence that, for computationally challenging regions of phase space, a trained ANN can replace existing numerical solvers, enabling fast and scalable simulations of many-body systems to shed light on outstanding phenomena such as the formation of black hole binary systems or the origin of the core collapse in dense star clusters.
Phylogenetic Modeling of Regulatory Element Turnover Based on Epigenomic Data
Authors: Dukler Noah , Huang Yi-Fei , Siepel Adam 
Published: March 2020

AbstractEvolutionary changes in gene expression are often driven by gains and losses of cis-regulatory elements (CREs). The dynamics of CRE evolution can be examined using multispecies epigenomic data, but so far such analyses have generally been descriptive and model-free. Here, we introduce a probabilistic modeling framework for the evolution of CREs that operates directly on raw chromatin immunoprecipitation and sequencing (ChIP-seq) data and fully considers the phylogenetic relationships among species. Our framework includes a phylogenetic hidden Markov model, called epiPhyloHMM, for identifying the locations of multiply aligned CREs, and a combined phylogenetic and generalized linear model, called phyloGLM, for accounting for the influence of a rich set of genomic features in describing their evolutionary dynamics. We apply these methods to previously published ChIP-seq data for the H3K4me3 and H3K27ac histone modifications in liver tissue from nine mammals. We find that enhancers are gained and lost during mammalian evolution at about twice the rate of promoters, and that turnover rates are negatively correlated with DNA sequence conservation, expression level, and tissue breadth, and positively correlated with distance from the transcription start site, consistent with previous findings. In addition, we find that the predicted dosage sensitivity of target genes positively correlates with DNA sequence constraint in CREs but not with turnover rates, perhaps owing to differences in the effect sizes of the relevant mutations. Altogether, our probabilistic modeling framework enables a variety of powerful new analyses.
Molecular architecture of the DNA-binding sites of the P-loop ATPases MipZ and ParA from Caulobacter crescentus
Authors: Corrales-Guerrero Laura , He Binbin , Refes Yacine , Panis Gaël , Bange Gert , Viollier Patrick H , Steinchen Wieland , Thanbichler Martin 
Published: March 2020

AbstractThe spatiotemporal regulation of chromosome segregation and cell division in Caulobacter crescentus is mediated by two different P-loop ATPases, ParA and MipZ. Both of these proteins form dynamic concentration gradients that control the positioning of regulatory targets within the cell. Their proper localization depends on their nucleotide-dependent cycling between a monomeric and a dimeric state and on the ability of the dimeric species to associate with the nucleoid. In this study, we use a combination of genetic screening, biochemical analysis and hydrogen/deuterium exchange mass spectrometry to comprehensively map the residues mediating the interactions of MipZ and ParA with DNA. We show that MipZ has non-specific DNA-binding activity that relies on an array of positively charged and hydrophobic residues lining both sides of the dimer interface. Extending our analysis to ParA, we find that the MipZ and ParA DNA-binding sites differ markedly in composition, although their relative positions on the dimer surface and their mode of DNA binding are conserved. In line with previous experimental work, bioinformatic analysis suggests that the same principles may apply to other members of the P-loop ATPase family. P-loop ATPases thus share common mechanistic features, although their functions have diverged considerably during the course of evolution.