bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic inference of the mating system of free-ranging domestic dogs
Authors: Natoli Eugenia , Bonanni Roberto , Cafazzo Simona , Mills Daniel S , Pontier Dominique , Pilot Małgorzata 
Published: February 2021

Abstract
Domestication has greatly changed the social and reproductive behavior of dogs relative to that of wild members of the genus Canis, which typically exhibit social monogamy and extended parental care. Unlike a typical gray wolf pack that consists of a single breeding pair and their offspring from multiple seasons, a group of free-ranging dogs (FRDs) can include multiple breeding individuals of both sexes. To understand the consequences of this shift in reproductive behavior, we reconstructed the genetic pedigree of an FRD population and assessed the kinship patterns in social groups, based on genome-wide single-nucleotide polymorphism genotypes. Consistent with behavioral observations, the mating system of the study population was characterized by polygynandry. Instead of the discreet family units observed in wolves, FRDs were linked by a network of kinship relationships that spread across packs. However, we also observed reproduction of the same male–female pairs in multiple seasons, retention of adult offspring in natal packs, and dispersal between neighboring packs—patterns in common with wolves. Although monogamy is the predominant mating system in wolves, polygyny and polyandry are occasionally observed in response to increased food availability. Thus, polygynandry of domestic dogs was likely influenced by the shift in ecological niche from an apex predator to a human commensal.
Inflated false discovery rate due to volcano plots: problem and solutions
Authors: Ebrahimpoor Mitra , Goeman Jelle J 
Published: February 2021

AbstractMotivationVolcano plots are used to select the most interesting discoveries when too many discoveries remain after application of Benjamini–Hochberg’s procedure (BH). The volcano plot suggests a double filtering procedure that selects features with both small adjusted $P$-value and large estimated effect size. Despite its popularity, this type of selection overlooks the fact that BH does not guarantee error control over filtered subsets of discoveries. Therefore the selected subset of features may include an inflated number of false discoveries.ResultsIn this paper, we illustrate the substantially inflated type I error rate of volcano plot selection with simulation experiments and RNA-seq data. In particular, we show that the feature with the largest estimated effect is a very likely false positive result. Next, we investigate two alternative approaches for multiple testing with double filtering that do not inflate the false discovery rate. Our procedure is implemented in an interactive web application and is publicly available.
Spawning substrate shift associated with the evolution of a female sexual characteristic in a family of fishes
Authors: Styga Joseph M , Welsh Daniel P 
Published: February 2021

AbstractBecause ‘primary’ sexual characteristics (i.e. those directly associated with reproduction) can be extremely variable, evolve quickly, and can be impacted by both natural and sexual selection, they are often considered excellent model systems in which to study evolution. Here, we explore the evolution of the anal sheath, a trait hypothesized to facilitate the release and proper placement of eggs on the spawning substrate, and its relationship to spawning habitat and maximum body size in a family of fish (Fundulidae). In addition to using phylogenetically informed statistics to determine the role of preferred spawning habitat and maximum body size on the evolution of anal sheath length, we reconstruct the evolutionary history of the anal sheath and preferred spawning habitat. We then test for significant phylogenetic signal and evolutionary rate shifts in the size of the anal sheath and the preferred spawning habitat. Our results indicate that preferred spawning habitat, and not maximum body length, significantly influences anal sheath size, which is associated with a significant phylogenetic signal, and an evolutionary rate similar to that of preferred spawning substrate. We discuss these results in terms of potential evolutionary mechanisms driving anal sheath length.
The Concept, Practice, Application, and Results of Locally Based Monitoring of the Environment
Authors: Danielsen Finn , Enghoff Martin , Poulsen Michael K , Funder Mikkel , Jensen Per M , Burgess Neil D 
Published: February 2021

AbstractLocally based monitoring is typically undertaken in areas in which communities have a close attachment to their natural resource base. We present a summary of work to develop a theoretical and practical understanding of locally based monitoring and we outline tests of this approach in research and practice over the past 20 years. Our tests show that locally based monitoring delivers credible data at local scale independent of external experts and can be used to inform local and national decision making within a short timeframe. We believe that monitoring conducted by and anchored in communities will gain in importance where scientist-led monitoring is sparse or too expensive to sustain and for ecosystem attributes in cases in which remote sensing cannot provide credible data. The spread of smartphone technology and online portals will further enhance the importance and usefulness of this discipline.
Characteristics and Outcome of Acute Heart Failure in Infective Endocarditis: Focus on Cardiogenic Shock
Authors: Pericàs Juan M , Hernández-Meneses Marta , Muñoz Patricia , Martínez-Sellés Manuel , Álvarez-Uria Ana , de Alarcón Arístides , Gutiérrez-Carretero Encarnación , Goenaga Miguel A , Zarauza Manuel J , Falces Carlos , Rodríguez-Esteban M Ángeles , Hidalgo-Tenorio Carmen , Hernández-Cabrera Michele , Miró Jose M ,   Spanish Collaboration on Endocarditis—Grupo de Apoyo al Manejo de la Endocarditis Infecciosa en España (GAMES)
Published: February 2021

Abstract

Background
Studies investigating the impact of cardiogenic shock (CS) on endocarditis are lacking.

Methods
Prospectively collected cohort from 35 Spanish centers (2008-2018). Logistic regression analyses were performed to identify risk factors for developing CS and predictors of mortality.

Results
Among 4856 endocarditis patients, 1652 (34%) had acute heart failure (AHF) and 244 (5%) CS. Compared with patients without AHF and AHF but no CS, patients with CS presented higher rates of surgery (40.5%, 52.5%, and 68%; P &lt; .001) and in-hospital mortality (16.3%, 39.1%, and 52.5%). Compared with patients with septic shock, CS patients presented higher rates of surgery (42.5% vs 68%; P &lt; .001) and lower rates of in-hospital and 1-year mortality (62.3% vs 52.5%, P = .008, and 65.3% vs 57.4%, P = .030). Severe aortic and mitral regurgitation (OR [95% CI], 2.47 [1.82-3.35] and 3.03 [2.26-4.07]; both P &lt; .001), left-ventricle ejection fraction &lt;60% (1.72; 1.22-2.40; P = .002), heart block (2.22; 1.41-3.47; P = .001), tachyarrhythmias (5.07; 3.13-8.19; P &lt; .001), and acute kidney failure (2.29; 1.73-3.03; P &lt; .001) were associated with higher likelihood of developing CS. Prosthetic endocarditis (2.03; 1.06 -3.88; P = .032), Staphylococcus aureus (3.10; 1.16 -8.30; P = .024), tachyarrhythmias (3.09; 1.50-10.13; P = .005), and not performing cardiac surgery (11.40; 4.83-26.90; P &lt; .001) were associated with a higher risk of mortality.

Conclusions
AHF is common among patients with endocarditis. CS is associated with high mortality and should be promptly identified and assessed for cardiac surgery.
Gitelman syndrome and ectopic calcification in the retina and joints
Authors: Ham Yeji , Mack Heather , Colville Deb , Harraka Philip , Savige Judy 
Published: February 2021

Abstract
Gitelman syndrome is a rare inherited renal tubular disorder with features that resemble thiazide use, including a hypokalemic metabolic alkalosis, hypomagnesemia, hypocalciuria and a low or normal blood pressure, hyperreninemia and hyperaldosteronism. Treatment is primarily correction of the potassium and magnesium levels. The diagnosis is confirmed with genetic testing but Gitelman syndrome is often not suspected. However, the association with ectopic calcification in the retina, blood vessels and chondrocalcinosis in the joints is a useful pointer to this diagnosis. Bilateral symmetrical whitish deposits of calcium pyrophosphate are visible superotemporally on ophthalmoscopy and retinal photography but are actually located beneath the retina in the sclerochoroid. Optical coherence tomography is even more sensitive for their detection. These deposits increase in size with time, but the rate of progression slows with long-term correction of the hypomagnesemia. Calcification may be complicated by atrophy of the overlying retina and visual loss. The deposits often correlate with ectopic calcification in the aorta and coronary and cerebral vessels. Chondrocalcinosis occurs in the large joints such as the knees. Ectopic calcification in Gitelman syndrome indicates the need for more aggressive management of Mg levels. Calcification is much less common in Bartter syndrome, which itself is rarer and associated less often with hypomagnesemia.
Engagement of Children who are Deaf or Hard-of-Hearing Attending Mainstream Schools
Authors: Todorov Michelle , Galvin Karyn , Klieve Sharon , Rickards Field 
Published: February 2021

Abstract
This study compared the observed and the self-reported engagement of 16 students who are Deaf or hard-of-hearing (DHH) attending mainstream schools to that of matched controls with typical hearing. Observed engagement was measured through observations in the classroom setting using the Mainstream Version of the Code for Instructional Structure and Student Academic Reponses. Self-reported engagement was measured using the Classroom Participation Questionnaire. The results revealed no significant differences for either observed or self-reported engagement between the DHH and the control groups; however, three individual DHH participants had lower levels of observed engagement compared to their matched controls. As such, including engagement in the evaluation of students who are DHH may be important for some individuals to provide a better understanding of the daily challenges they experience at school. Where needs are identified, the support that students who are DHH receive should include a specific focus on engagement to assist with their successful inclusion.
Is total aortic arch replacement with the frozen elephant trunk procedure reasonable in elderly patients?
Authors: Beckmann Erik , Martens Andreas , Kaufeld Tim , Natanov Ruslan , Krueger Heike , Haverich Axel , Shrestha Malakh 
Published: February 2021

Abstract

OBJECTIVES
Total aortic arch replacement is an invasive procedure with significant risks for complications. These risks are even higher in older, multimorbid patients. The current trends in demographic changes in western countries with an ageing population will aggravate this issue. In this study, we present our experience with total aortic arch replacement using the frozen elephant trunk (FET) technique in septuagenarians. We compared the results of septuagenarians with those of younger patients and analysed if there was an improvement in outcome over time.

METHODS
Between August 2001 and March 2020, 225 patients underwent non-urgent FET procedure at our institution. There were 75 patients aged ≥70 years (mean age 74 ± 4) who were assigned to group A, and 150 patients aged &lt;70 years (mean age of 57 ± 11) who were assigned to group B. In groups A and B, the indications for surgery were chronic dissection (21% vs 53%), aortic aneurysm (78% vs 45%) and penetrating atherosclerotic ulcer (1% vs 2%).

RESULTS
The rate for temporary dialysis was significantly higher in group A than in group B (29% vs 13%, P = 0.003), although the majority recovered kidney function. Rates for re-exploration for bleeding and stroke were comparable in both groups. In-hospital mortality was significantly higher in group A than in group B (24% vs 13%, P = 0.037). Logistic regression analysis showed that age &gt;70 years was an independent statistically significant risk factor for in-hospital mortality (odds ratio = 2.513, 95% confidence interval = 1.197–5.278, P-value = 0.015). Follow-up was complete for 100% of patients and comprised a total of 1073 patient-years with a mean follow-up time of 4.8 ± 4.5 years. The 1- and 5-year survival rates were 68% and 49% in group A, and 85% and 71% in group B, respectively (log rank, P &lt; 0.001). Survival did not significantly improve over time.

Discussion
Total aortic arch replacement using the FET technique has a significantly higher risk for perioperative morbidity and mortality in septuagenarians than in younger patients. Long-term survival is significantly impaired in older patients. We recommend thorough patient selection of those who require total aortic arch replacement, and optimization of perioperative management to improve outcomes.
Patterns of myocardial injury in recovered troponin-positive COVID-19 patients assessed by cardiovascular magnetic resonance
Authors: Kotecha Tushar , Knight Daniel S , Razvi Yousuf , Kumar Kartik , Vimalesvaran Kavitha , Thornton George , Patel Rishi , Chacko Liza , Brown James T , Coyle Clare , Leith Donald , Shetye Abhishek , Ariff Ben , Bell Robert , Captur Gabriella , Coleman Meg , Goldring James , Gopalan Deepa , Heightman Melissa , Hillman Toby , Howard Luke , Jacobs Michael , Jeetley Paramjit S , Kanagaratnam Prapa , Kon Onn Min , Lamb Lucy E , Manisty Charlotte H , Mathurdas Palmira , Mayet Jamil , Negus Rupert , Patel Niket , Pierce Iain , Russell Georgina , Wolff Anthony , Xue Hui , Kellman Peter , Moon James C , Treibel Thomas A , Cole Graham D , Fontana Marianna 
Published: February 2021

Abstract

Background
Troponin elevation is common in hospitalized COVID-19 patients, but underlying aetiologies are ill-defined. We used multi-parametric cardiovascular magnetic resonance (CMR) to assess myocardial injury in recovered COVID-19 patients.

Methods and results
One hundred and forty-eight patients (64 ± 12 years, 70% male) with severe COVID-19 infection [all requiring hospital admission, 48 (32%) requiring ventilatory support] and troponin elevation discharged from six hospitals underwent convalescent CMR (including adenosine stress perfusion if indicated) at median 68 days. Left ventricular (LV) function was normal in 89% (ejection fraction 67% ± 11%). Late gadolinium enhancement and/or ischaemia was found in 54% (80/148). This comprised myocarditis-like scar in 26% (39/148), infarction and/or ischaemia in 22% (32/148) and dual pathology in 6% (9/148). Myocarditis-like injury was limited to three or less myocardial segments in 88% (35/40) of cases with no associated LV dysfunction; of these, 30% had active myocarditis. Myocardial infarction was found in 19% (28/148) and inducible ischaemia in 26% (20/76) of those undergoing stress perfusion (including 7 with both infarction and ischaemia). Of patients with ischaemic injury pattern, 66% (27/41) had no past history of coronary disease. There was no evidence of diffuse fibrosis or oedema in the remote myocardium (T1: COVID-19 patients 1033 ± 41 ms vs. matched controls 1028 ± 35 ms; T2: COVID-19 46 ± 3 ms vs. matched controls 47 ± 3 ms).

Conclusions
During convalescence after severe COVID-19 infection with troponin elevation, myocarditis-like injury can be encountered, with limited extent and minimal functional consequence. In a proportion of patients, there is evidence of possible ongoing localized inflammation. A quarter of patients had ischaemic heart disease, of which two-thirds had no previous history. Whether these observed findings represent pre-existing clinically silent disease or de novo COVID-19-related changes remain undetermined. Diffuse oedema or fibrosis was not detected.
Breast milk urea as a nitrogen source for urease positiveBifidobacterium infantis
Authors: Schimmel Patrick , Kleinjans Lennart , Bongers Roger S , Knol Jan , Belzer Clara 
Published: February 2021

ABSTRACTHuman milk stimulates a health-promoting gut microbiome in infants. However, it is unclear how the microbiota salvages and processes its required nitrogen from breast milk. Human milk nitrogen sources such as urea could contribute to the composition of this early life microbiome. Urea is abundant in human milk, representing a large part of the non-protein nitrogen (NPN). We found that B. longum subsp. infantis (ATCC17930) can use urea as a main source of nitrogen for growth in synthetic medium and enzyme activity was induced by the presence of urea in the medium. We furthermore confirmed the expression of both urease protein subunits and accessory proteins of B. longum subsp. infantis through proteomics. To the same end, metagenome data were mined for urease-related genes. It was found that the breastfed infant's microbiome possessed more urease-related genes than formula fed infants (51.4:22.1; 2.3-fold increase). Bifidobacteria provided a total of 106 of urease subunit alpha alignments, found only in breastfed infants. These experiments show how an important gut commensal that colonizes the infant intestine can metabolize urea. The results presented herein further indicate how dietary nitrogen can determine bacterial metabolism in the neonate gut and shape the overall microbiome.
A new method for estimating the correlation of seismic waveforms based on the NTFT
Authors: Cheng Wei , Liu Lintao , Wang Guocheng 
Published: February 2021

SUMMARY
We propose a new correlation function called the similarity coefficient (SC) based on the normal time–frequency transform (NTFT) to evaluate the similarity between two non-stationary seismic signals as a function of the delay time. The SC is defined in the time–frequency spectrum of the NTFT, and the instantaneous phase and amplitude of each frequency component in a signal are used to calculate the SC. Our simulation experiments demonstrate that the SC method can effectively recognize similar signals compared to the conventional normalized cross-correlation coefficient (NCC) under high background noise conditions. The SC presents good robustness in identifying similar signals and performs well in the case of an extremely low signal-to-noise ratio (SNR), which makes it suitable for detecting weak seismic signals concealed by noise. As a real application case, we use the SC method to detect quasi-Love (QL) surface waves. QL waves are scattered Love waves and are important indicators for lateral anisotropic gradients in the upper mantle. We detect the QL waves at 21 stations deployed across Japan after the 23 December 2004 Mw 8.1 Macquarie earthquake by using the SC method. Obvious QL waves are observed at 19 stations, and we locate the Love-to-Rayleigh scatterers by applying the delay times between the QL and main Love waves. Our results show that the QL wave scatterers were mostly generated in two areas: Mariana subduction and Papua New Guinea. The observations of QL waves suggest the presence of lateral gradients in anisotropy beneath those two areas. The spatial distribution of the 13 scatterers in the Mariana subduction zone agrees well with the Mariana Island Arc, and we infer that the Mariana slab may have melted and coupled with the surrounding mantle at depth.
Effect of a church-based intervention on abstinence communication among African-American caregiver–child dyads: the role of gender of caregiver and child
Authors: Cederbaum Julie A , Kim Soojong , Zhang Jingwen , Jemmott John B , Jemmott Loretta S 
Published: February 2021

Abstract
Parent–child sexual-health communication is critical. Religious involvement is important in many African-American families, but can be a barrier to sexual-health communication. We tested a theory-based, culturally tailored intervention to increase sexual-abstinence communication among church-attending African-American parent–child dyads. In a randomized controlled trial, 613 parent–child dyads were randomly assigned to one of three 3-session interventions: (i) faith-based abstinence-only; (ii) non-faith-based abstinence-only; or (iii) attention-matched health-promotion control. Data were collected pre- and post-intervention, and 3-, 6-, 12- and 18-months post-intervention. Generalized-estimating-equations Poisson-regression models revealed no differences in communication by intervention arm. However, three-way condition � sex-of-child � sex-of-parent interactions on children’s reports of parent–child communication about puberty [IRR=0.065, 95% CI: (0.010, 0.414)], menstruation or wet dreams [IRR=0.103, 95% CI: (0.013, 0.825)] and dating [IRR=0.102, 95% CI: (0.016, 0.668)] indicated that the non-faith-based abstinence intervention’s effect on increasing communication was greater with daughters than with sons, when the parent was the father. This study highlights the importance of considering parent and child gender in the efficacy of parent–child interventions and the need to tailor interventions to increase fathers’ comfort with communication.
The pathogenic m.8993 T &gt; G mutation in mitochondrial ATP6 gene prevents proton release from the subunit c-ring rotor of ATP synthase
Authors: Su Xin , Dautant Alain , Rak Malgorzata , Godard François , Ezkurdia Nahia , Bouhier Marine , Bietenhader Maïlis , Mueller David M , Kucharczyk Roza , di Rago Jean-Paul , Tribouillard-Tanvier Déborah 
Published: February 2021

Abstract
The human ATP synthase is an assembly of 29 subunits of 18 different types, of which only two (a and 8) are encoded in the mitochondrial genome. Subunit a, together with an oligomeric ring of c-subunit (c-ring), forms the proton pathway responsible for the transport of protons through the mitochondrial inner membrane, coupled to rotation of the c-ring and ATP synthesis. Neuromuscular diseases have been associated to a number of mutations in the gene encoding subunit a, ATP6. The most common, m.8993 T &gt; G, leads to replacement of a strictly conserved leucine residue with arginine (aL156R). We previously showed that the equivalent mutation (aL173R) dramatically compromises respiratory growth of Saccharomyces cerevisiae and causes a 90% drop in the rate of mitochondrial ATP synthesis. Here, we isolated revertants from the aL173R strain that show improved respiratory growth. Four first-site reversions at codon 173 (aL173M, aL173S, aL173K and aL173W) and five second-site reversions at another codon (aR169M, aR169S, aA170P, aA170G and aI216S) were identified. Based on the atomic structures of yeast ATP synthase and the biochemical properties of the revertant strains, we propose that the aL173R mutation is responsible for unfavorable electrostatic interactions that prevent the release of protons from the c-ring into a channel from which protons move from the c-ring to the mitochondrial matrix. The results provide further evidence that yeast aL173 (and thus human aL156) optimizes the exit of protons from ATP synthase, but is not essential despite its strict evolutionary conservation.
Spectral Theory of Schrödinger Operators over Circle Diffeomorphisms
Authors: Jitomirskaya Svetlana , Kocić Saša 
Published: February 2021

Abstract
We initiate the study of Schrödinger operators with ergodic potentials defined over circle map dynamics, in particular over circle diffeomorphisms. For analytic circle diffeomorphisms and a set of rotation numbers satisfying Yoccoz’s ${{\mathcal{H}}}$ arithmetic condition, we discuss an extension of Avila’s global theory. We also give an abstract version and a short proof of a sharp Gordon-type theorem on the absence of eigenvalues for general potentials with repetitions. Coupled with the dynamical analysis, we obtain that, for every $C^{1+BV}$ circle diffeomorphism, with a super Liouville rotation number and an invariant measure $\mu $, and for $\mu $-almost all $x\in{{\mathbb{T}}}^1$, the corresponding Schrödinger operator has purely continuous spectrum for every Hölder continuous potential $V$.