bluuebunny/crossref_metadata_2025_split huggingface dataset:
Do Meristic Characters Used in Phylogenetic Analysis Evolve in an Ordered Manner?
Authors: Brocklehurst Neil , Haridy Yara 
Published: October 2020

Abstract
The use of ordered characters in phylogenetic analysis has been inconsistent throughout the history of phylogenetic inference. It has become more widespread in recent years, and some have advocated that all characters representing continuous or meristic traits should be ordered as a matter of course. Here, using the example of dental evolution, we examine two factors that may impact on whether meristic characters actually evolve in an ordered manner: the regulatory hierarchy governing the development of teeth that allows large sections of the entire tooth row to be suppressed in a single transition and regionalization of the tooth row where different modules have a degree of independence in their evolution. These are studied using both empirical and simulated data. Models of evolution of such characters are examined over molecular phylogenies to see if ordered or unordered models fit best. Simulations of tooth-row evolution are designed to incorporate changes in region size and multiple levels of developmental control to suppress individual regions or the entire row. The empirical analyses show that in a clade with largely homodont dentition the characters evolve in an ordered manner, but if dentition is heterodont with distinct regionalization their evolution better fits an unordered model. In the simulations, even if teeth are added and removed from the tooth row in an ordered manner, dividing the row into independently evolving modules can lead to characters covering multiple modules better fitting an unordered model of evolution. Adding the ability to suppress regions or the entire tooth row has a variable effect depending on the rates of suppression relative to the rates of addition and subtraction of individual teeth. We therefore advise not following a single policy when deciding whether to order meristic traits but to base the decision on a priori knowledge of the focal clade’s evolution and developmental biology. [Discrete characters; ordered characters; phylogeny; teeth.]
A novel epidermal gland type in lizards (α-gland): structural organization, histochemistry, protein profile and phylogenetic origins
Authors: Carvalho André L G , Jeckel Adriana M , Nisa Carolina , Luna María Celeste , Piantoni Carla 
Published: October 2020

AbstractChemical signalling is an essential component of the communication system of lizards, and epidermal glands are responsible for producing semiochemicals that regulate many behavioural interactions. Two types of epidermal glands have been previously described for lizards: follicular and generation glands. Generation glands are characterized by the aggregation of novel glandular cell types in the epithelium and the lack of a lumen or external pore. Despite the fact that several subtypes of generation glands have been recognized over the years, the morphology, taxonomic distribution, function and evolutionary origins of generation glands remain nearly unexplored in Neotropical clades. Here, we describe a novel escutcheon-type generation gland (‘α-gland’) for lizards of the South American family Tropiduridae, characterize its structural and ultrastructural organization, and study the homology of the constituent parts in a phylogenetic framework. The α-glands emerged in the ancestor of Eurolophosaurus, Plica, Strobilurus, Tropidurus and Uracentron, and are found in at least 39 species with diverse ecological habits. We preliminarily analysed the protein profile of α-glands and discovered differential expression of protein components between sexes. Our investigations change the general view about epidermal gland homology, leading us to argue that generation and follicular glands are possibly more closely related functionally and evolutionarily than previously thought.
Hyalorbilia oviparasitica Clade Detected in Field Soils Cropped to Sugar Beets and Enriched in the Presence of Heterodera schachtii and a Host Crop
Authors: Witte Hannes , Yang Jiue-in , Logan Geoffrey D. , Colindres Nicole B. , Peacock Beth B. , Smith Becker Jennifer , Ruegger Paul M. , Becker J. Ole , Borneman James 
Published: October 2020

This study endeavored to test two hypotheses: (i) Hyalorbilia oviparasitica and related species (H. oviparasitica clade) will be detected in sugar beet fields in California’s Imperial Valley and (ii) the population densities of these fungi will increase in the presence of their nematode host (Heterodera schachtii) and a host plant of this nematode. The H. oviparasitica clade includes potent hyperparasites of sedentary stages of plant-parasitic nematodes, which have the ability to substantially suppress the population densities of several endoparasitic nematode species. In this study, 21 of 25 Imperial Valley soils cropped to sugar beets harbored members of the H. oviparasitica clade. The population densities of these fungi increased, on average, approximately 10,000-fold in the presence of H. schachtii and its host Swiss Chard over one nematode generation. An rRNA ITS sequence analysis showed that members of the H. oviparasitica clade were the dominant group of fungi associated with H. schachtii females derived from these soils. These results provide evidence supporting the hypotheses. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Replacing defective thymus function
Authors: Kreins Alexandra Y. , Graham Davies E. 
Published: October 2020

Purpose of review
Transplantation of cultured postnatal allogeneic thymus has been successful for treating athymia, mostly associated with complete DiGeorge syndrome, for more than 20 years. Advances in molecular genetics provide opportunities for widening the range of athymic conditions that can be treated while advances in cell culture and organ/tissue regeneration may offer the prospect of alternative preparations of thymic tissue. There are potential broader applications of this treatment outside congenital athymia.

Recent findings
At the same time as further characterization of the cultured thymus product in terms of thymic epithelial cells and lymphoid composition, preclinical studies have looked at de-novo generation of thymic epithelial cells from stem cells and explored scaffolds for delivering these as three-dimensional structures. In the era of newborn screening for T-cell lymphopaenia, a broadening range of defects leading to athymia is being recognized and new assays should allow differentiation of these from haematopoietic cell defects, pending their genetic/molecular characterization. Evidence suggests that the tolerogenic effect of transplanted thymus could be exploited to improve outcomes after solid organ transplantation.

Summary
Thymus transplantation, the accepted standard treatment for complete DiGeorge syndrome is also appropriate for other genetic defects leading to athymia. Improved strategies for generating thymus may lead to better outcomes and broader application of this treatment.
Association of age at menarche with hypertension in rural Chinese women
Authors: Liu Dechen , Qin Pei , Liu Yu , Sun Xizhuo , Li Honghui , Wu Xiaoyan , Zhang Yanyan , Han Minghui , Qie Ranran , Huang Shengbing , Li Yang , Wu Yuying , Yang Xingjin , Feng Yifei , Zhao Yang , Hu Fulan , Zhang Ming , Lu Jie , Hu Dongsheng , Sun Liang 
Published: October 2020

Objective:
The study aimed to explore the association of age at menarche with hypertension and whether adiposity and insulin resistance mediated the association in rural Chinese women.

Methods:
We conducted a cross-sectional study enrolling 7518 women (median age 56 years) from a rural Chinese area from 2013 to 2014. Adiposity was measured by BMI and waist circumference, and insulin resistance was measured by the homeostasis model assessment of insulin resistance (HOMA-IR) index. Odds ratios (ORs) and 95% confidence limits (Cls) for the association of age at menarche with hypertension were estimated by using multivariate logistic regression models. The contribution of adiposity and insulin resistance to the association was estimated by mediation analysis.

Results:
Among 7518 women, 3187 (42.39%) had hypertension. Age at menarche was inversely associated with hypertension (per additional year of menarche, OR = 0.965, 95% Cl: 0.935–0.995). BMI or waist circumference and HOMA-IR completely mediated the association of age at menarche with hypertension (for BMI and HOMA-IR: total indirect effect: OR = 0.970, 95% Cl: 0.962–0.978 and direct effect: OR = 0.994, 95% Cl: 0.963–1.026; for waist circumference and HOMA-IR: total indirect effect: OR = 0.981, 95% Cl: 0.973–0.988 and direct effect: OR = 0.983, 95% Cl: 0.952–1.014).

Conclusion:
Early age at menarche was positively associated with hypertension. Adiposity and insulin resistance seemed to be two vital mediators of the association between age at menarche and hypertension in rural Chinese women.
Donor-specific antibodies in heart transplantation: can we afford the price or is it too steep to pay?
Authors: Nikolova Andriana P. , Kobashigawa Jon A. 
Published: October 2020

Purpose of review
One-third of patients awaiting heart transplant are sensitized and 25–35% of heart allograft recipients develop de novo DSAs. Solid phase assays for DSA measurement have facilitated wider use of antibody monitoring and as such, our experience with DSAs is continuously evolving.

Recent findings
DSAs continue to exhibit poor correlation with biopsy-proven rejection. Novel molecular technologies, such as cell-free DNA and the molecular microscope (MMDx, which detects rejection-associated intragraft mRNA transcripts), are emerging as more sensitive methods to capture subclinical graft injury. High-resolution typing techniques are providing insight into the differential immunogenicity of HLA classes through epitope and eplet analysis. As sensitization of the transplant population is continuing to rise, our repertoire of desensitization strategies is also expanding. However, there is an acute need of predictive algorithms to help forecast the responders and the durability of desensitization. Novel immunomodulatory therapies have allowed safely transplanting across a positive crossmatch with good short-term survival but reported greater degree of rejection and lower long-term graft survival.

Summary
Our experience of outcomes as pertaining to DSAs still originates primarily from single-center studies. Our field is confronted with the challenge to establish common practice algorithms for the monitoring and treatment of DSAs.
Prospects for high gain inertial fusion energy: an introduction to the first special edition
Authors: Norreys P. A. , Ridgers C. , Lancaster K. , Koepke M. , Tynan G. 
Published: October 2020

A European consortium of 15 laboratories across nine nations have worked together under the EUROFusion Enabling Research grants for the past decade with three principle objectives. These are: (a) investigating obstacles to ignition on megaJoule-class laser facilities; (b) investigating novel alternative approaches to ignition, including basic studies for fast ignition (both electron and ion-driven), auxiliary heating, shock ignition etc.; and (c) developing technologies that will be required in the future for a fusion reactor. The Hooke discussion meeting in March 2020 provided an opportunity to reflect on the progress made in inertial confinement fusion research world-wide to date. This first edition of two special issues seeks to identify paths forward to achieve high fusion energy gain.
This article is part of a discussion meeting issue ‘Prospects for high gain inertial fusion energy (part 1)’.
Progress and opportunities for inertial fusion energy in Europe
Authors: Tikhonchuk V. T. 
Published: October 2020

In this paper, I consider the motivations, recent results and perspectives for the inertial confinement fusion (ICF) studies in Europe. The European approach is based on the direct drive scheme with a preference for the central ignition boosted by a strong shock. Compared to other schemes, shock ignition offers a higher gain needed for the design of a future commercial reactor and relatively simple and technological targets, but implies a more complicated physics of laser–target interaction, energy transport and ignition. European scientists are studying physics issues of shock ignition schemes related to the target design, laser plasma interaction and implosion by the code developments and conducting experiments in collaboration with US and Japanese physicists, providing access to their installations Omega and Gekko XII. The ICF research in Europe can be further developed only if European scientists acquire their own academic laser research facility specifically dedicated to controlled fusion energy and going beyond ignition to the physical, technical, technological and operational problems related to the future fusion power plant. Recent results show significant progress in our understanding and simulation capabilities of the laser plasma interaction and implosion physics and in our understanding of material behaviour under strong mechanical, thermal and radiation loads. In addition, growing awareness of environmental issues has attracted more public attention to this problem and commissioning at ELI Beamlines the first high-energy laser facility with a high repetition rate opens the opportunity for qualitatively innovative experiments. These achievements are building elements for a new international project for inertial fusion energy in Europe.
This article is part of a discussion meeting issue ‘Prospects for high gain inertial fusion energy (part 1)’.
A simplified economic model for inertial fusion
Authors: Hawker Nicholas 
Published: October 2020

A simple model for the levelized cost of electricity (LCOE) of an inertial fusion power plant is developed. The model has 14 parameters. These have been designed to be technology agnostic, such that the model may be applied broadly to all variants of inertial fusion. It is also designed to allow easy use of proxies from existing technology. The variables related most intimately to the physics challenges of inertial fusion, such as gain and target cost, are treated as parameters such that requirements can be found without bringing complex physics into the model. A Monte Carlo approach is taken to explore the parameter space. The most important conclusion is that a combination of high gain (greater than 500) and high fusion energy yield per shot (greater than 5 GJ) together appear to unlock more cost competitive designs than those in the existing literature. Designs with LCOE as low as $25/MWh are found with optimistic but not obviously unrealistic inputs.This article is part of a discussion meeting issue ‘Prospects for high gain inertial fusion energy (part 1)'.
Vaginal dinoprostone versus placebo for pain relief during intrauterine device insertion: a systematic review and meta-analysis of randomized controlled trials
Authors: Abu-Zaid Ahmed , Alshahrani Majed S. , Albezrah Nisreen A. , Miski Najlaa T. , Aboudi Saud A. , Abuzaid Mohammed , Alomar Osama , Salem Hany , Al-Badawi Ismail A. , Baradwan Saeed 
Published: October 2020

AbstractObjectiveTo investigate the safety and efficacy of vaginal dinoprostone versus placebo in pain relief during intrauterine device (IUD) insertion.DesignSystematic review and meta-analysis of randomized placebo-controlled trials.SettingNot applicable.Patient(s)Women undergoing IUD insertion and receiving vaginal dinoprostone or placebo.Intervention(s)PubMed, Scopus, Web of Science, and Cochrane Library were screened from inception to 01-October-2020, using the following search strategy: (dinoprostone OR cervidil OR prepidil) AND (intrauterine device OR iud).Main outcome measure(s)IUD insertion related pain, patient satisfaction, provider ease of IUD insertion, and side effects.Result(s)Five studies met the study inclusion criteria, comprising 862 patients; equally 431 patients received vaginal dinoprostone and placebo. All studies had an overall low risk of bias. When compared to placebo, dinoprostone significantly correlated with decreased pain at tenaculum placement (SMD=−0.79, 95% CI [−1.43, −0.16], p=0.01), decreased pain at uterine sounding (SMD=−0.88, 95% CI [−1.54, −0.22], p=0.009), decreased pain at IUD insertion (SMD=−1.18, 95% CI [−1.74, −0.61], p<0.001), decreased need for additional analgesia (RR=0.34, 95% CI [0.22, 0.53], p<0.001), increased patient satisfaction (SMD=1.41, 95% CI [0.62, 2.20], p<0.001), and increased provider ease of IUD insertion (SMD=−1.17, 95% CI [−1.62, −0.73], p<0.001). Fever was statistically significantly higher in dinoprostone versus placebo group (RR=3.73, 95% CI [1.47, 9.44], p=0.006). All other side effects—including nausea, vomiting, shivering, diarrhea, abdominal cramps, vasovagal attack, uterine perforation, and postprocedural bleeding—did not substantially differ between both groups.ConclusionsThis first ever meta-analysis advocates that dinoprostone is safe, effective, and yields favorable analgesic outcomes during IUD insertion.
Chromosome-scale assembly of the genome ofSalix dunniireveals a male-heterogametic sex determination system on chromosome 7
Authors: He Li , Jia Kai-Hua , Zhang Ren-Gang , Wang Yuan , Shi Tian-Le , Li Zhi-Chao , Zeng Si-Wen , Cai Xin-Jie , Wagner Natascha Dorothea , Hörandl Elvira , Muyle Aline , Yang Ke , Charlesworth Deborah , Mao Jian-Feng 
Published: October 2020

AbstractSex determination systems in plants can involve either female or male heterogamety (ZW or XY, respectively). Here we used Illumina short reads, Oxford Nanopore Technologies (ONT) long reads, and Hi-C reads to assemble the first chromosome-scale genome of a female willow tree (Salix dunnii), and to predict genes using transcriptome sequences and available databases. The final genome sequence of 328 Mb in total was assembled in 29 contigs, and includes 31,501 genes. We inferred a male heterogametic sex determining factor on chromosome 7, suggesting that, unlike the female heterogamety of most species in the genusSalix, male heterogamety evolved in the subgenusSalix. TheS. dunniiX-linked region occupies about 3.21 Mb of chromosome 7, and is probably in a pericentromeric region. Our data suggest that this region is enriched for transposable element insertions, and about one third of its 124 protein-coding genes were gained via duplications from other genome regions. We detect purifying selection on the genes that were ancestrally present in the region, though some have been lost. Transcriptome data from female and male individuals show more male- than female-biased genes in catkin and leaf tissues, and indicate enrichment for male-biased genes in the pseudo-autosomal regions. Our study provides valuable genomic resources for studying sex chromosome evolution in Salicaceae family.
The effect of salt on the dynamics of CoV-2 RBD at ACE2
Authors: Peter E. K. , Schug A. 
Published: October 2020

ABSTRACTIn this article, we investigate the effect of electrolytes on the stability of the complex between the coronavirus type 2 spike protein receptor domain (CoV-2 RBD) and ACE2, which plays an important role in the activation cascade at the viral entry of CoV-2 into human cells. At the cellular surface, electrolytes play an important role, especially in the interaction of proteins near the membrane surface. Additionally, the binding interface of the CoV-2 RBD - ACE2 complex is highly hydrophilic. We simulated the CoV-2 RBD - ACE2 complex at varying salt concentrations over the concentration range from 0.03 M to 0.3 M of calcium and sodium chloride over an individual simulation length of 750 ns in 9 independent simulations (6.75µstotal). We observe that the CoV-2 RBD - ACE2 complex is stabilized independent of the salt concentration. We identify a strong negative electrostatic potential at the N-terminal part of CoV-2 RBD and we find that CoV-2 RBD binds even stronger at higher salt concentrations. We observe that the dynamics of the N-terminal part of CoV-2 RBD stabilize the protein complex leading to strong collective motions and a stable interface between CoV-2 RBD and ACE2. We state that the sequence of CoV-2 RBD might be optimized for a strong binding to ACE2 at varying salt concentrations at the cellular surface, which acts as a key component in the activation of CoV-2 for its viral entry.SIGNIFICANCEA novel coronavirus, coronavirus type 2 (CoV-2), was identified as primary cause for a worldwide pandemic of the severe acute respiratory syndrome (SARS CoV-2). The CoV-2 spike protein is a major target for the development of a vaccine and potential strategies to inhibit the viral entry into human cells. At the cellular surface, CoV-2 activation involves the direct interaction between ACE2 and CoV-2 RBD. At the cellular surface, electrolytes play an important role, especially in the interaction of proteins near the membrane surface. We thus investigate the effect of ion conditions on the interaction of the CoV-2 RBD - ACE2 complex and find stabilizing effects. We speculate that CoV-2 RBD is optimized for strong binding to ACE2 at varying salt concentrations.
Subjugating Translational Inhibition in Response to Ribosomal Protein Insufficiency by a Herpesvirus Ribosome-Associated Protein
Authors: Vink Elizabeth I. , Andrews John , Duffy Carol , Mohr Ian 
Published: October 2020

SUMMARYIn addition to being required for protein synthesis, ribosomes and ribosomal proteins (RPs) also regulate mRNA translation in uninfected and virus-infected cells. By individually depleting 85 RPs using RNAi, we found overall protein synthesis in uninfected primary fibroblasts was more sensitive to RP-depletion than those infected with herpes simplex virus-1 (HSV-1). Although representative RP-depletion (uL3, uS4, uL5) inhibited protein synthesis in cells infected with other DNA viruses, HSV-1-infected cell protein synthesis unexpectedly endured and required a single virus-encoded gene product, VP22. During individual RP-insufficiency, VP22-expressing HSV-1 replicated better than a VP22-deficient variant. Furthermore, VP22 cosedimented with ribosomes and polyribosomes in infected cells. This identifies VP22 as a virus-encoded, polyribosome-associated protein that compensates for RP-insufficiency to support viral protein synthesis and replication. Moreover, it reveals an unanticipated class of virus-encoded, ribosome-associated effectors that reduce the dependence of protein synthesis upon RPs and broadly support translation during physiological stress such as infection.
DRP1 IS REQUIRED FOR AGRP NEURONAL ACTIVITY AND FEEDING
Authors: Jin Sungho , Yoon Nal Ae , Liu Zhong-Wu , Horvath Tamas L. , Kim Jung Dae , Diano Sabrina 
Published: October 2020

AbstractThe hypothalamic orexigenic Agouti-related peptide (AgRP)-expressing neurons are crucial for the regulation of whole-body energy homeostasis. Here, we show that fasting-induced AgRP neuronal activation is associated with dynamin-related peptide 1 (Drp1)-mediated mitochondrial fission and mitochondrial fatty acid utilization in AgRP neurons. In line with this, mice lacking Drp1 in adult AgRP neurons (Drp1AgRPKO) show decrease in fasting-or ghrelin-induced AgRP neuronal activity and feeding and exhibited a significant decrease in body weight, fat mass, and feeding accompanied by a significant increase in energy expenditure. In support of the role for mitochondrial fission and fatty acids oxidation,Drp1AgRPKOmice showed attenuated palmitic acid-induced mitochondrial respiration. Altogether, our data revealed that mitochondrial dynamics and fatty acids oxidation in hypothalamic AgRP neurons is a critical mechanism for AgRP neuronal function and associated behavior.