bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nonintrusive methods for biomass estimation in aquaculture with emphasis on fish: a review
Authors: Li Daoliang , Hao Yinfeng , Duan Yanqing 
Published: October 2019

AbstractFish biomass estimation is one of the most common and important practices in aquaculture. The regular acquisition of fish biomass information has been identified as an urgent need for managers to optimize daily feeding, control stocking densities and ultimately determine the optimal time for harvesting. However, it is difficult to estimate fish biomass without human intervention because fishes are sensitive and move freely in an environment where visibility, lighting and stability are uncontrollable. Until now, fish biomass estimation has been mostly based on manual sampling, which is usually invasive, time‐consuming and laborious. Therefore, it is imperative and highly desirable to develop a noninvasive, rapid and cost‐effective means. Machine vision, acoustics, environmental DNA and resistivity counter provide the possibility of developing nonintrusive, faster and cheaper methods for in situ estimation of fish biomass. This article summarizes the development of these nonintrusive methods for fish biomass estimation over the past three decades and presents their basic concepts and principles. The strengths and weaknesses of each method are analysed and future research directions are also presented. Studies show that the applications of information technology such as advanced sensors and communication technologies have great significance to accelerate the development of new means and techniques for more effective biomass estimation. However, the accuracy and intelligence still need to be improved to meet intensive aquaculture requirements. Through close cooperation between fisheries experts and engineers, the precision and the level of intelligence for fish biomass estimation will be further improved based on the above methods.
Catherine de Medici’s grandmotherhood: the building of emotional and political intergenerational relationships
Authors: Paranque Estelle 
Published: October 2019

AbstractCatherine de Medici’s role in the French government as a queen consort, regent and political adviser has been thoroughly studied. Notwithstanding her evil reputation, which scholars have lately reassessed, Catherine was a talented and skilful politician who wrote thousands of letters to maintain her own and her sons’ authority both inside and outside of France.This paper aims to shed new light on Catherine’s complex representations and augment the existing historiography on her life. In addition to being an influential political figure, Catherine gave birth to ten children, some of whom subsequently produced children of their own. The paper focuses on the political significance of her grandmotherhood and how she used it to exercise political agency outside the borders of her realm by reviewing the letters she sent to her Franco‐Spanish granddaughters, the Spanish ambassador and other people who were intimately involved in her granddaughters’ lives, as well as other key sources. This analysis not only reveals a new image of Catherine – that of a caring grandmother rather than an evil, power‐hungry mother – but also highlights her close involvement in her granddaughters’ lives and the influence she was able to exert over the next generation of women in her family.
Consociationalism and Centripetalism: Friends or Foes?
Authors: Bogaards Matthijs 
Published: October 2019

AbstractTwo schools dominate the literature on democracy in divided societies: consociationalism and centripetalism. The first advocates group representation and power sharing while the second recommends institutions that promote multi‐ethnic parties. Although often presented as mutually exclusive choices, in reality many new democracies display a mix. Drawing on the experiences of Bosnia and Herzegovina, Burundi, Fiji, Lebanon, Malaysia, and Northern Ireland, this article examines the empirical and theoretical relationship between centripetalism and consociationalism. The aim is to explore the conditions under which they reinforce each other (friends) or work at cross‐purposes (foes). A better understanding of the interaction between consociational and centripetal elements in post‐conflict societies not only yields a more nuanced picture of institutional dynamics, but also holds lessons for institutional design.
A fast quadtree‐based terrain crack locating method that accounts for adjacency relationships
Authors: Li Chengming , Zhao Zhanjie , Sun Wei , Liu Zhendong 
Published: October 2019

AbstractThe repair of terrain cracks is an important process in multi‐resolution three‐dimensional terrain visualization, and rapid and accurate pinpointing of cracks between terrain blocks is of the utmost importance for this process. The existing quadtree‐based crack locating methods are generally slow and inefficient, as they require the traversal of terrain quadtrees to locate terrain cracks. In this research, we propose a fast quadtree‐based terrain crack locating method that accounts for adjacency information. First, terrain quadtrees are constructed that contain information regarding adjacency relationships. Second, dynamic updating is performed for terrain quadtrees and their adjacency information. Finally, terrain cracks are located by using the adjacencies of the quadtree nodes. This proposed method was experimentally validated via the terrain data of a mountainous region in Sichuan Province. The experimental results indicate that the proposed method can be used to efficiently and accurately locate terrain cracks with a strong performance in practical applications.
Independent origin of MIRNA genes controlling homologous target genes by partial inverted duplication of antisense‐transcribed sequences
Authors: Gramzow Lydia , Lobbes Dajana , Innard Nathan , Theißen Günter 
Published: October 2019

SummarySome microRNAs (miRNAs) are key regulators of developmental processes, mainly by controlling the accumulation of transcripts encoding transcription factors that are important for morphogenesis. MADS‐box genes encode a family of transcription factors which control diverse developmental processes in flowering plants. Here we study the convergent evolution of two MIRNA (MIR) gene families, named MIR444 and MIR824, targeting members of the same clade of MIKCC‐group MADS‐box genes. We show that these two MIR genes most likely originated independently in monocots (MIR444) and in Brassicales (eudicots, MIR824). We provide evidence that, in both cases, the future target gene was transcribed in antisense prior to the evolution of the MIR genes. Both MIR genes then likely originated by a partial inverted duplication of their target genes, resulting in natural antisense organization of the newly evolved MIR gene and its target gene at birth. We thus propose a model for the origin of MIR genes, MEPIDAS (MicroRNA Evolution by Partial Inverted Duplication of Antisense‐transcribed Sequences). MEPIDAS is a refinement of the inverted duplication hypothesis. According to MEPIDAS, a MIR gene evolves at a genomic locus at which the future target gene is also transcribed in the antisense direction. A partial inverted duplication at this locus causes the antisense transcript to fold into a stem–loop structure that is recognized by the miRNA biogenesis machinery to produce a miRNA that regulates the gene at this locus. Our analyses exemplify how to elucidate the origin of conserved miRNAs by comparative genomics and will guide future studies.Open Research Badge

This article has earned an Open Data Badge for making publicly available the digitally‐shareable data necessary to reproduce the reported results. The data is available at https://www.ncbi.nlm.nih.gov/genbank/
Actin‐spectrin scaffold supports open fenestrae in liver sinusoidal endothelial cells
Authors: Zapotoczny Bartlomiej , Braet Filip , Kus Edyta , Ginda‐Mäkelä Katarzyna , Klejevskaja Beata , Campagna Roberto , Chlopicki Stefan , Szymonski Marek 
Published: October 2019

AbstractFenestrae are open transmembrane pores that are a structural hallmark of healthy liver sinusoidal endothelial cells (LSECs). Their key role is the transport of solutes and macromolecular complexes between the sinusoidal lumen and the space of Disse. To date, the biochemical nature of the cytoskeleton elements that surround the fenestrae and sieve plates in LSECs remain largely elusive. Herein, we took advantage of the latest developments in atomic force imaging and super‐resolution fluorescence nanoscopy to define the organization of the supramolecular complex(es) that surround the fenestrae. Our data revealed that spectrin, together with actin, lines the inner cell membrane and provided direct structural support to the membrane‐bound pores. We conclusively demonstrated that diamide and iodoacetic acid (IAA) affect fenestrae number by destabilizing the LSEC actin‐spectrin scaffold. Furthermore, IAA induces rapid and repeatable switching between the open vs closed state of the fenestrae, indicating that the spectrin‐actin complex could play an important role in controlling the pore number. Our results suggest that spectrin functions as a key regulator in the structural preservation of the fenestrae, and as such, it might serve as a molecular target for altering transendothelial permeability.
Efficacy of therapeutic plasma exchange in reducing the incidence of recurrent pancreatitis related to familial chylomicronemia
Authors: Fitts Eric , Lee Phillip D. K. , Yates Sean G. 
Published: October 2019

BACKGROUNDFamilial chylomicronemia syndrome (FCS) is caused by a genetic defect in triglyceride (TG) metabolism that leads to severe hypertriglyceridemia, which in turn is associated with multiple morbidities and may cause severe pancreatitis that is both recurrent and progressive. Management of hypertriglyceridemia in FCS is challenging, as both dietary and medical interventions are often ineffective. Therapeutic plasma exchange (TPE) has been shown to rapidly decrease circulating levels of chylomicrons and TGs in patients presenting with acute hypertriglyceridemic‐associated pancreatitis. Conversely, limited evidence exists to suggest that prophylactic use of TPE is effective at preventing recurrence of acute pancreatitis.CASE REPORTHerein, we report our experience with the use of chronic, prophylactic TPE to reduce the incidence of recurrent acute pancreatitis in a patient with FCS.
Mutation and methylation status of KIT and TP53 in canine cutaneous and subcutaneous mast cell tumours
Authors: Vozdova Miluse , Kubickova Svatava , Fictum Petr , Cernohorska Halina , Fröhlich Jan , Rubes Jiri 
Published: October 2019

AbstractCutaneous and subcutaneous mast cell tumours (MCTs) are counted among the most frequent cancers in dogs. However, the genetic aetiology of their development is still mostly unknown, with the exception of KIT and tumor protein p53 (TP53) mutations reported in less than a half of cutaneous MCTs. In subcutaneous MCTs, no gene alterations were previously detected. We analysed KIT and TP53 mutations in cutaneous and subcutaneous MCTs, and identified methylated CpG sites in KIT and TP53 promoters and adjacent exon 1 regions. The mutation analysis focused on KIT exons 8, 9 and 11, and TP53 exons 5‐8, and revealed mutations in 26% and 7% cutaneous MCT cases, respectively. Moreover, we report a first case of KIT mutation ever detected in subcutaneous MCTs. KIT exon 11 mutations and high Kiupel and Patnaik grades were associated with reduced survival in this study. Both KIT and TP53 gene were generally unmethylated in canine cutaneous MCTs. A sporadic methylation of the CpG positions in KIT promoter and adjacent exon 1 was detected in 70.4% of cutaneous and 82% of subcutaneous MCTs. A sporadic methylation of the CpG positions in the TP53 promoter and exon 1 was observed in 36.8% of the analysed cutaneous MCT samples. Only in two subcutaneous MCTs, we observed more than 30% of clones showing KIT methylation at the CpG positions 13 or 14. The CpG position 14 is involved in a predicted binding site for Sp1 transcription factor. However, the significance of KIT promoter methylation at this specific position needs further evaluation.
A preoperative bupivacaine retrobulbar block offers superior antinociception compared with an intraoperative splash block in dogs undergoing enucleation
Authors: Zibura Ashley E. , Posner Lysa P. , Ru Hongyu , Westermeyer Hans D. 
Published: October 2019

AbstractPurposeInvestigate nociception differences in dogs undergoing enucleation administered bupivacaine either via preoperative retrobulbar block (pRB) or intraoperative splash block (iSB).MethodsProspective, randomized, double‐masked, clinical comparison study. Dogs undergoing unilateral enucleation were randomized to two groups: one received bupivacaine pRB and saline iSB of the same volume, and the other received saline pRB and bupivacaine iSB. The following intraoperative parameters were recorded: heart rate (HR), respiratory rate (RR), end‐tidal CO2 (EtCO2); systolic, mean, and diastolic arterial blood pressure (SAP, MAP, and DAP respectively); inspired end‐tidal isoflurane concentration (EtISOIns), and expired end‐tidal isoflurane concentration (EtISOExp). Pain scores were recorded pre‐ and postoperatively. Analgesic rescue was documented. Surgical hemorrhage and postoperative bruising and swelling were graded subjectively by the surgeon (HDW) and study coordinator (AEZ).ResultsA significant (P = .0399) increase from baseline in overall mean heart rate was recorded in iSB bupivacaine patients (n = 11) compared with pRB bupivacaine patients (n = 11), with no significant differences in other intraoperative physiologic parameters, or pain scores. More analgesic rescue events occurred in iSB bupivacaine patients compared to pRB bupivacaine patients. A near‐significant increase in intraoperative bleeding (P = .0519), and a significant increase in bruising (P = .0382) and swelling (P = .0223) was noted in the iSB bupivacaine group.ConclusionsPreoperative retrobulbar block bupivacaine is more effective than an iSB bupivacaine at controlling both intraoperative and postoperative nociception in dogs undergoing enucleation. Additionally, iSB causes more postoperative bruising and swelling and may be associated with increased intraoperative hemorrhage.
Morphology and morphometric relationships for sagitta otoliths in Lutjanus argentiventris (Pisces: Lutjanidae) and Hyporthodus acanthistius (Pisces: Serranidae) from the Colombian Pacific Ocean
Authors: Puentes-Granada Vladimir , Rojas Paola , Pavolini Giovanni , Gutierrez Carlos Fernando , Villa Angel Andres 
Published: October 2019

Fish earstones, or otoliths, are inner ear structures that can be studied to determine a fish’s age and are a source of taxonomically informative data. In the present work, sagitta otoliths of the Yellowtail snapper (Lutjanus argentiventris) and the Red grouper (Hyporthodus acanthistius) were collected in the Colombian Pacific, and their key morphological features were studied. Otoliths of the Yellow tail snapper were distinctly concave by their distal surface, revealing features shared with species of its genus (Lutjanus). Red grouper otoliths were elliptic and compressed laterally by their proximal surface, bearing similarities to those of other Serranid species. Morphometric relationships between otolith size weight and whole fish size and weight were also studied. In Red groupers significant statistical morphometric relationships between otolith and body features were found via power regression models; successfully relating otolith length with total fish length, otolith weight with total fish length, otolith length with total fish weight, and otolith weight with total fish weight. No significant morphometric relationships were found for the Yellow snapper data. In both fish species, otolith transversal sections proved best to identify its internal features and to distinguish otolith growth rings, as a method for determining the specimen’s age.
Investigating Instabilities in a Rotating Detonation Combustor Operating With Natural Gas–Hydrogen Fuel Blend—Effect of Air Preheat and Annulus Width
Authors: Roy Arnab , Bedick Clinton R. , Ferguson Donald H. , Sidwell Todd , Strakey Peter A. 
Published: October 2019

Abstract
Propagation characteristics of a detonation wave in an air-breathing rotating detonation combustor (RDC) using natural gas (NG)–hydrogen fuel blends is presented in this paper. Short-duration (∼up to 6 s) experiments were performed on a 152.4 mm OD uncooled RDC with two different annulus gap widths (5.08 mm and 7.62 mm) over a range of equivalence ratios (0.6–1.0) at varying inlet air temperatures (∼65–204 °C) and NG content (up to 15%) with precombustion operating pressure slightly above ambient. It was observed that the RDC, with an annulus gap width of 5.08 mm, was inherently unstable when NG was added to the hydrogen fuel while operating at precombustion pressures near ambient and at an inlet air temperature of 65 °C. Increasing the annulus gap width to 7.62 mm improved the stability of the detonation wave at similar temperatures and pressure permitting operation with as much as 5% NG by volume. While observed speeds of the detonation waves were still below theoretical values, an increase in inlet air temperature reduced the variability in wave speed. The frequency analysis thus explored in this study is an effort to quantify detonation instability in an RDC under varying operational envelope. The data presented are relevant toward developing strategies to sustain a stable detonation wave in an RDC using NG for land-based power generation.
Guidelines for Design of Dividing Manifolds With Discharge Uniformly Distributed at Different Positions Along the Device Axis
Authors: Yang Honggang , Wang Yi , Meng Xiaojing , Li Dong , Cai Xiaofan 
Published: October 2019

Abstract
For practical operation of dividing manifolds, the discharge uniformity is a property generally required. To investigate the dependence of discharge uniformity on the manifold geometry and operating conditions, analytical solution to the governing equation, Bajura's equation, was secured. Furthermore, examples were derived by substituting experimental data into the analytical solutions; the resultant curves of discharge distribution indicated essential agreement between the theoretical and experimental results. For evaluating the property of discharge distribution, a uniformity index, U, was introduced. The calculated results of U showed a well-defined dependence of uniformity on the dimensionless parameter, γ, and a maximum of U presented around 1.44 of γ.
Ad Lucem: QED parton distribution functions in the MMHT framework
Authors: Harland-Lang L. A. , Martin A. D. , Nathvani R. , Thorne R. S. 
Published: October 2019

Abstract
We present the MMHT2015qed PDF set, resulting from the inclusion of QED corrections to the existing set of MMHT Parton Distribution Functions (PDFs), and which contain the photon PDF of the proton. Adopting an input distribution from the LUXqed formulation, we discuss our methods of including QED effects for the full, coupled DGLAP evolution of all partons with QED at $${\mathcal {O}}(\alpha )$$O(α), $${\mathcal {O}}(\alpha \alpha _{S})$$O(ααS), $${\mathcal {O}}(\alpha ^2)$$O(α2). While we find consistency for the photon PDF of the proton with other recent sets, building on this we also present a set of QED corrected neutron PDFs and provide the photon PDF separated into its elastic and inelastic contributions. The effect of QED corrections on the other partons and the fit quality is investigated, and the sources of uncertainty for the photon are outlined. Finally we explore the phenomenological implications of this set, giving the partonic luminosities for both the elastic and inelastic contributions to the photon and the effect of our photon PDF on fits to high mass Drell–Yan production, including the photon-initiated channel.
HNF4α-Deficient Fatty Liver Provides a Permissive Environment for Sex-Independent Hepatocellular Carcinoma
Authors: Fekry Baharan , Ribas-Latre Aleix , Baumgartner Corrine , Mohamed Alaa M.T. , Kolonin Mikhail G. , Sladek Frances M. , Younes Mamoun , Eckel-Mahan Kristin L. 
Published: October 2019

Abstract

The incidence of hepatocellular carcinoma (HCC) is on the rise worldwide. Although the incidence of HCC in males is considerably higher than in females, the projected rates of HCC incidence are increasing for both sexes. A recently appreciated risk factor for HCC is the growing problem of nonalcoholic fatty liver disease, which is usually associated with obesity and the metabolic syndrome. In this study, we showed that under conditions of fatty liver, female mice were more likely to develop HCC than expected from previous models. Using an inducible knockout model of the tumor-suppressive isoform of hepatocyte nuclear factor 4 alpha (“P1-HNF4α”) in the liver in combination with prolonged high fat (HF) diet, we found that HCC developed equally in male and female mice as early as 38 weeks of age. Similar sex-independent HCC occurred in the “STAM” model of mice, in which severe hyperglycemia and HF feeding results in rapid hepatic lipid deposition, fibrosis, and ultimately HCC. In both sexes, reduced P1-HNF4α activity, which also occurs under chronic HF diet feeding, increased hepatic lipid deposition and produced a greatly augmented circadian rhythm in IL6, a factor previously linked with higher HCC incidence in males. Loss of HNF4α combined with HF feeding induced epithelial–mesenchymal transition in an IL6-dependent manner. Collectively, these data provide a mechanism-based working hypothesis that could explain the rising incidence of aggressive HCC.

Significance:
This study provides a mechanism for the growing incidence of hepatocellular carcinoma in both men and women, which is linked to nonalcoholic fatty liver disease.
A Breath of Fresh Air: Opening up the Lung Cancer Genome
Authors: Bowcock Anne M. 
Published: October 2019

Abstract
In this issue of Cancer Research, Wang and colleagues identify a large number of regulatory sites within the genomes of non–small cell lung cancers with a global scan for open chromatin (assaying for transposase-accessible chromatin with sequencing). They show that this type of profiling might substitute RNA sequencing in classifying lung cancer samples and in making predictions about prognosis. They also show experimentally that genome editing of some regulatory sites upregulates the expression of GSTM1 and GSTT1, which are required for detoxification of carcinogens and whose low expression levels are associated with lung cancer risk.
See related article by Wang et al., p. 4840
Sequencing the Events That Mediate Progression of Premalignant Lung Lesions
Authors: Merrick Daniel T. 
Published: October 2019

AbstractAnalysis of a large group of patients with multifocal premalignant disease by Krysan and colleagues in this issue of Cancer Research provides an informative view of the processes that may underlie progression of these lesions to invasive adenocarcinoma of the lung. The identification of the type and distribution of mutational changes reveals that common processes may be occurring within individuals but that these are generally unique between patients at risk for developing lung cancer. Furthermore, predicted neoantigens are identified and associated with characteristics of immune infiltrates supporting the role of alterations in adaptive immune surveillance in progression of these premalignant lesions. These findings provide critical insights that will help establish a foundation of knowledge for developing personalized prevention strategies with the potential to significantly impact overall mortality in lung cancer.See related article by Krysan et al., p. 5022