bluuebunny/crossref_metadata_2025_split huggingface dataset:
ESTIMATION OF THE COANCESTRY COEFFICIENT: BASIS FOR A SHORT-TERM GENETIC DISTANCE
Authors: Reynolds John , Weir B S , Cockerham C Clark 
Published: January 2021

ABSTRACT
A distance measure for populations diverging by drift only is based on the coancestry coefficient θ, and three estimators of the distance D = -ln(1 - θ) are constructed for multiallelic, multilocus data. Simulations of a monoecious population mating at random showed that a weighted ratio of single-locus estimators performed better than an unweighted average or a least squares estimator. Jackknifing over loci provided satisfactory variance estimates of distance values. In the drift situation, in which mutation is excluded, the weighted estimator of D appears to be a better measure of distance than others that have appeared in the literature.
SPECIFICITY OF TRANSPOSON Tn5 INSERTION
Authors: Berg Douglas E , Schmandt Margaret A , Lowe John B 
Published: January 2021

ABSTRACT
Genetic mapping studies had shown that the bacterial transposon Tn5 can insert into many sites in a gene, but that some sites are preferred. To begin understanding Tn5's insertion specificity at the molecular level, we selected transpositions of Tn5 from the Escherichia coli chromosome to the plasmid pBR322 and analyzed the resultant pBR322::Tn5 plasmids by restriction endonuclease digestion and DNA sequencing. Seventy-five insertions in the tet gene were found at 28 sites including one major hotspot (with 21 insertions) and four lesser hotspots (with four to ten insertions each). All five hotspots are within the first 300 of the 1250-base pair (bp) tet gene. In contrast, 31 independent insertions in the amp gene were found in at least 27 distinct sites.—Tn5 generates 9 bp target sequence duplications when it transposes. Such transposon-induced duplications are generally taken to indicate that cleavages of complementary target DNA strands are made 9 bp apart during transposition. DNA sequence analysis indicated that GC base pairs occupy positions 1 and 9 in the duplications at each of the five hotspots examined, suggesting a GC-cutting preference during Tn5 transposition.
Heritability and family-based GWAS analyses of the N-acyl ethanolamine and ceramide plasma lipidome
Authors: McGurk Kathryn A , Williams Simon G , Guo Hui , Watkins Hugh , Farrall Martin , Cordell Heather J , Nicolaou Anna , Keavney Bernard D 
Published: January 2021

Abstract
Signalling lipids of the N-acyl ethanolamine (NAE) and ceramide (CER) classes have emerged as potential biomarkers of cardiovascular disease (CVD). We sought to establish the heritability of plasma NAEs (including the endocannabinoid anandamide) and CERs, to identify common DNA variants influencing the circulating concentrations of the heritable lipids, and assess causality of these lipids in CVD using 2-sample Mendelian randomization (2SMR). Nine NAEs and 16 CERs were analyzed in plasma samples from 999 members of 196 British Caucasian families, using targeted ultra-performance liquid chromatography with tandem mass spectrometry. All lipids were significantly heritable (h2 = 36–62%). A missense variant (rs324420) in the gene encoding the enzyme fatty acid amide hydrolase (FAAH), which degrades NAEs, associated at genome-wide association study (GWAS) significance (P &lt; 5 × 10−8) with four NAEs (DHEA, PEA, LEA and VEA). For CERs, rs680379 in the SPTLC3 gene, which encodes a subunit of the rate-limiting enzyme in CER biosynthesis, associated with a range of species (e.g. CER[N(24)S(19)]; P = 4.82 × 10−27). We observed three novel associations between SNPs at the CD83, SGPP1 and DEGS1 loci, and plasma CER traits (P &lt; 5 × 10−8). 2SMR in the CARDIoGRAMplusC4D cohorts (60 801 cases; 123 504 controls) and in the DIAGRAM cohort (26 488 cases; 83 964 controls), using the genetic instruments from our family-based GWAS, did not reveal association between genetically determined differences in CER levels and CVD or diabetes. Two of the novel GWAS loci, SGPP1 and DEGS1, suggested a casual association between CERs and a range of haematological phenotypes, through 2SMR in the UK Biobank, INTERVAL and UKBiLEVE cohorts (n = 110 000–350 000).
Marmosets: Welfare, Ethical Use, and IACUC/Regulatory Considerations
Authors: Colman Ricki J , Capuano Saverio , Bakker Jaco , Keeley Jo , Nakamura Katsuki , Ross Corinna 
Published: January 2021

Abstract
Use of marmosets in biomedical research has increased dramatically in recent years due, in large part, to their suitability for transgenic applications and utility as models for neuroscience investigations. This increased use includes the establishment of new colonies and involvement of people new to marmoset research. To facilitate the use of the marmoset as a research model, we provide an overview of issues surrounding the ethics and regulations associated with captive marmoset research, including discussion of the history of marmosets in research, current uses of marmosets, ethical considerations related to marmoset use, issues related to importation of animals, and recommendations for regulatory oversight of gene-edited marmosets. To understand the main concerns that oversight bodies have regarding captive biomedical research with marmosets, we developed a brief, 15-question survey that was then sent electronically to academic and biomedical research institutions worldwide that were believed to house colonies of marmosets intended for biomedical research. The survey included general questions regarding the individual respondent’s colony, status of research use of the colony and institutional oversight of both the colony itself and the research use of the colony. We received completed surveys from a total of 18 institutions from North America, Europe, and Asia. Overall, there appeared to be no clear difference in regulatory oversight body concerns between countries/regions. One difference that we were able to appreciate was that while biomedical research with marmosets was noted to be either stable or decreasing in Europe, use was clearly increasing elsewhere.
Goeritz Groups of Bridge Decompositions
Authors: Hirose Susumu , Iguchi Daiki , Kin Eiko , Koda Yuya 
Published: January 2021

AbstractFor a bridge decomposition of a link in the $3$-sphere, we define the Goeritz group to be the group of isotopy classes of orientation-preserving homeomorphisms of the $3$-sphere that preserve each of the bridge sphere and link setwise. After describing basic properties of this group, we discuss the asymptotic behavior of the minimal pseudo-Anosov entropies. We then give an application to the asymptotic behavior of the minimal entropies for the original Goeritz groups of Heegaard splittings of the $3$-sphere and the real projective space.
MOVES – IV. Modelling the influence of stellar XUV-flux, cosmic rays, and stellar energetic particles on the atmospheric composition of the hot Jupiter HD 189733b
Authors: Barth P , Helling Ch , Stüeken E E , Bourrier V , Mayne N , Rimmer P B , Jardine M , Vidotto A A , Wheatley P J , Fares R 
Published: January 2021

ABSTRACT
Hot Jupiters provide valuable natural laboratories for studying potential contributions of high-energy radiation to pre-biotic synthesis in the atmospheres of exoplanets. In this fourth paper of the Multiwavelength Observations of an eVaporating Exoplanet and its Star (MOVES) programme, we study the effect of different types of high-energy radiation on the production of organic and pre-biotic molecules in the atmosphere of the hot Jupiter HD 189733b. Our model combines X-ray and UV observations from the MOVES programme and 3D climate simulations from the 3D Met Office Unified Model to simulate the atmospheric composition and kinetic chemistry with the STAND2019 network. Also, the effects of galactic cosmic rays and stellar energetic particles are included. We find that the differences in the radiation field between the irradiated dayside and the shadowed nightside lead to stronger changes in the chemical abundances than the variability of the host star’s XUV emission. We identify ammonium (NH4+) and oxonium (H3O+) as fingerprint ions for the ionization of the atmosphere by both galactic cosmic rays and stellar particles. All considered types of high-energy radiation have an enhancing effect on the abundance of key organic molecules such as hydrogen cyanide (HCN), formaldehyde (CH2O), and ethylene (C2H4). The latter two are intermediates in the production pathway of the amino acid glycine (C2H5NO2) and abundant enough to be potentially detectable by JWST.
Compressive Shack–Hartmann wavefront sensor based on deep neural networks
Authors: Jia Peng , Ma Mingyang , Cai Dongmei , Wang Weihua , Li Juanjuan , Li Can 
Published: January 2021

ABSTRACT
The Shack–Hartmann wavefront sensor is widely used to measure aberrations induced by atmospheric turbulence in adaptive optics systems. However, if strong atmospheric turbulence exists or the brightness of guide stars is low, the accuracy of wavefront measurements will be affected. In this work, we propose a compressive Shack–Hartmann wavefront sensing method. Instead of reconstructing wavefronts with slope measurements of all subapertures, our method reconstructs wavefronts with slope measurements of subapertures that have spot images with high signal-to-noise ratio. We further propose to use a deep neural network to accelerate the wavefront reconstruction speed. During the training stage of the deep neural network, we propose to add a drop-out layer to simulate the compressive sensing process, which could increase the development speed of our method. After training, the compressive Shack–Hartmann wavefront sensing method can reconstruct wavefronts at high spatial resolution with slope measurements from only a small number of subapertures. We integrate the straightforward compressive Shack–Hartmann wavefront sensing method with an image deconvolution algorithm to develop a high-order image restoration method. We use images restored by the high-order image restoration method to test the performance of our compressive Shack–Hartmann wavefront sensing method. The results show that our method can improve the accuracy of wavefront measurements and is suitable for real-time applications.
The nascent polypeptide in the 60S subunit determines the Rqc2-dependency of ribosomal quality control
Authors: Mizuno Masato , Ebine Shuhei , Shounai Okuto , Nakajima Shizuka , Tomomatsu Shota , Ikeuchi Ken , Matsuo Yoshitaka , Inada Toshifumi 
Published: January 2021

Abstract
Ribosome stalling at tandem CGA codons or poly(A) sequences activates quality controls for nascent polypeptides including ribosome-associated quality control (RQC) and no-go mRNA decay (NGD). In RQC pathway, Hel2-dependent uS10 ubiquitination and the RQC-trigger (RQT) complex are essential for subunit dissociation, and Ltn1-dependent ubiquitination of peptidyl-tRNA in the 60S subunit requires Rqc2. Here, we report that polytryptophan sequences induce Rqc2-independent RQC. More than 11 consecutive tryptophan residues induced RQC in a manner dependent on Hel2-mediated ribosome ubiquitination and the RQT complex. Polytryptophan sequence-mediated RQC was not coupled with CAT-tailing, and Rqc2 was not required for Ltn1-dependent degradation of the arrest products. Eight consecutive tryptophan residues located at the region proximal to the peptidyl transferase center in the ribosome tunnel inhibited CAT-tailing by tandem CGA codons. Polytryptophan sequences also induced Hel2-mediated canonical RQC-coupled NGD and RQC-uncoupled NGD outside the stalled ribosomes. We propose that poly-tryptophan sequences induce Rqc2-independent RQC, suggesting that CAT-tailing in the 60S subunit could be modulated by the polypeptide in the ribosome exit tunnel.
UV-A/B radiation rapidly activates photoprotective mechanisms in Chlamydomonas reinhardtii
Authors: Tokutsu Ryutaro , Fujimura-Kamada Konomi , Yamasaki Tomohito , Okajima Keisuke , Minagawa Jun 
Published: January 2021

Abstract
Conversion of light energy into chemical energy through photosynthesis in the chloroplasts of photosynthetic organisms is essential for photoautotrophic growth, and non-photochemical quenching (NPQ) of excess light energy prevents the generation of reactive oxygen species and maintains efficient photosynthesis under high light. In the unicellular green alga Chlamydomonas reinhardtii, NPQ is activated as a photoprotective mechanism through wavelength-specific light signaling pathways mediated by the phototropin (blue light) and ultra-violet (UV) light photoreceptors, but the biological significance of photoprotection activation by light with different qualities remains poorly understood. Here, we demonstrate that NPQ-dependent photoprotection is activated more rapidly by UV than by visible light. We found that induction of gene expression and protein accumulation related to photoprotection was significantly faster and greater in magnitude under UV treatment compared with that under blue- or red-light treatment. Furthermore, the action spectrum of UV-dependent induction of photoprotective factors implied that C. reinhardtii senses relatively long-wavelength UV (including UV-A/B), whereas the model dicot plant Arabidopsis (Arabidopsis thaliana) preferentially senses relatively short-wavelength UV (mainly UV-B/C) for induction of photoprotective responses. Therefore, we hypothesize that C. reinhardtii developed a UV response distinct from that of land plants.
The new role of musculoskeletal ultrasound in the treat-to-target management of juvenile idiopathic arthritis
Authors: Gohar Faekah , Windschall Daniel 
Published: January 2021

AbstractThis article reviews the role of musculoskeletal ultrasound (MSUS) for the diagnosis, monitoring and treat-to-target management of JIA. Technological advancements in MSUS allow more precise evaluation of arthritis, tenosynovitis and enthesitis versus clinical examination alone, which may assist treatment decisions. In adult studies, serum and synovial biomarkers have correlated with MSUS findings. Within paediatric rheumatology, significant developments in the definition of normal and pathology, a necessity for the future integration of MSUS into treat-to-target management, have already been reached or are underway, which in turn could allow tighter control of disease activity and earlier identification of treatment response and failure, bringing the goal of ‘precision medicine’ closer. Additionally, the utility of MSUS for the evaluation of subclinical disease remains an unexamined area of interest. ‘Ultrasound remission’ combined with clinical assessment and immunological markers could therefore potentially improve the treat-to-target management of JIA.
Asthma, severe acute respiratory syndrome coronavirus-2 and coronavirus disease 2019
Authors: Timberlake Dylan T. , Strothman Kasey , Grayson Mitchell H. 
Published: January 2021

Purpose of review
In December 2019, a novel respiratory illness caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first described and named coronavirus disease 2019 (COVID-19). Although the knowledge base surrounding COVID-19 and SARS-CoV-2 has grown rapidly, significant gaps in our knowledge remain and inaccurate information continues to circulate. This review will discuss the interaction between asthma and COVID-19 to provide a comprehensive understanding based on the currently available published data.

Recent findings
Non-SARS human coronaviruses (HCoVs) are a significant cause of asthma exacerbations, but SARS-CoV-2 does not appear to exacerbate asthma. Data thus far strongly suggest that patients with asthma are at no increased risk of infection with SARS-CoV-2 or more severe disease if infected with COVID-19. Although the data are extremely limited on inhaled corticosteroids and biologic medications, there remain no data suggesting that these therapeutics positively or negatively impact the severity or outcome of COVID-19.

Summary
Data are rapidly evolving regarding COVID-19 and asthma. At this time, asthma does not appear to positively or negatively affect outcomes of COVID-19; however, it is imperative that practitioners keep abreast of the changing literature as we await a vaccine and control of this pandemic.
Thickness of rectus abdominis measured by ultrasound in critically ill patients after abdominal surgery
Authors: Yang Ming-Chieh , Wang Yung-Chang , Chen I-Shu , Huang Wei-Chun 
Published: January 2021

BACKGROUND
Early identification of patients at high risk of prolonged mechanical ventilation is important in critical care. Sarcopenia, the loss of muscle mass and function, has been reported to be associated with extended mechanical ventilation and prolonged ICU stay. Although ultrasound is noninvasive and widely used in critical care, there is no standard method of using it to assess sarcopenia.

OBJECTIVES
The study aims to investigate the relationship between outcomes of critically ill patients and the ratio of BMI to the thickness of rectus abdominis measured by a standardised ultrasound examination.

DESIGN
A retrospective cohort study.

SETTING
Surgical ICU of a tertiary referral hospital, from October 2017 to June 2018. The thickness of rectus abdominis (RA) was measured while performing extended focused assessment sonography for trauma. BMI was divided by the thickness of rectus abdominis over the upper abdomen to derive the BMI-RA thickness ratio.

PATIENTS
Sixteen male and 11 female patients admitted to ICU after major abdominal surgery.

MAIN OUTCOME MEASURES
The primary outcome was in-hospital mortality, and the secondary outcomes were durations of mechanical ventilation, ICU stay and hospital stay. The disease severity, serum albumin level and BMI-RA thickness ratio were also analysed.

RESULTS
Ultrasound measurement was easy to perform without adverse effects. The BMI-RA thickness ratio was significantly higher in nonsurvivors and was associated with ICU stay, hospital stay and duration of mechanical ventilation. Multivariable logistic regression showed that the BMI-RA thickness ratio was a predictor of in-hospital mortality.

CONCLUSION
The BMI-RA thickness ratio is related to the outcomes of patients transferred to ICU after major abdominal surgery. Measuring the thickness of rectus abdominis by ultrasound is well tolerated and easy to perform in surgical ICU. Larger prospective studies are required to confirm current findings.
Mid-axillary transversus abdominis plane block and stress response after abdominal hysterectomy
Authors: Ismail Samina , Ahmed Aliya , Hoda Muhammad Q. , Asghar Samie , Habib Aysha , Aziz Aliya 
Published: January 2021

BACKGROUND
The hormonal response to surgical trauma can have detrimental effects on patients. Transversus abdominis plane (TAP) block, which can improve analgesia after total abdominal hysterectomy (TAH) might attenuate the peri-operative stress response.

OBJECTIVE
To evaluate the ability of the TAP block to reduce stress response, opioid consumption and pain following TAH and multimodal analgesia.

DESIGN
Randomised, placebo-controlled double-blind study.

SETTING
The current study was conducted at a university hospital from July 2016 to September 2017.

PATIENTS
Fifty patients scheduled for TAH were included. Anaesthesia and postoperative analgesia were standardised.

INTERVENTION
After induction of anaesthesia, patients were allocated into two groups: ultrasound-guided bilateral mid-axillary TAP block with 20 ml of bupivacaine 0.25% (Group T) or 0.9% saline (Group C).

MAIN OUTCOME MEASURES
Levels of free serum cortisol, metanephrine and normetanephrine at 60 min and 6, 12 and 24 h after surgical incision. Pain scores and opioid consumption during the first 24 h after surgery.

RESULTS
There was no statistically significant difference between the median [IQR] peri-operative levels of stress hormones and pain scores between groups. Compared with baseline value 9.90 [4.2 to 23.1], free serum median cortisol levels were significantly high at 6 h in Group T, 23.6 [10.1 to 42.9] P = 0.015 and Group C 23.6 [9.9 to 46.3] P = 0.014. Only Group C showed significant elevation from the baseline median levels of plasma metanephrine at 60 min, 52.8 [33.4 to 193.2] P = 0.001, 6 h, 92.70 [2.4 to 202.6] P = 0.005 and normetanephrine at 60 min 83.44 [28.98 to 114.86] P = 0.004, 6 h 78.62 [36.6 to 162.31] P = 0.0005 and 24 h 80.96 [8.6 to 110.5] P = 0.025. Mean ± SD opioid consumption was similar in both groups: 39.60 ± 14.87 in Group T vs. 43.68 ± 14.93 in Group C (P = 0.338).

CONCLUSION
Mid-axillary TAP block does not improve stress response and analgesia in patients undergoing TAH receiving multimodal analgesia.

TRAIL REGISTRATION
ClinicalTrial.gov identifier: NCT03443271.
Protective effect of sevoflurane on vascular endothelial glycocalyx in patients undergoing heart valve surgery
Authors: Fang Fu-Quan , Sun Jie-Hao , Wu Qiao-Lin , Feng Lin-Ya , Fan Yu-Xiu , Ye Jun-Xin , Gao Wei , He Guo-Liang , Wang Wei-Jian 
Published: January 2021

BACKGROUND
The glycocalyx plays an important physiological role and may be damaged during cardiopulmonary bypass. Sevoflurane can protect the glycocalyx; however, its relevance in a clinical setting is unknown.

OBJECTIVE
Glycocalyx degradation during cardiopulmonary bypass in patients was investigated. On the basis of the available experimental data, we hypothesised that sevoflurane-based anaesthesia would confer additional protection against cardiopulmonary bypass-induced glycocalyx damage.

DESIGN
Randomised controlled study.

SETTING
Clinical study at The First Affiliated Hospital of Wenzhou Medical University between June 2018 and March 2019.

PATIENTS
Fifty-one patients.

INTERVENTIONS
After intubation and mechanical ventilation, patients undergoing elective heart valve surgery were maintained under general anaesthesia with either propofol or sevoflurane during surgery.

MAIN OUTCOME MEASURES
Glycocalyx markers (such as syndecan-1, heparan sulphate and hyaluronan), sheddases responsible for the degradation of the endothelial glycocalyx (such as matrix metalloproteinase-9 and cathepsin-B), urine albumin-to-creatinine ratio and levels of lactic acid and myocardial enzymes were all measured. Postoperative mechanical ventilation time and length of stay in the cardiac care unit and hospital were also measured. Morbidity and mortality after 30 days and 1 year were evaluated.

RESULTS
The vascular endothelial glycocalyx was damaged during cardiopulmonary bypass. The glycocalyx damage in the sevoflurane group was less extensive than that in the propofol group. The urine albumin-to-creatinine ratio increased in both groups but was lower in the sevoflurane group. Enzymes including matrix metalloproteinase-9 and cathepsin-B were positively correlated with glycocalyx marker concentrations. After operation, the sevoflurane group showed lower levels of lactic acid and myocardial enzyme, as well as shorter duration of postoperative mechanical ventilation than the propofol group.

CONCLUSION
Sevoflurane can decrease glycocalyx degradation in patients undergoing heart valve surgery under cardiopulmonary bypass.

TRIAL REGISTRATION
Chinese Clinical Trial Registry, chictr.org.cn, identifier: ChiCTR1800016367.