bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrated analysis of three newly sequenced fern chloroplast genomes: Genome structure and comparative analysis
Authors: Fan Ruifeng , Ma Wei , Liu Shilei , Huang Qingyang 
Published: March 2021

AbstractBackgroundSome ferns have medicinal properties and are used in therapeutic interventions. However, the classification and phylogenetic relationships of ferns remain incompletely reported. Considering that chloroplast genomes provide ideal information for species identification and evolution, in this study, three unpublished and one published ferns were sequenced and compared with other ferns to obtain comprehensive information on their classification and evolution.Materials and MethodsThe complete chloroplast genomes of Dryopteris goeringiana (Kunze) Koidz, D. crassirhizoma Nakai, Athyrium brevifrons Nakai ex Kitagawa, and Polystichum tripteron (Kunze) Presl were sequenced using the Illumina HiSeq 4,000 platform. Simple sequence repeats (SSRs), nucleotide diversity analysis, and RNA editing were investigated in all four species. Genome comparison and inverted repeats (IR) boundary expansion and contraction analyses were also performed. The relationships among the ferns were studied by phylogenetic analysis based on the whole chloroplast genomes.ResultsThe whole chloroplast genomes ranged from 148,539 to 151,341 bp in size and exhibited typical quadripartite structures. Ten highly variable loci with parsimony informative (Pi) values of > 0.02 were identified. A total of 75–108 SSRs were identified, and only six SSRs were present in all four ferns. The SSRs contained a higher number of A + T than G + C bases. C‐to‐U conversion was the most common type of RNA editing event. Genome comparison analysis revealed that single‐copy regions were more highly conserved than IR regions. IR boundary expansion and contraction varied among the four ferns. Phylogenetic analysis showed that species in the same genus tended to cluster together with and had relatively close relationships.ConclusionThe results provide valuable information on fern chloroplast genomes that will be useful to identify and classify ferns, and study their phylogenetic relationships and evolution.
Extreme home range sizes among Eurasian lynx at the northern edge of their biogeographic range
Authors: Linnell John D.C. , Mattisson Jenny , Odden John 
Published: March 2021

AbstractEurasian lynx (Lynx lynx) have a wide distribution across Eurasia. The northern edge of this distribution is in Norway, where they reach up to 72 degrees north. We conducted a study of lynx space use in this region from 2007 to 2013 using GPS telemetry. The home range sizes averaged 2,606 (± 438 SE) km2 for males (n = 9 ranges) and 1,456 (± 179 SE) km2 for females (n = 24 ranges). These are the largest home ranges reported for any large felid, and indeed are only matched by polar bears, arctic living wolves, and grizzly bears among all the Carnivora. The habitat occupied was almost entirely treeless alpine tundra, with home ranges only containing from 20% to 25% of forest. These data have clear implications for the spatial planning of lynx management in the far north as the current management zones are located in unsuitable habitats and are not large enough to encompass individual lynx movements.
A Novel GABABR1a Receptor Electrochemical Biosensor Based on Gold Nanoparticles Chitosan‐horseradish Peroxidase
Authors: Zhao Xiaotong , Wei Lihui , Pang Guangchang , Xie Junbo 
Published: March 2021

AbstractA novel gamma aminobutyric acid type B receptor subunit 1a (GABABR1a) biosensor modified with double‐layer gold has been developed for the first time. In this work, the synthesized plasmid was transfected into HEK‐293T cells by liposome transfection, and the target protein GABABR1a was obtained. The horseradish peroxidase was used as a signal amplification system to produce a double‐layer gold modified GABABR1a receptor biosensor. The ligand gamma aminobutyric acid (GABA), jujuboside A and baclofen were detected by the time‐current method with the biosensor. The results showed that the action regularity of GABA, jujuboside A, and baclofen on GABABR1a receptor was fitted with hyperbolic fitting (R2 was 0.9740, 0.9770 and 0.9770, respectively). The double reciprocal method was used to figure out the affinity constant (Ka) of GABA, jujuboside A, and baclofen with the receptor, i. e. 2.1016×10−15 mol/L, 1.7601×10−14 mol/L, and 1.633×10−14 mol/L, respectively, indicating that these measured compounds exhibited different action strength on the receptor. Based on the above, this study will provide a basis for drug screening and will also provide a new idea and method for investigating quantitatively the interaction between receptors and ligands in the future.
Influence of normal force in metallic sealing
Authors: Fischer Felix , Murrenhoff Hubertus , Schmitz Katharina 
Published: March 2021

AbstractMetallic ball seat valves are an essential component in almost every hydraulic system in the form of check valves. Despite their wide usage in real‐life applications, the physical sealing mechanism is not yet fully understood and still debated. One promising method is the contact mechanics theory which has been developed by Persson et al. for rubber seals. It can predict the leakage of rubber seals successfully, but its application for metallic seals, where plastic deformation plays an import role, has only been developed recently and is not yet fully validated. This theory is combined with surface scans of investigated seats and simulations that are performed using the finite element method (FEM) for different geometric configurations. This combination allows an efficient calculation of the leakage of ball seat valves depending on their specific design and applied forces and pressures. In this work, the predictions by simulations according to Persson's theory are compared with experimental results. This comparison is done by analyzing the dependency of the leakage of ball seat valves in relation to applied normal forces and for different surfaces in contact. This validates the applicability of Persson's method in this field. The presented experimental method allows the measurement of the leakage of ball seat valves under realistic conditions.
A real‐world dataset and data simulation algorithm for automated fish species identification
Authors: Allken Vaneeda , Rosen Shale , Handegard Nils Olav , Malde Ketil 
Published: March 2021

AbstractDeveloping high‐performing machine learning algorithms requires large amounts of annotated data. Manual annotation of data is labour‐intensive, and the cost and effort needed are an important obstacle to the development and deployment of automated analysis. In a previous work, we have shown that deep learning classifiers can successfully be trained on synthetic images and annotations. Here, we provide a curated set of fish image data and backgrounds, the necessary software tools to generate synthetic images and annotations, and annotated real datasets to test classifier performance. The dataset is constructed from images collected using the Deep Vision system during two surveys from 2017 and 2018 that targeted economically important pelagic species in the Northeast Atlantic Ocean. We annotated a total of 1,879 images, randomly selected across trawl stations from both surveys, comprising 482 images of blue whiting, 456 images of Atlantic herring, 341 images of Atlantic mackerel, 335 images of mesopelagic fishes and 265 images containing a mixture of the four categories.
Low grade, indolent lymphomas of the head and neck: Comparative toxicity of standard versus very low dose radiation therapy
Authors: Chelius Monica , Chau Karen , Yang Joanna , Hajj Carla , Imber Brandon , Yahalom Joachim 
Published: March 2021

AbstractNational Comprehensive Cancer Network guidelines recommend radiation therapy (RT) for localized indolent non‐Hodgkin lymphomas (iNHL). Many referring physicians avoid RT to the head and neck (HN) due to fears of toxicity. Very low‐dose radiation (4 Gy) for select patients produces sustained local control and recently gained popularity. We compared early and late toxicities of standard 24–30 Gy to 4 Gy in patients with HN iNHL. We retrospectively analyzed 266 consecutive patients with HN iNHL receiving RT from 1994 to 2017. Patient characteristics, outcomes, and toxicities were collected from medical records. Early (≤2 months post‐RT) and late (>2 months post‐RT) toxicities were graded per Common Terminology Criteria for Adverse Events version 4. Grades 1–2 were defined as “low‐grade” and 3–4 “high‐grade.” Toxicity incidence was compared between 4 and >4 Gy, grouped by treated site (orbit, nonorbital head, neck, skin) and early versus late. Median follow‐up was 23 months (2–145) and 68 months (2–256) for 4Gy and >4 Gy cohorts, respectively. Median dose for the >4 Gy cohort was 30 Gy (10.5–54 Gy). Early and late toxicity incidences were lower in the 4 Gy cohort compared to >4 Gy across all RT‐sites: early toxicity, orbit, 42% versus 96%; nonorbital head, 24% versus 96%; neck, 22% versus 94%; skin, 31% versus 87%; late toxicity, orbit, 20% versus 71%; nonorbital head, 6% versus 66%; neck, 6% versus 57%; skin, 0% versus 46% (4 Gy vs. >4 Gy, respectively). Toxicities among both cohorts were largely low‐grade. High‐grade early and late toxicities did not occur in the 4 Gy cohort. There was 1 high‐grade early toxicity (Grade 3 dry mouth) and 17 high‐grade late toxicities (Grade 3 cataracts) in the >4 Gy cohort. RT to HN for iNHL is associated with minimal short‐ and long‐term toxicity and excellent local control among 4 Gy and >4 Gy treatments. In this setting, “toxicity” concerns should not deter oncologists from potentially curative RT. In select patients where toxicity remains a concern, very low dose 4 Gy could be considered.
Laparoendoscopic single‐site simple nephrectomy and reduced port procedure for inflammatory nonfunctioning kidney
Authors: Kaneko Go , Hattori Seiya , Shirotake Suguru , Kanao Kent , Hara Satoshi , Oyama Masafumi 
Published: March 2021

IntroductionTo describe laparoendoscopic single‐site simple nephrectomy and reduced port simple nephrectomy for inflammatory nonfunctioning kidney.Case presentationCase 1: a 58‐year‐old female with fever was referred to our hospital. Computed tomography demonstrated a markedly atrophic right kidney and mild hydronephrosis. Case 2: a 64‐year‐old male with a history of several intra‐abdominal surgeries visited our hospital with a complaint of left back pain and fever. Computed tomography demonstrated left marked hydronephrosis, thinning of renal parenchyma, and duplicated inferior vena cava. After antibiotic treatment, transperitoneal reduced port simple nephrectomy and retroperitoneal laparoendoscopic single‐site simple nephrectomy were performed in Case 1 and 2, respectively, because the function of the affected kidney was almost lost on renography. Although adhesion was slightly noted around the renal hilum in Case 1, neither conversion to laparotomy nor placement of additional ports was needed.ConclusionLaparoendoscopic single‐site simple nephrectomy and reduced port simple nephrectomy for inflammatory nonfunctioning kidney may be options for experienced laparoscopic surgeons.
ALG13 X‐linked intellectual disability: New variants, glycosylation analysis, and expanded phenotypes
Authors: Alsharhan Hind , He Miao , Edmondson Andrew C. , Daniel Earnest J. P. , Chen Jie , Donald Tyhiesia , Bakhtiari Somayeh , Amor David J. , Jones Elizabeth A. , Vassallo Grace , Vincent Marie , Cogné Benjamin , Deb Wallid , Werners Arend H. , Jin Sheng C. , Bilguvar Kaya , Christodoulou John , Webster Richard I. , Yearwood Katherine R. , Ng Bobby G. , Freeze Hudson H. , Kruer Michael C. , Li Dong , Raymond Kimiyo M. , Bhoj Elizabeth J. , Sobering Andrew K. 
Published: March 2021

AbstractPathogenic variants in ALG13 (ALG13 UDP‐N‐acetylglucosaminyltransferase subunit) cause an X‐linked congenital disorder of glycosylation (ALG13‐CDG) where individuals have variable clinical phenotypes that include developmental delay, intellectual disability, infantile spasms, and epileptic encephalopathy. Girls with a recurrent de novo c.3013C>T; p.(Asn107Ser) variant have normal transferrin glycosylation. Using a highly sensitive, semi‐quantitative flow injection‐electrospray ionization‐quadrupole time‐of‐flight mass spectrometry (ESI‐QTOF/MS) N‐glycan assay, we report subtle abnormalities in N‐glycans that normally account for <0.3% of the total plasma glycans that may increase up to 0.5% in females with the p.(Asn107Ser) variant. Among our 11 unrelated ALG13‐CDG individuals, one male had abnormal serum transferrin glycosylation. We describe seven previously unreported subjects including three novel variants in ALG13 and report a milder neurodevelopmental course. We also summarize the molecular, biochemical, and clinical data for the 53 previously reported ALG13‐CDG individuals. We provide evidence that ALG13 pathogenic variants may mildly alter N‐linked protein glycosylation in both female and male subjects, but the underlying mechanism remains unclear.
Combined use of creatinine and cystatin C improves the detection of renal dysfunction in children undergoing home parenteral nutrition
Authors: Matrat Lucie , Ruiz Mathias , Ecochard‐Dugelay Emmanuelle , Loras‐Duclaux Irène , Marotte Stéphanie , Heissat Sophie , Poinsot Pierre , Sellier‐Leclerc Anne‐Laure , Bacchetta Justine , Dubourg Laurence , Peretti Noël 
Published: March 2021

AbstractBackgroundRenal dysfunction can complicate home parenteral nutrition (HPN). The aims were, in the context of pediatric HPN, to assess renal function using the measured glomerular filtration rate (mGFR), determine the most accurate formula(s) to estimate GFR, and identify possible underlying mechanisms of renal impairment.MethodsA retrospective study was performed in 2 centers. Patients receiving HPN and aged 2–16 years without medical history of nephropathy were included. GFR was measured using iohexol clearance. Estimated GFR (eGFR) was calculated using creatinine, cystatin C–based, and combined (eGFRcr+cyst) Schwartz formulas.ResultsA total of 36 patients (18 females) were included; they received HPN for 8 (2–16) years. The primary digestive disease was short‐bowel syndrome for 16 (44%) patients, gastrointestinal motility disorder for 10 (28%), or congenital diarrhea for 10 (28%). The median (range) mGFR was 99 (33–136) ml/min/1.73 m2; 9 (25%) patients had mildly decreased mGFR (<90 and ≥60 ml/min/1.73 m2), and 2 (6%) had mildly to severely decreased mGFR (<60 ml/min/1.73 m2). The eGFRcr+cyst formula was the most accurate and precise to estimate GFR. A significant negative correlation between mGFR and PN duration was found for patients receiving PN for 6–7/7 days (P = .008). Activation of the renin‐angiotensin system was identified in 15 of 36 (42%) patients.ConclusionRenal dysfunction was frequent and correlated with the duration of PN only for patients with the most severe intestinal failure. The use of eGFRcr+cyst improves its detection in these patients. Chronic dehydration may be an underlying mechanism.
Investigation of laser‐induced grating spectroscopy of O2 for accurate temperature measurements towards applications in harsh environments
Authors: Hot Dina , Sahlberg Anna‐Lena , Alden Marcus , Li Zhongshan 
Published: March 2021

AbstractWe present an in‐depth investigation of laser‐induced grating spectroscopy (LIGS) for temperature measurements in practical applications using a narrow‐band dye laser with 760 nm wavelength and a pulse duration of 8 ns as the source for the pump beams creating the laser‐induced grating. The pump laser wavelength was set to be either resonant with the
transition from the
band of O2 for generation of thermal LIGS or nonresonant for generation of purely electrostrictive LIGS. Signals were generated in ambient air as well as in high‐pressure or high‐temperature dry air mixtures. Pump laser irradiances up to 11 GW/cm2 were used, which resulted in strong electrostrictive contribution to the overall LIGS signals at atmospheric pressure, with a low thermal contribution due to the weak absorption by the singlet O2
. The advantage and disadvantage of thermal or electrostrictive LIGS for temperature measurements are discussed, as well as potential applications in high‐pressure environments. Furthermore, the precision of the temperature measurement is discussed by comparing different analysis methods.
Predictors and significance of histologic response to neoadjuvant therapy for gastric cancer
Authors: Rajabnejad Ataollah , Vaida Florin , Valasek Mark , Razzaque Saqib , Fanta Paul , Horgan Santiago , Bouvet Michael , Lowy Andrew M. , Kelly Kaitlyn J. 
Published: March 2021

AbstractBackgroundPerioperative therapy is the standard‐of‐care for locally‐advanced gastric cancer but many patients do not respond. There are currently no known factors that predict response to therapy.MethodsThis was a retrospective study aimed to evaluate treatment effect grade (TEG) in patients with locally advanced gastric cancer treated with neoadjuvant therapy and surgery at a single center. Ordinal logistic regression was performed to identify predictors of TEG, scaled from 0 to 3.ResultsFifty patients were identified. The majority were male (n = 33) and 50% were Hispanic. The most common regimens given were: 5‐fluorouracil/leucovorin, oxaliplatin, and docetaxel (n = 23, 46%), epirubicin, cis‐ or oxaliplatin, and 5‐fluorouracil/leucovorin or Xeloda (n = 8, 16%), and 5‐fluorouracil/leucovorin and oxaliplatin (n = 9, 18%). Twenty‐seven patients (55%) had complete or partial response to therapy (TEG 0–2), and 23 patients (46%) had no response (TEG 3). Of numerous variables analyzed, only race and SRC histology were associated with TEG. TEG was associated with disease free, but not disease specific survival.ConclusionsIn this cohort, 46% of patients had no histologic response to therapy. SRC histology, and possibly race, should be considered in determination of optimal multidisciplinary regimens and in amount of therapy to be given upfront, as patients with SRC histology and those of non‐Asian race are less likely to respond to standard regimens.
Hydrophilic carrageenan functionalized magnetic carbon‐based framework linked by silane coupling agent for the enrichment of N‐glycopeptides from human saliva
Authors: Jin Xueting , Zhu Canhong , Wu Jiani , Yan Yinghua , Ding Chuan‐Fan , Tang Keqi , Zhang Di 
Published: March 2021

AbstractIn this work, a magnetic graphene material coated with mesoporous silica was selected as the substrate, 3‐glycidoxypropyltrimethoxysilane and polyethyleneimine were sequentially bonded through chemical reactions, and then carrageenan was successfully introduced by electrostatic interaction; finally, hydrophilic nanocomposite material was prepared. Due to the large number of hydrophilic groups, and polyethyleneimine was connected by means of chemical bonds, this material exhibits good hydrophilicity and stability for glycopeptide enrichment. In the actual enrichment process, nanomaterial exhibits high selectivity (1:500), high sensitivity (2 fmol), and good repeatability (five cycles). In addition, the synthesized material also shows a good enrichment effect in the face of actual complex biological samples, which captured 40 N‐glycopeptides from human saliva, indicating the application potential for enrichment of N‐glycopeptides.
Microglia‐derived galectin‐3 in neuroinflammation; a bittersweet ligand?
Authors: Rahimian Reza , Béland Louis‐Charles , Sato Sachiko , Kriz Jasna 
Published: March 2021

AbstractGalectins are soluble β‐galactoside‐binding proteins found in all multicellular organisms. Galectins may act as danger‐associated molecular patterns in innate immunity and/or as pattern‐recognition receptors that bind to pathogen‐associated molecular patterns. Among different galectin family members, galectin‐3 has been the focus of studies in neurodegenerative diseases in recent years. This lectin modulates brain innate immune responses, microglia activation patterns in physiological and pathophysiological settings in a context‐dependent manner. Galectin‐3 is considered as a pivotal tuner of macrophage and microglial activity. Indeed galectin‐3 acts as a double edged sword in neuroinflammatory context and this multimodal lectin has diverse roles in physiological and pathophysiological conditions. Better understanding of galectin‐3 physiology (its extracellular and intracellular actions) and structure (its C terminus vs. N terminus) is instrumental to design molecules that selectively modulate galectin‐3 function toward neuroprotective phenotypes. Several experimental studies using different approaches and methods have demonstrated both protective and deleterious effects of galectin‐3 in neuroinflammatory diseases. According to the crucial role of galectin‐3 in modulation of innate immune response in brain, it is an attractive target in drug discovery of neurodegenerative diseases. The current insight attempts to provide an updated and balanced discussion on the role of galectin‐3 as a complex endogenous immune modulator. This helps to have a better insight into the development of galectin‐3 modulators with translational value in different neurological disorders including stroke and neurodegenerative diseases, such as Alzheimer's disease, Huntington's disease and Parkinson's disease.
A fresh look at the dynamics of a flexible body application to substructuring for flexible multibody dynamics
Authors: Géradin Michel , Rixen Daniel J. 
Published: March 2021

AbstractThe general formulation of the dynamics of an elastic body undergoing arbitrary motion is revisited with emphasis on the orthogonality between rigid body motion and elastic deformation on the one hand, and on the appropriate definition of the relative velocities induced by elastic deformation on the other hand. A mixed displacement–velocity approach is adopted, thus allowing a local frame definition of velocities which results in simplification of the discretization and solution steps. The proposed formulation is applied to model reduction starting from a set of free‐free elastic modes and attachment modes. The Herting–Martinez component mode synthesis method is used to replace the modal intensities by a body‐frame nodal set of elastic degrees of freedom. A body‐to‐global frame transformation is then applied to the system equations in incremental form to avoid the use of Lagrange multipliers for expressing node‐to‐node connections. Examples are presented to assess the methodology proposed and its numerical implementation.