bluuebunny/crossref_metadata_2025_split huggingface dataset:
Landscape and evolutionary dynamics of Helitron transposons in plant genomes as well as construction of online database HelDB
Authors: Li Shu‐Fen , Zhang Xin‐Yu , Yang Long‐Long , Jia Ke‐Li , Li Jia‐Rong , Lan Li‐Na , Zhang Yu‐Lan , Li Ning , Deng Chuan‐Liang , Gao Wu‐Jun 
Published: November 2022

AbstractHelitron transposons play an important role in host genome evolution due to their ability to capture genes and regulatory elements. In this study, we developed a pipeline to identify and annotate Helitrons systematically from 358 plant and 178 animal high‐quality genomes. All these data were organized into HelDB, a database where Helitrons can be explored with a user‐friendly Web interface and related software. Based on these data, further analysis showed that the number or the cumulative length of Helitrons is positively correlated with genome size. Helitrons had experienced two expansion periods in plants, with the first occurring 20–30 Ma and peaking at approximately 24 Ma. The second expansion occurred in the last 4 million years. The expansions might be due to stimulation of paleogeographic environment. Detailed investigation of gene capture by Helitrons in Brassicaceae and Solanaceae plants showed that the captured genes showed diverse functions. Interestingly, metal ion binding function was enriched in these captured genes in most species. This phenomenon might be due to the need for binding of divalent metal ions to the Rep domain required for Helitron transposition. This study improves our knowledge of the landscape and evolution of Helitron transposons in plants and paves a way for further functional studies of this kind of transposable element.
Characterization of clinicopathologic and abdominal ultrasound findings in dogs with glucocorticoid deficient hypoadrenocorticism
Authors: Reagan Krystle L. , McLarty Ehren , Marks Stanley L. , Sebastian Jamie , McGill Jennifer , Gilor Chen 
Published: November 2022

AbstractBackgroundClinical findings of glucocorticoid‐deficient hypoadrenocorticism (GDH) can overlap with other diseases, presenting a diagnostic challenge.ObjectivesDescribe clinicopathologic and ultrasonographic features of dogs with GDH and those suspected of having GDH that had the disease ruled out.AnimalsSix hundred twenty‐three dogs.MethodsRecords from dogs with suspected GDH between 2003 and 2018 were reviewed. Dogs with hyperkalemia or hyponatremia were excluded. Dogs were categorized as controls when the resting serum cortisol or post‐ACTH cortisol concentration were > 2 μg/dL. Clinicopathologic and ultrasonographic features were compared between groups. The optimal cut‐point, area under the receiver operating characteristic curve (AUC), sensitivity, and specificity were calculated for individual features used to detect GDH.ResultsDogs were categorized as GDH (n = 29) or controls (n = 594). Lymphocyte count (>1750 cells/L; sensitivity, 96.6%; 95% confidence interval [CI], 82.8%‐99.8%; specificity, 60.3%; 95% CI, 56.3%‐64.1%; AUC, 0.828; 95% CI, 0.762‐0.894) and albumin/globulin ratio (<1.081; sensitivity, 86.2%; 95% CI, 69.4%‐94.5%; specificity, 78.8%; 95% CI, 75.3%‐81.9%; AUC, 0.886; 95% CI, 0.827‐0.944) had the highest discriminatory power between groups. Left adrenal gland width <0.39 cm was 80% (95% CI, 58.4%‐91.9%) sensitive and 82.4% (95% CI, 74.2‐88.4) specific for GDH. Serum cobalamin concentrations and ultrasonographic abnormalities of the GI tract were not different between groups.Conclusion and Clinical ImportanceNo single variable could be used to confidently rule out GDH and obviate the need for cortisol testing in dogs with a clinical presentation consistent with GDH.
Canine and feline P‐glycoprotein deficiency: What we know and where we need to go
Authors: Mealey Katrina L. , Owens Jane G. , Freeman Elaine 
Published: November 2022

AbstractIn 2001 the molecular genetic basis of so‐called “ivermectin sensitivity” in herding breed dogs was determined to be a P‐glycoprotein deficiency caused by a genetic variant of the MDR1 (ABCB1) gene often called “the MDR1 mutation.” We have learned a great deal about P‐glycoprotein's role in drug disposition since that discovery, namely that P‐glycoprotein transports many more drugs than just macrocyclic lactones that P‐glycoprotein mediated drug transport is present in more places than just the blood brain barrier, that some cats have a genetic variant of MDR1 that results in P‐glycoprotein deficiency, that P‐glycoprotein dysfunction can occur as a result of drug–drug interactions in any dog or cat, and that the concept of P‐glycoprotein “inhibitors” versus P‐glycoprotein substrates is somewhat arbitrary and artificial. This paper will review these discoveries and discuss how they impact drug selection and dosing in dogs and cats with genetically mediated P‐glycoprotein deficiency or P‐glycoprotein dysfunction resulting from drug–drug interactions.
Network analysis with either Illumina or MinION reveals that detecting vertebrate species requires metabarcoding of iDNA from a diverse fly community
Authors: Srivathsan Amrita , Loh Rebecca Ker , Ong Elliott James , Lee Leshon , Ang Yuchen , Kutty Sujatha Narayanan , Meier Rudolf 
Published: November 2022

AbstractDNA obtained from invertebrates (iDNA) can be metabarcoded in order to survey vertebrate communities. However, little attention has been paid to the interaction between the invertebrate and vertebrate species. Here, we tested for specialization by sampling the dung and carrion fly community of a swamp forest remnant along a disturbance gradient (10 sites: 80–310 m from a road). Approximately, 60% of the baited 407 flies yielded 294 vertebrate identifications based on two COI fragments and 16S. A bipartite network analysis found no statistically significant specialization in the interactions between fly and vertebrate species, but uncommon fly species can carry the signal for vertebrate species that are otherwise difficult to detect with iDNA. A spatial analysis revealed that most of the 20 vertebrate species reported in this study could be detected within 150 m of the road (18 spp.) and that the fly community sourced for iDNA was unexpectedly rich (24 species, 3 families). They carried DNA for rare and common species inhabiting different layers of the forest (ground‐dwelling: wild boar, Sunda pangolin, skinks, rats; arboreal: long‐tailed macaque, Raffles' banded langur; flying: pin‐striped tit‐babbler, olive‐winged bulbul). All our results were obtained with a new, greatly simplified iDNA protocol that eliminates DNA extraction by obtaining template directly through dissolving fly faeces and regurgitates with water. Lastly, we show that MinION‐ and Illumina‐based metabarcoding yield similar results. We conclude by urging more studies that use different baits and involve experiments that are capable of revealing the dispersal capabilities of the flies carrying the iDNA.
Parents' Separation: What is the Effect on Parents' and Children's Time Investments?*
Authors: Le Forner Hélène 
Published: November 2022

AbstractThis paper investigates the effect of parental separation on children's allocation of their time and on the time spent with their parents. Based on detailed time‐use diaries from the Panel Study of Income Dynamics – Child Development Supplement, I estimate an individual fixed‐effect model and find that being in a single‐parent family decreases time with a parent accessible by 18% of a standard deviation (3 hours 30 minutes per week). Time spent with both parents together and alone with the non‐custodial parent is greatly affected, but the custodial parent partially compensates for this decrease. The decrease in time with a parent actively engaged in activities is, however, not statistically significant. Younger children continue spending as much time with their parents after separation. Effects on boys and girls differ, but this difference depends on the type of parental time investment we consider. Time spent with a grandparent acts as a recovery channel in single‐mother families. Time with a step‐parent increases but does not lead to an accumulation of parental time.
Phenotypic variability in LAMA3‐associated amelogenesis imperfecta
Authors: Wang Shih‐Kai , Zhang Hong , Wang Yin‐Lin , Seymen Figen , Koruyucu Mine , Simmer James P. , Hu Jan C.‐C. 
Published: November 2022

AbstractObjectiveAmelogenesis imperfecta (AI) is defined as inherited enamel malformations. LAMA3 (laminin alpha‐3) encodes a critical protein component of the basement membrane (laminin‐332). Individuals carrying heterozygous LAMA3 mutations have previously been shown to have localized enamel defects. This study aimed to define clinical phenotypes and to discern the genetic etiology for four AI kindreds.Materials and MethodsWhole‐exome analyses were conducted to search for sequence variants associated with the disorder, and micro‐computed tomography (μCT) to characterize the enamel defects.ResultsThe predominant enamel phenotype was generalized thin enamel with defective pits and grooves. Horizonal bands of hypoplastic enamel with chalky‐white discoloration and enamel hypomineralization were also observed and demonstrated by μCT analyses of affected teeth. Four disease‐causing LAMA3 mutations (NM_198129.4:c.3712dup; c.5891dup; c.7367del; c.9400G > C) were identified. Compound heterozygous MMP20 mutations (NM_004771.4:c.539A > G; c.692C > T) were also found in one proband with more severe enamel defects, suggesting a mutational synergism on disease phenotypes. Further analyses of the AI‐causing mutations suggested that both α3A (short) and α3B (long) isoforms of LAMA3 are essential for enamel formation.ConclusionsHeterozygous LAMA3 mutations can cause generalized enamel defects (AI1A) with variable expressivity. Laminin‐332 is critical not only for appositional growth but also enamel maturation.
Implication of Changes in the Imaging Measurements after Mechanically Aligned Total Knee Arthroplasty
Authors: Cheng Long , Ren Peng , Zheng Qingyuan , Ni Ming , Geng Lei , Wang Yi‐Ming , Zhang Guo‐Qiang 
Published: November 2022

ObjectiveImaging measurements allow assessment of the mechanical alignment before and after total knee arthroplasty (TKA). The changes in radiographic parameters in each period of time within 1 year after TKA has been poorly understood. The purpose of this study was to examine the timing and causes of imaging changes in lower extremity force lines after total knee arthroplasty with mechanical alignment.MethodsA total of 93 mechanically‐aligned TKA were radiographically examined before, 3 days, 3 months, and 1 year after surgery. Radiographic parameters included hip‐knee angle (HKA), lateral distal femoral angle (LDFA), medial proximal tibial angle (MPTA), knee joint line orientation (KJLO), ankle joint line orientation (AJLO), the knee joint line relative to ankle joint line angle (KJLTA) and midpoints of the ankle distance (MAD). Paired t‐test were used to analyze the changes of these imaging parameters, By establishing a simple tibial model, the time points of changes in the imaging parameters after TKA was determined, with an attempt to understand the post‐TKA changes in these imaging parameters.ResultsStatistically significant differences were found between the preoperative data and the data measured 3 days after surgery in HKA, LDFA, MPTA, MAD, KJLTA, AJLO (P < 0.05) while KJLO exhibited no significant difference (P = 0.089). There existed significant differences between the data measured 3 days and the measurements taken 3 months after operation in HKA, MPTA, KJLTA, KJLO, AJLO (P < 0.05), whereas LDFA and MAD showed no significant difference (P > 0.05). Significant differences were revealed between the data measured 3 months and those collected 1 year after surgery in LDFA, MPTA, AJLO, KJLTA (P < 0.05) but HKA, KJLO, AJLO showed no significant differences (P > 0.05). The tibial model was made to look into the changes in postoperative imaging parameters. ΔMAD and postoperative AJLO were calculated to verify the model and hypothesis.ConclusionsPostoperative changes in radiographic parameters and tibial models showed that the lower extremities were in an unnatural state within 1 year after TKA. The changes in the lower extremities force line were the results of the gradual adaptation of the lower extremities to TKA and the lateral swing of the extremities (3°) after surgery. Imaging data 1 year after surgery should be taken into account in the explanation of post‐TKA changes in lower limb force lines.
Correctly responding to reasons while being means‐end incoherent
Authors: Schneider Leonhard 
Published: November 2022

AbstractThis paper argues that Reason Responsiveness (RR) accounts of rationality, proposed for example by Benjamin Kiesewetter and Error Lord, fail to explain structural irrationality (i.e., the irrationality involved in holding incoherent attitudes). Proponents of RR hold that rationality consists in correctly responding to available reasons. Structural irrationality, they argue, is just a “by‐product” of incorrect reason‐responding. Applying this idea to cases of means–end incoherence, this paper shows that RR accounts must rely on a certain transmission principle. Roughly, this amounts to the principle that necessarily, if (1) A has decisive available reason to intend to E and (2) A has decisive available reason to believe that intending to M is necessary for E‐ing, it follows that (3) A has decisive available reason to intend to M. By considering an example, this paper argues that even the most plausible version of this transmission principle does not hold true. It follows that one can correctly respond to one's available reasons while being means–end incoherent.
Special IMM groups
Authors: Groves Daniel , Manning Jason Fox 
Published: November 2022

AbstractItaliano–Martelli–Migliorini recently constructed hyperbolic groups which have non‐hyperbolic subgroups of finite type. Using a closely related construction, Llosa Isenrich–Martelli–Py constructed hyperbolic groups with subgroups of type but not . We observe that these hyperbolic groups can be chosen to be special in the sense of Haglund–Wise.
Spatiotemporal modelling reveals geometric dependence of AMPAR dynamics on dendritic spine morphology
Authors: Bell Miriam K. , Lee Christopher T. , Rangamani Padmini 
Published: November 2022

AbstractThe modification of neural circuits depends on the strengthening and weakening of synaptic connections. Synaptic strength is often correlated to the density of the ionotropic, glutamatergic receptors, AMPARs, (α‐amino‐3‐hydroxy‐5‐methyl‐4‐isoxazolepropionic acid receptors) at the postsynaptic density (PSD). While AMPAR density is known to change based on complex biological signalling cascades, the effect of geometric factors such as dendritic spine shape, size and curvature remain poorly understood. In this work, we developed a deterministic, spatiotemporal model to study the dynamics of AMPARs during long‐term potentiation (LTP). This model includes a minimal set of biochemical events that represent the upstream signalling events, trafficking of AMPARs to and from the PSD, lateral diffusion in the plane of the spine membrane, and the presence of an extrasynaptic AMPAR pool. Using idealized and realistic spine geometries, we show that the dynamics and increase of bound AMPARs at the PSD depends on a combination of endo‐ and exocytosis, membrane diffusion, the availability of free AMPARs and intracellular signalling interactions. We also found non‐monotonic relationships between spine volume and the change in AMPARs at the PSD, suggesting that spines restrict changes in AMPARs to optimize resources and prevent runaway potentiation.
imageKey points
Synaptic plasticity involves dynamic biochemical and physical remodelling of small protrusions called dendritic spines along the dendrites of neurons.
Proper synaptic functionality within these spines requires changes in receptor number at the synapse, which has implications for downstream neural functions, such as learning and memory formation.
In addition to being signalling subcompartments, spines also have unique morphological features that can play a role in regulating receptor dynamics on the synaptic surface.
We have developed a spatiotemporal model that couples biochemical signalling and receptor trafficking modalities in idealized and realistic spine geometries to investigate the role of biochemical and biophysical factors in synaptic plasticity.
Using this model, we highlight the importance of spine size and shape in regulating bound AMPA receptor dynamics that govern synaptic plasticity, and predict how spine shape might act to reset synaptic plasticity as a built‐in resource optimization and regulation tool.
Oral combined contraceptives induce liver mitochondrial reactive oxygen species and whole‐body metabolic adaptations in female mice
Authors: Fuller Kelly N. Z. , McCoin Colin S. , Stierwalt Harrison , Allen Julie , Gandhi Shivam , Perry Christopher G. R. , Jambal Purevsuren , Shankar Kartik , Thyfault John P. 
Published: November 2022

AbstractCompared to age‐matched men, pre‐menopausal women show greater resilience against cardiovascular disease (CVD), hepatic steatosis, diabetes and obesity – findings that are widely attributed to oestrogen. However, meta‐analysis data suggest that current use of oral combined contraceptives (OC) is a risk factor for myocardial infarction, and OC use further compounds with metabolic disease risk factors to increase CVD susceptibility. While mitochondrial function in tissues such as the liver and skeletal muscle is an emerging mechanism by which oestrogen may confer its protection, effects of OC use on mitochondria and metabolism in the context of disease risk remain unexplored. To answer this question, female C57Bl/6J mice were fed a high fat diet and treated with vehicle or OCs for 3, 12 or 20 weeks (n = 6 to 12 per group) at a dose and ratio that mimic the human condition of cycle cessation in the low oestrogen, high progesterone stage. Liver and skeletal muscle mitochondrial function (respiratory capacity, H2O2, coupling) was measured along with clinical outcomes of cardiometabolic disease such as obesity, glucose tolerance, hepatic steatosis and aortic atherosclerosis. The main findings indicate that regardless of treatment duration, OCs robustly increase hepatic mitochondrial H2O2 levels, likely due to diminished antioxidant capacity, but have no impact on muscle mitochondrial H2O2. Furthermore, OC‐treated mice had lower adiposity and hepatic triglyceride content compared to control mice despite reduced wheel running, spontaneous physical activity and total energy expenditure. Together, these studies describe tissue‐specific effects of OC use on mitochondria as well as variable impacts on markers of metabolic disease susceptibility.
imageKey points
Oestrogen loss in women increases risk for cardiometabolic diseases, a link that has been partially attributed to negative impacts on mitochondria and energy metabolism.
To study the effect of oral combined contraceptives (OCs) on hepatic and skeletal muscle mitochondria and whole‐body energy metabolism, we used an animal model of OCs which mimics the human condition of cessation of hormonal cycling in the low oestrogen, high progesterone state.
OC‐treated mice have increased hepatic mitochondrial oxidative stress and decreased physical activity and energy expenditure, despite displaying lower adiposity and liver fat at this time point.
These pre‐clinical data reveal tissue‐specific effects of OCs that likely underlie the clinical findings of increased cardiometabolic disease in women who use OCs compared to non‐users, when matched for obesity.
Uncertainty Quantification of Computational Flutter Estimates of a Compressor Cascade
Authors: Rauseo Marco , Zhao Fanzhou , Vahdati Mehdi , Rendu Quentin 
Published: November 2022

Abstract
Aeroelastic instabilities such as flutter can greatly limit the operating range and safety of modern aircraft engines. Current computational methods have a central role in the evaluation of turbomachinery blades stability, but can be affected by errors if the investigated flow conditions break model assumptions or are particularly sensitive to small changes in flow variables. In this paper, a machine learning based method is proposed to quantify the uncertainty of computational aerodynamic damping predictions. The test case employed for this study is a two dimensional compressor cascade, which resembles most of the relevant aeroelastic features of modern fan and compressor blades. A random forest based model is trained and tested to construct a mapping between input features and aerodynamic damping, both obtained from linearised CFD computations. The input features concern simple, physically relevant quantities that are available early on in design stage. The results show that the machine learnt model can produce predictions, by interpolating within the range of input features, with a coefficient of determination R2 ≈ 0.94. Moreover, the predictions are enhanced with a measure of uncertainty in terms of confidence intervals. The results show that the confidence intervals can accurately portray the sensitivity of aerodynamic damping with respect to the flow variables. Finally, to underline the relevance of such an approach during design, the model is applied to obtain a conservative flutter boundary on a compressor map, providing a safer operating margin.
Simulation of the HiPowAR Gas-Steam Power Generation System Using Ammonia as Fuel
Authors: Cammarata Alberto , Colbertaldo Paolo , Campanari Stefano 
Published: November 2022

Abstract
This work presents a simulation activity on an innovative power generation cycle, developed within the EU Horizon 2020 project HiPowAR, using ammonia as fuel for an oxy-combustion process in a membrane reactor. The key advantages of the system are the low compression requirement, typical of steam cycles, and the large expander inlet temperature, typical of gas turbine cycles. The analysis explores the options of cooled or uncooled expander, either adopting a steam-cooled turbine made of conventional Ni-based alloys or using high temperature-resistant ceramic matrix composite (CMC) materials. The simulations show that, with a reactor outlet temperature of 1350°C, a cooled system could reach up to 48.2% efficiency, with limited additional advantages when further increasing the temperature. At the same temperature level, the uncooled system could instead achieve 52.5% efficiency, allowing also a substantial system simplification. However, since the expanded mixture contains nearly 90%mol steam, the use of CMC materials is made difficult by degradation issues and would require the development of suitable barrier coatings.
A MATLAB Based Set of Functions for Finding Thermodynamic Properties and Solving Gas Turbine and Other Thermodynamics Problems
Authors: Volino Ralph J. 
Published: November 2022

Abstract
A new set of MATLAB based functions have been written for providing fluid property data and solving thermodynamics problems. One function utilizes NIST property tables for pure real fluids (e.g. water, various refrigerants, propane, etc.), and provides desired properties when provided with any two other independent properties. Properties can be obtained for liquids, vapors, and two-phase mixtures. Another function provides properties for a range of pure ideal gases using NASA functions for specific heats. Enthalpies are referenced to include the heat of formation, so the function is useful for solving combustion problems. A third function utilizes the ideal gas function to provide ideal gas properties for dry air, assuming a mixture of 78% N2, 21% O2, and 1% Ar by volume. A fourth function uses the air and real fluid functions to provide properties for moist air. Additional functions are available to generate property plots. All functions can be used with the SI or the U.S. Customary unit systems. The functions are described, and examples are provided in which they are used to solve thermodynamics problems. When used in conjunction with built-in MATLAB commands, the new functions are useful for parametric and optimization studies. The full package, including function codes and data files, requires 2.5 MB of disk space and is available at no cost.