bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nucleolar release of rDNA repeats for repair involves SUMO-mediated untethering by the Cdc48/p97 segregase
Authors: Capella Matías , Mandemaker Imke K. , Martín Caballero Lucía , den Brave Fabian , Pfander Boris , Ladurner Andreas G. , Jentsch Stefan , Braun Sigurd 
Published: August 2021

AbstractRibosomal RNA genes (rDNA) are highly unstable and susceptible to rearrangement due to their repetitive nature and active transcriptional status. Sequestration of rDNA in the nucleolus suppresses uncontrolled recombination. However, broken repeats must be first released to the nucleoplasm to allow repair by homologous recombination. Nucleolar release of broken rDNA repeats is conserved from yeast to humans, but the underlying molecular mechanisms are currently unknown. Here we show that DNA damage induces phosphorylation of the CLIP-cohibin complex, releasing membrane-tethered rDNA from the nucleolus in Saccharomyces cerevisiae. Downstream of phosphorylation, SUMOylation of CLIP-cohibin is recognized by Ufd1 via its SUMO-interacting motif, which targets the complex for disassembly through the Cdc48/p97 chaperone. Consistent with a conserved mechanism, UFD1L depletion in human cells impairs rDNA release. The dynamic and regulated assembly and disassembly of the rDNA-tethering complex is therefore a key determinant of nucleolar rDNA release and genome integrity.
Macroscopic weavable fibers of carbon nanotubes with giant thermoelectric power factor
Authors: Komatsu Natsumi , Ichinose Yota , Dewey Oliver S. , Taylor Lauren W. , Trafford Mitchell A. , Yomogida Yohei , Wehmeyer Geoff , Pasquali Matteo , Yanagi Kazuhiro , Kono Junichiro 
Published: August 2021

AbstractLow-dimensional materials have recently attracted much interest as thermoelectric materials because of their charge carrier confinement leading to thermoelectric performance enhancement. Carbon nanotubes are promising candidates because of their one-dimensionality in addition to their unique advantages such as flexibility and light weight. However, preserving the large power factor of individual carbon nanotubes in macroscopic assemblies has been challenging, primarily due to poor sample morphology and a lack of proper Fermi energy tuning. Here, we report an ultrahigh value of power factor (14 ± 5 mW m−1 K−2) for macroscopic weavable fibers of aligned carbon nanotubes with ultrahigh electrical and thermal conductivity. The observed giant power factor originates from the ultrahigh electrical conductivity achieved through excellent sample morphology, combined with an enhanced Seebeck coefficient through Fermi energy tuning. We fabricate a textile thermoelectric generator based on these carbon nanotube fibers, which demonstrates high thermoelectric performance, weavability, and scalability. The giant power factor we observe make these fibers strong candidates for the emerging field of thermoelectric active cooling, which requires a large thermoelectric power factor and a large thermal conductivity at the same time.
The missing linker between SUN5 and PMFBP1 in sperm head-tail coupling apparatus
Authors: Zhang Ying , Liu Chao , Wu Bingbing , Li Liansheng , Li Wei , Yuan Li 
Published: August 2021

AbstractThe sperm head-to-tail coupling apparatus (HTCA) ensures sperm head-tail integrity while defective HTCA causes acephalic spermatozoa, rendering males infertile. Here, we show that CENTLEIN is indispensable for HTCA integrity and function, and that inactivation of CENTLEIN in mice leads to sperm decapitation and male sterility. We demonstrate that CENTLEIN directly interacts with both SUN5 and PMFBP1, two proteins localized in the HTCA and related with acephalic spermatozoa syndrome. We find that the absence of Centlein sets SUN5 and PMFBP1 apart, the former close to the sperm head and the latter in the decapitated tail. We show that lack of Sun5 results in CENTLEIN and PMFBP1 left in the decapitated tail, while disruption of Pmfbp1 results in SUN5 and CENTLEIN left on the detached sperm head. These results demonstrate that CENTLEIN cooperating with SUN5 and PMFBP1 participates in the HTCA assembly and integration of sperm head to the tail, indicating that impairments of CENTLEIN might be associated with acephalic spermatozoa syndrome in humans.
Tuning the performance of a micrometer-sized Stirling engine through reservoir engineering
Authors: Roy Niloyendu , Leroux Nathan , Sood A. K. , Ganapathy Rajesh 
Published: August 2021

AbstractColloidal heat engines are paradigmatic models to understand the conversion of heat into work in a noisy environment - a domain where biological and synthetic nano/micro machines function. While the operation of these engines across thermal baths is well-understood, how they function across baths with noise statistics that is non-Gaussian and also lacks memory, the simplest departure from the thermal case, remains unclear. Here we quantified the performance of a colloidal Stirling engine operating between an engineered memoryless non-Gaussian bath and a Gaussian one. In the quasistatic limit, the non-Gaussian engine functioned like a thermal one as predicted by theory. On increasing the operating speed, due to the nature of noise statistics, the onset of irreversibility for the non-Gaussian engine preceded its thermal counterpart and thus shifted the operating speed at which power is maximum. The performance of nano/micro machines can be tuned by altering only the nature of reservoir noise statistics.
Episodic construction of the early Andean Cordillera unravelled by zircon petrochronology
Authors: Jara José Joaquín , Barra Fernando , Reich Martin , Leisen Mathieu , Romero Rurik , Morata Diego 
Published: August 2021

AbstractThe subduction of oceanic plates beneath continental lithosphere is responsible for continental growth and recycling of oceanic crust, promoting the formation of Cordilleran arcs. However, the processes that control the evolution of these Cordilleran orogenic belts, particularly during their early stages of formation, have not been fully investigated. Here we use a multi-proxy geochemical approach, based on zircon petrochronology and whole-rock analyses, to assess the early evolution of the Andes, one of the most remarkable continental arcs in the world. Our results show that magmatism in the early Andean Cordillera occurred over a period of ~120 million years with six distinct plutonic episodes between 215 and 94 Ma. Each episode is the result of a complex interplay between mantle, crust, slab and sediment contributions that can be traced using zircon chemistry. Overall, the magmatism evolved in response to changes in the tectonic configuration, from transtensional/extensional conditions (215–145 Ma) to a transtensional regime (138–94 Ma). We conclude that an external (tectonic) forcing model with mantle-derived inputs is responsible for the episodic plutonism in this extensional continental arc. This study highlights the use of zircon petrochronology in assessing the multimillion-year crustal scale evolution of Cordilleran arcs.
Soft robotic constrictor for in vitro modeling of dynamic tissue compression
Authors: Paek Jungwook , Song Joseph W. , Ban Ehsan , Morimitsu Yuma , Osuji Chinedum O. , Shenoy Vivek B. , Huh Dan Dongeun 
Published: August 2021

AbstractHere we present a microengineered soft-robotic in vitro platform developed by integrating a pneumatically regulated novel elastomeric actuator with primary culture of human cells. This system is capable of generating dynamic bending motion akin to the constriction of tubular organs that can exert controlled compressive forces on cultured living cells. Using this platform, we demonstrate cyclic compression of primary human endothelial cells, fibroblasts, and smooth muscle cells to show physiological changes in their morphology due to applied forces. Moreover, we present mechanically actuatable organotypic models to examine the effects of compressive forces on three-dimensional multicellular constructs designed to emulate complex tissues such as solid tumors and vascular networks. Our work provides a preliminary demonstration of how soft-robotics technology can be leveraged for in vitro modeling of complex physiological tissue microenvironment, and may enable the development of new research tools for mechanobiology and related areas.
Patient-specific computational simulation of coronary artery bifurcation stenting
Authors: Zhao Shijia , Wu Wei , Samant Saurabhi , Khan Behram , Kassab Ghassan S. , Watanabe Yusuke , Murasato Yoshinobu , Sharzehee Mohammadali , Makadia Janaki , Zolty Daniel , Panagopoulos Anastasios , Burzotta Francesco , Migliavacca Francesco , Johnson Thomas W. , Lefevre Thierry , Lassen Jens Flensted , Brilakis Emmanouil S. , Bhatt Deepak L. , Dangas George , Chiastra Claudio , Stankovic Goran , Louvard Yves , Chatzizisis Yiannis S. 
Published: August 2021

AbstractPatient-specific and lesion-specific computational simulation of bifurcation stenting is an attractive approach to achieve individualized pre-procedural planning that could improve outcomes. The objectives of this work were to describe and validate a novel platform for fully computational patient-specific coronary bifurcation stenting. Our computational stent simulation platform was trained using n = 4 patient-specific bench bifurcation models (n = 17 simulations), and n = 5 clinical bifurcation cases (training group, n = 23 simulations). The platform was blindly tested in n = 5 clinical bifurcation cases (testing group, n = 29 simulations). A variety of stent platforms and stent techniques with 1- or 2-stents was used. Post-stenting imaging with micro-computed tomography (μCT) for bench group and optical coherence tomography (OCT) for clinical groups were used as reference for the training and testing of computational coronary bifurcation stenting. There was a very high agreement for mean lumen diameter (MLD) between stent simulations and post-stenting μCT in bench cases yielding an overall bias of 0.03 (− 0.28 to 0.34) mm. Similarly, there was a high agreement for MLD between stent simulation and OCT in clinical training group [bias 0.08 (− 0.24 to 0.41) mm], and clinical testing group [bias 0.08 (− 0.29 to 0.46) mm]. Quantitatively and qualitatively stent size and shape in computational stenting was in high agreement with clinical cases, yielding an overall bias of < 0.15 mm. Patient-specific computational stenting of coronary bifurcations is a feasible and accurate approach. Future clinical studies are warranted to investigate the ability of computational stenting simulations to guide decision-making in the cardiac catheterization laboratory and improve clinical outcomes.
Underlying SUSY in a generalized Jaynes–Cummings model
Authors: Maldonado-Villamizar F. H. , González-Gutiérrez C. A. , Villanueva-Vergara L. , Rodríguez-Lara B. M. 
Published: August 2021

AbstractWe present a general qubit-boson interaction Hamiltonian that describes the Jaynes–Cummings model and its extensions as a single Hamiltonian class. Our model includes non-linear processes for both the free qubit and boson field as well as non-linear, multi-boson excitation exchange between them. It shows an underlying algebra with supersymmetric quantum mechanics features allowing an operator based diagonalization that simplifies the calculations of observables. As a practical example, we show the evolution of the population inversion and the boson quadratures for an initial state consisting of the qubit in the ground state interacting with a coherent field for a selection of cases covering the standard Jaynes–Cummings model and some of its extensions including Stark shift, Kerr-like, intensity dependent coupling, multi-boson exchange and algebraic deformations.
Morphological variation of the deciduous second molars in the Baka Pygmies
Authors: Šimková Petra G. , Weber Gerhard W. , Ramirez Rozzi Fernando V. , Slimani Lotfi , Sadoine Jérémy , Fornai Cinzia 
Published: August 2021

AbstractThe Baka Pygmies are known for their short stature resulting from a reduced growth rate during infancy. They are peculiar also for their teeth erupt earlier than in any other African population, and their posterior dentition is larger than in non-Pygmy populations. However, the Baka’s dental morphology, like several other aspects of their biology, is still understudied. Here, we explore the variation of the Baka’s deciduous upper and lower second molars (dm2s) in comparison to a geographically heterogeneous human sample by means of 3D geometric morphometrics and analysis of dental traits. Our results show that the different populations largely overlap based on the shape of their dm2s, especially the lower ones. Their distal region and the height of the dentinal crown differ the most, with the Baka showing the most extreme range of variation. Upper and lower dm2s covary to a great extent (RV = 0.82). The Baka’s and South Americans’ dm2s were confirmed among the largest in our sample. Despite the Baka’s unique growth pattern, long-lasting isolation, and extreme dental variation, it is not possible to distinguish them from other populations based on their dm2s’ morphology only.
Diagnostic and prognostic implications of 2018 guideline for the diagnosis of idiopathic pulmonary fibrosis in clinical practice
Authors: Choe Jooae , Kwon Byoung Soo , Do Kyung-Hyun , Hwang Hee Sang , Song Jin Woo , Chae Eun Jin 
Published: August 2021

AbstractThe purpose of this study was to evaluate the implications of the 2018 updated guideline for the diagnosis of idiopathic pulmonary fibrosis (IPF) in clinical practice compared to 2011 guideline. This study involved 535 patients including 339 IPF and 196 non-IPF, and we retrospectively evaluated CT classifications of usual interstitial pneumonia (UIP) by two guidelines. Interobserver agreement of 2018 criteria showed moderate reliability (κ = 0.53) comparable to 2011 (κ = 0.56) but interobserver agreement for probable UIP was fair (κ = 0.40). CT pattern of indeterminate for UIP was associated with better prognosis compared with the other groups (adjusted hazard ratio [HR] = 0.36, p < 0.001). Compared to possible UIP, probable UIP demonstrated a lower positive predictive value (PPV, 62.9% vs 65.8%). In analysis of patients with CT patterns of non-definite UIP, diagnosing IPF when CT pattern showed probable UIP with lymphocyte count ≤ 15% in BAL fluid, and either male sex or age ≥ 60 years showed a high specificity of 90.6% and a PPV of 80.8% in the validation cohort. The 2018 criteria provide better prognostic stratification than the 2011 in patients with possible UIP. BAL fluid analysis can improve the diagnostic certainty for IPF diagnosis in patients with probable UIP CT pattern.
Autonomous navigation of a magnetic colonoscope using force sensing and a heuristic search algorithm
Authors: Huang Hao-En , Yen Sheng-Yang , Chu Chia-Feng , Suk Fat-Moon , Lien Gi-Shih , Liu Chih-Wen 
Published: August 2021

AbstractThis paper presents an autonomous navigation system for cost-effective magnetic-assisted colonoscopy, employing force-based sensors, an actuator, a proportional–integrator controller and a real-time heuristic searching method. The force sensing system uses load cells installed between the robotic arm and external permanent magnets to derive attractive force data as the basis for real-time surgical safety monitoring and tracking information to navigate the disposable magnetic colonoscope. The average tracking accuracy on magnetic field navigator (MFN) platform in x-axis and y-axis are 1.14 ± 0.59 mm and 1.61 ± 0.45 mm, respectively, presented in mean error ± standard deviation. The average detectable radius of the tracking system is 15 cm. Three simulations of path planning algorithms are presented and the learning real-time A* (LRTA*) algorithm with our proposed directional heuristic evaluation design has the best performance. It takes 75 steps to complete the traveling in unknown synthetic colon map. By integrating the force-based sensing technology and LRTA* path planning algorithm, the average time required to complete autonomous navigation of a highly realistic colonoscopy training model on the MFN platform is 15 min 38 s and the intubation rate is 83.33%. All autonomous navigation experiments are completed without intervention by the operator.
Comparison of gene expression in the red imported fire ant (Solenopsis invicta) under different temperature conditions
Authors: Vatanparast Mohammad , Puckett Robert T. , Choi Deuk-Soo , Park Youngjin 
Published: August 2021

AbstractThe red imported fire ant (RIFA), Solenopsis invicta Buren is native to South America and is known as a global problematic invasive species. This study focused on the molecular response of RIFA by comparing gene expression profiles after exposing ants to low (10 °C) and high (40 °C) temperature stress and comparing them to untreated controls (30 °C). A total of 99,085 unigenes (the clustered non-redundant transcripts that are filtered from the longest assembled contigs) were obtained, of which 19,154 were annotated with gene descriptions, gene ontology terms, and metabolic pathways. 86 gene ontology (GO) functional sub-groups and 23 EggNOG terms resulted. Differentially expressed genes (DEGs) with log2FC ≥ 10 were screened and were compared at different temperatures. We found 203, 48, and 66 specific DEGs co-regulated at 10, 20, and 40 °C. Comparing transcriptome profiles for differential gene expression resulted in various DE genes, including cytochrome P450, NADH dehydrogenase subunit 1, cuticle protein and heat shock protein (HSP), which have previously been reported to be involved in cold and high temperature resistance. GO analysis revealed that antioxidant activity is up-regulated under high temperature stress. We verified the RNA-seq data by qPCR on 20 up- and down-regulated DEGs. These findings provide a basis for future understanding of the adaptation mechanisms of RIFA and the molecular mechanisms underlying the response to low and high temperatures.
The ERAP1 active site cannot productively access the N-terminus of antigenic peptide precursors stably bound onto MHC class I
Authors: Mavridis George , Mpakali Anastasia , Zoidakis Jerome , Makridakis Manousos , Vlahou Antonia , Kaloumenou Eleni , Ziotopoulou Angeliki , Georgiadis Dimitris , Papakyriakou Athanasios , Stratikos Efstratios 
Published: August 2021

AbstractProcessing of N-terminally elongated antigenic peptide precursors by Endoplasmic Reticulum Aminopeptidase 1 (ERAP1) is a key step in antigen presentation and the adaptive immune response. Although ERAP1 can efficiently process long peptides in solution, it has been proposed that it can also process peptides bound onto Major Histocompatibility Complex I molecules (MHCI). In a previous study, we suggested that the occasionally observed “ontο MHCI” trimming by ERAP1 is likely due to fast peptide dissociation followed by solution trimming, rather than direct action of ERAP1 onto the MHCI complex. However, other groups have proposed that ERAP1 can trim peptides covalently bound onto MHCI, which would preclude peptide dissociation. To explore this interaction, we constructed disulfide-linked MHCI-peptide complexes using HLA-B*08 and a 12mer kinetically labile peptide, or a 16mer carrying a phosphinic transition-state analogue N-terminus with high-affinity for ERAP1. Kinetic and biochemical analyses suggested that while both peptides could access the ERAP1 active site when free in solution, they were unable to do so when tethered in the MHCI binding groove. Our results suggest that MHCI binding protects, rather than promotes, antigenic peptide precursor trimming by ERAP1 and thus solution trimming is the more likely model of antigenic peptide processing.
Galerkin finite element analysis of magneto two-phase nanofluid flowing in double wavy enclosure comprehending an adiabatic rotating cylinder
Authors: Al-Kouz Wael , Bendrer Bilal Abdel-Illah , Aissa Abderrahmane , Almuhtady Ahmad , Jamshed Wasim , Nisar Kottakkaran Sooppy , Mourad Abed , Alshehri Nawal A. , Zakarya Mohammed 
Published: August 2021

AbstractIn this work, the finite element method is employed to simulate heat transfer and irreversibilities in a mixed convection two-phase flow through a wavy enclosure filled with water–alumina nanoliquid and contains a rotating solid cylinder in the presence of a uniform magnetic field. Impact of the variations of undulations number (0 ≤ N ≤ 5), Ra (103 ≤ Ra ≤ 106), Ha (0 ≤ Ha ≤ 100), and angular rotational velocity (− 500 ≤ Ω ≤ 500) were presented. Isotherms distribution, streamlines and isentropic lines are displayed. The governing equations are verified by using the Galerkin Finite Element Method (GFEM). The Nusselt numbers are calculated and displayed graphically for several parametric studies. The computational calculations were carried out using Buongiorno's non-homogeneous model. To illustrate the studied problem, a thorough discussion of the findings was conducted. The results show the enhacement of the maximum value of the flow function and the heat transfer process by increasing the value of Rayleigh number. Furthermore the irreversibility is primarily governed by the heat transfer component and the increment of the waviness of the active surfaces or the cylinder rotational velocity or hartmann number will suppress the fluid motion and hinders the heat transfer process.
Tokorhabditis n. gen. (Rhabditida, Rhabditidae), a comparative nematode model for extremophilic living
Authors: Kanzaki Natsumi , Yamashita Tatsuya , Lee James Siho , Shih Pei-Yin , Ragsdale Erik J. , Shinya Ryoji 
Published: August 2021

AbstractLife in extreme environments is typically studied as a physiological problem, although the existence of extremophilic animals suggests that developmental and behavioral traits might also be adaptive in such environments. Here, we describe a new species of nematode, Tokorhabditistufae, n. gen., n. sp., which was discovered from the alkaline, hypersaline, and arsenic-rich locale of Mono Lake, California. The new species, which offers a tractable model for studying animal-specific adaptations to extremophilic life, shows a combination of unusual reproductive and developmental traits. Like the recently described sister group Auanema, the species has a trioecious mating system comprising males, females, and self-fertilizing hermaphrodites. Our description of the new genus thus reveals that the origin of this uncommon reproductive mode is even more ancient than previously assumed, and it presents a new comparator for the study of mating-system transitions. However, unlike Auanema and almost all other known rhabditid nematodes, the new species is obligately live-bearing, with embryos that grow in utero, suggesting maternal provisioning during development. Finally, our isolation of two additional, molecularly distinct strains of the new genus—specifically from non-extreme locales—establishes a comparative system for the study of extremophilic traits in this model.