bluuebunny/crossref_metadata_2025_split huggingface dataset:
Postnatal skeletal growth is driven by the epiphyseal stem cell niche: potential implications to pediatrics
Authors: Chagin Andrei S. , Newton Phillip T. 
Published: December 2019

AbstractChildren’s longitudinal growth is facilitated by the activity of the growth plates, cartilage discs located near the ends of the long-bones. In order to elongate these bones, growth plates must continuously generate chondrocytes. Two recent studies have demonstrated that there are stem cells and a stem cell niche in the growth plate, which govern the generation of chondrocytes during the postnatal growth period. The niche, which allows stem cells to renew, appears at the same time as the secondary ossification center (SOC) matures into a bone epiphysis. Thus, the mechanism of chondrocyte generation differs substantially between neonatal and postnatal age, i.e., before and after the formation of the mineralized epiphyses. Hence, at the neonatal age bone growth is based on a consumption of chondro-progenitors whereas postnatally it is based on the activity of the stem cell niche. Here we discuss potential implications of these observations in relation to longitudinal growth, including the effects of estrogens, nutrition and growth hormone.
The novel circCLK3/miR-320a/FoxM1 axis promotes cervical cancer progression
Authors: Hong Hanqing , Zhu Hai , Zhao Shujun , Wang Kaili , Zhang Nan , Tian Yun , Li Yan , Wang Yaping , Lv Xiaofeng , Wei Tianxiang , Liu Yan , Fan Suzhen , Liu Yang , Li Yuan , Cai Aojie , Jin Shuo , Qin Qiaohong , Li Hongyu 
Published: December 2019

AbstractAs a new class of non-coding RNA, circular RNAs (circRNAs) play crucial roles in the development and progression of various cancers. However, the detailed functions of circRNAs in cervical cancer have seldom been reported. In this study, circRNA sequence was applied to detect the differentially expressed circRNAs between cervical cancer tissues and adjacent normal tissues. The relationships between circCLK3 level with clinicopathological characteristics and prognosis were analyzed. In vitro CCK-8, cell count, cell colony, cell wound healing, transwell migration and invasion, and in vivo tumorigenesis and lung metastasis models were performed to evaluate the functions of circCLK3. The pull-down, RNA immunoprecipitation (RIP), luciferase reporter and rescue assays were employed to clarify the interaction between circCLK3 and miR-320a and the regulation of miR-320a on FoxM1. We found that the level of circCLK3 was remarkably higher in cervical cancer tissues than in adjacent normal tissues, and closely associated with tumor differentiation, FIGO stage and depth of stromal invasion. Down-regulated circCLK3 evidently inhibited cell growth and metastasis of cervical cancer in vitro and in vivo, while up-regulated circCLK3 significantly promoted cell growth and metastasis in vitro and in vivo. The pull-down, luciferase reporter and RIP assays demonstrated that circCLK3 directly bound to and sponge miR-320a. MiR-320a suppressed the expression of FoxM1 through directly binding to 3′UTR of FoxM1 mRNA. In addition, FoxM1 promoted cell proliferation, migration, and invasion of cervical cancer, while miR-320a suppressed cell proliferation, migration, and invasion through suppressing FoxM1, and circCLK3 enhanced cell proliferation, migration and invasion through sponging miR-320a and promoting FoxM1 expression. In summary, circCLK3 may serve as a novel diagnostic biomarker for disease progression and a promising molecular target for early diagnoses and treatments of cervical cancer.
Amorphization activated ruthenium-tellurium nanorods for efficient water splitting
Authors: Wang Juan , Han Lili , Huang Bolong , Shao Qi , Xin Huolin L. , Huang Xiaoqing 
Published: December 2019

AbstractPursuing active and durable water splitting electrocatalysts is of vital significance for solving the sluggish kinetics of the oxygen evolution reaction (OER) process in energy supply. Herein, theoretical calculations identify that the local distortion-strain effect in amorphous RuTe2 system abnormally sensitizes the Te-pπ coupling capability and enhances the electron-transfer of Ru-sites, in which the excellent inter-orbital p-d transfers determine strong electronic activities for boosting OER performance. Thus, a robust electrocatalyst based on amorphous RuTe2 porous nanorods (PNRs) is successfully fabricated. In the acidic water splitting, a-RuTe2 PNRs exhibit a superior performance, which only require a cell voltage of 1.52 V to reach a current density of 10 mA cm−2. Detailed investigations show that the high density of defects combine with oxygen atoms to form RuOxHy species, which are conducive to the OER. This work offers valuable insights for constructing robust electrocatalysts based on theoretical calculations guided by rational design and amorphous materials.
Involvement of condensin in cellular senescence through gene regulation and compartmental reorganization
Authors: Iwasaki Osamu , Tanizawa Hideki , Kim Kyoung-Dong , Kossenkov Andrew , Nacarelli Timothy , Tashiro Sanki , Majumdar Sonali , Showe Louise C. , Zhang Rugang , Noma Ken-ichi 
Published: December 2019

AbstractSenescence is induced by various stimuli such as oncogene expression and telomere shortening, referred to as oncogene-induced senescence (OIS) and replicative senescence (RS), respectively, and accompanied by global transcriptional alterations and 3D genome reorganization. Here, we demonstrate that the human condensin II complex participates in senescence via gene regulation and reorganization of euchromatic A and heterochromatic B compartments. Both OIS and RS are accompanied by A-to-B and B-to-A compartmental transitions, the latter of which occur more frequently and are undergone by 14% (430 Mb) of the human genome. Mechanistically, condensin is enriched in A compartments and implicated in B-to-A transitions. The full activation of senescence genes (SASP genes and p53 targets) requires condensin; its depletion impairs senescence markers. This study describes that condensin reinforces euchromatic A compartments and promotes B-to-A transitions, both of which are coupled to optimal expression of senescence genes, thereby allowing condensin to contribute to senescent processes.
Optical nanomanipulation on solid substrates via optothermally-gated photon nudging
Authors: Li Jingang , Liu Yaoran , Lin Linhan , Wang Mingsong , Jiang Taizhi , Guo Jianhe , Ding Hongru , Kollipara Pavana Siddhartha , Inoue Yuji , Fan Donglei , Korgel Brian A. , Zheng Yuebing 
Published: December 2019

AbstractConstructing colloidal particles into functional nanostructures, materials, and devices is a promising yet challenging direction. Many optical techniques have been developed to trap, manipulate, assemble, and print colloidal particles from aqueous solutions into desired configurations on solid substrates. However, these techniques operated in liquid environments generally suffer from pattern collapses, Brownian motion, and challenges that come with reconfigurable assembly. Here, we develop an all-optical technique, termed optothermally-gated photon nudging (OPN), for the versatile manipulation and dynamic patterning of a variety of colloidal particles on a solid substrate at nanoscale accuracy. OPN takes advantage of a thin surfactant layer to optothermally modulate the particle-substrate interaction, which enables the manipulation of colloidal particles on solid substrates with optical scattering force. Along with in situ optical spectroscopy, our non-invasive and contactless nanomanipulation technique will find various applications in nanofabrication, nanophotonics, nanoelectronics, and colloidal sciences.
Dodecagonal bilayer graphene quasicrystal and its approximants
Authors: Yu Guodong , Wu Zewen , Zhan Zhen , Katsnelson Mikhail I. , Yuan Shengjun 
Published: December 2019

AbstractDodecagonal bilayer graphene quasicrystal has 12-fold rotational order but lacks translational symmetry which prevents the application of band theory. In this paper, we study the electronic and optical properties of graphene quasicrystal with large-scale tight-binding calculations involving more than ten million atoms. We propose a series of periodic approximants which reproduce accurately the properties of quasicrystal within a finite unit cell. By utilizing the band-unfolding method on the smallest approximant with only 2702 atoms, the effective band structure of graphene quasicrystal is derived. The features, such as the emergence of new Dirac points (especially the mirrored ones), the band gap at $$M$$M point and the Fermi velocity are all in agreement with recent experiments. The properties of quasicrystal states are identified in the Landau level spectrum and optical excitations. Importantly, our results show that the lattice mismatch is the dominant factor determining the accuracy of layered approximants. The proposed approximants can be used directly for other layered materials in honeycomb lattice, and the design principles can be applied for any quasi-periodic incommensurate structures.
Atomistic simulation of carbohydrate-protein complex formation: Hevein-32 domain
Authors: Solanke Charles Oluremi , Trapl Dalibor , Šućur Zoran , Mareška Václav , Tvaroška Igor , Spiwok Vojtěch 
Published: December 2019

AbstractInteractions between proteins and their small molecule ligands are of great importance for the process of drug design. Here we report an unbiased molecular dynamics simulation of systems containing hevein domain (HEV32) with N-acetylglucosamine mono-, di- or trisaccharide. Carbohydrate molecules were placed outside the binding site. Three of six simulations (6 × 2 μs) led to binding of a carbohydrate ligand into the binding mode in agreement with the experimentally determined structure. Unbinding was observed in one simulation (monosaccharide). There were no remarkable intermediates of binding for mono and disaccharide. Trisaccharide binding was initiated by formation of carbohydrate-aromatic CH/π interactions. Our results indicate that binding of ligands followed the model of conformational selection because the conformation of the protein ready for ligand binding was observed before the binding. This study extends the concept of docking by dynamics on carbohydrate-protein interactions.
Preconditioning the Initial State of Feeder-free Human Pluripotent Stem Cells Promotes Self-formation of Three-dimensional Retinal Tissue
Authors: Kuwahara Atsushi , Yamasaki Suguru , Mandai Michiko , Watari Kenji , Matsushita Keizo , Fujiwara Masayo , Hori Yoriko , Hiramine Yasushi , Nukaya Daiki , Iwata Miki , Kishino Akiyoshi , Takahashi Masayo , Sasai Yoshiki , Kimura Toru 
Published: December 2019

AbstractA three-dimensional retinal tissue (3D-retina) is a promising graft source for retinal transplantation therapy. We previously demonstrated that embryonic stem cells (ESCs) can generate 3D-retina in vitro using a self-organizing stem cell culture technique known as SFEBq. Here we show an optimized culture method for 3D-retina generation from feeder-free human pluripotent stem cells (hPSCs). Although feeder-free hPSC-maintenance culture was suitable for cell therapy, feeder-free hPSC-derived aggregates tended to collapse during 3D-differentiation culture. We found that the initial hPSC state was a key factor and that preconditioning of the hPSC state by modulating TGF-beta and Shh signaling improved self-formation of 3D-neuroepithelium. Using the preconditioning method, several feeder-free hPSC lines robustly differentiated into 3D-retina. In addition, changing preconditioning stimuli in undifferentiated hPSCs altered the proportions of neural retina and retinal pigment epithelium, important quality factors for 3D-retina. We demonstrated that the feeder-free hiPSC-derived 3D-retina differentiated into rod and cone photoreceptors in vitro and in vivo. Thus, preconditioning is a useful culture methodology for cell therapy to direct the initial hPSC state toward self-organizing 3D-neuroepithelium.
Retrospective auditory cues can improve detection of near-threshold visual targets
Authors: Rimsky-Robert Daphné , Störmer Viola , Sackur Jérôme , Sergent Claire 
Published: December 2019

AbstractRecent studies have demonstrated that visually cueing attention towards a stimulus location after its disappearance can facilitate visual processing of the target and increase task performance. Here, we tested whether such retro-cueing effects can also occur across different sensory modalities, as cross-modal facilitation has been shown in pre-cueing studies using auditory stimuli prior to the onset of a visual target. In the present study, participants detected low-contrast Gabor patches in a speeded response task. These patches were presented in the left or right visual periphery, preceded or followed by a lateralized and task-irrelevant sound at 4 stimulus-onset asynchronies (SOA; −600 ms, −150 ms, +150 ms, +450 ms). We found that pre-cueing at the −150 ms SOA led to a general increase in detection performance irrespective of the sound’s location relative to the target. On top of this temporal effect, sound-cues also had a spatially specific effect, with further improvement when cue and target originated from the same location. Critically, the temporal effect was absent, but the spatial effect was present in the short-SOA retro-cueing condition (+150 ms). Drift-diffusion analysis of the response time distributions allowed us to better characterize the evidenced effects. Overall, our results show that sounds can facilitate visual processing, both pre- and retro-actively, indicative of a flexible and multisensory attentional system that underlies our conscious visual experience.
TRANSNAP: a web database providing comprehensive information on Japanese pear transcriptome
Authors: Koshimizu Shizuka , Nakamura Yukino , Nishitani Chikako , Kobayashi Masaaki , Ohyanagi Hajime , Yamamoto Toshiya , Yano Kentaro 
Published: December 2019

AbstractJapanese pear (Pyrus pyrifolia) is a major fruit tree in the family Rosaceae and is bred for fruit production. To promote the development of breeding strategies and molecular research for Japanese pear, we sequenced the transcripts of Japanese pear variety ‘Hosui’. To exhaustively collect information of total gene expression, RNA samples from various organs and stages of Japanese pear were sequenced by three technologies, single-molecule real-time (SMRT) sequencing, 454 pyrosequencing, and Sanger sequencing. Using all those reads, we determined comprehensive reference sequences of Japanese pear. Then, their protein sequences were predicted, and biological functional annotations were assigned. Finally, we developed a web database, TRANSNAP (http://plantomics.mind.meiji.ac.jp/nashi), which is the first web resource of Japanese pear omics information. This database provides highly reliable information via a user-friendly web interface: the reference sequences, gene functional annotations, and gene expression profiles from microarray experiments. In addition, based on sequence comparisons among Japanese, Chinese and European pears, similar protein sequences among the pears and species-specific proteins in Japanese pear can be quickly and efficiently identified. TRANSNAP will aid molecular research and breeding in Japanese pear, and its information is available for comparative analysis among other pear species and families.
Elucidating the correlations between cancer initiation times and lifetime cancer risks
Authors: Teimouri Hamid , Kochugaeva Maria P. , Kolomeisky Anatoly B. 
Published: December 2019

AbstractCancer is a genetic disease that results from accumulation of unfavorable mutations. As soon as genetic and epigenetic modifications associated with these mutations become strong enough, the uncontrolled tumor cell growth is initiated, eventually spreading through healthy tissues. Clarifying the dynamics of cancer initiation is thus critically important for understanding the molecular mechanisms of tumorigenesis. Here we present a new theoretical method to evaluate the dynamic processes associated with the cancer initiation. It is based on a discrete-state stochastic description of the formation of tumors as a fixation of cancerous mutations in tissues. Using a first-passage analysis the probabilities for the cancer to appear and the times before it happens, which are viewed as fixation probabilities and fixation times, respectively, are explicitly calculated. It is predicted that the slowest cancer initiation dynamics is observed for neutral mutations, while it is fast for both advantageous and, surprisingly, disadvantageous mutations. The method is applied for estimating the cancer initiation times from experimentally available lifetime cancer risks for different types of cancer. It is found that the higher probability of the cancer to occur does not necessary lead to the faster times of starting the cancer. Our theoretical analysis helps to clarify microscopic aspects of cancer initiation processes.
Diet-induced leukocyte telomere shortening in a baboon model for early stage atherosclerosis
Authors: Karere Genesio M. , Mahaney Michael C. , Newman Deborah E. , Riojas Angelica M. , Christensen Clint , Birnbaum Shifra , VandeBerg John L. , Cox Laura 
Published: December 2019

AbstractReported associations between leukocyte telomere length (LTL) attrition, diet and cardiovascular disease (CVD) are inconsistent. This study explores effects of prolonged exposure to a high cholesterol high fat (HCHF) diet on LTL in a baboon model of atherosclerosis. We measured LTL by qPCR in pedigreed baboons fed a chow (n = 105) or HCHF (n = 106) diet for 2 years, tested for effects of diet on LTL, and association between CVD risk factors and atherosclerotic lesions with LTL. Though not different at baseline, after 2 years median LTL is shorter in HCHF fed baboons (P < 0.0001). Diet predicts sex- and age-adjusted LTL and LTL attrition (P = 0.0009 and 0.0156, respectively). Serum concentrations of CVD biomarkers are associated with LTL at the 2-year endpoint and LTL accounts approximately 6% of the variance in aortic lesions (P = 0.04). Although heritable at baseline (h2 = 0.27, P = 0.027) and after 2 years (h2 = 0.46, P = 0.0038), baseline LTL does not predict lesion extent after 2 years. Atherogenic diet influences LTL, and LTL is a potential biomarker for early atherosclerosis. Prolonged exposure to an atherogenic diet decreases LTL and increases LTL attrition, and shortened LTL is associated with early-stage atherosclerosis in pedigreed baboons.
Coupled whole-body rhythmic entrainment between two chimpanzees
Authors: Lameira Adriano R. , Eerola Tuomas , Ravignani Andrea 
Published: December 2019

AbstractDance is an icon of human expression. Despite astounding diversity around the world’s cultures and dazzling abundance of reminiscent animal systems, the evolution of dance in the human clade remains obscure. Dance requires individuals to interactively synchronize their whole-body tempo to their partner’s, with near-perfect precision. This capacity is motorically-heavy, engaging multiple neural circuitries, but also dependent on an acute socio-emotional bond between partners. Hitherto, these factors helped explain why no dance forms were present amongst nonhuman primates. Critically, evidence for conjoined full-body rhythmic entrainment in great apes that could help reconstruct possible proto-stages of human dance is still lacking. Here, we report an endogenously-effected case of ritualized dance-like behaviour between two captive chimpanzees – synchronized bipedalism. We submitted video recordings to rigorous time-series analysis and circular statistics. We found that individual step tempo was within the genus’ range of “solo” bipedalism. Between-individual analyses, however, revealed that synchronisation between individuals was non-random, predictable, phase concordant, maintained with instantaneous centi-second precision and jointly regulated, with individuals also taking turns as “pace-makers”. No function was apparent besides the behaviour’s putative positive social affiliation. Our analyses show a first case of spontaneous whole-body entrainment between two ape peers, thus providing tentative empirical evidence for phylogenies of human dance. Human proto-dance, we argue, may have been rooted in mechanisms of social cohesion among small groups that might have granted stress-releasing benefits via gait-synchrony and mutual-touch. An external sound/musical beat may have been initially uninvolved. We discuss dance evolution as driven by ecologically-, socially- and/or culturally-imposed “captivity”.
Bronchial epithelium repair by Esculentin-1a-derived antimicrobial peptides: involvement of metalloproteinase-9 and interleukin-8, and evaluation of peptides’ immunogenicity
Authors: Cappiello Floriana , Ranieri Danilo , Carnicelli Veronica , Casciaro Bruno , Chen Han-Tang , Ferrera Loretta , Di Y. Peter , Mangoni Maria Luisa 
Published: December 2019

AbstractThe airway epithelium is seriously damaged upon pulmonary Pseudomonas aeruginosa infection, especially in cystic fibrosis (CF) sufferers. Therefore, the discovery of novel anti-infective agents accelerating healing of infected injured tissues is crucial. The antipseudomonal peptides esculentin-1a(1–21)NH2 and its diastereomer Esc(1–21)-1c (Esc peptides) hold promise in this respect. In fact, they stimulate airway epithelial wound repair, but no mechanistic insights are available. Here we demonstrated that this process occurs through promotion of cell migration by an indirect activation of epidermal growth factor receptor mediated by metalloproteinases. Furthermore, we showed an increased expression of metalloproteinase 9, at both gene and protein levels, in peptide-treated bronchial epithelial cells with a functional or mutated form of CF transmembrane conductance regulator. In addition, the two peptides counteracted the inhibitory effect of Pseudomonas lipopolysaccharide (mimicking an infection condition) on the wound healing activity of the airway epithelium, and they enhanced the production of interleukin-8 from both types of cells. Finally, no immunogenicity was discovered for Esc peptides, suggesting their potential safety for clinical usage. Besides representing a step forward in understanding the molecular mechanism underlying the peptide-induced wound healing activity, these studies have contributed to highlight Esc peptides as valuable therapeutics with multiple functions.