bluuebunny/crossref_metadata_2025 huggingface dataset:
Stretchable and colorless freestanding microwire arrays for transparent solar cells with flexibility
Authors: Kang Sung Bum , Kim Ji-Hwan , Jeong Myeong Hoon , Sanger Amit , Kim Chan Ul , Kim Chil-Min , Choi Kyoung Jin
Published: December 2019

Transparent solar cells (TSCs) are emerging devices that combine the advantages of visible transparency and light-to-electricity conversion. Currently, existing TSCs are based predominantly on organics, dyes, and perovskites; however, the rigidity and color-tinted transparent nature of those devices strongly limit the utility of the resulting TSCs for real-world applications. Here, we demonstrate a flexible, color-neutral, and high-efficiency TSC based on a freestanding form of n-silicon microwires (SiMWs). Flat-tip SiMWs with controllable spacing are fabricated via deep-reactive ion etching and embedded in a freestanding transparent polymer matrix. The light transmittance can be tuned from ~10 to 55% by adjusting the spacing between the microwires. For TSCs, a heterojunction is formed with a p-type polymer in the top portion of the n-type flat-tip SiMWs. Ohmic contact with an indium-doped ZnO film occurs at the bottom, and the side surface has an Al2O3 passivation layer. Furthermore, slanted-tip SiMWs are developed by a novel solvent-assisted wet etching method to manipulate light absorption. Finite-difference time-domain simulation revealed that the reflected light from slanted-tip SiMWs helps light-matter interactions in adjacent microwires. The TSC based on the slanted-tip SiMWs demonstrates 8% efficiency at a visible transparency of 10% with flexibility. This efficiency is the highest among Si-based TSCs and comparable with that of state-of-the-art neutral-color TSCs based on organic–inorganic hybrid perovskite and organics. Moreover, unlike others, the stretchable and transparent platform in this study is promising for future TSCs.
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

Children’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

As 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

Pursuing 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

Senescence 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

Constructing 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

Dodecagonal 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

Interactions 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

A 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

Recent 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

Japanese 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

Cancer 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

Reported 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

Dance 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

The 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.
Effect of ALDH2 on Sleep Disturbances in Patients with Parkinson’s Disease
Authors: Lin Chia-Yen , Yu Rwei-Ling , Wu Ruey-Meei , Tan Chun-Hsiang
Published: December 2019

Monoamine neurotransmitters play essential roles in the regulation of arousal and sleep. Impaired metabolism of monoamine neurotransmitters could result in the accumulation of neurotoxic aldehyde metabolites and, hence, neuronal degeneration. Aldehyde dehydrogenases play an important role in the metabolism of the neurotoxic aldehyde metabolites, including the aldehyde metabolites of dopamine, serotonin, and noradrenaline. Deficient aldehyde dehydrogenase 2 (ALDH2) has been suggested to result in the accumulation of these biogenic aldehydes. An ALDH2 single nucleotide polymorphism (SNP), rs671 (A), results in significantly reduced ALDH2 enzyme activity. A total of 83 Parkinson’s disease (PD) patients were recruited in this study. In addition to the genotypes of rs671, the patients were assessed with the PD sleep scale-2nd version (PDSS-2) and the Epworth sleepiness scale (ESS) for symptoms of daytime and nocturnal sleep disturbances. The patients carrying rs671 (A) had more frequent dozing while lying down to rest in the afternoon (ESS item5) (F = 7.308, p = 0.008) than the rs671 (GG) patients. The patients with rs671 (A) reported a trend toward more frequent difficulty staying asleep than the patients with rs671 (GG). (F = 3.278, p = 0.074). The results indicate that patients carrying allele rs671 (A) are more likely to experience impairment in the regulation of arousal and sleep. The results also support the hypothesis that the accumulation of neurotoxic monoamine neurotransmitter aldehyde metabolites secondary to reduced ALDH2 enzyme activity may cause more severe monoaminergic neuronal loss and, hence, more severe symptoms in the regulation of wakefulness and sleep.
Shape-dependent toxicity and mineralization of hydroxyapatite nanoparticles in A7R5 aortic smooth muscle cells
Authors: Huang Ling-Hong , Sun Xin-Yuan , Ouyang Jian-Ming
Published: December 2019

Vascular smooth muscle cell damage is a key step in inducing vascular calcification that yields hydroxyapatite (HAP) as a major product. The effect of the shape of HAP on the damage to vascular smooth muscle cells has yet to be investigated. In this study, we compared the differences in toxicity of four various morphological nano-HAP crystals, namely, H-Rod, H-Needle, H-Sphere, and H-Plate, in rat aortic smooth muscle cells (A7R5). The sizes of these crystals were 39 nm × 115 nm, 41 nm ×189 nm, 56 nm × 56 nm, and 91 nm × 192 nm, respectively. Results showed that all HAPs decreased cell viability, disorganized cell morphology, disrupted cell membranes, increased intracellular reactive oxygen species concentration, decreased mitochondrial membrane potential, decreased lysosome integrity, increased alkaline phosphatase activity, and increased intracellular calcium concentration, resulting in cell necrosis. The cytotoxicity of the four kinds of HAP was ranked as follows: H-Plate > H-Sphere > H-Needle > H-Rod. The cytotoxicity of each crystal was positively correlated with the following factors: large specific surface area, high electrical conductivity and low surface charge. HAP accelerated calcium deposits on the A7R5 cell surface and induced the expression of osteogenic proteins, such as BMP-2, Runx2, OCN, and ALP. The crystals with high cytotoxicity caused more calcium deposits on the cell surface, higher expression levels of osteogenic protein, and stronger osteogenic transformation abilities. These findings elucidated the relationship between crystal shape and cytotoxicity and provided theoretical references for decreasing the risks of vascular calcification.
Integrated species–phenon trees: visualizing infraspecific diversity within lineages
Authors: Zehady Abdullah Khan , Fordham Barry G. , Ogg James G.
Published: December 2019

The unprecedented detail with which contemporary molecular phylogenetics are visualizing infraspecific relationships within living species and species complexes cannot as yet be reliably extended into deep time. Yet paleontological systematics has routinely dealt in (mainly) morphotaxa envisaged in various ways to have been components of past species lineages. Bridging these perspectives can only enrich both. We present a visualization tool that digitally depicts infraspecific diversity within species through deep time. Our integrated species–phenon tree merges ancestor–descendant trees for fossil morphotaxa (phena) into reconstructed phylogenies of lineages (species) by expanding the latter into “species boxes” and placing the phenon trees inside. A key programming strategy to overcome the lack of a simple overall parent–child hierarchy in the integrated tree has been the progressive population of a species–phenon relationship map which then provides the graphical footprint for the overarching species boxes. Our initial case has been limited to planktonic foraminfera via Aze & others’ important macroevolutionary dataset. The tool could potentially be appropriated for other organisms, to detail other kinds of infraspecific granularity within lineages, or more generally to visualize two nested but loosely coupled trees.
Exploring inflammatory signatures in arthritic joint biopsies with Spatial Transcriptomics
Authors: Carlberg Konstantin , Korotkova Marina , Larsson Ludvig , Catrina Anca I. , Ståhl Patrik L. , Malmström Vivianne
Published: December 2019

Lately it has become possible to analyze transcriptomic profiles in tissue sections with retained cellular context. We aimed to explore synovial biopsies from rheumatoid arthritis (RA) and spondyloarthritis (SpA) patients, using Spatial Transcriptomics (ST) as a proof of principle approach for unbiased mRNA studies at the site of inflammation in these chronic inflammatory diseases. Synovial tissue biopsies from affected joints were studied with ST. The transcriptome data was subjected to differential gene expression analysis (DEA), pathway analysis, immune cell type identification using Xcell analysis and validation with immunohistochemistry (IHC). The ST technology allows selective analyses on areas of interest, thus we analyzed morphologically distinct areas of mononuclear cell infiltrates. The top differentially expressed genes revealed an adaptive immune response profile and T-B cell interactions in RA, while in SpA, the profiles implicate functions associated with tissue repair. With spatially resolved gene expression data, overlaid on high-resolution histological images, we digitally portrayed pre-selected cell types in silico. The RA displayed an overrepresentation of central memory T cells, while in SpA effector memory T cells were most prominent. Consequently, ST allows for deeper understanding of cellular mechanisms and diversity in tissues from chronic inflammatory diseases.
Using mechanistic models for the clinical interpretation of complex genomic variation
Authors: Peña-Chilet María , Esteban-Medina Marina , Falco Matias M. , Rian Kinza , Hidalgo Marta R. , Loucera Carlos , Dopazo Joaquín
Published: December 2019

The sustained generation of genomic data in the last decade has increased the knowledge on the causal mutations of a large number of diseases, especially for highly penetrant Mendelian diseases, typically caused by a unique or a few genes. However, the discovery of causal genes in complex diseases has been far less successful. Many complex diseases are actually a consequence of the failure of complex biological modules, composed by interrelated proteins, which can happen in many different ways, which conferring a multigenic nature to the condition that can hardly be attributed to one or a few genes. We present a mechanistic model, Hipathia, implemented in a web server that allows estimating the effect that mutations, or changes in the expression of genes, have over the whole system of human signaling and the corresponding functional consequences. We show several use cases where we demonstrate how different the ultimate impact of mutations with similar loss-of-function potential can be and how the potential pathological role of a damaged gene can be inferred within the context of a signaling network. The use of systems biology-based approaches, such as mechanistic models, allows estimating the potential impact of loss-of-function mutations occurring in proteins that are part of complex biological interaction networks, such as signaling pathways. This holistic approach provides an elegant alternative to gene-centric approaches that can open new avenues in the interpretation of the genomic variability in complex diseases.
Hierarchical habitat-use by an endangered steppe bird in fragmented landscapes is associated with large connected patches and high food availability
Authors: Gómez-Catasús Julia , Garza Vicente , Morales Manuel B. , Traba Juan
Published: December 2019

Multidimensional approaches must be employed when addressing habitat use patterns. In this study, we aim to elucidate the hierarchical nature of space use by species inhabiting fragmented landscapes, using the threatened Dupont’s lark (Chersophilus duponti). The intensity of space use by Dupont’s lark was estimated using the Kernel Density Function on territory locations in 2015. We measured descriptors of habitat quality at metapopulation (connectivity and patch size), landscape (land-use types and anthropogenic disturbance) and microhabitat-scale (plant structure and composition, herbivore abundance and food availability) at 37 sampling stations. We fitted a Partial Least Squares Regression (PLSR) which yielded two components, accounting for 81% of total variance. Metapopulation-scale factors had the greatest explanatory power (32%), followed by microhabitat (17%) landscape (10%) and spatial predictors (3.6%). Connectivity and patch size were key factors explaining habitat use, and wind farms had a negative effect. At microhabitat-scale, space use was positively associated withColeoptera, Orthoptera, AraneaeandDipterabiomass, but negatively withFormicidaeandBlattodeabiomass, the cover ofStipa spp, Koeleria vallesianaand moss. This research highlights the hierarchical nature of habitat use in fragmented landscapes. Therefore, conservation measures should ensure connectivity, guarantee a minimum patch size, and improve habitat quality within patches.
Tunable three-way topological energy-splitter
Authors: Makwana Mehul P. , Chaplain Gregory
Published: December 2019

Strategically combining four structured domains creates the first ever three-way topological energy-splitter; remarkably, this is only possible using a square, or rectangular, lattice, and not the graphene-like structures more commonly used in valleytronics. To achieve this effect, the two mirror symmetries, present within all fully-symmetric square structures, are broken; this leads to two nondistinct interfaces upon which valley-Hall states reside. These interfaces are related to each other via the time-reversal operator and it is this subtlety that allows us to ignite the third outgoing lead. The geometrical construction of our structured medium allows for the three-way splitter to be adiabatically converted into a wave steerer around sharp bends. Due to the tunability of the energies directionality by geometry, our results have far-reaching implications for applications such as beam-splitters, switches and filters across wave physics.
Safety and efficacy of risedronate for patients with esophageal varices and liver cirrhosis: a non-randomized clinical trial
Authors: Lima Talles Bazeia , Santos Lívia Alves Amaral , Nunes Hélio Rubens de Carvalho , Silva Giovanni Faria , Caramori Carlos Antonio , Qi Xingshun , Romeiro Fernando Gomes
Published: December 2019

Despite the high prevalence of osteoporosis in liver cirrhosis, the indication of bisphosphonates for patients with esophageal varices has been avoided due to risk of digestive mucosal damage. Therefore, this study aimed to evaluate the safety profile of risedronate treatment for patients with osteoporosis, liver cirrhosis and esophageal varices with low risk of bleeding. A total of 120 patients were allocated into two groups according to their bone mineral density measured by dual-energy X-ray absorptiometry. In the intervention group, 57 subjects with osteoporosis received oral risedronate at 35 mg weekly plus daily calcium and vitamin D supplementation. In the control group, 63 subjects with osteopenia received only calcium and vitamin D. The groups received the treatment for one year and underwent surveillance endoscopies at six and 12 months, as well as a control dual-energy X-ray absorptiometry after a 12-month follow-up. The study received Institutional Review Board approval. The groups had not only comparable Model for End-stage Liver Disease score and esophageal varices degree, but also similar incidence of digestive adverse effects. A significant improvement was achieved in the intervention group in the lumbar spine T score (p < 0.001). The results suggest that risedronate may be safely used in liver cirrhosis and esophageal varices with low bleeding risk under endoscopic surveillance, thus allowing bone mass recovery.
Improving sentence reading performance in Chinese children with developmental dyslexia by training based on visual attention span
Authors: Zhao Jing , Liu Hanlong , Li Jiaxiao , Sun Haixia , Liu Zhanhong , Gao Jing , Liu Yuan , Huang Chen
Published: December 2019

Deficits in the visual attention span (VAS) are thought to hamper reading performance in dyslexic individuals. However, the causal relationship between VAS deficits and reading disability remains unclear. The present study attempts to address this issue by using a VAS-based intervention to explore the possible influence of VAS on reading processes in Chinese children with dyslexia. Given the influence of the heterogeneity of dyslexia on intervention effects, VAS-impaired dyslexic and VAS-intact dyslexic individuals were separately trained. Therefore, there were five groups of participants in this study, including 10 trained dyslexic individuals with VAS deficits and 10 untrained dyslexic individuals with VAS dysfunction as the baseline reference, 10 trained and 10 untrained dyslexic individuals with an intact VAS, and fourteen age-matched normal readers for reference of normal level. All participants completed reading measures and a visual 1-back task, reflecting VAS capacity with non-verbal stimuli and non-verbal responses, before and after VAS-based training. VAS-based training tasks included a length estimation task regarding the bottom-up attention, visual search and digit cancelling tasks targeting top-down attentional modulation, and visual tracking tasks to train eye-movement control. The results showed that visual training only helped improve VAS skills in VAS-impaired dyslexic individuals receiving training. Meanwhile, their silent sentence reading accuracy improved after training, and there was a significant relationship between training improvements in VAS function and reading performance. The current findings suggest that VAS-based training has a far-transfer effect on linguistic level (i.e., fluent reading). These findings suggest the possibility that VAS-related training may help children with dyslexia improve their reading skills.
Author Correction: Spatial distribution of decadal ice-thickness change and glacier stored water loss in the Upper Ganga basin, India during 2000–2014
Authors: Bandyopadhyay Debmita , Singh Gulab , Kulkarni Anil V.
Published: December 2019

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Non-contact physiological monitoring of preterm infants in the Neonatal Intensive Care Unit
Authors: Villarroel Mauricio , Chaichulee Sitthichok , Jorge João , Davis Sara , Green Gabrielle , Arteta Carlos , Zisserman Andrew , McCormick Kenny , Watkinson Peter , Tarassenko Lionel
Published: December 2019

The implementation of video-based non-contact technologies to monitor the vital signs of preterm infants in the hospital presents several challenges, such as the detection of the presence or the absence of a patient in the video frame, robustness to changes in lighting conditions, automated identification of suitable time periods and regions of interest from which vital signs can be estimated. We carried out a clinical study to evaluate the accuracy and the proportion of time that heart rate and respiratory rate can be estimated from preterm infants using only a video camera in a clinical environment, without interfering with regular patient care. A total of 426.6 h of video and reference vital signs were recorded for 90 sessions from 30 preterm infants in the Neonatal Intensive Care Unit (NICU) of the John Radcliffe Hospital in Oxford. Each preterm infant was recorded under regular ambient light during daytime for up to four consecutive days. We developed multi-task deep learning algorithms to automatically segment skin areas and to estimate vital signs only when the infant was present in the field of view of the video camera and no clinical interventions were undertaken. We propose signal quality assessment algorithms for both heart rate and respiratory rate to discriminate between clinically acceptable and noisy signals. The mean absolute error between the reference and camera-derived heart rates was 2.3 beats/min for over 76% of the time for which the reference and camera data were valid. The mean absolute error between the reference and camera-derived respiratory rate was 3.5 breaths/min for over 82% of the time. Accurate estimates of heart rate and respiratory rate could be derived for at least 90% of the time, if gaps of up to 30 seconds with no estimates were allowed.
Tunable super- and subradiant boundary states in one-dimensional atomic arrays
Authors: Zhang Anwei , Wang Luojia , Chen Xianfeng , Yakovlev Vladislav V. , Yuan Luqi
Published: December 2019

Efficient manipulation of quantum states is a key step towards applications in quantum information, quantum metrology, and nonlinear optics. Recently, atomic arrays have been shown to be a promising system for exploring topological quantum optics and robust control of quantum states, where the inherent nonlinearity is included through long-range hoppings. Here we show that a one-dimensional atomic array in a periodic magnetic field exhibits characteristic properties associated with an effective two-dimensional Hofstadter-butterfly-like model. Our work points out super- and sub-radiant topological edge states localized at the boundaries of the atomic array despite featuring long-range interactions, and opens an avenue of exploring an interacting quantum optical platform with synthetic dimensions.
Effect of semolina pudding prepared fromstarch branching enzyme IIaandbmutant wheat on glycaemic responsein vitroandin vivo: a randomised controlled pilot study
Authors: Corrado Marina , Cherta-Murillo Anna , Chambers Edward S. , Wood Abigail J. , Plummer Amy , Lovegrove Alison , Edwards Cathrina H. , Frost Gary S. , Hazard Brittany A.
Published: December 2019

The starch characteristics of raw semolina determinesbeIIa/b-AB pudding digestibilityin vitroand glycaemic indexin vivo.
Calcium relieves fluoride-induced bone damage through the PI3K/AKT pathway
Authors: Wang Jinming , Xu Huimiao , Cheng Xiaofang , Yang Jiarong , Yan Zipeng , Ma Haili , Zhao Yangfei , Ommati Mohammad Mehdi , Manthari Ram Kumar , Wang Jundong
Published: December 2019

Bone is the main target of fluorosis, and it has been perfectly elaborated that a moderate dosage of calcium (Ca) can alleviate bone fluorosis.
Selective chemical adsorption of Cd(ii) on silica covalently decorated with a β-ketoenol-thiophene-furan receptor
Authors: Tighadouini Said , Radi Smaail , Garcia Yann
Published: December 2019

Nowadays, porous hybrid materials are considered as potential reservoirs of metallic species in environmental clean-up technologies.
Preparation of a Ti0.7W0.3O2/TiO2 nanocomposite interfacial photocatalyst and its photocatalytic degradation of phenol pollutants in wastewater
Authors: Dong Zemin , Zhou Rendan , Xiong Leyan , Li Han , Liu Qiang , Zheng Longzhen , Guo Zanru , Deng Zhaoxiang
Published: December 2019

The Ti0.7W0.3O2/TiO2 nanocomposite interfacial photocatalyst was designed and prepared for the photocatalytic degradation of phenol pollutants in wastewater.
Orbital hybridization-induced band offset phenomena in NixCd1−xO thin films
Authors: Das Arkaprava , Singh Deobrat , Saini C. P. , Ahuja Rajeev , Kaur Anumeet , Aliukov Sergei
Published: December 2019

The band gap enhancement with a reduction in orbital hybridization has been deeply investigated for Ni-doped CdO thin films.
Nanoparticle-mediated chiral light chaos based on non-Hermitian mode coupling
Authors: Liu Zeng-Xing , You Cai , Wang Bao , Dong Huafeng , Xiong Hao , Wu Ying
Published: December 2019

Chiral light chaos in a whispering-gallery-mode microresonator based on nanoparticle-induced non-Hermitian mode coupling.
Self-healing conductive hydrogels: preparation, properties and applications
Authors: Deng Zexing , Wang Hong , Ma Peter X. , Guo Baolin
Published: December 2019

The self-healing mechanism and applications of conductive self-healing hydrogels are summarized and their future development direction is presented.
Switching of regioselectivity in base-mediated diastereoselective annulation of 2,3-epoxy tosylates and their N-tosylaziridine analogs with 2-mercaptobenzimidazole
Authors: Das Arup Jyoti , Borgohain Hemi , Sarma Bipul , Das Sajal Kumar
Published: December 2019

Benzimidazole-based tricyclic compounds have been synthesized via base-mediated diastereoselective cyclization of 2,3-epoxy tosylates and their N-tosylaziridine analogs with 2-mercaptobenzimidazole.
Highly selective staining and quantification of intracellular lipid droplets with a compact push–pull fluorophore based on benzothiadiazole
Authors: Suarez S. Israel , Warner Caroline C. , Brown-Harding Heather , Thooft Andrea M. , VanVeller Brett , Lukesh John C.
Published: December 2019

A robust lipophilic dye, based on the structures of the benzothiadiazole heterocycle, was shown to be a potent fluorescent stain for the selective imaging of lipid droplets (LDs) within both live and fixed human cells.
Stable and sensitive amino-functionalized graphene/polyaniline nanofiber composites for room-temperature carbon dioxide sensing
Authors: Abdali Hanan , Heli Bentolhoda , Ajji Abdellah
Published: December 2019

This article describes the preparation and characterization of amino-functionalized graphene (AmG)/polyaniline (PANI)/poly(methyl methacrylate) (PMMA) nanofiber mats along with the efficiency of these nanofiber composites as a new material for sensing carbon dioxide (CO2) gas.
Evaluation of disinfection byproduct formation from extra- and intra-cellular algal organic matters during chlorination after Fe(vi) oxidation
Authors: Dong Feilong , Lin Qiufeng , Li Cong , Zhang Tuqiao
Published: December 2019

Blue-green algae commonly bloom in fresh water in summer, producing extra- and intra-cellular algal organic matters, which are important precursors for disinfection byproduct (DBP) formation.
Silica from diatom frustules as anode material for Li-ion batteries
Authors: Norberg Andreas Nicolai , Wagner Nils Peter , Kaland Henning , Vullum-Bruer Fride , Svensson Ann Mari
Published: December 2019

Silica derived from algae was used as anode material in Li-ion batteries, giving a capacity of more than 700 mA h g−1.
Electronic and optical properties of Janus ZrSSe by density functional theory
Authors: Vu Tuan V. , Tong Hien D. , Tran Duy Phu , Binh Nguyen T. T. , Nguyen Chuong V. , Phuc Huynh V. , Do Hoat M. , Hieu Nguyen N.
Published: December 2019

In the present work, we investigate systematically the electronic and optical properties of Janus ZrSSe using first-principles calculations.
Inhibiting effect of CO2 on the oxidative combustion thermodynamics of coal
Authors: Ren Li-Feng , Li Qing-Wei , Deng Jun , Yang Xiao , Ma Li , Wang Wei-Feng
Published: December 2019

The effect of carbon dioxide and oxygen concentration on thermal behavior of coal oxidation and combustion of coal were investigated using an STA449F3 thermal analysis experiment.