bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sustained CO2-photoreduction activity and high selectivity over Mn, C-codoped ZnO core-triple shell hollow spheres
Authors: Sayed Mahmoud , Xu Feiyan , Kuang Panyong , Low Jingxiang , Wang Shengyao , Zhang Liuyang , Yu Jiaguo 
Published: August 2021

AbstractSolar conversion of CO2 into energy-rich products is one of the sustainable solutions to lessen the global energy shortage and environmental crisis. Pitifully, it is still challenging to attain reliable and affordable CO2 conversion. Herein, we demonstrate a facile one-pot approach to design core-triple shell Mn, C-codoped ZnO hollow spheres as efficient photocatalysts for CO2 reduction. The Mn ions, with switchable valence states, function as “ionized cocatalyst” to promote the CO2 adsorption and light harvesting of the system. Besides, they can capture photogenerated electrons from the conduction band of ZnO and provide the electrons for CO2 reduction. This process is continuous due to the switchable valence states of Mn ions. Benefiting from such unique features, the prepared photocatalysts demonstrated fairly good CO2 conversion performance. This work is endeavoured to shed light on the role of ionized cocatalyst towards sustainable energy production.
LineageOT is a unified framework for lineage tracing and trajectory inference
Authors: Forrow Aden , Schiebinger Geoffrey 
Published: August 2021

AbstractUnderstanding the genetic and epigenetic programs that control differentiation during development is a fundamental challenge, with broad impacts across biology and medicine. Measurement technologies like single-cell RNA-sequencing and CRISPR-based lineage tracing have opened new windows on these processes, through computational trajectory inference and lineage reconstruction. While these two mathematical problems are deeply related, methods for trajectory inference are not typically designed to leverage information from lineage tracing and vice versa. Here, we present LineageOT, a unified framework for lineage tracing and trajectory inference. Specifically, we leverage mathematical tools from graphical models and optimal transport to reconstruct developmental trajectories from time courses with snapshots of both cell states and lineages. We find that lineage data helps disentangle complex state transitions with increased accuracy using fewer measured time points. Moreover, integrating lineage tracing with trajectory inference in this way could enable accurate reconstruction of developmental pathways that are impossible to recover with state-based methods alone.
Large-scale and high-resolution mass spectrometry-based proteomics profiling defines molecular subtypes of esophageal cancer for therapeutic targeting
Authors: Liu Wei , Xie Lei , He Yao-Hui , Wu Zhi-Yong , Liu Lu-Xin , Bai Xue-Feng , Deng Dan-Xia , Xu Xiu-E , Liao Lian-Di , Lin Wan , Heng Jing-Hua , Xu Xin , Peng Liu , Huang Qing-Feng , Li Cheng-Yu , Zhang Zhi-Da , Wang Wei , Zhang Guo-Rui , Gao Xiang , Wang Shao-Hong , Li Chun-Quan , Xu Li-Yan , Liu Wen , Li En-Min 
Published: August 2021

AbstractEsophageal cancer (EC) is a type of aggressive cancer without clinically relevant molecular subtypes, hindering the development of effective strategies for treatment. To define molecular subtypes of EC, we perform mass spectrometry-based proteomic and phosphoproteomics profiling of EC tumors and adjacent non-tumor tissues, revealing a catalog of proteins and phosphosites that are dysregulated in ECs. The EC cohort is stratified into two molecular subtypes—S1 and S2—based on proteomic analysis, with the S2 subtype characterized by the upregulation of spliceosomal and ribosomal proteins, and being more aggressive. Moreover, we identify a subtype signature composed of ELOA and SCAF4, and construct a subtype diagnostic and prognostic model. Potential drugs are predicted for treating patients of S2 subtype, and three candidate drugs are validated to inhibit EC. Taken together, our proteomic analysis define molecular subtypes of EC, thus providing a potential therapeutic outlook for improving disease outcomes in patients with EC.
Global view on the metabolism of RNA poly(A) tails in yeast Saccharomyces cerevisiae
Authors: Tudek Agnieszka , Krawczyk Paweł S. , Mroczek Seweryn , Tomecki Rafał , Turtola Matti , Matylla-Kulińska Katarzyna , Jensen Torben Heick , Dziembowski Andrzej 
Published: August 2021

AbstractThe polyadenosine tail (poly[A]-tail) is a universal modification of eukaryotic messenger RNAs (mRNAs) and non-coding RNAs (ncRNAs). In budding yeast, Pap1-synthesized mRNA poly(A) tails enhance export and translation, whereas Trf4/5-mediated polyadenylation of ncRNAs facilitates degradation by the exosome. Using direct RNA sequencing, we decipher the extent of poly(A) tail dynamics in yeast defective in all relevant exonucleases, deadenylases, and poly(A) polymerases. Predominantly ncRNA poly(A) tails are 20-60 adenosines long. Poly(A) tails of newly transcribed mRNAs are 50 adenosine long on average, with an upper limit of 200. Exonucleolysis by Trf5-assisted nuclear exosome and cytoplasmic deadenylases trim the tails to 40 adenosines on average. Surprisingly, PAN2/3 and CCR4-NOT deadenylase complexes have a large pool of non-overlapping substrates mainly defined by expression level. Finally, we demonstrate that mRNA poly(A) tail length strongly responds to growth conditions, such as heat and nutrient deprivation.
Exclusive and ultrasensitive detection of formaldehyde at room temperature using a flexible and monolithic chemiresistive sensor
Authors: Jo Yong Kun , Jeong Seong-Yong , Moon Young Kook , Jo Young-Moo , Yoon Ji-Wook , Lee Jong-Heun 
Published: August 2021

AbstractFormaldehyde, a probable carcinogen, is a ubiquitous indoor pollutant, but its highly selective detection has been a long-standing challenge. Herein, a chemiresistive sensor that can detect ppb-level formaldehyde in an exclusive manner at room temperature is designed. The TiO2 sensor exhibits under UV illumination highly selective detection of formaldehyde and ethanol with negligible cross-responses to other indoor pollutants. The coating of a mixed matrix membrane (MMM) composed of zeolitic imidazole framework (ZIF-7) nanoparticles and polymers on TiO2 sensing films removed ethanol interference completely by molecular sieving, enabling an ultrahigh selectivity (response ratio > 50) and response (resistance ratio > 1,100) to 5 ppm formaldehyde at room temperature. Furthermore, a monolithic and flexible sensor is fabricated successfully using a TiO2 film sandwiched between a flexible polyethylene terephthalate substrate and MMM overlayer. Our work provides a strategy to achieve exclusive selectivity and high response to formaldehyde, demonstrating the promising potential of flexible gas sensors for indoor air monitoring.
The role of oxygen-permeable ionomer for polymer electrolyte fuel cells
Authors: Jinnouchi Ryosuke , Kudo Kenji , Kodama Kensaku , Kitano Naoki , Suzuki Takahisa , Minami Saori , Shinozaki Kazuma , Hasegawa Naoki , Shinohara Akihiro 
Published: August 2021

AbstractIn recent years, considerable research and development efforts are devoted to improving the performance of polymer electrolyte fuel cells. However, the power density and catalytic activities of these energy conversion devices are still far from being satisfactory for large-scale operation. Here we report performance enhancement via incorporation, in the cathode catalyst layers, of a ring-structured backbone matrix into ionomers. Electrochemical characterizations of single cells and microelectrodes reveal that high power density is obtained using an ionomer with high oxygen solubility. The high solubility allows oxygen to permeate the ionomer/catalyst interface and react with protons and electrons on the catalyst surfaces. Furthermore, characterizations of single cells and single-crystal surfaces reveal that the oxygen reduction reaction activity is enhanced owing to the mitigation of catalyst poisoning by sulfonate anion groups. Molecular dynamics simulations indicate that both the high permeation and poisoning mitigation are due to the suppression of densely layered folding of polymer backbones near the catalyst surfaces by the incorporated ring-structured matrix. These experimental and theoretical observations demonstrate that ionomer’s tailored molecular design promotes local oxygen transport and catalytic reactions.
Multiregional genetic evolution of metastatic uveal melanoma
Authors: Rodriguez Daniel A. , Yang Jessica , Durante Michael A. , Shoushtari Alexander N. , Moschos Stergios J. , Wrzeszczynski Kazimierz O. , Harbour J. William , Carvajal Richard D. 
Published: August 2021

AbstractUveal melanoma (UM) is the most common primary intraocular malignancy in adults and leads to deadly metastases for which there is no approved treatment. Genetic events driving early tumor development are well-described, but those occurring later during metastatic progression remain poorly understood. We performed multiregional genomic sequencing on 22 tumors collected from two patients with widely metastatic UM who underwent rapid autopsy. We observed multiple seeding events from the primary tumors, metastasis-to-metastasis seeding, polyclonal seeding, and late driver variants in ATM, KRAS, and other genes previously unreported in UM. These findings reveal previously unrecognized temporal and anatomic complexity in the genetic evolution of metastatic uveal melanoma, and they highlight the distinction between early and late phases of UM genetic evolution with implications for novel therapeutic approaches.
Prognostic biomarkers of Parkinson’s disease in the Spanish EPIC cohort: a multiplatform metabolomics approach
Authors: Gonzalez-Riano Carolina , Saiz Jorge , Barbas Coral , Bergareche Alberto , Huerta José Mª , Ardanaz Eva , Konjevod Marcela , Mondragon Elisabet , Erro M. E. , Chirlaque M. Dolores , Abilleira Eunate , Goñi-Irigoyen Fernando , Amiano Pilar 
Published: August 2021

AbstractThe lack of knowledge about the onset and progression of Parkinson’s disease (PD) hampers its early diagnosis and treatment. Metabolomics might shed light on the PD imprint seeking a broader view of the biochemical remodeling induced by this disease in an early and pre-symptomatic stage and unveiling potential biomarkers. To achieve this goal, we took advantage of the great potential of the European Prospective Study on Nutrition and Cancer (EPIC) cohort to apply metabolomics searching for early diagnostic PD markers. This cohort consisted of healthy volunteers that were followed for around 15 years until June 2011 to ascertain incident PD. For this untargeted metabolomics-based study, baseline preclinical plasma samples of 39 randomly selected individuals that developed PD (Pre-PD group) and the corresponding control group were analyzed using a multiplatform approach. Data were statistically analyzed and exposed alterations in 33 metabolites levels, including significantly lower levels of free fatty acids (FFAs) in the preclinical samples from PD subjects. These results were then validated by adopting a targeted HPLC-QqQ-MS approach. After integrating all the metabolites affected, our finding revealed alterations in FFAs metabolism, mitochondrial dysfunction, oxidative stress, and gut–brain axis dysregulation long before the development of PD hallmarks. Although the biological purpose of these events is still unknown, the remodeled metabolic pathways highlighted in this work might be considered worthy prognostic biomarkers of early prodromal PD. The findings revealed by this work are of inestimable value since this is the first study conducted with samples collected many years before the disease development.
Open-access quantitative MRI data of the spinal cord and reproducibility across participants, sites and manufacturers
Authors: Cohen-Adad Julien , Alonso-Ortiz Eva , Abramovic Mihael , Arneitz Carina , Atcheson Nicole , Barlow Laura , Barry Robert L. , Barth Markus , Battiston Marco , Büchel Christian , Budde Matthew , Callot Virginie , Combes Anna J. E. , De Leener Benjamin , Descoteaux Maxime , de Sousa Paulo Loureiro , Dostál Marek , Doyon Julien , Dvorak Adam , Eippert Falk , Epperson Karla R. , Epperson Kevin S. , Freund Patrick , Finsterbusch Jürgen , Foias Alexandru , Fratini Michela , Fukunaga Issei , Gandini Wheeler-Kingshott Claudia A. M. , Germani Giancarlo , Gilbert Guillaume , Giove Federico , Gros Charley , Grussu Francesco , Hagiwara Akifumi , Henry Pierre-Gilles , Horák Tomáš , Hori Masaaki , Joers James , Kamiya Kouhei , Karbasforoushan Haleh , Keřkovský Miloš , Khatibi Ali , Kim Joo-Won , Kinany Nawal , Kitzler Hagen H. , Kolind Shannon , Kong Yazhuo , Kudlička Petr , Kuntke Paul , Kurniawan Nyoman D. , Kusmia Slawomir , Labounek René , Laganà Maria Marcella , Laule Cornelia , Law Christine S. , Lenglet Christophe , Leutritz Tobias , Liu Yaou , Llufriu Sara , Mackey Sean , Martinez-Heras Eloy , Mattera Loan , Nestrasil Igor , O’Grady Kristin P. , Papinutto Nico , Papp Daniel , Pareto Deborah , Parrish Todd B. , Pichiecchio Anna , Prados Ferran , Rovira Àlex , Ruitenberg Marc J. , Samson Rebecca S. , Savini Giovanni , Seif Maryam , Seifert Alan C. , Smith Alex K. , Smith Seth A. , Smith Zachary A. , Solana Elisabeth , Suzuki Y. , Tackley George , Tinnermann Alexandra , Valošek Jan , Van De Ville Dimitri , Yiannakas Marios C. , Weber II Kenneth A. , Weiskopf Nikolaus , Wise Richard G. , Wyss Patrik O. , Xu Junqian 
Published: August 2021

AbstractIn a companion paper by Cohen-Adadet al. we introduce thespine genericquantitative MRI protocol that provides valuable metrics for assessing spinal cord macrostructural and microstructural integrity. This protocol was used to acquire a single subject dataset across 19 centers and a multi-subject dataset across 42 centers (for a total of 260 participants), spanning the three main MRI manufacturers: GE, Philips and Siemens. Both datasets are publicly available via git-annex. Data were analysed using the Spinal Cord Toolbox to produce normative values as well as inter/intra-site and inter/intra-manufacturer statistics. Reproducibility for thespine genericprotocol was high across sites and manufacturers, with an average inter-site coefficient of variation of less than 5% for all the metrics. Full documentation and results can be found athttps://spine-generic.rtfd.io/. The datasets and analysis pipeline will help pave the way towards accessible and reproducible quantitative MRI in the spinal cord.
Synthesis, characterisation and thermo-physical properties of highly stable graphene oxide-based aqueous nanofluids for potential low-temperature direct absorption solar applications
Authors: Cham sa-ard Wisut , Fawcett Derek , Fung Chun Che , Chapman Peter , Rattan Supriya , Poinern Gerrard Eddy Jai 
Published: August 2021

AbstractTwo types of highly stable 0.1% graphene oxide-based aqueous nanofluids were synthesised and investigated. The first nanofluid (GO) was prepared under the influence of ultrasonic irradiation without surfactant. The second nanofluid was treated with tetra ethyl ammonium hydroxide to reduce the graphene oxide to form reduced graphene oxide (RGO) during ultrasonic irradiation. The GO and RGO powders were characterised by various techniques such as field emission scanning electron microscopy, transmission electron microscopy, X-ray diffraction and Raman. Also UV–visible absorption spectroscopy was carried out and band gap energies were determined. Optical band gap energies for indirect transitions ranged from 3.4 to 4.4 eV and for direct transitions they ranged between 2.2 and 3.7 eV. Thermal conductivity measurements of the GO-based aqueous nanofluid revealed an enhancement of 9.5% at 40 °C compared to pure water, while the RGO-based aqueous nanofluid at 40 °C had a value 9.23% lower than pure water. Furthermore, the photothermal response of the RGO-based aqueous nanofluid had a temperature increase of 13.5 °C, (enhancement of 60.2%) compared to pure water, the GO-based aqueous nanofluid only displayed a temperature rise of 10.9 °C, (enhancement of 46.6%) after 20 min exposure to a solar irradiance of 1000 W m−2. Both nanofluid types displayed good long-term stability, with the GO-based aqueous nanofluid having a zeta potential of 30.3 mV and the RGO-based aqueous nanofluid having a value of 47.6 mV after 6 months. The good dispersion stability and photothermal performance makes both nanofluid types very promising working fluids for low-temperature direct absorption solar collectors.
Toll-like receptor-4 null mutation causes fetal loss and fetal growth restriction associated with impaired maternal immune tolerance in mice
Authors: Chan Hon Y. , Moldenhauer Lachlan M. , Groome Holly M. , Schjenken John E. , Robertson Sarah A. 
Published: August 2021

AbstractMaternal immune adaptation to accommodate pregnancy depends on sufficient availability of regulatory T (Treg) cells to enable embryo implantation. Toll-like receptor 4 is implicated as a key upstream driver of a controlled inflammatory response, elicited by signals in male partner seminal fluid, to initiate expansion of the maternal Treg cell pool after mating. Here, we report that mice with null mutation in Tlr4 (Tlr4−/−) exhibit impaired reproductive outcomes after allogeneic mating, with reduced pregnancy rate, elevated mid-gestation fetal loss, and fetal growth restriction, compared to Tlr4+/+ wild-type controls. To investigate the effects of TLR4 deficiency on early events of maternal immune adaptation, TLR4-regulated cytokines and immune regulatory microRNAs were measured in the uterus at 8 h post-mating by qPCR, and Treg cells in uterus-draining lymph nodes were evaluated by flow cytometry on day 3.5 post-coitum. Ptgs2 encoding prostaglandin-endoperoxide synthase 2, cytokines Csf2, Il6, Lif, and Tnf, chemokines Ccl2, Cxcl1, Cxcl2, and Cxcl10, and microRNAs miR-155, miR-146a, and miR-223 were induced by mating in wild-type mice, but not, or to a lesser extent, in Tlr4−/− mice. CD4+ T cells were expanded after mating in Tlr4+/+ but not Tlr4−/− mice, with failure to expand peripheral CD25+FOXP3+ NRP1− or thymic CD25+FOXP3+ NRP1+ Treg cell populations, and fewer Treg cells expressed Ki67 proliferation marker and suppressive function marker CTLA4. We conclude that TLR4 is an essential mediator of the inflammation-like response in the pre-implantation uterus that induces generation of Treg cells to support robust pregnancy tolerance and ensure optimal fetal growth and survival.
Phylogeography, colouration, and cryptic speciation across the Indo-Pacific in the sea urchin genus Echinothrix
Authors: Coppard Simon E. , Jessop Holly , Lessios Harilaos A. 
Published: August 2021

AbstractThe sea urchins Echinothrix calamaris and Echinothrix diadema have sympatric distributions throughout the Indo-Pacific. Diverse colour variation is reported in both species. To reconstruct the phylogeny of the genus and assess gene flow across the Indo-Pacific we sequenced mitochondrial 16S rDNA, ATPase-6, and ATPase-8, and nuclear 28S rDNA and the Calpain-7 intron. Our analyses revealed that E. diadema formed a single trans-Indo-Pacific clade, but E. calamaris contained three discrete clades. One clade was endemic to the Red Sea and the Gulf of Oman. A second clade occurred from Malaysia in the West to Moorea in the East. A third clade of E. calamaris was distributed across the entire Indo-Pacific biogeographic region. A fossil calibrated phylogeny revealed that the ancestor of E. diadema diverged from the ancestor of E. calamaris ~ 16.8 million years ago (Ma), and that the ancestor of the trans-Indo-Pacific clade and Red Sea and Gulf of Oman clade split from the western and central Pacific clade ~ 9.8 Ma. Time since divergence and genetic distances suggested species level differentiation among clades of E. calamaris. Colour variation was extensive in E. calamaris, but not clade or locality specific. There was little colour polymorphism in E. diadema.
Efficacy of sealants and bonding materials during fixed orthodontic treatment to prevent enamel demineralization: a systematic review and meta-analysis
Authors: Kamber R. , Meyer-Lueckel H. , Kloukos D. , Tennert C. , Wierichs R. J. 
Published: August 2021

AbstractTo analyse clinical studies investigating coating agents such as sealants and other bonding materials to prevent the initiation or inhibit the progress of white spot lesions (WSL) during orthodontic treatment with fixed appliances. Electronic databases (Pubmed, CENTRAL, EMBASE) were screened for studies. No language restrictions were applied. Study selection, data extraction and quality assessment were done in duplicate. Primary outcome included assessment of WSL with visual-tactile assessment and/or laser fluorescence measurements. Twenty-four studies with 1117 patients (age: 11–40 years) and 12,809 teeth were included. Overall, 34 different sealants or bonding materials were analysed. Fourteen studies analysed fluoride and 14 studies non-fluoride releasing materials. Meta-analysis for visual tactile assessment revealed that sealants significantly decreased the initiation of WSL compared to untreated control (RR [95%CI] = 0.70 [0.53; 0.93]; very low level of evidence). Materials releasing fluoride did not decrease initiation of WSL compared to those with no fluoride release (RR [95%CI] = 0.84 [0.70; 1.01]; very low level of evidence). For laser fluorescence measurements no meta-analysis could be performed. The use of sealants seems to be effective in preventing the initiation of post-orthodontic WSL. Furthermore, there is no evidence supporting that fluoride-releasing sealants or bonding materials are more effective than those without fluoride release. No gold standard prevention strategy to prevent WSL during treatment with fixed orthodontic appliances has been established yet. However, based on only a limited number of studies the use of sealants seems to be effective in preventing the initiation of post-orthodontic WSL.