bluuebunny/crossref_metadata_2025_split huggingface dataset:
Addressing the batch effect issue for LC/MS metabolomics data in data preprocessing
Authors: Liu Qin , Walker Douglas , Uppal Karan , Liu Zihe , Ma Chunyu , Tran ViLinh , Li Shuzhao , Jones Dean P. , Yu Tianwei 
Published: August 2020

AbstractWith the growth of metabolomics research, more and more studies are conducted on large numbers of samples. Due to technical limitations of the Liquid Chromatography–Mass Spectrometry (LC/MS) platform, samples often need to be processed in multiple batches. Across different batches, we often observe differences in data characteristics. In this work, we specifically focus on data generated in multiple batches on the same LC/MS machinery. Traditional preprocessing methods treat all samples as a single group. Such practice can result in errors in the alignment of peaks, which cannot be corrected by post hoc application of batch effect correction methods. In this work, we developed a new approach that address the batch effect issue in the preprocessing stage, resulting in better peak detection, alignment and quantification. It can be combined with down-stream batch effect correction methods to further correct for between-batch intensity differences. The method is implemented in the existing workflow of the apLCMS platform. Analyzing data with multiple batches, both generated from standardized quality control (QC) plasma samples and from real biological studies, the new method resulted in feature tables with better consistency, as well as better down-stream analysis results. The method can be a useful addition to the tools available for large studies involving multiple batches. The method is available as part of the apLCMS package. Download link and instructions are athttps://mypage.cuhk.edu.cn/academics/yutianwei/apLCMS/.
Integrated [18F]FDG PET/MRI demonstrates the iron-related bone-marrow physiology
Authors: Tsujikawa Tetsuya , Oikawa Hiroshi , Tasaki Toshiki , Hosono Naoko , Tsuyoshi Hideaki , Rahman Mahmudur G. M. , Yoshida Yoshio , Yamauchi Takahiro , Kimura Hirohiko , Okazawa Hidehiko 
Published: August 2020

AbstractWe identified predictors for bone-marrow [18F]FDG uptake and MR signals among complete blood count, C-reactive protein (CRP), and anthropometric factors, and demonstrated the bone-marrow physiology using integrated [18F]FDG-PET/MRI. 174 oncology patients without bone-marrow lesions underwent whole-body [18F]FDG-PET/MRI. The standardized uptake value (SUV), apparent diffusion coefficient (ADC), proton density fat-fraction (PDFF), and a reciprocal of T2* relaxation time (R2*) were measured in lumbar vertebrae (L3–5) and bilateral ilia. Vertebrae, pelvis, and ribs were evaluated by 3-point visual scoring on DWI. The association of the PET/MR features with the predictors was examined. Multi-regression analyses identified CRP as the strongest predictor for lumbar and iliac SUVs (standardized coefficient: β = 0.31 and β = 0.38, respectively), and for lumbar and iliac R2* (β = 0.31 and β = 0.46, respectively). In contrast, age was the strongest factor influencing lumbar and iliac ADCs (β = 0.23 and β = 0.21, respectively), and lumbar and iliac PDFFs (β = 0.53 and β = 0.54, respectively). Regarding DWI-visual scores, age was the strongest predictor for vertebrae (β = − 0.47), and the red cell distribution width (RDW) was the strongest predictor for pelvis and ribs (β = 0.33 and β = 0.47, respectively). The bone-marrow [18F]FDG uptake and R2* reflect anemia of inflammation (increased granulopoiesis and reduced iron metabolism), whereas bone-marrow DWI and PDFF reflect age and anemia-responsive erythropoiesis.
An integrated drug repurposing strategy for the rapid identification of potential SARS-CoV-2 viral inhibitors
Authors: Trezza Alfonso , Iovinelli Daniele , Santucci Annalisa , Prischi Filippo , Spiga Ottavia 
Published: August 2020

AbstractThe Coronavirus disease 2019 (COVID-19) is an infectious disease caused by the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2). The virus has rapidly spread in humans, causing the ongoing Coronavirus pandemic. Recent studies have shown that, similarly to SARS-CoV, SARS-CoV-2 utilises the Spike glycoprotein on the envelope to recognise and bind the human receptor ACE2. This event initiates the fusion of viral and host cell membranes and then the viral entry into the host cell. Despite several ongoing clinical studies, there are currently no approved vaccines or drugs that specifically target SARS-CoV-2. Until an effective vaccine is available, repurposing FDA approved drugs could significantly shorten the time and reduce the cost compared to de novo drug discovery. In this study we attempted to overcome the limitation of in silico virtual screening by applying a robust in silico drug repurposing strategy. We combined and integrated docking simulations, with molecular dynamics (MD), Supervised MD (SuMD) and Steered MD (SMD) simulations to identify a Spike protein – ACE2 interaction inhibitor. Our data showed that Simeprevir and Lumacaftor bind the receptor-binding domain of the Spike protein with high affinity and prevent ACE2 interaction.
Smart textiles for multimodal wearable sensing using highly stretchable multiplexed optical fiber system
Authors: Leal-Junior Arnaldo , Avellar Leticia , Frizera Anselmo , Marques Carlos 
Published: August 2020

AbstractThis paper presents the development and application of a multiparameter, quasi-distributed smart textile based on embedded highly stretchable polymer optical fiber (POF) sensors. The POF is fabricated using the light polymerization spinning process, resulting a highly stretchable optical fiber, so-called LPS-POF, with Young’s modulus and elastic limits of 15 MPa and 17%, respectively. The differential scanning calorimetry shows a thermal stability of the LPS-POF in temperature range of 13–40 °C. The developed sensors are based on the optical power variation, which results in a fully portable and low-cost technique. In order to obtain a multiplexed sensor system, a technique based on flexible light emitting diodes (LEDs) on–off keying modulation is applied, where each LED represents the response of one sensor. The smart textile comprises of LPS-POF and three flexible LEDs embedded in neoprene textile fabric. The performance of the system is evaluated for temperature, transverse force and angular displacement detection at different planes. The sensors presented high linearity (mean determination coefficient of 0.99) and high repeatability (inter-measurement deviations below 5%). The sensor is also applied in activity detection, where the principal component analysis (PCA) was applied in the sensors responses and, in conjunction with clustering techniques such as k-means, indicate the possibility of detecting basic activities such as walking, sitting on a chair and squatting.
Amygdalin based G-6-P synthase inhibitors as novel preservatives for food and pharmaceutical products
Authors: Lather Amit , Sharma Sunil , Khatkar Anurag 
Published: August 2020

AbstractG-6-P synthase enzyme has been involved in the synthesis of the microbial cell wall, and its inhibition may lead to the antimicrobial effect. In the present study, we designed a library of amygdalin derivatives, and two most active derivatives selected on the basis of various parameters viz. dock score, binding energy, and ADMET data using molecular docking software (Schrodinger’s Maestro). The selected derivatives were synthesized and evaluated for their antioxidant and antimicrobial potential against several Gram (+ ve), Gram (−ve), as well as fungal strains. The results indicated that synthesized compounds exhibited good antioxidant, antimicrobial, and better preservative efficacy in food preparation as compared to the standard compounds. No significant differences were observed in different parameters as confirmed by Kruskal–Wallis test (p < 0.05). Docking results have been found in good correlation with experimental wet-lab data. Moreover, the mechanistic insight into the docking poses has also been explored by binding interactions of amygdalin derivative inside the dynamic site of G-6-P synthase.
Ionic liquid-assisted cellulose coating of chitosan hydrogel beads and their application as drug carriers
Authors: Song Myung-Hee , Pham Thi Phuong Thuy , Yun Yeoung-Sang 
Published: August 2020

AbstractThe present study proposes a simple yet effective method of cellulose coating onto chitosan (CS) hydrogel beads and application thereof as drug carriers. The beads were coated with cellulose dissolved in 1-ethyl-3-methylimidazolium acetate, an ionic liquid (IL) via a one-pot one-step process. Water molecules present in the CS beads diffused outward upon contact with the cellulose–IL mixture and acted as an anti-solvent. This allowed the surface of the beads to be coated with the regenerated cellulose. The regenerated cellulose was characterized by FE-SEM, FT-IR, and XRD analyses. To test potential application of the cellulose-coated CS hydrogel beads as a drug carrier, verapamil hydrochloride (VRP), used as a model drug, was impregnated into the beads. When the VRP-impregnated beads were immersed in the simulated gastric fluid (pH 1.2), the VRP was released in an almost ideal linear pattern. This easily fabricated cellulose-coated CS beads showed the possibility for application as carriers for drug release control.
Clinical features of irreversible rejection after allogeneic uterus transplantation in cynomolgus macaques
Authors: Kisu Iori , Emoto Katsura , Masugi Yohei , Yamada Yohei , Matsubara Kentaro , Obara Hideaki , Matoba Yusuke , Banno Kouji , Kato Yojiro , Saiki Yoko , Itagaki Iori , Kawamoto Ikuo , Iwatani Chizuru , Murase Mitsuru , Nakagawa Takahiro , Tsuchiya Hideaki , Ishigaki Hirohito , Urano Hiroyuki , Ema Masatsugu , Ogasawara Kazumasa , Aoki Daisuke , Nakagawa Kenshi , Shiina Takashi 
Published: August 2020

AbstractUterus transplantation (UTx) is a potential option for women with uterine factor infertility to have a child. The clinical features indicating irreversible rejection of the uterus are unknown. In our experimental series of allogeneic UTx in cynomolgus macaques, six female macaques were retrospectively examined, which were unresponsive to treatment with immunosuppressants (i.e. irreversible rejection). Clinical features including general condition, hematology, uterine size, indocyanine green (ICG) fluorescence imaging by laparotomy, and histopathological findings of the removed uterus were evaluated. In all cases, general condition was good at the time of diagnosis of irreversible rejection and thereafter. Laboratory evaluation showed temporary increases in white blood cells, lactate dehydrogenase and C-reactive protein, then these levels tended to decrease gradually. In transabdominal ultrasonography, the uterus showed time-dependent shrinkage after transient swelling at the time of diagnosis of irreversible rejection. In laparotomy, a whitish transplanted uterus was observed and enhancement of the transplanted uterus was absent in ICG fluorescence imaging. Histopathological findings in each removed uterus showed hyalinized fibrosis, endometrial deficit, lymphocytic infiltration and vasculitis. These findings suggest that uterine transplantation rejection is not fatal, in contrast to rejection of life-supporting organs. Since the transplanted uterus with irreversible rejection atrophies naturally, hysterectomy may be unnecessary.
Promotional effect of magnesium oxide for a stable nickel-based catalyst in dry reforming of methane
Authors: Al-Fatesh Ahmed S. , Kumar Rawesh , Fakeeha Anis H. , Kasim Samsudeen O. , Khatri Jyoti , Ibrahim Ahmed A. , Arasheed Rasheed , Alabdulsalam Muhamad , Lanre Mahmud S. , Osman Ahmed I. , Abasaeed Ahmed E. , Bagabas Abdulaziz 
Published: August 2020

AbstractThe generation of synthesis gas (hydrogen and carbon monoxide mixture) from two global warming gases of carbon dioxide and methane via dry reforming is environmentally crucial and for the chemical industry as well. Herein, magnesium-promoted NiO supported on mesoporous zirconia, 5Ni/xMg–ZrO2 (x = 0, 3, 5, 7 wt%) were prepared by wet impregnation method and then were tested for syngas production via dry reforming of methane. The reaction temperature at 800 °C was found more catalytically active than that at 700 °C due to the endothermic feature of reaction which promotes efficient CH4 catalytic decomposition over Ni and Ni–Zr interface as confirmed by CH4–TSPR experiment. NiO–MgO solid solution interacted with ZrO2 support was found crucial and the reason for high CH4 and CO2 conversions. The highest catalyst stability of the 5Ni/3Mg–ZrO2 catalyst was explained by the ability of CO2 to partially oxidize the carbon deposit over the surface of the catalyst. A mole ratio of hydrogen to carbon monoxide near unity (H2/CO ~ 1) was obtained over 5Ni/ZrO2 and 5Ni/5Mg–ZrO2, implying the important role of basic sites. Our approach opens doors for designing cheap and stable dry reforming catalysts from two potent greenhouse gases which could be of great interest for many industrial applications, including syngas production and other value-added chemicals.
Application of unmanned aerial vehicle (UAV) thermal infrared remote sensing to identify coal fires in the Huojitu coal mine in Shenmu city, China
Authors: He Xiaoyuan , Yang Xingke , Luo Zheng , Guan Tao 
Published: August 2020

AbstractChina is a major coal-producing country that consumes large amounts of coal every year. Due to the existence of many small coal kilns using backward mining methods, numerous worked-out areas have been formed. The coal mines were abandoned with no mitigation, so air penetrates into the roadways and contacts the coal seams; as a result, the residual coal seams spontaneously ignite to form coal fires. These coal fires have burned millions of tons of valuable coal resources and caused serious environmental problems. To implement fire suppression more effectively, coal fire detection is a key technology. In this paper, thermal infrared remote sensing from unmanned aerial vehicle combined with a surface survey is used to identify the range of coal fires in the Huojitu coal mine in Shenmu city. The scopes and locations of the fire zones are preliminarily delineated, which provides an accurate basis for the development of fire suppression projects.
Dispersion-free extraction of In(III) from HCl solutions using a supported liquid membrane containing the HA324H+Cl− ionic liquid as the carrier
Authors: Alguacil Francisco José , López Félix Antonio 
Published: August 2020

AbstractBy reaction of HCl and the tertiary amine HA324, an ionic liquid denoted HA324H+Cl− was generated and used in the transport of indium(III) from HCl solutions. Metal transport experiments were carried out with a supported liquid membrane, and several variables affecting the permeation of indium(III) across the membrane were tested: stirring speed, metal and acid concentrations in the feed solutions and the carrier concentration in the supported organic solution. The metal transport results were also compared with those obtained using different carriers in the solid support. A model that described indium(III) transport across the membrane was proposed, and the corresponding diffusional parameters were estimated.
High-throughput microCT scanning of small specimens: preparation, packing, parameters and post-processing
Authors: Hipsley Christy A. , Aguilar Rocio , Black Jay R. , Hocknull Scott A. 
Published: August 2020

AbstractHigh-resolution X-ray microcomputed tomography, or microCT (μCT), enables the digital imaging of whole objects in three dimensions. The power of μCT to visualize internal features without disarticulation makes it particularly valuable for the study of museum collections, which house millions of physical specimens documenting the spatio-temporal patterns of life. Despite the potential for comparative analyses, most μCT studies include limited numbers of museum specimens, due to the challenges of digitizing numerous individuals within a project scope. Here we describe a method for high-throughput μCT scanning of hundreds of small (< 2 cm) specimens in a single container, followed by individual labelling and archival storage. We also explore the effects of various packing materials and multiple specimens per capsule to minimize sample movement that can degrade image quality, and hence μCT investment. We demonstrate this protocol on vertebrate fossils from Queensland Museum, Australia, as part of an effort to track community responses to climate change over evolutionary time. This system can be easily modified for other types of wet and dry material amenable to X-ray attenuation, including geological, botanical and zoological samples, providing greater access to large-scale phenotypic data and adding value to global collections.
FAM46C/TENT5C functions as a tumor suppressor through inhibition of Plk4 activity
Authors: Kazazian Karineh , Haffani Yosr , Ng Deanna , Lee Chae Min Michelle , Johnston Wendy , Kim Minji , Xu Roland , Pacholzyk Karina , Zih Francis Si-Wah , Tan Julie , Smrke Alannah , Pollett Aaron , Wu Hannah Sun-Tsi , Swallow Carol Jane 
Published: August 2020

AbstractPolo like kinase 4 (Plk4) is a tightly regulated serine threonine kinase that governs centriole duplication. Increased Plk4 expression, which is a feature of many common human cancers, causes centriole overduplication, mitotic irregularities, and chromosomal instability. Plk4 can also promote cancer invasion and metastasis through regulation of the actin cytoskeleton. Herein we demonstrate physical interaction of Plk4 with FAM46C/TENT5C, a conserved protein of unknown function until recently. FAM46C localizes to centrioles, inhibits Plk4 kinase activity, and suppresses Plk4-induced centriole duplication. Interference with Plk4 function by FAM46C was independent of the latter’s nucleotidyl transferase activity. In addition, FAM46C restrained cancer cell invasion and suppressed MDA MB-435 cancer growth in a xenograft model, opposing the effect of Plk4. We demonstrate loss of FAM46C in patient-derived colorectal cancer tumor tissue that becomes more profound with advanced clinical stage. These results implicate FAM46C as a tumor suppressor that acts by inhibiting Plk4 activity.
Pheromone components affect motivation and induce persistent modulation of associative learning and memory in honey bees
Authors: Baracchi David , Cabirol Amélie , Devaud Jean-Marc , Haase Albrecht , d’Ettorre Patrizia , Giurfa Martin 
Published: August 2020

AbstractSince their discovery in insects, pheromones are considered as ubiquitous and stereotyped chemical messengers acting in intraspecific animal communication. Here we studied the effect of pheromones in a different context as we investigated their capacity to induce persistent modulations of associative learning and memory. We used honey bees, Apis mellifera, and combined olfactory conditioning and pheromone preexposure with disruption of neural activity and two-photon imaging of olfactory brain circuits, to characterize the effect of pheromones on olfactory learning and memory. Geraniol, an attractive pheromone component, and 2-heptanone, an aversive pheromone, improved and impaired, respectively, olfactory learning and memory via a durable modulation of appetitive motivation, which left odor processing unaffected. Consistently, interfering with aminergic circuits mediating appetitive motivation rescued or diminished the cognitive effects induced by pheromone components. We thus show that these chemical messengers act as important modulators of motivational processes and influence thereby animal cognition.
Sigmoidally hydrochromic molecular porous crystal with rotatable dendrons
Authors: Yamagishi Hiroshi , Nakajima Sae , Yoo Jooyoung , Okazaki Masato , Takeda Youhei , Minakata Satoshi , Albrecht Ken , Yamamoto Kimihisa , Badía-Domínguez Irene , Oliva Maria Moreno , Delgado M. Carmen Ruiz , Ikemoto Yuka , Sato Hiroyasu , Imoto Kenta , Nakagawa Kosuke , Tokoro Hiroko , Ohkoshi Shin-ichi , Yamamoto Yohei 
Published: August 2020

AbstractVapochromic behaviour of porous crystals is beneficial for facile and rapid detection of gaseous molecules without electricity. Toward this end, tailored molecular designs have been established for metal–organic, covalent-bonded and hydrogen-bonded frameworks. Here, we explore the hydrochromic chemistry of a van der Waals (VDW) porous crystal. The VDW porous crystal VPC-1 is formed from a novel aromatic dendrimer having a dibenzophenazine core and multibranched carbazole dendrons. Although the constituent molecules are connected via VDW forces, VPC-1 maintains its structural integrity even after desolvation. VPC-1 exhibits reversible colour changes upon uptake/release of water molecules due to the charge transfer character of the constituent dendrimer. Detailed structural analyses reveal that the outermost carbazole units alone are mobile in the crystal and twist simultaneously in response to water vapour. Thermodynamic analysis suggests that the sigmoidal water sorption is induced by the affinity alternation of the pore surface from hydrophobic to hydrophilic.
Exploring the mechanism of Radix Rhei Et Rhizome intervention in intracerebral hemorrhage based on systematic pharmacology and proteomics strategy
Authors: Zhu Xiaofei , Long Zhiyong , Bao Tingting , Liu Liang , Yang Kailin 
Published: August 2020

Abstract
Objective: To explore the mechanism of Radix Rhei Et Rhizome (Dahuang, DH) intervention in intracerebral hemorrhage (ICH) based on systematic pharmacology and proteomics strategy.
Methods: The systematic pharmacological strategies were utilized to find the bioactive compounds of Radix Rhei Et Rhizome, predict its potential targets, and collect ICH’s disease genes; then, the Cytoscape 3.7.1 software was applied for network construction and network topology analysis. After that, in-depth analysis of the proteomics data of Radix Rhei Et Rhizome intervention in ICH was performed to complement and validate the results of systematic pharmacological predictions.
Results: A total of three major networks were constructed in the present study: (1) compound–compound target network of Radix Rhei Et Rhizome, (2) DH-ICH PPI network, (3) proteomics proteins’ PPI network. These three major networks have been analyzed by network topology, and several small networks derived (such as signaling pathway networks). The enrichment analysis showed that Radix Rhei Et Rhizome can intervene in several biological process (such as inflammation, smooth muscle proliferation, platelet activation, blood pressure regulation, angiogenesis, hypoxia, and inflammatory response of leukocytes), signaling pathway (such as FoxO signaling pathway, complement and coagulation cascades, cGMP-PKG signaling pathway, and Rap1 signaling pathway), and reactome pathway (such as signaling by interleukins, interleukin-4 and interleukin-13 signaling, nuclear receptor transcription pathway, and platelet activation).
Conclusion: Radix Rhei Et Rhizome may intervene in ICH-related biological process, signaling pathway, and reactome pathway found in this research so as to achieve the effect of treating ICH related injuries.