bluuebunny/crossref_metadata_2025_split huggingface dataset:
Orthodontic patients’ oral hygiene compliance by utilizing a smartphone application (Brush DJ): a randomized clinical trial
Authors: Farhadifard Homa , Soheilifar Sepideh , Farhadian Maryam , Kokabi Hadi , Bakhshaei Anahita 
Published: November 2020

AbstractConsidering the widespread use of smartphones and their applications (apps), as well as the undeniable role of reminders and apps in behavioral interventions, this study aimed to assess the efficacy of a smartphone app (Brush DJ) for oral hygiene compliance of patients with fixed orthodontic appliances. In this randomized clinical trial, 120 patients between 15 to 25 years who had just started fixed orthodontic treatment were randomly divided into two groups (n = 60). Control patients received conventional oral hygiene instruction, while patients in the intervention group were asked to use the Brush DJ smartphone app, after receiving conventional oral hygiene instruction. The plaque index (PI) and gingival index (GI) were measured at baseline (T0), and at 4 weeks (T1), 8 weeks (T2) and 12 weeks (T3) after the onset of study. A questionnaire was given to all patients to assess the frequency and duration of tooth brushing per day, and the frequency of app usage and reminder noticing in the intervention group. Improvements in PI and GI were noted in the intervention group; while these parameters increased in the control group. Significant differences were noted in PI and GI changes between the two groups (p < 0.001). Brushing frequency and duration were positively correlated with app usage during the follow-up period. Ultimately, we believe that smartphone apps, as motivators and reminders, can greatly help in improving the orthodontic patients’ oral hygiene compliance, especially in adolescents
Deletion of the deISGylating enzyme USP18 enhances tumour cell antigenicity and radiosensitivity
Authors: Pinto-Fernandez Adan , Salio Mariolina , Partridge Tom , Chen Jianzhou , Vere George , Greenwood Helene , Olie Cyriel Sebastiaan , Damianou Andreas , Scott Hannah Claire , Pegg Henry Jack , Chiarenza Alessandra , Díaz-Saez Laura , Smith Paul , Gonzalez-Lopez Claudia , Patel Bhavisha , Anderton Emma , Jones Neil , Hammonds Tim R. , Huber Kilian , Muschel Ruth , Borrow Persephone , Cerundolo Vincenzo , Kessler Benedikt M. 
Published: November 2020

AbstractBackgroundInterferon (IFN) signalling pathways, a key element of the innate immune response, contribute to resistance to conventional chemotherapy, radiotherapy, and immunotherapy, and are often deregulated in cancer. The deubiquitylating enzyme USP18 is a major negative regulator of the IFN signalling cascade and is the predominant human protease that cleaves ISG15, a ubiquitin-like protein tightly regulated in the context of innate immunity, from its modified substrate proteins in vivo.MethodsIn this study, using advanced proteomic techniques, we have significantly expanded the USP18-dependent ISGylome and proteome in a chronic myeloid leukaemia (CML)-derived cell line. USP18-dependent effects were explored further in CML and colorectal carcinoma cellular models.ResultsNovel ISGylation targets were characterised that modulate the sensing of innate ligands, antigen presentation and secretion of cytokines. Consequently, CML USP18-deficient cells are more antigenic, driving increased activation of cytotoxic T lymphocytes (CTLs) and are more susceptible to irradiation.ConclusionsOur results provide strong evidence for USP18 in regulating antigenicity and radiosensitivity, highlighting its potential as a cancer target.
Long noncoding RNA ASB16-AS1 inhibits adrenocortical carcinoma cell growth by promoting ubiquitination of RNA-binding protein HuR
Authors: Long Bo , Yang Xufei , Xu Xixia , Li Xiaoxin , Xu Xinjie , Zhang Xuebin , Zhang Shuyang 
Published: November 2020

AbstractAdrenocortical carcinoma is one of the aggressive malignancies and it originates from the cortex of adrenal gland. Dysregulation of long non-coding RNA plays important roles in the development of adrenocortical carcinoma. Here, we found that lncRNA ASB16-AS1 was down-regulated in adrenocortical carcinoma and ASB16-AS1 functions as tumor suppressor in vitro and in vivo. We then found that IGF1R and CDK6 are regulated by ASB16-AS1 in adrenocortical carcinoma cells by transcriptome RNA sequencing. ASB16-AS1 associates with RNA-binding protein HuR (ELAVL1) as revealed by RNA pull-down following mass spectrometry. Also, ASB16-AS1 inhibits HuR expression post-translationally by promoting its ubiquitination. ASB16-AS1 regulates IGF1R and CDK6 mRNA expression through RNA-binding protein HuR. We then found that inhibition of ASB16-AS1 attenuates the binding of ubiquitin E3 ligase BTRC to HuR and subsequently inhibits HuR protein unbiquitination and degradation. BTRC knock-down could reverse the effect of AB16-AS1 on HuR, CDK6, and IGF1R levels. Collectively, these results demonstrate that ASB16-AS1 regulates adrenocortical carcinoma cell proliferation and tackling the level of ASB16-AS1 may be developed to treat adrenocortical carcinoma.
Genome-wide methylation sequencing identifies progression-related epigenetic drivers in myelodysplastic syndromes
Authors: Zhou Jing-dong , Zhang Ting-juan , Xu Zi-jun , Deng Zhao-qun , Gu Yu , Ma Ji-chun , Wen Xiang-mei , Leng Jia-yan , Lin Jiang , Chen Su-ning , Qian Jun 
Published: November 2020

AbstractThe potential mechanism of myelodysplastic syndromes (MDS) progressing to acute myeloid leukemia (AML) remains poorly elucidated. It has been proved that epigenetic alterations play crucial roles in the pathogenesis of cancer progression including MDS. However, fewer studies explored the whole-genome methylation alterations during MDS progression. Reduced representation bisulfite sequencing was conducted in four paired MDS/secondary AML (MDS/sAML) patients and intended to explore the underlying methylation-associated epigenetic drivers in MDS progression. In four paired MDS/sAML patients, cases at sAML stage exhibited significantly increased methylation level as compared with the matched MDS stage. A total of 1090 differentially methylated fragments (DMFs) (441 hypermethylated and 649 hypomethylated) were identified involving in MDS pathogenesis, whereas 103 DMFs (96 hypermethylated and 7 hypomethylated) were involved in MDS progression. Targeted bisulfite sequencing further identified that aberrant GFRA1, IRX1, NPY, and ZNF300 methylation were frequent events in an additional group of de novo MDS and AML patients, of which only ZNF300 methylation was associated with ZNF300 expression. Subsequently, ZNF300 hypermethylation in larger cohorts of de novo MDS and AML patients was confirmed by real-time quantitative methylation-specific PCR. It was illustrated that ZNF300 methylation could act as a potential biomarker for the diagnosis and prognosis in MDS and AML patients. Functional experiments demonstrated the anti-proliferative and pro-apoptotic role of ZNF300 overexpression in MDS-derived AML cell-line SKM-1. Collectively, genome-wide DNA hypermethylation were frequent events during MDS progression. Among these changes, ZNF300 methylation, a regulator of ZNF300 expression, acted as an epigenetic driver in MDS progression. These findings provided a theoretical basis for the usage of demethylation drugs in MDS patients against disease progression.
Ultrasound-guided platelet-rich plasma injection and multimodality ultrasound examination of peripheral nerve crush injury
Authors: Zhu Yaqiong , Jin Zhuang , Wang Jing , Chen Siming , Hu Yongqiang , Ren Ling , Wang Yu , Song Qing , Tian Xiaoqi , Xie Fang , Peng Jiang , Peng Nan , Luo Yukun , Wang Yuexiang 
Published: November 2020

AbstractUltrasound-guided platelet-rich plasma (PRP) injection is able to make up for the limitations of applying a single growth factor. The goal of this study was to investigate the effects of serial ultrasound-guided PRP injections of the appropriate concentration on the treatment of sciatic nerve crush injury, and explore the value of multimodality ultrasound techniques in evaluating the prognosis of crushed peripheral nerve. In vitro, optimal concentration of PRP (from 150%, 250%, 450%, and 650%) was screened due for its maximal effect on proliferation and neurotrophic function of Schwann cells (SCs). In vivo, ninety rabbits were equally and randomly divided into normal control, model, PRP-2.5×, PRP-4.5×, and PRP-6.5× groups. The neurological function and electrophysiological recovery evaluation, and the comparison of the multimodality ultrasound evaluation with the histological results of sciatic nerve crush injury were performed to investigate the regenerative effects of PRP at different concentrations on the sciatic nerve crush injury. Our results showed that the PRP with a 4.5-fold concentration of whole blood platelets could significantly stimulate the proliferation and secretion of SCs and nerve repair. The changes in stiffness and blood perfusion were positively correlated with the collagen area percentage and VEGF expression in the injured nerve, respectively. Thus, serial ultrasound-guided PRP injections at an appropriate concentration accelerates the recovery of axonal function. Multimodality ultrasound techniques provide a clinical reference for prognosis by allowing the stiffness and microcirculation perfusion of crush-injured peripheral nerves to be quantitatively evaluated.
Dynamics of picosecond laser ablation for surgical treatment of colorectal cancer
Authors: Beck R. J. , Bitharas I. , Hand D. P. , Maisey T. , Moore A. J. , Shires M. , Thomson R. R. , West N. P. , Jayne D. G. , Shephard J. D. 
Published: November 2020

AbstractEndoluminal surgery for the treatment of colorectal neoplasia is typically carried out using electrocautery tools which imply limited precision and the risk of harm through collateral thermal damage to the adjacent healthy tissue. As a potential alternative, we present the successful colonic epithelial laser ablation by means of picosecond laser pulses. Laser ablation studies performed in ex-vivo colon tissue result in cavities with comparable thickness to early stage colorectal cancers. The corresponding histology sections exhibit only minimal collateral damage to the surrounding tissue and the depth of the ablation can be controlled precisely by means of the pulse energy. High-speed imaging has been used for the first time to visualize picosecond laser ablation of cancerous tissue in a clinically relevant model. This information was correlated with histopathology and optical surface profilometry revealing the dynamic nature of the laser tissue interaction and the need for temporal or spatial separation of pulses for optimum efficacy with regards to tissue removal. Overall, the application of picosecond laser pulses to ablate endoluminal bowel lesions demonstrates significantly improved precision and reduced thermal damage to the adjacent tissue in comparison to conventional procedures and hence will enable more precise surgical treatment of cancers.
Quantitative comparison of the biomass-degrading enzyme repertoires of five filamentous fungi
Authors: Arntzen Magnus Ø. , Bengtsson Oskar , Várnai Anikó , Delogu Francesco , Mathiesen Geir , Eijsink Vincent G. H. 
Published: November 2020

AbstractThe efficiency of microorganisms to degrade lignified plants is of great importance in the Earth’s carbon cycle, but also in industrial biorefinery processes, such as for biofuel production. Here, we present a large-scale proteomics approach to investigate and compare the enzymatic response of five filamentous fungi when grown on five very different substrates: grass (sugarcane bagasse), hardwood (birch), softwood (spruce), cellulose and glucose. The five fungi included the ascomycetes Aspergillus terreus, Trichoderma reesei, Myceliophthora thermophila, Neurospora crassa and the white-rot basidiomycete Phanerochaete chrysosporium, all expressing a diverse repertoire of enzymes. In this study, we present comparable quantitative protein abundance values across five species and five diverse substrates. The results allow for direct comparison of fungal adaptation to the different substrates, give indications as to the substrate specificity of individual carbohydrate-active enzymes (CAZymes), and reveal proteins of unknown function that are co-expressed with CAZymes. Based on the results, we present a quantitative comparison of 34 lytic polysaccharide monooxygenases (LPMOs), which are crucial enzymes in biomass deconstruction.
Exceptional sulfur and iron isotope enrichment in millimetre-sized, early Palaeozoic animal burrows
Authors: Harazim Dario , Virtasalo Joonas J. , Denommee Kathryn C. , Thiemeyer Nicolas , Lahaye Yann , Whitehouse Martin J. 
Published: November 2020

AbstractPyrite-δ34S and -δ56Fe isotopes represent highly sensitive diagnostic paleoenvironmental proxies that express high variability at the bed (< 10 mm) scale that has so far defied explanation by a single formative process. This study reveals for the first time the paleoenvironmental context of exceptionally enriched pyrite-δ34S and -δ56Fe in bioturbated, storm-reworked mudstones of an early Ordovician storm-dominated delta (Tremadocian Beach Formation, Bell Island Group, Newfoundland). Very few studies provide insight into the low-temperature sulfur and iron cycling from bioturbated muddy settings for time periods prior to the evolution of deep soil horizons on land. Secondary ion mass spectroscopy (SIMS) analyses performed on Beach Formation muddy storm event beds reveal spatially distinct δ34S and δ56Fe values in: (a) tubular biogenic structures and trails (δ34S ~ +40‰; δ56Fe ~ −0.5‰), (b) silt-filled Planolites burrows (δ34S ~ +40‰; δ56Fe ~ +0.5 to + 2.1‰), and (c) non-bioturbated mudstone (δ34S ~ +35‰; δ56Fe ~ +0.5‰). δ34S values of well above + 40.0‰ indicate at least some pyrite precipitation in the presence of a 34S-depleted pore water sulfide reservoir, via closed system (Raleigh-type) fractionation. The preferential enrichment of 56Fe in Planolites burrows is best explained via microbially-driven liberation of Fe(II) from solid iron parent phases and precipitation from a depleted 54Fe dissolved Fe(II) reservoir. Rigorous sedimentological analysis represents a gateway to critically test the paleoenvironmental models describing the formation of a wide range of mudstones and elucidates the origins of variability in the global stable S and Fe isotope record.
Morphology, ultrastructure, genomics, and phylogeny of Euplotes vanleeuwenhoeki sp. nov. and its ultra-reduced endosymbiont “Candidatus Pinguicoccus supinus” sp. nov.
Authors: Serra Valentina , Gammuto Leandro , Nitla Venkatamahesh , Castelli Michele , Lanzoni Olivia , Sassera Davide , Bandi Claudio , Sandeep Bhagavatula Venkata , Verni Franco , Modeo Letizia , Petroni Giulio 
Published: November 2020

AbstractTaxonomy is the science of defining and naming groups of biological organisms based on shared characteristics and, more recently, on evolutionary relationships. With the birth of novel genomics/bioinformatics techniques and the increasing interest in microbiome studies, a further advance of taxonomic discipline appears not only possible but highly desirable. The present work proposes a new approach to modern taxonomy, consisting in the inclusion of novel descriptors in the organism characterization: (1) the presence of associated microorganisms (e.g.: symbionts, microbiome), (2) the mitochondrial genome of the host, (3) the symbiont genome. This approach aims to provide a deeper comprehension of the evolutionary/ecological dimensions of organisms since their very first description. Particularly interesting, are those complexes formed by the host plus associated microorganisms, that in the present study we refer to as “holobionts”. We illustrate this approach through the description of the ciliateEuplotes vanleeuwenhoekisp. nov. and its bacterial endosymbiont “CandidatusPinguicoccus supinus” gen. nov., sp. nov. The endosymbiont possesses an extremely reduced genome (~ 163 kbp); intriguingly, this suggests a high integration between host and symbiont.
Characteristics of temperature evolution from 1960 to 2015 in the Three Rivers’ Headstream Region, Qinghai, China
Authors: Liu Xiaoqiong , Zhang Yuyang , Liu Yansui , Zhao Xinzheng , Zhang Jian , Rui Yang 
Published: November 2020

AbstractThe cumulative anomaly analysis, the ensemble empirical mode decomposition (EEMD), the Bernaola Galvan heuristic segmentation algorithm (BGSA), the Le Page test, the moving t test at different sub-series scales, and the quasi-periodic oscillations (QPOs) were used to demonstrate the statistical characteristics of the temperature changes in the study area from 1960 to 2015. The results were as follows: the temperatures varied obviously among subregions and seasons and they generally increased; the climate tendency rates of autumn mean temperatures were higher than those of summer and spring; additionally, the temperatures in the three subregions of the Three Rivers’ Headstream Region (THRHR) were relatively low in the 1960s, especially in the early 1960s, followed by those in the 1970s, and the annual mean temperature has been increasing since the mid-late 1980s, especially in the middle 1990s. The results of EEMD showed that the QPOs of the annual mean temperature series in the study area were mainly quasi-3 years, quasi-5–8 years, quasi-12–15 years, and quasi-35–38 years. The results of the annual mean temperature series mutational sites showed that a significant warming mutation began in approximately 1997; and the mutational sites of seasonal mean temperature series in the three subregions of the THRHR all began in the middle and late 1990s. The prediction result of the temperature series trend based on multiple methods showed that the warming persistence of annual and seasonal mean temperature series would be stronger, and their seasonal and regional differences were obvious.
Fabrication of selective and sensitive chemical sensor probe based on ternary nano-formulated CuO/MnO2/Gd2O3 spikes by hydrothermal approach
Authors: Rahman Mohammed M. , Alam M. M. , Asiri Abdullah M. , Opo Firoz A. D. M. 
Published: November 2020

AbstractIn this approach, thin spikes (NSs) of ternary nano-formulated mixed CuO/MnO2/Gd2O3were synthesized by the hydrothermal approach for efficient detection of 3-methoxyphenyl hydrazine (3-MPHyd) chemical from various environmental samples. The NSs were systematically characterized by using XPS, EDS, TEM, FTIR, UV/vis, and XRD. The fabricated NSs onto the glassy carbon electrode (GCE) was successfully applied for the selective and sensitive detection of 3-MPHyd in the phosphate buffer system (PBS), which displayed the highest sensitivity, good selectivity with ultra-trace detection limit, high stability, good reproducibility, and quick response time. The real environmental samples were tested for validation from stand point of the ternary doped nanomaterials for sensing in the practical applications using by electrochemical method.
Pivotal role of DPYSL2A in KLF4-mediated monocytic differentiation of acute myeloid leukemia cells
Authors: Noura Mina , Morita Ken , Kiyose Hiroki , Matsuo Hidemasa , Nishinaka-Arai Yoko , Kurokawa Mineo , Kamikubo Yasuhiko , Adachi Souichi 
Published: November 2020

AbstractAlthough the biological importance of Krüppel-like factor 4 (KLF4) transcription factor in the terminal differentiation of hematopoietic cells to the monocytes has been well established, the underlying mechanisms remain elusive. To clarify the molecular basis of KLF4-mediated monocytic differentiation, we performed detailed genetic studies in acute myeloid leukemia (AML) cells. Here, we report that dihydropyrimidinase like 2 (DPYSL2), also known as CRMP2, is a novel key differentiation mediator downstream of KLF4 in AML cells. Interestingly, we discovered that KLF4-mediated monocytic differentiation is selectively dependent on one specific isoform, DPYSL2A, but not on other DPYSL family genes. Terminal differentiation to the monocytes and proliferation arrest in AML cells induced by genetic or pharmacological upregulation of KLF4 were significantly reversed by short hairpin RNA (shRNA)-mediated selective depletion of DPYSL2A. Chromatin immunoprecipitation assay revealed that KLF4 associates with the proximal gene promoter of DPYSL2A and directly transactivates its expression. Together with the unique expression patterns of KLF4 and DPYSL2 limited to the differentiated monocytes in the hematopoietic system both in human and mouse, the identified KLF4-DPYSL2 axis in leukemia cells may serve as a potential therapeutic target for the development of novel differentiation therapies for patients with AML.
Cholesteryl ester levels are elevated in the caudate and putamen of Huntington’s disease patients
Authors: Phillips Gabrielle R. , Hancock Sarah E. , Brown Simon H. J. , Jenner Andrew M. , Kreilaus Fabian , Newell Kelly A. , Mitchell Todd W. 
Published: November 2020

AbstractHuntington’s disease (HD) is an autosomal dominant neurodegenerative illness caused by a mutation in the huntingtin gene (HTT) and subsequent protein (mhtt), to which the brain shows a region-specific vulnerability. Disturbances in neural cholesterol metabolism are established in HD human, murine and cell studies; however, cholesteryl esters (CE), which store and transport cholesterol in the brain, have not been investigated in human studies. This study aimed to identify region-specific alterations in the concentrations of CE in HD. The Victorian Brain Bank provided post-mortem tissue from 13 HD subjects and 13 age and sex-matched controls. Lipids were extracted from the caudate, putamen and cerebellum, and CE were quantified using targeted mass spectrometry. ACAT 1 protein expression was measured by western blot. CE concentrations were elevated in HD caudate and putamen compared to controls, with the elevation more pronounced in the caudate. No differences in the expression of ACAT1 were identified in the striatum. No remarkable differences in CE were detected in HD cerebellum. The striatal region-specific differences in CE profiles indicate functional subareas of lipid disturbance in HD. The increased CE concentration may have been induced as a compensatory mechanism to reduce cholesterol accumulation.
Field evaporation and atom probe tomography of pure water tips
Authors: Schwarz T. M. , Weikum E. M. , Meng K. , Hadjixenophontos E. , Dietrich C. A. , Kästner J. , Stender P. , Schmitz G. 
Published: November 2020

AbstractMeasuring biological samples by atom probe tomography (APT) in their natural environment, i.e. aqueous solution, would take this analytical method, which is currently well established for metals, semi-conductive materials and non-metals, to a new level. It would give information about the 3D chemical structure of biological systems, which could enable unprecedented insights into biological systems and processes, such as virus protein interactions. For this future aim, we present as a first essential step the APT analysis of pure water (Milli-Q) which is the main component of biological systems. After Cryo-preparation, nanometric water tips are field evaporated with assistance by short laser pulses. The obtained data sets of several tens of millions of atoms reveal a complex evaporation behavior. Understanding the field evaporation process of water is fundamental for the measurement of more complex biological systems. For the identification of the individual signals in the mass spectrum, DFT calculations were performed to prove the stability of the detected molecules.