bluuebunny/crossref_metadata_2025_split huggingface dataset:
ThicknessTool: automated ImageJ retinal layer thickness and profile in digital images
Authors: Maidana Daniel E. , Notomi Shoji , Ueta Takashi , Zhou Tianna , Joseph Danica , Kosmidou Cassandra , Caminal-Mitjana Josep Maria , Miller Joan W. , Vavvas Demetrios G. 
Published: October 2020

AbstractTo develop an automated retina layer thickness measurement tool for the ImageJ platform, to quantitate nuclear layers following the retina contour. We developed the ThicknessTool (TT), an automated thickness measurement plugin for the ImageJ platform. To calibrate TT, we created a calibration dataset of mock binary skeletonized mask images with increasing thickness masks and different rotations. Following, we created a training dataset and performed an agreement analysis of thickness measurements between TT and two masked manual observers. Finally, we tested the performance of TT measurements in a validation dataset of retinal detachment images. In the calibration dataset, there were no differences in layer thickness between measured and known thickness masks, with an overall coefficient of variation of 0.00%. Training dataset measurements of immunofluorescence retina nuclear layers disclosed no significant differences between TT and any observer’s average outer nuclear layer (ONL) (p = 0.998), inner nuclear layer (INL) (p = 0.807), and ONL/INL ratio (p = 0.944) measurements. Agreement analysis showed that bias between TT vs. observers’ mean was lower than between any observers’ mean against each other in the ONL (0.77 ± 0.34 µm vs 3.25 ± 0.33 µm) and INL (1.59 ± 0.28 µm vs 2.82 ± 0.36 µm). Validation dataset showed that TT can detect significant and true ONL thinning (p = 0.006), more sensitive than manual measurement capabilities (p = 0.069). ThicknessTool can measure retina nuclear layers thickness in a fast, accurate, and precise manner with multi-platform capabilities. In addition, the TT can be customized to user preferences and is freely available to download.
Centrifugal granulation behavior in metallic powder fabrication by plasma rotating electrode process
Authors: Zhao Yufan , Cui Yujie , Numata Haruko , Bian Huakang , Wako Kimio , Yamanaka Kenta , Aoyagi Kenta , Chiba Akihiko 
Published: October 2020

AbstractIn recent years, spherical powders with no or minimal internal pores fabricated by the plasma rotating electrode process (PREP) have been highly recommended for powder-type additive manufacturing. Most research on PREP is aimed at establishing relationship between PREP parameters and powder size. However, almost no dedicated research on granulation behavior has been conducted so far. In the present study, PREP experiments of Ti64 and SUS316 alloys were carried out. Numerical modeling based on computational thermo-fluid dynamics was developed to analyze the granulation behavior. In particular, the roles of the additionally introduced gas blast and the morphology of the electrode end surface in fluid granulation were preliminarily investigated. The study showed that in addition to the electrode's rotating speed and diameter, manipulating the plasma arc current (i.e., the melting rate) could also be an effective way to control the PREP-powder size. According to the simulation, there were competing actions of the gas blast affecting the powder size. The gas blast created disturbance on the fluid and deepened the depression of the electrode end surface, which facilitated powder refinement. However, the cooling effect enhanced the fluid stability and hindered fluid granulation. The conclusions indicated the possibility of using various methods to manipulate PREP-powder size.
Proteomic signatures of acute oxidative stress response to paraquat in the mouse heart
Authors: Dostal Vishantie , Wood Silas D. , Thomas Cody T. , Han Yu , Lau Edward , Lam Maggie P. Y. 
Published: October 2020

AbstractThe heart is sensitive to oxidative damage but a global view on how the cardiac proteome responds to oxidative stressors has yet to fully emerge. Using quantitative tandem mass spectrometry, we assessed the effects of acute exposure of the oxidative stress inducer paraquat on protein expression in mouse hearts. We observed widespread protein expression changes in the paraquat-exposed heart especially in organelle-containing subcellular fractions. During cardiac response to acute oxidative stress, proteome changes are consistent with a rapid reduction of mitochondrial metabolism, coupled with activation of multiple antioxidant proteins, reduction of protein synthesis and remediation of proteostasis. In addition to differential expression, we saw evidence of spatial reorganizations of the cardiac proteome including the translocation of hexokinase 2 to more soluble fractions. Treatment with the antioxidants Tempol and MitoTEMPO reversed many proteomic signatures of paraquat but this reversal was incomplete. We also identified a number of proteins with unknown function in the heart to be triggered by paraquat, suggesting they may have functions in oxidative stress response. Surprisingly, protein expression changes in the heart correlate poorly with those in the lung, consistent with differential sensitivity or stress response in these two organs. The results and data set here could provide insights into oxidative stress responses in the heart and avail the search for new therapeutic targets.
A new glioma grading model based on histopathology and Bone Morphogenetic Protein 2 mRNA expression
Authors: Zhou Kaijia , Zhao Zheng , Li Shouwei , Liu Yanwei , Li Guanzhang , Jiang Tao 
Published: October 2020

AbstractGlioma, the most common form of primary malignant brain tumors, is graded based solely on histopathological appearance, which has led to prognostic discrepancies. This study aimed to establish a new glioma grading model by analyzing the expression of Bone Morphogenetic Protein 2 (BMP2) mRNA in patients with gliomas as well, named the Histopathological-BMP2 (HB) system. Clinical information was collected from 692 patients from the Chinese Glioma Genome Atlas database. According to pathological glioma subtypes and the expression of BMP2 mRNA in tumor tissues, the new subtypes HBs, HBh, HBm and HB1 were established, with BMP2 expression highest in HBs and lowest in HB1. Survival periods were analyzed. Based on this, the expression of three BMP2 receptors (BMPR1A, BMPR1B, and BMPR2) was also analyzed, which was related to the prognosis of patients. This new classification model was validated in further groups of patients from the CGGA database (n = 291) and the Cancer Genome Atlas (n = 625). A new glioma grade (HB grade) based on histopathology and BMP2 expression can predict the prognosis of glioma patients, with BMPR1B and BMPR2 expression indicating a different prognosis in different types of gliomas. The higher the concentration of BMP2, the better the prognosis of patients.
Variation of rhizosphere bacterial community diversity in the desert ephemeral plant Ferula sinkiangensis across environmental gradients
Authors: Zhang Tao , Wang Zhongke , Lv Xinhua , Dang Hanli , Zhuang Li 
Published: October 2020

AbstractFerula sinkiangensis (F. sinkiangensis) is a desert short-lived medicinal plant, and its number is rapidly decreasing. Rhizosphere microbial community plays an important role in plant growth and adaptability. However, F. sinkiangensis rhizosphere bacterial communities and the soil physicochemical factors that drive the bacterial community distribution are currently unclear. On this study, based on high-throughput sequencing, we explored the diversity, structure and composition of F. sinkiangensis rhizosphere bacterial communities at different slope positions and soil depths and their correlation with soil physicochemical properties. Our results revealed the heterogeneity and changed trend of F. sinkiangensis rhizosphere bacterial community diversity and abundance on slope position and soil depth and found Actinobacteria (25.5%), Acidobacteria (16.9%), Proteobacteria (16.6%), Gemmatimonadetes (11.5%) and Bacteroidetes (5.8%) were the dominant bacterial phyla in F. sinkiangensis rhizosphere soil. Among all soil physicochemical variables shown in this study, there was a strong positive correlation between phosphorus (AP) and the diversity of rhizosphere bacterial community in F. sinkiangensis. In addition, Soil physicochemical factors jointly explained 24.28% of variation in F. sinkiangensis rhizosphere bacterial community structure. Among them, pH largely explained the variation of F. sinkiangensis rhizosphere bacterial community structure (5.58%), followed by total salt (TS, 5.21%) and phosphorus (TP, 4.90%).
Evaluation of NDEL1 oligopeptidase activity in blood and brain in an animal model of schizophrenia: effects of psychostimulants and antipsychotics
Authors: Nani João V. , Lee Richard S. , Yonamine Camila M. , Sant’Anna Osvaldo A. , Juliano Maria A. , Gadelha Ary , Mari Jair J. , Hayashi Mirian A. F. 
Published: October 2020

AbstractNuclear distribution element-like 1 (NDEL1) enzyme activity is important for neuritogenesis, neuronal migration, and neurodevelopment. We reported previously lower NDEL1 enzyme activity in blood of treated first episode psychosis and chronic schizophrenia (SCZ) compared to healthy control subjects, with even lower activity in treatment resistant chronic SCZ patients, implicating NDEL1 activity in SCZ. Herein, higher NDEL1 activity was observed in the blood and several brain regions of a validated animal model for SCZ at baseline. In addition, long-term treatment with typical or atypical antipsychotics, under conditions in which SCZ-like phenotypes were reported to be reversed in this animal model for SCZ, showed a significant NDEL1 activity reduction in blood and brain regions which is in line with clinical data. Importantly, these results support measuring NDEL1 enzyme activity in the peripheral blood to predict changes in NDEL1 activity in the CNS. Also, acute administration of psychostimulants, at levels reported to induce SCZ-like phenotype in normal rat strains, increased NDEL1 enzyme activity in blood. Therefore, alterations in NDEL1 activity after treatment with antipsychotics or psychostimulants may suggest a possible modulation of NDEL1 activity secondary to neurotransmission homeostasis and provide new insights into the role of NDEL1 in SCZ pathophysiology.
Detection of functional deterioration in glaucoma by trend analysis using comprehensive overlapping clusters of locations
Authors: Gardiner Stuart K. , Mansberger Steven L. 
Published: October 2020

AbstractDetecting rapid visual field deterioration is crucial for individuals with glaucoma. Cluster trend analysis detects visual field deterioration with higher sensitivity than global analyses by using predefined non-overlapping subsets of visual field locations. However, it may miss small defects that straddle cluster borders. This study introduces a comprehensive set of overlapping clusters, and assesses whether this further improves progression detection. Clusters were defined as locations from where ganglion cell axons enter the optic nerve head within a θ° wide sector, centered at 1º intervals, for various θ. Deterioration in eyes with or at risk of glaucomatous visual field loss was “detected” if ≥ Nθ clusters had deteriorated with p < pCluster, chosen empirically to give 95% specificity based on permuting the series. Nθ was chosen to minimize the time to detect subsequently-confirmed deterioration in ≥ 1/3rd of eyes. Times to detect deterioration were compared using Cox survival models. Biannual series were available for 422 eyes of 214 participants. Predefined non-overlapping clusters detected subsequently-confirmed change in ≥ 1/3rd of eyes in 3.41 years (95% confidence interval 2.75–5.48 years). After equalizing specificity, no criteria based on comprehensive overlapping clusters detected deterioration significantly sooner. The quickest was 3.13 years (2.69–4.65) for θ° = 20° and Nθ = 25, but the comparison with non-overlapping clusters had p = 0.672. Any improvement in sensitivity for detecting deterioration when using a comprehensive set of overlapping clusters was negated by the need to maintain equal specificity. The existing cluster trend analysis using predefined non-overlapping clusters provides a useful tool for monitoring visual field progression.
Sex differences in the association between chronotype and risk of depression
Authors: Kim Kyung Min , Han Seung Min , Heo Kyoung , Kim Won-Joo , Chu Min Kyung 
Published: October 2020

AbstractInformation on sex differences in the association between chronotype and depression is scarce. We aimed to investigate these differences using data from the Korea National Health and Nutrition Examination Survey in 2016. Chronotypes were categorised based on mid-sleep time on free days corrected by sleep debt accumulated on workdays (MSFsc): early type, < mean MSFsc − 1 standard deviation (SD); intermediate type, between mean MSFsc − 1 SD and MSFsc + 1 SD; and late type, > mean MSFsc + 1 SD. A Patient Health Questionnaire-9 score of ≥ 10 indicated depression. Among 5550 non-shift working adults aged 19–80 years, the prevalence rates of depression in the early, intermediate, and late chronotype groups were 7.4%, 4.5%, and 9.3%, respectively. Women with late chronotype (odds ratio [OR] = 2.9, 95% confidence interval [CI] = 1.8–4.7) showed a higher risk of depression than women with intermediate chronotype after adjusting for covariates. Women with early chronotype did not show a significant difference in depression risk (OR = 1.3, 95% CI = 0.9–2.0). In conclusion, late chronotype is associated with an increased risk of depression in women but not in men. Early chronotype is not associated with depression in women or men.
Intrinsic multiplication rate variation and plasticity of human blood stage malaria parasites
Authors: Stewart Lindsay B. , Diaz-Ingelmo Ofelia , Claessens Antoine , Abugri James , Pearson Richard D. , Goncalves Sonia , Drury Eleanor , Kwiatkowski Dominic P. , Awandare Gordon A. , Conway David J. 
Published: October 2020

AbstractPathogen multiplication rate is theoretically an important determinant of virulence, although often poorly understood and difficult to measure accurately. We show intrinsic asexual blood stage multiplication rate variation of the major human malaria parasite Plasmodium falciparum to be associated with blood-stage infection intensity in patients. A panel of clinical isolates from a highly endemic West African population was analysed repeatedly during five months of continuous laboratory culture, showing a range of exponential multiplication rates at all timepoints tested, mean rates increasing over time. All isolates had different genome sequences, many containing within-isolate diversity that decreased over time in culture, but increases in multiplication rates were not primarily attributable to genomic selection. New mutants, including premature stop codons emerging in a few isolates, did not attain sufficiently high frequencies to substantially affect overall multiplication rates. Significantly, multiplication rate variation among the isolates at each of the assayed culture timepoints robustly correlated with parasite levels seen in patients at clinical presentation, indicating innate parasite control of multiplication rate that contributes to virulence.
Nacre toughening due to cooperative plastic deformation of stacks of co-oriented aragonite platelets
Authors: Loh Hyun-Chae , Divoux Thibaut , Gludovatz Bernd , Gilbert Pupa U. P. A. , Ritchie Robert O. , Ulm Franz-Josef , Masic Admir 
Published: October 2020

AbstractNacre’s structure-property relationships have been a source of inspiration for designing advanced functional materials with both high strength and toughness. These outstanding mechanical properties have been mostly attributed to the interplay between aragonite platelets and organic matrices in the typical brick-and-mortar structure. Here, we show that crystallographically co-oriented stacks of aragonite platelets, in both columnar and sheet nacre, define another hierarchical level that contributes to the toughening of nacre. By correlating piezo-Raman and micro-indentation results, we quantify the residual strain energy associated with strain hardening capacity. Our findings suggest that the aragonite stacks, with characteristic dimensions of around 20 µm, effectively store energy through cooperative plastic deformation. The existence of a larger length scale beyond the brick-and-mortar structure offers an opportunity for a more efficient implementation of biomimetic design.
Water soluble selenometabolome of Cardamine violifolia
Authors: Ouerdane Laurent , Both Eszter Borbála , Xiang Jiqian , Yin Hongqing , Kang Yu , Shao Shuxun , Kiszelák Katalin , Jókai Zsuzsa , Dernovics Mihály 
Published: October 2020

Abstract
Low molecular weight selenium containing metabolites in the leaves of the selenium hyperaccumulator Cardamine violifolia (261 mg total Se per kg d.w.) were targeted in this study. One dimensional cation exchange chromatography coupled to ICP-MS was used for purification and fractionation purposes prior to LC-Unispray-QTOF-MS analysis. The search for selenium species in full scan spectra was assisted with an automated mass defect based filtering approach. Besides selenocystathionine, selenohomocystine and its polyselenide derivative, a total number of 35 water soluble selenium metabolites other than selenolanthionine were encountered, including 30 previously unreported compounds. High occurrence of selenium containing hexoses was observed, together with the first assignment of N-glycoside derivatives of selenolanthionine. Quantification of the most abundant selenium species, selenolanthionine, was carried out with an ion pairing LC – post column isotope dilution ICP-MS setup, which revealed that this selenoamino acid accounted for 30% of the total selenium content of the leaf (78 mg (as Se) per kg d.w.).
A rational study on the geometric and electronic properties of single-atom catalysts for enhanced catalytic performance
Authors: Xue Qi , Xie Yi , Wu Simson , Wu Tai-Sing , Soo Yun-Liang , Day Sarah , Tang Chiu C. , Man Ho W. , Yuen Sha T. , Wong Kwok-yin , Wang Ying , Lo Benedict T. W. , Tsang Shik C. E. 
Published: October 2020

We investigate the geometric and electronic properties of single-atom catalysts (SACs) for electrocatalytic CO2 reduction reaction (eCO2RR).
Immune-related miRNA signature identifies prognosis and immune landscape in head and neck squamous cell carcinomas
Authors: Ma Bo , Li Hui , Qiao Jia , Meng Tao , Yu Riyue 
Published: October 2020

Abstract
Background: Head and neck squamous cell carcinoma (HNSCC) is recognised as an immune active cancer, but little is known about the role of microRNAs (miRNAs) in it. In the present study, we aim to determine a prognostic and immune-related miRNAs signature (IRMS) in HNSCC.
Methods: Spearman correlation analysis was used to screen out prognostic immune-related miRNAs based on single-sample gene set enrichment analysis (ssGSEA). Least absolute shrinkage and selection operator (LASSO) Cox regression model was used to establish IRMS in HNSCC. Then, the influence of the IRMS on HNSCC was comprehensively analysed.
Results: We obtained 11 prognostic immune-related miRNAs based on ssGSEA. Then an IRMS integrated with six miRNAs was established through LASSO Cox regression analysis. The stratification survival analysis indicated that IRMS was independent from other characteristics and performed favourably in the overall survival (OS) prediction. The function annotation suggested that IRMS was highly associated with the immune-related response biological processes and pathways which are so important for tumorigenesis of HNSCC. Moreover, the nomogram demonstrated that our model was identified as an independent prognostic factor. In addition, we found that IRMS was significantly correlated with the immune infiltration and expression of critical immune checkpoints, indicating that the poor prognosis might be caused partly by immunosuppressive microenvironment.
Conclusion: We established a novel IRMS, which exhibited a potent prognostic value and could be representative of immune status in HNSCC.
„… das klassische Problem ist zu sagen, man ist ja jetzt palliativ“ – Versorgung am Lebensende an den Schnittstellen zur hausärztlichen Versorgung in ländlich geprägten Regionen – eine qualitative multiperspektivische Studie
Authors: Schrader Sophie , van Baal Katharina , Schleef Tanja , Schneider Nils , Afshar Kambiz , Müller-Mundt Gabriele 
Published: October 2020

Zusammenfassung
Ziel der Studie Exploration der palliativen Versorgung am Lebensende in zwei ländlich geprägten Landkreisen Niedersachsens.
Methodik Qualitative Interviews mit Expert*innen der regionalen Palliativversorgung (z. B. Mitarbeiter*innen von Hospizen, spezialisierten ambulanten Palliativdiensten, Palliativstationen) an den Schnittstellen zur hausärztlichen Versorgung wurden inhaltsanalytisch ausgewertet.
Ergebnisse Interviewt wurden 28 Expert*innen (75 % weiblich). Sie betonten vier Aspekte: Um die Begleitung am Lebensende zu sichern, gilt es 1) dem Mangel an Hausärzt*innen und Pflegefachpersonen zu begegnen, 2) die an der Versorgung beteiligten Professionen für palliative Bedürfnisse und den Bedarf zu sensibilisieren, um Maßnahmen frühzeitig einzuleiten, und 3) die Aufklärung und Information von Patient*innen und Angehörigen über eine palliative Versorgung zu verbessern, sowie 4) die Vernetzung und Kooperation der an der Palliativversorgung beteiligten Professionen zu stärken.
Schlussfolgerung Die Versorgung am Lebensende ist eng mit der Sicherstellung der hausärztlichen und pflegerischen Versorgung verknüpft. In der allgemeinen Palliativversorgung ist die frühzeitige Identifikation palliativer Bedürfnisse und des Bedarfs zentral.
Impact of Endodontic Instrumentation on Surface Roughness of Various Nickel-Titanium Rotary Files
Authors: Zafar Muhammad Sohail 
Published: October 2020

AbstractObjectives The aim of the present study was to evaluate the surface roughness (SR) of various nickel-titanium (NiTi) rotary endodontic instruments (ProTaper Next [PTN], WaveOne Gold [WOG], and ProTaper Gold [PTG]) before and after root canal instrumentation.Materials and Methods For each type (PTN, WOG, and PTG), the endodontic instrumentation was performed using extracted mandibular molar teeth’s curved mesial root canals (curvature: 20–40 degrees) after determining the working length. Each NiTi file was cleaned, and sterilized following preparation of four root canals and characterized for surface properties before and after endodontic instrumentation using a contact-mode three-dimensional surface profiler. The data were analyzed statistically using Statistical Package for the Social Sciences for SR parameters including average surface roughness value (Sa), root mean square roughness (Sq), and peak to valley height (Sz).Results Preinstrumentation assessment revealed a significant difference for all the three SR variables (p < 0.05) for the cutting blade and the flute area. WOG instruments showed the highest SR values (p = 0.000). The postinstrumentation assessment revealed significant differences in SR values in the blade and the flute between the three groups (p < 0.05), with WOG and PTG exhibiting the highest values in the blade and flute sections, respectively.Conclusions The SR parameters of intact PTN, WOG, and PTG NiTi files vary and that was increased following the endodontic instrumentation.