bluuebunny/crossref_metadata_2025_split huggingface dataset:
Electron microscopy dataset for the recognition of nanoscale ordering effects and location of nanoparticles
Authors: Boiko Daniil A. , Pentsak Evgeniy O. , Cherepanova Vera A. , Ananikov Valentine P. 
Published: March 2020

AbstractA unique ordering effect has been observed in functional catalytic nanoscale materials. Instead of randomly arranged binding to the catalyst surface, metal nanoparticles show spatially ordered behavior resulting in formation of geometrical patterns. Understanding of such nanoscale materials and analysis of corresponding microscopy images will never be comprehensive without appropriate reference datasets. Here we describe the first dataset of electron microscopy images comprising individual nanoparticles which undergo ordering on a surface towards the formation of geometrical patterns. The dataset developed in this study spans three levels of nanoscale organization: (i) individual nanoparticles (1–5 nm) and arrays of nanoparticles (5–20 nm), (ii) ordering effects (20–200 nm) and (iii) complex patterns (from nm to μm scales). The described dataset for the first time provides a possibility for the development of machine learning algorithms to study the unique phenomena of nanoparticles ordering and hierarchical organization.
Processing citizen science- and machine-annotated time-lapse imagery for biologically meaningful metrics
Authors: Jones Fiona M. , Arteta Carlos , Zisserman Andrew , Lempitsky Victor , Lintott Chris J. , Hart Tom 
Published: March 2020

AbstractTime-lapse cameras facilitate remote and high-resolution monitoring of wild animal and plant communities, but the image data produced require further processing to be useful. Here we publish pipelines to process raw time-lapse imagery, resulting in count data (number of penguins per image) and ‘nearest neighbour distance’ measurements. The latter provide useful summaries of colony spatial structure (which can indicate phenological stage) and can be used to detect movement – metrics which could be valuable for a number of different monitoring scenarios, including image capture during aerial surveys. We present two alternative pathways for producing counts: (1) via the Zooniverse citizen science project Penguin Watch and (2) via a computer vision algorithm (Pengbot), and share a comparison of citizen science-, machine learning-, and expert- derived counts. We provide example files for 14 Penguin Watch cameras, generated from 63,070 raw images annotated by 50,445 volunteers. We encourage the use of this large open-source dataset, and the associated processing methodologies, for both ecological studies and continued machine learning and computer vision development.
Oxytocin Receptors Regulate Social Preference in Zebrafish
Authors: Landin Jenny , Hovey Daniel , Xu Bo , Lagman David , Zettergren Anna , Larhammar Dan , Kettunen Petronella , Westberg Lars 
Published: March 2020

AbstractWith a strong tendency to socialise, the zebrafish is a useful model to study social behaviour, with implications for better treatments of social impairments, for instance in autism spectrum disorders. Although oxytocin is crucial for social behaviour in mammals, the importance of the fish orthologue – isotocin or zebrafish oxytocin (zOT) – for social behaviour in zebrafish is unclear. The aims of this study were firstly, to elucidate the receptor specificity of zOT and the related vasotocin or zebrafish vasopressin (zVP; the orthologue of mammalian vasopressin) and the nonpeptidergic oxytocin receptor antagonist L-368,899, and secondly to investigate if L-368,899 inhibits social preference in zebrafish. The potencies of ligands were evaluated for zOT/zVP family receptors in HEK293 cells. Adult and larval zebrafish were treated with L-368,899 or vehicle and subsequently assessed for social behaviour and anxiety (adults only). The antagonist L-368,899 specifically inhibited the two zOT receptors, but not the two zVP-1 receptors. The antagonist decreased social preference in adult and larval zebrafish. It did not affect anxiety in adults. These results indicate that endogenous zOT, and possibly zVP, is involved in social behaviour in zebrafish via either or both of the two zOT receptors, and show promise for future explorations of the anatomy and evolution of networks underlying social behaviour.
25-years Trends and Risk factors related to Surgical Outcomes of Giant Retinal Tear-Rhegmatogenous Retinal Detachments
Authors: Ting Daniel S. W. , Foo Valencia H. X. , Tan Tien-En , Sie Nicole M. , Wong Chee Wai , Tsai Andrew S. H. , Tan Gavin S. W. , Lim Laurence S. , Yeo Ian Y. S. , Wong Doric W. K. , Ong Sze Guan , Wong Edmund Y. M. , Ang Chong Lye , Lee Shu Yen 
Published: March 2020

AbstractTo describe the 25-year surgical trends, long-term outcomes and risk factors affecting the outcomes of giant retinal tear-related rhegmatogenous retinal detachments (GRT-RRD). Patients’ demographics, pre-operative characteristics, risk factors, operative procedures and post-operative outcomes were collected and divided into three groups – Group A: 1991 to 2015 (overall); Group B: 1991 to 2005, and Group C: 2006 to 2015. Functional and anatomical successes were monitored over a 5-year period. Multivariate logistic regression analysis was performed to identify the risk factors related to functional and anatomical success.127 eyes of 127 patients were included in the study. At 5th year, 69.4% patients had visual acuity (VA) < logMAR 1.0 with 87.5% primary anatomical success rate. While the functional outcome remained the same between group B and C, there was an increase in the anatomical success from 89.7% to 100%, albeit not statistically significant. Patients with worse presenting VA, 150 degrees or more of giant retina tear, macula-detached status and presence of PVR were associated with VA of> logMAR 1.0 (all p < 0.05). The types of surgery (TPPV vs combined SB/TPPV), number of breaks, lens extraction and additional cryotherapy were not associated with the functional or anatomical success. In conclusion, the GRT-RRD functional and structural outcomes were comparable between 1991–2005 and 2006–2015, albeit a statistically insignificant improvement of anatomical outcome over the past 25 years. Worse presenting VA, 150 degrees or more of giant retinal tear, detached macula and presence of PVR were associated with poorer visual outcome.
A high-resolution polarimeter formed from inexpensive optical parts
Authors: Harvie A. J. , Phillips T. W. , deMello J. C. 
Published: March 2020

AbstractWe describe a high resolution laser polarimeter built from commodity optical components. The optical rotation angle is determined by measuring the phase difference between two harmonically modulated polarised laser beams – an ‘object beam’ that passes through the sample under test and a ‘reference beam’ that bypasses the sample. The complete polarimeter may be assembled from low cost off-the-shelf parts for less than £300 (UK Sterling). Data acquisition and analysis are carried out on a microcontroller running an efficient algorithm based on the sliding Discrete Fourier Transform. Despite its low cost, the polarimeter is a fully automatic, research-grade instrument with an accuracy of ±0.0013° and a precision of ±0.0028° – comparable to far costlier commercial instruments. The polarimeter’s ease of use, compact size, fast measurement times and high angular resolution make it a capable and versatile tool for analytical science, while its low cost means it is ideally suited for use in resource-constrained environments and process monitoring. The polarimeter is released here as open hardware, with technical diagrams, a full parts list, and source code for its firmware included as Supplementary Information.
Hypoplasia of cerebellar afferent networks in Down syndrome revealed by DTI-driven tensor based morphometry
Authors: Lee Nancy Raitano , Nayak Amritha , Irfanoglu M. Okan , Sadeghi Neda , Stoodley Catherine J. , Adeyemi Elizabeth , Clasen Liv S. , Pierpaoli Carlo 
Published: March 2020

AbstractQuantitative magnetic resonance imaging (MRI) investigations of brain anatomy in children and young adults with Down syndrome (DS) are limited, with no diffusion tensor imaging (DTI) studies covering that age range. We used DTI-driven tensor based morphometry (DTBM), a novel technique that extracts morphometric information from diffusion data, to investigate brain anatomy in 15 participants with DS and 15 age- and sex-matched typically developing (TD) controls, ages 6–24 years (mean age ~17 years). DTBM revealed marked hypoplasia of cerebellar afferent systems in DS, including fronto-pontine (middle cerebellar peduncle) and olivo-cerebellar (inferior cerebellar peduncle) connections. Prominent gray matter hypoplasia was observed in medial frontal regions, the inferior olives, and the cerebellum. Very few abnormalities were detected by classical diffusion MRI metrics, such as fractional anisotropy and mean diffusivity. Our results highlight the potential importance of cerebro-cerebellar networks in the clinical manifestations of DS and suggest a role for DTBM in the investigation of other brain disorders involving white matter hypoplasia or atrophy.
Sustained virological response to hepatitis C therapy does not decrease the incidence of systemic lupus erythematosus or rheumatoid arthritis
Authors: Hsu Wei-Fan , Chen Chi-Yi , Tseng Kuo-Chih , Lai Hsueh-Chou , Kuo Hsing-Tao , Hung Chao-Hung , Tung Shui-Yi , Wang Jing-Houng , Chen Jyh-Jou , Lee Pei-Lun , Chien Rong-Nan , Lin Chun-Yen , Yang Chi-Chieh , Lo Gin-Ho , Tai Chi-Ming , Lin Chih-Wen , Kao Jia-Horng , Liu Chun-Jen , Liu Chen-Hua , Yan Sheng-Lei , Bair Ming-Jong , Su Wei-Wen , Chu Cheng-Hsin , Chen Chih-Jen , Lo Ching-Chu , Cheng Pin-Nan , Chiu Yen-Cheng , Wang Chia-Chi , Cheng Jin-Shiung , Tsai Wei-Lun , Lin Han-Chieh , Huang Yi-Hsiang , Tsai Pei-Chien , Huang Jee-Fu , Dai Chia-Yen , Chuang Wan-Long , Yu Ming-Lung , Peng Cheng-Yuan 
Published: March 2020

AbstractIn patients with chronic hepatitis C (CHC), the effects of baseline characteristics, virological profiles, and therapeutic outcome to pegylated interferon plus ribavirin (PR) therapy on autoimmune diseases are unknown. Taiwanese Chronic Hepatitis C Cohort is a nationwide hepatitis C virus registry cohort comprising 23 hospitals of Taiwan. A total of 12,770 CHC patients receiving PR therapy for at least 4 weeks between January 2003 and December 2015 were enrolled and their data were linked to the Taiwan National Health Insurance Research Database for studying the development of 10 autoimmune diseases. The mean follow-up duration was 5.3 ± 2.9 years with a total of 67,930 person-years, and the annual incidence of systemic lupus erythematosus (SLE) or rheumatoid arthritis (RA) was 0.03%. Other autoimmune diseases were not assessable due to few events. Body mass index ≥24 kg/m2 was an independent predictor of the low incidence of SLE or RA (hazard ratio 0.40, 95% confidence interval 0.17–0.93, p = 0.034). A sustained virological response (SVR) to PR therapy was not associated with the low incidence of SLE or RA in any subgroup analysis. CHC patients achieving SVR to PR therapy did not exhibit an impact on the incidence of SLE or RA compared with non-SVR patients.
Mid- to long-wave infrared computational spectroscopy with a graphene metasurface modulator
Authors: Shrestha Vivek Raj , Craig Benjamin , Meng Jiajun , Bullock James , Javey Ali , Crozier Kenneth B. 
Published: March 2020

AbstractIn recent years there has been much interest concerning the development of modulators in the mid- to long-wave infrared, based on emerging materials such as graphene. These have been frequently pursued for optical communications, though also for other specialized applications such as infrared scene projectors. Here we investigate a new application for graphene modulators in the mid- to long-wave infrared. We demonstrate, for the first time, computational spectroscopy in the mid- to long-wave infrared using a graphene-based metasurface modulator. Furthermore, our metasurface device operates at low gate voltage. To demonstrate computational spectroscopy, we provide our algorithm with the measured reflection spectra of the modulator at different gate voltages. We also provide it with the measured reflected light power as a function of the gate voltage. The algorithm then estimates the input spectrum. We show that the reconstructed spectrum is in good agreement with that measured directly by a Fourier transform infrared spectrometer, with a normalized mean-absolute-error (NMAE) of 0.021.
Retinal Organoids derived from hiPSCs of an AIPL1-LCA Patient Maintain Cytoarchitecture despite Reduced levels of Mutant AIPL1
Authors: Lukovic Dunja , Artero Castro Ana , Kaya Koray Dogan , Munezero Daniella , Gieser Linn , Davó-Martínez Carlota , Corton Marta , Cuenca Nicolás , Swaroop Anand , Ramamurthy Visvanathan , Ayuso Carmen , Erceg Slaven 
Published: March 2020

AbstractAryl hydrocarbon receptor-interacting protein-like 1 (AIPL1) is a photoreceptor-specific chaperone that stabilizes the effector enzyme of phototransduction, cGMP phosphodiesterase 6 (PDE6). Mutations in the AIPL1 gene cause a severe inherited retinal dystrophy, Leber congenital amaurosis type 4 (LCA4), that manifests as the loss of vision during the first year of life. In this study, we generated three-dimensional (3D) retinal organoids (ROs) from human induced pluripotent stem cells (hiPSCs) derived from an LCA4 patient carrying a Cys89Arg mutation in AIPL1. This study aimed to (i) explore whether the patient hiPSC-derived ROs recapitulate LCA4 disease phenotype, and (ii) generate a clinically relevant resource to investigate the molecular mechanism of disease and safely test novel therapies for LCA4 in vitro. We demonstrate reduced levels of the mutant AIPL1 and PDE6 proteins in patient organoids, corroborating the findings in animal models; however, patient-derived organoids maintained retinal cell cytoarchitecture despite significantly reduced levels of AIPL1.
Optical coherence tomography angiography as a novel approach to contactless evaluation of sublingual microcirculation: A proof of principle study
Authors: Hessler Michael , Nelis Pieter , Ertmer Christian , Alnawaiseh Maged , Lehmann Florian , Schmidt Christina , Kampmeier Tim-Gerald , Rehberg Sebastian Willy , Arnemann Philip-Helge , Rovas Alexandros 
Published: March 2020

AbstractMicrocirculatory disorders are crucial in pathophysiology of organ dysfunction in critical illness. Evaluation of sublingual microcirculation is not routinely conducted in daily practice due to time-consuming analysis and susceptibility to artifacts. We investigated the suitability of optical coherence tomography angiography (OCTA) for contactless evaluation of sublingual microcirculation. Sublingual microcirculation was imaged in 10 healthy volunteers, using an OCTA device and an incident dark field (IDF) illumination microscopy (current gold standard). OCTA images were analyzed with regard to flow density and perfused vessel density (PVDbyOCTA). IDF videos were analyzed following current recommendations. Flow density was automatically extracted from OCTA images (whole en face 48.9% [43.2; 54.5]; central ring 52.6% [43.6; 60.6]). PVDbyOCTA did not differ from the PVD calculated from IDF videos (PVDbyOCTA 18.6 mm/mm² [18.0; 21.7]) vs. PVDbyIDF 21.0 mm/mm² [17.5; 22.9]; p = 0.430). Analysis according to Bland-Altman revealed a mean bias of 0.95 mm/mm² (95% Confidence interval −1.34 to 3.25) between PVDbyOCTA and PVDbyIDF with limits of agreement of −5.34 to 7.24 mm/mm². This study is the first to demonstrate the suitability of OCTA for evaluating sublingual microcirculation. Comparison of the perfused vessel density between methods showed a plausible level of agreement.
Fungal Cell Wall and Methyl-β–Cyclodextrin Synergistically Enhance Paclitaxel Biosynthesis and Secretion in Corylus avellana Cell Suspension Culture
Authors: Farhadi Siamak , Moieni Ahmad , Safaie Naser , Sabet Mohammad Sadegh , Salehi Mina 
Published: March 2020

AbstractPaclitaxel is the top-selling chemotherapeutic drug used for the treatment of lung, ovarian and breast cancer as well as Kaposi’s sarcoma. Cell suspension culture (CSC) of Corylus avellana has been addressed as a promising alternative for producing paclitaxel. In this study, endophytic fungus strain YEF33 was isolated from Taxus baccata and identified as Coniothyrium palmarum. The effects of the elicitors derived from this fungus including cell extract, culture filtrate and cell wall (CW) and also chitin, alone or in combination with Methyl-β-Cyclodextrin (MBCD), on paclitaxel biosynthesis in C. avellana CSC were assayed for the first time. CW of C. palmarum was the most efficient fungal elicitor for paclitaxel biosynthesis in C. avellana CSC. The results revealed that MBCD affected paclitaxel biosynthesis differently depending on fungal elicitor type and vice versa. MBCD, either alone or in combination with fungal elicitors, induced a high secretion of paclitaxel, suggesting the decrement of toxicity and retro-inhibition processes of paclitaxel for cells. The joint effects of C. palmarum CW (2.5% (v/v) on 17th day) and 50 mM MBCD synergistically enhanced paclitaxel biosynthesis (402.4 µg l−1; 5.8-fold), 78.6% of which (316.5 µg l−1) were secreted into culture medium, a level 146% higher than that in control.
Renal carcinoma CD105−/CD44− cells display stem-like properties in vitro and form aggressive tumors in vivo
Authors: Fiedorowicz M. , Khan M. I. , Strzemecki D. , Orzeł J. , Wełniak-Kamińska M. , Sobiborowicz A , Wieteska M. , Rogulski Z. , Cheda L. , Wargocka-Matuszewska W. , Kilian K. , Szczylik C. , Czarnecka A. M. 
Published: March 2020

AbstractClear cell renal cell carcinoma (ccRCC) is the most common kidney cancer. Prognosis for ccRCC is generally poor since it is largely resistant to chemo- and radiotherapy. Many studies suggested that cancer stem cells/tumor initiating cells (CSCs/TICs) are responsible for development of tumor, disease progression, aggressiveness, metastasis and drug resistance. However, tumorigenic potential of CSCs/TICs isolated from established RCC cell lines – basic ccRCC research model – has never been investigatedin vivo. CD105+, CD105−, CD44+ and CD44− as well as CD44−/CD105− CD44+/CD105+ and CD44−/CD105+ cells were isolated from Caki-1 RCC cell line, confirming coexistence of multiple subpopulations of stem-related phenotype in stable cell line. Sorted cells were injected subcutaneously into NOD SCID mice and tumor growth was monitored with MRI and PET/CT. Tumor growth was observed after implantation of CD105+, CD44+, CD44−, CD44−/CD105+ and CD44−/CD105− but not CD105− or CD44+/CD105+. Implantation of CD44−/CD105− cells induced tumors that were characterized by longer T1 and distinct metabolic pattern than other tumors. All the tumors were characterized by low uptake of [18F]FDG. CD105+ and CD44− tumors expresses Nanog and Oct-4, while CD44− tumors additionally expressed endothelial cell marker - CD31.
In vitro modelling of alveolar repair at the air-liquid interface using alveolar epithelial cells derived from human induced pluripotent stem cells
Authors: van Riet Sander , Ninaber Dennis K. , Mikkers Harald M. M. , Tetley Teresa D. , Jost Carolina R. , Mulder Aat A. , Pasman Thijs , Baptista Danielle , Poot André A. , Truckenmüller Roman , Mummery Christine L. , Freund Christian , Rottier Robbert J. , Hiemstra Pieter S. 
Published: March 2020

AbstractResearch on acute and chronic lung diseases would greatly benefit from reproducible availability of alveolar epithelial cells (AEC). Primary alveolar epithelial cells can be derived from human lung tissue but the quality of these cells is highly donor dependent. Here, we demonstrated that culture of EpCAM+ cells derived from human induced pluripotent stem cells (hiPSC) at the physiological air-liquid interface (ALI) resulted in type 2 AEC-like cells (iAEC2) with alveolar characteristics. iAEC2 cells expressed native AEC2 markers (surfactant proteins and LPCAT-1) and contained lamellar bodies. ALI-iAEC2 were used to study alveolar repair over a period of 2 weeks following mechanical wounding of the cultures and the responses were compared with those obtained using primary AEC2 (pAEC2) isolated from resected lung tissue. Addition of the Wnt/β-catenin activator CHIR99021 reduced wound closure in the iAEC2 cultures but not pAEC2 cultures. This was accompanied by decreased surfactant protein expression and accumulation of podoplanin-positive cells at the wound edge. These results demonstrated the feasibility of studying alveolar repair using hiPSC-AEC2 cultured at the ALI and indicated that this model can be used in the future to study modulation of alveolar repair by (pharmaceutical) compounds.
Geodynamic subduction models constrained by deep earthquakes beneath the Japan Sea and eastern China
Authors: Čížková Hana , Zahradník Jiří , Liu Junqing , Bina Craig R. 
Published: March 2020

AbstractDetails of Pacific plate subduction under the Japan Sea and associated current seismicity remain challenging. Seismic tomography reveals a continuous slab dipping at ~30° down to ~600 km, and earthquake mechanisms point to down-dip compression. Further, the slab is lying at the 660-km discontinuity, and this zone is aseismic. We suggest that this pattern results from the slab’s negative thermal buoyancy, resistance of the viscous lower mantle, and buoyancy forces associated with the phase transitions at 410 km and 660 km. Our model comprises an ageing subducting plate, nonlinear rheology and major phase transitions. The model explains the observed low dip angle of the slab and predicts a detailed stress pattern related to bending down to 450 km, followed by unbending as the slab is laid flat upon the 660 km boundary. Remarkably, in the bending/unbending regions, down-dip compression occurs close to the slab top/bottom, respectively. As only down-dip compression is observed, we argue that the earthquakes are mapping the top and bottom of the slab. The absence of seismicity in the flat-lying slab is explained by significantly lower stresses and higher temperatures. With this new knowledge, increasingly accurate seismic locations will considerably improve images of finite-extent slab geometry.
Oral lichen planus interactome reveals CXCR4 and CXCL12 as candidate therapeutic targets
Authors: Rivera César , Crisóstomo Mariangela Fernanda , Peña Carolina , González-Díaz Paulina , González-Arriagada Wilfredo Alejandro 
Published: March 2020

AbstractToday, we face difficulty in generating new hypotheses and understanding oral lichen planus due to the large amount of biomedical information available. In this research, we have used an integrated bioinformatics approach assimilating information from data mining, gene ontologies, protein–protein interaction and network analysis to predict candidate genes related to oral lichen planus. A detailed pathway analysis led us to propose two promising therapeutic targets: the stromal cell derived factor 1 (CXCL12) and the C-X-C type 4 chemokine receptor (CXCR4). We further validated our predictions and found that CXCR4 was upregulated in all oral lichen planus tissue samples. Our bioinformatics data cumulatively support the pathological role of chemokines and chemokine receptors in oral lichen planus. From a clinical perspective, we suggest a drug (plerixafor) and two therapeutic targets for future research.