bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of machine learning-based clinical decision support system for hepatocellular carcinoma
Authors: Choi Gwang Hyeon , Yun Jihye , Choi Jonggi , Lee Danbi , Shim Ju Hyun , Lee Han Chu , Chung Young-Hwa , Lee Yung Sang , Park Beomhee , Kim Namkug , Kim Kang Mo 
Published: September 2020

AbstractThere is a significant discrepancy between the actual choice for initial treatment option for hepatocellular carcinoma (HCC) and recommendations from the currently used BCLC staging system. We develop a machine learning-based clinical decision support system (CDSS) for recommending initial treatment option in HCC and predicting overall survival (OS). From hospital records of 1,021 consecutive patients with HCC treated at a single centre in Korea between January 2010 and October 2010, we collected information on 61 pretreatment variables, initial treatment, and survival status. Twenty pretreatment key variables were finally selected. We developed the CDSS from the derivation set (N = 813) using random forest method and validated it in the validation set (N = 208). Among the 1,021 patients (mean age: 56.9 years), 81.8% were male and 77.0% had positive hepatitis B BCLC stages 0, A, B, C, and D were observed in 13.4%, 26.0%, 18.0%, 36.6%, and 6.3% of patients, respectively. The six multi-step classifier model was developed for treatment decision in a hierarchical manner, and showed good performance with 81.0% of accuracy for radiofrequency ablation (RFA) or resection versus not, 88.4% for RFA versus resection, and 76.8% for TACE or not. We also developed seven survival prediction models for each treatment option. Our newly developed HCC-CDSS model showed good performance in terms of treatment recommendation and OS prediction and may be used as a guidance in deciding the initial treatment option for HCC.
Optical tracking and laser-induced mortality of insects during flight
Authors: Keller Matthew D. , Norton Bryan J. , Farrar David J. , Rutschman Phil , Marvit Maclen , Makagon Arty 
Published: September 2020

AbstractAddressing the need for novel insect observation and control tools, the Photonic Fence detects and tracks mosquitoes and other flying insects and can apply lethal doses of laser light to them. Previously, we determined lethal exposure levels for a variety of lasers and pulse conditions on anesthetized Anopheles stephensi mosquitoes. In this work, similar studies were performed while the subjects were freely flying within transparent cages two meters from the optical system; a proof-of-principle demonstration of a 30 m system was also performed. From the dose–response curves of mortality data created as a function of various beam diameter, pulse width, and power conditions at visible and near-infrared wavelengths, the visible wavelengths required significantly lower laser exposure than near infrared wavelengths to disable subjects, though near infrared sources remain attractive given their cost and retina safety. The flight behavior of the subjects and the performance of the tracking system were found to have no impact on the mortality outcomes for pulse durations up to 25 ms, which appears to be the ideal duration to minimize required laser power. The results of this study affirm the practicality of using optical approaches to protect people and crops from pestilent flying insects.
Bidirectional alterations in antibiotics susceptibility in Staphylococcus aureus—Pseudomonas aeruginosa dual-species biofilm
Authors: Trizna Elena Y. , Yarullina Maria N. , Baidamshina Diana R. , Mironova Anna V. , Akhatova Farida S. , Rozhina Elvira V. , Fakhrullin Rawil F. , Khabibrakhmanova Alsu M. , Kurbangalieva Almira R. , Bogachev Mikhail I. , Kayumov Airat R. 
Published: September 2020

AbstractIn mixed infections, the bacterial susceptibility differs significantly compared to monocultures of bacteria, and generally the concentrations of antibiotics required for the treatment increases drastically. For S. aureus and P. aeruginosa dual species biofilms, it has been numerously reported that P. aeruginosa decreases S. aureus susceptibility to a broad range of antibiotics, including beta-lactams, glycopeptides, aminoglycosides, macrolides, while sensitizes to quinolones via secretion of various metabolites. Here we show that S. aureus also modulates the susceptibility of P. aeruginosa to antibiotics in mixed cultures. Thus, S. aureus—P. aeruginosa consortium was characterized by tenfold increase in susceptibility to ciprofloxacin and aminoglycosides compared to monocultures. The same effect could be also achieved by the addition of cell-free culture of S. aureus to P. aeruginosa biofilm. Moreover, similar increase in antibiotics efficacy could be observed following addition of S. aureus suspension to the P. aeruginosa mature biofilm, compared to P. aeruginosa monoculture, and vice versa. These findings open promising perspectives to increase the antimicrobial treatment efficacy of the wounds infected with nosocomial pathogens by the transplantation of the skin residential microflora.
Pluripotent stem cell model of Shwachman–Diamond syndrome reveals apoptotic predisposition of hemoangiogenic progenitors
Authors: Hamabata Takayuki , Umeda Katsutsugu , Kouzuki Kagehiro , Tanaka Takayuki , Daifu Tomoo , Nodomi Seishiro , Saida Satoshi , Kato Itaru , Baba Shiro , Hiramatsu Hidefumi , Osawa Mitsujiro , Niwa Akira , Saito Megumu K. , Kamikubo Yasuhiko , Adachi Souichi , Hashii Yoshiko , Shimada Akira , Watanabe Hiroyoshi , Osafune Kenji , Okita Keisuke , Nakahata Tatsutoshi , Watanabe Kenichiro , Takita Junko , Heike Toshio 
Published: September 2020

AbstractShwachman–Diamond syndrome (SDS), an autosomal recessive disorder characterized by bone marrow failure, exocrine pancreatic insufficiency, and skeletal abnormalities, is caused by mutations in the Shwachman–Bodian–Diamond syndrome (SBDS) gene, which plays a role in ribosome biogenesis. Although the causative genes of congenital disorders frequently involve regulation of embryogenesis, the role of the SBDS gene in early hematopoiesis remains unclear, primarily due to the lack of a suitable experimental model for this syndrome. In this study, we established induced pluripotent stem cells (iPSCs) from patients with SDS (SDS-iPSCs) and analyzed their in vitro hematopoietic and endothelial differentiation potentials. SDS-iPSCs generated hematopoietic and endothelial cells less efficiently than iPSCs derived from healthy donors, principally due to the apoptotic predisposition of KDR+CD34+ common hemoangiogenic progenitors. By contrast, forced expression of SBDS gene in SDS-iPSCs or treatment with a caspase inhibitor reversed the deficiency in hematopoietic and endothelial development, and decreased apoptosis of their progenitors, mainly via p53-independent mechanisms. Patient-derived iPSCs exhibited the hematological abnormalities associated with SDS even at the earliest hematopoietic stages. These findings will enable us to dissect the pathogenesis of multiple disorders associated with ribosomal dysfunction.
Probability distribution of copy number alterations along the genome: an algorithm to distinguish different tumour profiles
Authors: Esteves Luísa , Caramelo Francisco , Ribeiro Ilda Patrícia , Carreira Isabel M. , de Melo Joana Barbosa 
Published: September 2020

AbstractCopy number alterations (CNAs) comprise deletions or amplifications of fragments of genomic material that are particularly common in cancer and play a major contribution in its development and progression. High resolution microarray-based genome-wide technologies have been widely used to detect CNAs, generating complex datasets that require further steps to allow for the determination of meaningful results. In this work, we propose a methodology to determine common regions of CNAs from these datasets, that in turn are used to infer the probability distribution of disease profiles in the population. This methodology was validated using simulated data and assessed using real data from Head and Neck Squamous Cell Carcinoma and Lung Adenocarcinoma, from the TCGA platform. Probability distribution profiles were produced allowing for the distinction between different phenotypic groups established within that cohort. This method may be used to distinguish between groups in the diseased population, within well-established degrees of confidence. The application of such methods may be of greater value in the clinical context both as a diagnostic or prognostic tool and, even as a useful way for helping to establish the most adequate treatment and care plans.
Molecular imaging and deep learning analysis of uMUC1 expression in response to chemotherapy in an orthotopic model of ovarian cancer
Authors: Zhao Hongwei , Hayat Hasaan , Ma Xiaohong , Fan Daguang , Wang Ping , Moore Anna 
Published: September 2020

AbstractArtificial Intelligence (AI) algorithms including deep learning have recently demonstrated remarkable progress in image-recognition tasks. Here, we utilized AI for monitoring the expression of underglycosylated mucin 1 (uMUC1) tumor antigen, a biomarker for ovarian cancer progression and response to therapy, using contrast-enhanced in vivo imaging. This was done using a dual-modal (magnetic resonance and near infrared optical imaging) uMUC1-specific probe (termed MN-EPPT) consisted of iron-oxide magnetic nanoparticles (MN) conjugated to a uMUC1-specific peptide (EPPT) and labeled with a near-infrared fluorescent dye, Cy5.5. In vitro studies performed in uMUC1-expressing human ovarian cancer cell line SKOV3/Luc and control uMUC1low ES-2 cells showed preferential uptake on the probe by the high expressor (n = 3, p < .05). A decrease in MN-EPPT uptake by SKOV3/Luc cells in vitro due to uMUC1 downregulation after docetaxel therapy was paralleled by in vivo imaging studies that showed a reduction in probe accumulation in the docetaxel treated group (n = 5, p < .05). The imaging data were analyzed using deep learning-enabled segmentation and quantification of the tumor region of interest (ROI) from raw input MRI sequences by applying AI algorithms including a blend of Convolutional Neural Networks (CNN) and Fully Connected Neural Networks. We believe that the algorithms used in this study have the potential to improve studying and monitoring cancer progression, amongst other diseases.
Development of the muographic tephra deposit monitoring system
Authors: Tanaka Hiroyuki K. M. 
Published: September 2020

AbstractMeasurements of volcanic tephra fallout deposits provide useful information about the magnitude and intensity of explosive volcanic eruptions and potential for remobilization of deposits as dangerous volcanic flows. However, gathering information in the vicinity of erupting craters is extremely dangerous, and moreover, it is often quite difficult to determine deposit thickness proximal to volcanic craters because the thickness of the deposit is too great to easily measure; thus, airborne remote sensing technologies have generally been utilized during the intermission between eruptions. As an alternative tool, a muographic tephra deposit monitoring system was developed in this work. Here we report the performance of this system by applying the muographic data acquired at Sakurajima volcano, Japan as an example. By assuming the average density of the deposit was 2.0 g cm−3, the deposit thicknesses measured with muography were in agreement with the airborne results, indicating that volcanic fallout built up within the upper river basin, showed its potential for monitoring the episodic tephra fallouts even during eruptions.
Actin bundles play a different role in shaping scales compared to bristles in the mosquito Aedes aegypti
Authors: Djokic Sanja , Bakhrat Anna , Tsurim Ido , Urakova Nadya , Rasgon Jason L. , Abdu Uri 
Published: September 2020

AbstractInsect epithelial cells contain cellular extensions such as bristles, hairs, and scales. These cellular extensions are homologous structures that differ in morphology and function. They contain actin bundles that dictate their cellular morphology. While the organization, function, and identity of the major actin-bundling proteins in bristles and hairs are known, this information on scales is unknown. In this study, we characterized the development of scales and the role of actin bundles in the mosquito, Aedes aegypti. We show that scales undergo drastic morphological changes during development, from a cylindrical to flat shape with longer membrane invagination. Scale actin-bundle distribution changes from the symmetrical organization of actin bundles located throughout the bristle membrane to an asymmetrical organization. By chemically inhibiting actin polymerization and by knocking out the forked gene in the mosquito (Ae-Forked; a known actin-bundling protein) by CRISPR-Cas9 gene editing, we showed that actin bundles are required for shaping bristle, hair, and scale morphology. We demonstrated that actin bundles and Ae-Forked are required for bristle elongation, but not for that of scales. In scales, actin bundles are required for width formation. In summary, our results reveal, for the first time, the developmental process of mosquito scale formation and also the role of actin bundles and actin-bundle proteins in scale morphogenesis. Moreover, our results reveal that although scale and bristle are thought to be homologous structures, actin bundles have a differential requirement in shaping mosquito scales compared to bristles.
Driving the polar spin reorientation transition of ultrathin ferromagnets with antiferromagnetic–ferromagnetic phase transition of nearby FeRh alloy film
Authors: Dróżdż P. , Ślęzak M. , Janus W. , Szpytma M. , Nayyef H. , Kozioł-Rachwał A. , Freindl K. , Wilgocka-Ślęzak D. , Korecki J. , Ślęzak T. 
Published: September 2020

AbstractWe show that in-plane to out-of-plane magnetization switching of a ferromagnetic layer can be driven by antiferromagnetic–ferromagnetic phase transition in a nearby FeRh system. For FeRh/Au/FeAu trilayers, the impact of the magnetic phase transition of FeRh onto the perpendicular magnetization of monoatomic FeAu superlattices is transferred across the Au spacer layer via interlayer magnetic coupling. The polar spin reorientation process of the FeAu spins driven by the magnetic phase transition in the FeRh reveals its major features; namely it is reversible and displays hysteresis.
Infant gut microbiota characteristics generally do not modify effects of lipid-based nutrient supplementation on growth or inflammation: secondary analysis of a randomized controlled trial in Malawi
Authors: Hughes Riley L. , Arnold Charles D. , Young Rebecca R. , Ashorn Per , Maleta Ken , Fan Yue-Mei , Ashorn Ulla , Chaima David , Malamba-Banda Chikondi , Kable Mary E. , Dewey Kathryn G. 
Published: September 2020

AbstractAn unhealthy gut microbial community may act as a barrier to improvement in growth and health outcomes in response to nutritional interventions. The objective of this analysis was to determine whether the infant microbiota modified the effects of a randomized controlled trial of lipid-based nutrient supplements (LNS) in Malawi on growth and inflammation at 12 and 18 months, respectively. We characterized baseline microbiota composition of fecal samples at 6 months of age (n = 506, prior to infant supplementation, which extended to 18 months) using 16S rRNA gene sequencing of the V4 region. Features of the gut microbiota previously identified as being involved in fatty acid or micronutrient metabolism or in outcomes relating to growth and inflammation, especially in children, were investigated. Prior to correction for multiple hypothesis testing, the effects of LNS on growth appeared to be modified by Clostridium (p-for-interaction = 0.02), Ruminococcus (p-for-interaction = 0.007), and Firmicutes (p-for-interaction = 0.04) and effects on inflammation appeared to be modified by Faecalibacterium (p-for-interaction = 0.03) and Streptococcus (p-for-interaction = 0.004). However, after correction for multiple hypothesis testing these findings were not statistically significant, suggesting that the gut microbiota did not alter the effect of LNS on infant growth and inflammation in this cohort.
Machine learning improves the prediction of febrile neutropenia in Korean inpatients undergoing chemotherapy for breast cancer
Authors: Cho Bum-Joo , Kim Kyoung Min , Bilegsaikhan Sanchir-Erdene , Suh Yong Joon 
Published: September 2020

AbstractFebrile neutropenia (FN) is one of the most concerning complications of chemotherapy, and its prediction remains difficult. This study aimed to reveal the risk factors for and build the prediction models of FN using machine learning algorithms. Medical records of hospitalized patients who underwent chemotherapy after surgery for breast cancer between May 2002 and September 2018 were selectively reviewed for development of models. Demographic, clinical, pathological, and therapeutic data were analyzed to identify risk factors for FN. Using machine learning algorithms, prediction models were developed and evaluated for performance. Of 933 selected inpatients with a mean age of 51.8 ± 10.7 years, FN developed in 409 (43.8%) patients. There was a significant difference in FN incidence according to age, staging, taxane-based regimen, and blood count 5 days after chemotherapy. The area under the curve (AUC) built based on these findings was 0.870 on the basis of logistic regression. The AUC improved by machine learning was 0.908. Machine learning improves the prediction of FN in patients undergoing chemotherapy for breast cancer compared to the conventional statistical model. In these high-risk patients, primary prophylaxis with granulocyte colony-stimulating factor could be considered.
Effects of dietary polyunsaturated fatty acid sources on expression of lipid-related genes in bovine milk somatic cells
Authors: Vargas-Bello-Pérez Einar , Cancino-Padilla Nathaly , Geldsetzer-Mendoza Carolina , Morales María Sol , Leskinen Heidi , Garnsworthy Philip C. , Loor Juan J. , Romero Jaime 
Published: September 2020

AbstractThe objective of this study was to compare the effect of contrasting sources of dietary n-6 and n-3 PUFA on expression of genes related to lipid metabolism in dairy cows. During 63 days, fifteen lactating cows were assigned to a control or basal diet containing no added lipid (n = 5 cows); and treatment diets supplemented with SO (n = 5 cows; unrefined soybean oil; 2.9% of DM) or FO (n = 5 cows; fish oil manufactured from salmon oil; 2.9% of DM). Plasma for fatty acid (FA) analysis and milk somatic cells (MSC) were obtained from all cows at the beginning of the study (day 0) and on days 21, 42 and 63. Plasma was used to determine FA transport dynamics. Compared with control and FO, plasma from SO had increased contents of C18:1 cis-9, C18:1 trans-11, C18:2 cis-9, trans-11 and total monounsaturated FA. On the other hand, compared with control and SO, FO increased plasma contents of C20:3 n-3, C20:3 n-6, C20:4 n-6, C20:5 n-3, C22:6 n-3 and total polyunsaturated FA. Moreover, plasma C18:3 n-3 and C20:5 n-3 increased over time for all diets. Compared with control, SO downregulated ACACA, INSIG1, and DGAT1, whereas FO downregulated ACACA, PPARGC1, LPIN1 and FABP3 on day 63, in MSC. At different time-points, SO and FO downregulated genes related to synthesis and intracellular transport of FA, synthesis of triglycerides, and transcription factors.
Direct identification of a mutation in OsSh1 causing non-shattering in a rice (Oryza sativa L.) mutant cultivar using whole-genome resequencing
Authors: Li Feng , Komatsu Akira , Ohtake Miki , Eun Heesoo , Shimizu Akemi , Kato Hiroshi 
Published: September 2020

AbstractLoss of seed shattering has been regarded as a key step during crop domestication. Mutagenesis contributes to the development of novel crop cultivars with a desired seed-shattering habit in a relatively short period of time, but also to uncovering the genetic architecture of seed shattering. ‘Minamiyutaka’, a non-shattering indica rice cultivar, was developed from the easy-shattering cultivar ‘Moretsu’ by mutation breeding via gamma-ray irradiation. In present study, we observed significant differences in shattering habit, breaking tensile strength, and abscission zone structure between ‘Moretsu’ and ‘Minamiyutaka’. Whole-genome mutation analysis of ‘Minamiyutaka’ newly identified a 13-bp deletion causing defective splicing in exon 3 of the OsSh1 gene which has previously been referred to as a candidate for controlling seed shattering. Using CRISPR/Cas9 gene editing, we demonstrated that loss-of-function mutation in OsSh1 causes non-shattering in rice. Furthermore, gene expression analysis suggests that OsSh1 may function downstream of qSH1, a known key gene involved in abscission zone differentiation. Nucleotide diversity analysis of OsSh1 in wild rice accessions and cultivars revealed that OsSh1 has been under strong selection during rice domestication, and a missense mutation might have contributed to the reduction of seed shattering from the wild progenitors to cultivated rice.
Aryl hydrocarbon receptor antagonism before reperfusion attenuates cerebral ischaemia/reperfusion injury in rats
Authors: Kwon Jae-Im , Heo Hwon , Ham Su Jeong , Chae Yeon Ji , Lee Do-Wan , Kim Sang Tae , Min Joongkee , Sung Yu Sub , Kim Kyung Won , Choi Yoonseok , Woo Dong Cheol , Woo Chul-Woong 
Published: September 2020

AbstractAryl hydrocarbon receptor (AhR) antagonism can mitigate cellular damage associated with cerebral ischaemia and reperfusion (I/R) injury. This study investigated the neuroprotective effects of AhR antagonist administration before reperfusion in a rat stroke model and influence of the timing of AhR antagonist administration on its neuroprotective effects. Magnetic resonance imaging (MRI) was performed at baseline, immediately after, and 3, 8, and 24 h after ischaemia in the sham, control (I/R injury), TMF10 (trimethoxyflavone [TMF] administered 10 min post-ischaemia), and TMF50 (TMF administered 50 min post-ischaemia) groups. The TMF treatment groups had significantly fewer infarcts than the control group. At 24 h, the relative apparent diffusion coefficient values of the ischaemic core and peri-infarct region were significantly higher and relative T2 values were significantly lower in the TMF10 groups than in the control group. The TMF treatment groups showed significantly fewer terminal deoxynucleotidyl transferase dUTP nick-end labelling positive (+) cells (%) in the peri-infarct region than the control group. This study demonstrated that TMF treatment 10 or 50 min after ischaemia alleviated brain damage. Furthermore, the timing of AhR antagonist administration affected the inhibition of cellular or vasogenic oedema formation caused by a transient ischaemic stroke.