bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tailored optical propulsion forces for controlled transport of resonant gold nanoparticles and associated thermal convective fluid flows
Authors: Rodrigo José A. , Angulo Mercedes , Alieva Tatiana 
Published: October 2020

AbstractNoble metal nanoparticles illuminated at their plasmonic resonance wavelength turn into heat nanosources. This phenomenon has prompted the development of numerous applications in science and technology. Simultaneous optical manipulation of such resonant nanoparticles could certainly extend the functionality and potential applications of optothermal tools. In this article, we experimentally demonstrate optical transport of single and multiple resonant nanoparticles (colloidal gold spheres of radius 200 nm) directed by tailored transverse phase-gradient forces propelling them around a 2D optical trap. We show how the phase-gradient force can be designed to efficiently change the speed of the nanoparticles. We have found that multiple hot nanoparticles assemble in the form of a quasi-stable group whose motion around the laser trap is also controlled by such optical propulsion forces. This assembly experiences a significant increase in the local temperature, which creates an optothermal convective fluid flow dragging tracer particles into the assembly. Thus, the created assembly is a moving heat source controlled by the propulsion force, enabling indirect control of fluid flows as a micro-optofluidic tool. The existence of these flows, probably caused by the temperature-induced Marangoni effect at the liquid water/superheated water interface, is confirmed by tracking free tracer particles migrating towards the assembly. We propose a straightforward method to control the assembly size, and therefore its temperature, by using a nonuniform optical propelling force that induces the splitting or merging of the group of nanoparticles. We envision further development of microscale optofluidic tools based on these achievements.
Progress in the mechanism and targeted drug therapy for COPD
Authors: Wang Cuixue , Zhou Jiedong , Wang Jinquan , Li Shujing , Fukunaga Atsushi , Yodoi Junji , Tian Hai 
Published: October 2020

AbstractChronic obstructive pulmonary disease (COPD) is emphysema and/or chronic bronchitis characterised by long-term breathing problems and poor airflow. The prevalence of COPD has increased over the last decade and the drugs most commonly used to treat it, such as glucocorticoids and bronchodilators, have significant therapeutic effects; however, they also cause side effects, including infection and immunosuppression. Here we reviewed the pathogenesis and progression of COPD and elaborated on the effects and mechanisms of newly developed molecular targeted COPD therapeutic drugs. Among these new drugs, we focussed on thioredoxin (Trx). Trx effectively prevents the progression of COPD by regulating redox status and protease/anti-protease balance, blocking the NF-κB and MAPK signalling pathways, suppressing the activation and migration of inflammatory cells and the production of cytokines, inhibiting the synthesis and the activation of adhesion factors and growth factors, and controlling the cAMP-PKA and PI3K/Akt signalling pathways. The mechanism by which Trx affects COPD is different from glucocorticoid-based mechanisms which regulate the inflammatory reaction in association with suppressing immune responses. In addition, Trx also improves the insensitivity of COPD to steroids by inhibiting the production and internalisation of macrophage migration inhibitory factor (MIF). Taken together, these findings suggest that Trx may be the ideal drug for treating COPD.
Light-sheet fluorescence imaging charts the gastrula origin of vascular endothelial cells in early zebrafish embryos
Authors: Pang Meijun , Bai Linlu , Zong Weijian , Wang Xu , Bu Ye , Xiong Connie , Zheng Jiyuan , Li Jieyi , Gao Weizheng , Feng Zhiheng , Chen Liangyi , Zhang Jue , Cheng Heping , Zhu Xiaojun , Xiong Jing-Wei 
Published: October 2020

AbstractIt remains challenging to construct a complete cell lineage map of the origin of vascular endothelial cells in any vertebrate embryo. Here, we report the application of in toto light-sheet fluorescence imaging of embryos to trace the origin of vascular endothelial cells (ECs) at single-cell resolution in zebrafish. We first adapted a previously reported method to embryo mounting and light-sheet imaging, created an alignment, fusion, and extraction all-in-one software (AFEIO) for processing big data, and performed quantitative analysis of cell lineage relationships using commercially available Imaris software. Our data revealed that vascular ECs originated from broad regions of the gastrula along the dorsal–ventral and anterior–posterior axes, of which the dorsal–anterior cells contributed to cerebral ECs, the dorsal–lateral cells to anterior trunk ECs, and the ventral–lateral cells to posterior trunk and tail ECs. Therefore, this work, to our knowledge, charts the first comprehensive map of the gastrula origin of vascular ECs in zebrafish, and has potential applications for studying the origin of any embryonic organs in zebrafish and other model organisms.
A large-scale optical microscopy image dataset of potato tuber for deep learning based plant cell assessment
Authors: Biswas Sumona , Barma Shovan 
Published: October 2020

AbstractWe present a new large-scale three-fold annotated microscopy image dataset, aiming to advance the plant cell biology research by exploring different cell microstructures including cell size and shape, cell wall thickness, intercellular space, etc. in deep learning (DL) framework. This dataset includes 9,811 unstained and 6,127 stained (safranin-o, toluidine blue-o, and lugol’s-iodine) images with three-fold annotation including physical, morphological, and tissue grading based on weight, different section area, and tissue zone respectively. In addition, we prepared ground truth segmentation labels for three different tuber weights. We have validated the pertinence of annotations by performing multi-label cell classification, employing convolutional neural network (CNN), VGG16, for unstained and stained images. The accuracy has been achieved up to 0.94, while, F2-score reaches to 0.92. Furthermore, the ground truth labels have been verified by semantic segmentation algorithm using UNet architecture which presents the mean intersection of union up to 0.70. Hence, the overall results show that the data are very much efficient and could enrich the domain of microscopy plant cell analysis for DL-framework.
The Building Data Genome Project 2, energy meter data from the ASHRAE Great Energy Predictor III competition
Authors: Miller Clayton , Kathirgamanathan Anjukan , Picchetti Bianca , Arjunan Pandarasamy , Park June Young , Nagy Zoltan , Raftery Paul , Hobson Brodie W. , Shi Zixiao , Meggers Forrest 
Published: October 2020

AbstractThis paper describes an open data set of 3,053 energy meters from 1,636 non-residential buildings with a range of two full years (2016 and 2017) at an hourly frequency (17,544 measurements per meter resulting in approximately 53.6 million measurements). These meters were collected from 19 sites across North America and Europe, with one or more meters per building measuring whole building electrical, heating and cooling water, steam, and solar energy as well as water and irrigation meters. Part of these data was used in the Great Energy Predictor III (GEPIII) competition hosted by the American Society of Heating, Refrigeration, and Air-Conditioning Engineers (ASHRAE) in October-December 2019. GEPIII was a machine learning competition for long-term prediction with an application to measurement and verification. This paper describes the process of data collection, cleaning, and convergence of time-series meter data, the meta-data about the buildings, and complementary weather data. This data set can be used for further prediction benchmarking and prototyping as well as anomaly detection, energy analysis, and building type classification.
Vaginal microbiota evaluation and prevalence of key pathogens in ecuadorian women: an epidemiologic analysis
Authors: Salinas Ana María , Osorio Verónica Gabriela , Pacha-Herrera David , Vivanco Juan S. , Trueba Ana Francisca , Machado António 
Published: October 2020

AbstractVaginal infection is a gynecological problem in women of reproductive age with multiple health outcomes. The most common forms of infection include bacterial vaginosis (BV), vulvovaginal candidiasis (VC), and aerobic vaginitis (AV). Our main goals were to evaluate different types of vaginal infections in Ecuadorian women in a large urban area (Quito) and to characterize the vaginal microbiota colonization by opportunistic species. We collected vaginal swabs and epidemiological surveys from 414 women from June 2016 to July of 2017. We analyzed vaginal samples for the presence of any vaginal infection. The microbiological examination was done through Gram-stain, wet mount smears, and polymerase chain reaction (PCR) assays using primers for target genes, such as 16S rRNA (Atopobium vaginae, Mobiluncus mulieris, and Gardnerella species), ddl (Enterococcus faecalis), adk (Escherichia coli) and KER1 (Candida albicans) genes. Most women showed a healthy vaginal microbiota (66.7%). Nearly one-tenth (10.4%) of the participants had intermediate microbiota, and the remaining women (22.9%) had a single vaginal infection (BV, AV, or VC) or coinfections. From the 95 participants that had an infection, AV was the main diagnosed vaginal infection (51.6%), followed by BV (24.2%) and finally VC (7.4%). The remaining women (16.8%) showed coinfections, being BV and AV the most common coinfection. Using univariable logistic regression analyses we found an increased odds of healthy microbiota in women with a sexual partner (P = 0.02, OR = 1.64). Also, women in a free union relationship (P = 0.000, OR = 16.65) had an increased odds of having coinfections. On the other hand, the use of birth control (condom OR = 0.388 or other contraceptive method OR = 0.363) was associated with significantly lower odds of intermediate microbiota (P ≤ 0.05). We found no statistically significant differences between women with infection and a particular group age. Using multivariate logistic regression analyses we initially found an increased odds of having BV in women with M. mulieris (P = 0.020, OR = 4.98) and Gardnerella species (P = 0.010, OR = 4.16). Women with E. coli showed an increased odds of having AV (P = 0.009, OR = 2.81). The presence of C. albicans in women showed an increased odds of having VC (P = 0.007, OR = 17.94). Finally, women with M. mulieris showed a reverse odds of having healthy microbiota (P = 0.008, OR = 0.06). We found no statistically significant differences between women with symptomatic and asymptomatic infections or the presence of Enterococcus faecalis. We found using logistic regression analyses that M. mulieris was the most prevalent opportunistic pathogen among women with vaginal infection. Further studies should evaluate the possibility to use M. mulieris as a potential key predictor for vaginal infections.
Machine learning for endoleak detection after endovascular aortic repair
Authors: Talebi Salmonn , Madani Mohammad H. , Madani Ali , Chien Ashley , Shen Jody , Mastrodicasa Domenico , Fleischmann Dominik , Chan Frandics P. , Mofrad Mohammad R. K. 
Published: October 2020

AbstractDiagnosis of endoleak following endovascular aortic repair (EVAR) relies on manual review of multi-slice CT angiography (CTA) by physicians which is a tedious and time-consuming process that is susceptible to error. We evaluate the use of a deep neural network for the detection of endoleak on CTA for post-EVAR patients using a novel data efficient training approach. 50 CTAs and 20 CTAs with and without endoleak respectively were identified based on gold standard interpretation by a cardiovascular subspecialty radiologist. The Endoleak Augmentor, a custom designed augmentation method, provided robust training for the machine learning (ML) model. Predicted segmentation maps underwent post-processing to determine the presence of endoleak. The model was tested against 3 blinded general radiologists and 1 blinded subspecialist using a held-out subset (10 positive endoleak CTAs, 10 control CTAs). Model accuracy, precision and recall for endoleak diagnosis were 95%, 90% and 100% relative to reference subspecialist interpretation (AUC = 0.99). Accuracy, precision and recall was 70/70/70% for generalist1, 50/50/90% for generalist2, and 90/83/100% for generalist3. The blinded subspecialist had concordant interpretations for all test cases compared with the reference. In conclusion, our ML-based approach has similar performance for endoleak diagnosis relative to subspecialists and superior performance compared with generalists.
Epithelial layer unjamming shifts energy metabolism toward glycolysis
Authors: DeCamp Stephen J. , Tsuda Victor M. K. , Ferruzzi Jacopo , Koehler Stephan A. , Giblin John T. , Roblyer Darren , Zaman Muhammad H. , Weiss Scott T. , Kılıç Ayşe , De Marzio Margherita , Park Chan Young , Ogassavara Nicolas Chiu , Mitchel Jennifer A. , Butler James P. , Fredberg Jeffrey J. 
Published: October 2020

AbstractIn development of an embryo, healing of a wound, or progression of a carcinoma, a requisite event is collective epithelial cellular migration. For example, cells at the advancing front of a wound edge tend to migrate collectively, elongate substantially, and exert tractions more forcefully compared with cells many ranks behind. With regards to energy metabolism, striking spatial gradients have recently been reported in the wounded epithelium, as well as in the tumor, but within the wounded cell layer little is known about the link between mechanical events and underlying energy metabolism. Using the advancing confluent monolayer of MDCKII cells as a model system, here we report at single cell resolution the evolving spatiotemporal fields of cell migration speeds, cell shapes, and traction forces measured simultaneously with fields of multiple indices of cellular energy metabolism. Compared with the epithelial layer that is unwounded, which is non-migratory, solid-like and jammed, the leading edge of the advancing cell layer is shown to become progressively more migratory, fluid-like, and unjammed. In doing so the cytoplasmic redox ratio becomes progressively smaller, the NADH lifetime becomes progressively shorter, and the mitochondrial membrane potential and glucose uptake become progressively larger. These observations indicate that a metabolic shift toward glycolysis accompanies collective cellular migration but show, further, that this shift occurs throughout the cell layer, even in regions where associated changes in cell shapes, traction forces, and migration velocities have yet to penetrate. In characterizing the wound healing process these morphological, mechanical, and metabolic observations, taken on a cell-by-cell basis, comprise the most comprehensive set of biophysical data yet reported. Together, these data suggest the novel hypothesis that the unjammed phase evolved to accommodate fluid-like migratory dynamics during episodes of tissue wound healing, development, and plasticity, but is more energetically expensive compared with the jammed phase, which evolved to maintain a solid-like non-migratory state that is more energetically economical.
Comprehensive analysis of the expression of SLC30A family genes and prognosis in human gastric cancer
Authors: Guo Yongdong , He Yutong 
Published: October 2020

AbstractThe solute carrier 30 (SLC30) family genes play a fundamental role in various cancers. However, the diverse expression patterns, prognostic value, and potential mechanism of SLC30A family genes in gastric cancer (GC) remain unknown. Herein, we analyzed the expression and survival data of SLC30A family genes in GC patients using multiple bioinformatic approaches. Expression data of SLC30A family genes for GC patients were extracted from the Cancer Genome Atlas (TCGA) and genetic alteration frequency assessed by using cBioportal database. And validated the expression of SLC30A family genes in GC tissues and corresponding normal tissues. The prognostic value of SLC30A family genes in gastric cancer patients were explored using Kaplan–Meier plotter database. Functional enrichment analysis performed using DAVID database and clusterProfiler package. And ssGSEA algorithm was performed to explore the relationship between the SLC30A family genes and the infiltration of immune cells. We found that the median expression levels of SLC30A1-3, 5–7, and 9 were significantly upregulated in gastric cancer tissues compared to non-cancerous tissues, while SLC30A4 was downregulated. Meanwhile, SLC30A1-7, and 9 were significantly correlated with advanced tumor stage and nodal metastasis status, SLC30A5-7, and 9–10 were significantly related to the Helicobacter pylori infection status of GC patients. High expression of five genes (SLC30A1, 5–7, and 9) was significantly correlated with better overall survival (OS), first progression survival (FPS), and post progression survival (PPS). Conversely, upregulated SLC30A2-4, 8, and 10 expression was markedly associated with poor OS, FP and PPS. And SLC30A family genes were closely associated with the infiltration of immune cells. The present study implied that SLC30A5 and 7 may be potential biomarkers for predicting prognosis in GC patients, SLC30A2 and 3 play an oncogenic role in GC patients and could provide a new strategy for GC patients treatment.
Structural modeling of GSK3β implicates the inactive (DFG-out) conformation as the target bound by TDZD analogs
Authors: Balasubramaniam Meenakshisundaram , Mainali Nirjal , Bowroju Suresh Kuarm , Atluri Paavan , Penthala Narsimha Reddy , Ayyadevera Srinivas , Crooks Peter A. , Shmookler Reis Robert J. 
Published: October 2020

AbstractGlycogen synthase kinase-3β (GSK3β) controls many physiological pathways, and is implicated in many diseases including Alzheimer’s and several cancers. GSK3β-mediated phosphorylation of target residues in microtubule-associated protein tau (MAPTAU) contributes to MAPTAU hyperphosphorylation and subsequent formation of neurofibrillary tangles. Inhibitors of GSK3β protect against Alzheimer’s disease and are therapeutic for several cancers. A thiadiazolidinone drug, TDZD-8, is a non-ATP-competitive inhibitor targeting GSK3β with demonstrated efficacy against multiple diseases. However, no experimental data or models define the binding mode of TDZD-8 with GSK3β, which chiefly reflects our lack of an established inactive conformation for this protein. Here, we used metadynamic simulation to predict the three-dimensional structure of the inactive conformation of GSK3β. Our model predicts that phosphorylation of GSK3β Serine9 would hasten the DFG-flip to an inactive state. Molecular docking and simulation predict the TDZD-8 binding conformation of GSK3β to be inactive, and are consistent with biochemical evidence for the TDZD-8–interacting residues of GSK3β. We also identified the pharmacophore and assessed binding efficacy of second-generation TDZD analogs (TDZD-10 and Tideglusib) that bind GSK3β as non-ATP-competitive inhibitors. Based on these results, the predicted inactive conformation of GSK3β can facilitate the identification of novel GSK3β inhibitors of high potency and specificity.
Increased estrogen to androgen ratio enhances immunoglobulin levels and impairs B cell function in male mice
Authors: Aguilar-Pimentel Juan Antonio , Cho Yi-Li , Gerlini Raffaele , Calzada-Wack Julia , Wimmer Maria , Mayer-Kuckuk Philipp , Adler Thure , Schmidt-Weber Carsten B. , Busch Dirk H. , Fuchs Helmut , Gailus-Durner Valérie , Ollert Markus , Hrabě de Angelis Martin , Ohlsson Claes , Poutanen Matti , Teperino Raffaele , Strauss Leena 
Published: October 2020

AbstractSex steroids, such as estrogens and androgens, are important regulators of the humoral immune response. Studies in female mice have demonstrated that alteration of circulating estrogen concentration regulates antibody-mediated immunity. As males have normally little endogenous estrogen, we hypothesized that in males high estrogens and low androgens affect the immune system and enhance the allergic inflammatory response. Here, we studied transgenic male mice expressing human aromatase (AROM+). These animals have a high circulating estrogen to androgen ratio (E/A), causing female traits such as gynecomastia. We found that AROM+ male mice had significantly higher plasma immunoglobulin levels, particularly IgE. Flow cytometry analyses of splenocytes revealed changes in mature/immature B cell ratio together with a transcriptional upregulation of the Igh locus. Furthermore, higher proliferation rate and increased IgE synthesis after IgE class-switching was found. Subsequently, we utilized an ovalbumin airway challenge model to test the allergic response in AROM+ male mice. In line with above observations, an increase in IgE levels was measured, albeit no impact on immune cell infiltration into the lungs was detected. Together, our findings suggest that high circulating E/A in males significantly alters B cell function without any significant enhancement in allergic inflammation.
Interplay among p21Waf1/Cip1, MUSASHI-1 and Krüppel-like factor 4 in activation of Bmi1-CreER reserve intestinal stem cells after gamma radiation-induced injury
Authors: Orzechowska Emilia J. , Katano Takahito , Bialkowska Agnieszka B. , Yang Vincent W. 
Published: October 2020

AbstractGamma radiation is a commonly used adjuvant treatment for abdominally localized cancer. Since its therapeutic potential is limited due to gastrointestinal (GI) syndrome, elucidation of the regenerative response following radiation-induced gut injury is needed to develop a preventive treatment. Previously, we showed that Krüppel-like factor 4 (KLF4) activates certain quiescent intestinal stem cells (ISCs) marked by Bmi1-CreER to give rise to regenerating crypts following γ irradiation. In the current study, we showed that γ radiation-induced expression of p21Waf1/Cip1 in Bmi1-CreER cells is likely mitigated by MUSASHI-1 (MSI1) acting as a negative regulator of p21Waf1/Cip1 mRNA translation, which promotes exit of the Bmi1-CreER cells from a quiescent state. Additionally, Bmi1-specific Klf4 deletion resulted in decreased numbers of MSI1+ cells in regenerating crypts compared to those of control mice. We showed that KLF4 binds to the Msi1 promoter and activates its expression in vitro. Since MSI1 has been shown to be crucial for crypt regeneration, this finding elucidates a pro-proliferative role of KLF4 during the postirradiation regenerative response. Taken together, our data suggest that the interplay among p21Waf1/Cip1, MSI1 and KLF4 regulates Bmi1-CreER cell survival, exit from quiescence and regenerative potential upon γ radiation-induced injury.