bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fully stretchable active-matrix organic light-emitting electrochemical cell array
Authors: Liu Jia , Wang Jiechen , Zhang Zhitao , Molina-Lopez Francisco , Wang Ging-Ji Nathan , Schroeder Bob C. , Yan Xuzhou , Zeng Yitian , Zhao Oliver , Tran Helen , Lei Ting , Lu Yang , Wang Yi-Xuan , Tok Jeffrey B.-H. , Dauskardt Reinhold , Chung Jong Won , Yun Youngjun , Bao Zhenan 
Published: July 2020

AbstractIntrinsically and fully stretchable active-matrix-driven displays are an important element to skin electronics that can be applied to many emerging fields, such as wearable electronics, consumer electronics and biomedical devices. Here, we show for the first time a fully stretchable active-matrix-driven organic light-emitting electrochemical cell array. Briefly, it is comprised of a stretchable light-emitting electrochemical cell array driven by a solution-processed, vertically integrated stretchable organic thin-film transistor active-matrix, which is enabled by the development of chemically-orthogonal and intrinsically stretchable dielectric materials. Our resulting active-matrix-driven organic light-emitting electrochemical cell array can be readily bent, twisted and stretched without affecting its device performance. When mounted on skin, the array can tolerate to repeated cycles at 30% strain. This work demonstrates the feasibility of skin-applicable displays and lays the foundation for further materials development.
Anatomically and functionally distinct thalamocortical inputs to primary and secondary mouse whisker somatosensory cortices
Authors: El-Boustani Sami , Sermet B. Semihcan , Foustoukos Georgios , Oram Tess B. , Yizhar Ofer , Petersen Carl C. H. 
Published: July 2020

AbstractSubdivisions of mouse whisker somatosensory thalamus project to cortex in a region-specific and layer-specific manner. However, a clear anatomical dissection of these pathways and their functional properties during whisker sensation is lacking. Here, we use anterograde trans-synaptic viral vectors to identify three specific thalamic subpopulations based on their connectivity with brainstem. The principal trigeminal nucleus innervates ventral posterior medial thalamus, which conveys whisker-selective tactile information to layer 4 primary somatosensory cortex that is highly sensitive to self-initiated movements. The spinal trigeminal nucleus innervates a rostral part of the posterior medial (POm) thalamus, signaling whisker-selective sensory information, as well as decision-related information during a goal-directed behavior, to layer 4 secondary somatosensory cortex. A caudal part of the POm, which apparently does not receive brainstem input, innervates layer 1 and 5A, responding with little whisker selectivity, but showing decision-related modulation. Our results suggest the existence of complementary segregated information streams to somatosensory cortices.
Predicting and affecting response to cancer therapy based on pathway-level biomarkers
Authors: Ben-Hamo Rotem , Jacob Berger Adi , Gavert Nancy , Miller Mendy , Pines Guy , Oren Roni , Pikarsky Eli , Benes Cyril H. , Neuman Tzahi , Zwang Yaara , Efroni Sol , Getz Gad , Straussman Ravid 
Published: July 2020

AbstractIdentifying robust, patient-specific, and predictive biomarkers presents a major obstacle in precision oncology. To optimize patient-specific therapeutic strategies, here we couple pathway knowledge with large-scale drug sensitivity, RNAi, and CRISPR-Cas9 screening data from 460 cell lines. Pathway activity levels are found to be strong predictive biomarkers for the essentiality of 15 proteins, including the essentiality of MAD2L1 in breast cancer patients with high BRCA-pathway activity. We also find strong predictive biomarkers for the sensitivity to 31 compounds, including BCL2 and microtubule inhibitors (MTIs). Lastly, we show that Bcl-xL inhibition can modulate the activity of a predictive biomarker pathway and re-sensitize lung cancer cells and tumors to MTI therapy. Overall, our results support the use of pathways in helping to achieve the goal of precision medicine by uncovering dozens of predictive biomarkers.
Real-time gap-free dynamic waveform spectral analysis with nanosecond resolutions through analog signal processing
Authors: Konatham Saikrishna Reddy , Maram Reza , Romero Cortés Luis , Chang Jun Ho , Rusch Leslie , LaRochelle Sophie , Guillet de Chatellus Hugues , Azaña José 
Published: July 2020

AbstractReal-time tracking of a waveform frequency content is essential for detection and analysis of fast rare events in communications, radar, radio astronomy, spectroscopy, sensing etc. This requires a method that can provide real-time spectrum analysis (RT-SA) of high-speed waveforms in a continuous and gap-free fashion. Digital signal processing is inefficient to perform RT-SA over instantaneous frequency bandwidths above the sub-GHz range and/or to track spectral changes faster than a few microseconds. Analog dispersion-induced frequency-to-time mapping enables RT-SA of short isolated pulse-like signals but cannot be extended to continuous waveforms. Here, we propose a universal analog processing approach for time-mapping a gap-free spectrogram −the prime method for dynamic frequency analysis− of an incoming arbitrary waveform, based on a simple sampling and dispersive delay scheme. In experiments, the spectrograms of GHz-bandwidth microwave signals are captured at a speed of ~5×109 Fourier transforms per second, allowing to intercept nanosecond-duration frequency transients in real time. This method opens new opportunities for dynamic frequency analysis and processing of high-speed waveforms.
Automated design of a convolutional neural network with multi-scale filters for cost-efficient seismic data classification
Authors: Geng Zhi , Wang Yanfei 
Published: July 2020

AbstractGeoscientists mainly identify subsurface geologic features using exploration-derived seismic data. Classification or segmentation of 2D/3D seismic images commonly relies on conventional deep learning methods for image recognition. However, complex reflections of seismic waves tend to form high-dimensional and multi-scale signals, making traditional convolutional neural networks (CNNs) computationally costly. Here we propose a highly efficient and resource-saving CNN architecture (SeismicPatchNet) with topological modules and multi-scale-feature fusion units for classifying seismic data, which was discovered by an automated data-driven search strategy. The storage volume of the architecture parameters (0.73 M) is only ~2.7 MB, ~0.5% of the well-known VGG-16 architecture. SeismicPatchNet predicts nearly 18 times faster than ResNet-50 and shows an overwhelming advantage in identifying Bottom Simulating Reflection (BSR), an indicator of marine gas-hydrate resources. Saliency mapping demonstrated that our architecture captured key features well. These results suggest the prospect of end-to-end interpretation of multiple seismic datasets at extremely low computational cost.
Effects of climate change on the movement of future landfalling Texas tropical cyclones
Authors: Hassanzadeh Pedram , Lee Chia-Ying , Nabizadeh Ebrahim , Camargo Suzana J. , Ma Ding , Yeung Laurence Y. 
Published: July 2020

AbstractThe movement of tropical cyclones (TCs), particularly around the time of landfall, can substantially affect the resulting damage. Recently, trends in TC translation speed and the likelihood of stalled TCs such as Harvey have received significant attention, but findings have remained inconclusive. Here, we examine how the June-September steering wind and translation speed of landfalling Texas TCs change in the future under anthropogenic climate change. Using several large-ensemble/multi-model datasets, we find pronounced regional variations in the meridional steering wind response over North America, but―consistently across models―stronger June-September-averaged northward steering winds over Texas. A cluster analysis of daily wind patterns shows more frequent circulation regimes that steer landfalling TCs northward in the future. Downscaling experiments show a 10-percentage-point shift from the slow-moving to the fast-moving end of the translation-speed distribution in the future. Together, these analyses indicate increases in the likelihood of faster-moving landfalling Texas TCs in the late 21st century.
Persistent telomere cohesion protects aged cells from premature senescence
Authors: Azarm Kameron , Bhardwaj Amit , Kim Eugenie , Smith Susan 
Published: July 2020

AbstractHuman telomeres are bound by the telomere repeat binding proteins TRF1 and TRF2. Telomere shortening in human cells leads to a DNA damage response that signals replicative senescence. While insufficient loading of TRF2 at shortened telomeres contributes to the DNA damage response in senescence, the contribution of TRF1 to senescence induction has not been determined. Here we show that counter to TRF2 deficiency-mediated induction of DNA damage, TRF1 deficiency serves a protective role to limit induction of DNA damage induced by subtelomere recombination. Shortened telomeres recruit insufficient TRF1 and as a consequence inadequate tankyrase 1 to resolve sister telomere cohesion. Our findings suggest that the persistent cohesion protects short telomeres from inappropriate recombination. Ultimately, in the final division, telomeres are no longer able to maintain cohesion and subtelomere copying ensues. Thus, the gradual loss of TRF1 and concomitant persistent cohesion that occurs with telomere shortening ensures a measured approach to replicative senescence.
Integrated pharmaco-proteogenomics defines two subgroups in isocitrate dehydrogenase wild-type glioblastoma with prognostic and therapeutic opportunities
Authors: Oh Sejin , Yeom Jeonghun , Cho Hee Jin , Kim Ju-Hwa , Yoon Seon-Jin , Kim Hakhyun , Sa Jason K. , Ju Shinyeong , Lee Hwanho , Oh Myung Joon , Lee Wonyeop , Kwon Yumi , Li Honglan , Choi Seunghyuk , Han Jang Hee , Chang Jong Hee , Choi Eunsuk , Kim Jayeon , Her Nam-Gu , Kim Se Hoon , Kang Seok-Gu , Paek Eunok , Nam Do-Hyun , Lee Cheolju , Kim Hyun Seok 
Published: July 2020

AbstractThe prognostic and therapeutic relevance of molecular subtypes for the most aggressive isocitrate dehydrogenase 1/2 (IDH) wild-type glioblastoma (GBM) is currently limited due to high molecular heterogeneity of the tumors that impedes patient stratification. Here, we describe a distinct binary classification ofIDHwild-type GBM tumors derived from a quantitative proteomic analysis of 39IDHwild-type GBMs as well asIDHmutant and low-grade glioma controls. Specifically, GBM proteomic cluster 1 (GPC1) tumors exhibit Warburg-like features, neural stem-cell markers, immune checkpoint ligands, and a poor prognostic biomarker, FKBP prolyl isomerase 9 (FKBP9). Meanwhile, GPC2 tumors show elevated oxidative phosphorylation-related proteins, differentiated oligodendrocyte and astrocyte markers, and a favorable prognostic biomarker, phosphoglycerate dehydrogenase (PHGDH). Integrating these proteomic features with the pharmacological profiles of matched patient-derived cells (PDCs) reveals that the mTORC1/2 dual inhibitor AZD2014 is cytotoxic to the poor prognostic PDCs. Our analyses will guide GBM prognosis and precision treatment strategies.
Engineering monocyte/macrophage−specific glucocerebrosidase expression in human hematopoietic stem cells using genome editing
Authors: Scharenberg Samantha G. , Poletto Edina , Lucot Katherine L. , Colella Pasqualina , Sheikali Adam , Montine Thomas J. , Porteus Matthew H. , Gomez-Ospina Natalia 
Published: July 2020

AbstractGaucher disease is a lysosomal storage disorder caused by insufficient glucocerebrosidase activity. Its hallmark manifestations are attributed to infiltration and inflammation by macrophages. Current therapies for Gaucher disease include life−long intravenous administration of recombinant glucocerebrosidase and orally-available glucosylceramide synthase inhibitors. An alternative approach is to engineer the patient’s own hematopoietic system to restore glucocerebrosidase expression, thereby replacing the affected cells, and constituting a potential one-time therapy for this disease. Here, we report an efficient CRISPR/Cas9-based approach that targets glucocerebrosidase expression cassettes with a monocyte/macrophage-specific element to the CCR5 safe-harbor locus in human hematopoietic stem and progenitor cells. The targeted cells generate glucocerebrosidase-expressing macrophages and maintain long-term repopulation and multi-lineage differentiation potential with serial transplantation. The combination of a safe-harbor and a lineage-specific promoter establishes a universal correction strategy and circumvents potential toxicity of ectopic glucocerebrosidase in the stem cells. Furthermore, it constitutes an adaptable platform for other lysosomal enzyme deficiencies.
The Seminavis robusta genome provides insights into the evolutionary adaptations of benthic diatoms
Authors: Osuna-Cruz Cristina Maria , Bilcke Gust , Vancaester Emmelien , De Decker Sam , Bones Atle M. , Winge Per , Poulsen Nicole , Bulankova Petra , Verhelst Bram , Audoor Sien , Belisova Darja , Pargana Aikaterini , Russo Monia , Stock Frederike , Cirri Emilio , Brembu Tore , Pohnert Georg , Piganeau Gwenael , Ferrante Maria Immacolata , Mock Thomas , Sterck Lieven , Sabbe Koen , De Veylder Lieven , Vyverman Wim , Vandepoele Klaas 
Published: July 2020

AbstractBenthic diatoms are the main primary producers in shallow freshwater and coastal environments, fulfilling important ecological functions such as nutrient cycling and sediment stabilization. However, little is known about their evolutionary adaptations to these highly structured but heterogeneous environments. Here, we report a reference genome for the marine biofilm-forming diatom Seminavis robusta, showing that gene family expansions are responsible for a quarter of all 36,254 protein-coding genes. Tandem duplications play a key role in extending the repertoire of specific gene functions, including light and oxygen sensing, which are probably central for its adaptation to benthic habitats. Genes differentially expressed during interactions with bacteria are strongly conserved in other benthic diatoms while many species-specific genes are strongly upregulated during sexual reproduction. Combined with re-sequencing data from 48 strains, our results offer insights into the genetic diversity and gene functions in benthic diatoms.
Structure-based machine-guided mapping of amyloid sequence space reveals uncharted sequence clusters with higher solubilities
Authors: Louros Nikolaos , Orlando Gabriele , De Vleeschouwer Matthias , Rousseau Frederic , Schymkowitz Joost 
Published: July 2020

AbstractThe amyloid conformation can be adopted by a variety of sequences, but the precise boundaries of amyloid sequence space are still unclear. The currently charted amyloid sequence space is strongly biased towards hydrophobic, beta-sheet prone sequences that form the core of globular proteins and by Q/N/Y rich yeast prions. Here, we took advantage of the increasing amount of high-resolution structural information on amyloid cores currently available in the protein databank to implement a machine learning approach, named Cordax (https://cordax.switchlab.org), that explores amyloid sequence beyond its current boundaries. Clustering by t-Distributed Stochastic Neighbour Embedding (t-SNE) shows how our approach resulted in an expansion away from hydrophobic amyloid sequences towards clusters of lower aliphatic content and higher charge, or regions of helical and disordered propensities. These clusters uncouple amyloid propensity from solubility representing sequence flavours compatible with surface-exposed patches in globular proteins, functional amyloids or sequences associated to liquid-liquid phase transitions.
Association between Serum Essential Metal Elements and the Risk of Schizophrenia in China
Authors: Ma Jiahui , Yan Lailai , Guo Tongjun , Yang Siyu , Liu Yaqiong , Xie Qing , Ni Dawei , Wang Jingyu 
Published: July 2020

AbstractNumerous essential metal elements (EMEs) are necessary to maintain the proper function of human body. In this case-control study, we investigated the associations of 11 EMEs [Calcium (Ca), potassium (K), magnesium (Mg), sodium (Na), manganese (Mn), selenium (Se), cobalt (Co), Molybdenum (Mo), copper (Cu), zinc (Zn), and iron (Fe)] in serum with the risk of schizophrenia. We recruited first-episode and drug-naïve schizophrenic patients (cases = 99) and age-sex-matched normal subjects (controls = 99) from Tangshan, Hebei Province, China. The 11 EMEs in serum from cases and controls were quantified by inductively coupled plasma atomic emission spectrometry and inductively coupled plasma mass spectrometry. We observed that a higher level of Mn (OR = 2.390; 95%CI: 1.504–3.796) and lower levels of Ca (OR = 0.939; 95%CI: 0.890–0.990), Mg (OR = 0.806; 95%CI: 0.669–0.972), Na (OR = 0.995; 95%CI: 0.993–0.998), and Se (OR = 0.954; 95%CI: 0.937–0.972) were associated with an elevated risk of schizophrenia. Dose–response relationships between serum EME concentrations and the risk of schizophrenia were observed in most of the schizophrenia-associated EMEs. Moreover, the serum concentrations of these schizophrenia-associated EMEs in patients were correlated with the severity of their clinical symptoms. Significant correlations were found between EMEs and biomarkers associated with schizophrenia related to metabolic and oxidative stress. This study suggested that the concentration and profile of EMEs were different between schizophrenic patients and normal controls and revealed potential metabolisms associated with EMEs and schizophrenia, suggesting EMEs might act as biomarkers of schizophrenia to improve the current situation of diagnosis and treatment.
Recursive Consensus Clustering for novel subtype discovery from transcriptome data
Authors: Sonpatki Pranali , Shah Nameeta 
Published: July 2020

AbstractLarge-scale transcriptomic data is used by biologists for the discovery of new molecular patterns or cell subpopulations. Clustering is one of the most popular methods for dimensionality reduction and data analysis for large scale datasets. The major problem while clustering the data is the selection of the optimal number of clusters (k) for each dataset and to discover new insights from it. We have developed Recursive Consensus Clustering (RCC), an unsupervised clustering algorithm for novel subtype discovery from both bulk and single-cell datasets. RCC is available as an R package and facilitates the generation of new biological insights through intuitive visualization of clustering results.
Cytosolic phospholipase A2-α participates in lipid body formation and PGE2 release in human neutrophils stimulated with an l-amino acid oxidase from Calloselasma rhodostoma venom
Authors: Paloschi Mauro Valentino , Lopes Jéssica Amaral , Boeno Charles Nunes , Silva Milena Daniela Souza , Evangelista Jaína Rodrigues , Pontes Adriana Silva , da Silva Setúbal Sulamita , Rego Cristina Matiele Alves , Néry Neriane Monteiro , Ferreira e Ferreira Alex Augusto , Pires Weverson Luciano , Felipin Kátia Paula , Ferreira Gabriel Eduardo Melim , Bozza Patrícia Torres , Zuliani Juliana Pavan 
Published: July 2020

AbstractCr-LAAO, an l-amino acid oxidase isolated from Calloselasma rhodosthoma snake venom, has been demonstrated as a potent stimulus for neutrophil activation and inflammatory mediator production. However, the mechanisms involved in Cr-LAAO induced neutrophil activation has not been well characterized. Here we investigated the mechanisms involved in Cr-LAAO-induced lipid body (also known as lipid droplet) biogenesis and eicosanoid formation in human neutrophils. Using microarray analysis, we show for the first time that Cr-LAAO plays a role in the up-regulation of the expression of genes involved in lipid signalling and metabolism. Those include different members of phospholipase A2, mostly cytosolic phospholipase A2-α (cPLA2-α); and enzymes involved in prostaglandin synthesis including cyclooxygenases 2 (COX-2), and prostaglandin E synthase (PTGES). In addition, genes involved in lipid droplet formation, including perilipin 2 and 3 (PLIN 2 and 3) and diacylglycerol acyltransferase 1 (DGAT1), were also upregulated. Furthermore, increased phosphorylation of cPLA2-α, lipid droplet biogenesis and PGE2 synthesis were observed in human neutrophils stimulated with Cr-LAAO. Treatment with cPLA2-α inhibitor (CAY10650) or DGAT-1 inhibitor (A922500) suppressed lipid droplets formation and PGE2 secretion. In conclusion, we demonstrate for the first time the effects of Cr-LAAO to regulate neutrophil lipid metabolism and signalling.
Comparison of 68Ga-PSMA-617 PET/CT with mpMRI for the detection of PCa in patients with a PSA level of 4–20 ng/ml before the initial biopsy
Authors: Li Yu , Han Donghui , Wu Peng , Ren Jing , Ma Shuaijun , Zhang Jingliang , Song Wei , Lin Xiaoyu , Jiao Dian , Shi Shengjia , Yang Fa , Wu Jieheng , Meng Ping , Wen Weihong , Kang Fei , Wang Jing , Qin Weijun 
Published: July 2020

AbstractThe study was aimed at assessing the diagnostic performance of 68Ga-PSMA-617 PET/CT in the detection of prostate cancer (PCa) in patients with a prostate-specific antigen (PSA) level of 4–20 ng/ml and to compare its efficacy with that of multiparametric MRI (mpMRI). We analyzed the data of 67 consecutive patients with PSA levels of 4–20 ng/ml who almost simultaneously underwent 68Ga-PSMA-617 PET/CT and mpMRI. 68Ga-PSMA-617 PET/CT and mpMRI diagnostic performances were compared via receiver operating characteristic (ROC) curve analysis. Of the 67 suspected PCa cases, 33 had pathologically confirmed PCa. 68Ga-PSMA-617 PET/CT showed a patient-based sensitivity, specificity, and positive and negative predictive values (PPVs and NPVs) of 87.88%, 88.24%, 87.88%, and 88.24%, respectively. The corresponding values for mpMRI were 84.85%, 52.94%, 63.64%, and 78.26%. The area under the curve values for 68Ga-PSMA-617 PET/CT and mpMRI were 0.881 and 0.689, respectively. 68Ga-PSMA-617 PET/CT showed a better diagnostic performance than mpMRI in the detection of PCa in patients with PSA levels of 4–20 ng/ml.
GL261 luciferase-expressing cells elicit an anti-tumor immune response: an evaluation of murine glioma models
Authors: Sanchez Victoria E. , Lynes John P. , Walbridge Stuart , Wang Xiang , Edwards Nancy A. , Nwankwo Anthony K. , Sur Hannah P. , Dominah Gifty A. , Obungu Arnold , Adamstein Nicholas , Dagur Pradeep K. , Maric Dragan , Munasinghe Jeeva , Heiss John D. , Nduom Edjah K. 
Published: July 2020

AbstractPreclinical models that reliably recapitulate the immunosuppressive properties of human gliomas are essential to assess immune-based therapies. GL261 murine glioma cells are widely used as a syngeneic animal model of glioma, however, it has become common practice to transfect these cells with luciferase for fluorescent tumor tracking. The aim of this study was to compare the survival of mice injected with fluorescent or non-fluorescent GL261 cells and characterize the differences in their tumor microenvironment. Mice were intracranially implanted with GL261, GL261 Red-FLuc or GL261-Luc2 cells at varying doses. Cytokine profiles were evaluated by proteome microarray and Kaplan–Meier survival analysis was used to determine survival differences. Median survival for mice implanted with 5 × 104 GL261 cells was 18 to 21 days. The GL261 Red-FLuc implanted mice cells did not reach median survival at any tumor dose. Mice injected with 3 × 105 GL261-Luc2 cells reached median survival at 23 days. However, median survival was significantly prolonged to 37 days in mice implanted with 5 × 104 GL261-Luc2 cells. Additionally, proteomic analyses revealed significantly elevated inflammatory cytokines in the supernatants of the GL261 Red-FLuc cells and GL261-Luc2 cells. Our data suggest that GL261 Red-FLuc and GL261-Luc2 murine models elicit an anti-tumor immune response by increasing pro-inflammatory modulators.