bluuebunny/crossref_metadata_2025_split huggingface dataset:
Embryonic progenitor pools generate diversity in fine-scale excitatory cortical subnetworks
Authors: Ellender Tommas J. , Avery Sophie V. , Mahfooz Kashif , Scaber Jakub , von Klemperer Alexander , Nixon Sophie L. , Buchan Matthew J. , van Rheede Joram J. , Gatti Aleksandra , Waites Cameron , Pavlou Hania J. , Sims David , Newey Sarah E. , Akerman Colin J. 
Published: November 2019

AbstractThe mammalian neocortex is characterized by a variety of neuronal cell types and precise arrangements of synaptic connections, but the processes that generate this diversity are poorly understood. Here we examine how a pool of embryonic progenitor cells consisting of apical intermediate progenitors (aIPs) contribute to diversity within the upper layers of mouse cortex. In utero labeling combined with single-cell RNA-sequencing reveals that aIPs can generate transcriptionally defined glutamatergic cell types, when compared to neighboring neurons born from other embryonic progenitor pools. Whilst sharing layer-associated morphological and functional properties, simultaneous patch clamp recordings and optogenetic studies reveal that aIP-derived neurons exhibit systematic biases in both their intralaminar monosynaptic connectivity and the post-synaptic partners that they target within deeper layers of cortex. Multiple cortical progenitor pools therefore represent an important factor in establishing diversity amongst local and long-range fine-scale glutamatergic connectivity, which generates subnetworks for routing excitatory synaptic information.
Application of convolutional neural networks to breast biopsies to delineate tissue correlates of mammographic breast density
Authors: Mullooly Maeve , Ehteshami Bejnordi Babak , Pfeiffer Ruth M. , Fan Shaoqi , Palakal Maya , Hada Manila , Vacek Pamela M. , Weaver Donald L. , Shepherd John A. , Fan Bo , Mahmoudzadeh Amir Pasha , Wang Jeff , Malkov Serghei , Johnson Jason M. , Herschorn Sally D. , Sprague Brian L. , Hewitt Stephen , Brinton Louise A. , Karssemeijer Nico , van der Laak Jeroen , Beck Andrew , Sherman Mark E. , Gierach Gretchen L. 
Published: November 2019

AbstractBreast density, a breast cancer risk factor, is a radiologic feature that reflects fibroglandular tissue content relative to breast area or volume. Its histology is incompletely characterized. Here we use deep learning approaches to identify histologic correlates in radiologically-guided biopsies that may underlie breast density and distinguish cancer among women with elevated and low density. We evaluated hematoxylin and eosin (H&E)-stained digitized images from image-guided breast biopsies (n = 852 patients). Breast density was assessed as global and localized fibroglandular volume (%). A convolutional neural network characterized H&E composition. In total 37 features were extracted from the network output, describing tissue quantities and morphological structure. A random forest regression model was trained to identify correlates most predictive of fibroglandular volume (n = 588). Correlations between predicted and radiologically quantified fibroglandular volume were assessed in 264 independent patients. A second random forest classifier was trained to predict diagnosis (invasive vs. benign); performance was assessed using area under receiver-operating characteristics curves (AUC). Using extracted features, regression models predicted global (r = 0.94) and localized (r = 0.93) fibroglandular volume, with fat and non-fatty stromal content representing the strongest correlates, followed by epithelial organization rather than quantity. For predicting cancer among high and low fibroglandular volume, the classifier achieved AUCs of 0.92 and 0.84, respectively, with epithelial organizational features ranking most important. These results suggest non-fatty stroma, fat tissue quantities and epithelial region organization predict fibroglandular volume. The model holds promise for identifying histological correlates of cancer risk in patients with high and low density and warrants further evaluation.
Food authentication from shotgun sequencing reads with an application on high protein powders
Authors: Haiminen Niina , Edlund Stefan , Chambliss David , Kunitomi Mark , Weimer Bart C. , Ganesan Balasubramanian , Baker Robert , Markwell Peter , Davis Matthew , Huang B. Carol , Kong Nguyet , Prill Robert J. , Marlowe Carl H. , Quintanar André , Pierre Sophie , Dubois Geraud , Kaufman James H. , Parida Laxmi , Beck Kristen L. 
Published: November 2019

AbstractHere we propose that using shotgun sequencing to examine food leads to accurate authentication of ingredients and detection of contaminants. To demonstrate this, we developed a bioinformatic pipeline, FASER (Food Authentication from SEquencing Reads), designed to resolve the relative composition of mixtures of eukaryotic species using RNA or DNA sequencing. Our comprehensive database includes >6000 plants and animals that may be present in food. FASER accurately identified eukaryotic species with 0.4% median absolute difference between observed and expected proportions on sequence data from various sources including sausage meat, plants, and fish. FASER was applied to 31 high protein powder raw factory ingredient total RNA samples. The samples mostly contained the expected source ingredient, chicken, while three samples unexpectedly contained pork and beef. Our results demonstrate that DNA/RNA sequencing of food ingredients, combined with a robust analysis, can be used to find contaminants and authenticate food ingredients in a single assay.
A quantitative description of the transition between intuitive altruism and rational deliberation in iterated Prisoner’s Dilemma experiments
Authors: Gallotti Riccardo , Grujić Jelena 
Published: November 2019

AbstractWhat is intuitive: pro-social or anti-social behaviour? To answer this fundamental question, recent studies analyse decision times in game theory experiments under the assumption that intuitive decisions are fast and that deliberation is slow. These analyses keep track of the average time taken to make decisions under different conditions. Lacking any knowledge of the underlying dynamics, such simplistic approach might however lead to erroneous interpretations. Here we model the cognitive basis of strategic cooperative decision making using the Drift Diffusion Model to discern between deliberation and intuition and describe the evolution of the decision making in iterated Prisoner’s Dilemma experiments. We find that, although initially people’s intuitive decision is to cooperate, rational deliberation quickly becomes dominant over an initial intuitive bias towards cooperation, which is fostered by positive interactions as much as frustrated by a negative one. However, this initial pro-social tendency is resilient, as after a pause it resets to the same initial value. These results illustrate the new insight that can be achieved thanks to a quantitative modelling of human behavior.
Associations of parental age with offspring all-cause and cause-specific adult mortality
Authors: Carslake David , Tynelius Per , van den Berg Gerard J. , Davey Smith George 
Published: November 2019

AbstractPeople are having children later in life. The consequences for offspring adult survival have been little studied due to the need for long follow-up linked to parental data and most research has considered offspring survival only in early life. We used Swedish registry data to examine all-cause and cause-specific adult mortality (293,470 deaths among 5,204,433 people, followed up to a maximum of 80 years old) in relation to parental age. For most common causes of death adult survival was improved in the offspring of older parents (HR for all-cause survival was 0.96 (95% CI: 0.96, 0.97) and 0.98 (0.97, 0.98) per five years of maternal and paternal age, respectively). The childhood environment provided by older parents may more than compensate for any physiological disadvantages. Within-family analyses suggested stronger benefits of advanced parental age. This emphasises the importance of secular trends; a parent’s later children were born into a wealthier, healthier world. Sibling-comparison analyses can best assess individual family planning choices, but our results suggested a vulnerability to selection bias when there is extensive censoring. We consider the numerous causal and non-causal mechanisms which can link parental age and offspring survival, and the difficulty of separating them with currently available data.
A dose response model for quantifying the infection risk of antibiotic-resistant bacteria
Authors: Chandrasekaran Srikiran , Jiang Sunny C. 
Published: November 2019

AbstractQuantifying the human health risk of microbial infection helps inform regulatory policies concerning pathogens, and the associated public health measures. Estimating the infection risk requires knowledge of the probability of a person being infected by a given quantity of pathogens, and this relationship is modeled using pathogen specific dose response models (DRMs). However, risk quantification for antibiotic-resistant bacteria (ARB) has been hindered by the absence of suitable DRMs for ARB. A new approach to DRMs is introduced to capture ARB and antibiotic-susceptible bacteria (ASB) dynamics as a stochastic simple death (SD) process. By bridging SD with data from bench experiments, we demonstrate methods to (1) account for the effect of antibiotic concentrations and horizontal gene transfer on risk; (2) compute total risk for samples containing multiple bacterial types (e.g., ASB, ARB); and (3) predict if illness is treatable with antibiotics. We present a case study of exposure to a mixed population of Gentamicin-susceptible and resistant Escherichia coli and predict the health outcomes for varying Gentamicin concentrations. Thus, this research establishes a new framework to quantify the risk posed by ARB and antibiotics.
Impact of Direct Acting Antivirals on Survival in Patients with Chronic Hepatitis C and Hepatocellular Carcinoma
Authors: Kamp William M. , Sellers Cortlandt M. , Stein Stacey , Lim Joseph K. , Kim Hyun S. 
Published: November 2019

AbstractWith the increasing use of direct-acting antivirals (DAA) for treatment of chronic hepatitis C virus (HCV) infection, we looked at the impact of DAA use and 12-week sustained viral response (SVR12) in patients with hepatocellular carcinoma (HCC) and HCV. This is a retrospective analysis of 969 HCC patients diagnosed from 2005 to 2016 at an urban tertiary-care hospital. Kaplan-Meier curves and multivariable Cox proportional hazards models were used to assess survival. Median overall survival of the cohort was 24.2 months. 470 patients had HCV (56%). 123 patients received DAA therapies for HCV (26.2%), 83 of whom achieved SVR12 (67.4%). HCV-positive and HCV-negative patients had similar survival, 20.7 months vs 17.4 months (p = 0.22). Patients receiving DAA therapy had an overall survival of 71.8 months vs 11.6 months for patients without (p < 0.0001). DAA patients who achieved SVR12 had an overall survival of 75.6 months vs. 26.7 months in the non SVR12 group (p < 0.0001). Multivariable analysis revealed AJCC, Child-Pugh Score, MELD, tumor size, tumor location, cancer treatment type, receiving DAA treatment and achieving SVR12 had independent influence on survival (p < 0.05). This suggests DAA therapy and achieving SVR12 is associated with increased overall survival in HCV patients with HCC.
Correlative light and scanning electron microscopy (CLSEM) for analysis of bacterial infection of polarized epithelial cells
Authors: Kommnick Carina , Lepper Andrea , Hensel Michael 
Published: November 2019

AbstractInfection of mammalian host cells by bacterial pathogens is a highly dynamic process and microscopy is instrumental to reveal the cellular and molecular details of host-pathogen interactions. Correlative light and electron microscopy (CLEM) combines the advantages of three-dimensional live cell imaging with ultrastructural analysis. The analyses of adhesion to, and invasion of polarized epithelial cells by pathogens often deploys scanning electron microscopy (SEM), since surface structures of the apical brush border can be analyzed in detail. Most available CLEM approaches focus on relocalization of separated single cells in different imaging modalities, but are not readily applicable to polarized epithelial cell monolayers, since orientation marks on substrate are overgrown during differentiation. To address this problem, we developed a simple and convenient workflow for correlative light and scanning electron microscopy (CLSEM), using gold mesh grids as carrier for growth of epithelial cell monolayers, and for imaging infection. The approach allows fast live cell imaging of bacterial infection of polarized cells with subsequent analyses by SEM. As examples for CLSEM applications, we investigated trigger invasion by Salmonella enterica, zipper invasion by Listeria monocytogenes, and the enterocyte attachment and effacement phenotype of enteropathogenic Escherichia coli. Our study demonstrates the versatile use of gold mesh grids for CLSEM of the interaction of bacterial pathogens with the apical side of polarized epithelial cells.
Tadalafil Treatment Improves Inflammation, Cognitive Function, And Mismatch Negativity Of Patients With Low Urinary Tract Symptoms And Erectile Dysfunction
Authors: Urios Amparo , Ordoño Felipe , García-García Raquel , Mangas-Losada Alba , Leone Paola , José Gallego Juan , Cabrera-Pastor Andrea , Megías Javier , Fermin Ordoño Juan , Felipo Vicente , Montoliu Carmina 
Published: November 2019

AbstractPatients with Benign prostatic hyperplasia, low urinary tract symptoms, and erectile dysfunction (BPH/LUTS-ED) present chronic inflammation. We studied in patients with BPH/LUTS-ED the effect of tadalafil treatment (5 mg/day) on changes in peripheral inflammation, cognitive function, and the auditory evoked potential, “mismatch negativity” (MMN). Nine patients with BPH/LUTS-ED and 12 controls performed psychometric tests, MMN. IL-6, IL-17, IL-18, cGMP and CD4+CD28− autoreactive T-cells were measured in blood. Patients with BPH/LUTS-ED performed psychometric tests, MMN, and blood extraction at baseline and after tadalafil treatment. Patients with BPH/LUTS-ED showed increased CD4+CD28− autoreactive T-cells (p < 0.05), and higher levels of pro-inflammatory interleukins IL-6 (p < 0.001), IL-17 and IL-18 (p < 0.05), compared to controls. Patients got lower scores than controls in psychometric tests assessing mental processing speed and attention (p < 0.05), and showed lower amplitude (p < 0.01) and area (p < 0.05) of MMN wave than controls. Inflammatory, psychometric and electrophysiological parameters were normalized after tadalafil treatment. In conclusion, there is a pro-inflammatory environment in blood in patients with BPH/LUTS-ED which would induce cognitive impairment and alter MMN. Phosphodiesterase-5 inhibition with tadalafil exerts anti-inflammatory effects and ameliorates cognitive function and MMN parameters. Tadalafil could be a promising candidate for chronic treatment in other inflammatory pathologies associated with mild cognitive impairment.
Cooling history and emplacement of a pyroxenitic lava as proxy for understanding Martian lava flows
Authors: Murri Mara , Domeneghetti Maria C. , Fioretti Anna M. , Nestola Fabrizio , Vetere Francesco , Perugini Diego , Pisello Alessandro , Faccenda Manuele , Alvaro Matteo 
Published: November 2019

AbstractTerrestrial analogues are often investigated to get insights into the geological processes occurring on other planetary bodies. Due to its thickness and petrological similarities, the pyroxenitic layer of the 120m-thick magmatic pile Theo’s Flow (Archean Abitibi greenstone belt Ontario, Canada), has always been regarded as the terrestrial analogue for Martian nakhlites. However, its origin and cooling history and, as a consequence those of nakhlites, have always been a matter of vigorous debate. Did this lava flow originate from a single magmatic event similar to those supposed to occur on Mars or do the different units derive from multiple eruptions? We demonstrate, by a combination of geothermometric constraints on augite single crystals and numerical simulations, that Theo’s Flow has been formed by multiple magma emplacements that occurred at different times. This discovery supports the idea that the enormous lava flows with similar compositions observed on Mars could be the result of a process where low viscosity lavas are emplaced during multiple eruptions. This has profound implications for understanding the multiscale mechanisms of lava flow emplacement on Earth and other planetary bodies.
Exploring anticancer activity of structurally modified benzylphenoxyacetamide (BPA); I: Synthesis strategies and computational analyses of substituted BPA variants with high anti-glioblastoma potential
Authors: Stalinska Joanna , Houser Lisa , Rak Monika , Colley Susan B. , Reiss Krzysztof , Jursic Branko S. 
Published: November 2019

AbstractStructural variations of the benzylphenoxyacetamide (BPA) molecular skeleton were explored as a viable starting point for designing new anti-glioblastoma drug candidates. Hand-to-hand computational evaluation, chemical modifications, and cell viability testing were performed to explore the importance of some of the structural properties in order to generate, retain, and improve desired anti-glioblastoma characteristics. It was demonstrated that several structural features are required to retain the anti-glioblastoma activity, including a carbonyl group of the benzophenone moiety, as well as 4′-chloro and 2,2-dimethy substituents. In addition, the structure of the amide moiety can be modified in such a way that desirable anti-glioblastoma and physical properties can be improved. Via these structural modifications, more than 50 compounds were prepared and tested for anti-glioblastoma activity. Four compounds were identified (HR28, HR32, HR37, and HR46) that in addition to HR40 (PP1) from our previous study, have been determined to have desirable physical and biological properties. These include high glioblastoma cytotoxicity at low μM concentrations, improved water solubility, and the ability to penetrate the blood brain barrier (BBB), which indicate a potential for becoming a new class of anti-glioblastoma drugs.
Rotational Three-dimensional OCTA: a Notable New Imaging Tool to Characterize Type 3 Macular Neovascularization
Authors: Borrelli Enrico , Sacconi Riccardo , Klose Gerd , de Sisternes Luis , Bandello Francesco , Querques Giuseppe 
Published: November 2019

AbstractThis study explored whether rotational three-dimensional (3D) visualization of optical coherence tomography angiography (OCTA) volume data may yield valuable information regarding type 3 macular neovascularization (MNV). In this retrospective, cross-sectional study, we collected data from 15 eyes (13 patients) with treatment-naïve type 3 MNV in their post-nascent stage and age-related macular degeneration (AMD). Subjects were imaged with the SS-OCT system (PLEX Elite 9000, Carl Zeiss Meditec Inc., Dublin, CA, USA). The OCTA volume data were processed with a prototype volume projection removal algorithm and then analyzed using volumetric visualization techniques in order to obtain a 3D visualization of the region occupied by type 3 MNV. The two-dimensional and three-dimensional OCTA images were investigated. Mean ± SD age was 75.1 ± 7.4 years. BCVA was 0.42 ± 0.21 LogMAR in the study eyes. Considering the cohort of analyzed eyes, on rotational 3D OCTA images, a total of 35 neovascular lesions (vs 22 lesions detected on 2D OCTA images) rising from the deep vascular complex and variably spanning the outer retinal layers and eventually reaching the RPE/sub-RPE space were detected. Nine of 35 lesions had a saccular shape, while the remaining cases had a filiform shape. On rotational 3D OCTA images, these lesions were inclined on the three planes, instead of perpendicular to the RPE/Bruch’s membrane. In conclusion, this study used an algorithm to obtain rotational three-dimensional visualization of type 3 MNV. This approach seems to increase the detection rate for these lesions and to be useful to offer new insight into type 3 MNV.
Immune cell type, cell activation, and single cell heterogeneity revealed by label-free optical methods
Authors: Pavillon Nicolas , Smith Nicholas I. 
Published: November 2019

AbstractMeasurement techniques that allow the global analysis of cellular responses while retaining single-cell sensitivity are increasingly needed in order to understand complex and dynamic biological processes. In this context, compromises between sensitivity, degree of multiplexing, throughput, and invasiveness are often unavoidable. We present here a noninvasive optical approach that can retrieve quantitative biomarkers of both morphological and molecular phenotypes of individual cells, based on a combination of quantitative phase imaging and Raman spectroscopy measurements. We then develop generalized statistical tools to assess the influence of both controlled (cell sub-populations, immune stimulation) and uncontrolled (culturing conditions, animal variations, etc.) experimental parameters on the label-free biomarkers. These indicators can detect different macrophage cell sub-populations originating from different progenitors as well as their activation state, and how these changes are related to specific differences in morphology and molecular content. The molecular indicators also display further sensitivity that allow identification of other experimental conditions, such as differences between cells originating from different animals, allowing the detection of outlier behaviour from given cell sub-populations.
The origin of the exceptionally low activation energy of oxygen vacancy in tantalum pentoxide based resistive memory
Authors: Hur Ji-Hyun 
Published: November 2019

AbstractIt is well known that collective migrations of oxygen vacancies in oxide is the key principle of resistance change in oxide-based resistive memory (OxRAM). The practical usefulness of OxRAM mainly arises from the fact that these oxygen vacancy migrations take place at relatively low operating voltages. The activation energy of oxygen vacancy migration, which can be inferred from the operational voltage of an OxRAM, is much smaller compared to the experimentally measured activation energy of oxygen, and the underlying mechanism of the discrepancy has not been highlighted yet. We ask this fundamental question in this paper for tantalum oxide which is one of the most commonly employed oxides in OxRAMs and try the theoretical answer based on the first-principles calculations. From the results, it is proven that the exceptionally large mobility of oxygen vacancy expected by the switching model can be well explained by the exceptionally low activation barrier of positively charged oxygen vacancy within the two-dimensional substructure.