bluuebunny/crossref_metadata_2025_split huggingface dataset:
DIALib: an automated ion library generator for data independent acquisition mass spectrometry analysis of peptides and glycopeptides
Authors: Phung Toan K. , Zacchi Lucia F , Schulz Benjamin L. 
Published: July 2019

AbstractData Independent Acquisition (DIA) Mass Spectrometry (MS) workflows allow unbiased measurement of all detectable peptides from complex proteomes, but require ion libraries for interrogation of peptides of interest. These DIA ion libraries can be theoretical or built from peptide identification data from Data Dependent Acquisition (DDA) MS workflows. However, DDA libraries derived from empirical data rely on confident peptide identification, which can be challenging for peptides carrying complex post-translational modifications. Here, we present DIALib, software to automate the construction of peptide and glycopeptide Data Independent Acquisition ion Libraries. We show that DIALib theoretical ion libraries can identify and measure diverse N- and O-glycopeptides from yeast and mammalian glycoproteins without prior knowledge of the glycan structures present. We present proof-of-principle data from a moderately complex yeast cell wall glycoproteome and a simple mixture of mammalian glycoproteins. We also show that DIALib libraries consisting only of glycan oxonium ions can quickly and easily provide a global compositional glycosylation profile of the detectable “oxoniome” of glycoproteomes. DIALib will help enable DIA glycoproteomics as a complementary analytical approach to DDA glycoproteomics.
Cyborg Organoids: Implantation of Nanoelectronics via Organogenesis for Tissue-Wide Electrophysiology
Authors: Li Qiang , Nan Kewang , Le Floch Paul , Lin Zuwan , Sheng Hao , Liu Jia 
Published: July 2019

ABSTRACTTissue-wide electrophysiology with single-cell and millisecond spatiotemporal resolution is critical for heart and brain studies, yet issues arise from invasive, localized implantation of electronics that destructs the well-connected cellular networks within matured organs. Here, we report the creation of cyborg organoids: the three-dimensional (3D) assembly of soft, stretchable mesh nanoelectronics across the entire organoid by cell-cell attraction forces from 2D-to-3D tissue reconfiguration during organogenesis. We demonstrate that stretchable mesh nanoelectronics can grow into and migrate with the initial 2D cell layers to form the 3D structure with minimal interruptions to tissue growth and differentiation. The intimate contact of nanoelectronics to cells enables us to chronically and systematically observe the evolution, propagation and synchronization of the bursting dynamics in human cardiac organoids through their entire organogenesis.
Systematic Description of 3q29 Duplication Syndrome Reveals New Syndromic Phenotypes: Results from the 3q29 Registry
Authors: Pollak Rebecca M , Zinsmeister Michael C , Murphy Melissa M , Zwick Michael E ,   the Emory 3q29 Project, Mulle Jennifer G 
Published: July 2019

ABSTRACT3q29 duplication syndrome (3q29Dup) is a rare genomic disorder caused by the reciprocal duplication of the 1.6 Mb 3q29 deletion syndrome region. Case reports indicate the 3q29Dup is likely to be pathogenic, but because no systematic study of the syndrome exists, the full range of manifestations is not well-understood. To develop a better understanding of 3q29 duplication syndrome, we used the 3q29 registry (https://3q29deletion.patientcrossroads.org/) to ascertain 31 individuals with 3q29Dup, the largest cohort ever surveyed in a systematic way. For comparison, we ascertained 117 individuals with the reciprocal 3q29 deletion syndrome (3q29Del) and 64 typically developing controls. We used a custom medical and demographic questionnaire to assess physical and developmental phenotypes, and two standardized instruments, the Social Responsiveness Scale (SRS) and Achenbach Behavior Checklists (CBCL/ABCL), to assess social disability. We find that our 3q29Dup participants report a high rate of problems in the first year of life (80.6%), including feeding problems (58%), failure to gain weight (42%), hypotonia (39%), and respiratory distress (29%). In early childhood, learning problems (87.1%) and seizures (25.8%) are common. Additionally, we find a rate of self-reported ASD diagnoses (39%) similar to that previously identified in 3q29Del (29%), and the granular characteristics of social disability measured using the SRS and CBCL/ABCL are comparable between 3q29Dup and 3q29Del. This is the most comprehensive description of 3q29Dup to date. Our findings can be used to develop evidence-based strategies for early intervention and management of 3q29 duplication syndrome.
PACVr: Plastome Assembly Coverage Visualization in R
Authors: Gruenstaeudl Michael , Jenke Nils 
Published: July 2019

ABSTRACTBackgroundThe circular, quadripartite structure of plastid genomes which includes two inverted repeat regions renders the automatic assembly of plastid genomes challenging. The correct assembly of plastid genomes is a prerequisite for the validity of subsequent analyses on plastid genome structure and evolution. Plastome-based phylogenetic or population genetic investigations, for example, require the precise identification of DNA sequence and length to determine the location of nucleotide polymorphisms. The average coverage depth of a genome assembly is often used as an indicator for assembly quality. Visualizing coverage depth across a draft genome allows users to inspect the quality of the assembly and, where applicable, identify regions of reduced assembly confidence. Based on such visualizations, users can conduct a local re-assembly or other forms of targeted error correction. Few, if any, contemporary software tools can visualize the coverage depth of a plastid genome assembly while taking its quadripartite structure into account, despite the interplay between genome structure and assembly quality. A software tool is needed that visualizes the coverage depth of a plastid genome assembly on a circular, quadripartite map of the plastid genome.ResultsWe introduce ‘PACVr’, an R package that visualizes the coverage depth of a plastid genome assembly in relation to the circular, quadripartite structure of the genome as well as to the individual plastome genes. The tool allows visualizations on different scales using a variable window approach and also visualizes the equality of gene synteny in the inverted repeat regions of the plastid genome, thus providing an additional measure of assembly quality. As a tool for plastid genomics, PACVr provides the functionality to identify regions of coverage depth above or below user-defined threshold values and helps to identify non-identical IR regions. To allow easy integration into bioinformatic workflows, PACVr can be directly invoked from a Unix shell, thus facilitating its use in automated quality control. We illustrate the application of PACVr on two empirical datasets and compare the resulting visualizations with alternative software tools for displaying plastome sequencing coverage.ConclusionsPACVr provides a user-friendly tool to visualize (a) the coverage depth of a plastid genome assembly on a circular, quadripartite plastome map and in relation to individual plastome genes, and (b) the equality of gene synteny in the inverted repeat regions. It, thus, contributes to optimizing plastid genome assemblies and increasing the reliability of publicly available plastome sequences, especially in light of incongruence among the visualization results of alternative software tools. The software, example datasets, technical documentation, and a tutorial are available with the package at https://github.com/michaelgruenstaeudl/PACVr.
StructureDistiller: Structural relevance scoring increases resilience of contact maps to false positive predictions
Authors: Bittrich Sebastian , Schroeder Michael , Labudde Dirk 
Published: July 2019

AbstractProtein folding and structure prediction are two sides of the same coin. We propose contact maps and the related techniques of constraint-based structure reconstruction as unifying aspect of both processes. The presented Structural Relevance (SR) score quantifies the contribution of individual contacts and residues to structural integrity.It is demonstrated that entries of a contact map are not equally relevant for structural integrity. Structure prediction methods should explicitly consider the most relevant contacts for optimal performance because they effectively double resilience toward false positively predicted contacts. Furthermore, knowledge of the most relevant contacts significantly increases reconstruction fidelity on sparse contact maps by 0.4 Å.Protein folding is commonly characterized with spatial and temporal resolution: some residues are Early Folding while others are Highly Stable with respect to unfolding events. Using the proposed SR score, we demonstrate that folding initiation and structure stabilization are distinct processes.
Cross-kingdom recognition of bacterial small RNAs induces transgenerational pathogenic avoidance
Authors: Kaletsky Rachel , Moore Rebecca S. , Parsons Lance L. , Murphy Coleen T. 
Published: July 2019

AbstractWe recently discovered that C. elegans can pass on a learned avoidance of pathogenic Pseudomonas aeruginosa (PA14) to four generations of its progeny. This transgenerational inheritance is bacterial species-specific, but how C. elegans recognizes and distinguishes different bacteria and transmits this information to future generations is not apparent. Here we show that small RNAs purified from pathogenic PA14 are sufficient not only to induce avoidance of pathogens in mothers, but also to confer transgenerational inheritance of this species-specific behavior for four generations, all without direct contact with pathogenic bacteria. This behavior requires the small RNA transporters SID-1 and SID-2, RNA interference pathway components, the piRNA Piwi/Argonaute pathway, a functioning germline, and TGF-β ligand daf-7 expression in the ASI sensory neuron. Our results suggest that C. elegans “reads” small RNAs expressed by pathogenic bacteria, and uses this information to induce an escape behavior that lasts for four additional generations. C. elegans may have evolved this trans-kingdom signaling system to avoid pathogens in abundant classes of bacteria in its environment and its microbiome.
Dynamic regulation of chromatin accessibility by pluripotency transcription factors across the cell cycle
Authors: Friman Elias T. , Deluz Cédric , Meireles-Filho Antonio C.A. , Govindan Subashika , Gardeux Vincent , Deplancke Bart , Suter David M. 
Published: July 2019

AbstractThe pioneer activity of transcription factors allows for opening of inaccessible regulatory elements and has been extensively studied in the context of cellular differentiation and reprogramming. In contrast, the function of pioneer activity in self-renewing cell divisions and across the cell cycle is poorly understood. Here we assessed the interplay between OCT4 and SOX2 in controlling chromatin accessibility of mouse embryonic stem cells. We found that OCT4 and SOX2 operate in a largely independent manner even at co-occupied sites, and that their cooperative binding is mostly mediated indirectly through regulation of chromatin accessibility. Controlled protein degradation strategies revealed that the uninterrupted presence of OCT4 is required for post-mitotic re-establishment and interphase maintenance of chromatin accessibility, and that highly OCT4-bound enhancers are particularly vulnerable to transient loss of OCT4 expression. Our study sheds light on the constant pioneer activity required to maintain the dynamic pluripotency regulatory landscape in an accessible state.
Negative Regulation of Autophagy by UBA6-BIRC6–Mediated Ubiquitination of LC3
Authors: Jia Rui , Bonifacino Juan S. 
Published: July 2019

AbstractAlthough the process of autophagy has been extensively studied, the mechanisms that regulate it remain insufficiently understood. The ability to manipulate autophagy is important not only for addressing fundamental biological questions, but also for its possible application to the treatment of various human diseases. To identify novel regulators of autophagy, we performed a whole-genome CRISPR/Cas9 knockout screen in H4 human neuroblastoma cells gene-edited to express the endogenous autophagy effector LC3B fused to a tandem of GFP and mCherry. Using this methodology, we identified the ubiquitin-activating (E1) enzyme UBA6 and the hybrid ubiquitin-conjugating (E2)/ubiquitin-ligase (E3) enzyme BIRC6 as important autophagy regulators. We found that these two enzymes cooperate to monoubiquitinate LC3B on lysine-51, targeting it for degradation by the proteasome. Knockout of UBA6 or BIRC6 increased the levels of LC3B as well as autophagic flux under conditions of nutrient deprivation or protein synthesis inhibition. Moreover, depletion of UBA6 or BIRC6 KO decreased the formation of aggresome-like induced structures in H4 cells, and aggregates of an α-synuclein mutant in the axon of rat hippocampal neurons. These findings demonstrate that UBA6 and BIRC6 negatively regulate autophagy by limiting the availability of LC3B, possibly to prevent the deleterious effects of excessive autophagy. Inhibition of UBA6 or BIRC6, on the other hand, could be used to enhance autophagic clearance of protein aggregates in neurodegenerative disorders.
HBMITool: a user-friendly software for labeling Human Brain Microscopy Images
Authors: Wang Hungju , Grinberg Lea T , Alegro Maryana 
Published: July 2019

AbstractOne of the most popular tools for quantifying protein expression is Immunofluorescence (IF). Although IF is widely applied in drug discovery research and assessing disease mechanisms, it has great room for improvement on the task of analyzing human postmortem brain samples. IF analysis of postmortem human tissue relies mostly on manual interaction, which is often error-prone and leading to low inter and intra-observer reproducibility. The high level of autofluorescence caused by accumulation of lipofuscin pigment during aging impedes systematic analyses of human postmortem brain samples. A method for automating cell counting and classification in IF microscopy of human postmortem brains was proposed before, which speeds up the quantification task while improving reproducibility. To correct for misclassified cells by the algorithm, we created HBFMTool, a software package that ease the process of editing the result produced by cell detection/classification algorithm.
Differential expansion microscopy
Authors: Pernal Sebastian P. , Liyanaarachchi Asiri , Gatti Domenico L. , Formosa Brent , Pulvender Rishika , Kuhn Eric R. , Ramos Rafael , Naik Akshata R. , George Kathleen , Arslanturk Suzan , Taatjes Douglas J. , Jena Bhanu P. 
Published: July 2019

AbstractExpansion microscopy (ExM) involves the use of hydration-competent polymers to physically expand biological specimens approximately 4-fold linear increase to achieve 70 nanometer resolution using an ordinary diffraction limited optical microscope. Optimal conditions however for antigen retention during the expansion process and the relative expansion between organelles within cells has remained unclear. It is reported that different tissues expand to different extents, suggesting that although isotropic expansion is believed to occur, different subcellular compartments with different composition would undergo anisotropic or differential expansion (DiEx). Consequently, there would be distortion of the native shape and size of subcellular compartments upon expansion, parameters which are critical in assessing cellular states in health and disease. Here we report optimal fixation and expansion conditions that retain structural integrity of cells while exhibiting up to 8-fold linear and therefore 512-fold volumetric expansion. Anisotropic expansion is observed not just between tissues, but between different subcellular compartments and even within subcellular compartments. Combining image analysis and machine learning, we provide an approach for the rapid and precise measurement of cellular and subcellular structures in expanded tissue. Using both manual and computation assessment of morphometric parameters, we demonstrate expansion to be anisotropic and name this method differential expansion microscopy (DiExM).
The tumor immune response is not compromised by mesenchymal stromal cells in humanized mice
Authors: Moquin-Beaudry Gaël , Colas Chloé , Li Yuanyi , Bazin Renée , Guimond Jean V. , Haddad Elie , Beauséjour Christian 
Published: July 2019

ABSTRACTTherapeutic uses of mesenchymal stromal cells (MSCs) have emerged over the past decade. Yet, their effect on tumor growth remains highly debated, particularly in an immune competent environment. Here, we wanted to investigate the impact of human umbilical cord MSCs (hUC-MSCs) on tumor growth in humanized mice generated by the adoptive transfer of peripheral blood mononuclear cells (Hu-AT) or the co-transplantation of hematopoietic stem cells and human thymic tissue (Hu-BLT). Our results showed that the growth and immune rejection of engineered human tumors was not altered by the injection of hUC-MSCs in immune-deficient or humanized mice respectively. This was observed whether tumor cells were injected subcutaneously or intravenously and independently of the injection route of the hUC-MSCs. Moreover, only in Hu-BLT mice did hUC-MSCs have some effects on the tumor immune infiltrate, yet without altering tumor growth. These results demonstrate that hUC-MSCs do not promote tumor growth and neither do they prevent tumor infiltration and rejection by immune cells in humanized mice.
Fluid-structure interaction analysis of transient convection heat transfer in a cavity containing inner solid cylinder and flexible right wall
Authors: Alsabery Ammar I. , Saleh Habibis , Ghalambaz Mohammad , Chamkha Ali J. , Hashim Ishak 
Published: July 2019

Purpose
This paper aims to investigate the fluid structure interaction analysis of conjugate natural convection in a square containing internal solid cylinder and flexible right wall.

Design/methodology/approach
The right wall of the cavity is flexible, which can be deformed due to the interaction with the natural convection flow in the cavity. The top and bottom walls of the cavity are insulated while the right wall is cold and the left wall is partially heated. The governing equations for heat, flow and elastic wall, as well as the grid deformation are written in Arbitrary Lagrangian–Eulerian formulation. The governing equations along with their boundary conditions are solved using the finite element method.

Findings
The results of the present study show that the presence of the solid cylinder strongly affects the transient solution at the initial times. The natural convection flow changes the shape of the flexible right wall of the cavity into S shape wall due to the interaction of the flow and the structure. It is found that the increase of the flexibility of the right wall increases the average Nusselt number of the hot wall up to 2 per cent.

Originality/value
To the best of the authors' knowledge, the unsteady natural convection in an enclosure having a flexible wall and inner solid cylinder has never been reported before.
Comparison of the experimental and numerical analyses of silver nanofluid under influence of strong magnetic field
Authors: Fornalik-Wajs Elzbieta , Roszko Aleksandra , Donizak Janusz , Kraszewska Anna 
Published: July 2019

Purpose
Nanofluids’ properties made them interesting for various areas like engineering, medicine or cosmetology. Discussed here, research pertains to specific problem of heat transfer enhancement with application of the magnetic field. The main idea was to transfer high heat rates with utilization of nanofluids including metallic non-ferrous particles. The expectation was based on changed nanofluid properties. However, the results of experimental analysis did not meet it. The heat transfer effect was smaller than in the case of base fluid. The only way to understand the process was to involve the computational fluid dynamics, which could help to clarify this issue. The purpose of this research is deep understanding of the external magnetic field effect on the nanofluids heat transfer.

Design/methodology/approach
In presented experimental and numerical studies, the water and silver nanofluids were considered. From the numerical point of view, three approaches to model the nanofluid in the strong magnetic field were used: single-phase Euler, Euler–Euler and Euler–Lagrange. In two-phase approach, the momentum transfer equations for individual phases were coupled through the interphase momentum transfer term expressing the volume force exerted by one phase on the second one.

Findings
Therefore, the results of numerical simulation predicted decrease of convection heat transfer for nanofluid with respect to pure water, which agreed with the experimental results. The experimental and numerical results are in good agreement with each other, which confirms the right choice of two-phase approach in analysis of nanofluid thermo-magnetic convection.

Originality/value
The Euler–Lagrange exhibit the best matching with the experimental results.
Numerical simulation of the interaction between a vortex ring and a bubble plume
Authors: Nguyen Van Luc , Degawa Tomohiro , Uchiyama Tomomi 
Published: July 2019

Purpose
This paper aims to provide discussions of a numerical method for bubbly flows and the interaction between a vortex ring and a bubble plume.

Design/methodology/approach
Small bubbles are released into quiescent water from a cylinder tip. They rise under the buoyant force, forming a plume. A vortex ring is launched vertically upward into the bubble plume. The interactions between the vortex ring and the bubble plume are numerically simulated using a semi-Lagrangian–Lagrangian approach composed of a vortex-in-cell method for the fluid phase and a Lagrangian description of the gas phase.

Findings
A vortex ring can transport the bubbles surrounding it over a distance significantly depending on the correlative initial position between the bubbles and the core center. The motion of some bubbles is nearly periodic and gradually extinguishes with time. These bubble trajectories are similar to two-dimensional-helix shapes. The vortex is fragmented into multiple regions with high values of Q, the second invariant of velocity gradient tensor, settling at these regional centers. The entrained bubbles excite a growth rate of the vortex ring's azimuthal instability with a formation of the second- and third-harmonic oscillations of modes of 16 and 24, respectively.

Originality/value
A semi-Lagrangian–Lagrangian approach is applied to simulate the interactions between a vortex ring and a bubble plume. The simulations provide the detail features of the interactions.