bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of Soft Tissue Materials for Simulation Development
Authors: Caldwell Julia , Mooney James J. 
Published: October 2019

Introduction
To meet unique demands and stretch budgets, simulations will often be made rather than purchased. Although 3-dimensional printing can be useful, there are significant physical limitations of these materials. This project is intended to begin examining the physical properties of materials used in casting/molding that may be useful for simulant soft tissue creation.

Methods
A variety of materials (foams and rubbers, urethanes and silicones, ballistic and food grade gels) were cast in standardized forms for analysis and visualized via computed tomography scanner and ultrasound (US). Each sample was also tested using 18ga and 22ga needles to determine force required for penetration.

Results
Silicone rubbers were generally well visualized via US, with computed tomography imaging showing between 100 and 200 Hounsfield units. Ballistic and food grade gels measured in the areas of −175 and 8 Hounsfield units, respectively, while being clear under US. Foams, particularly the urethane, demonstrated low Hounsfield units and were essentially opaque to US because of air cell artifact. Needle force requirements ranged from 0.05 to 23.34 N. Gels and foams were in the lower range, but there was overlap with the silicone. The use of additives in the silicones allowed for a wide range of needle forces and tactile experiences.

Conclusions
Silicone and urethane materials can mimic soft tissues, for both imaging and interventions. Although there is significant potential for independent production of custom, high-fidelity simulants, further work is required to identify preferable combinations of materials and optimal techniques for their use.
Critical role of de novo LTD in the formation and maintenance of hippocampal CA1 place-cell fields
Authors: Ashby Donovan M , Seamans Jeremy K , Wang Yu Tian 
Published: October 2019

AbstractSynaptic plasticity mechanisms may help shape hippocampal place field representations of novel environments, yet direct evidence for how this occurs is lacking. Using multi-channel recordings in freely moving rats, we demonstrate that novelty exploration results in widespread de novo long-term depression (LTD) at hippocampal CA1 synapses in a pathway-specific manner, while blockade of LTD expression impairs the maintenance of newly formed place fields. This study therefore reveals an unrecognized role for LTD in the formation and maintenance of hippocampal place fields in novel environments.
miR-206 family is important for mitochondrial and muscle function, but not essential for myogenesis in vitro
Authors: Przanowska Roza K. , Sobierajska Ewelina , Su Zhangli , Jensen Kate , Przanowski Piotr , Nagdas Sarbajeet , Kashatus Jennifer A. , Kashatus David F. , Bhatnagar Sanchita , Lukens John R. , Dutta Anindya 
Published: October 2019

AbstractmiR-206, miR-1a-1 and miR-1a-2 are induced during differentiation of skeletal myoblasts and promote myogenesis in vitro. miR-206 is required for skeletal muscle regeneration in vivo. Although this microRNA family is hypothesized to play an essential role in differentiation, a triple knockout of the three genes has not been done to test this hypothesis. We report that triple KO C2C12 myoblasts generated using CRISPR/Cas9 method differentiate despite the expected de-repression of the microRNA targets. Surprisingly, their mitochondrial function is diminished. Triple KO mice demonstrate partial embryonic lethality, most likely due to the role of miR-1a in cardiac muscle differentiation. Two triple KO mice survive and grow normally to adulthood with smaller myofiber diameter and diminished physical performance. Thus, unlike other microRNAs important in other differentiation pathways, the miR-206 family is not absolutely essential for myogenesis and is instead a modulator of optimal differentiation of skeletal myoblasts.
Multivariate pattern analysis techniques for electroencephalography data to study interference effects
Authors: López-García David , Sobrado Alberto , Peñalver José M. G. , Górriz Juan Manuel , Ruz María 
Published: October 2019

AbstractA central challenge in cognitive neuroscience is to understand the neural mechanisms that underlie the capacity to control our behavior according to internal goals. Flanker tasks, which require responding to stimuli surrounded by distracters that trigger incompatible action tendencies, are frequently used to measure this conflict. Even though the interference generated in these situations has been broadly studied, multivariate analysis techniques can shed new light into the underlying neural mechanisms. The current study is an initial approximation to adapt an interference Flanker paradigm embedded in a Demand-Selection Task to a format that allows measuring concurrent high-density electroencephalography. We used multivariate pattern analysis (MVPA) to decode conflictrelated neural processes associated with congruent or incongruent target events in a time-frequency resolved way. Our results replicate findings obtained with other analysis approaches and offer new information regarding the dynamics of the underlying mechanisms, which show signs of reinstantiation. Our findings, some of which could not had been obtained with classic analytical strategies, open novel avenues of research.
Phase separation by ssDNA binding protein controlledviaprotein-protein and protein-DNA interactions
Authors: Harami Gábor M. , Kovács Zoltán J. , Pancsa Rita , Pálinkás János , Baráth Veronika , Tárnok Krisztián , Málnási-Csizmadia András , Kovács Mihály 
Published: October 2019

ABSTRACTBacterial single stranded (ss) DNA-binding proteins (SSB) are essential for the replication and maintenance of the genome. SSBs share a conserved ssDNA-binding domain, a less conserved intrinsically disordered linker (IDL) and a highly conserved C-terminal peptide (CTP) motif that mediates a wide array of protein-protein interactions with DNA-metabolizing proteins. Here we show that theE. coliSSB protein forms liquid-liquid phase separated condensates in cellular-like conditions through multifaceted interactions involving all structural regions of the protein. SSB, ssDNA and SSB-interacting molecules are highly concentrated within the condensates, whereas phase separation is overall regulated by the stoichiometry of SSB and ssDNA. Together with recent results on subcellular SSB localization patterns, our results point to a conserved mechanism by which bacterial cells store a pool of SSB and SSB-interacting proteins. Dynamic phase separation enables rapid mobilization of this protein pool to protect exposed ssDNA and repair genomic loci affected by DNA damage.
Automated cryo-lamella preparation for high-throughput in-situ structural biology
Authors: Buckley Genevieve , Gervinskas Gediminas , Taveneau Cyntia , Venugopal Hari , Whisstock James C. , de Marco Alex 
Published: October 2019

AbstractCryo-transmission electron tomography (cryo-ET) in association with cryo-focused ion beam (cryo-FIB) milling enables structural biology studies to be performed directly within the cellular environment. Cryo-preserved cells are milled and a lamella with a thickness of 200-300 nm provides an electron transparent window suitable for cryo-ET imaging. Cryo-FIB milling is an effective method, but it is a tedious and time-consuming process, which typically results in ~10 lamellae per day. Here, we introduce an automated method to reproducibly prepare cryo-lamellae on a grid and reduce the amount of human supervision. We tested the routine on cryo-preserved Saccharomyces cerevisiae and demonstrate that this method allows an increased throughput, achieving a rate of 5 lamellae/hour without the need to supervise the FIB milling. We demonstrate that the quality of the lamellae is consistent throughout the preparation and their compatibility with cryo-ET analyses.
Fully automated, sequential focused ion beam milling for cryo-electron tomography
Authors: Zachs Tobias , Medeiros João M. , Schertel Andreas , Weiss Gregor L. , Hugener Jannik , Pilhofer Martin 
Published: October 2019

AbstractCryo-electron tomography (cryoET) has become a powerful technique at the interface of structural biology and cell biology, with the unique ability to determine structures of macromolecular complexes in their cellular context. A major limitation of cryoET is its restriction to relatively thin samples. Sample thinning by cryo-focused ion beam (cryoFIB) milling has significantly expanded the range of samples that can be analyzed by cryoET. Unfortunately, cryoFIB milling is low-throughput, time-consuming and manual. Here we report a method for fully automated sequential cryoFIB preparation of high-quality lamellae, including rough milling and polishing. We reproducibly applied this method to eukaryotic and bacterial model organisms, and show that the resulting lamellae are suitable for cryoET imaging and subtomogram averaging. Since our method reduces the time required for lamella preparation and minimizes the need for user input, we envision the technique will render previously inaccessible projects feasible.
Somatic selection of poorly differentiating variant stem cell clones could be a key to human ageing
Authors: Bodmer Walter F. , Crouch Daniel J. M. 
Published: October 2019

AbstractAny replicating system in which heritable variants with differing replicative potentials can arise is subject to a Darwinian evolutionary process. The continually replicating adult tissue stem cells that control the integrity of many tissues of long-lived, multicellular, complex vertebrate organisms, including humans, constitute such a replicating system. Our suggestion is that somatic selection for mutations (or stable epigenetic changes) that cause an increased rate of adult tissue stem cell proliferation, and their long-term persistence, at the expense of normal differentiation, is a major key to the ageing process. Once an organism has passed the reproductive age, there is no longer any significant counterselection at the organismal level to this inevitable cellular level Darwinian process.Author ContributionsWFB conceived the project. WFB and DJMC wrote the manuscript.
Human CST complex protects replication fork stability by directly blocking MRE11 degradation of nascent strand DNA
Authors: Lyu Xinxing , Lei Kai-Hang , Shiva Olga , Chastain Megan , Chi Peter , Chai Weihang 
Published: October 2019

AbstractDegradation and collapse of stalled replication forks are main sources of genome instability, yet the molecular mechanism for protecting forks from degradation/collapse is not well understood. Here, we report that human CST (CTC1-STN1-TEN1), a single-stranded DNA binding protein complex, localizes at stalled forks and protects forks from MRE11 nuclease degradation upon replication perturbation. CST deficiency causes nascent strand degradation, ssDNA accumulation after fork stalling, and delay in replication recovery, leading to cellular sensitivity to fork stalling agents. Purified CST binds to 5’ overhangs and directly blocks MRE11 degradation in vitro, and the DNA binding ability of CST is required for blocking MRE11-mediated nascent strand degradation. Finally, we uncover that CST and BRCA2 form non-overlapping foci upon fork stalling, and CST inactivation is synthetic with BRCA2 deficiency in inducing genome instability. Collectively, our findings identify CST as an important fork protector to preserve genome integrity under replication perturbation.
Insects as phyllosphere microbiome engineers: effects of aphids on a plant pathogen
Authors: Smee Melanie R. , Real-Ramirez Imperio , Hendry Tory A. 
Published: October 2019

AbstractInsect herbivores are common in the phyllosphere, the above-ground parts of plants, and encounter diverse plant-associated bacteria there, yet how these organisms interact remains largely unknown. Strains of the bacteriumPseudomonas syringaegrow well epiphytically and have been shown to grow within and kill hemipteran insects like the pea aphid,Acyrthosiphon pisum. Aphids are hypothesized to be an alternative host for these epiphytic bacteria but it is unclear if aphids provide fitness benefits to these bacterial pathogens. To determine if epiphytic bacteria could be adapted for infecting aphids, we characterized 21 strains ofP. syringaefor epiphytic ability and virulence to pea aphids and found that the two traits were positively correlated. For a subset of strains, we tested if the bacteria derived a fitness benefit from the presence of aphids. Some strains benefited significantly, with up to 18.9% higher population densities when aphids were present, and lower starting population density was predictive of higher benefit from aphid presence. However, further investigation found that honeydew, the sugary waste product of aphids, and not growth in aphids, increasedP. syringaegrowth on leaves. This suggests that aphids may be important microbiome engineers in the phyllosphere, but evolutionarily dead-ends for epiphytic bacteria.
Usefulness of a familiarity signal during recognition depends on test format: Neurocognitive evidence for a core assumption of the CLS framework
Authors: Bader Regine , Mecklinger Axel , Meyer Patric 
Published: October 2019

AbstractFamiliarity-based discrimination between studied target items and similar foils in yes/no recognition memory tests is relatively poor. According to the complementary learning systems (CLS) framework this is due do a relatively small difference in familiarity strength between these two item classes. The model, however, also predicts that when targets and corresponding similar foils are presented next to each other in a forced-choice corresponding (FCC) test format, familiarity values for targets and foils can be directly compared because in each trial, targets are reliably more familiar than their corresponding foils. In contrast, when forced-choice displays contain non-corresponding foils (FCNC) which are similar to other studied items (but not the target), familiarity should not be diagnostic because familiarity values are not directly comparable (as in yes/no-tasks). We compared ERP old/new effects (ERPs of targets vs. foils) when participants were tested with FCC vs. FCNC displays after having intentionally encoded pictures of objects. As predicted, the mid-frontal old/new effect which is associated with familiarity was significantly larger in FCC compared to FCNC displays. Moreover, the target-foil amplitude difference predicted the accuracy of the recognition judgment in a given trial. This is one of the very few studies which support the assumption of the CLS framework that the test format can influence the diagnosticity of familiarity. Moreover, it implies that the mid-frontal old/new effect does not reflect the mean difference in the familiarity signal itself between studied and non-studied items but reflects the task-adequate assessment of the familiarity signal.
Establishment of chromatin accessibility by the conserved transcription factor Grainy head is developmentally regulated
Authors: Nevil Markus , Gibson Tyler J. , Bartolutti Constantine , Iyengar Anusha , Harrison Melissa M 
Published: October 2019

AbstractThe dramatic changes in gene expression required for development necessitate the establishment ofcis-regulatory modules defined by regions of accessible chromatin. Pioneer transcription factors have the unique property of binding closed chromatin and facilitating the establishment of these accessible regions. Nonetheless, much of how pioneer transcription factors coordinate changes in chromatin accessibility during development remains unknown. To determine whether pioneer-factor function is intrinsic to the protein or whether pioneering activity is developmentally modulated, we studied the highly conserved, essential transcription factor, Grainy head (Grh). Grh is expressed throughoutDrosophiladevelopment and functions as a pioneer factor in the larvae. We demonstrated that Grh remains bound to condensed mitotic chromosomes, a property shared with other pioneer factors. By assaying chromatin accessibility in embryos lacking either maternal or zygotic Grh at three stages of development, we discovered that Grh is not required for chromatin accessibility in early embryogenesis, in contrast to its essential functions later in development. Our data reveal that the pioneering activity of Grh is temporally regulated and is likely influenced by additional factors expressed at a given developmental stage.
Computational genomics of brain tumors: identification and characterization of glioma candidate biomarkers through multi-omics integrative molecular profiling
Authors: Liu Lin , Wang Guangyu , Wang Liguo , Yu Chunlei , Li Mengwei , Song Shuhui , Hao Lili , Ma Lina , Zhang Zhang 
Published: October 2019

AbstractGlioma is one of the most common malignant brain tumors and exhibits low resection rate and high recurrence risk. Although a large number of glioma studies powered by high-throughput sequencing technologies have led to massive multi-omics datasets, there lacks of comprehensive integration of glioma datasets for uncovering candidate biomarker genes. In this study, we collected a large-scale assemble of multi-omics multi-cohort datasets from worldwide public resources, involving a total of 16,939 samples across 19 independent studies. Through comprehensive multi-omics molecular profiling across different datasets, we revealed thatPRKCG(Protein Kinase C Gamma), a brain-specific gene detectable in cerebrospinal fluid, is closely associated with glioma. Specifically, it presents lower expression and higher methylation in glioma samples compared with normal samples.PRKCGexpression/methylation change from high to low is indicative of glioma progression from low-grade to high-grade and high RNA expression is suggestive of good survival. Importantly,PRKCGin combination withMGMTis effective to predict survival outcomes after TMZ chemotherapy in a more precise manner. Collectively,PRKCGbears the great potential for glioma diagnosis, prognosis and therapy, andPRKCG-like genes may represent a set of important genes associated with different molecular mechanisms in glioma tumorigenesis. Accordingly, our study indicates the importance of computational integrative multi-omics data analysis and represents a data-driven scheme toward precision tumor subtyping and accurate personalized healthcare.Author SummaryGlioma is a type of brain tumors that represents one of the most lethal human malignancies with little chance for recovery. Nowadays, more and more studies have adopted high-throughput sequencing technologies to decode the molecular profiles of glioma from different omics levels, accordingly resulting in massive glioma datasets generated from different projects and laboratories throughout the world. Therefore, it has become crucially important on how to make full use of these valuable datasets for computational identification of glioma candidate biomarker genes in aid of precision tumor subtyping and accurate personalized treatment. In this study, we comprehensively integrated glioma datasets from all over the world and performed multi-omics molecular data mining. We revealed thatPRKCG, a brain-specific gene abundantly expressed in cerebrospinal fluid, bears the great potential for glioma diagnosis, prognosis and treatment prediction, which has been consistently observed on multiple independent datasets. In the era of big data, our study highlights the significance of computational integrative data mining toward precision medicine in cancer research.
Cell surface mechanics gate stem cell differentiation
Authors: Bergert Martin , Lembo Sergio , Milovanović Danica , Börmel Mandy , Neveu Pierre , Diz-Muñoz Alba 
Published: October 2019

AbstractCell differentiation typically occurs with concomitant shape transitions to enable specialized functions. To adopt a different shape, cells need to change the mechanical properties of their surface. However, whether conversely cell surface mechanics control the process of differentiation has been relatively unexplored. Here, we show that membrane mechanics gate the exit from naïve pluripotency of mouse embryonic stem cells. By measuring membrane tension during differentiation, we find that naïve stem cells release their plasma membrane from the underlying actin cortex when transitioning to a primed state. By mechanically tethering the plasma membrane to the cortex with a synthetic signalling-inert linker, we demonstrate that preventing this detachment forces stem cells to retain their naïve pluripotent state. We thus identify a decrease in membrane-to-cortex attachment as a new cell-intrinsic mechanism that is essential for stem cells to exit pluripotency.
The enhanced participant-driven photo elicitation method for everyday life health information behaviour research
Authors: Feng Yuanyuan 
Published: October 2019

Purpose
The purpose of this paper is to report the design and implementation of the enhanced participant-driven photo elicitation method in a qualitative interview study, to assess the performance of the method to investigate a research topic in everyday life health information behaviour and to provide insights on how to effectively use this method in future research.

Design/methodology/approach
The author embedded the enhanced participant-driven photo elicitation in a qualitative interview study to examine people’s everyday life health information behaviour with activity tracking technology. The author assessed the types of visual data collected by the method, categories of elicitation enabled by the method and how the method contributed to key research findings of the interview study.

Findings
The enhanced participant-driven photo elicitation generated rich, unique and meaningful data that would be otherwise difficult to collect through conventional qualitative interviews. The method also elicited explanation, rationalisation and reflection during the interviews, which enriched and triangulated key research findings. This work validated the benefits of the general photo elicitation method such as aiding participants’ recall of experiences, enriching research findings and improving research validity. It also demonstrated that the enhancement techniques used in this study could generate rich and even research data across interviews.

Originality/value
This paper describes the design and implementation of the enhanced participant-driven photo elicitation method to augment a qualitative interview study with activity tracker users. The author provides recommendations for researchers to take full advantage of the method in future everyday life health information behaviour research.