bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hematological and Neurological Expressed 1 (HN1): a predictive and pharmacodynamic biomarker of metformin response in endometrial cancers
Authors: Bateman Nicholas W. , Teng Pang-ning , Hope Erica , Hood Brian L. , Oliver Julie , Ao Wei , Zhou Ming , Wang Guisong , Tommarello Domenic , Wilson Katlin , Conrads Kelly A. , Hamilton Chad A. , Darcy Kathleen M. , Casablanca Yovanni , Maxwell G. Larry , Bae-Jump Victoria , Conrads Thomas P. 
Published: April 2019

AbstractPreoperative use of metformin in obese women with endometrioid endometrial cancer (EEC) reduces tumor proliferation and inhibits the mammalian target of rapamycin (mTOR) pathway, though is only effective in select cases. This study sought to identify a predictive and/or pharmacodynamic proteomic signature of metformin response to tailor its pharmacologic use. Matched pre- and post-metformin treated tumor tissues from a recently completed phase 0 window trial of metformin in EEC patients (ClinicalTrials.gov:NCT01911247), were analyzed by mass spectrometry (MS)-based proteomic and immunohistochemical analyses. Hematological and neurological expressed 1 (HN1) was significantly elevated in metformin responders (n=13) versus non-responders (n=7), which was also found to decrease in abundance in metformin responders following treatment; observations that were verified by immunohistochemical staining for HN1. Metformin response and loss of HN1 was assessed in RL95-2 and ACI-181 endometrial cancer cell lines. We further identified that silencing of HN1 abundance does not alter cellular response to metformin or basal cell proliferation, but that HN1 abundance does decrease in response to metformin treatment in RL95-2 and ACI-181 endometrial cancer cell lines. These data suggest that HN1 represents a predictive and pharmacodynamic biomarker of metformin response that, if validated in larger patient populations, may enable pre-operative EEC patient stratification to metformin treatment and the ability to monitor patient response.Novelty and ImpactHematological and Neurological Expressed 1 (HN1) is elevated in endometrioid endometrial cancer (EEC) patients that respond to metformin vs non-responders and decreases after treatment. HN1 decreases after metformin treatment of EEC cells in vitro, but is not necessary for metformin response or proliferation. We report HN1 as a novel predictive and pharmacodynamic biomarker of metformin response in EEC that may enable pre-operative EEC patient stratification to metformin treatment and the ability to monitor patient response.
Modeling unitary fields and the single-neuron contribution to local field potentials in the hippocampus
Authors: Teleńczuk Maria , Teleńczuk Bartosz , Destexhe Alain 
Published: April 2019

AbstractSynaptic currents represent a major contribution to the local field potential (LFP) in brain tissue, but the respective contribution of excitatory and inhibitory synapses is not known. Here, we provide estimates of this contribution by using computational models of hippocampal pyramidal neurons, constrained by in vitro recordings. We focus on the unitary LFP (uLFP) generated by single neurons in the CA3 region of the hippocampus. We first reproduce experimental results for hippocampal basket cells, and in particular how inhibitory uLFP are distributed within hippocampal layers. Next, we calculate the uLFP generated by pyramidal neurons, using morphologically-reconstructed CA3 pyramidal cells. The model shows that the excitatory uLFP is of small amplitude, smaller than inhibitory uLFPs. Indeed, when the two are simulated together, inhibitory uLFPs mask excitatory uLFPs, which might create the illusion that the inhibitory field is generated by pyramidal cells. These results provide an explanation for the observation that excitatory and inhibitory uLFPs are of the same polarity, in vivo and in vitro. These results also show that somatic inhibitory currents are large contributors of the LFP, which is important information to interpret this signal. Finally, the results of our model might form the basis of a simple method to compute the LFP, which could be applied to point neurons for each cell type, thus providing a simple biologically-grounded method to calculate LFPs from neural networks.
Image3C: a multimodal image-based and label independent integrative method for single-cell analysis
Authors: Accorsi Alice , Box Andrew C. , Peuß Robert , Wood Christopher , Alvarado Alejandro Sánchez , Rohner Nicolas 
Published: April 2019

AbstractImage-based cell classification has become a common tool to identify phenotypic changes in cell populations. However, this methodology is limited to organisms possessing well characterized species-specific reagents (e.g., antibodies) that allow cell identification, clustering and convolutional neural network (CNN) training. In the absence of such reagents, the power of image-based classification has remained mostly off-limits to many research organisms. We have developed an image-based classification methodology we named Image3C (Image-Cytometry Cell Classification) that does not require species-specific reagents nor pre-existing knowledge about the sample. Image3C combines image-based flow cytometry with an unbiased, high-throughput cell cluster pipeline and CNN integration. Image3C exploits intrinsic cellular features and non-species-specific dyes to perform de novo cell composition analysis and to detect changes in cellular composition between different conditions. Therefore, Image3C expands the use of imaged-based analyses of cell population composition to research organisms in which detailed cellular phenotypes are unknown or for which species-specific reagents are not available.Impact statementImage3C analyzes cell populations through image-based clustering and neural network training, which allows single-cell analysis in research organisms devoid of species-specific reagents or pre-existing knowledge on cell phenotypes.
Suction feeding performance and prey escape response interact to determine feeding success in larval fish
Authors: Sommerfeld Noam , Holzman Roi 
Published: April 2019

AbstractThe survival of larval marine fishes during early development is strongly dependent on their ability to capture prey. Most larval fish capture prey by expanding their mouth cavity, generating a “suction flow” that draws the prey into their mouth. Larval fish dwell in a hydrodynamic regime of low Reynolds numbers, which has been shown to impede their ability to capture non-evasive prey. However, the marine environment is characterized by an abundance of evasive prey such as Copepods. These organisms can sense the hydrodynamic disturbance created by approaching predators and perform high-acceleration escape maneuvers. Using a 3D high-speed video system, we characterized the interaction between 8-33 day post hatchingSparus auratalarvae and prey from a natural zooplankton assemblage that contained evasive prey, and assessed the factors that determine the outcome of these interactions. Larvae showed strong selectivity for large prey that was moving prior to the initialization of the strike. As previously shown in studies with non-evasive prey, larval feeding success increased with increasing Reynolds numbers. However, larval feeding success was also strongly dependent on the prey’s escape response. Feeding success was lower for larger, more evasive prey, indicating that larvae might be challenged in capturing their preferred prey. The kinematics of successful strikes resulted in shorter response time but higher hydrodynamic signature available for the prey. Thus, despite being “noisier”, successful strikes on evasive prey depended on preceding the prey’s escape response. Our results show that larval performance, rather than larval preferences, determines their diet during early development.
Evidence for a multi-level trophic organization of the human gut microbiome
Authors: Wang Tong , Goyal Akshit , Dubinkina Veronika , Maslov Sergei 
Published: April 2019

AbstractThe human gut microbiome is a complex ecosystem, in which hundreds of microbial species and metabolites coexist, in part due to an extensive network of cross-feeding interactions. However, both the large-scale trophic organization of this ecosystem, and its effects on the underlying metabolic flow, remain unexplored. Here, using a simplified model, we provide quantitative support for a multi-level trophic organization of the human gut microbiome, where microbes consume and secrete metabolites in multiple iterative steps. Using a manually-curated set of metabolic interactions between microbes, our model suggests about four trophic levels, each characterized by a high level-to-level metabolic transfer of byproducts. It also quantitatively predicts the typical metabolic environment of the gut (fecal metabolome) in approximate agreement with the real data. To understand the consequences of this trophic organization, we quantify the metabolic flow and biomass distribution, and explore patterns of microbial and metabolic diversity in different levels. The hierarchical trophic organization suggested by our model can help mechanistically establish causal links between the abundances of microbes and metabolites in the human gut.
Growth and selection of the cyanobacterium Synechococcus sp. PCC 7002 using alternative nitrogen and phosphorus sources
Authors: Selão Tiago Toscano , Włodarczyk Artur , Nixon Peter J. , Norling Birgitta 
Published: April 2019

AbstractCyanobacteria, such as Synechococcus sp. PCC 7002 (Syn7002), are promising chassis strains for “green” biotechnological applications as they can be grown in seawater using oxygenic photosynthesis to fix carbon dioxide into biomass. Their other major nutritional requirements for efficient growth are sources of nitrogen (N) and phosphorus (P). As these organisms are more economically cultivated in outdoor open systems, there is a need to develop cost-effective approaches to prevent the growth of contaminating organisms, especially as the use of antibiotic selection markers is neither economically feasible nor ecologically desirable due to the risk of horizontal gene transfer. Here we have introduced a synthetic melamine degradation pathway into Syn7002 and evolved the resulting strain to efficiently use the nitrogen-rich xenobiotic compound melamine as the sole N source. We also show that expression of phosphite dehydrogenase in the absence of its cognate phosphite transporter permits growth of Syn7002 on phosphite and can be used as a selectable marker in Syn7002. We combined these two strategies to generate a strain that can grow on melamine and phosphite as sole N and P sources, respectively. This strain is able to resist deliberate contamination in large excess and should be a useful chassis for metabolic engineering and biotechnological applications using cyanobacteria.
Stimulation of cardiac fibroblast Piezo1 channels opposes myofibroblast differentiation and induces IL-6 secretion via Ca2+-mediated p38 MAP kinase activation
Authors: Blythe Nicola M. , Stylianidis Vasili , Ludlow Melanie J. , Gilbert Hamish T. J. , Evans Elizabeth L. , Cuthbertson Kevin , Foster Richard , Swift Joe , Li Jing , Drinkhill Mark J. , van Nieuwenhoven Frans A. , Porter Karen E. , Beech David J. , Turner Neil A. 
Published: April 2019

AbstractPiezo1 is a mechanosensitive cation channel with widespread physiological importance; however its role in the heart is poorly understood. Cardiac fibroblasts are responsible for preserving the structural integrity of the myocardium and play a key role in regulating its repair and remodeling following stress or injury. We investigated expression and function of Piezo1 in cultured human and mouse cardiac fibroblasts. RT-PCR studies confirmed expression ofPiezo1mRNA in cardiac fibroblasts at similar levels to endothelial cells. Fura-2 intracellular Ca2+measurements validated Piezo1 as a functional ion channel that was activated by the Piezo1 agonist, Yoda1. Yoda1-induced Ca2+entry was inhibited by Piezo1 blockers (gadolinium, ruthenium red) and the Ca2+response was reduced proportionally by Piezo1 siRNA knockdown or in cells fromPiezo1+/−mice. Investigation of Yoda1 effects on selected remodeling genes indicated that Piezo1 activation opposed cardiac fibroblast differentiation; data confirmed by functional collagen gel contraction assays. Piezo1 activation using Yoda1 or mechanical stretch also increased the expression of interleukin-6 (IL-6), a mechanosensitive pro-hypertrophic and pro-fibrotic cytokine, in a Piezo1-dependent manner. Multiplex kinase activity profiling combined with kinase inhibitor studies and phospho-specific western blotting, established that Piezo1 activation stimulated IL-6 secretion via a pathway involving p38 MAP kinase, downstream of Ca2+entry. In summary, this study reveals that cardiac fibroblasts express functional Piezo1 channels coupled to reduced myofibroblast activation and increased secretion of paracrine signaling molecules that can modulate cardiac remodeling.
neoANT-HILL: an integrated tool for identification of potential neoantigens
Authors: Coelho Ana Carolina M F , Fonseca André L , Martins Danilo L , da Cunha Lucas M , Lins Paulo B R , de Souza Sandro J 
Published: April 2019

AbstractCancer neoantigens have attracted great interest in immunotherapy due to their ability to elicit antitumoral immune responses. These antigens are formed due to somatic mutations in the cancer genome that result in alterations of the original protein. Although current technological advances in neoantigen identification, it remains a challenging and a large number of false-positive continue to exist. In the current work, we present neoANT-HILL, an automatized user-friendly tool that integrates several immunogenomic analysis to improve neoantigens detection from NGS data. The program input can be a file with somatic mutations called and/or RNA-seq data. Our tool was applied on somatic mutations of melanoma dataset from TCGA and found that neoANT-HILL was able to predicted potential neoantigens. The software is available on github athttps://github.com/neoanthill/neoANT-HILL.
Differential characterization of physiological and biochemical responses during drought stress in finger millet varieties
Authors: Mukami Asunta , Ngetich Alex , Mweu Cecilia , Oduor Richard O. , Muthangya Mutemi , Mbinda Wilton Mwema 
Published: April 2019

AbstractDrought is the most perilous abiotic stress that affects finger millet growth and productivity worldwide. For the successful production of finger millet, selection of drought tolerant varieties is necessary and critical stages under drought stress, germination and early seedling growth, ought to be fully understood. This study investigated the physiological and biochemical responses of six finger millet varieties (GBK043137, GBK043128, GBK043124, GBK043122, GBK043094 and GBK043050) under mannitol-induced drought stress. Seeds were germinated on sterile soil and irrigated with various concentrations of mannitol (200, 400 and 600 mM) for two weeks. Comparative analysis in terms of relative water content (RWC), chlorophyll, proline, and malondialdehyde (MDA) contents were measured the physiological and biochemical characteristics of drought stress. The results showed that increased level of drought stress seriously decreased germination and early seedling growth of finger millet varieties. However, root growth was increased. In addition, exposition to drought stress triggered a significant decrease in relative water content and chlorophyll content reduction the biochemical parameters assay showed less reduction of relative water content. Furthermore, oxidative damage indicating parameters such as proline concentration and MDA content increased. Varieties GBK043137 and GBK043094 were less affected by drought as shown by significant change in the physiological parameters. Our findings reveal the difference and linkage between the physiological responses of finger millet to drought and are vital for breeding and selection of drought tolerant varieties of finger millet. Further investigations on genomic and molecular to deeply insight the detail mechanisms of drought tolerance in finger millet need to explored.
Multiplexed and Inducible Gene Modulation in Human Pluripotent Stem Cells by CRISPR Interference and Activation
Authors: Hazelbaker Dane Z. , Beccard Amanda , Mazzucato Patrizia , Angelini Gabriella , Messana Angelica , Lam Daisy , Eggan Kevin , Barrett Lindy E. 
Published: April 2019

ABSTRACTCRISPR-Cas9-mediated gene interference (CRISPRi) and activation (CRISPRa) approaches hold promise for functional genomic studies and genome-wide screens in human pluripotent stem cells (hPSCs). However, in contrast to CRISPR-Cas9 nuclease approaches, the efficiency of CRISPRi/a depends on continued expression of the dead Cas9 (dCas9) effector and guide RNA (gRNA), which can vary substantially depending on transgene design and delivery. Here, we design new fluorescently labeledpiggyBac(PB) vectors to deliver robust and stable expression of multiplexed gRNAs. In addition, we generate hPSC lines harboring AAVS1-integrated, inducible and fluorescent dCas9-KRAB and dCas9-VPR transgenes to allow for accurate quantification and tracking of cells that express both the dCas9 effectors and gRNAs. We then employ these systems to target theTCF4gene and conduct a rigorous assessment of expression levels of the dCas9 effectors, gRNAs and targeted gene. Collectively, these data provide proof-of-principle application of a stable, multiplexed PB gRNA delivery system that can be widely exploited to further enable genome engineering studies in hPSCs. Paired with diverse CRISPR tools including our dual fluorescence CRISPRi/a cell lines, this system would facilitate functional dissection of individual genes and pathways as well as larger-scale screens for studies of development and disease.
Reliability, sensitivity and predictive value of fMRI during multiple object tracking as a marker of cognitive training gain in combination with tDCS in stroke survivors
Authors: Kolskår Knut K. , Richard Geneviève , Alnæs Dag , Dørum Erlend S. , Sanders Anne-Marthe , Ulrichsen Kristine M. , Sánchez Jennifer Monereo , Ihle-Hansen Hege , Nordvik Jan E. , Westlye Lars T. 
Published: April 2019

AbstractComputerized cognitive training (CCT) combined with transcranial direct current stimulation (tDCS) has showed some promise in alleviating cognitive impairments in patients with brain disorders, but the robustness and possible mechanisms are unclear. In this prospective double-blind randomized clinical trial, we investigated the feasibility and effectiveness of combining CCT and tDCS, and tested the predictive value of and training-related changes in fMRI-based brain activation during attentive performance (multiple object tracking) obtained at inclusion, before initiating training, and after the three-weeks intervention in chronic stroke patients (> 6 months since hospital admission). Patients were randomized to one of two groups, receiving CCT and either (1) tDCS targeting left dorsolateral prefrontal cortex (1 mA), or (2) sham tDCS, with 40s active stimulation (1 mA) before fade out of the current. 77 patients were enrolled in the study, 54 completed the cognitive training, and 48 completed all training and MRI sessions. We found significant improvement in performance across all trained tasks, but no additional gain of tDCS. fMRI-based brain activation showed high reliability, and higher cognitive performance was associated with increased tracking-related activation in the dorsal attention network (DAN) and default mode network (DMN) as well as anterior cingulate after compared to before the intervention. We found no significant associations between cognitive gain and brain activation measured before training or in the difference in activation after intervention. Combined, these results show significant training effects on trained cognitive tasks in stroke survivors, with no clear evidence of additional gain of concurrent tDCS.
Augmenting Quadriplegic Hand Function Using a Sensorimotor Demultiplexing Neural Interface
Authors: Ganzer PD , Colachis SC , Schwemmer MA , Friedenberg DA , Swiftney CE , Jacobowitz AF , Weber DJ , Bockbrader MA , Sharma G 
Published: April 2019

AbstractBackgroundThe sense of touch is a key component of motor function. Severe spinal cord injury (SCI) should essentially eliminate sensory information transmission to the brain, that originates from skin innervated from below the lesion. We assessed the hypothesis that, following SCI, residual hand sensory information is transmitted to the brain, can be decoded amongst competing sensorimotor signals, and used to enhance the sense of touch via an intracortically controlled closed-loop brain-computer interface (BCI) system.MethodsExperiments were performed with a participant who has an AIS-A C5 SCI and an intracortical recording array implanted in left primary motor cortex (M1). Sensory stimulation and standard clinical sensorimotor functional assessments were used throughout a series of several mechanistic experiments.FindingsOur results demonstrate that residual afferent hand sensory signals surprisingly reach human primary motor cortex and can be simultaneously demultiplexed from ongoing efferent motor intention, enabling closed-loop sensory feedback during brain-computer interface (BCI) operation. The closed-loop sensory feedback system was able to detect residual sensory signals from up to the C8 spinal level. Using the closed-loop sensory feedback system enabled significantly enhanced object touch detection, sense of agency, movement speed, and other sensorimotor functions.InterpretationTo our knowledge, this is the first demonstration of simultaneously decoding multiplexed afferent and efferent activity from human cortex to control multiple assistive devices, constituting a ‘sensorimotor demultiplexing’ BCI. Overall, our results support the hypothesis that sub-perceptual neural signals can be decoded reliably and transformed to conscious perception, significantly augmenting function.FundingInternal funding was provided for this study from Battelle Memorial Institute and The Ohio State University Center for Neuromodulation.
The influence of feeding behaviour and temperature on the capacity of mosquitoes to transmit malaria
Authors: Suh Eunho , Grossman Marissa K. , Waite Jessica L. , Dennington Nina L. , Sherrard-Smith Ellie , Churcher Thomas S. , Thomas Matthew B. 
Published: April 2019

AbstractInsecticide-treated bed nets reduce malaria transmission by limiting contact between mosquito vectors and human hosts when mosquitoes feed during the night. However, malaria vectors can also feed in the early evening and in the morning when people are not protected. Here, we explored how timing of blood feeding interacts with environmental temperature to influence the capacity of Anopheles mosquitoes to transmit the human malaria parasite, Plasmodium falciparum. We found no effect of biting time itself on the proportion of mosquitoes that became infectious (vector competence) at constant temperature. However, when mosquitoes were maintained under more realistic fluctuating temperatures there was a significant increase in competence for mosquitoes feeding in the evening, and a significant reduction in competence for those feeding in the morning, relative to those feeding at midnight. These effects appear to be due to thermal sensitivity of malaria parasites during the initial stages of parasite development within the mosquito, and the fact that mosquitoes feeding in the evening experience cooling temperatures during the night, whereas mosquitoes feeding in the morning quickly experience warming temperatures that are inhibitory to parasite establishment. A transmission dynamics model illustrates that such differences in competence could have important implications for disease endemicity, the extent of transmission that persists in the presence of bed nets, and the epidemiological impact of behavioural resistance. These results indicate the interaction of temperature and feeding behaviour to be a major ecological determinant of the vectorial capacity of malaria mosquitoes.