bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dasatinib Plus Quercetin on Uterine Age-Related Dysfunction and Fibrosis in Mice
Authors: Cavalcante Marcelo B. , Saccon Tatiana D. , Nunes Allancer D. C. , Kirkland James L. , Tchkonia Tamara , Schneider Augusto , Masternak Michal M. 
Published: October 2019

AbstractFemale reproductive function is negatively impacted by age. Animal and human studies show that fibrosis of the uterus contributes to gestational outcomes. Collagen deposition in the myometrial and endometrial layers is the main change related to uterine aging. Senolytic therapies are a potential option for reducing diseases and health complications related to aging. We investigated effects of aging and the senolytic drug combination of dasatinib plus quercetin (D+Q) on uterine fibrosis. A total of 40 mice, 20 young females (03-months) and 20 old females (18-months), were analyzed. Young (Y) and old (O) animals were divided into groups of 10 mice, with one treatment (T) group (YT and OT) and another control (C) group (YC and OC). Comparative analysis ofPi3k/Akt1/mTorand p53 gene expression among the 4 groups was performed to test effects of age and treatment on collagen deposition in uterine tissue. Uterine levels of microRNAs (miR34a, miR34b, miR34c, miR146a, miR449a, miR21a, miR126a, and miR181b) were evaluated. Aging promoted downregulation of genes of thePi3k/Akt1/mTorsignaling pathway (p=0.005, p=0.031, and p=0.028, respectively) as well as a reduction in expression of miR34c (p=0.029), miR126a (p=0.009), and miR181b (p=0.007). D+Q treatment increased p53 gene expression (p=0.041) and decreased levels of miR34a (p=0.016). Our results demonstrate a role for thePi3k/Akt1/mTorsignaling pathway in uterine aging and suggest for the first time a possible anti-fibrotic effect in the uterus of D+Q senolytic therapy.
The impact of respiratory gating on improving volume measurement of murine lung tumors in micro-CT imaging
Authors: Blocker S. J. , Holbrook M. D. , Mowery Y. M. , Sullivan D. C. , Badea C. T. 
Published: October 2019

ABSTRACTSmall animal imaging has become essential in evaluating new cancer therapies as they are translated from the preclinical to clinical domain. However, preclinical imaging faces unique challenges that emphasize the gap between mouse and man. One example is the difference in breathing patterns and breath-holding ability, which can dramatically affect tumor burden assessment in lung tissue. As part of a co-clinical trial studying immunotherapy and radiotherapy in sarcomas, we are using micro-CT of the lungs to detect and measure metastases as a metric of disease progression. To effectively utilize metastatic disease detection as a metric of progression, we have addressed the impact of respiratory gating during micro-CT acquisition on improving lung tumor detection and volume quantitation. Accuracy and precision of lung tumor measurements with and without respiratory gating were studied by performing experiments with in vivo images, simulations, and a pocket phantom. When performing test-retest studies in vivo, the variance in volume calculations was 5.9% in gated images and 15.8% in non-gated images, compared to 2.9% in post-mortem images. Sensitivity of detection was examined in images with simulated tumors, demonstrating that reliable sensitivity (true positive rate (TPR) ≥ 90%) was achievable down to 1.0 mm3 lesions with respiratory gating, but was limited to ≥ 8.0 mm3 in non-gated images. Finally, a clinically-inspired “pocket phantom” was used during in vivo mouse scanning to aid in refining and assessing the gating protocols. Application of respiratory gating techniques reduced variance of repeated volume measurements and significantly improved the accuracy of tumor volume quantitation in vivo.
Towards implementation of AI in New Zealand national screening program: Cloud-based, Robust, and Bespoke
Authors: Xie Li , Yang Song , Squirrell David , Vaghefi Ehsan 
Published: October 2019

AbstractConvolutional Neural Networks (CNN)s have become a prominent method of AI implementation in medical classification tasks. Grading Diabetic Retinopathy (DR) has been at the forefront of the development of AI for ophthalmology. However, major obstacles remain in the generalization of these CNN’s onto real-world DR screening programs. We believe these difficulties are due to use of 1) small training datasets (<5,000 images), 2) private and ‘curated’ repositories, 3) offline CNN implementation methods, while 4) relying on accuracy measured as area under the curve (AUC) as the sole measure of CNN performance.To address these issues, the public EyePACS Kaggle Diabetic Retinopathy dataset was uploaded onto Microsoft Azure™ cloud platform. Two CNNs were trained as a “Quality Assurance”, and a “Classifier”. The “Classifier” CNN performance was then tested both on ‘un-curated’ as well as the ‘curated’ test set created by the “Quality Assessment” CNN. Finally, the sensitivity of the “Classifier” CNNs was boosted post-training using two post-training techniques.Our “Classifier” CNN proved to be robust, as its performance was similar on ‘curated’ and ‘uncurated’ sets. The implementation of ‘cascading thresholds’ and ‘max margin’ techniques led to significant improvements in the “Classifier” CNN’s sensitivity, while also enhancing the specificity of other grades.
Does training method matter?: Evidence for the negative impact of aversive-based methods on companion dog welfare
Authors: Vieira de Castro Ana Catarina , Fuchs Danielle , Pastur Stefania , de Sousa Liliana , Olsson I Anna S 
Published: October 2019

ABSTRACTThere is a growing number of dogs kept as companion animals, and the methods by which they are trained range broadly from those using mostly positive punishment and negative reinforcement (aversive-based methods) to those using primarily positive reinforcement (reward-based methods). Although the use of aversive-based methods has been strongly criticized for negatively affecting dog welfare, these claims do not find support in solid scientific evidence. Previous research on the subject lacks companion dog-focused research, investigation of the entire range of aversive-based techniques (beyond shock-collars), objective measures of welfare, and long-term welfare studies. The aim of the present study was to perform a comprehensive evaluation of the short- and long-term effects of aversive- and reward-based training methods on companion dog welfare. Ninety-two companion dogs were recruited from three reward-based (Group Reward, n=42) and four aversive-based (Group Aversive, n=50) dog training schools. For the short-term welfare assessment, dogs were video recorded for three training sessions and six saliva samples were collected, three at home (baseline levels) and three after the training sessions (post-training levels). Video recordings were then used to examine the frequency of stress-related behaviors (e.g., lip lick, yawn) and the overall behavioral state of the dog (e.g., tense, relaxed), and saliva samples were analyzed for cortisol concentration. For the long-term welfare assessment, dogs performed a cognitive bias task. Dogs from Group Aversive displayed more stress-related behaviors, spent more time in tense and low behavioral states and more time panting during the training sessions, showed higher elevations in cortisol levels after training and were more ‘pessimistic’ in the cognitive bias task than dogs from Group Reward. These findings indicate that the use of aversive-based methods compromises the welfare of companion dogs in both the short- and the long-term.
Comprehensive fitness maps of Hsp90 show widespread environmental dependence
Authors: Flynn Julia M. , Rossouw Ammeret , Cote-Hammarlof Pamela A. , Fragata Ines , Mavor David , Hollins Carl , Bank Claudia , Bolon Daniel N.A. 
Published: October 2019

ABSTRACTGene-environment interactions have long been theorized to influence molecular evolution. However, the environmental dependence of most mutations remains unknown. Using deep mutational scanning, we engineered yeast with all 44,604 single codon changes encoding 14,160 amino acid variants in Hsp90 and quantified growth effects under standard conditions and under five stress conditions. To our knowledge these are the largest determined comprehensive fitness maps of point mutants. The growth of many variants differed between conditions, indicating that environment can have a large impact on Hsp90 evolution. Multiple variants provided growth advantages under individual conditions, however these variants tended to exhibit growth defects in other environments. The diversity of Hsp90 sequences observed in extant eukaryotes preferentially contains variants that supported robust growth under all tested conditions. Rather than favoring substitutions in individual conditions, the long-term selective pressure on Hsp90 may have been that of fluctuating environments, leading to robustness under a variety of conditions.
Efference copy is necessary for the attenuation of self-generated touch
Authors: Kilteni Konstantina , Engeler Patrick , Ehrsson H. Henrik 
Published: October 2019

AbstractA self-generated touch feels less intense than an external touch of the exact same intensity. According to a prevalent computational theory of motor control, this attenuation occurs because the brain uses internal forward models to predict the somatosensory consequences of our movements using a copy of the motor command, i.e., the efference copy. These tactile predictions are then used to suppress the perceived intensity of the actual tactile feedback. Despite being highly influential, the core assumption of theory has never been tested; that is, whether the efference copy is necessary for somatosensory attenuation. A possible alternative hypothesis is that a predictable contact of two of one’s own body parts is sufficient. Using a psychophysical task, we quantified the attenuation of touch applied on the participants’ left index finger when the touch was triggered by the active or passive movement of the participants’ right index finger and when it was externally generated in the absence of any movement. We observed somatosensory attenuation only when the touch was triggered by the voluntary movement of the participants’ finger. In contrast, during the passive movement, the intensity of the touch was perceived to be as strong as when the touch was externally triggered. In both active and passive movement conditions, the participants showed the same discrimination capacity. Electromyographic recordings confirmed minimal activity of the right hand during the passive movement. Together, our results suggest that the efference copy is necessary for computing the somatosensory predictions that produce the attenuation of self-generated touch.
Mitochondrial pyruvate carrier is required for optimal brown fat thermogenesis
Authors: Panic Vanja , Pearson Stephanie , Banks James , Tippetts Trevor S. , Lee Sanghoon , Simcox Judith , Geoghegan Gisela , Bensard Claire , van Ry Tyler , Holland Will L. , Summers Scott , Cox James , Ducker Greg , Rutter Jared , Villanueva Claudio J. 
Published: October 2019

AbstractBrown adipose tissue (BAT) is composed of thermogenic cells that convert chemical energy into heat to help maintain a constant body temperature and counteract metabolic disease in mammals. The metabolic adaptations required for thermogenesis are not fully understood. Here we explore how steady state levels of metabolic intermediates are altered in brown adipose tissue in response to cold exposure. Transcriptome and metabolome analysis revealed changes in pathways involved in amino acid, glucose, and TCA cycle metabolism. Using isotopic labeling experiments, we found that activated brown adipocytes increased labeling of pyruvate and TCA cycle intermediates from U13C-glucose. Although glucose oxidation has been implicated as being essential for thermogenesis, its requirement for efficient thermogenesis has not been directly tested. Here we show that mitochondrial pyruvate uptake is essential for optimal thermogenesis, as conditional deletion ofMpc1in brown adipocytes leads to impaired cold adaptation. Isotopic labeling experiments using U13C-glucose showed that loss of MPC1 led to impaired labeling of TCA cycle intermediates, while labeling of glycolytic intermediates was unchanged. Loss of MPC1 in BAT increased 3-hydroxybutyrate levels in blood and BAT in response to the cold, suggesting that ketogenesis provides an alternative fuel source that partially compensates for impaired mitochondrial oxidation of cytosolic pyruvate. Collectively, these studies highlight that complete glucose oxidation is essential for optimal brown fat thermogenesis.
HDAC6 promotes self-renewal and migration/invasion of rhabdomyosarcoma
Authors: Pham Thao Q. , Robinson Kristin , Xu Lin , Skapek Stephen X. , Chen Eleanor Y. 
Published: October 2019

ABSTRACTRhabdomyosarcoma (RMS) is a devastating pediatric sarcoma. The survival outcomes remain poor for patients with relapsed or metastatic disease. Effective targeted therapy is lacking due to our limited knowledge of the underlying cellular and molecular mechanisms leading to disease progression. In this study, we used functional assays in vitro and in vivo (zebrafish and xenograft mouse models) to demonstrate the crucial role of HDAC6, a cytoplasmic histone deacetylase, in driving RMS tumor growth, self-renewal and migration/invasion. Treatment with the HDAC6-selective inhibitor, Tubastatin A, recapitulates the HDAC6 loss-of-function phenotypes. HDAC6 regulates cytoskeletal dynamics to promote tumor cell migration and invasion. RAC1, a Rho family GTPase, is an essential mediator of HDAC6 function, and is necessary and sufficient for RMS cell migration and invasion. High expression of RAC1 correlates with poor clinical prognosis in RMS patients. Targeting the HDAC6-RAC1 axis represents a promising therapeutic option for improving survival outcomes of RMS patients.
Cytokine and Growth Factor Response in a Rat Model of Radiation Induced Injury to the Submental Muscles
Authors: King Suzanne N. , Al-Quran Zakariyya , Hurley Justin , Wang Brian , Dunlap Neal 
Published: October 2019

ABSTRACTSubmental muscles (i.e. mylohyoid and geniohyoid) play a vital role during swallowing, protecting the airway from ingested material. To design therapies to reduce the functional deficits associated with radiation treatment relies in part on our understanding of the changes in the cytokine and growth factor response that can impact muscle function. The purpose of this study is to quantify changes in the inflammatory, pro-fibrotic, and pro-angiogenic factors following 48Gy of fractionated radiation to the mylohyoid muscle. We hypothesized that (1) irradiation will provoke increases in TGF-1β and MMP-2 mRNA in the mylohyoid muscle; and (2) muscles surrounding the target location (i.e. geniohyoid and digastric muscles) will exhibit similar alterations in their gene expression profiles. Rats were exposed to 6 fractions of 8Gy using a 6MeV electron beam on a clinical linear accelerator. The highest dose curve was focused at the mylohyoid muscle. After 2-and 4-weeks post-radiation, the mylohyoid, geniohyoid, and digastric muscles were harvested. Expression of TNF-α, IFNγ, IL-1β, IL-6, TGF-1β, VEGF, MMP-2, and MMP-9 mRNA was analyzed via PCR and/or RT-PCR. TGF-1β, MMP-2, and IL-6 expression was upregulated in the irradiated mylohyoid compared to nonirradiated controls. No notable changes in TNF-α, IFNγ, and IL-1β mRNA expression was observed in irradiated muscles. Differing expression profiles were found in the surrounding muscles post-radiation. Results demonstrated that irradiation provokes molecular signals involved in the regulation of the extracellular matrix, which could lead to fibrosis or atrophy in the swallowing muscle after radiation.
CreLite: An Optogenetically Controlled Cre/loxP System Using Red Light
Authors: Yen Shuo-Ting , Trimmer Kenneth A. , Aboul Nader , Mullen Rachel D. , Culver James C. , Dickinson Mary E. , Behringer Richard R. , Eisenhoffer George T. 
Published: October 2019

ABSTRACTPrecise manipulation of gene expression with temporal and spatial control is essential for functional studies and the determination of cell lineage relationships in complex biological systems. The Cre-loxP system is commonly used for gene manipulation at desired times and places. However, specificity is dependent on the availability of tissue- or cell-specific regulatory elements used in combination with Cre or CreER (tamoxifen-inducible). Here we present CreLite, an optogenetically-controlled Cre system using red light in developing zebrafish embryos. Cre activity is disabled by splitting Cre and fusing the inactive halves with the Arabidopsis thaliana red light-inducible binding partners, PhyB and PIF6. In addition, PhyB-PIF6 binding requires phycocyanobilin (PCB), providing an additional layer of control. Upon exposure to red light (660 nm) illumination, the PhyB-CreC and PIF6-CreN fusion proteins come together in the presence of PCB to restore Cre activity. Red-light exposure of transgenic zebrafish embryos harboring a Cre-dependent multi-color fluorescent protein reporter (ubi:zebrabow) injected with CreLite mRNAs and PCB, resulted in Cre activity as measured by the generation of multi-spectral cell labeling in various tissues, including heart, skeletal muscle and epithelium. We show that CreLite can be used for gene manipulations in whole embryos or small groups of cells at different stages of development. CreLite provides a novel optogenetic tool for precise temporal and spatial control of gene expression in zebrafish embryos that may also be useful in cell culture, ex vivo organ culture, and other animal models for developmental biology studies.
Inference and effects of barcode multiplets in droplet-based single-cell assays
Authors: Lareau Caleb A. , Ma Sai , Duarte Fabiana M. , Buenrostro Jason D. 
Published: October 2019

AbstractA widespread assumption for single-cell analyses specifies that one cell’s nucleic acids are predominantly captured by one oligonucleotide barcode. However, we show that ∼13-21% of cell barcodes from the 10x Chromium scATAC-seq assay may have been derived from a droplet with more than one oligonucleotide sequence, which we call “barcode multiplets”. We demonstrate that barcode multiplets can be derived from at least two different sources. First, we confirm that ∼4% of droplets from the 10x platform may contain multiple beads. Additionally, we find that ∼5-7% of beads may contain multiple oligonucleotide barcodes. We show that this artifact can confound single-cell analyses, including the interpretation of clonal diversity and proliferation of intra-tumor lymphocytes. Overall, our work provides a conceptual and computational framework to identify and assess the impacts of barcode multiplets in single-cell data.
More than DNA methylation: does pleiotropy drive the complex pattern of evolution ofDnmt1?
Authors: Amukamara Ashley U. , Washington Joshua T. , Sanchez Zachary , McKinney Elizabeth C. , Moore Allen J. , Schmitz Robert J. , Moore Patricia J. 
Published: October 2019

AbstractDNA methylation is an important chromatin modification that can stably alter gene expression in cells and maintain genome integrity in plants and vertebrates. The function of DNA methylation outside of these well-studied systems, however, is unclear. Insects, in particular, represent an understudied group. Variation in the level of DNA methylation and gains and losses in the maintenance methyltransferase, DNMT1, across the insect tree of life suggests that there is much we don’t understand about DMNT1 function and evolution. One constant across the studies examining patterns ofDnmt1expression in insects is that expression is consistently high in reproductive tissues compared to somatic tissue. The explanation for this has been that DNMT1 is required in tissues that have high levels of cell division. Our previous study found that downregulation ofDnmt1expression in the milkweed bugOncopeltus fasciatusresults in the expected reduction of DNA methylation, no global changes in gene expression reflecting changes in DNA methylation, and the loss of the ability to produce viable oocytes. Here, we show that females treated with ds-Dnmt1RNA during larval development have a more extreme phenotype; they lack oocytes entirely but develop a normal somatic ovary. Our results indicate a specific role for DNMT1 in the formation of gametes and are consistent with data from other systems, includingTribolium castaneum, a species does not have DNA methylation. We propose that DNMT1 has multiple functional roles in addition to methylating DNA, which explains its complex patterns of evolution, and suggests that previous inferences of causation from associations are premature.
Feedback control of morphogen gradient scale
Authors: Zhu Yilun , Qiu Yuchi , Chen Weitao , Nie Qing , Lander Arthur D. 
Published: October 2019

SUMMARYGradients of the morphogen decapentaplegic (Dpp) patternDrosophilawing imaginal discs, establishing gene expression boundaries at specific locations. As discs grow, Dpp gradients expand, keeping relative boundary positions approximately stationary. Such scaling fails in mutants forPentagone(pent), a gene repressed by Dpp that encodes a diffusible protein that expands Dpp gradients. Although these properties fit a recent mathematical model of automatic gradient scaling, we show here that Pent lacks a property essential to that model—the ability to spread with minimal loss throughout the morphogen field. Instead, Pent’s actions appear confined to within a few cell diameters of its site of synthesis, and can be phenocopied by manipulating non-diffusible targets of Pent strictly within the Pent expression domain. Through genetic manipulation and mathematical modeling we develop an alternative model of scaling, driven by feedback down-regulation of Dpp receptors and co-receptors. Among the model’s predictions is a size limit beyond which scaling fails—something we observe directly in wing discs.
Heterogeneity of satellite cells implicates DELTA1/NOTCH2 signaling in self-renewal
Authors: Yartseva Valeria , Goldstein Leonard D. , Rodman Julia , Kates Lance , Chen Mark Z. , Chen Ying-Jiun J. , Foreman Oded , Siebel Christopher W. , Modrusan Zora , Peterson Andrew S. , Jovičić Ana 
Published: October 2019

SUMMARYHow satellite cells and their progenitors balance differentiation and self-renewal to achieve sustainable tissue regeneration is not well understood. A major roadblock to understanding satellite cell fate decisions has been the difficulty to study this process in vivo. By visualizing expression dynamics of myogenic transcription factors during early regeneration in vivo, we identified the time point at which cells undergo decisions to differentiate or self-renew. Single-cell RNA sequencing revealed heterogeneity of satellite cells during both muscle homeostasis and regeneration, including a subpopulation enriched in Notch2 receptor expression. Furthermore, we reveal that differentiating cells express the Dll1 ligand. Using antagonistic antibodies we demonstrate that the DLL1 and NOTCH2 signaling pair is required for satellite cell self-renewal. Thus, differentiating cells provide the self-renewing signal during regeneration, enabling proportional regeneration in response to injury while maintaining the satellite cell pool. These findings have implications for therapeutic control of muscle regeneration.