bluuebunny/crossref_metadata_2025_split huggingface dataset:
DICER1 regulates antibacterial function of epididymis by modulating transcription of β-defensins
Authors: Tang Chunhua , Ni Minjie , Xie Shengsong , Zhang Yao , Zhang Chaobao , Ni Zimei , Chu Chen , Wu Ligang , Zhou Yuchuan , Zhang Yonglian 
Published: September 2018

AbstractDICER1 is a key enzyme responsible for the maturation of microRNAs. Recent evidences suggested that DICER1 and microRNAs expressed in epididymis were involved in the control of male fertility. However, the exact mechanism remains to be elucidated. Here, we created a mouse line by targeted disruption of Dicer1 gene in the principal cells of distal caput epididymis. Our data indicated that a set of β-defensin genes were downregulated by DICER1 rather than by microRNAs. Moreover, DICER1 was significantly enriched in the promoter of β-defensin gene and controlled transcription. Besides, the antibacterial ability of the adult epididymis significantly declined upon Dicer1 deletion both in vitro and in vivo. And a higher incidence of reproductive defect was observed in middle-aged Dicer1−/− males. These results suggest that DICER1 plays an important role in transcription of β-defensin genes, which are associated with the natural antibacterial properties in a microRNA-independent manner, and further impacts the male fertility.
Naming Violence in United States Colonialism
Authors: Spence Taylor 
Published: September 2018

Abstract
This article reexamines a highly public dispute between a powerful and well-connected Episcopal bishop and his missionary priest, men both central to the government’s campaign of war and assimilation against Indigenous Peoples in the Northern Great Plains of the nineteenth-century United States. The bishop claimed that the priest had engaged in sexual intercourse with a Dakota woman named “Scarlet House,” and used this allegation to remove the priest from his post. No historian ever challenged this claim and asked who Scarlet House was. Employing Dakota-resourced evidence, government and church records, linguistics, and onomastics, this study reveals that in actuality there was no such person as Scarlet House. Furthermore, at the time of the incident, the person in question was not a woman but a child. The church created a fictional personage to cover up what was taking place at the agency: sexual violence against children. After “naming” this violence, this article makes four key historical contributions about the history of US settler colonialism: It documents Dakota Peoples’ agency, by demonstrating how they adapted their social structures to the harrowing conditions of the US mission and agency system. It situates the experiences of two Dakota families within the larger context of settler-colonial conquest in North America, revealing the generational quality of settler-colonial violence. It shows how US governmental policies actually enabled sexual predation against children and women. And, it argues that “naming violence” means both rendering a historical account of the sexual violence experienced by children and families in the care of the US government and its agents, as well as acknowledging how this violence has rippled out through communities and across generations.
Sustaining enhanced condensation on hierarchical mesh-covered surfaces
Authors: Wen Rongfu , Xu Shanshan , Zhao Dongliang , Yang Lixin , Ma Xuehu , Liu Wei , Lee Yung-Cheng , Yang Ronggui 
Published: September 2018

Abstract
Controlling the solid–liquid–vapor tri-phase interface is of fundamental importance for a broad range of industrial applications including biomedical engineering, energy production and utilization, environmental control, water production, and thermal management. Although a lot of progress has been made over the past few decades on surface manipulation for promoting droplet removal, it is challenging to accelerate both droplet growth and surface refreshing for enhancing vapor-to-liquid condensation. Here we present a superhydrophobic hierarchical mesh-covered (hi-mesh) surface to enable continuous sucking flow of liquid condensate, which achieves fourfold-higher droplet growth and 36.8% faster surface refreshing compared to the state-of-the-art dropwise condensation. Unprecedented enhanced condensation heat transfer is observed to be sustained over a wide range of surface subcooling on the hi-mesh surfaces. This demonstration of sustained enhanced condensation enhancement is not only of fundamental scientific importance, but also provides a viable strategy for large-scale deployment of micro/nanostructured surfaces in a diverse range of technologies.
Intraductal patient derived xenografts of estrogen receptor positive (ER+) breast cancer recapitulate the histopathological spectrum and metastatic potential of human lesions
Authors: Fiche Maryse , Scabia Valentina , Battista Laura , Treboux Assia , Stravodimou Athina , Zaman Khalil ,   RLS, Ayyannan Ayyakannu , Sflomos George , Brisken Cathrin 
Published: September 2018

AbstractEstrogen receptor α positive (ER+) or “luminal” breast cancers were notoriously difficult to establish as patient-derived xenografts (PDXs). We and others recently demonstrated that the microenvironment is critical for ER+ tumor cells; by grafting them into milk ducts >90% take rates are achieved and many features of the human disease are recapitulated. This intra-ductal (ID) approach holds promise for personalized medicine, yet human and murine stroma are organized differently and this and other species specificities may limit the value of this model. Here, we analyzed 21 ER+ ID-PDXs histopathologically. We find that ID-PDXs vary in extent and define four histopathological patterns: flat, lobular,in situ, and invasive, which occur in pure and combined forms. The ID-PDXs replicate earlier stages of tumor development than their clinical counterparts. Micrometastases are already detected when lesions appearin situ. Tumor extent, histopathological patterns, and metastatic load correlate with biological properties of their tumors of origin. Our findings add evidence to the validity of the intraductal model forin vivostudies of ER+ breast cancer and raise the intriguing possibility that tumor cell dissemination may occur earlier than currently thought.Conflict of interest statement:The authors declare no conflict of interest.
Differential Gene Expression Analysis of a Small Colony Variant ofEscherichia coliK-12
Authors: Paratore Anthony W. , Santos Victors , Bibis Stergios , Hirshfield Irvin N. 
Published: September 2018

AbstractAs persistent residents of planktonic bacterial cultures, small colony variants (SCVs) constitute a slow-growing subpopulation with atypical colony morphology and unusual biochemical characteristics that, in the case of clinical isolates, cause latent and recurrent infections. We propose a novel blueprint for the formation ofE. coliSCVs through DNA microarray analysis, coupled with complete genome sequencing and verification by qRT-PCR. While others have used DNA microarrays to study quorum sensing inE. coliSCVs, our work represents the first proposal for a combination of novel mutations, amplified by a differential shift in expression of select gene groups that work in concert to establish and maintain the SCV phenotype. This combination of genetic and expression events fall under selective pressure, leading to unequal fitness in our strain, SCV IH9 versus its parental strain, BW7261 (a MG1655 descendant). We hypothesize that this combination of events would ordinarily be lethal for bacteria, but instead confers a survival advantage to SCV IH9 due to its slow growth and resistance to acidic and oxidative stress challenges.
Template-free detection and classification of heterogeneous membrane-bound complexes in cryo-electron tomograms
Authors: Martinez-Sanchez Antonio , Kochovski Zdravko , Laugks Ulrike , Borgloh Johannes Meyer zum Alten , Chakraborty Saikat , Pfeffer Stefan , Baumeister Wolfgang , Lucic Vladan 
Published: September 2018

AbstractWith faithful sample preservation and direct imaging of fully hydrated biological material, cryo-electron tomography (cryo-ET) provides an accurate representation of molecular architecture of cells. However, detection and precise localization of macromolecular complexes within cellular environments is aggravated by the presence of many molecular species and molecular crowding. We developed a template-free image processing procedure for accurate tracing of complex networks of densities in cryo-electron tomograms, a comprehensive and automated detection of heterogeneous membrane-bound complexes and an unsupervised classification. Applying this procedure to tomograms of intact cells and isolated endoplasmic reticulum (ER), we detected and classified small protein complexes like the ER protein translocons, which were not detected by other methods before. This classification provided sufficiently homogeneous particle sets and initial references to allow subsequent de novo subtomogram averaging. Therefore the procedure presented allows a comprehensive detection and a structural analysis of complexes in their native state. In addition, we present structural evidence that different ribosome-free translocon species are present at the ER membrane, determine their 3D structure, and show that they have different localization patterns forming nanodomains.
Optogenetics enables real-time spatiotemporal control over spiral wave dynamics in an excitable cardiac system
Authors: Majumder Rupamanjari , Feola Iolanda , Teplenin Alexander S. , de Vries Antoine A. F. , Panfilov Alexander V. , Pijnappels Daniël A. 
Published: September 2018

AbstractPropagation of non-linear waves is key to the functioning of diverse biological systems. Such waves can organize into spirals, rotating around a core, whose properties determine the overall wave dynamics. Theoretically, manipulation of a spiral wave core should lead to full spatiotemporal control over its dynamics. However, this theory lacks supportive evidence (even at a conceptual level), making it thus a long-standing hypothesis. Here, we propose a new phenomenological concept that involves artificially dragging spiral waves by their cores, to prove the afore-mentioned hypothesis in silico, with subsequent in vitro validation in optogenetically-modified monolayers of rat atrial cardiomyocytes. We thereby connect previously established, but unrelated concepts of spiral wave attraction, anchoring and unpinning to demonstrate that core manipulation, through controlled displacement of heterogeneities in excitable media, allows forced movement of spiral waves along pre-defined trajectories. Consequently, we impose real-time spatiotemporal control over spiral wave dynamics in a biological system.
Lessons learned when looking for non-neutral ecological processes in the built environment: the bacterial and fungal microbiota of shower tiles
Authors: Adams Rachel I. , Lymperopoulou Despoina L. 
Published: September 2018

AbstractWith periodic pulses of water, bathroom showers represent a habitat in the built environment with a high potential for microbial growth. We set out to apply a neutral model of microbial community assembly and to identify deviations from the model that would indicate non-neutral dynamics, such as selective pressures for individual taxa, in this particular indoor habitat. Following a cleaning event, the bacterial and fungal microbiota of the shower stalls in two residences in the San Francisco Bay Area were observed over a four-week period. We observed strong differences in composition between houses, preventing us from combining samples and thus limiting our statistical power. We also identified different aspects of the sampling scheme that could be improved, including increasing the sampling area (to ensure sufficient biomass) and increasing the number of replicates within an individual shower. The data from this pilot study indicate that immigrants to the built environment arising from human shedding dominate the shower ecosystem and that growth conditions are relatively unfavorable despite the water availability. We offer suggestions on how to improve the studying and sampling of microbes in indoor environments.
Genetic differences between Coccidioides spp. and closely related nonpathogenic Onygenales
Authors: Kirkland Theo N. 
Published: September 2018

AbstractCoccidioides spp. are dimorphic, pathogenic fungi that can cause severe human and animal disease. Like the other primary fungal pathogens, animal infection results in a morphologic transformation from the environmental mycelial phase to a tissue phase, known as a spherule. The sequencing and annotation of Coccidioides spp. and the genomes of several nonpathogenic Onygenales species allows comparisons that provide clues about the Coccidioides spp. genes that might be involved in pathogenesis. The analysis in this study is a gene by gene orthology comparison. Although there were few differences in the size of genes families in the Coccidioides spp.-specific group compared to the genes shared by Coccidioides spp. and nonpathogenic Onygenales, there were a number of differences in the characterization of the two types of genes. Many more Coccidioides spp.-specific genes are up-regulated expression in spherules. Coccidioides spp.-specific genes more often lacked functional annotation and were more often classified as orphan genes. Analysis by random forest machine learning confirmed that high numbers of orthologs and high levels of expression in hyphae were predictive of common genes, while high levels of expression in spherules and more nonsynonymous predicted Coccidioides spp.-specific genes. Review of individual genes in the Coccidioides spp.-specific group identified a histidine kinase, two thioredoxin genes, a calmodulin gene and ureidoglycolate hydrolase. Hopefully, identification of these genes will be useful for pursuing potential Coccidioides spp. virulence genes in the future.
Ultrasensitive molecular controllers for quasi-integral feedback
Authors: Samaniego Christian Cuba , Franco Elisa 
Published: September 2018

AbstractFeedback control has enabled the success of automated technologies by mitigating the effects of variability, unknown disturbances, and noise. Similarly, feedback loops in biology reduce the impact of noise and help shape kinetic responses, but it is still unclear how to rationally design molecular controllers that approach the performance of controllers in traditional engineering applications, in particular the performance of integral controllers. Here, we describe a strategy to build molecular quasi-integral controllers by following two design principles: (1) a highly ultrasensitive response, which guarantees a small steady-state error, and (2) a tunable ultrasensitivity threshold, which determines the system equilibrium point (reference). We describe a molecular reaction network, which we name Brink motif, that satisfies these requirements by combining sequestration and an activation/deactivation cycle. We show that if ultrasensitivity conditions are satisfied, this motif operates as a quasi-integral controller and promotes homeostatic behavior of the closed-loop system (robust tracking of the input reference while rejecting disturbances). We propose potential biological implementations of Brink controllers and we illustrate different example applications with computational models.
Co-SELECT reveals sequence non-specific contribution of DNA shape to transcription factor binding in vitro
Authors: Pal Soumitra , Hoinka Jan , Przytycka Teresa M. 
Published: September 2018

AbstractUnderstanding the principles of DNA binding by transcription factors (TFs) is of primary importance for studying gene regulation. Recently, several lines of evidence suggested that both DNA sequence and shape contribute to TF binding. However, the question if in the absence of any sequence similarity to the binding motif, DNA shape can still increase probability of binding was yet to be addressed.To address this challenge, we developed Co-SELECT, a computational approach to analyze the results of in vitro HT-SELEX experiments for TF-DNA binding. Specifically, the presence of motif-free sequences in late HT-SELEX rounds and their enrichment in weak binders allowed us to detect evidence for the role of DNA shape features in TF binding.Our approach revealed that, even in the absence of the sequence motif, TFs have propensity to weakly bind to DNA molecules enriched in specific shape features. Surprisingly, we also found that some properties of DNA shape contribute to promiscuous binding of all tested TF families. Strikingly, such promiscuously bound shapes correspond to the most frequent shape formed by the DNA. We propose that this promiscuous binding facilitates diffusing of TFs along the DNA molecule before it is locked in its binding site.
Is faster always better? The walking speed-dependency of gait variability in bilateral vestibulopathy
Authors: McCrum Christopher , Lucieer Florence , van de Berg Raymond , Willems Paul , Fornos Angélica Pérez , Guinand Nils , Karamanidis Kiros , Kingma Herman , Meijer Kenneth 
Published: September 2018

AbstractStudy of balance and gait deficits associated with vestibulopathy is important for improving clinical care and is critical to our understanding of the vestibular contributions to gait and balance control. Previous studies report a speed-dependency of the vestibular contributions to gait, so we examined the walking speed effects on gait variability in healthy young and older adults and in adults with bilateral vestibulopathy (BVP). Forty-four people with BVP, 12 healthy young adults and 12 healthy older adults completed walking trials at 0.4m/s to 1.6m/s in 0.2m/s intervals on a dual belt, instrumented treadmill. Using a motion capture system and kinematic data, the means and coefficients of variation for step length, time, width and double support time were calculated. The BVP group also completed a video head impulse test and examinations of ocular and cervical vestibular evoked myogenic potentials and dynamic visual acuity. Walking speed significantly affected all assessed gait parameters. Step length variability at slower speeds and step width variability at faster speeds were the most distinguishing parameters between the healthy participants and people with BVP, and within people with BVP with different locomotor capacities. We observed for step width variability, specifically, an apparent persistent importance of vestibular function at increasing speeds. Gait variability was not associated with the clinical vestibular tests. Our results indicate that gait variability at multiple walking speeds has potential as an assessment tool for vestibular interventions.New & Noteworthy:Walking speed significantly but differentially affects gait variability in healthy adults and in adults with bilateral vestibulopathy. Gait variability at different speeds distinguishes between participants with and without bilateral vestibulopathy, but also between more and less able walkers with bilateral vestibulopathy. Specifically, for step width variability, an apparent persistent importance of vestibular function at increasing walking speeds was observed. Gait variability was generally not correlated with clinical tests of vestibular function.
A lysosomal dimmer switch regulates cellular quiescence depth
Authors: Fujimaki Kotaro , Li Ruoyan , Chen Hengyu , Croce Kimiko Della , Zhang Hao Helen , Xing Jianhua , Bai Fan , Yao Guang 
Published: September 2018

ABSTRACTNumerous physiological and pathological phenomena are associated with the quiescent state of a cell. Cellular quiescence is a heterogeneous resting state; cells in deep than shallow quiescence require stronger growth stimulation to exit quiescence and reenter the cell cycle. Despite the importance of quiescent cells such as stem and progenitor cells to tissue homeostasis and repair, cellular mechanisms controlling the depth of cellular quiescence are poorly understood. Here we began by analyzing transcriptome changes as rat embryonic fibroblasts moved progressively deeper into quiescence under increasingly longer periods of serum starvation. We found that lysosomal gene expression was significantly upregulated in deep than shallow quiescence, which compensated for gradually reduced autophagy flux observed during quiescence deepening. Consistently, we show that inhibiting lysosomal function drove cells deeper into quiescence and eventually into a senescence-like irreversibly arrested state. By contrast, increasing lysosomal function progressively pushed cells into shallower quiescence. That is, lysosomal function modulates quiescence depth continuously like a dimmer switch. Mechanistically, we show that lysosomal function prevents quiescence deepening by reducing oxidative stress in the cell. Lastly, we show that a gene expression signature developed by comparing deep and shallow quiescent cells can correctly classify senescent and aging cells in a wide array of cell lines in vitro and tissues in vivo, suggesting that quiescence deepening, senescence, and aging may share common regulatory mechanisms.
Morphogenesis and differentiation of embryonic vascular smooth muscle cells in zebrafish
Authors: Whitesell Thomas R. , Chrystal Paul , Ryu Jae-Ryeon , Munsie Nicole , Grosse Ann , French Curtis , Workentine Matthew L. , Li Rui , Zhu Lihua Julie , Waskiewicz Andrew , Lehmann Ordan J. , Lawson Nathan D. , Childs Sarah J. 
Published: September 2018

AbstractDespite the critical role of vascular mural cells (smooth muscle cells and pericytes) in supporting the endothelium of blood vessels, we know little of their early morphogenesis and differentiation.foxc1b:EGFPexpressing cells in zebrafish associate with the vascular endothelium (kdrl) and co-express a smooth muscle marker (acta2), but not a pericyte marker (pdgfrβ). The expression offoxc1bin early peri-endothelial mesenchymal cells allows us to follow the morphogenesis of mesenchyme intoacta2expressing vascular smooth muscle cells. We show that mural cells expressing different markers associate with vessels of different diameters, depending on their embryonic location and developmental timing, suggesting marker expression is predictive of functional differences. We identify gene expression signatures for an enriched vascular smooth muscle cell population (foxc1b + acta2)and all smooth muscle(acta2)using fluorescence-activated cell sorting and RNA-Seq. Finally, we demonstrate that progressive loss offoxc1a/foxc1bresults in decreased smooth muscle cell coverage. Together, our data highlight the early cellular dynamics and transcriptome profiles of smooth muscle cellsin vivo,usingfoxc1bas a unique tool to probe vascular smooth muscle cell differentiation.Summary StatementTracing the morphogenesis and transcriptome of early vascular smooth muscle cells using foxc1b
NUCOME: A Comprehensive Database of Nucleosome Organizations in Mammalian Genomes
Authors: Chen Xiaolan , Yang Hui , Zhang Yong 
Published: September 2018

AbstractNucleosome organization is involved in many regulatory activities in various organisms. However, studies integrating nucleosome organizations in mammalian genomes are very limited mainly due to the lack of comprehensive data management. Here, we presentNUCOME, which is the first database to organize publicly available MNase-seq data resource and manage unified processed datasets covering various cell types in human and mouse. TheNUCOMEprovides standard, qualified and informative nucleosome organization data at the genome scale and at any genomic regions for users’ downstream analyses.NUCOMEis freely available athttp://compbio.tongji.edu.cn/NUCOME/.