bluuebunny/crossref_metadata_2025_split huggingface dataset:
Noise Reconsidered
Authors: Rivers Patrick , Fulton Will 
Published: August 2018

Abstract
Recordings by Public Enemy (PE) from the late 1980s and early 1990s have dominated academic writing on hip hop beat making. Scholarly attention has been drawn to their sample-filled sonic signature, created by the Bomb Squad production team, which was deemed to align with the group’s role as vanguards for the use of hip hop as a platform for social justice and black consciousness. When surveying the historical development of hip hop production practices, however, there is a paradoxical relationship in regard to how their work is positioned in the historiography of the genre. This chapter addresses the development of PE’s sound within the context of late 1980s hip hop, suggesting that PE’s sonic signature was an outlier rather than illustrative of the common practice of beat making. Drawing on new interviews with PE members and other key hip hop recordists of the era, an examination of the technology and process of the Bomb Squad, and musical analysis of two recordings—“Bring the Noise” and “Brothers Gonna Work It Out”—this chapter positions “organized noise” within the landscape of contemporaneous hip hop production styles and considers ways in which historical distance has compelled a reassessment of PE in academia.
“I’m Ready to Die”
Authors: Calvente Lisa B. Y. 
Published: August 2018

Abstract
This chapter highlights the significance of the Notorious B.I.G.’s music as a product of neoliberal racism and as resistance through embodied acts of solidarity, love, and death. The chapter locates the Notorious B.I.G. within the modernity/coloniality relationship and the neoliberal landscape of post-1975 New York City in order to emphasize the importance of Black radical performance at this conjunctural moment. It then turns to the Notorious B.I.G.’s embodied critique of necessary death, the killing of Blackness both socially and physically. It highlights how this critique is performed through the interplay of sound and content (lyrics, delivery, sampling, and especially call and response). The chapter argues B.I.G.’s performances and his play on and of death produce affective moments of loving Blackness as subversive action.
The Superior Paraolivary Nucleus
Authors: Magnusson Anna K. , Gómez-Álvarez Marcelo 
Published: August 2018

Abstract
This chapter summarizes the current concepts of the superior paraolivary nucleus (SPON)—a structure embedded in the superior olivary complex in the mammalian auditory brainstem. SPON is driven by input pathways from two of the most temporally secure neurons in the brain: the octopus cells in the cochlear nucleus and the neurons of the medial nucleus of the trapezoid body. These inputs activate spiking activity that marks the onset and offset of sound, the latter based on a rebound depolarization mechanism. This makes the SPON an excellent detector of transient sound energy. Robust detection of the coarse sound pattern over time further gives SPON the capacity to track the temporal envelope of complex sounds with supreme precision. Since the SPON circuitry is constant in mammals and resilient to sensory perturbation, it indicates its high survival value. A possible neuroevolutionary role of SPON in the processing of vocalizations is discussed.
James and Epistemic Pluralism
Authors: Skrupskelis Ignas Kęstutis 
Published: August 2018

Abstract
James’s account of truth is pluralistic. He holds that there are different kinds of truth, with truth by correspondence being only one. He does not provide a complete list of the kinds. Central for James is the problem of reference because of his concern to refute Royce’s argument for the Absolute. Referential assertions are true if and only if there are experienceable paths which if traversed would lead into the presence of the object. Such assertions anchor knowledge. Scientific theories are true if they are anchored—that is, fit the facts, can be integrated into the established system of beliefs, and are simpler and more fruitful than any alternatives. Religious beliefs cannot be in conflict with facts and science. But they must carry with them a sense of authority and illumination and meet our moral needs. The will to believe is not a question of truth, but it allows us to hold “over-beliefs,” at our own risk, so as not to impoverish human experience.
Whole blood transcriptome analysis reveals footprints of cattle adaptation to sub-arctic conditions
Authors: Pokharel Kisun , Weldenegodguad Melak , Popov Ruslan , Honkatukia Mervi , Huuki Hanna , Lindeberg Heli , Peippo Jaana , Reilas Tiina , Zarovnyaev Stepan , Kantanen Juha 
Published: August 2018

SummaryIndigenous cattle breeds in northern Eurasia have adapted to harsh climate conditions. The local breeds are important genetic resources with cultural and historical heritages, and therefore, their preservation and genetic characterization are important. In this study, we aim to identify genes and biological processes that are important for their adaptation to the cold and harsh conditions. For this purpose, we profiled the whole-blood transcriptome of two native breeds and one commercial breed using high-throughput RNA sequencing. More than 15,000 genes were identified, of which 2, 89, and 162 genes were significantly upregulated exclusively in Northern Finncattle, Yakutian cattle and Holstein cattle, respectively. The functional classification of these significantly differentially expressed genes identified several biological processes and pathways related to signalling mechanisms, cell differentiation, and host-pathogen interactions that, in general, point towards immunity and disease resistance mechanisms. The gene expression pattern observed in Northern Finncattle was more similar to that of Yakutian cattle, despite sharing similar living conditions as the Holstein cattle included in our study. In conclusion, our study identified unique biological processes in these breeds that help them to adapt and survive in sub-arctic environments.
Functional In vivo Single-cell Transcriptome (FIST) Analysis Reveals Molecular Properties of Light-Sensitive Neurons in Mouse V1
Authors: Liu Jianwei , Pan Na , Sun Le , Wang Mengdi , Zhang Junjing , Zuo Zhentao , He Sheng , Wu Qian , Wang Xiaoqun 
Published: August 2018

ABSTRACTVision formation is classically based on projections from the retinal ganglion cells (RGC) to the lateral geniculate nucleus (LGN) and the primary visual cortex (V1). Although the cellular information of the retina and the LGN has been widely studied, the transcriptome profiles of single neurons with specific functions in V1 still remain unknown. Some neurons in mouse V1 are tuned to light stimulus. To determine the molecular properties of light-stimulated neurons in layer 2/3 of V1, we developed a method of functionalin vivosingle-cell transcriptome (FIST) analysis that integrates sensory evoked calcium imaging, whole-cell electrophysiological patch-clamp recordings, single-cell mRNA sequencing and three-dimensional morphological characterization in a live mouse, based on a two-photon microscope system. In our study, 58 individual cells from layer 2/3 of V1 were identified as either light-sensitive (LS) or non-light-sensitive (NS) by single-cell light-evoked calcium evaluation and action potential spiking. The contents of every single cell after individual functional tests were aspirated through the patch-clamp pipette for mRNA sequencing. Furthermore, the three-dimensional (3-D) morphological characterizations of the neurons were reconstructed in the live mouse after the whole-cell recordings. Our sequencing results indicated that V1 neurons with high expression of genes related to transmission regulation, such asRtn4r,Nr4a1,and genes involved in membrane transport, such as Na+/K+ATPase, NMDA-type glutamatergic receptor, preferentially respond to light stimulation. Our findings demonstrate the ability of FIST analysis to characterize the functional, morphological and transcriptomic properties of a single cell in alive animal, thereby providing precise neuronal information and predicting its network contribution in the brain.
Deterministic Nature of Cellular Position Noise DuringC. elegansEmbryogenesis
Authors: Li Xiaoyu , Zhao Zhiguang , Xu Weina , Fan Rong , Xiao Long , Ma Xuehua , Du Zhuo 
Published: August 2018

ABSTRACTIndividuals with identical genotypes exhibit great phenotypic variability known as biological noise, which has broad implications. While molecular-level noise has been extensively studied, in-depth analysis of cellular-level noise is challenging. Here, we present a systems-level quantitative and functional analysis of noise in cellular position during embryogenesis, an important phenotype indicating differentiation and morphogenesis. We show that cellular position noise is deterministic, stringently regulated by intrinsic and extrinsic mechanisms. The noise level is determined by cell lineage identity and is coupled to developmental properties including embryonic localization, cell contact, and left-right symmetry. Cells follow a concordant low-high-low pattern of noise dynamics, and fate specification triggers a global down-regulation of noise that provide a noise-buffering strategy. Noise is stringently regulated throughout embryogenesis, especially during cell division and cell adhesion and gap junctions function to restrict noise. Collectively, our study reveals system properties and regulatory mechanisms of cellular noise control during development.
Voxelwise encoding models with non-spherical multivariate normal priors
Authors: Nunez-Elizalde Anwar O. , Huth Alexander G. , Gallant Jack L. 
Published: August 2018

AbstractPredictive models for neural or fMRI data are often fit using regression methods that employ priors on the model parameters. One widely used method is ridge regression, which employs a spherical Gaussian prior that assumes equal and independent variance for all parameters. However, a spherical prior is not always optimal or appropriate. There are many cases where expert knowledge or hypotheses about the structure of the model parameters could be used to construct a better prior. In these cases, non-spherical Gaussian priors can be employed using a generalized form of ridge known as Tikhonov regression. Yet Tikhonov regression is only rarely used in neuroscience. In this paper we discuss the theoretical basis for Tikhonov regression, demonstrate a computationally efficient method for its application, and show several examples of how Tikhonov regression can improve predictive models for fMRI data. We also show that many earlier studies have implicitly used Tikhonov regression by linearly transforming the regressors before performing ridge regression.
Enhanced axonal Neuregulin-1 type-III signaling ameliorates disease severity in a CMT1B mouse model
Authors: Scapin Cristina , Ferri Cinzia , Pettinato Emanuela , Zambroni Desiree , Bianchi Francesca , Carro Ubaldo Del , Belin Sophie , Caruso Donatella , Mitro Nico , Pellegatta Marta , Taveggia Carla , Schwab Markus H. , Nave Klaus-Armin , Feltri M. Laura , Wrabetz Lawrence , D’Antonio Maurizio 
Published: August 2018

ABSTRACTCharcot–Marie–Tooth neuropathies (CMTs) are a group of genetic disorders that affect the peripheral nervous system (PNS) with heterogeneous pathogenesis and no available treatment. Axonal Neuregulin 1 type III (Nrg1TIII) drives peripheral nerve myelination by activating downstream signaling pathways such as PI3K/Akt and MAPK/Erk that converge on master transcriptional regulators of myelin genes, such as Krox20. We reasoned that modulating Nrg1TIII activity may constitute a general therapeutic strategy to treat CMTs that are characterized by reduced levels of myelination. Here, we show that genetic overexpression of Nrg1TIII ameliorates neurophysiological and morphological parameters in a mouse model of demyelinating CMT1B, without exacerbating the toxic gain of function that underlies the neuropathy. Intriguingly, the mechanism appears not to be related to Krox20 or myelin gene upregulation, but rather to a beneficial rebalancing in the stoichiometry of myelin lipids and proteins. Finally, we provide proof of principle that stimulating Nrg1TIII signaling, by pharmacological suppression of the Nrg1TIII inhibitor TACE/ADAM17, also ameliorates the neuropathy. Thus, modulation of Nrg1TIII by TACE/ADAM17 inhibition may represent a general treatment for hypomyelinating neuropathies.
Human frontoparietal cortex represents behaviorally-relevant target status during invariant object recognition
Authors: Henderson Margaret , Serences John T. 
Published: August 2018

AbstractSearching for items that are useful given current goals, or “target” recognition, requires an observer to generalize across identity-preserving transformations such as viewpoint changes, as well as to incorporate contextual information. While past work has found target recognition signals in areas of ventral visual cortex, it is not clear whether these signals support performance on demanding tasks that require invariant, flexible search. Here, we used a task that required subjects to match novel object stimuli based on invariant features (identity and viewpoint). Based on multivariate fMRI analyses, the data suggest that the multiple-demand (MD) network, including sub-regions of parietal and frontal cortex, encodes invariant representations of an object’s status as a target. Furthermore, target information in MD regions, but not early or ventral visual cortex, was higher on correct compared to incorrect trials, suggesting a strong link between MD target signals and behavior.
Reliable variant calling during runtime of Illumina sequencing
Authors: Loka Tobias P. , Tausch Simon H. , Renard Bernhard Y. 
Published: August 2018

AbstractThe sequential paradigm of data acquisition and analysis in next-generation sequencing leads to high turnaround times for the generation of interpretable results. We combined a novel real-time read mapping algorithm with fast variant calling to obtain reliable variant calls still during the sequencing process. Thereby, our new algorithm allows for accurate read mapping results for intermediate cycles and supports large reference genomes such as the complete human reference. This enables the combination of real-time read mapping results with complex follow-up analysis. In this study, we showed the accuracy and scalability of our approach by applying real-time read mapping and variant calling to seven publicly available human whole exome sequencing datasets. Thereby, up to 89% of all detected SNPs were already identified after 40 sequencing cycles while showing similar precision as at the end of sequencing. Final results showed similar accuracy to those of conventionalpost-hocanalysis methods. When compared to standard routines, our live approach enables considerably faster interventions in clinical applications and infectious disease outbreaks. Besides variant calling, our approach can be adapted for a plethora of other mapping-based analyses.
Dragotcytosis: Elucidation of the Mechanism forCryptococcus neoformansMacrophage-to-Macrophage Transfer
Authors: Dragotakes Quigly , Fu Man Shun , Casadevall Arturo 
Published: August 2018

AbstractCryptococcus neoformansis a pathogenic yeast capable of a unique and intriguing form of cell-to-cell transfer between macrophage cells. The mechanism for cell-to-cell transfer is not understood. Here we imaged macrophages with CellTracker Green CMFDA-labeled cytosol to ascertain whether cytosol was shared between donor and acceptor macrophages. Analysis of several transfer events detected no transfer of cytosol from donor to acceptor macrophages. However, blocking Fc and complement receptors resulted in a major diminution of cell-to-cell transfer events. The timing cell-to-cell transfer (11.17 min) closely approximated the sum of phagocytosis (4.18 min) and exocytosis (6.71 min) times. We propose that macrophage cell-to-cell transfer represents a non-lytic exocytosis event followed by phagocytosis into a macrophage that is in close proximity and name this process Dragotcytosis (Dragot is a Greek surname meaning ‘Sentinel’) as it represents sharing of a microbe between two sentinel cells of the innate immune system.
Superior dispersal ability leads to persistent ecological dominance by Candida pseudoglaebosa in the Sarracenia purpurea metacommunity
Authors: Boynton Primrose J. , Peterson Celeste N. , Pringle Anne 
Published: August 2018

AbstractA large number of descriptive surveys document changes in microbial communities over time, but direct evidence for the ecological processes mediating succession or causing ecological dominance remains rare. Differential dispersal may be a key mechanism. We surveyed microbial diversity within a metacommunity of pitchers of the model carnivorous plant Sarracenia purpurea and discovered the yeast Candida pseudoglaebosa as ecologically dominant. Its frequency in the metacommunity increased over the growing season, and it was not replaced by other taxa. We next measured its competitive ability in a manipulative laboratory experiment and tracked its dispersal over time in nature. Despite its dominance, C. pseudoglaebosa is not a superior competitor. Instead, it is a superior disperser: it arrives in pitchers earlier, and disperses into more pitchers, than other taxa. Differential dispersal across the spatially structured metacommunity of individual pitchers emerges as a key driver of the continuous dominance of C. pseudoglaebosa during succession.
A conserved role of the insulin-like signaling pathway in uric acid pathologies revealed in Drosophila melanogaster
Authors: Lang Sven , Bose Neelanjan , Wilson Kenneth A. , Brackman Deanna J. , Hilsabeck Tyler , Watson Mark , Beck Jennifer N. , Sharma Amit , Chen Ling , Killilea David W. , Ho Sunita , Kahn Arnold , Giacomini Kathleen , Stoller Marshall L. , Chi Thomas , Kapahi Pankaj 
Published: August 2018

SummaryElevated uric acid (UA) is a key factor for disorders, including gout or kidney stones and result from abrogated expression of Urate Oxidase (Uro) and diet. To understand the genetic pathways influencing UA metabolism we established a Drosophila melanogaster model with elevated UA using Uro knockdown. Reduced Uro expression resulted in the accumulation of UA concretions and diet-dependent shortening of lifespan. Inhibition of insulin-like signaling (ILS) pathway genes reduced UA and concretion load. In humans, SNPs in the ILS genes AKT2 and FOXO3 were associated with UA levels or gout, supporting a conserved role for ILS in modulating UA metabolism. Downstream of the ILS pathway UA pathogenicity was mediated partly by NADPH Oxidase, whose inhibition attenuated the reduced lifespan and concretion accumulation. Thus, genes in the ILS pathway represent potential therapeutic targets for treating UA associated pathologies, including gout and kidney stones.HighlightsIn Drosophila high uric acid (UA) levels shorten lifespan and cause UA aggregationConserved in flies and humans, the ILS pathway associates with UA pathologiesFoxO dampens concretion formation by reducing UA levels and ROS formationInhibition of NOX alleviates the lifespan attenuation and UA aggregation
Evaluation of a Dual Isolation Width Acquisition (DIWA) method for isobaric labelling ratio decompression
Authors: Roumeliotis Theodoros I. , Weisser Hendrik , Choudhary Jyoti S. 
Published: August 2018

ABSRACTIsobaric labelling is a highly precise approach for protein quantification. However, due to the isolation interference problem, isobaric tagging suffers from ratio underestimation at the MS2 level. The use of narrow isolation widths is a rational approach to alleviate the interference problem; however, this approach compromises proteome coverage. We reasoned that although a very narrow isolation window will result in loss of peptide fragment ions, the reporter ion signals will be retained for a significant portion of the spectra. Based on this assumption we have designed a Dual Isolation Width Acquisition (DIWA) method, in which each precursor is first fragmented with HCD using a standard isolation width for peptide identification and preliminary quantification, followed by a second MS2 HCD scan using a much narrower isolation width for the acquisition of quantitative spectra with reduced interference. We leverage the quantification obtained by the “narrow” scans to build linear regression models and apply these to decompress the fold-changes measured at the “standard” scans. We evaluate the DIWA approach using a nested two species/gene knockout TMT-6plex experimental design and discuss the perspectives of this approach.
Atypical flexibility in dynamic functional connectivity quantifies the severity in autism spectrum disorder
Authors: Harlalka Vatika , Bapi Raju S. , Vinod P.K. , Roy Dipanjan 
Published: August 2018

AbstractResting-state functional connectivity (FC) analyses have shown atypical connectivity in autism spectrum disorder (ASD) as compared to typically developing (TD). However, this view emerges from investigating static FC overlooking the age, disease phenotype and their interaction in the whole brain transient connectivity patterns. Contrasting with most extant literature in the present study, we investigated precisely how age and disease phenotypes factors into dynamic changes in functional connectivity of TD and ASD using resting-state functional magnetic resonance imaging (rs-fMRI) data stratified into three cohorts: children (7–11 years) and adolescents (12–17 years), and adults (18+) for the analysis. The dynamic variability in the connection strength and the modular organization in terms of measures: flexibility, cohesion strength and disjointness were explored for each subject to characterize the differences between ASD and TD.In ASD, we observed significantly higher inter-subject dynamic variability in connection strength as compared to TD. This hypervariability relates to the symptom severity in ASD. We found that whole-brain flexibility correlates with static modularity only in TD. Further, we observed a core-periphery organization in the resting-state, with Sensorimotor and Visual regions in the rigid core; and DMN and attention areas in the flexible periphery. TD also develops a more cohesive organization of sensorimotor areas. However, in ASD we found a strong positive correlation of symptom severity with the flexibility of rigid areas and with disjointness of sensorimotor areas. The regions of the brain showing the high predictive power of symptom severity were distributed across the cortex, with stronger bearings in the frontal, motor and occipital cortices. Our study demonstrates that the dynamic framework best characterizes the variability in ASD.