bluuebunny/crossref_metadata_2025_split huggingface dataset:
Generalizable EEG encoding models with naturalistic audiovisual stimuli
Authors: Desai Maansi , Holder Jade , Villarreal Cassandra , Clark Nat , Hamilton Liberty S. 
Published: January 2021

AbstractIn natural conversations, listeners must attend to what others are saying while ignoring extraneous background sounds. Recent studies have used encoding models to predict electroencephalography (EEG) responses to speech in noise-free listening situations, sometimes referred to as “speech tracking” in EEG. Researchers have analyzed how speech tracking changes with different types of background noise. It is unclear, however, whether neural responses from noisy and naturalistic environments can be generalized to more controlled stimuli. If encoding models for noisy, naturalistic stimuli are generalizable to other tasks, this could aid in data collection from populations who may not tolerate listening to more controlled, less-engaging stimuli for long periods of time. We recorded non-invasive scalp EEG while participants listened to speech without noise and audiovisual speech stimuli containing overlapping speakers and background sounds. We fit multivariate temporal receptive field (mTRF) encoding models to predict EEG responses to pitch, the acoustic envelope, phonological features, and visual cues in both noise-free and noisy stimulus conditions. Our results suggested that neural responses to naturalistic stimuli were generalizable to more controlled data sets. EEG responses to speech in isolation were predicted accurately using phonological features alone, while responses to noisy speech were more accurate when including both phonological and acoustic features. These findings may inform basic science research on speech-in-noise processing. Ultimately, they may also provide insight into auditory processing in people who are hard of hearing, who use a combination of audio and visual cues to understand speech in the presence of noise.Significance StatementUnderstanding spoken language in natural environments requires listeners to parse acoustic and linguistic information in the presence of other distracting stimuli. However, most studies of auditory processing rely on highly controlled stimuli with no background noise, or with background noise inserted at specific times. Here, we compare models where EEG data are predicted based on a combination of acoustic, phonetic, and visual features in highly disparate stimuli – sentences from a speech corpus, and speech embedded within movie trailers. We show that modeling neural responses to highly noisy, audiovisual movies can uncover tuning for acoustic and phonetic information that generalizes to simpler stimuli typically used in sensory neuroscience experiments.
Sampling from Disentangled Representations of Single-Cell Data Using Generative Adversarial Networks
Authors: Yu Hengshi , Welch Joshua D. 
Published: January 2021

AbstractDeep generative models, including variational autoencoders (VAEs) and generative adversarial networks (GANs), have achieved remarkable successes in generating and manipulating highdimensional images. VAEs excel at learning disentangled image representations, while GANs excel at generating realistic images. Here, we systematically assess disentanglement and generation performance on single-cell gene expression data and find that these strengths and weaknesses of VAEs and GANs apply to single-cell gene expression data in a similar way. We also develop MichiGAN1, a novel neural network that combines the strengths of VAEs and GANs to sample from disentangled representations without sacrificing data generation quality. We learn disentangled representations of two large singlecell RNA-seq datasets [13, 68] and use MichiGAN to sample from these representations. MichiGAN allows us to manipulate semantically distinct aspects of cellular identity and predict single-cell gene expression response to drug treatment.
Analysis of a “Split-and-Stuttering” Module of an Assembly Line Polyketide Synthase
Authors: Guzman Katarina M. , Yuet Kai P. , Lynch Stephen R. , Liu Corey W. , Khosla Chaitan 
Published: January 2021

AbstractNotwithstanding the “one-module-one-elongation-cycle” paradigm of assembly line polyketide synthases (PKSs), some PKSs harbor modules that iteratively elongate their substrates through a defined number of cycles. While some insights into module iteration, also referred to as “stuttering”, have been derived throughin vivoandin vitroanalysis of a few PKS modules, a general understanding of the mechanistic principles underlying module iteration remains elusive. This report serves as the first interrogation of a stuttering module from atrans-AT subfamily PKS that is also naturally split across two polypeptides. Previous work has shown that Module 5 of the NOCAP (nocardiosisassociatedpolyketide) synthase iterates precisely three times in the biosynthesis of its polyketide product, resulting in an alltrans-configured triene moiety in the polyketide product. Here we describe the intrinsic catalytic properties of this NOCAP synthase module. Through complementary experimentsin vitroand inE. coli, the “split-and-stuttering” module was shown to catalyze up to five elongation cycles, although its dehydratase domain ceased to function after three cycles. Unexpectedly, the central olefinic group of this truncated product had acisconfiguration. Our findings set the stage for further in-depth analysis of a structurally and functionally unusual PKS module with contextual biosynthetic plasticity.TOC/Abstract Graphic
Real-Time, Direct Classification of Nanopore Signals with SquiggleNet
Authors: Bao Yuwei , Wadden Jack , Erb-Downward John R. , Ranjan Piyush , Zhou Weichen , McDonald Torrin L. , Mills Ryan E. , Boyle Alan P. , Dickson Robert P. , Blaauw David , Welch Joshua D. 
Published: January 2021

AbstractOxford Nanopore sequencers provide results in real time as DNA passes through a nanopore and can eject a molecule after it has been partly sequenced. However, the computational challenge of deciding whether to keep or reject a molecule in real time has limited the application of this capability. We present SquiggleNet, the first deep learning model that can classify nanopore reads directly from their electrical signals. SquiggleNet operates faster than the DNA passes through the pore, allowing real-time classification and read ejection. When given the amount of sequencing data generated in one second, the classifier achieves significantly higher accuracy than base calling followed by sequence alignment. Our approach is also faster and requires an order of magnitude less memory than approaches based on alignment. SquiggleNet distinguished human from bacterial DNA with over 90% accuracy, generalized to unseen species, identified bacterial species in a human respiratory meta genome sample, and accurately classified sequences containing human long interspersed repeat elements.
Targeting primary and metastatic uveal melanoma with a G protein inhibitor
Authors: Onken Michael D. , Makepeace Carol M. , Kaltenbronn Kevin M. , Choi Joelle , Hernandez-Aya Leonel , Weilbaecher Katherine N. , Piggott Kisha D. , Rao P. Kumar , Yuede Carla M , Dixon Alethia J. , Osei-Owusu Patrick , Cooper John A. , Blumer Kendall J. 
Published: January 2021

AbstractUveal melanoma (UM) is the most common intraocular tumor in adults. Nearly half of UM patients develop metastatic disease and often succumb within months because effective therapy is lacking. A novel therapeutic approach has been suggested by the discovery that UM cell lines driven by mutant constitutively active Gq or G11 can be targeted by FR900359 (FR) or YM-254890, which are bioavailable, selective inhibitors of the Gq/11/14 subfamily of heterotrimeric G proteins. Here, we have addressed the therapeutic potential of FR for UM. We found that FR inhibited all oncogenic Gq/11 mutants reported in UM. FR arrested growth of all Gq/11-driven UM cell lines tested, but induced apoptosis only in a few. Similarly, FR inhibited growth of, but did not efficiently kill, UM tumor cells from biopsies of primary or metastatic tumors. FR evoked melanocytic redifferentiation of UM tumor cells with low (class 1), but not high (class 2), metastatic potential. FR administered systemically below its LD50 strongly inhibited growth of PDX-derived class 1 and class 2 UM tumors in mouse xenograft models, and reduced blood pressure transiently. FR did not regress xenografted UM tumors, or significantly affect heart rate, liver function, hematopoiesis, or behavior. These results indicated the existence of a therapeutic window in which FR can be explored for treating UM, and potentially other diseases caused by constitutively active Gq/11.
Regulation of neurofilament length and transport by a dynamic cycle of polymer severing and annealing
Authors: Uchida Atsuko , Peng Juan , Brown Anthony 
Published: January 2021

ABSTRACTNeurofilaments are space-filling cytoskeletal polymers that are transported into axons where they accumulate during development to expand axon caliber. We previously described novel severing and end-to-end annealing mechanisms in neurons that alter neurofilament length. To explore the functional significance of neurofilament length, we developed a long-term multi-field time-lapse method to track the movement of fluorescently tagged neurofilaments in axons of cultured neurons for up to 30 minutes. All filaments moved rapidly, but long filaments paused and reversed more often, resulting in little net movement, whereas short filaments moved persistently for long distances, pausing and reversing less often. Long filaments severed more frequently, generating shorter filaments, and short filaments annealed more frequently, generating longer filaments. Thus, neurofilament length is regulated by a dynamic cycle of severing and annealing and this influences neurofilament transport. Site-directed mutagenesis to mimic phosphorylation at four known phosphorylation sites in the head domain of neurofilament protein L generated shorter neurofilaments that moved more frequently. A non-phosphorylatable mutant had the opposite effect. Treatment of cultured neurons with activators of protein kinase A, which phosphorylates three of these sites, increased neurofilament severing. This effect was blocked by the non-phosphorylatable mutant. We propose that focal destabilization of intermediate filaments by N-terminal phosphorylation of their constituent polypeptides at specific locations along their length may be a general enzymatic mechanism for severing this class of cytoskeletal polymers. Our data suggest a novel mechanism for the control of neurofilament transport and accumulation in axons based on regulation of neurofilament polymer length.SUMMARYNeurofilaments are space-filling cytoskeletal polymers that are transported into axons where they accumulate to expand axon caliber, which is an important determinant of axonal conduction velocity. We reported previously that neurofilaments can lengthen and shorten by novel end-to-end annealing and severing mechanisms. Here, we show that neurofilament annealing and severing are robust phenomena in cultured neurons that act antagonistically to dynamically regulate neurofilament length, which in turn regulates their transport. In addition, we present evidence for a novel enzymatic mechanism of intermediate filament severing based on site-directed phosphorylation of the neurofilament subunit proteins. We propose that modulation of neurofilament length by annealing and severing may be a mechanism for the regulation of neurofilament transport and accumulation in axons.
Tropism of SARS-CoV-2 for Developing Human Cortical Astrocytes
Authors: Andrews Madeline G. , Mukhtar Tanzila , Eze Ugomma C. , Simoneau Camille R. , Perez Yonatan , Mostajo-Radji Mohammed A. , Wang Shaohui , Velmeshev Dmitry , Salma Jahan , Kumar G. Renuka , Pollen Alex A. , Crouch Elizabeth E. , Ott Melanie , Kriegstein Arnold R. 
Published: January 2021

AbstractThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) readily infects a variety of cell types impacting the function of vital organ systems, with particularly severe impact on respiratory function. It proves fatal for one percent of those infected. Neurological symptoms, which range in severity, accompany a significant proportion of COVID-19 cases, indicating a potential vulnerability of neural cell types. To assess whether human cortical cells can be directly infected by SARS-CoV-2, we utilized primary human cortical tissue and stem cell-derived cortical organoids. We find significant and predominant infection in cortical astrocytes in both primary and organoid cultures, with minimal infection of other cortical populations. Infected astrocytes had a corresponding increase in reactivity characteristics, growth factor signaling, and cellular stress. Although human cortical cells, including astrocytes, have minimal ACE2 expression, we find high levels of alternative coronavirus receptors in infected astrocytes, including DPP4 and CD147. Inhibition of DPP4 reduced infection and decreased expression of the cell stress marker, ARCN1. We find tropism of SARS-CoV-2 for human astrocytes mediated by DPP4, resulting in reactive gliosis-type injury.
Adherence to quarantine protocols to prevent the spread of COVID-19: the mediating effect of intrinsic and extrinsic motivations
Authors: Suplico-Jeong Luz , Bautista Jr Reynaldo Altillo , Guillen Jr Nelson Borrega , Murad Noel Sajid 
Published: January 2021

PurposeIloilo province was singled out as a model province in the Philippines because of its ability to prevent the spread of COVID-19. This study aims to examine the factors that influenced Iloilo residents' adherence to quarantine protocols.Design/methodology/approachA total of 334 Iloilo residents joined the survey. Using the theory of planned behavior (TPB), the results suggest a significant impact of attitude on adherence to quarantine protocols, while subjective norm, self-efficacy and controllability were not significant.FindingsThis study suggests that attitude predicts adherence to quarantine protocols. Further, the results showed that intrinsic motivation mediated the relationship between (1) attitude and adherence to quarantine protocols and (2) subjective norm and adherence to quarantine protocols. This implies that intrinsic motivation such as staying alive can encourage a resident to adhere to quarantine protocols.Research limitations/implicationsSubsequent research should also consider how to mitigate the effects of similar public health crises in the future.Practical implicationsThe study implies that intrinsic motivation such as staying alive can encourage a resident to follow quarantine protocol given this pandemic.Social implicationsHealth campaigns can lead to a more favorable attitude toward quarantine protocols adherence. Given the value of subjective norm, campaigns can also frame quarantine protocols adherence as socially responsible behavior. This can be used to target provinces with the highest risk of infection within the population. These insights can be used by local government units (LGUs), media and other stakeholders to encourage residents to adhere to quarantine protocols.Originality/valueThis study provides insights that can be used by the LGUs, media and other stakeholders to encourage residents to follow quarantine protocols.
Parent-adolescent communication on sexual and reproductive health among school adolescents of Woldia town, Ethiopia by the year 2019
Authors: Masresha Seteamlak Adane , Alen Gedefaw Diress 
Published: January 2021

PurposeThe purpose of this paper is to assess the magnitude of parent-adolescent communication on sexual and reproductive health (SRH) issues and its association with gender and premarital sexual practice among school adolescents of Woldia town.Design/methodology/approachSchool-based cross-sectional study was conducted on 368 unmarried secondary and preparatory school adolescents (15–19 years) in Woldia town. Simple random sampling was employed to select study participants. Self-administered questionnaire was used. Data were entered by EPI-Data version 3.0.2 and analyzed by using SPSS version 20.FindingsIn this study, 56.3% of school adolescents had parental communication on sexual and reproductive health issues. The result of this study showed that adolescents who had history of sexual intercourse where 64% less likely to communicate with parents on sexual and reproductive health issues (AOR: 0.36 95% CI: 0.20, 0.65), but there was no association between gender and sexual and reproductive health communication between adolescent and parent (AOR: 1.06, 95% CI: 0.64, 1.75).Originality/valueParent-adolescent communication about sexual matters is one of the means that encourages adolescents to adopt responsible sexual behavior. Many children in Africa are uncomfortable to have a communication about sexual and reproductive health issues with their parents because the subject is a taboo topic in most homes.
Turbulent flow with nonequilibrium chemical reaction in single snorkel RH
Authors: Chen Shifu , Lei Hong , Wang Meng , Ding Changyou , Dou Weixue , Chang Lishan 
Published: January 2021

Purpose
The reported mathematical models of gas–liquid flow in single snorkel Rheinstahl–Heraeus (SSRH) are based on the assumption of steady Ar-molten steel flow. The purpose of this paper is to develop a mathematical model to describe the unsteady turbulent flow (CO-Ar-molten steel) with nonequilibrium decarburization reaction.

Design/methodology/approach
On the base of the finite volume method, the computational fluid dynamics software CFX is used to predict the unsteady fluid flow, the spatial distributions of CO/argon gas and carbon element. The water model experiment and the industrial experiment are carried out to verify the mathematical models.

Findings
A two-way coupling model (T-WCM) based on algebraic slip model is developed to investigate the coupling phenomena. The related results show that T-WCM is more rigorous and accurate than one-way coupling model in predicting carbon content of molten steel. The amount of CO gas, which can enhance turbulent flow and mass transfer, is about three times the argon gas blown into SSRH.

Originality/value
CO gas is the key factor in investigating the transport phenomena. This study fully reveals the truth about the unsteady gas-liquid flow in SSRH. It is necessary to adopt T-WCM based on algebraic slip model to describe the CO-Ar-molten steel flow phenomenon.
The empowering role of hospitable telemedicine experience in reducing isolation and anxiety: evidence from the COVID-19 pandemic
Authors: Cheng Yusi , Wei Wei , Zhong Yunying , Zhang Lu 
Published: January 2021

PurposeThis paper aims to explore how hospitable telemedicine services empowered patients during the COVID-19. Expanding from the technology aspect, this research integrated the philosophy of hospitality organizational culture by including factors related to human-human interaction as significant predictors for patients’ sense of empowerment (perceived competence and control) in coping with their emotional stress (anxiety and isolation).Design/methodology/approachSurvey data were obtained from 409 general consumers who have used video-based virtual consultation since February 2020. Stepwise multiple regression and simple linear regression analyses were used for hypotheses testing.FindingsThe results reveal that the doctors’ reliability, responsiveness and empathy significantly predict patients’ perceived competence and control. Perceived usefulness and convenience of telemedicine technology enhance patients’ perceived competence and control. Patients’ sense of empowerment significantly reduces their anxiety and sense of isolation.Research limitations/implicationsTo fully understand the role of hospitality in people’s telemedicine experiences, future studies are encouraged to not only examine the patients-clinicians interactions but also explore the patients-support staff interactions.Practical implicationsHealth care providers’ “bed-side” manners empower patients in managing their emotional stress. Health care providers should be trained for their empathetic ability and communication skills. Strategies such as collaborating with hospitality schools and business schools can be implemented to help build medical student’s patient-centric attitudes and skills.Originality/valueThis paper provided empirical evidence for the value of hospitality in health care and offered useful suggestions for health care providers, especially by empowering vulnerable people during catastrophic events such as COVID-19.
Making #blacklivesmatter in universities: a viewpoint on social policy education
Authors: Bennett Bindi , Ravulo Jioji J. , Ife Jim , Gates Trevor G. 
Published: January 2021

PurposeThe purpose of this viewpoint article is to consider the #BlackLivesMatter movement within the Aboriginal Australian struggle for equality, sovereignty and human rights. Indigenous sovereignty has been threatened throughout Australia's history of colonization. We provide a viewpoint and recommendations for social policy education and practice.Design/methodology/approachWe provide commentary and interpretation based upon the lived experience of Black, Indigenous and Other People of Color (BIPOC) co-authors, co-authors who are Allies, extant literature and practice wisdom as social policy educators.FindingsUniversities are sources of knowledge production, transmission and consumption within society. We provide critical recommendations for what social policy education within universities can address human rights and the #BlackLivesMatter movement.Originality/valueCulturally responsive inclusion for BIPOC has only just begun in Australia and globally within the context of the #BlackLivesMatter movement. This paper adds critical conversation and recommendations for what social policy programs might do better to achieve universities' teaching and learning missions.
The future is now: calling for a focus on temporal issues in information system research
Authors: Venkatesh Viswanath , Sykes Tracy Ann , Aljafari Ruba , Poole Marshall Scott 
Published: January 2021

PurposeAs information systems (IS) phenomena continue to emerge and evolve in our ever-changing economic and social contexts, researchers need to increase their focus on time in order to enrich our theories. The purpose of this paper is to present broad suggestions for IS researchers about how they can direct some of their research efforts to consider, conceptualize and incorporate time into research endeavors and how they might be mindful about considering and specifying time-related scope conditions of their research efforts.Design/methodology/approachThe authors synthesize empirical studies and discuss three distinct yet related frameworks of time and the benefits they can provide. The authors choose two research streams that reflect dynamic economic and social contexts – namely, enterprise systems and social networks – to illustrate how time and frameworks of time can be leveraged in our theory development and research design.FindingsThe authors demonstrate that limited research in IS has incorporated a rich conceptualization and/or discussion of time. The authors build on this gap to highlight guidelines that researchers can adopt to enrich their view of time.Originality/valueGiven the dynamic nature of IS phenomena and the increased availability of longitudinal data, the authors’ suggestions aim to urge and guide IS researchers about ways in which they can incorporate time into their theory and study designs.