bluuebunny/crossref_metadata_2025_split huggingface dataset:
Social Listening: A Thematic Analysis of COVID-19 Discussion on Social Media
Authors: Afolabi Sulaimon , Folorunso Sakinat Oluwabukonla , Bunyula Zinia Siphosethu , Banjo Oluwatobi Oluwaseyi , Matshika Sibusiso Sydney , Warrie Warrie Usenobong , Ngqambela Naledi , Adepoju Ayodeji Emmanuel , Rabophala Hendrica , Abimbola Olawale Victor , Olanipekun Michael Segun , Odukoya Adedayo Lateef 
Published: July 2020

AbstractCOVI-19 is a variant of coronavirus diseases that has destabilised the entire world and whose cure as at mid-2020 has become elusive. Social media is ablaze with discussions around the pandemic. There is the dire need to delineate the on-going conversations on the infection with the intention of creating awareness on people’s reaction, opinion, action and recommendation that are inimical to the wellbeing of the populace. Hence, this study is geared towards performing thematic analysis of the discussions on social media about COVID-19. We programmatically retrieved data from twitter between 1st March, 2020 to 30th June 2020 with covid-19 related keywords. We processed the data and later categorised them into themes that evolved from the tweets namely Herbs and Vegetables as COVID-10 Panacea, Self-Medication Due to Prescription by Non-Medical Practitioners on Social Media, Conspiracy Theories on COVID-19 and Fear and Anxiety Associated with COVID-19. The results show that many are resulting to herbs to protect themselves against the disease; taking drugs without doctor’s prescription; believing in conspiracy theories and having certain degree of fear.
Salt and Health: Public awareness, attitudes and practices in Sri Lanka to inform a behavior change communication campaign to reduce dietary salt
Authors: Jayatilleke Achala , Gunawardena Nalika , de Silva Angela , Wickramasinghe Champika , Gamlath Lakshman , Siriwardena Thilak , Kumarapeli Vindya , Vidanapathirana Janaki , Gunawardena Shanthi , Alagiyawanna AMAAP , Talagala Ishanka , Wickramasinghe Aravinda , Kumari Prabha , Ranatunga Prasad , Dhanapala Sapumal , Pendse Razia 
Published: July 2020

AbstractBackgroundSri Lankan citizens consume almost double the recommended daily amount of salt. Objective of this study was to assess the knowledge, attitudes and practices related to health effects of dietary salt among adults and adolescents in Sri Lanka to inform a national behavior change communication campaign.MethodsWe conducted a descriptive household survey among adults (n=1016) and adolescents (n=505) in 10 districts. An, interviewer administered questionnaire was used for data collection. The approximate amount of dietary salt intake of the individuals was estimated based on household purchases.FindingsThe recommended salt limit was identified by 40% of the population. Majority, adults (90.8%) and adolescents (86.1%) knew the adverse health effects of high salt intake. Although household monthly purchase of salt indicated consumption is much higher than recommended, 48.3% of adults and 45.9% of adolescents believed that they consume ‘just the right’ amount. Discretionary salt added to home cooking was a major contributor to intake, with approximately half (50%) adding salt when cooking rice, the staple. For health-related information most preferred (adults - 72%, adolescents – 69%) media is television.InterpretationThe study identified gaps as well strengths in knowledge, attitudes and practices of Sri Lankans related to salt and health and recommends that the communication campaign include specific messaging to address gaps and leveraging on strengths. The survey identified adult females to be a key target group for the campaign and television is recommended as the mode of delivery.
Voxel-level Classification of Prostate Cancer Using a Four-Compartment Restriction Spectrum Imaging Model
Authors: Feng Christine H , Conlin Christopher C , Batra Kanha , Rodríguez-Soto Ana E , Karunamuni Roshan , Simon Aaron , Kuperman Joshua , Rakow-Penner Rebecca , Hahn Michael E , Dale Anders M , Seibert Tyler M 
Published: July 2020

AbstractPurposeDiffusion MRI is integral to detection of prostate cancer (PCa), but conventional ADC cannot capture the complexity of prostate tissues. A four-compartment restriction spectrum imaging (RSI4) model was recently found to optimally characterize pelvic diffusion signals, and the model coefficient for the slowest diffusion compartment, RSI4-C1, yielded greatest tumor conspicuity. In this study, RSI4-C1 was evaluated as a quantitative voxel-level classifier of PCa.MethodsThis was a retrospective analysis of 46 men who underwent an expanded-acquisition pelvic MRI for suspected PCa. Twenty-three men had no detectable cancer on biopsy or clinical follow-up; the other 23 had biopsy-proven PCa corresponding to a lesion on MRI (PI-RADS category 3-5). High-confidence cancer voxels were delineated by expert consensus, using imaging data and biopsy results. The entire prostate was considered benign in patients with no detectable cancer. Diffusion images were used to calculate RSI4-C1 and conventional ADC. Voxel-level discrimination of PCa from benign prostate tissue was assessed via receiver operating characteristic (ROC) curves generated by bootstrapping with patient-level case resampling. Specifically, we compared RSI4-C1 and conventional ADC on mean (and 95% CI) for two metrics: area under the curve (AUC) and false-positive rate for a sensitivity of 90% (FPR90). Classifier images were also compared.ResultsRSI4-C1 outperformed conventional ADC, with greater AUC [0.977 (0.951-0.991) vs. 0.921 (0.873-0.949)] and lower FPR90 [0.033 (0.009-0.083) vs. 0.201 (0.131-0.300)].ConclusionRSI4-C1 yielded a quantitative, voxel-level classifier of PCa that was superior to conventional ADC. RSI classifier images with a low false-positive rate might improve PCa detection.
Predicting the Emergence of SARS-CoV-2 Clades
Authors: Jain Siddharth , Xiao Xiongye , Bogdan Paul , Bruck Jehoshua 
Published: July 2020

ABSTRACTEvolution is a process of change where mutations in the viral RNA are selected based on their fitness for replication and survival. Given that current phylogenetic analysis of SARS-CoV-2 identifies new viral clades after they exhibit evolutionary selections, one wonders whether we can identify the viral selection and predict the emergence of new viral clades? Inspired by the Kolmogorov complexity concept, we propose a generative complexity (algorithmic) framework capable to analyze the viral RNA sequences by mapping the multiscale nucleotide dependencies onto a state machine, where states represent subsequences of nucleotides and state-transition probabilities encode the higher order interactions between these states. We apply computational learning and classification techniques to identify the active state-transitions and use those as features in clade classifiers to decipher the transient mutations (still evolving within a clade) and stable mutations (typical to a clade). As opposed to current analysis tools that rely on the edit distance between sequences and require sequence alignment, our method is computationally local, does not require sequence alignment and is robust to random errors (substitution, insertions and deletions). Relying on the GISAID viral sequence database, we demonstrate that our method can predict clade emergence, potentially aiding with the design of medications and vaccines.
An alternative binding mode of IGHV3-53 antibodies to the SARS-CoV-2 receptor binding domain
Authors: Wu Nicholas C. , Yuan Meng , Liu Hejun , Lee Chang-Chun D. , Zhu Xueyong , Bangaru Sandhya , Torres Jonathan L. , Caniels Tom G. , Brouwer Philip J.M. , van Gils Marit J. , Sanders Rogier W. , Ward Andrew B. , Wilson Ian A. 
Published: July 2020

ABSTRACTIGHV3-53-encoded neutralizing antibodies are commonly elicited during SARS-CoV-2 infection and target the receptor-binding domain (RBD) of the spike (S) protein. Such IGHV3-53 antibodies generally have a short CDR H3 due to structural constraints in binding the RBD (mode A). However, a small subset of IGHV3-53 antibodies to the RBD contain a longer CDR H3. Crystal structures of two IGHV3-53 neutralizing antibodies here demonstrate that a longer CDR H3 can be accommodated in a different binding mode (mode B). These two classes of IGHV3-53 antibodies both target the ACE2 receptor binding site, but with very different angles of approach and molecular interactions. Overall, these findings emphasize the versatility of IGHV3-53 in this common antibody response to SARS-CoV-2, where conserved IGHV3-53 germline-encoded features can be combined with very different CDR H3 lengths and light chains for SARS-CoV-2 RBD recognition and virus neutralization.
Hybrid optogenetic and electrical stimulation for greater spatial resolution and temporal fidelity of cochlear activation
Authors: Thompson Alex C. , Wise Andrew K. , Hart William L. , Needham Karina , Fallon James B. , Gunewardene Niliksha , Stoddart Paul R. , Richardson Rachael T. 
Published: July 2020

AbstractCompared to electrical stimulation, optogenetic stimulation has the potential to improve the spatial precision of neural activation in neuroprostheses, but it requires intense light and has relatively poor temporal kinetics. We tested the effect of hybrid stimulation, which is the combination of subthreshold optical and electrical stimuli, on spectral and temporal fidelity in the cochlea by recording multiunit activity in the inferior colliculus of channelrhodopsin (H134R variant) transgenic mice. Pulsed light or biphasic electrical pulses were delivered to cochlear spiral ganglion neurons of acutely deafened mice, either as individual stimuli or as hybrid stimuli for which the timing of the electrical pulse had a varied delay relative to the start of the optical pulse. Facilitation occurred when subthreshold electrical stimuli were applied at the end of, or up to 3.75 ms after subthreshold optical pulses. The spread of activation resulting from hybrid stimulation was significantly narrower than electrical-only and optical-only stimulation (p<0.01), measured at equivalent suprathreshold levels of loudness that are relevant to cochlear implant users. Furthermore, temporal fidelity, measured as maximum following rates to 300 ms pulse trains bursts up to 240 Hz, was 2.4-fold greater than optical-only stimulation (p<0.05). By significantly improving spectral resolution of electrical- and optical-only stimulation and the temporal fidelity of optical-only stimulation, hybrid stimulation has the potential to increase the number of perceptually independent stimulating channels in a cochlear implant.
Antiviral effects of miRNAs in extracellular vesicles against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and mutations in SARS-CoV-2 RNA virus
Authors: Park Jae Hyun , Choi Yuri , Lim Chul-Woo , Park Ji-Min , Yu Shin-Hye , Kim Yujin , Han Hae Jung , Kim Chun-Hyung , Song Young-Sook , Kim Chul , Moon Jisook 
Published: July 2020

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus 2019 (COVID-19). No treatment is available. Micro-RNAs (miRNAs) in mesenchymal stem cell-derived extracellular vesicles (MSC-EVs) are potential novel therapeutic agents because of their ability to regulate gene expression by inhibiting mRNA. Thus, they may degrade the RNA genome of SARS-CoV-2. EVs can transfer miRNAs to recipient cells and regulate conditions within them. MSC-EVs harbor major therapeutic miRNAs that play important roles in the biological functions of virus-infected host cells. Here, we examined their potential impact on viral and immune responses. MSC-EVs contained 18 miRNAs predicted to interact directly with the 3’ UTR of SARS-CoV-2. These EVs suppressed SARS-CoV-2 replication in Vero E6 cells. In addition, five major miRNAs suppressed virus activity in a luciferase reporter assay by binding the 3’ UTR. MSC-EVs showed strong regenerative effects and potent anti-inflammatory activity which may prevent lethal cytokine storms. We confirmed that EVs regulated inflammatory responses by several cell types, including human brain cells that express the viral receptor ACE2, suggesting that the brain may be targeted by SARS-CoV-2. miRNAs in MSC-EVs have several advantages as therapeutic agents against SARS-CoV-2: 1) they bind specifically to the viral 3’ UTR, and are thus unlikely to have side effects; 2) because the 3’ UTR is highly conserved and rarely mutates, MSC-EV miRNAs could be used against novel variants arising during viral replication; and 3) unique cargoes carried by MSC-EVs can have diverse effects, such as regenerating damaged tissue and regulating immunity.
The landscape of micro-inversions provides clues for population genetic analysis of humans
Authors: Qu Li , Wang Luotong , He Feifei , Han Yilun , Yang Longshu , Wang May D. , Zhu Huaiqiu 
Published: July 2020

AbstractBackgroundVariations in the human genome have been studied extensively. However, little is known about the role of micro-inversions (MIs), generally defined as small (<100 bp) inversions, in human evolution, diversity, and health. Depicting the pattern of MIs among diverse populations is critical for interpreting human evolutionary history and obtaining insight into genetic diseases.ResultsIn this paper, we explored the distribution of MIs in genomes from 26 human populations and 7 nonhuman primate genomes and analyzed the phylogenetic structure of the 26 human populations based on the MIs. We further investigated the functions of the MIs located within genes associated with human health. With hg19 as the reference genome, we detected 6,968 MIs among the 1,937 human samples and 24,476 MIs among the 7 nonhuman primate genomes. The analyses of MIs in human genomes showed that the MIs were rarely located in exonic regions. Nonhuman primates and human populations shared only 82 inverted alleles, and Africans had the most inverted alleles in common with nonhuman primates, which was consistent with the “Out of Africa” hypothesis. The clustering of MIs among the human populations also coincided with human migration history and ancestral lineages.ConclusionsWe propose that MIs are potential evolutionary markers for investigating population dynamics. Our results revealed the diversity of MIs in human populations and showed that they are essential to constructing human population relationships and have a potential effect on human health.
Tracking mitochondrial density and positioning along a growing neuronal process in individualC. elegansneuron using a long-term growth and imaging microfluidic device
Authors: Mondal Sudip , Dubey Jyoti , Awasthi Anjali , Sure Guruprasad Reddy , Koushika Sandhya P. 
Published: July 2020

AbstractThe long cellular architecture of neurons requires regulation in part through transport and anchoring events to distribute intracellular organelles. During development, cellular and sub-cellular events such as organelle additions and their recruitment at specific sites on the growing axons occur over different time scales and often show inter-animal variability thus making it difficult to identify specific phenomena in population averages. To measure the variability in sub-cellular events such as organelle positions, we developed a microfluidic device to feed and immobilizeC. elegansfor high-resolution imaging over several days. The microfluidic device enabled long-term imaging of individual animals and allowed us to investigate organelle density using mitochondria as a testbed in a growing neuronal processin vivo. Sub-cellular imaging of an individual neuron in multiple animals, over 36 hours in our microfluidic device, shows the addition of new mitochondria along the neuronal process and an increase in the accumulation of synaptic vesicles at synapses, both organelles with important roles in neurons. Long-term imaging of individualC. eleganstouch receptor neurons identifies addition of new mitochondria and interacts with other moving mitochondria only through fission and fusion events. The addition of new mitochondria takes place along the entire neuronal process length and the threshold for the addition of a new mitochondrion is when the average separation between the two pre-existing mitochondria exceeds 24 micrometers.
NBS1-CtIP–Mediated DNA End Resection Regulates cGAS Binding to Micronuclei
Authors: Abdisalaam Salim , Mukherjee Shibani , Bhattacharya Souparno , Sinha Debapriya , Kumari Sharda , Sadek Hesham A. , Ortega Janice , Li Guo-Min , Asaithamby Aroumougame 
Published: July 2020

AbstractCyclic GMP-AMP synthase (cGAS), an important component of immune signaling, is hyperactivated in cells defective for DNA damage response (DDR) signaling. However, a direct role for DDR factors in the regulation of cGAS functions is mostly unknown. Here, we provide novel evidence that Nijmegen breakage syndrome 1 (NBS1) protein, a well-studied DNA double-strand break (DSB) sensor, in coordination with ATM, a protein kinase, and CtBP-interacting protein (CtIP), a DNA end resection factor, functions as an upstream regulator of cGAS binding to micronuclei. Upon NBS1 binding to micronuclei via its fork-head–associated domain, it recruits ATM and CtIP via its N- and C-terminal domains, respectively. Subsequently, ATM stabilizes NBS1’s interaction with micronuclei, and CtIP converts DSB ends into single-strand DNA ends, and these two key events preclude cGAS from binding to micronuclei. Notably, we show that purified cGAS cannot form a complex with DNA substrates that mimic resected DNA ends in vitro. Thus, NBS1 together with its binding partners modify the chromatin architecture of the micronuclei and that plays a critical role in cGAS’s binding to micronuclei.
A Conserved TCRβ signature dominates a highly polyclonal T-cell expansion during the acute phase of a murine malaria infection
Authors: Smith Natasha L. , Nahrendorf Wiebke , Sutherland Catherine , Mooney Jason P. , Thompson Joanne , Spence Philip J. , Cowan Graeme J. M. 
Published: July 2020

AbstractCD4+αβ T-cells are key mediators of the immune response to a firstPlasmodiuminfection, undergoing extensive activation and splenic expansion during the acute phase of an infection. However, the clonality and clonal composition of this expansion has not previously been described. Using a comparative infection model, we sequenced the splenic CD4+T-cell receptor repertoires generated over the time-course of aPlasmodium chabaudiinfection. We show through repeat replicate experiments, single-cell RNA-seq, and analyses of independent RNA-seq data, that following a first infection – within a highly polyclonal expansion – T-effector repertoires are consistently dominated by TRBV3 gene usage. Clustering by sequence similarity, we find the same dominant clonal signature is expanded across replicates in the acute phase of an infection, revealing a conserved pathogen-specific T-cell response that is consistently a hallmark of a first infection, but not expanded upon re-challenge. Determining the host or parasite factors driving this conserved response may uncover novel immune targets for malaria therapeutic purposes.
Transcription factor binding process is the primary driver of noise in gene expression
Authors: Parab Lavisha , Pal Sampriti , Dhar Riddhiman 
Published: July 2020

AbstractNoise in expression of individual genes gives rise to variations in activity of cellular pathways and generates heterogeneity in cellular phenotypes. Phenotypic heterogeneity has important implications for antibiotic persistence, mutation penetrance, cancer growth and therapy resistance. Specific molecular features such as presence of the TATA box sequence and promoter nucleosome occupancy have been associated with noise. However, the relative importance of these features in noise regulation has not yet been assessed. In addition, how well these features can predict noise also remains unclear. Here through an integrated statistical model of gene expression noise in yeast we found that the number of regulating transcription factors (TFs) was a key predictor of noise. With an increase in the number of regulatory TFs, we observed a rise in the number of TFs that bound cooperatively. In addition, increased number of TFs meant more overlaps in TF binding sites that caused competition between TFs for binding to the same region of the promoter. Through modeling of TF binding to promoter and applying stochastic simulations, we demonstrated that competition and cooperation among TFs could increase noise. Thus, our work uncovers a process of noise regulation that arises out of the dynamics of gene regulation and is not dependent on any specific transcription factor or specific promoter sequence.
Intrathecal catheter implantation decreases cerebrospinal fluid dynamics in cynomolgus monkeys
Authors: Khani Mohammadreza , Fu Audrey Q. , Pluid Joshua , Gibbs Christina P. , Oshinski John N. , Xing Tao , Stewart Gregory R. , Zeller Jillynne R. , Martin Bryn A. 
Published: July 2020

AbstractA detailed understanding of the CSF dynamics is essential for testing and evaluation of intrathecal drug delivery. Preclinical work using large-animal models (e.g., monkeys, dogs and sheep) has great utility for defining spinal drug distribution/pharmacokinetics and provide an important tool for defining safety. In this study, we investigated the impact of catheter implantation in the sub-dural space on CSF flow dynamics in Cynomolgus monkeys. Magnetic resonance imaging (MRI) was performed before and after catheter implantation to quantify the differences based on catheter placement location in the cervical compared to the lumbar spine. Several geometric and hydrodynamic parameters were calculated based on the 3D segmentation and flow analysis. Hagen-Poiseuille equation was used to investigate the impact of catheter implantation on flow reduction and hydraulic resistance. A linear mixed-effects model was used in this study to investigate if there is a statistically significant difference between cervical and lumbar implantation, or between two MRI time points. Results showed that geometric parameters did not change statistically across MRI measurement time points and did not depend on catheter location. However, catheter insertion did have a significant impact on the hydrodynamic parameters and the effect was greater with the cervical implantation. CSF flow rate decreased up to 54.7% when the catheter located in the cervical region. The maximum flow rate reduction in the lumbar implantation group was 21%. Overall, lumbar catheter implantation disrupted CSF dynamics to a lesser degree than cervical catheter implantation and this effect remained up to two weeks post-catheter implantation