bluuebunny/crossref_metadata_2025_split huggingface dataset:
Scale Invariance in fNIRS as a Measurement of Cognitive Load
Authors: Zhuang Chu , Meidenbauer Kimberly L. , Kardan Omid , Stier Andrew J. , Choe Kyoung Whan , Cardenas-Iniguez Carlos , Huppert Theodore J. , Berman Marc G. 
Published: September 2021

AbstractScale invariant neural dynamics are a relatively new but effective means of measuring changes in brain states as a result of varied cognitive load and task difficulty. This study is the first to test whether scale invariance (as measured by the Hurst exponent,H) can be used with functional near-infrared spectroscopy (fNIRS) to quantify cognitive load. We analyzedHextracted from the fNIRS time series while participants completed an N-back working memory task. Consistent with what has been demonstrated in fMRI, the current results showed that scale-invariance analysis significantly differentiated between task and rest periods as calculated from both oxy- (HbO) and deoxy-hemoglobin (HbR) concentration changes. Results from both channel-averagedHand a multivariate partial least squares approach (Task PLS) demonstrated higherHduring the 1-back task than the 2-back task. These results were stronger forHderived from HbR than from HbO. As fNIRS is relatively portable and robust to motion-related artifacts, these preliminary results shed light on the promising future of measuring cognitive load in real life settings.Author SummaryScale invariance reflects a pattern of self-similarity (or fractalness) across a time series of brain data. In human neuroscience studies using EEG and fMRI, higher scale invariance has been associated with individuals being in a state of minimal cognitive effort or while performing a relatively easy task compared to doing something more challenging. Functional near-infrared spectroscopy (fNIRS) is a flexible neuroimaging technique that can be used in naturalistic settings and measures the same underlying biological signal as fMRI. We expected that, if scale invariant brain states are indeed robust indicators of cognitive load or task difficulty, we should be able to replicate previous findings in fNIRS. Consistent with this hypothesis, we find that more scale invariant brain states are indeed associated with less cognitively demanding and more restful brain states in fNIRS data. This finding opens up a wide array of potential applications for monitoring cognitive load and fatigue in real-life settings, such as during driving, learning in schools, or during interpersonal interactions.
Multiscale affinity maturation simulations to elicit broadly neutralizing antibodies against HIV
Authors: Sprenger Kayla G. , Conti Simone , Ovchinnikov Victor , Chakraborty Arup K. , Karplus Martin 
Published: September 2021

AbstractThe design of vaccines against highly mutable pathogens, such as HIV and influenza, requires a detailed understanding of how the adaptive immune system responds to encountering multiple variant antigens (Ags). Here, we describe a multiscale model of B cell receptor (BCR) affinity maturation that employs actual BCR nucleotide sequences and treats BCR/Ag interactions in atomistic detail. We apply the model to simulate the maturation of a broadly neutralizing Ab (bnAb) against HIV. Starting from a germline precursor sequence of the VRC01 anti-HIV Ab, we simulate BCR evolution in response to different vaccination protocols and different Ags, which were previously designed by us. The simulation results provide qualitative guidelines for future vaccine design and reveal unique insights into bnAb evolution against the CD4 binding site of HIV. Our model makes possible direct comparisons of simulated BCR populations with results of deep sequencing data, which will be explored in future applications.Author SummaryVaccination has saved more lives than any other medical procedure, and the impending end of the COVID-19 pandemic is also due to the rapid development of highly efficacious vaccines. But, we do not have robust ways to develop vaccines against highly mutable pathogens. For example, there is no effective vaccine against HIV, and a universal vaccine against diverse strains of influenza is also not available. The development of immunization strategies to elicit antibodies that can neutralize diverse strains of highly mutable pathogens (so-called ‘broadly neutralizing antibodies’, or bnAbs) would enable the design of universal vaccines against such pathogens, as well as other viruses that may emerge in the future. In this paper, we present an agent-based model of affinity maturation – the Darwinian process by which antibodies evolve against a pathogen – that, for the first time, enables thein silicoinvestigation of real germline nucleotide sequences of antibodies known to evolve into potent bnAbs, evolving against real amino acid sequences of HIV-based vaccine-candidate proteins. Our results provide new insights into bnAb evolution against HIV, and can be used to qualitatively guide the future design of vaccines against highly mutable pathogens.
Thalamic bursts modulate cortical synchrony locally to switch between states of global functional connectivity in a cognitive task
Authors: Portoles Oscar , Blesa Manuel , van Vugt Marieke , Cao Ming , Borst Jelmer P. 
Published: September 2021

AbstractPerforming a cognitive task requires going through a sequence of functionally diverse stages. Although it is typically assumed that these stages are characterized by distinct states of cortical synchrony that are triggered by sub-cortical events, little reported evidence supports this hypothesis. To test this hypothesis, we first identified cognitive stages in single-trial MEG data of an associative recognition task, showing with a novel method that each stage begins with local modulations of synchrony followed by a state of directed functional connectivity. Second, we developed the first whole-brain model that can simulate cortical synchrony throughout a task. The model suggests that the observed synchrony is caused by thalamocortical bursts at the onset of each stage, targeted at cortical synapses and interacting with the structural anatomical connectivity. These findings confirm that cognitive stages are defined by distinct states of cortical synchrony and explains the network-level mechanisms necessary for reaching stage-dependent synchrony states.Author summaryA novel machine-learning method was applied to unveil the dynamics of local and cortex-wide neural coordination underlying the fundamental cognitive processes involved in a memory task. To explain how neural activity – and ultimately behavior – was coordinated throughout the task, we developed a whole-brain model that incorporates cognitive mechanisms, anatomy, and neural biophysics. Similar models are used with resting state data, however, simulating a cognitive task remained elusive. The model showed that sub-cortical pulses at the onset of cognitive processes – as hypothesized by cognitive and neurophysiological theories – were sufficient to switch between the states of neural coordination observed. These findings have implications to understand goal-directed cognitive processing and the mechanisms to reach states of neural coordination.
The SARS-CoV-2 spike (S) and the orthoreovirus p15 cause neuronal and glial fusion
Authors: Martinez-Marmol Ramon , Giordano-Santini Rosina , Kaulich Eva , Cho Ann-Na , Riyadh Md Asrafuzzaman , Robinson Emilija , Balistreri Giuseppe , Meunier Frédéric A. , Ke Yazi D. , Ittner Lars M. , Hilliard Massimo A. 
Published: September 2021

AbstractNumerous enveloped viruses use specialized surface molecules called fusogens to enter host cells1. During virus replication, these fusogens decorate the host cells membrane enabling them the ability to fuse with neighboring cells, forming syncytia that the viruses use to propagate while evading the immune system. Many of these viruses, including the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), infect the brain and may cause serious neurological symptoms through mechanisms which remain poorly understood2–4. Here we show that expression of either the SARS-CoV-2 spike (S) protein or p15 protein from the baboon orthoreovirus is sufficient to induce fusion between interconnected neurons, as well as between neurons and glial cells. This phenomenon is observed across species, from nematodes to mammals, including human embryonic stem cells-derived neurons and brain organoids. We show that fusion events are progressive, can occur between distant neurites, and lead to the formation of multicellular syncytia. Finally, we reveal that in addition to intracellular molecules, fusion events allow diffusion and movement of large organelles such as mitochondria between fused neurons. Our results provide important mechanistic insights into how SARS-CoV-2 and other viruses could affect the nervous system circuitries causing neurological symptoms.
CARD8 inflammasome sensitization through DPP9 inhibition enhances NNRTI-triggered killing of HIV-1-infected cells
Authors: Clark Kolin , Wang Qiankun , Shan Liang 
Published: September 2021

AbstractNon-nucleoside reverse transcriptase inhibitors (NNRTIs) induce pyroptosis of HIV-1 infected CD4+T cells through induction of intracellular viral protease activation, which then activates the CARD8 inflammasome. Due to high concentrations of NNRTIs being required for efficient CARD8 activation and elimination of HIV-1-infected cells, it is important to elucidate ways to sensitize the CARD8 inflammasome to NNRTI-induced activation. We show that this sensitization can be done through chemical inhibition of the CARD8 negative regulator DPP9. DPP9 inhibitor Val-boroPro (VbP) can act synergistically with NNRTIs to increase their efficacy in killing HIV-1-infected cells. We also show that VbP is able to partially overcome issues with NNRTI resistance and is capable of killing infected cells without the presence of NNRTIs. This offers a promising strategy for enhancing NNRTI efficacy in elimination of HIV-1 reservoirs in patients.
Co-expression analysis to identify key modules and hub genes associated with COVID19 in Platelets
Authors: Alarabi Ahmed B. , Mohsen Attayeb , Mizuguchi Kenji , Alshbool Fatima Z. , Khasawneh Fadi T. 
Published: September 2021

AbstractThe severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) is a highly contagious virus that causes a severe respiratory disease known as Corona virus disease 2019 (COVID19). Indeed, COVID19 increases the risk of cardiovascular occlusive/thrombotic events and is linked to poor outcomes. The pathophysiological processes underlying COVID19-induced thrombosis are complex, and remain poorly understood. To this end, platelets play important roles in regulating our cardiovascular system, including via contributions to coagulation and inflammation. There is an ample of evidence that circulating platelets are activated in COVID19 patients, which is a primary driver of the thrombotic outcome observed in these patients. However, the comprehensive molecular basis of platelet activation in COVID19 disease remains elusive, which warrants more investigation. Hence, we employed gene co-expression network analysis combined with pathways enrichment analysis to further investigate the aforementioned issues. Our study revealed three important gene clusters/modules that were closely related to COVID19. Furthermore, enrichment analysis showed that these three modules were mostly related to platelet metabolism, protein translation, mitochondrial activity, and oxidative phosphorylation, as well as regulation of megakaryocyte differentiation, and apoptosis, suggesting a hyperactivation status of platelets in COVID19. We identified the three hub genes from each of three key modules according to their intramodular connectivity value ranking, namely: COPE, CDC37, CAPNS1, AURKAIP1, LAMTOR2, GABARAP MT-ND1, MT-ND5, and MTRNR2L12. Collectively, our results offer a new and interesting insight into platelet involvement in COVID19 disease at the molecular level, which might aid in defining new targets for treatment of COVID19–induced thrombosis.key pointsCo-expression analysis of platelet RNAseq from COVID19 patients show distinct clusters of genes (modules) that are highly correlated to COVID19 disease.Identifying these modules might help in understanding the mechanism of thrombosis in COVID19 patients
The methodology used to deliver information literacy instruction by a select group of academic librarians: a case study
Authors: Harrison Simone Julie-Ann , Deans Mark-Jeffery O'niel 
Published: September 2021

PurposeThe purpose of the study is to highlight the need for academic librarians to incorporate effective methodologies in their delivery of information literacy instruction.Design/methodology/approachThe researchers conducted a qualitative research using a case study approach. A nonprobability or purposive sampling method was employed in this research to select five participants. Semistructured interviews and observation were used to garner data from the sample.FindingsThe findings of the study revealed that the support required by distance education and face-to-face students is typically the same. An examination of the findings pointed to the fact that some students may be demotivated in information literacy instruction sessions because of an overload of information, which leads to frustration and poor performance.Practical implicationsThe findings of the study highlight the need for Caribbean academic librarians to incorporate effective methodologies in their delivery of information literacy instruction and provide an analytical view of how these methodologies may impact performance, understanding and the overall work produced by both students and faculty.Originality/valueResearch on the topic specific to the Caribbean is limited; therefore, research of this nature provides useful strategies that academic librarians may use in developing stellar information literacy programs in the Caribbean to help both students and faculty members achieve excellence.
Revisiting the role of inflation in financial development: unveiling non-linear and moderating effects
Authors: Ehigiamusoe Kizito Uyi , Narayanan Suresh , Poon Wai-Ching 
Published: September 2021

PurposeThis paper aims to examine the non-linear impact of inflation on financial development, and the moderating role of GDP in the relationship between inflation and financial development in a panel of 125 countries.Design/methodology/approachIt employs the dynamic common correlated effects (CCE) that can control for heterogeneity and cross-sectional dependence. This technique enables us to conduct both panel and country-specific analyses.FindingsThough there is no significant evidence that inflation has a non-linear impact on financial development in the panel, the country-specific estimations reveal that inflation has a non-linear impact on financial development in 66 countries. The results also show that GDP mitigates the detrimental effect of inflation on financial development in 45 countries. An insight into the non-linear relationship between inflation and financial development is crucial for policy decision-making. Besides, knowledge of the moderating role of GDP in the relationship between financial development and inflation is fundamental for policy formulations.Originality/valueAlthough the extant literature has shown that the inflation rate plays a negative role in financial development, the literature overlooked the non-linear relationship between the two variables. Besides, the studies have not considered the role of GDP in moderating the impact of the inflation rate on financial development. This study fills these gaps in the existing body of finance literature.
Mapping and measuring spatial connectivity of the pathways to home-based businesses within informal urban contexts
Authors: Thai Ha Minh Hai , Stevens Quentin , Rogers Judy 
Published: September 2021

PurposeThis paper presents a mixed methodology to map and analyse the spatial connectivity of the everyday pathways that link the doorway of an individual's home–work locations to the local main commercial street. These pathways include public streets, semi-private lanes, alleys and stairs.Design/methodology/approachPathways within different morphological areas in Hanoi, Vietnam, are used as examples to illustrate the development and application of the methodology. The methodology, adapted from Conzenian, typological, and space syntax methods, combined with observations and interviews, seeks to overcome several identified limitations of each of these approaches for understanding pedestrians' horizontal and vertical movement patterns within urban settings.FindingsAnalytical diagrams of pathways are developed on figure-ground maps of the neighbourhoods and three-dimensional projections of circulation spaces within buildings. Scatter plots are used to analyse the distribution of collected samples according to their business types and distances to local main streets. Field observations and interviews with homeowners revealed the critical influence of the pathways' spatial characteristics on home-based businesses' operations.Originality/valueThe methods developed here are potentially useful for urban morphologists and urban designers in decoding the intricacies of informal urban settings and understanding their socio-economic significance for users.
The reestablishment of Mosul's city fabric: an approach to computational hybridization
Authors: Alani Mostafa , Kahera Akel Ismail 
Published: September 2021

PurposeThis paper aims out to analyze the confluence of spatial analysis and computational design strategies to support the reestablishment of Mosul's city housing fabric. According to a UN-Habitat report, Mosul suffered from catastrophic losses on an urban scale, resulting in a housing crisis that requires a large-scale response. However, the need for immediate shelters might lead to a rapid, uninformed reconstruction process, causing the loss of the architectural identity that the city accumulated over the years.Design/methodology/approachThe study utilizes a two-phase sequential research method. In Phase 1, the study applies space syntax techniques to transform the floor plans of the collected traditional and contemporary houses into “quantifiable data.” This phase aims to identify design criteria that capture the “spatial configuration” of both types of houses. In the subsequent phase, the study utilizes the identified design criteria to develop a genetic algorithm inspired by traditional and contemporary practice that facilitates an informed design process.FindingsThe outcome of the study indicates that informed computational synthesis can assist in generating multiplicities floor plan layouts that mimic the inner spatial configuration of existing traditional courtyard houses and contemporary noncourtyard houses. In addition, the developed genetic algorithm was able to generate hybridized design solutions that have been spatially validated.Originality/valueThe study concludes with observations linking informed computational synthesis to the postwar construction process as a remedial methodology to analyze and redesign Mosul's city fabric in an informed, affordable and accessible fashion.
Contour- and Texture-based analysis for victim identification in forensic odontology
Authors: Jaffino G. , Prabin Jose J. 
Published: September 2021

PurposeForensic dentistry is the application of dentistry in legal proceedings that arise from any facts relating to teeth. The ultimate goal of forensic odontology is to identify the individual when there are no other means of identification such as fingerprint, Deoxyribonucleic acid (DNA), iris, hand print and leg print. The purpose of selecting dental record is for the teeth to be able to withstand decomposition, heat degradation up to 1600 °C. Dental patterns are unique for every individual. This work aims to analyze the contour shape extraction and texture feature extraction of both radiographic and photographic dental images for person identification.Design/methodology/approachTo achieve an accurate identification of individuals, the missing tooth in the radiograph has to be identified before matching of ante-mortem (AM) and post-mortem (PM) radiographs. To identify whether the missing tooth is a molar or premolar, each tooth in the given radiograph has to be classified using a k-nearest neighbor (k-NN) classifier; then, it is matched with the universal tooth numbering system. In order to make exact person identification, this research work is mainly concentrate on contour shape extraction and texture feature extraction for person identification. This work aims to analyze the contour shape extraction and texture feature extraction of both radiographic and photographic images for individual identification. Then, shape matching of AM and PM images is performed by similarity and distance metric for accurate person identification.FindingsThe experimental results are analyzed for shape and feature extraction of both radiographic and photographic dental images. From this analysis, it is proved that the higher hit rate performance is observed for the active contour shape extraction model, and it is well suited for forensic odontologists to identify a person in mass disaster situations.Research limitations/implicationsForensic odontology is a branch of human identification that uses dental evidence to identify the victims. In mass disaster circumstances, contours and dental patterns are very useful to extract the shape in individual identification.Originality/valueThe experimental results are analyzed both the contour shape extraction and texture feature extraction of both radiographic and photographic images. From this analysis, it is proved that the higher hit rate performance is observed for the active contour shape extraction model and it is well suited for forensic odontologists to identify a person in mass disaster situations. The findings provide theoretical and practical implications for individual identification of both radiographic and photographic images with a view to accurate identification of the person.