bluuebunny/crossref_metadata_2025_split huggingface dataset:
A filamentous phage triggers antiviral responses in cystic fibrosis basal airway epithelial cells
Authors: Popescu Medeea C , Haddock Naomi L , Burgener Elizabeth B , Rojas-Hernandez Laura S , Kaber Gernot , Hargil Aviv , Bollyky Paul L , Milla Carlos E 
Published: September 2022

AbstractBasal airway epithelial cells are a multipotent stem cell population which gives rise to several airway cell types. Basal cells are known to be critical to airway epithelium homeostasis and repair, and altered basal cell phenotypes have been reported in cystic fibrosis and idiopathic pulmonary fibrosis. However, very little is known about how basal cells respond to stimuli in the cystic fibrosis airway environment. Cystic fibrosis patients experience chronic infection with Pseudomonas aeruginosa and contain both high quantities of lipopolysaccharide (LPS) as well as the filamentous bacteriophage Pf produced by biofilm-state P. aeruginosa in the airway. In this study, we sought to investigate the transcriptional responses of human basal cells from both healthy controls and patients with cystic fibrosis to LPS and Pf phage. Basal cells from wildtype and cystic fibrosis donors were cultured in vitro and exposed to LPS and/or Pf phage, followed by single-cell sequencing on the 10x platform. We report that basal cells show strong antiviral responses and neutrophil chemokine production in response to Pf phage. We validate these findings in additional donors by qRT-PCR and show that Pf phage is internalized by basal cells. We also show that Pf decreases basal cell migration and proliferation. We demonstrate that Pf phage, a bacteria-infecting virus which does not replicate in mammalian cells, is taken up by basal cells and activates immune responses. Further studies are needed to determine the impact of this antiviral response to bacterial clearance.Author SummaryWhen we experience a lung infection or injury, the stem cells of the airway—called basal epithelial cells—are crucial for healing the affected tissue. Basal cells proliferate and migrate to close gaps in the epithelium and replace injured and dead cells. We are also learning that basal cells can directly contribute to the immune response against lung pathogens, although little is understood about how basal cells sense viruses and bacteria, and what molecules they secrete in response. In our work, we sought to investigate the role that basal cells play in the course of an infection with the common human pathogen Pseudomonas aeruginosa. We stimulated basal cells with lipopolysaccharide (LPS), a potent immunogen produced by Pseudomonas, as well as the Pseudomonas-infecting virus Pf4. We have previously shown that Pf4, which is produced in high amounts by lung-infecting Pseudomonas, affects the immune response to this bacterium. In our work here, we show that Pf4 is recognized as a virus by basal cells and changes the transcriptional response to LPS, derailing the antibacterial immune response to Pseudomonas. These findings raise the question of whether other bacteria-infecting viruses alter immune responses, and how these viruses interact with other airway cells.
“Lead (Pb) impairs thyroid hormone mediated changes in brain development and body length in Xenopus laevis tadpoles”
Authors: Dahora Lara I. , Robinson Alayna M. , Buenaventura Christopher , Bailey Hannah , Thompson Christopher K. 
Published: September 2022

ABSTRACTLead (Pb) poisoning during early development is associated with behavioral and cognitive deficits, but the specific mechanisms by which Pb impairs brain development are not fully understood. One potential mechanism is that Pb poisoning may impair thyroid hormone (TH)- mediated changes in brain development To address this issue, we performed experiments to assess the effects of Pb poisoning on (TH) -dependent changes in cellular and molecular mechanisms in the developing Xenopus laevis tadpole brain. We treated stage 48 tadpoles to combinations of 1000 ppb Pb bath for seven days and added one of three different concentrations of thyroxine (T4) for the final two days of treatment. We found that lead exposure decreased body length, including in T4-treated tadpoles. We also performed immuno-staining for proliferative marker pH3 and found that Pb disrupts T4-induced increases in neuronal proliferation. Finally, we used syGlass VR data visualization software to measure volume of the forebrain, midbrain, and hindbrain in 3D and found that Pb exposure impaired T4-mediated changes in brain volume. Last, we found that Pb poisoning reduced the T4-mediated increase in proliferating cell nuclear antigen (PCNA), a TH-sensitive gene. These results illustrate that Pb poisoning impairs some TH-dependent changes in the developing brain.
Transcription factors interact with RNA to regulate genes
Authors: Oksuz Ozgur , Henninger Jonathan E , Warneford-Thomson Robert , Zheng Ming M , Erb Hailey , Overholt Kalon J , Hawken Susana Wilson , Banani Salman F , Lauman Richard , Vancura Adrienne , Robertson Anne L , Hannett Nancy M , Lee Tong I , Zon Leonard I. , Bonasio Roberto , Young Richard A. 
Published: September 2022

SummaryTranscription factors (TFs) orchestrate the gene expression programs that define each cell’s identity. The canonical TF accomplishes this with two domains, one that binds specific DNA sequences and the other that binds protein coactivators or corepressors. We find that at least half of TFs also bind RNA, doing so through a previously unrecognized domain with sequence and functional features analogous to the arginine-rich motif of the HIV transcriptional activator Tat. RNA-binding contributes to TF function by promoting the dynamic association between DNA, RNA and TF on chromatin. TF-RNA interactions are a conserved feature essential for vertebrate development and disrupted in disease. We propose that the ability to bind DNA, RNA and protein is a general property of many TFs and is fundamental to their gene regulatory function.
Uncovering the Mechanism of the Proton-Coupled Fluoride Transport in the CLCF Antiporter
Authors: Mills Kira R. , Torabifard Hedieh 
Published: September 2022

AbstractFluoride is a natural antibiotic abundantly present in the environment and, in micromolar concentrations, is able to inhibit enzymes necessary for bacteria to survive. However, as is the case with many antibiotics, bacteria have evolved resistance methods, including through the use of recently discovered membrane proteins. One such protein is the CLCF F-/H+ antiporter protein, a member of the CLC superfamily of anion-transport proteins, most notably known for their ability to transport chloride ions. While it possesses many similarities to the other CLC proteins, it also differs in several key ways, and though previous studies have examined this F- transporter, many questions are still left unanswered. To reveal details of the transport mechanism used by CLCF, we have employed molecular dynamics simulations and umbrella sampling calculations. Our results have led to several discoveries, including the mechanism of proton import and how it is able to aid in the fluoride export. Additionally, we have determined the role of the previously identified residues Glu118, Glu318, Met79, and Tyr396. This work is among the first computational studies of the CLCF F-/H+ antiporter and is the first to propose a mechanism which couples both the proton and anion transport.
Characterising modulatory effects of transcranial random noise stimulation using the perceptual template model
Authors: Gotsis Stephanie , van Boxtel Jeroen , Teufel Christoph , Edwards Mark , Christensen Bruce 
Published: September 2022

AbstractNeural noise is an inherent property of all nervous systems. However, the mechanisms by which such random and fluctuating neural activity influences perception are still unclear. To elucidate the relationship between neural noise and perceptual performance we require techniques that can safely manipulate neural noise in humans. Transcranial random noise stimulation (tRNS), a form of electrical brain stimulation, has been proposed to increase neural noise according to principles of stochastic resonance (SR); where small to moderate intensities of tRNS improve performance, while higher intensities are detrimental. To date, high intensity (i.e., >2mA) tRNS effects on neural noise levels have not been directly quantified, nor have the detrimental effects proposed by SR been demonstrated in early visual processing. For this purpose, we applied a maximum current intensity of 3mA high-frequency tRNS to the visual cortex (V1) during an orientation discrimination task across increasing external visual noise levels, and fit the perceptual template model to contrast thresholds to quantify intrinsic mechanisms related to noise underlying changes in perceptual performance. We found that tRNS generally worsened perceptual performance by increasing observer’s internal noise and reducing the ability to filter external noise compared to sham. While most observers experienced detrimental effects, others demonstrated improved perceptual performance (i.e., reduced internal noise and better noise filtering). Preliminary evidence suggests that individual baseline internal noise levels may drive the observed beneficial or detrimental observer responses to tRNS. These findings have important implications for the application of tRNS to investigate the impact of internal noise and noise filtering processes on perception.
Cytoophidia safeguard binucleation of Drosophila male accessory gland cells
Authors: You Dong-Dong , Zhou Xiao-Li , Wang Qiao-Qi , Liu Ji-Long 
Published: September 2022

ABSTRACTAlthough most cells are mononuclear, the nucleus can exist in the form of binucleate or even multinucleate to respond to different physiological processes. The male accessory gland of Drosophila is the organ that produces semen, and its main cells are binucleate. Here we observe that CTP synthase (CTPS) forms filamentous cytoophidia in binuclear main cells, primarily located at the cell boundary. In CTPSH355A, a point mutation that destroys the formation of cytoophidia, we find that the nucleation mode of the main cells changes, including mononucleates and vertical distribution of binucleates. Although the overexpression of CTPSH355A can restore the level of CTPS protein, it will neither form cytoophidia nor eliminate the abnormal nucleation pattern. Therefore, our data indicate that there is an unexpected functional link between the formation of cytoophidia and the maintenance of binucleation in Drosophila main cells.
Structural and Immunological Similarities Between the Metacyclic and Bloodstream Form Variant Surface Glycoproteins of the African Trypanosome
Authors: Chandra Monica , Đaković Sara , Foti Konstantina , Zeelen Johan , van Straaten Monique , Aresta-Branco Francisco , Tihon Eliane , Lübbehusen Nicole , Ruppert Thomas , Glover Lucy , Papavasiliou F. Nina , Stebbins C. Erec 
Published: September 2022

AbstractDuring infection of mammalian hosts, African trypanosomes thwart immunity using antigenic variation of the dense Variant Surface Glycoprotein (VSG) coat, accessing a large repertoire of thousands of genes and pseudogenes and switching to antigenically distinct copies. The parasite is transferred to mammalian hosts through the bite of the tsetse fly. In the salivary glands of the fly, the pathogen adopts the metacyclic form and expresses a limited repertoire of VSG genes specific to that developmental stage. It has remained unknown whether the metacyclic VSGs possess distinct properties associated with this particular and discrete phase of the parasite life cycle. We show here using bioinformatic, crystallographic, and immunological analyses of three metacyclic VSGs that they closely mirror the known classes of bloodstream form VSGs both in structure and in the immunological responses they elicit.
Travelling waves observed in MEG data can be explained by two discrete sources
Authors: Zhigalov Alexander , Jensen Ole 
Published: September 2022

AbstractGrowing evidence suggests that travelling waves are functionally relevant for cognitive operations in the brain. Several electroencephalography (EEG) studies report on a perceptual alpha-echo, representing the brain response to a random visual flicker, propagating as a travelling wave across the cortical surface. In this study, we ask if the propagating activity of the alpha-echo is best explained by a set of discrete sources mixing at the sensor level rather than a cortical travelling wave. To this end, we presented participants with gratings modulated by random noise and simultaneously acquired the ongoing MEG. The perceptual alpha-echo was estimated using the temporal response function linking the visual input to the brain response. At the group level, we observed a spatial decay of the amplitude of the alpha-echo with respect to the sensor where the alpha-echo was the largest. Importantly, the propagation latencies consistently increased with the distance. Interestingly, the propagation of the alpha-echoes was predominantly centro-lateral, while EEG studies reported mainly posterior-frontal propagation. Moreover, the propagation speed of the alpha-echoes derived from the MEG data was around 10 m/s, which is higher compared to the 2 m/s reported in EEG studies. Using source modelling, we found an early component in the primary visual cortex and a phase-lagged late component in the parietal cortex, which may underlie the travelling alpha-echoes at the sensor level. We then simulated the alpha-echoes using realistic EEG and MEG forward models by placing two sources in the parietal and occipital cortices in accordance with our empirical findings. The two-source model could account for both the direction and speed of the observed alpha-echoes in the EEG and MEG data. Our results demonstrate that the propagation of the perceptual echoes observed in EEG and MEG data can be explained by two sources mixing at the scalp level equally well as by a cortical travelling wave. This conclusion however does not put into question continuous travelling waves reported in intracranial recordings.
Subject independent emotion recognition using EEG and physiological signals – a comparative study
Authors: Arthanarisamy Ramaswamy Manju Priya , Palaniswamy Suja 
Published: September 2022

PurposeThe aim of this study is to investigate subject independent emotion recognition capabilities of EEG and peripheral physiological signals namely: electroocoulogram (EOG), electromyography (EMG), electrodermal activity (EDA), temperature, plethysmograph and respiration. The experiments are conducted on both modalities independently and in combination. This study arranges the physiological signals in order based on the prediction accuracy obtained on test data using time and frequency domain features.Design/methodology/approachDEAP dataset is used in this experiment. Time and frequency domain features of EEG and physiological signals are extracted, followed by correlation-based feature selection. Classifiers namely – Naïve Bayes, logistic regression, linear discriminant analysis, quadratic discriminant analysis, logit boost and stacking are trained on the selected features. Based on the performance of the classifiers on the test set, the best modality for each dimension of emotion is identified.Findings The experimental results with EEG as one modality and all physiological signals as another modality indicate that EEG signals are better at arousal prediction compared to physiological signals by 7.18%, while physiological signals are better at valence prediction compared to EEG signals by 3.51%. The valence prediction accuracy of EOG is superior to zygomaticus electromyography (zEMG) and EDA by 1.75% at the cost of higher number of electrodes. This paper concludes that valence can be measured from the eyes (EOG) while arousal can be measured from the changes in blood volume (plethysmograph). The sorted order of physiological signals based on arousal prediction accuracy is plethysmograph, EOG (hEOG + vEOG), vEOG, hEOG, zEMG, tEMG, temperature, EMG (tEMG + zEMG), respiration, EDA, while based on valence prediction accuracy the sorted order is EOG (hEOG + vEOG), EDA, zEMG, hEOG, respiration, tEMG, vEOG, EMG (tEMG + zEMG), temperature and plethysmograph.Originality/valueMany of the emotion recognition studies in literature are subject dependent and the limited subject independent emotion recognition studies in the literature report an average of leave one subject out (LOSO) validation result as accuracy. The work reported in this paper sets the baseline for subject independent emotion recognition using DEAP dataset by clearly specifying the subjects used in training and test set. In addition, this work specifies the cut-off score used to classify the scale as low or high in arousal and valence dimensions. Generally, statistical features are used for emotion recognition using physiological signals as a modality, whereas in this work, time and frequency domain features of physiological signals and EEG are used. This paper concludes that valence can be identified from EOG while arousal can be predicted from plethysmograph.
Exploring the psychological contract breach of nurses in healthcare: an exploratory study
Authors: Gulzar Saba , Hussain Kanwal , Akhlaq Ather , Abbas Zuhair , Ghauri Shagufta 
Published: September 2022

PurposeRecent advancements in the field of organizational psychology have transformed the employees’ perceptions related to the reactions of the employment relationship. The main aim of the study is to explore the consequences of psychological contracts among the nursing staff and how to provide better patient care and quality service in the health-care system as nurses play a pivotal role in the context of Pakistan. Significantly, this study attempts to bridge the research gap by exploring consequences of psychological contracts. Drawing on the social exchange theory, this study examined the psychological contracts of nurses and their reactions to the perceived violation.Design/methodology/approachThis research adopted a qualitative method and was based on an exploratory approach. Data were collected through in-depth semi-structured interviews from 21 nurses working in public, private and charity hospitals in Karachi, Pakistan. The thematic content analysis is employed for the analysis of data by using NVivo software.FindingsThe study identified the relational and transactional elements related to the psychological contract of nurses who predominantly consisted of supervisor support, autonomy, tangible/intangible rewards and trust. The intrinsic motivation which relates to their devotion to work was found as an additional element to balance their psychological contract. This research also establishes that the psychological contract of nurses is being violated in their work settings.Practical implicationsBy highlighting the importance of psychological contract breach, the findings demonstrate that health-care institutions should take measures to cope with psychological contract breach issues at the workplace.Originality/valueThis study contributes to the body of knowledge by exploring psychological contract breach. Substantially, there are rare studies conducted on psychological contract breach among nurses in developing country context (Pakistan). However, this study adds to the previous studies related to the psychological contract of nurses in the context of Pakistan by using social exchange theories. Finally, this study enables the management of healthcare to balance the psychological contract issues effectively.
An integrated building information modeling (BIM)-based lifecycle-oriented framework for sustainable building design
Authors: Kylili Angeliki , Georgali Phoebe-Zoe , Christou Petros , Fokaides Paris 
Published: September 2022

Purpose
The built environment is taking enormous leaps towards its digitalization. Computer-aided tools such as building information modeling (BIM) are found in the forefront of this evolution, playing a critical role in creating the foundations for the upcoming development of smart low-carbon cities. However, the potential of BIM is still untapped – links will need to be created among the available and forthcoming methodologies under one integral operational system. The purpose of this paper is to present an integrated BIM-based life cycle-oriented framework for achieving sustainable constructions at the pre-construction phase. The developed framework represents an example of the approaches that the construction industry will need to adopt to integrate the different tools under an integrated smart city context.

Design/methodology/approach
The methodological approach follows the development of four same-volume different-configuration three-dimensional BIM designs, which are coupled with life cycle assessment (LCA) tools for establishing sustainable building design.

Findings
The results of this paper indicated that the choice of building design and shape can play a significant role in reducing the embodied energy and embodied carbon of buildings, achieving a reduction of up to 15% compared to a reference building of same volume and gross floor area.

Originality/value
The originality of this paper is found in its approach application by coupling three-dimensional BIM models with LCA data, the use of reinforcement detailing in an nD BIM study and the employment of country-specific LCA databases.
Novel and simplified implementation of digital high-power pulsed MIG welding power supply with LLC resonant converter
Authors: Wu Kaiyuan , Huang Hao , Chen Ziwei , Zeng Min , Yin Tong 
Published: September 2022

Purpose
This paper aims to overcome the limitations of low efficiency, low power density and strong electromagnetic interference (EMI) of the existing pulsed melt inert gas (MIG) welding power supply. So a novel and simplified implementation of digital high-power pulsed MIG welding power supply with LLC resonant converter is proposed in this work.

Design/methodology/approach
A simple parallel full-bridge LLC resonant converter structure is used to design the digital power supply with high welding current, low arc voltage, high open-circuit voltage and a wide range of arc loads, by effectively exploiting the variable load and high-power applications of LLC resonant converter.

Findings
The efficiency of each converter can reach up to 92.3%, under the rated operating condition. Notably, with proposed scheme, a short-circuit current mutation of 300 A can stabilize at 60 A within 8 ms. Furthermore, the pulsed MIG welding test shows that a stable welding process with 280 A peak current can be realized and a well-formed weld bead can be obtained, thereby verifying the feasibility of LLC resonant converter for pulsed MIG welding power supply.

Originality/value
The high efficiency, high power density and weak EMI of LLC resonant converter are conducive to the further optimization of pulsed MIG welding power supply. Consequently, a high performance welding power supply is implemented by taking adequate advantages of LLC resonant converter, which can provide equipment support for exploring better pulsed MIG welding processes.