bluuebunny/crossref_metadata_2025_split huggingface dataset:
In situ Patch-seq analysis of microglia reveals a lack of stress genes as found in FACS-isolated microglia
Authors: Bakina Olga , Conrad Thomas , Mitic Nina , Vidal Ramon Oliveira , Obrusnik Tessa , Sai Somesh , Nolte Christiane , Semtner Marcus , Kettenmann Helmut 
Published: March 2023

AbstractWe applied the patch-seq technique to harvest transcripts from individual microglial cells from cortex, hippocampus and corpus callosum of acute brain slices from adult mice. After recording membrane currents with the patch-clamp technique, the cytoplasm was collected via the pipette and underwent adapted SMART-seq2 preparation with subsequent sequencing. On average, 4138 genes were detected in 113 cells from hippocampus, corpus callosum and cortex, including microglia markers such asTmem119, P2ry12andSiglec-H. Comparing our dataset to previously published single cell mRNA sequencing data from FACS-isolated microglia indicated that two clusters of cells were absent in our patch-seq dataset. Pathway analysis of marker genes in FACS-specific clusters revealed association with microglial activation and stress response. This indicates that under normal conditions microgliain situlack transcripts associated with a stress-response, and that the microglia-isolation procedure by mechanical dissociation and FACS triggers the expression of genes related to activation and stress.
Evolution of a Functionally Intact but Antigenically Distinct DENV Fusion Loop
Authors: Meganck Rita M. , Zhu Deanna , Dong Stephanie , Snoderly-Foster Lisa J. , Dalben Yago R. , Thiono Devina , White Laura J. , DeSilva Aravinda M. , Baric Ralph S. , Tse Longping V. 
Published: March 2023

ABSTRACTA hallmark of Dengue virus (DENV) pathogenesis is the potential for antibody-dependent enhancement, which is associated with deadly DENV secondary infection, complicates the identification of correlates of protection, and negatively impacts the safety and efficacy of DENV vaccines. ADE is linked to antibodies targeting the fusion loop (FL) motif of the envelope protein, which is completely conserved in mosquito-borne flaviviruses and required for viral entry and fusion. In the current study, we utilized saturation mutagenesis and directed evolution to engineer a functional variant with a mutated FL (D2-FL) which is not neutralized by FL-targeting monoclonal antibodies. The FL mutations were combined with our previously evolved prM cleavage site to create a mature version of D2-FL (D2-FLM), which evades both prM- and FL-Abs but retains sensitivity to other type-specific and quaternary cross-reactive (CR) Abs. CR serum from heterotypic (DENV4) infected non-human primates (NHP) showed lower neutralization titers against D2-FL and D2-FLM than isogenic wildtype DENV2 while similar neutralization titers were observed in serum from homotypic (DENV2) infected NHP. We propose D2-FL and D2-FLM as valuable tools to delineate CR Ab subtypes in serum as well as an exciting platform for safer live attenuated DENV vaccines suitable for naïve individuals and children.
A gene network implicated in the joint-muscle pain, brain fog, chronic fatigue, and bowel irregularity of Ehlers-Danlos and “long” COVID19 syndromes
Authors: Wilson Golder N. 
Published: March 2023

AbstractObjectivesCharacterization of tissue laxityanddysautonomia symptoms in Ehlers-Danlos syndrome (EDS) uncovered similarities with those of post-infectious SARS-CoV-2 or long COVID19, prompting detailed comparison of their findings and influencing genes.MethodsHolistic assessment of 1261 EDS outpatients for 120 history-physical findings populated a deidentified database that includes 568 patients with 317 variant genes obtained by commercial NextGen sequencing. Findings were compared to 15 of long COVID19 compiled in an extensive review, genes to 104 associated with COVID19 severity in multiple molecular studies.ResultsFifteen symptoms common to Ehlers-Danlos versus long COVID19 ranged from brain fog (27-80 versus 30-70%), chronic fatigue (38-91; 30-60%), dyspnea (32-52; 29-52%) to irritable bowel (67-89; 14-78%), muscle weakness (22-49; 15-25%), and arthritis (32-94; 15-27%). Genes relevant to EDS included 6 identical to those influencing COVID19 severity (F2,LIFR,NLRP3,STAT1,T1CAM1,TNFRSF13B) and 18 similar includingPOLG-POLD4,SLC6A2-SLC6A20, andNFKB1-NFKB2. Both gene sets had broad genomic distribution, many mitochondrial genes influencing EDS and many involved with immunity-inflammation modifying COVID19 severity. Recurring DNA variants in EDS that merit evaluation in COVID19 resistance include those impacting connective tissue elements--51 inCOL5(joint), 29 inCOL1/2/9/11(bone), 13 inCOL3(vessel), and 18 inFBN1(vessel-heart)--or neural function--93 in mitochondrial DNA, 28 inCOL6/12, 16 inSCN9A/10A/11A, 14 inPOLG, and 11 in genes associated with porphyria.ConclusionsHolistic ascertainment of finding pattern and exome variation in EDS defined tissue laxity, neuromuscular, and autonomic correlations that transcend single abnormalities or types. Implied networks of nuclear and mitochondrial genes are linked to findings like brain fog, fatigue, and frailty in EDS, their similarity to long COVID19 supporting shared therapies for disorders affecting a minimum 0.1% of the global population.
Quantification of measurable residual disease using duplex sequencing in adults with acute myeloid leukemia
Authors: Dillon Laura W. , Higgins Jake , Nasif Hassan , Othus Megan , Beppu Lan , Smith Thomas H. , Schmidt Elizabeth , Valentine Charles C. , Salk Jesse J. , Wood Brent L , Erba Harry P. , Radich Jerald P. , Hourigan Christopher S. 
Published: March 2023

AbstractThe presence of measurable residual disease (MRD) is strongly associated with treatment outcomes in acute myeloid leukemia (AML). Despite the correlation with clinical outcomes, MRD assessment has yet to be standardized or routinely incorporated into clinical trials. Discrepancies have been observed between different techniques for MRD assessment and there remains a need to compare centralized, high-quality multiparametric flow cytometry (MFC) and ultrasensitive next-generation sequencing (NGS) in AML patients with diverse mutational profiles. In 62 patients with AML, aged 18-60, in first complete remission after intensive induction therapy on the randomized phase 3 SWOG-S0106 clinical trial, MRD detection by MFC was compared with a 29 gene panel utilizing duplex sequencing (DS), an NGS method that generates double-stranded consensus sequences to reduce false positive errors. Using DS, detection of a persistent mutation utilizing defined criteria was seen in 22 (35%) patients and was strongly associated with higher rates of relapse (68% vs 13% at year 5; HR, 8.8; 95% CI, 3.2-24.5; P<0.001) and decreased survival (32% vs 82% at year 5; HR, 5.6; 95% CI, 2.3-13.8; P<0.001). MRD as defined by DS strongly outperformed MFC, which was observed in 10 (16%) patients and marginally associated with higher rates of relapse (50% vs 30% at year 5; HR, 2.4; 95% CI, 0.9-6.7; P=0.087) and decreased survival (40% vs 68% at year 5; HR, 2.5; 95% CI, 1.0-6.3; P=0.059). Furthermore, the prognostic significance of DS MRD status at the time of remission was similar on both randomized arms of the trial, predicting S0106 clinical trial outcomes. These findings suggest that DS is a powerful tool that could be used in patient management and for early treatment assessment in clinical trials.
Siglecs in the Porcine Oviduct and Sialylated Ligands on Sperm: Roles in the Formation of the Sperm Reservoir
Authors: Molina Leonardo M. , Pepi Lauren E. , Shajahan Asif , Doungkamchan Kankanit , Azadi Parastoo , McKim Daniel B. , Miller David J. 
Published: March 2023

AbstractDuring mammalian insemination, most of the deposited sperm are lost by retrograde flow or the female reproductive tract’s immune response. Once semen enters the uterus, seminal fluid and sperm elicit leukocyte infiltration that contributes to the elimination of sperm in the uterus. However, unlike the uterus, invading sperm do not trigger a phagocytic response in the oviduct in the absence of dysfunction or disease states. Thus, the oviduct possesses a distinct immunological microenvironment that tolerates sperm while maintaining the capacity to respond to pathogens. It has been suggested that sperm glycocalyx contributes to innate oviductal tolerance, but the cell and molecular mechanisms are not understood. The current investigation focused on the role of sialic acid-containing glycoconjugates on sperm and their potential to elicit innate tolerance via cognate sialic acid-binding immunoglobulin-type lectins (Siglecs) expressed in the oviduct. In this manuscript, we report our discovery of eight Siglecs (Siglecs-1, -2, -3, -5, -10, -11, -14, -15) expressed in the lower pig oviduct, five of which are known for immune inhibitory functions (Siglecs-2, -3, -5, -10, and -11) and how these may play a role in achieving sperm-induced immune suppression in the oviduct microenvironment. Mass spectrometry profiling of porcine sperm revealed the presence of a mixture of α2,3 and α2,6 linked sialic acids with α2,3-linked sialic acids as the dominant linkage. Of the detected glycans, several sialic acid-containing glycoconjugates were identified as potential ligands for Siglecs (among O-linked glycans: NeuAc1GalNAc1, NeuGc1GalNAc1, NeuAc2Gal1GalNAc1; attached to glycolipids: NeuAc2Gal1GalNAc1Gal1Glc1, Fuc1Gal1GalNAc1NeuAc1Gal1Glc1). This is the first report of Siglec expression in the mammalian oviduct and total glycan analysis of porcine sperm. The results of this study reveal the potential for a sperm-sialoglycan and oviductal-Siglec axis that may contribute to the distinct immunophysiology of the oviduct fundamentally required for undisrupted reproduction in mammals.
An efficient, scarless, selection-free technology for phage engineering
Authors: Goren Moran G , Mahata Tridib , Qimron Udi 
Published: March 2023

AbstractMany phage engineering technologies, mainly based on the CRISPR-Cas system, have been recently developed. Here we present a method to genetically engineer theEscherichia coliphages T5, T7, and P1 by adapting a technology, called pORTMAGE, developed for engineering bacterial genomes. The technology comprises ofE. coliharboring a plasmid encoding a potent recombinase and a gene transiently silencing a repair system. Oligonucleotides with the desired phage mutation are electroporated intoE. colifollowed by infection of the target bacteriophage. The high efficiency of this technology, ranging from 1-14% of desired recombinants, allows low-throughput screening for the desired mutant. We demonstrated the use of this technology for single-base substitutions, for deletions of 50 bases, for insertions of 20 bases, and for three different phages. The technology may be adjusted for use across many bacterial and phage strains.
Dual stop codon suppression in mammalian cells with genomically integrated genetic code expansion machinery
Authors: Meineke Birthe , Heimgärtner Johannes , Caridha Rozina , Block Matthias F , Kimler Kyle J , Pires Maria F , Landreh Michael , Elsässer Simon J 
Published: March 2023

ABSTRACTGenetic code expansion via stop codon suppression is a powerful strategy to engineer proteins. Pyrrolysyine-tRNA (tRNAPyl)/pyrrolysyl-tRNA synthetase (PylRS) pairs from methanogenic archaea and engineered bacterial tRNA/aminoacyl-tRNA synthetases (aaRS) pairs are used for site-specific incorporation of noncanonical amino acids (ncAAs) in response to stop codons in mammalian cells. Routinely, ncAA incorporation is achieved by transient expression of the tRNA/aaRS pair leading to heterogeneous suppression. Genomic integration of tRNA/aaRS expression cassettes for more homogenous, adjustable and reproducible levels of protein, containing one or more ncAA, will greatly benefit protein engineering, chemical control and imaging applications in mammalian cells. Here, we demonstrate that piggyBac-mediated genomic integration of archaeal tRNAPyl/PylRS or bacterial tRNA/aaRS pairs, using a modular plasmid design with multi-copy tRNA arrays, allows for homogeneous and efficient, genetically encoded ncAA incorporation in diverse mammalian cell lines. We assess opportunities and limitations of using ncAAs for fluorescent labeling applications in stable cell lines. We explore simultaneous suppression of ochre and opal stop codons and finally incorporate two distinct ncAAs with mutually orthogonal click chemistries for site-specific, dual fluorophore labeling of a cell surface receptor on live mammalian cells.
The mitotic surveillance pathway requires PLK1-dependent 53BP1 displacement from kinetochores
Authors: Burigotto Matteo , Vigorito Vincenza , Mattivi Alessia , Gliech Colin , Ghetti Sabrina , Bisio Alessandra , Lolli Graziano , Holland Andrew J. , Fava Luca L. 
Published: March 2023

Abstract53BP1 acts at the crossroads between DNA repair and p53-mediated stress response. With its interactor USP28, it is part of the mitotic surveillance pathway (MSP), a sensor that monitors the duration of cell division, promoting p53-dependent cell cycle arrest when a critical time threshold is surpassed. 53BP1 dynamically associates with kinetochores, being recruited during prophase, and then undergoing a time-dependent loss of affinity. However, the relevance of this behaviour remains unclear. Here, we identify CENP-F as an interaction partner and kinetochore receptor for 53BP1. By engineering human cells with a CENP-F point mutation, we demonstrate that preventing 53BP1 kinetochore localization does not reduce MSP proficiency. Strikingly, however, preventing the loss of 53BP1 from the kinetochore by inhibiting Polo-like kinase 1 (PLK1) restrains MSP activity, a phenomenon that is abrogated in the CENP-F mutant condition. Taken together, we demonstrate that kinetochore-loaded 53BP1 represents an MSP functionally inhibited state and that PLK1-dependent re-localization of 53BP1 represents an important layer of MSP regulation.
CSR, monitoring cost and firm performance during COVID-19: balancing organizational legitimacy and agency cost
Authors: Yadav Sandeep , Srivastava Jagriti 
Published: March 2023

Purpose
COVID-19 induced uncertainty in the firms’ business transactions, financial markets and product-market competition, causing a severe organizational legitimacy crisis. Using the organizational legitimacy perspective and agency theory, this paper aims to study the relationship between prior corporate social responsibility (CSR) activities, monitoring cost (MC) and firm performance.

Design/methodology/approach
This study uses a quarterly panel (16,924 firm-quarter observations from 61 countries for CSR and 53,345 firm-quarter observations from 55 countries for MC) for 14 quarters from January 2018 to June 2021. This study uses panel fixed-effect regression models to estimate the effect of CSR activities and MC (measured as audit fees) on firm performance during the COVID-19 period.

Findings
This study finds a U-shaped relationship between CSR and firm performance. This relationship is strengthened during COVID-19. In contrast, this study finds an inverted U-shaped relationship between firm MC and firm performance. However, this relationship is weakened during the pandemic.

Originality/value
This study contributes to theory and practice on maintaining organizational legitimacy and reducing agency costs during the pandemic. This study shows that firms’ prior legitimacy-gaining practices, such as CSR activities and MC, provide an opportunity to increase firm value. To balance agency costs and legitimacy benefits, firm managers also need to identify the optimal level of CSR activities and MC.
A longitudinal study investigating changing implicit leadership theory in an Irish business school
Authors: Berkery Elaine , Ryan Nuala F. 
Published: March 2023

Purpose
The purpose of this study is to investigate changing implicit leadership theories (ILTs) within a business student population over a ten-year period.

Design/methodology/approach
Students from the same business student population rated men, women and managers in general, using Schein’s Descriptive Index, first during the academic year 2008–2009 and again in 2018–2019.

Findings
In Sample 1, the authors found multiple ILTs, male students gender typed the managerial role in favour of men, while female students held a more gender egalitarian view of the managerial role. In Sample 2, the authors found evidence that ILTs are starting to converge, as neither the male nor female sample gender typed the managerial role.

Practical implications
These results aid the understanding of the ILTs that these graduating professionals bring into their new full-time organisations.

Originality/value
The analysis of data from the same population using the same measurement at ten-year intervals, along with the findings that male students no longer gender type the managerial role in the most recent round of data collection, are original contributions to the literature.
Text classification in tourism and hospitality – a deep learning perspective
Authors: Liu Jun , Hu Sike , Mehraliyev Fuad , Liu Haolong 
Published: March 2023

Purpose
This study aims to investigate the current state of research using deep learning methods for text classification in the tourism and hospitality field and to propose specific guidelines for future research.

Design/methodology/approach
This study undertakes a qualitative and critical review of studies that use deep learning methods for text classification in research fields of tourism and hospitality and computer science. The data was collected from the Web of Science database and included studies published until February 2022.

Findings
Findings show that current research has mainly focused on text feature classification, text rating classification and text sentiment classification. Most of the deep learning methods used are relatively old, proposed in the 20th century, including feed-forward neural networks and artificial neural networks, among others. Deep learning algorithms proposed in recent years in the field of computer science with better classification performance have not been introduced to tourism and hospitality for large-scale dissemination and use. In addition, most of the data the studies used were from publicly available rating data sets; only two studies manually annotated data collected from online tourism websites.

Practical implications
The applications of deep learning algorithms and data in the tourism and hospitality field are discussed, laying the foundation for future text mining research. The findings also hold implications for managers regarding the use of deep learning in tourism and hospitality. Researchers and practitioners can use methodological frameworks and recommendations proposed in this study to perform more effective classifications such as for quality assessment or service feature extraction purposes.

Originality/value
The paper provides an integrative review of research in text classification using deep learning methods in the tourism and hospitality field, points out newer deep learning methods that are suitable for classification and identifies how to develop different annotated data sets applicable to the field. Furthermore, foundations and directions for future text classification research are set.
Exploring crucial social media marketing factors for improving customer satisfaction and customer loyalty in bed and breakfast sectors in Taiwan
Authors: Nalluri Venkateswarlu , Yang Kai-Fu , Chen Long-Sheng , Yang Tzung-Yu Kevin 
Published: March 2023

Purpose
The Bed and Breakfast (B&B) enterprises generally lack sufficient human resources and time to conduct research on important social media marketing factors for visitors’ satisfaction and visitors’ intentions. Therefore, this study aims to provide crucial social media marketing and factors and service quality elements for improving customer satisfaction and customer loyalty in B&B sectors. This study also provides some recommendations for attracting more visitors and increasing customer satisfaction and customer loyalty through social media.

Design/methodology/approach
First, social media marketing factors and service quality elements were identified through the systematic literature review. Then these identified factors and elements were used to design a survey questionnaire for collecting data. The research data included responses of 64 B&B enterprises and 625 customers. The collected data was analyzed by feature selection approaches including Decision Tree algorithm and Information Gain to identify the key factors for improving customer satisfaction and customer loyalty.

Findings
The findings of this study determined that featured choice is an important social media marketing factor, and assurance is the common service quality element for both B&B enterprises and their customers in terms of satisfaction and loyalty.

Originality/value
This study adds a value to the growing literature on customer satisfaction and loyalty in B&B sectors by exploring key social media marketing factors and service quality elements. The study reveals several implications for theories and practices. The findings hopefully help B&B enterprises better social media marketing with less workforce and budget.
Enhance pick-and-place performance using multimodal interaction in operation environment
Authors: Guo Xinwei , Chen Yang 
Published: March 2023

Purpose
Currently, the vision and depth information obtained from the eye-to-hand RGB-D camera can apply to the reconstruction of the three-dimensional (3D) environment for a robotic operation workspace. The reconstructed 3D space contributes to a symmetrical and equal observation view for robots and humans, which can be considered a digital twin (DT) environment. The purpose of this study is to enhance the robot skill in the physical workspace, although the artificial intelligence (AI) technique has high performance of the robotic operation in the known environments.

Design/methodology/approach
A multimodal interaction framework is proposed in DT operation environments.

Findings
A fast image-based target segmentation technique is combined in the 3D reconstruction of the robotic operation environment from the eye-to-hand camera, thus expediting the 3D DT environment generation without accuracy loss. A multimodal interaction interface is integrated into the DT environment.

Originality/value
The users are supported to operate the virtual objects in the DT environment using speech, mouse and keyboard simultaneously. The humans’ operations in 3D DT virtual space are recorded, and cues are provided for the robot’s operations in practice.
Impact of US-China trade war on Asian economies: neural network multilayer perceptron approach
Authors: Rahman Mohd Nayyer , Iqbal Badar Alam , Rahman Nida 
Published: March 2023

Purpose
This study aims to find the impact of the trade war between the USA and China on Asian economies. Apart from macroeconomic variables associated with trade, this study explicitly creates a trade war scenario and trade war participant dummies. Using the neural network multilayer perceptron, this study checks for the causal linkages between the predictors and target output for the panel of Asian economies and the USA.

Design/methodology/approach
A conceptual model of the after effects of trade war in a quadrant is developed. Variables related to trade and tariffs are included in the study for a panel of 19 Asian economies. The feedforward structure of neural network analysis is used to identify strong and weak predictors of trade war.

Findings
The hidden layers of the multilayer perceptron reveal the inconsistency in linkages for the predictors’ services exports, tariff measures, anti-dumping measures, trade war scenario dummy with gross domestic product. The findings suggest that to curtail the impact of the trade war on Asian economies, predictors with neural evidence must be paid due weightage in policy determination and trade agreements.

Originality/value
The study applies a novel and little explored AI/ML technique of Neural Network analysis with training of 70% observations. The paper will provide opportunity for other researchers to explore techniques of AI/ML in trade studies.