bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antimalarial Drug Resistance Profiling ofPlasmodium falciparumInfections in India Using Next-Generation Sequencing
Authors: Kale Sonal , Uplekar Swapna M. , Bandyopadhyay Nabamita , Rao Pavitra N. , Ali Syed Z. , Sharma S.K. , Tandel Nikunj , Patel Ankita , Singh Ranvir , Dank Aaron , Ravishankaran Sangamithra , Lakshmi Priya G Sri , Asokan Aswin , Eapen Alex , Singh Om. P. , Carlton Jane M. , Mallick Prashant K. 
Published: April 2023

AbstractBackgroundTracking the emergence and spread of antimalarial drug resistance has become critical to sustaining progress towards the control and eventual elimination of malaria in South Asia, especially India.MethodsAn amplicon sequencing protocol was used for high-throughput molecular surveillance of antimalarial drug resistance in a total of 158 isolates at three sites in India: Chennai, Nadiad and Rourkela. Five genes of thePlasmodium falciparumimplicated in antimalarial resistance were investigated here;Pfcrtfor chloroquine resistance,Pfdhfrfor pyrimethamine resistance,Pfdhpsfor sulfadoxine resistance,Pfk13for artemisinin resistance andPfmdr1for resistance to multiple antimalarials.ResultsMutations in the propeller domain of PfK13 were observed in two samples only, however these mutations are not validated for artemisinin resistance. A high proportion of parasites from theP. falciparumdominant site Rourkela showed wild-typePfcrtandPfdhfrhaplotypes, while mutantPfcrtandPfdhfrhaplotypes were fixed at theP. vivaxdominant sites Chennai and Nadiad. The wild-type PfDHPS haplotype was predominant across all study sites. Finally, we observed the largest proportion of suspected multi-clonal infections at Rourkela, which has the highest transmission ofP. falciparumamong our study sites.ConclusionThis is the first simultaneous high-throughput next generation sequencing of five completeP. falciparumgenes from infected patients in India.
Tissue-specific vulnerability to apoptosis in Machado-Joseph disease
Authors: Ferreira Ana F. , Raposo Mafalda , Shaw Emily D. , Ashraf Naila S. , Medeiros Filipa , Brilhante Maria de Fátima , Perkins Matthew , Vasconcelos João , Kay Teresa , do Carmo Costa Maria , Lima Manuela 
Published: April 2023

AbstractMachado-Joseph disease (MJD) is a dominant neurodegenerative disease caused by an expanded CAG repeat in theATXN3gene encoding the ataxin-3 protein. Several cellular processes, including transcription and apoptosis, are disrupted in MJD. To gain further insights into the extent of dysregulation of mitochondrial apoptosis in MJD, and to evaluate if expression alterations of specific apoptosis genes/proteins could be used as transcriptional biomarkers of disease, the levels ofBCL2, BAXandTP53and theBCL2/BAXratio, an indicator of susceptibility to apoptosis, were assessed in blood andpost-mortembrain samples from MJD subjects and MJD transgenic mice and controls. While patients show reduced levels of bloodBCL2transcripts, this measurement displays low accuracy to discriminate patients from matched controls. However, increased levels of bloodBAXtranscripts and decreasedBCL2/BAXratio are associated with earlier onset, indicating a possible association with MJD pathogenesis.Post-mortemMJD brains show increasedBCL2/BAXtranscript ratio in the dentate cerebellar nucleus (DCN) and increased BCL2/BAX insoluble protein ratio in the DCN and pons, suggesting that in these regions, severely affected by degeneration in MJD, cells show signs of apoptosis resistance. Interestingly, a follow-up study of 18 patients further shows that bloodBCL2andTP53transcript levels increase over time in MJD patients. Furthermore, while the similar levels of bloodBCL2, BAX, andTP53transcripts observed in preclinical subjects and controls is mimicked by pre-symptomatic MJD mice, the expression profile of these genes in patient brains is partially replicated by symptomatic MJD mice. Globally, our findings indicate that there is tissue-specific vulnerability to apoptosis in MJD subjects and that this tissue dependent behavior is partially replicated in a MJD mouse model.
Predicting splicing patterns from the transcription factor binding sites in the promoter with deep learning
Authors: Lin Tzu-Chieh , Tsai Cheng-Hung , Shiau Cheng-Kai , Huang Jia-Hsin , Tsai Huai-Kuang 
Published: April 2023

AbstractBackgroundAlternative splicing is a crucial mechanism of post-transcriptional modification responsible for the transcriptome plasticity and proteome diversity of a metazoan cell. Although many splicing regulations around the exon/intron regions have been discovered, the relationship between promoter-bound transcription factors and the downstream alternative splicing remains largely unexplored.ResultsIn this study, we present computational approaches to decipher the regulation relationship connecting the promoter-bound transcription factor binding sites (TFBSs) and the splicing patterns. We curated a fine data set, including DNase I hypersensitive sites sequencing and transcriptome in fifteen human tissues from ENCODE. Specifically, we proposed different representations of TF binding context and splicing patterns to tackle the associations between the promoter and downstream splicing events. Our results demonstrated that the convolutional neural network (CNN) models learned from the TF binding changes in the promoter to predict the splicing pattern changes. Furthermore, through anin silicoperturbation-based analysis of the CNN models, we identified several TFs that considerably reduced the model performance of splicing prediction.ConclusionIn conclusion, our finding highlights the potential role of promoter-bound TFBSs in influencing the regulation of downstream splicing patterns and provides insights for discovering alternative splicing regulations.
Evolutionary trajectories of secondary replicons in multipartite genomes
Authors: Dranenko Natalia O. , Rodina Aleksandra D. , Demenchuk Yaroslav V. , Gelfand Mikhail S. , Bochkareva Olga O. 
Published: April 2023

AbstractMost bacterial genomes have a single chromosome that may be supplemented by smaller, dispensable plasmids. However, approximately 10% of bacteria with completely sequenced genomes, mostly pathogens and plant symbionts, have more than one stable large replicon. Some secondary replicons are species-specific, carrying pathogenicity or symbiotic factors. Other replicons are common on at least the genus level, carry house-keeping genes, and may have a size of several million base pairs.We analyzed the abundance and sizes of large secondary replicons in different groups of bacteria and identified two patterns in the evolution of multipartite genomes. In nine genera of four families,Pseudoalteromonadaceae, Burkholderiaceae, Vibrionaceae, andBrucellaceae, we observed a positive correlation between the sizes of the chromosome and the secondary replicon with the slope in the range of 0.6–1.2. This indicates that in these genera the replicons evolve in a coordinated manner, with comparable rates of gene gain/loss, hence supporting classification of such secondary replicons as ‘chromids’. The second, more common pattern, features gene gains and losses mainly occurring in the primary replicon, yielding a stable size of the secondary replicon. Such secondary replicons are usually present in only a low fraction of the genus’ species. Hence, such replicons behave as ‘megaplasmids’. A mixed situation was observed in symbiotic genera from theRhizobiaceaefamily where the large secondary replicons are of stable size, but present in all species. These results may provide a general framework for understanding the evolution of genome complexity in prokaryotes.SignificanceLarge secondary replicons are observed in representatives of many taxonomic groups of bacteria. Traditionally, they are referred to assecond chromosomes, chromids, ormegaplasmids, with little consistency, in particular because their evolution remains understudied. Here we demonstrate that the sizes of secondary replicons follow two main evolutionary trends: replicons whose size scales linearly with the size of the main chromosome (the suggested termchromids) typically contain numerous essential genes (rRNA, tRNA, ribosomal proteins), while large secondary replicons of stable size (termedmegaplasmids) contain fewer or none such genes.
Boosting BDNF in muscle rescues impaired axonal transport in a mouse model of DI-CMTC peripheral neuropathy
Authors: Rhymes Elena R. , Simkin Rebecca L. , Qu Ji , Villarroel-Campos David , Surana Sunaina , Tong Yao , Shapiro Ryan , Burgess Robert W. , Yang Xiang-Lei , Schiavo Giampietro , Sleigh James N. 
Published: April 2023

AbstractCharcot-Marie-Tooth disease (CMT) is a genetic peripheral neuropathy caused by mutations in many functionally diverse genes. The aminoacyl-tRNA synthetase (ARS) enzymes, which transfer amino acids to partner tRNAs for protein synthesis, represent the largest protein family genetically linked to CMT aetiology, suggesting pathomechanistic commonalities. Dominant intermediate CMT type C (DI-CMTC) is caused byYARS1mutations driving a toxic gain-of-function in the encoded tyrosyl-tRNA synthetase (TyrRS), which is mediated by exposure of consensus neomorphic surfaces through conformational changes of the mutant protein. In this study, we first showed that human DI-CMTC-causing TyrRSE196Kmis-interacts with the extracellular domain of the BDNF receptor TrkB, an aberrant association we have previously characterised for several mutant glycyl-tRNA synthetases linked to CMT type 2D (CMT2D). We then performed temporal neuromuscular assessments ofYarsE196Kmice modelling DI-CMT. We determined thatYarsE196Khomozygotes display a selective, age-dependent impairment inin vivoaxonal transport of neurotrophin-containing signalling endosomes, phenocopying CMT2D mice. This impairment is replicated by injection of recombinant TyrRSE196K, but not TyrRSWT, into muscles of wild-type mice. Augmenting BDNF in DI-CMTC muscles, through injection of recombinant protein or muscle-specific gene therapy, resulted in complete axonal transport correction. Therefore, this work identifies a non-cell autonomous pathomechanism common to ARS-related neuropathies, and highlights the potential of boosting BDNF levels in muscles as a therapeutic strategy.
Glial Draper signaling triggers cross-neuron plasticity in bystander neurons after neuronal cell death
Authors: Wang Yupu , Zhang Ruiling , Huang Sihao , Valverde Parisa Tajalli-Tehrani , Lobb-Rabe Meike , Ashley James , Venkatasubramanian Lalanti , Carrillo Robert A. 
Published: April 2023

AbstractNeuronal cell death and subsequent brain dysfunction are hallmarks of aging and neurodegeneration, but how the nearby healthy neurons (bystanders) respond to the cell death of their neighbors is not fully understood. In theDrosophilalarval neuromuscular system, bystander motor neurons can structurally and functionally compensate for the loss of their neighbors by increasing their axon terminal size and activity. We termed this compensation as cross-neuron plasticity, and in this study, we demonstrated that theDrosophilaengulfment receptor, Draper, and the associated kinase, Shark, are required in glial cells. Surprisingly, overexpression of the Draper-I isoform boosts cross-neuron plasticity, implying that the strength of plasticity correlates with Draper signaling. Synaptic plasticity normally declines as animals age, but in our system, functional cross-neuron plasticity can be induced at different time points, whereas structural cross-neuron plasticity can only be induced at early stages. Our work uncovers a novel role for glial Draper signaling in cross-neuron plasticity that may enhance nervous system function during neurodegeneration and provides insights into how healthy bystander neurons respond to the loss of their neighboring neurons.
Unbiased spectral cytometry immunome characterization predicts COVID-19 mRNA vaccine failure in older adults and patients with lymphoid malignancies
Authors: H-Vazquez Juan , Cal-Sabater Paloma , Arribas-Rodríguez Elisa , Fiz-López Aida , Perez-Segurado Candido , Martín-Muñoz Álvaro , Prado Ángel De , de la Fuente Graciani Ignacio , González Sonia Pérez , Gutiérrez Sara , Tellería Pablo , Novoa Cristina , Rello Silvia Rojo , Garcia-Blesa Antonio , Sedano Rosa , Martínez García Ana María , Pérez Sonsoles Garcinuño , Domínguez-Gil Marta , García Cristina Hernán , Guerra Mª Mercedes , Muñoz-Sánchez Eduardo , Barragan-Pérez Cristina , Morales Soraya Diez , Donnarumma Oriana Casazza , Pollo Daniel Ramos , Solla Natalia Santamarta , Álvarez Manzanares Paula Mª , Bravo Sara , Alonso Cristina García , Nieto Ángel Tesedo , López Moreno Elisabet Carmen , Cabrera Sanz María Esther , Olmedo Sara Borge , de Paula Ortiz Miguel , Asenjo Alberto Castellanos , Alonso Jenifer Gay , Garrote José A. , Arranz Eduardo , Eiros José María , Santiago Fernando Rescalvo , Villegas Carolina Quevedo , Tamayo Eduardo , Orduña Antonio , Dueñas Carlos , Peñarrubia María Jesús , Cuesta-Sancho Sara , Montoya María , Bernardo David 
Published: April 2023

ABSTRACTCOVID-19 affects the population unequally with a higher impact on aged and immunosuppressed people. Hence, we assessed the effect of SARS-CoV-2 vaccination in immune compromised patients (older adults and oncohematologic patients), compared with healthy counterparts. While the acquired humoral and cellular memory did not predict subsequent infection 18 months after full immunization, spectral and computational cytometry revealed several subsets within the CD8+T-cells, B-cells, NK cells, monocytes and CD45RA+CCR7-Tγδ cells differentially expressed in further infected and non-infected individuals not just following immunization, but also prior to that. Of note, up to 7 subsets were found within the CD45RA+CCR7-Tγδ population with some of them being expanded and other decreased in subsequently infected individuals. Moreover, some of these subsets also predicted COVID-induced hospitalization in oncohematologic patients. Therefore, we hereby have identified several cellular subsets that, even before vaccination, strongly related to COVID-19 vulnerability as opposed to the acquisition of cellular and/or humoral memory following vaccination with SARS-CoV- 2 mRNA vaccines.SUMMARYAn in depth and unbiased spectral cytometry characterization of the immune system before and after COVID-19 vaccination can predict not just subsequent PCR-confirmed infection, but also COVID-induced hospitalization in immune compromised patients.
Accountability and music: accounting, emotions and responses to the 1913 concert for Giuseppe Verdi
Authors: Giovannoni Elena , Giorgino Maria Cleofe , Di Pietra Roberto 
Published: April 2023

PurposeThis study aims to explore the engagement between accounting and music in the social and relational construction of accountability. The authors conceive this construction as a dynamic and recursive interplay between the giving of different accounts and the responses that these accounts provoke. The authors investigate the emotional dimension of this interplay, as it is also triggered by music, feeding back into how accountability is constructed and evolves over time.Design/methodology/approachThis study relies upon a historical analysis of archival and secondary sources about the main music concert organized in 1913 by the founder of “Accademia Chigiana”, one of the leading music academies in Italy. The concert celebrated the first centenary of the birth of Giuseppe Verdi, a worldwide famous Italian music composer, and icon of Italian national sentiment.FindingsThis study shows that music and accounting were profoundly intertwined in the social and relational construction of accountability for the 1913 concert. Accountability evolved through different accounts, also linked to music, and the complex emotional reactions these accounts provoked in the audiences, citizens, media and institutions, leading to always further responses and accounts in the ongoing construction of accountability.Originality/valueThis study extends prior literature on the chameleonic nature of accountability, as well as on its relational and emotional dimensions. The study shows that accountability is relationally constructed and evolves over time through the giving of accounts and the emotional reaction they provoke from others, feeding into further responses and accounts of the accountable subject. The authors show how the chameleonic nature of accountability permeates not only the accounts and the relations of accountability but also the subjects giving and demanding the accounts: these subjects change as chameleons through their interactions and emotions, feeding into the dynamic construction of accountability. The authors also show how arts, like music, can participate in the chameleonic nature of accountability and of its subjects, precisely by engaging with their emotional reactions and responses.
Modeling and verification of helicopter roll-on takeoff based on optimal control theory
Authors: Deng JingHui , Chen Jinhe , Wang ZhengZhong 
Published: April 2023

Purpose
The paper aims to establish a comprehensive optimization analysis model for a helicopter roll on the ground and take off based on optimal control method. The trajectory and control of the entire process are studied, and the key factors affecting the helicopter takeoff distance are analyzed.

Design/methodology/approach
First, based on the equivalent stiffness and damping, the landing gear model is established, and a six-degree-of-freedom helicopter model is formed. Then, the simulation of the roll-on takeoff is transformed into a nonlinear optimal control problem (NOCP). Meanwhile, a hybrid single-multiple shooting method-based transcription process is used for discretizing the problem, leading to a finite nonlinear programming model, which is solved by sequential quadratic programming. Finally, the process was calculated and compared with flight test data, which verified the feasibility of the NOCP. The influence of takeoff weight, takeoff power and liftoff airspeed on the takeoff distance of the helicopter was analyzed.

Findings
The results show that the takeoff weight can be increased by 17% under the maximum takeoff power, which is roll-on takeoff at an altitude of 0 m. When the helicopter takes off with the maximum weight at an altitude of 5000 m, the liftoff airspeed should be over 49.2 km/h.

Originality/value
The novelty of this paper lies in the comprehensive consideration of helicopter taxiing and taking-off phases, and the application of optimal control theory to establish a comprehensive analysis model, which can quickly analyze the maximum takeoff weight, takeoff distance, optimal liftoff speed and so on. Meanwhile, the method is verified based on the flight data.
Exploring the economics of conversational search sessions
Authors: Ghosh Souvick , Gogoi Julie , Chua Kristen 
Published: April 2023

PurposeTurn-taking is beneficial to conversational search success, but the increase in turns and time can also increase the cognitive load of the user. Therefore, in this research paper, the authors view conversational search sessions through the lens of economic theory and use the economic models of search to analyze the various costs and benefits of information-seeking interactions.Design/methodology/approachFirst, the authors built a cost-benefit model for conversational search sessions by defining action types and performing an intellectual mapping of actual sessions into sequences of these actions (using thematic analyses). The authors used the hypothesized cost and benefit actions (obtained from the user-system dialogs), along with the number of turns, utterances and time-related parameters, to propose the mathematical model. Next, the authors tested the model empirically by comparing the model scores to the user satisfaction and task success scores (collected through questionnaires). By representing each session as a bag of actions, the authors developed linear regression models to predict task success and user satisfaction.FindingsThrough feature analysis and significance testing, the authors identify the different parameters that contribute significantly to user satisfaction and task success scores. Error analysis shows that the model predicts task success and user satisfaction reasonably well, with the average prediction error being 0.5 for both (on a 5-point scale).Originality/valueThe authors' research is an initial step toward building a mathematical model for predicting user satisfaction and task success in conversational search sessions.
How to do the right thing
Authors: Messer Ron Peter 
Published: April 2023

Purpose
This paper aims to make suggestions for addressing the apparent failure of business schools to communicate good ethical decision-making skills to students studying in postsecondary institutions.

Design/methodology/approach
At the beginning of university management classes, a form is distributed to students outlining a short scenario that requires a course of action. The two questions asked, based on this decision context, are (i) is it ethical to offer bribes to secure construction contracts in countries where this practice is considered an acceptable way of conducting business and (ii) has the student completed an ethics course at the university?

Findings
The scenario described is what occurred at SNC Lavalin, a Canadian construction company that was charged and convicted with offering illegal inducements to foreign officials (in Libya) to secure large government construction contracts. Ethically, the “right” decision would be to not offer bribes; this is because they are illegal when offered both in the Canada and in foreign jurisdictions. The response results to the survey questionnaire showed that 21% of the students thought that bribery was acceptable, if it was a customary business practice in the country where the transaction occurred, and 93% of these students had taken an ethics course. It was interesting to note that almost all the students, who had not taken a business ethics courses, thought that bribery is not acceptable under the circumstances described.

Originality/value
To address the apparent failure to communicate good ethical decision-making skills, this essay suggests that when teaching business ethics, there should a clearer focus on (i) the distinction between morality and ethics; (ii) the problem posed by relativism; and (iii) the reasoning behind ethical standards. This approach is novel in that it makes sense from the perspective of both a business practitioner and university educator.