bluuebunny/crossref_metadata_2025_split huggingface dataset:
Convergent evolution of noxious heat sensing by TRPA5, a novel class of heat sensor inRhodnius prolixus
Authors: Liénard Marjorie A. , Baez-Nieto David , Tsai Cheng-Chia , Valencia-Montoya Wendy A. , Werin Balder , Johanson Urban , Lassance Jean-Marc , Pan Jen Q. , Yu Nanfang , Pierce Naomi E. 
Published: May 2023

ABSTRACTAs ectotherms, insects need a multifaceted repertoire of heat-sensitive receptors to monitor environmental temperatures and finely control behavioral thermoregulation. Here, we show thatTRPA5genes, a class of ankyrin transient receptor potential channels lost in genomes of model fruit flies or mosquitoes, are widespread across insect orders, and encode a previously uncharacterized type of heat receptors. We demonstrate that RpTRPA5B, a TRPA5 channel of the triatomine bugRhodnius prolixus(Insect: Hemiptera), primary vector of Chagas disease, forms a homo-tetrameric channel displaying a uniquely high thermosensitivity. The channel biophysical determinants include a large channel activation enthalpy change (72 kcal/mol), a high temperature coefficient (Q10= 25), and temperature-induced currents from 53 °C to 68 °C (T0.5= 58.6 °C)in vitro,similar to mammalian noxious TRPV heat receptors. Monomeric and tetrameric predictions of the ion channel architecture show reliable and conserved structural parallels with fruit fly dTRPA1, albeit depicting structural uniqueness from dTRPA, Painless and Pyrexia in the ankyrin repeat domain and the channel selectivity filter, potential modulator regions of functional characteristics of TRPs. The channel activation response, structural features and ubiquitous sensory tissue expression delineate a potential thermosensitive physiological niche close to that ofPyrexiagenes, lost during the evolution of true bugs. Overall, the finding ofTRPA5genes as a class of temperature-activated receptor illustrates the dynamic evolution of a large family of insect molecular heat detectors, with TRPs as promising multimodal sensory targets for triatomine vector control.
Fibrous finite element modeling of the optic nerve head region
Authors: Islam Mohammad R. , Ji Fengting , Bansal Manik , Hua Yi , Sigal Ian A. 
Published: May 2023

AbstractThe optic nerve head (ONH) region at the posterior pole of the eye is supported by a fibrous structure of collagen fiber bundles. Discerning how the fibrous structure determines the region biomechanics is crucial to understand normal physiology, and the roles of biomechanics on vision loss. The fiber bundles within the ONH structure exhibit complex three-dimensional (3D) organization and continuity across the various tissue components. Computational models of the ONH, however, usually represent collagen fibers in a homogenized fashion without accounting for their continuity across tissues, fibers interacting with each other and other synergistic effects in a fibrous structure. We present a novel fibrous finite element (FFE) model of the ONH that incorporates discrete collagen fiber bundles and their histology-based 3D organization to study ONH biomechanics as a fibrous structure. The FFE model was constructed using polarized light microscopy data of porcine ONH cryosections, representing individual fiber bundles in the sclera, dura and pia maters with beam elements and canal tissues as continuum structures. The FFE model mimics the histological in-plane orientation and width distributions of collagen bundles as well as their continuity across different tissues. Modeling the fiber bundles as linear materials, the FFE model predicts the nonlinear ONH response observed in an inflation experiment from the literature. The model also captures important microstructural mechanisms including fiber interactions and long-range strain transmission among bundles that have not been considered before. The FFE model presented here advances our understanding of the role of fibrous collagen structure in the ONH biomechanics.Statement of SignificanceThe microstructure and mechanics of the optic nerve head (ONH) are central to ocular physiology. Histologically, the ONH region exhibits a complex continuous fibrous structure of collagen bundles. Understanding the role of the fibrous collagen structure on ONH biomechanics requires high-fidelity computational models previously unavailable. We present a novel computational model of the ONH that incorporates histology-based fibrous collagen structure derived from polarized light microscopy images. The model predictions agree with experiments in the literature, and provide insight into important microstructural mechanisms of fibrous tissue biomechanics, such as long-range strain transmission along fiber bundles. Our model can be used to study the microstructural basis of biomechanical damage and the effects of collagen remodeling in glaucoma.
RAmbler:de novogenome assembly of complex repetitive regions
Authors: Chakravarty Sakshar , Logsdon Glennis , Lonardi Stefano 
Published: May 2023

ABSTRACTComplex repetitive regions (also called segmental duplications) in eukaryotic genomes often contain essential functional and regulatory information. Despite remarkable algorithmic progress in genome assembly in the last twenty years, modernde novoassemblers still struggle to accurately reconstruct these highly repetitive regions. When sequenced reads will be long enough to span all repetitive regions, the problem will be solved trivially. However, even the third generation of sequencing technologies on the market cannot yet produce reads that are sufficiently long (and accurate) to span every repetitive region in large eukaryotic genomes.In this work, we introduce a novel algorithm called RAmbler to resolve complex repetitive regions based on high-quality long reads (i.e., PacBio HiFi). We first identify repetitive regions by mapping the HiFi reads to the draft genome assembly and by detecting un-usually high mapping coverage. Then, (i) we compute thek-mers that are expected to occur only once in the genome (i.e., single copyk-mers, which we callunikmers), (ii) we barcode the HiFi reads based on the presence and the location of their unikmers, (iii) we compute an overlap graph solely based on shared barcodes, (iv) we reconstruct the sequence of the repetitive region by traversing the overlap graph.We present an extensive set of experiments comparing the performance of RAmbler against Hifiasm, HiCANU and Verkko on synthetic HiFi reads generated over a wide range of repeat lengths, number of repeats, heterozygosity rates and depth of sequencing (over 140 data sets). Our experimental results indicate that RAmbler outperforms Hifiasm, HiCANU and Verkko on the large majority of the inputs. We also show that RAmbler can resolve several long tandem repeats inArabidopsis thalianausing real HiFi reads.The code for RAmbler is available athttps://github.com/sakshar/rambler.CCS CONCEPTSApplied computing→Bioinformatics;Computational genomics;Molecular sequence analysis; •Theory of computation→ Graph algorithms analysis.
Exploration of an enzyme-product mapping approach for plant-derived diterpene synthases
Authors: Zhao Yalan , Liang Yupeng , Han Xiulin , Wen Mengliang 
Published: May 2023

AbstractPlant-derived diterpene synthases (PdiTPSs) play a critical role in the formation of structurally and functionally diverse diterpenoids. However, the relationship between PdiTPSs and the specificity or promiscuity of their products remains unclear. To explore this correlation, the sequences of 199 functionally characterized PdiTPSs and their corresponding 3D structures were collected and manually corrected. Using this compiled annotated database, the correlations among PdiTPSs sequences, domains, structures and their corresponding products were comprehensively analyzed. However, utilizing sequence similarity network (SSN), phylogenetic trees, and structural topology features alone was insufficient for effective functional classification of PdiTPSs as these methods could not establish a clear mapping between the enzymes and products. Surprisingly, residues verified to play a function through mutagenesis experiments were located within 8Å of the substrate. Aromatic residues surrounding the substrate exhibited selectivity towards its chemical structure. Specifically, tryptophan (W) was preferentially located around the linear substrate geranylgeranyl pyrophosphate (GGPP), while phenylalanine (F) and tyrosine (Y) were preferentially located around the initial cyclized diterpene intermediate. This analysis revealed the functional space of residues surrounding the substrate of PdiTPSs, most of which have not been experimentally explored. These findings provide guidance for screening specific residues for mutation studies to change the catalytic products of PdiTPSs, allowing us to better understand the correlation between PdiTPSs and their products.
RNA tertiary structure modeling with BRiQ potential in CASP15
Authors: Chen Ke , Zhou Yaoqi , Wang Sheng , Xiong Peng 
Published: May 2023

AbstractWe describe the modeling method for RNA tertiary structures employed by team AIchemy_RNA2 in the 15thCritical Assessment of Protein Structure Prediction (CASP15). The method consists of the following steps. Firstly, secondary structure information was derived from various manually-verified sources. With this information, the full length RNA was fragmented into structural motifs. The structures of each motif were predicted and then assembled into the full structure. To reduce the searching conformational space, a RNA structure was organized into an optimal base folding tree. And to further improve the sampling efficiency, the energy surface was smoothed at high temperatures during the Monte Carlo sampling to make it easier to move across the energy barrier. The statistical potential energy function BRiQ was employed during Monte Carlo energy optimization.
A patient-centered view of symptoms, functional impact, and priorities in post-COVID-19 syndrome: Cross-sectional results from the Québec Action Post-COVID cohort
Authors: Mayo Nancy , Brouillette Marie-Josée , Falcone Emilia Liana , Fellows Lesley K 
Published: May 2023

ABSTRACTBackgroundHealth services planning and mechanism-focused research would benefit from a clearer picture of symptoms, impact, and personal priorities in post-COVID-19 syndrome (PCS). This study aimed to provide estimates of the symptom, function, and quality of life (QOL) impact of PCS.MethodsPeople living in Quebec, aged ≥18, were eligible for the Québec Action for/pour le Post-COVID (QAPC) study if they had symptoms lasting more than 4 weeks post-acute SARS-CoV-2 infection, with or without a positive COVID-19 test. Recruitment was through conventional and social media between September 2022-January 2023. Standardized and individualized questionnaires, in French or English, were accessed through an online portal. We report cross-sectional results from the baseline visit of the first 414 participants in this ongoing longitudinal study.ResultsIndividuals spontaneously reported symptoms attributable to an average of 4.5 organ systems. Fatigue was most frequent. Effects on function and quality of life were moderate to severe, and had already persisted for a year or more in the majority. Personal intervention priorities included fatigue and post-exercise malaise, cognitive symptoms, shortness of breath, and impaired taste and smell. Women and men were similar on PCS impact, while older age was associated with lower impact.InterpretationSymptom clusters defined a range of severity, with fatigue a pervasive symptom at all levels of severity. Participants in this study are likely to be representative of those seeking health care for post-COVID-19 symptoms in Canada and the results can inform next steps for clinical, research, and health services planning.
Wastewater surveillance suggests unreported Mpox cases in a low-prevalence area
Authors: Oghuan Jeremiah , Chavarria Carlos , Vanderwal Scout R. , Gitter Anna , Ojaruega Akpevwe Amanda , Monserrat Carlos , Bauer Cici X. , Brown Eric L. , Cregeen Sara Javornik , Deegan Jennifer , Hanson Blake M. , Tisza Michael , Ocaranza Hector I , Balliew John , Maresso Anthony W. , Rios Janelle , Boerwinkle Eric , Mena Kristina D. , Wu Fuqing 
Published: May 2023

AbstractWastewater surveillance has emerged as a valuable tool for monitoring infectious disease agents including SARS-CoV-2 and Mpox virus. However, detecting the Mpox virus in wastewater is particularly challenging due to its relatively low prevalence in the community. In this study, we detected Mpox virus in wastewater from a US-Mexico border city with a low prevalence of Mpox disease during February and March 2023 using real-time PCR assays targeting the C22L, F3L, and F8L genes. An increasing trend of viral concentration was observed 1∼2 weeks earlier than when the Mpox case was reported. Further sequencing and epidemiological analysis provided supporting evidence for unreported Mpox infections in the city. This study showcases a combined approach with multiple molecular assays for efficient detection of the Mpox virus in wastewater in a low-prevalence area. The findings emphasize the value of wastewater surveillance as a timely identification tool for infectious diseases in low-prevalence areas, and the need for heightened vigilance to control the spread of infectious diseases in such settings.
False positive glycopeptide identification via in-FAIMS fragmentation
Authors: Rangel-Angarita Valentina , Mahoney Keira E. , Kwon Catherine , Sarker Raibat , Lucas Taryn M. , Malaker Stacy A. 
Published: May 2023

AbstractHigh-field asymmetric waveform ion mobility spectrometry (FAIMS) separates glycopeptides in the gas phase prior to mass spectrometry (MS) analysis, thus offering the potential to analyze glycopeptides without prior enrichment. Several studies have demonstrated the ability of FAIMS to enhance glycopeptide detection but have primarily focused on N-glycosylation. Here, we evaluated FAIMS for O-glycoprotein and mucin-domain glycoprotein analysis using samples of varying complexity. We demonstrated that FAIMS was useful in increasingly complex samples, as it allowed for the identification of more glycosylated species. However, during our analyses, we observed a phenomenon called “in FAIMS fragmentation” (IFF) akin to in source fragmentation but occurring during FAIMS separation. FAIMS experiments showed a 2-5-fold increase in spectral matches from IFF compared to control experiments. These results were also replicated in previously published data, indicating that this is likely a systemic occurrence when using FAIMS. Our study highlights that although there are potential benefits to using FAIMS separation, caution must be exercised in data analysis because of prevalent IFF, which may limit its applicability in the broader field of O-glycoproteomics.Graphical abstract
A moderated mediation model of smart-device use: work–family conflict and well-being by age
Authors: Haar Jarrod , Wilkinson Simon 
Published: May 2023

PurposeSmart device use for work during family time is a growing issue of concern and is likely exacerbated by the COVID-19 pandemic. The authors test a broad range of well-being outcomes (job anxiety, job depression and insomnia) to extend the literature. Work–family conflict was included as a mediator with age as a moderator.Design/methodology/approachThe study uses representative data from 422 New Zealand employees across a wide range of occupations, sectors, and industries from late 2020. Confirmatory factor analysis (CFA) of the data was used and moderated mediation analysis was conducted.FindingsOverall, hypotheses were supported, with mWork positively influencing work–family and family–work conflict, and all well-being outcomes. Work–family and family–work conflict acted as mediators and age interacted with mWork leading to more conflict for older workers. Finally, moderated mediation effects were supported with age acting as a boundary condition, whereby the indirect effect of mWork on well-being outcomes increases as age increases.Research limitations/implicationsThe findings highlight the danger of using mobile devices to work in family time and highlight the additional risks for older workers.Originality/valueThe mWork literature has a limited focus on well-being outcomes, and the New Zealand data provides insights from a largely underrepresented population in the literature. Further, the use of age as a moderator of mWork towards well-being outcomes provides further originality.
The effect of political connections and governance on credit ratings: substitution versus complementary view: case of Tunisian firm
Authors: Bouaine Wided , Alaya Karima , Slim Chokri 
Published: May 2023

PurposeThe objective of this paper is to study the impact of political connection and governance on credit rating and whether there is a substitution or complementary relationship between them.Design/methodology/approachIn order to achieve the objective, a succession of eight ordered probit regressions has been carried out. Moderating variables between the political connection and governance characteristics were introduced. The whole population is taken as a sample, i.e., 27 Tunisian companies that are evaluated by FITSH NORTH AFRICA agencies over a period of 10 years (2009–2018).FindingsThe outcomes are mixed. They show that the political connection does not always influence credit rating; the size and board independence always improves credit rating; the duality between the functions affects credit rating; whereas the majorities’ proportion does not influence credit rating; and a substitution between the political connection and the governance characteristics is validated.Research limitations/implicationsLike any other research, our results are factors of our measures and variable choice and depends heavily on the how these variables were conceived. Also, although our number of observations responds to the statistical result generalization requirements, our sample remains relatively narrow with 27 companies only.Practical implicationsIn practice, the research will allow investors to have a better vision upon the future of their investments based on whether to develop their governance system or promote political networking. It will also prompt lenders to look beyond ratings and consider factors such as political connections to make a rational judgment on their future placements.Social implicationsThis study leads us to find various solutions: the establishment of credit agencies that take into consideration all the data of all the operators taken as a whole (bank, leasing company, and factoring). It encourages the reorganization of the Tunisian banking sector through mergers for example.Originality/valueThis study is a pioneer in the credit rating field in Tunisia, where the source of debt financing is the most used by all enterprises across all sectors. This study extends the literature of political connection effectiveness, independent directors, board size, in improving corporate performance and credit rating.
An analysis of comment letters on a new, stand-alone standard for audits of less complex entities’ financial statements
Authors: Haapamäki Elina Elisabet , Mäki Juha 
Published: May 2023

PurposeThe objective of this paper is to extend the debate on audit quality in the less complex entity (LCE) context by analyzing comment letters submitted to the International Auditing and Assurance Standards Board (IAASB). The IAASB has drafted a new, stand-alone standard for audits of LCEs’ financial statements.Design/methodology/approachThe Gioia method is utilized to conduct the qualitative analysis. This enables the material to shine and provide a comprehensive picture of the important aspects of the comment letters about the International Standard on Auditing (ISA) for LCEs. A content analysis of the 145 comment letters is conducted to identify the extent of the support for and the arguments against the new, stand-alone draft standard for audits of LCEs’ financial statements. In addition, this study considers how the comment letters describe the respondents’ views on audit quality in relation to the new standard. Finally, the tone of the comment letters and audit quality arguments is investigated.FindingsThe findings provide a useful framework of the most frequently used arguments supporting and opposing the ISA for LCEs. Within the themes identified, a wide variety of issues and concerns are discussed. The results reveal that the arguments in the comment letters are contradictory. For instance, when discussing audit quality, those interest groups that perceived many positive opportunities in the adoption of the ISA for LCEs thought that the audit quality would increase. Conversely, those interest groups that were skeptical about the success of the ISA for LCEs argued that the audit quality could be compromised by the general prejudice that the ISA for LCEs might be perceived as a lower-quality audit with fewer procedures.Originality/valueThis paper is, to the best of the authors’ knowledge, the first to examine the content of comment letters in the context of a new, stand-alone standard for audits of LCEs. The international audience can utilize the results in the context of the widely discussed issue of reducing LCEs’ auditing obligations. This study aims to contribute to the two streams of accounting literature concerning audit quality and political lobbying.
Attitude, repurchase intention and brand loyalty toward halal cosmetics
Authors: Hussain Khalil , Fayyaz Muhammad Shahzeb , Shamim Amjad , Abbasi Amir Zaib , Malik Sana Jawed , Abid Muhammad Farrukh 
Published: May 2023

Purpose
This study aims to investigate consumer brand loyalty toward halal cosmetics using the theory of planned behavior through repurchase intention, which is primarily relying on the consumer’s attitude toward halal cosmetics. Important predictors such as trust on halal cosmetics, quality of halal cosmetics and religious beliefs of millennial Muslim female consumers shape consumer attitude.

Design/methodology/approach
The present study used the quantitative research design and deductive approach to collect the data from 275 halal cosmetics users in Pakistan by using a judgmental sampling approach.

Findings
Findings of the study provide useful insights for both theory and practice. The results support product quality, religious belief and trust on halal cosmetics as predictors of consumer’s attitude toward halal cosmetics that further develop consumers’ repurchase intention, which in turn enhances their overall brand loyalty. Besides, the findings also show that consumer repurchase intention has a mediating effect between consumer attitude toward halal cosmetics and consumer brand loyalty.

Practical implications
The current study helps in advancing practitioners’ understanding of female consumers’ brand loyalty in the halal cosmetics context. This study is considered to be greatly helpful for managers to gain knowledge about how repurchase intention and brand loyalty of millennial Muslim female consumers can be developed in the halal cosmetics segment, especially in the case of Pakistan.

Originality/value
Brand loyalty has been investigated by previous studies through different predictors and antecedents. This study contributes to the literature of brand loyalty by empirically examining and validating the different antecedents of consumer attitude that are accountable for creating consumer brand loyalty in the domain of halal cosmetics within the Pakistani cultural context. The current study also enhances the previous scholarly understanding on halal cosmetics by investigating the mediating role of consumer repurchase intention of halal cosmetics that further extends the discussion for both theory and practice.