bluuebunny/crossref_metadata_2025_split huggingface dataset:
RawHash: Enabling Fast and Accurate Real-Time Analysis of Raw Nanopore Signals for Large Genomes
Authors: Firtina Can , Ghiasi Nika Mansouri , Lindegger Joel , Singh Gagandeep , Cavlak Meryem Banu , Mao Haiyu , Mutlu Onur 
Published: January 2023

AbstractNanopore sequencers generate electrical raw signals in real-time while sequencing long genomic strands. These raw signals can be analyzed as they are generated, providing an opportunity for real-time genome analysis. An important feature of nanopore sequencing, Read Until, can eject strands from sequencers without fully sequencing them, which provides opportunities to computationally reduce the sequencing time and cost. However, existing works utilizing Read Until either 1) require powerful computational resources that may not be available for portable sequencers or 2) lack scalability for large genomes, rendering them inaccurate or ineffective.We propose RawHash, the first mechanism that can accurately and efficiently perform real-time analysis of nanopore raw signals for large genomes using a hash-based similarity search. To enable this, RawHash ensures the signals corresponding to the same DNA content lead to the same hash value, regardless of the slight variations in these signals. RawHash achieves an accurate hash-based similarity search via an effective quantization of the raw signals such that signals corresponding to the same DNA content have the same quantized value and, subsequently, the same hash value.We evaluate RawHash on three applications: 1) read mapping, 2) relative abundance estimation, and 3) contamination analysis. Our evaluations show that RawHash is the only tool that can provide high accuracy and high throughput for analyzing large genomes in real-time. When compared to the state-of-the-art techniques, UNCALLED and Sigmap, RawHash provides 1) 25.8× and 3.4× better average throughput and 2) significantly better accuracy for large genomes, respectively. Source code is available athttps://github.com/CMU-SAFARI/RawHash.
TheMedicago truncatulanodule-specific cysteine-rich peptides, NCR343 and NCR-new35 are required for the maintenance of rhizobia in nitrogen-fixing nodules
Authors: Horváth Beatrix , Güngör Berivan , Tóth Mónika , Domonkos Ágota , Ayaydin Ferhan , Saifi Farheen , Chen Yuhui , Biró János Barnabás , Bourge Mickael , Szabó Zoltán , Tóth Zoltán , Chen Rujin , Kaló Péter 
Published: January 2023

SummaryIn the nodules of Inverted Repeat-Lacking Clade legumes, includingM. truncatula, nitrogen-fixing rhizobia undergo terminal differentiation resulting in elongated and endoreduplicated bacteroids specialised for nitrogen fixation. This irreversible transition of rhizobia is mediated by host produced nodule-specific cysteine-rich (NCR) peptides, of which about 700 are encoded in theM. truncatulagenome. Some of these NCR peptides, NCR169, NCR211 and NCR247, are essential for nitrogen-fixing symbiosis.The analysis of bacteroid and symbiotic host cell differentiation revealed that the symbiotic phenotype ofM. truncatulamutants,Mtsym19,Mtsym20and NF-FN9363, were defective likewise in the formerly studiedncrmutants,Mtdnf4-1andMtdnf7-2. The incomplete differentiation of bacteroids triggered premature senescence of rhizobia in the nitrogen fixation zones of mutant nodules.Mtsym19andMtsym20mutants are defective in the same peptide NCR-new35 and the lack ofNCR343is responsible for the ineffective symbiosis of NF-FN9363.The activity ofNCR-new35is significantly lower and limited to the transition zone of the nodule compared with other crucialNCRs. The fluorescent protein-tagged version of NCR343 and NCR-new35 localize to the symbiotic compartment. Our discovery added two additional members to the group ofNCRgenes essential for nitrogen–fixing symbiosis inM. truncatula.
Cognitive and neural bases of salience-driven incidental learning
Authors: Sun Sai , Yu Hongbo , Wang Shuo , Yu Rongjun 
Published: January 2023

AbstractHumans incidentally adjust their behavioral strategies along feedback dimensions even without explicit reasons to do so. How it occurs may depend on stable individual preferences and contextual factors, such as visual salience. We here examined how task-irrelevant visual salience exerts influence on attention and valuation systems that further drives incidental learning. We first established the baseline behavior with no salience emphasis in Exp.1. We then highlighted either the utility or performance dimension of the chosen outcome usingcolorsin Exp.2. We demonstrated that the difference in switching frequency increased along the salient dimension, confirming a strong salience effect. Moreover, the salience effect was abolished when directional information of feedback was removed in Exp.3, suggesting that the observed salience effect is specific to directional feedback. We then generalized our findings usingtextemphasis in Exp.4 and replicated the non-specific salience effects in Exp.5 with simultaneous eye-tracking. The fixation difference between chosen and unchosen values was enhanced along the feedback-specific salient dimension (Exp.4) but kept unchanged when removing directional information (Exp.5). Moreover, behavioral switching correlates with fixation difference, confirming that salience guides attention and further drives incidental learning. Lastly, our neuroimaging study (Exp.6) showed that the striatum subregions encoded salience-based outcome evaluation, while the vmPFC encoded salience-based behavioral adjustments. The connectivity of the vmPFC-ventral striatum accounted for individual differences in utility-driven, whereas the vmPFC-dmPFC for performance-driven behavioral adjustments. Our results provide a neurocognitive account of how task-irrelevant visual salience drives incidental learning by involving attention and the frontal-striatal valuation systems.
4-methylumbelliferone enhances neuroplasticity in the central nervous system: potential oral treatment for SCI
Authors: Irvine Sîan F. , Gigout Sylvain , Štěpánková Kateřina , Varea Noelia Martinez , Urdzíková Lucia Machová , Jendelová Pavla , Kwok Jessica C. F. 
Published: January 2023

AbstractPerineuronal nets (PNNs) are specialised extracellular matrix (ECM) structures that act as key plasticity regulators to the central nervous system. Removal of PNNs using chondroitinase ABC injections restores plasticity, however, there are limitations to its application to due to its enzymatic nature. Here, we explore the use of a small molecule 4-methylumbelliferone (4-MU) as an alternative non-invasive strategy to reversibly remove PNNs and enhance plasticity. Oral administration of 4-MU for 10 days successfully and dynamically removed PNNsin vitro. While 4-MU, preferentially downregulated hyaluronan in the spinal cord, a down-regulation of chondroitin sulphate proteoglycans is also observed in the cortex. Long term administration for 8-weeks administration revealed a partial removal of PNNs, and that injury-induced mechanisms promoting cortical structural plasticity are linked to endogenous modulation of ECM molecules. 4-MU is a new tool to unravel the limits of normal and pathological PNN-mediated plasticity.
Heterologous expression of genes from a heterocystous cyanobacterial endosymbiont highlights organic carbon exchange with its diatom host
Authors: Nieves-Morión Mercedes , Camargo Sergio , Bardi Sepehr , Ruiz María Teresa , Flores Enrique , Foster Rachel A. 
Published: January 2023

ABSTRACTA few genera of diatoms are widespread and thrive in low nutrient waters of the open ocean due to their close association with N2-fixing, filamentous heterocyst-forming cyanobacteria. In one of these symbioses, the symbiont,Richelia euintracellularis, has penetrated the cell envelope of the host,Hemiaulus hauckii, and lives inside the host cytoplasm. How the partners interact, including how the symbiont sustains high rates of N2fixation is unstudied. SinceR. euintracellularishas evaded isolation, heterologous expression of genes in model laboratory organisms was performed to identify the function of proteins from the endosymbiont. Gene complementation of a cyanobacterial invertase mutant and expression of the protein inEscherichia colishowed thatR. euintracellularisHH01 possesses a neutral invertase that splits sucrose producing glucose and fructose. Several solute binding proteins (SBPs) of ABC transporters encoded in the genome ofR. euintracellularisHH01 were expressed inE. coliand their substrates were characterized. The selected SBPs directly linked the host as the source of several substrates, e.g., sugars (sucrose, galactose), amino acids (glutamate, phenylalanine) and a polyamine (spermidine), to support the cyanobacterial symbiont. Finally, transcripts of genes encoding the invertase and SBPs were consistently detected in wild populations ofH. hauckiicollected from multiple stations and depths in the western tropical North Atlantic. Our results support the idea that the diatom host provides the endosymbiotic cyanobacterium with organic carbon to fuel N2fixation. This knowledge is key to understand the physiology of the globally significantH. hauckii-R. euintracellularissymbiosis.SIGNIFICANCEDiatom diazotroph associations (DDAs) between diatoms and N2-fixing bacteria (diazotrophs) have a relevant impact on N2fixation-based production, but the mechanisms underlying their integrated N2and CO2fixation remain unstudied. In the association between the diatomHemiaulus hauckii(host) and the N2-fixing, heterocyst-forming cyanobacteriumRichelia euintracellularis(endosymbiont), the cyanobacterium is uncultivable. Here we used heterologous expression of genes from the endosymbiont to identify the function of proteins involved in the utilization of organic carbon from the host. The importance of these proteins was also confirmed by estimating gene expression in environmental samples. Our results show that the metabolisms of the symbiotic partners are integrated allowing the host to sustain the physiology of the endosymbiont for an important ecological role.
A bacterial tungsten-containing aldehyde oxidoreductase forms an enzymatic decorated protein nanowire
Authors: Winiarska Agnieszka , Ramírez-Amador Fidel , Hege Dominik , Gemmecker Yvonne , Prinz Simone , Hochberg Georg , Heider Johann , Szaleniec Maciej , Schuller Jan Michael 
Published: January 2023

AbstractAldehyde oxidoreductases (AOR) are tungsten enzymes catalysing the oxidation of many different aldehydes to the corresponding carboxylic acids. In contrast to other known AORs, the enzyme from the denitrifying betaproteobacteriumAromatoleum aromaticum(AORAa) consists of three different subunits (AorABC) and utilizes NAD as electron acceptor. Here we reveal that the enzyme forms filaments of repeating AorAB protomers which are capped by a single NAD-binding AorC subunit, based on solving its structure via cryo-electron microscopy. The polyferredoxin-like subunit AorA oligomerizes to an electron-conducting nanowire that is decorated with enzymatically active and W-cofactor (W-co) containing AorB subunits. Our structure further reveals the binding mode of the native substrate benzoate in the AorB active site. This, together with QM:MM-based modelling for the coordination of the W-co, enables formulation of catalytic mechanism hypothesis that paves the way for further engineering of AOR for applications in synthetic biology and biotechnology.
Epigenetic signature of human immune aging: the GESTALT study
Authors: Roy Roshni , Kuo Pei-Lun , Candia Julián , Sarantopoulou Dimitra , Ubaida-Mohien Ceereena , Hernandez Dena , Kaileh Mary , Arepalli Sampath , Singh Amit , Bektas Arsun , Kim Jaekwan , Moore Ann Zenobia , Tanaka Toshiko , McKelvey Julia , Zukley Linda , Nguyen Cuong , Wallace Tonya , Dunn Christopher , Wood William , Piao Yulan , Coletta Christopher , De Supriyo , Sen Jyoti Misra , Weng Nan-ping , Sen Ranjan , Ferrucci Luigi 
Published: January 2023

ABSTRACTAge-associated DNA methylation in blood cells convey information on health status. However, the mechanisms that drive these changes in circulating cells and their relationships to gene regulation are unknown. We identified age-associated DNA methylation sites in six purified blood borne immune cell types (naïve B, naïve CD4+and CD8+T cells, granulocytes, monocytes and NK cells) collected from healthy individuals interspersed over a wide age range. Of the thousand of age-associated sites, only 350 sites were differentially methylated in the same direction in all cell types and validated in an independent longitudinal cohort. Genes close to age-associated hypomethylated sites were enriched for collagen biosynthesis and complement cascade pathways, while genes close to hypermethylated sites mapped to neuronal pathways. In-silico analyses showed that in most cell types, the age-associated hypo- and hypermethylated sites were enriched for ARNT (HIF1β) and REST transcription factor motifs respectively, which are both master regulators of hypoxia response. To conclude, despite spatial heterogeneity, there is a commonality in the putative regulatory role with respect to transcription factor motifs and histone modifications at and around these sites. These features suggest that DNA methylation changes in healthy aging may be adaptive responses to fluctuations of oxygen availability.
Hierarchical clinical decision support for breast cancer care empowered with Bayesian networks
Authors: Alomran Omran , Qiu Robin , Yang Hui 
Published: January 2023

PurposeBreast cancer is a global public health dilemma and the most prevalent cancer in the world. Effective treatment plans improve patient survival rates and well-being. The five-year survival rate is often used to develop treatment selection and survival prediction models. However, unlike other types of cancer, breast cancer patients can have long survival rates. Therefore, the authors propose a novel two-level framework to provide clinical decision support for treatment selection contingent on survival prediction.Design/methodology/approachThe first level classifies patients into different survival periods using machine learning algorithms. The second level has two models with different survival rates (five-year and ten-year). Thus, based on the classification results of the first level, the authors employed Bayesian networks (BNs) to infer the effect of treatment on survival in the second level.FindingsThe authors validated the proposed approach with electronic health record data from the TriNetX Research Network. For the first level, the authors obtained 85% accuracy in survival classification. For the second level, the authors found that the topology of BNs using Causal Minimum Message Length had the highest accuracy and area under the ROC curve for both models. Notably, treatment selection substantially impacted survival rates, implying the two-level approach better aided clinical decision support on treatment selection.Originality/valueThe authors have developed a reference tool for medical practitioners that supports treatment decisions and patient education to identify patient treatment preferences and to enhance patient healthcare.
I can’t always get what I want: low power, service customer (dis)engagement and wellbeing
Authors: Abboud Liliane , Bruce Helen L. , Burton Jamie 
Published: January 2023

Purpose
This paper aims to examine experiences of low customer power in service interactions and the impact of those experiences on customers’ engagement and disengagement towards a firm. It subsequently identifies how such experiences may affect customers’ wellbeing.

Design/methodology/approach
The authors conducted visual elicitation interviews with 30 customers of a range of services. Data were analysed thematically using abductive reasoning.

Findings
Low customer power is influenced by several factors perceived by customers as associated with the firm and/or the context of the customer–firm relationship. Results show that low power drives negative customer engagement and may result in behavioural disengagement. Low customer power, negative engagement and disengagement can have negative implications for customers’ eudaimonic (physical and financial) and hedonic wellbeing.

Research limitations/implications
Future studies might explore specific service contexts and power dynamics across service ecosystems and should further analyse the implications of these relationships on firms’ strategic organisational responses.

Practical implications
Firms should monitor customer power and explore means of enhancing the wellbeing of their customers through strategies designed to increase customer power, thus, reducing negative customer engagement and avoiding detrimental impact on customer wellbeing.

Originality/value
This study reframes discussions on low customer power in relation to firms and its impact on firms and customers. It identifies low customer power as a key variable in the study of customer engagement, disengagement and wellbeing.
How attractive are internship advertisements to prospective applicants? A mixed-method examination through the lens of employer branding
Authors: Plakhotnik Maria S. , Shmaytser Kristina S. , Feofilov Kirill A. 
Published: January 2023

PurposeThe purpose of this study was to investigate attractiveness of internship advertisements to the prospective applicants through the lens of employer branding. By giving attention to internship attractiveness, universities and companies expand current collaborations around internship provision to enhance student internship experiences, satisfaction and employment prospects and to foster long-term sustainability of internship programs.Design/methodology/approachThe study used a mixed-methods design employing a concurrent triangulation strategy. The authors conducted a content analysis of 94 internship listings published in the largest Russian job portal, HeadHunter, and collected surveys from 274 prospective interns.FindingsThe study shows a mismatch between employer branding strategies and prospective interns' perceptions of employer attractiveness. Companies emphasize economic value and visual identity as well as functional attributes, while prospective interns prioritize development value and symbolic attributes. The findings suggest internship advertisements do not appeal to potential applicants.Research limitations/implicationsThe results are limited to business students from specific universities in Russia, so further research is needed to include students with different majors and from other countries. The study is also limited to advertisements available via a large online job portal. A comparative analysis of effectiveness of various communication channels for internship promotion could yield useful results.Practical implicationsCareer center advisors, academic program directors and internship coordinators should work with company leaders, human resources and marketing decision-makers, and recruitment specialists to better understand interns' drivers of attraction and audit the internship advertisements. Employers could use the study results to strengthen recruiting messages and, hence, attractiveness of the employer brand to potential interns.Originality/valueThe study contributes by applying the employer branding theory to an understudied population of interns, hence providing new insights into internships as collaboration between universities and companies. By focusing on internship positions, which differ from full-time permanent positions across many aspects, including the positions' duration, pay, supervision and purpose, the study assists in understanding the distinct drivers of attraction of interns, which are missing from published research on the topic.
Teachers' perceptions of school principals' role in tackling the pandemic crisis
Authors: Kafa Antonios 
Published: January 2023

PurposeThis paper reports the findings of a qualitative study on teachers' perspective about school principals' role during the pandemic in the context of Greece. In particular, information is provided on school principals' communication and leadership aspects in tackling the pandemic crisis as well as the obstacles observed in this particular setting.Design/methodology/approachData were collected through the focus group interview tool and included 19 teachers from primary and secondary education in Greece. Due to the circumstances of the pandemic crisis, the interview process was held using the Zoom software environment. The data collection tools included a common semi-structured interview protocol developed specifically for this study based on the current theoretical sources of school principals' role in tackling the pandemic crisis.FindingsThe findings of this study indicated the important aspects of trust, collaboration, and positive climate, together with school principals' external dimension that included the outreach of the local community, parents, private organizations, etc. during the pandemic crisis. Finally, obstacles connected to the students' lack of technological equipment were also observed and addressed by school principals.Research limitations/implicationsThe findings of this study could not be generalized since the study proceeded with convenience sampling. Furthermore, the data were collected while the world was in lockdown during the second pandemic wave.Originality/valueThis piece of research adds to the empirical aspect of school principals' role during the pandemic crisis from a different perspective and reports that researching school principals' role in tackling crises has grown considerably.
The effect of FDI on domestic entrepreneurship: the case of greenfield investment and cross-border M&A activities
Authors: Nguyen Ngoc Minh 
Published: January 2023

PurposeThe paper examines the impact of foreign direct investment (FDI), either greenfield investment or cross-border mergers and acquisitions (M&As), on domestic entrepreneurship.Design/methodology/approachThis paper uses a panel dataset of 104 countries over ten years from 2006 to 2015 and multiple econometric techniques to control for potential endogeneity bias.FindingsFDI, both in the form of greenfield investment and cross-border M&As, exerts positive spillover that encourages domestic entrepreneurial activities. While the benefit of greenfield investment in entrepreneurship is more pronounced in countries with higher levels of market capacity and institutional support, that of cross-border M&As is not influenced by these factors. On the other hand, human capital is important in promoting the positive effects of both types of FDI, and unless the level of human capital in the host economies reaches a certain threshold, greenfield investment can adversely affect domestic entrepreneurship.Practical implicationsPolicies toward FDI need to focus on promoting the driving forces behind FDI spillover to counteract the potential negative crowding-out effect of FDI.Originality/valueThe paper contributes to the existing literature investigating the impact of FDI on domestic entrepreneurship by distinguishing between the two FDI modes of entry and taking into account the moderating effects of sociopolitical characteristics of the host economies.