bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiparametric MRI Along with Machine Learning Informs on Molecular Underpinnings, Prognosis, and Treatment Response in Pediatric Low-Grade Glioma
Authors: Fathi Kazerooni Anahita , Kraya Adam , Rathi Komal S. , Kim Meen Chul , Vossough Arastoo , Khalili Nastaran , Familiar Ariana , Gandhi Deep , Khalili Neda , Kesherwani Varun , Haldar Debanjan , Anderson Hannah , Jin Run , Mahtabfar Aria , Bagheri Sina , Guo Yiran , Li Qi , Huang Xiaoyan , Zhu Yuankun , Sickler Alex , Lueder Matthew R. , Phul Saksham , Koptyra Mateusz , Storm Phillip B. , Ware Jeffrey B. , Song Yuanquan , Davatzikos Christos , Foster Jessica , Mueller Sabine , Fisher Michael J. , Resnick Adam C. , Nabavizadeh Ali 
Published: April 2024

AbstractIn this study, we present a comprehensive radiogenomic analysis of pediatric low-grade gliomas (pLGGs), combining treatment-naïve multiparametric MRI and RNA sequencing. We identified three immunological clusters using XCell enrichment scores, highlighting an ‘immune-hot’ group correlating with poorer prognosis, suggesting potential benefits from immunotherapies. A radiomic signature predicting immunological profiles showed balanced accuracies of 81.5% and 84.4% across discovery and replication cohorts, respectively. Our clinicoradiomic model predicted progression-free survival with concordance indices of 0.71 and 0.77 in these cohorts, and the clinicoradiomic scores correlated with treatment response (p = 0.001). We also explored germline variants and transcriptomic pathways related to clinicoradiomic risk, identifying those involved in tumor growth and immune responses. This is the first radiogenomic analysis in pLGGs that enhances prognostication by prediction of immunological profiles, assessment of patients’ risk of progression, prediction of treatment response to standard-of-care therapies, and early stratification of patients to identify potential candidates for novel therapies targeting specific pathways.
An efficient gene targeting system using Δku80and functional analysis of Cyp51A inTrichophyton rubrum
Authors: Ishii Masaki , Yamada Tsuyoshi , Ohata Shinya 
Published: April 2024

AbstractTrichophyton rubrumis one of the most frequently isolated fungi in patients with dermatophytosis. Despite its clinical significance, the molecular mechanisms of drug resistance and pathogenicity ofT. rubrumremain to be elucidated because of the lack of genetic tools, such as efficient gene targeting systems. In this study, we generated aT. rubrumstrain that lacks the nonhomologous end-joining-related geneku80(Δku80) and then developed a highly efficient genetic recombination system with gene targeting efficiency that was 46 times higher than that using the wild-type strain. Cyp51A and Cyp51B are 14-α-lanosterol demethylase isozymes inT. rubrumthat promote ergosterol biosynthesis and are the targets of azole antifungal drugs. The expression ofcyp51AmRNA was induced by the addition of the azole antifungal drug efinaconazole, whereas no such induction was detected forcyp51B, suggesting that Cyp51A functions as an azole-responsive Cyp51 isozyme. To explore the contribution of Cyp51A to susceptibility to azole drugs, the neomycin phosphotransferase (nptII) gene cassette was inserted into thecyp51A3′-UTR region of Δku80to destabilize the mRNA ofcyp51A. In this mutant, although the expression level ofcyp51AmRNA was comparable to that of the parent strain, the induction ofcyp51AmRNA expression by efinaconazole was diminished. The minimum inhibitory concentration for several azole drugs of this strain was reduced, suggesting that dermatophyte Cyp51A contributes to the tolerance for azole drugs. These findings suggest that an efficient gene targeting system using Δku80inT. rubrumis applicable for analyzing genes encoding drug targets.Key PointsA novel gene targeting system using Δku80strain was established inT. rubrumCyp51A inT. rubrumresponds to the azole antifungal drug efinaconazoleCyp51A contributes to azole drug tolerance inT. rubrum
Jumbo phages possess independent synthesis and utilization systems of NAD+
Authors: Li Cunyuan , Liu Kaiping , Gu Chengxiang , Li Ming , Zhou Ping , Chen Linxing , Sun Shize , Li Xiaoyue , Wang Limin , Ni Wei , Li Meng , Hu Shengwei 
Published: April 2024

AbstractJumbo phages, phages with genomes >200 kbp, contain some unique genes for successful reproduction in their bacterial hosts. Due to complex and massive genomes analogous to those of small-celled bacteria, how do jumbo phages complete their life cycle remain largely undefined. In this study, we assembled 668 high-quality jumbo phage genomes from over 15 TB of intestinal metagenomic data from 955 samples of five animal species (cow, sheep, pig, horse, and deer). Within them, we obtained a complete genome of 716 kbp in length, which is the largest phage genome so far reported in the gut environments. Interestingly, 174 out of the 668 jumbo phages were found to encode all genes required for synthesis of NAD+by the salvage pathway or Preiss-Handler pathway, referred as NAD-jumbo phage. Besides synthesis genes of NAD+, these NAD-jumbo phages also encode at least 15 types of NAD+-consuming enzyme genes involved in DNA replication, DNA repair, and counterdefense, suggesting that these phages not only have the capacity to synthesize NAD+but also redirect NAD+metabolism towards phage propagation need in hosts. Phylogenetic analysis and environmental survey indicated NAD-jumbo phages are widely present in the Earth’s ecosystems, including the human gut, lakes, salt ponds, mine tailings, and seawater. In summary, this study expands our understanding of the diversity and survival strategies of phages, and in-depth study of the NAD-jumbo phages is crucial for understanding their role in ecological regulation.
Safety of Repeated Low-Level Red-Light Therapy for Myopia: A Systematic Review
Authors: Chen Yanping , Chen Shida , Xiong Ruilin , Yang Shaopeng , Liu Riqian , Zhu Ziyu , Xiang Kaidi , Congdon Nathan , Wang Wei 
Published: April 2024

AbstractTopicExisting evidence for the safety of repeated low-level red-light (RLRL) therapy for myopia control.Clinical relevanceRecent trials show RLRL therapy is effective in the prevention and control of myopia. Establishing its safety profile is necessary prior to widespread clinical implementation.MethodsWe conducted a systematic review (International Prospective Register of Systematic Reviews, CRD42024516676) of articles across seven databases from inception through February 10, 2024, with keywords related to myopia and RLRL therapy. Pooled safety outcomes and risk-to-benefit ratios were reported, and incidence of side effects was compared with other anti-myopia interventions. Quality appraisal was performed using the Cochrane Risk of Bias Tool.ResultsAmong 689 screened articles, 20 studies (2.90%; eleven randomized controlled trials, four non-randomized controlled trials, one post-trial study, one single-arm study, one retrospective study and two case reports of identical patient.; median duration 9 months, longest 24 months) were analysed, encompassing 2,380 participants aged 3-18 years and 1,436 individuals undergoing RLRL therapy. Two case reports described an identical patient with reversible decline in visual acuity and optical coherence tomography (OCT) abnormalities, completely resolved 4 months after treatment cessation. No cases of permanent vision loss were reported. Temporary afterimage was the most common ocular symptom following treatment, resolving within 6 minutes in reported studies. The number needed to harm outweighed the number needed to treat by a ratio of 12.7-21.4 for a person with −3D to −8D myopia treated with RLRL therapy. Incidence of side effects from RLRL was 0.088 per 100 patient-years (95% confidence interval [CI], 0.02-0.50), comparable to spectacles designed for myopia reduction (0.22; 95% CI, 0.09-0.51; P=0.385), and significantly lower than for low-dose atropine (7.32; 95% CI, 6.65-8.05; P<0.001), orthokeratology (20.6; 95% CI, 16.7-25.0; P<0.001), other anti-myopia contact lens (19.3; 95% CI, 17.6-21.1; P<0.001).ConclusionNo irreversible visual function loss or ocular structural damage was identified with RLRL. Fundus photography and OCT before and during therapy, alongside home monitoring of visual acuity and duration of afterimages, are necessary to identify side effects. Further adequately-powered studies of longer duration are needed to evaluate long-term safety of RLRL.
A Pilot-Scale Process for the Extraction of Raffinose-Oligosaccharides from Pulse Protein Concentrates
Authors: Garbers Philipp , Gaber Sara M. , Tyl Catrin , Sahlstrøm Stefan , Knutsen Svein H. , Westereng Bjørge 
Published: April 2024

AbstractPlant protein concentrates have gained popularity in recent years as part of a shift towards healthier and sustainable food production. Their production via dry fractionation is well established and leads to a protein ingredient that is also rich in raffinose family oligosaccharides (RFOs). Although these can cause gut discomfort, they might also serve as a valuable substrate fowr growth of probiotic bacteria or as substrate in other biotechnological applications. By using a process including mildly acidic extraction, separation and sequential filtration, a carbohydrate fraction enriched in RFOs was isolated from peas (48 %) and faba beans (26 %) on a kilogram scale. Simultaneously a fraction with elevated protein concentration (5-6 % increase compared to the starting material) and only minor changes in amino acid composition is produced. This process could serve ingredient manufacturers that seek to reduce RFOs in protein concentrates or to produce RFOs for biotechnological or chemical conversion towards new products. It also has potential to reduce the amount of acid and base compared to protein isolate production through wet fractionation. Furthermore, the whole process was performed with industrially relevant and scalable equipment.Graphic for table of contents
Long-term fasting remodels gut microbial metabolism and host metabolism
Authors: Ducarmon QR , Grundler F , Giannopoulou C , Loumé A , Karcher N , Larralde M , Romano S , MacArthur MR , Mitchell SJ , Wilhelmi de Toledo F , Zeller G , Mesnage R 
Published: April 2024

AbstractLong-term fasting has become a promising research subject for its potential of treating and preventing metabolic diseases. However, little is known about its impact on the functional capacity of the gut microbiome and the combined effect on the serum metabolome. Here, we demonstrate extensive remodelling of the gut microbial ecosystem in humans (n=92) after an average of 9.8 days of fasting (∼250 kcal / day). Fasting transiently affected the relative abundance of the majority of bacterial species (306 decreased and 210 increased out of 772). Species changes could largely be explained by their genomic repertoire of carbohydrate-active enzymes (CAZymes), which were investigated here for the first time. Fasting induced extensive abundance changes in CAZyme families, depleting families with dietary fibre substrates and increasing families with host-derived glycan substrates. Likewise, we observed extensive changes in the serum metabolome, with 382 out of 721 metabolites significantly affected (246 increased and 136 decreased). In-depth metagenome-metabolome co-variation analysis suggestedOscillibacterspecies to be key producers of indole-3-propionic acid, a crucial metabolite for cardiometabolic health. Together, our results provide an unprecedented view on the impact of long-term fasting on gut microbiome composition and function.
Discovery of RNA-Protein Molecular Clamps Using Proteome-Wide Stability Assays
Authors: Goldstein Stanley I. , Fan Alice C. , Wang Zihao , Naineni Sai K. , Cencic Regina , Garcia-Gutierrez Steve B. , Patel Kesha , Huang Sidong , Brown Lauren E. , Emili Andrew , Porco John A. 
Published: April 2024

ABSTRACTUncompetitive inhibition is an effective strategy for suppressing dysregulated enzymes and their substrates, but discovery of suitable ligands depends on often-unavailable structural knowledge and serendipity. Hence, despite surging interest in mass spectrometry-based target identification, proteomic studies of substrate-dependent target engagement remain sparse. Herein, we describe a strategy for the discovery of substrate-dependent ligand binding. Using proteome integral solubility alteration (PISA) assays, we show that simple biochemical additives can enable detection of RNA-protein-small molecule complexes in native cell lysates. We apply our approach to rocaglates, molecules that specifically clamp RNA to eukaryotic translation initiation factor 4A (eIF4A), DEAD-box helicase 3X (DDX3X), and potentially other members of the DEAD-box (DDX) helicase family. To identify unexpected interactions, we used a target class-specific thermal window and compared ATP analog and RNA base dependencies for key rocaglate-DDX interactions. We report and validate novel DDX targets of high-profile rocaglates – including the clinical candidate Zotatifin – using limited proteolysis-mass spectrometry and fluorescence polarization (FP) experiments. We also provide structural insight into divergent DDX3X affinities between synthetic rocaglates. Taken together, our study provides a model for screening uncompetitive inhibitors using a chemical proteomics approach and uncovers actionable DDX clamping targets, clearing a path towards characterization of novel molecular clamps and associated RNA helicases.
Proteomic analysis of the Aggregation Factor from the spongeClathria (Microciona) proliferasuggests an ancient protein domain toolkit for allorecognition in animals
Authors: Ruperti Fabian , Dzieciatkowska Monika , Pankey M. Sabrina , Asensio Cedric S. , Anselmetti Dario , Fernàndez-Busquets Xavier , Nichols Scott A. 
Published: April 2024

AbstractThe discovery that sponges (Porifera) can fully regenerate from aggregates of dissociated cells launched them as one of the earliest experimental models for cell adhesion and allorecognition studies in animals. This process depends on an extracellular glycoprotein complex called the Aggregation Factor (AF). However, our understanding of how animal adhesion and allorecognition mechanisms first evolved is complicated by the fact that the known components of the AF are thought to be unique to sponges. We used label-free quantitative proteomics to identify additional AF components and interacting proteins in the classical modelClathria proliferaand compare them to proteins involved in cell interactions in Bilateria. Our results confirm MAFp3/p4 as the primary components of the AF, but implicate related proteins with calx-beta and wreath domains as additional components. Using AlphaFold, we unveiled close structural similarities of AF components to distant homologs in other animals, previously masked by the stark decay of sequence similarity. The wreath domain, believed to be unique to the AF, was predicted to contain a central beta-sandwich of the same organization as the vWFD domain in extracellular, gel-forming gly-coproteins in other animals. Additionally, we co-purified candidate AF-interacting proteins that share a conserved C-terminus, containing divergent Ig-like and Fn3 domains, a combination also known from IgCAMs. One of these, MAFAP1, may function to link the AF to the surface of cells. Our results highlight the existence of an ancient toolkit of conserved protein domains regulating cell-cell and cell-ECM interactions in all animals, and likely reflect a common origin of cell-adhesion and allorecognition.
The moderating role of individual and social resources in gender effect on entrepreneurial growth aspirations
Authors: Nyakudya Frederick Wedzerai , Mickiewicz Tomasz , Theodorakopoulos Nicholas 
Published: April 2024

PurposeThis study aims to examine how the effect of gender on entrepreneurial growth aspirations is moderated differently by individual resources (human and financial capital) compared to those within the social environment (availability of entrepreneurial knowledge and role models).Design/methodology/approachA multilevel estimator is used to investigate the determinants of growth aspirations of owners-managers of nascent start-ups. The Global Entrepreneurship Monitor database is employed, covering the period 2007–2019, with 99,000 useable cases drawn from 95 countries.FindingsThe results suggest that individual financial resources and human capital have positive effects on entrepreneurial growth aspirations; yet these effects are weaker for female entrepreneurs relative to males. In contrast, the impact of the availability of entrepreneurial social knowledge and role models on their growth aspirations is more positive than for male entrepreneurs.Originality/valueThis study offers a novel insight into entrepreneurial growth ambition, as it utilises a global perspective to scrutinise whether individual and social resources contribute differently to male versus female growth-aspirations, employing a multilevel approach. It also integrates insights from the resource-based view and from the relevant business literature on entrepreneurs’ gender to develop theoretical explanations.
Unveiling buyers’ preferences for privately developed affordable housing: a study in Kolkata, India
Authors: Biswas Sujoy , Mukerji Arjun 
Published: April 2024

Purpose
The purpose of this study is to examine the buyers’ preferences influencing the purchase of privately developed affordable housing in Kolkata and to determine whether unsold houses result from misalignment with these preferences.

Design/methodology/approach
The literature review and user-opinion survey identified 119 independent variables that indicate buyers’ preferences. A questionnaire survey of 383 households in affordable housing units from 32 housing complexes in Kolkata recorded buyers’ preferences and satisfaction against the independent variables grouped under five levels of characteristics. The product weights of variables derived from the rank sum method and percentage satisfaction give the Utility Score. Multivariate regression and univariate linear regressions were conducted to determine the significance of each Level of characteristics and each variable, identifying the significant variables that would affect the sale of affordable houses.

Findings
The multivariate regression analysis has indicated that 68.56% of the variation in the percentage of unsold houses was explained by the five utility scores, which affirms that misalignment with buyers’ preferences significantly affects the sale of privately developed affordable houses. Furthermore, building and neighbourhood-level utility show the highest significance as predictors, while city-level and miscellaneous utility have moderate significance, but housing complex-level utility lacks statistical significance.

Originality/value
This study addresses a research gap in privately developed affordable housing in Kolkata, enhancing understanding of buyer preferences in this segment.
Aggressive CSR strategy and CSR awarding: managerial opportunism versus social activism
Authors: Gerged Ali Meftah , Kuzey Cemil , Uyar Ali , Karaman Abdullah S. 
Published: April 2024

PurposeDespite the extensive body of research on absolute corporate social responsibility (CSR) performance, limited attention has been given to the distinct concepts of optimal and aggressive CSR engagement, as well as their associations with CSR awarding. This study aims to differentiate between optimal and aggressive CSR engagement and examine their relationship with CSR awarding while considering the moderating influence of board characteristics from the perspectives of stakeholder and agency theories.Design/methodology/approachThis empirical analysis draws on an international dataset comprising 43,803 observations from nine sectors across 41 countries. We employ a least squares dummy variable regression approach that accounts for country, industry and year effects to conduct the analysis.FindingsThe results reveal that engagement in aggressive CSR activities beyond the optimal level leads to the generation of a social reputation through CSR awarding. However, the influence of board characteristics on this relationship is significant. Specifically, the presence of a dedicated CSR committee encourages CSR awarding in the context of aggressive CSR engagement. Conversely, board independence constrains the relationship between aggressive CSR engagement and CSR awarding. Notably, board gender diversity does not have a discernible impact on this connection.Practical implicationsOur evidence provides valuable insights to help firms seeking to enhance their social reputation through CSR activities better allocate their resources and avoid unnecessary financial commitments.Originality/valueThis study advances the current understanding by exploring the relationship between aggressive CSR engagement and the recognition of CSR awards. Furthermore, it scrutinises the factors that dictate when such aggressive CSR engagement translates into enhanced social reputation, as evidenced by the attainment of CSR awards.
Managerial rationality, dysfunctional cognition and organizational decision comprehensiveness
Authors: Scholtes Christian , Trif Sabina , Curseu Petru Lucian 
Published: April 2024

PurposeOur study aims to explore the interplay between dysfunctional cognitive schemas and rationality for decision comprehensiveness in organizational strategic decisions.Design/methodology/approachWe used a cross-sectional design in which we evaluated individual decision rationality using an objective decision competence test and dysfunctional cognitive schemas in a sample of 270 managers (145 women with an average age of 41 years old). In addition, we asked managers to rate the decision comprehensiveness of their organization’s strategic decision processes.FindingsOur findings support the detrimental impact of dysfunctional cognition in strategic decision-making in such a way that the association between individual managerial rationality and the comprehensiveness of organizational strategic decisions was positive only when managers reported low dysfunctional cognition, while when managers reported high levels of dysfunctional cognitive schemas, the association between rationality and comprehensiveness was negative.Originality/valueOur study provides initial empirical evidence for the interplay between dysfunctional cognition and managerial rationality in strategic decision processes, and it opens venues for future research to explore the detrimental role of dysfunctional cognitive schemas in strategy processes.
When do we think farther and deeper? Interacting impacts of accountability focus and organizational learning on proactive policy orientation
Authors: Lee Junesoo , Choi Heungsuk 
Published: April 2024

PurposeThis study attempts to answer the question: “how are the two drivers, accountability focus and organizational learning, independently and interactively associated with public agencies’ proactive policy orientation?” The first driver is the multiple accountabilities that public agencies pursue: (1) bureaucratic, (2) legal, (3) professional and (4) political. The second driver is the organizational learning activities of public agencies: (1) socialization, (2) externalization, (3) combination and (4) internalization.Design/methodology/approachFor data, 800 respondents from the public agencies in South Korea were surveyed.FindingsThe analysis provided several findings: (1) the discretionary accountabilities (professional and political) have a greater positive influence on the proactive policy orientation; (2) the conventional accountabilities (legal and bureaucratic) tend to have negative impacts on the proactive policy orientation and (3) among the four types of accountability, legal accountability can be more significantly complemented by organizational learning activities, which can enable both visionary and realistic administration in a balanced manner.Originality/valueThis study provides a unique insight on how organizational proactivity can be ensured through the interactions of organizational accountabilities and organizational learning.