bluuebunny/crossref_metadata_2025_split huggingface dataset:
Temporal integration by multi‐level regularities fosters the emergence of dynamic conscious experience
Authors: Hu Ruichen , Li Shuo , Yuan Peijun , Wang Ying , Jiang Yi 
Published: January 2024

AbstractThe relationship between integration and awareness is central to contemporary theories and research on consciousness. Here, we investigated whether and how information integration over time, by incorporating the underlying regularities, contributes to our awareness of the dynamic world. Using binocular rivalry, we demonstrated that structured visual streams, constituted by shape, motion, or idiom sequences containing perceptual‐ or semantic‐level regularities, predominated over their nonstructured but otherwise matched counterparts in the competition for visual awareness. Despite the apparent resemblance, a substantial dissociation of the observed rivalry advantages emerged between perceptual‐ and semantic‐level regularities. These effects stem from nonconscious and conscious temporal integration processes, respectively, with the former but not the latter being vulnerable to perturbations in the spatiotemporal integration window. These findings corroborate the essential role of structure‐guided information integration in visual awareness and highlight a multi‐level mechanism where temporal integration by perceptually and semantically defined regularities fosters the emergence of continuous conscious experience.
Patients with a high defibrillation threshold: Approaches to management
Authors: Vidal Margenat Alejandro , Zedan Ahmed , Schubert Scott , Gopani Srushti , Hariharan Ramesh 
Published: January 2024

AbstractImplantable cardioverter‐defibrillators (ICDs) have revolutionized the prognosis for patients at elevated risk of ventricular tachyarrhythmias. For safety, defibrillation should be effective with a minimum of 10 J below the device's maximum energy. While modern ICDs rarely deliver ineffective shocks in primary prevention, the surge in managing severe heart failure patients has led to an increased number of patients with high defibrillation thresholds (DFTs). This article elucidates the potential causes of high DFT, including clinical factors, lead and device placement, the presence of a Left Ventricular Assist Device (LVAD), prolonged ventricular arrhythmias, shock vectors, waveform tilt, medications, and manufacturer‐specific options. We also detail management strategies, highlighting alternative shock coil placements, practical recommendations, and case studies from our institution. Our management algorithm suggests addressing preventable causes, re‐evaluating coil positions, considering non‐invasive system modifications, upgrading to a higher‐capacity device, and adding extra coil(s).
Endo‐1,4‐beta‐xylanase 1 (MoXYL1) secreted by Magnaporthe oryzae triggers defense responses and induces cell death in rice
Authors: Lee Gi Hyun , Min Cheol Woo , Yoo Ju Soon , Jang Jeong Woo , Yoon Jinmi , Cho Lae‐Hyeon , Wang Yiming , Jeon Jong‐Seong , Gupta Ravi , Kim Sun Tae 
Published: January 2024

AbstractThe rice blast fungus Magnaporthe oryzae devastates cultivated rice (Oryza sativa L.), causing extensive crop losses. Despite being a major pathogen, information on this pathosystem, especially on the proteins associated with fungal pathogenicity and host defense response, is relatively scarce. Utilizing liquid chromatography‐mass spectrometry (LC–MS/MS), we identified 123 in planta‐secreted M. oryzae proteins in rice leaves and screened for their cell death‐inducing activity. Biochemical characterization of these M. oryzae proteins revealed an endo‐1,4‐beta‐xylanase (MoXYL1), which induces cell death in Nicotiana benthamiana leaves and H2O2 accumulation in rice suspension‐cultured cells. Transgenic rice plants (PDUF26::MoXYL1) expressing MoXYL1 driven by rice DOMAIN OF UNKNOWN FUNCTION PROTEIN 26 (DUF26) promoter enhanced expression of pathogen‐responsive and hormone‐related genes, and resistance to the M. oryzae and Cochliobolus miyabeanus. Data‐independent acquisition (DIA) MS‐based proteomics of wild‐type and PDUF26::MoXYL1 rice revealed 1,833 significantly modulated rice proteins upon M. oryzae infection. Among these, 219 proteins showed a significant increased abundance exclusively in PDUF26::MoXYL1 transgenic rice, while 410 proteins showed increased abundance in both wild‐type and PDUF26::MoXYL1. Notably, xylanase inhibitor proteins, pathogenesis‐related proteins, and other proteins associated with jasmonic acid biosynthesis exhibited increased abundance in response to M. oryzae. Based on these results, we proposed a putative signaling network induced by MoXYL1 and M. oryzae. In summary, our findings highlight the crucial role of MoXYL1 in inducing rice defense and in potentially enhancing rice disease resistance against fungal pathogens.
ABA‐induced interplant drought cuing
Authors: Falik Omer , Kersting Lennart , Novoplansky Ariel 
Published: January 2024

AbstractPlants possess the ability to detect, integrate, and react to myriad signals and cues regarding imminent challenges and opportunities. In this study, we investigated whether unstressed plants can adaptively respond to cues emitted by neighbouring plants treated with abscisic acid (ABA) and if they can subsequently induce adaptive responses in additional unstressed neighbours. Triplets of split‐root Pisum sativum plants were grown in rows. The findings reveal that, under drought conditions, cues from ABA‐treated plants enhanced the survival of both immediately adjacent target plants and more distantly located relayed target plants. However, this cueing adversely impacted the performance of plants growing under sufficient water availability. These findings hold potential implications for our understanding of the role of interplant communication in plant interactions, as well as its effects on the survival and performance of plants in both natural and agricultural settings.
A framework for date palm (Phoenix dactylifera L.) tissue regeneration and stable transformation
Authors: Zhang Yasha , Patankar Himanshu , Aljedaani Fatima , Blilou Ikram 
Published: January 2024

AbstractThe date palm is a resilient, socioeconomically valuable desert fruit tree renowned for its heat, drought, and salinity tolerance. Date palm fruits are rich in nutrients and antioxidants, and their beneficial health properties can mitigate current and future food security challenges. However, it is challenging to improve date palm production through conventional breeding methods due to its slow growth. Date palm seeds do not produce true‐to‐type progeny, and commercial propagation relies on direct organogenesis from maternal tissue. Consequently, numerous economically important and valuable cultivars are lost due to tissue recalcitrance and challenges in inducing cell dedifferentiation and regeneration. Moreover, genetic engineering of date palms is currently impossible due to the lack of a stable genetic transformation protocol. This hampers the development of genetic resources in date palms.This study established a tissue culture pipeline and a genetic transformation protocol for various commercially important date palm cultivars. We used the non‐invasive visual reporter RUBY and four morphogenic regulators to validate and improve date palm transformation potential. We found that the date palm BABY‐BOOM (PdBBM) and the WOUND INDUCED DEDIFFERENTIATION (PdWIND1) enhanced transformation efficacy. We show that PdBBM can induce embryogenesis in hormone‐free media and regenerate roots and shoots in recalcitrant varieties. On the other hand, PdWIND1 maintained embryogenic cells in their undifferentiated state. Our study provides a foundation for genetically improving date palms and a potential solution for preserving economically valuable varieties.
‘Rules of engagement’: Does competition drive engagement in faculty development
Authors: Buckley Emily , Cooke John , Whelton Helen , Barrett Aileen 
Published: January 2024

AbstractIntroductionFaculty development (FD) is integral to the implementation of educational programmes. However, attracting new faculty is challenging. Competition is a motivator for learning at an undergraduate level; however, incorporating competition to engage faculty in continued FD has not been explored. In the context of a new strategy to embed in situ simulation in postgraduate education across our healthcare group, and drawing on motivational theory, we asked ‘does competition drive engagement in new FD initiatives?’MethodsWe conducted semi‐structured interviews with nine healthcare professionals (HCPs) who had participated in an in situ simulation ‘SimStars’ competition. Guided by thematic analysis and borrowing from constructivist grounded theory, we explored participants' motivations for entering a competition, their experiences of competition throughout their education and how this process impacted on their engagement in FD.ResultsThree overarching concepts arose and challenged our understanding of the role of competition as a motivator: (1) ‘Competition is a necessary evil’; (2) ‘It really is the taking part that counts’; and (3) ‘Teamwork makes the dream work’. In contrast to previously published work, our results suggest participants view competition negatively and as a means to career progression. However, the opportunity to work as part of an (interprofessional) team towards a goal, and to develop a new skill (i.e. the process), was more motivating for participants than ‘winning’ a competition.ConclusionCompetition may not provide a motivation for HCPs to engage in FD and may be a barrier. Providing collaboration opportunities, faculty coaching and the chance to develop new skills could enhance engagement.
Green Revolution dwarfing Rht genes negatively affected wheat floral traits related to cross‐pollination efficiency
Authors: Schierenbeck Matías , Alqudah Ahmad M. , Lantos Edit , Avogadro Evangelina G. , Simón María Rosa , Börner Andreas 
Published: January 2024

SUMMARYHybrid breeding is a promising strategy to quickly improve wheat yield and stability. Due to the usefulness of the Rht ‘Green Revolution’ dwarfing alleles, it is important to gain a better understanding of their impact on traits related to hybrid development. Traits associated with cross‐pollination efficiency were studied using Near Isogenic Lines carrying the different sets of alleles in Rht genes: Rht1 (semi‐dwarf), Rht2 (semi‐dwarf), Rht1 + 2 (dwarf), Rht3 (extreme dwarf), Rht2 + 3 (extreme dwarf), and rht (tall) during four growing seasons. Results showed that the extreme dwarfing alleles Rht2 + 3, Rht3, and Rht1 + 2 presented the greatest effects in all the traits analyzed. Plant height showed reductions up to 64% (Rht2 + 3) compared to rht. Decreases up to 20.2% in anther length and 33% in filament length (Rht2 + 3) were observed. Anthers extrusion decreased from 40% (rht) to 20% (Rht1 and Rht2), 11% (Rht3), 8.3% (Rht1 + 2), and 6.5% (Rht2 + 3). Positive correlations were detected between plant height and anther extrusion, anther, and anther filament lengths, suggesting the negative effect of dwarfing alleles. Moreover, the magnitude of these negative impacts depends on the combination of the alleles: Rht2 + 3 > Rht3/Rht1 + 2 > Rht2/Rht1 > rht (tall). Reductions were consistent across genotypes and environments with interactions due to magnitude effects. Our results indicate that Rht alleles are involved in multiple traits of interest for hybrid wheat production and the need to select alternative sources for reduced height/lodging resistance for hybrid breeding programs.
Iteration of Cox rings of klt singularities
Authors: Braun Lukas , Moraga Joaquín 
Published: January 2024

AbstractIn this article, we study the iteration of Cox rings of klt singularities (and Fano varieties) from a topological perspective. Given a klt singularity , we define the iteration of Cox rings of . The first result of this article is that the iteration of Cox rings of a klt singularity stabilizes for large enough. The second result is a boundedness one, we prove that for an ‐dimensional klt singularity , the iteration of Cox rings stabilizes for , where only depends on . Then, we use Cox rings to establish the existence of a simply connected factorial canonical (or scfc) cover of a klt singularity, with general fiber being an extension of a finite group by an algebraic torus. The scfc cover generalizes both the universal cover and the iteration of Cox rings. We prove that the scfc cover dominates any sequence of quasi‐étale finite covers and reductive abelian quasi‐torsors of the singularity. We characterize when the iteration of Cox rings is smooth and when the scfc cover is smooth. We also characterize when the spectrum of the iteration coincides with the scfc cover. Finally, we give a complete description of the regional fundamental group, the iteration of Cox rings, and the scfc cover of klt singularities of complexity one. Analogous versions of all our theorems are also proved for Fano‐type morphisms. To extend the results to this setting, we show that the Jordan property holds for the regional fundamental group of Fano‐type morphisms.
Improved Design of an Orthogonal-Axis-Type Precession Motion Ball Reducer
Authors: Terada Hidetsugu , Makino Koji , Wada Yuma , Nagai Takeshi 
Published: January 2024

Abstract
To realize a no-backlash reducer for a small-size orthogonal-axis output, a novel design of a precession motion ball reducer is proposed. This reducer consists of a precession-motion-generating section, a motion direction converting section of the precession motion, and a reduced output-generating section. To avoid cutting tool interference, two types of distorted spatial circular grooves are located on the outer spherical surface of a precession rotor. Furthermore, the grooves of the reduced rotation generating section are profiled on the spherical surface at the output side of the precession motion rotor, which is different from the previous precession ball reducer. In this research, the equations for the groove loci of the precession motion generation, motion direction conversion, and reduced-rotation generation, which are located on the outer spherical surfaces, are proposed. The output rotating direction can be determined using the relationship between the input and output rotation angles of the precession motion direction converting groove. The prototype reducer is confirmed to smoothly rotate. Furthermore, at the hysteresis loss characteristic test, that is better than the backlash characteristic of a general orthogonal-axis output-type speed reducer with bevel gears.
“Deoxy” to be or “Desoxy” not to be—a century-old tale in the history of DNA nomenclature
Authors: Sharma Gaurav , Chodvadiya Jaimin , Malik Indranil 
Published: January 2024

ABSTRACT

This commentary discusses a comprehensive history of the first-ever use of pertinent words directly related to DNA, such as desoxyribose, deoxyribose, desoxyribonucleic acid, and deoxyribonucleic acid. With almost 100 years of the identification and nomenclature of desoxyribose sugar and desoxyribonucleic acid, the term “desoxy” continues to see limited use. We hope that whenever young researchers come across the sporadic occurrence of “desoxy” in any published text, they will not consider it a mistake.
Inducing vulnerability to InhA inhibition restores isoniazid susceptibility in drug-resistant
Mycobacterium tuberculosis
Authors: Harrison Gregory A. , Wang Erin R. , Cho Kevin , Mreyoud Yassin , Sarkar Souvik , Almqvist Fredrik , Patti Gary J. , Stallings Christina L. 
Published: January 2024

ABSTRACT

Of the approximately 10 million cases of
Mycobacterium tuberculosis
(
Mtb
) infections each year, over 10% are resistant to the frontline antibiotic isoniazid (INH). INH resistance is predominantly caused by mutations that decrease the activity of the bacterial enzyme KatG, which mediates the conversion of the pro-drug INH to its active form INH-NAD. We previously discovered an inhibitor of
Mtb
respiration, C10, that enhances the bactericidal activity of INH, prevents the emergence of INH-resistant mutants, and re-sensitizes a collection of INH-resistant mutants to INH through an unknown mechanism. To investigate the mechanism of action of C10, we exploited the toxicity of high concentrations of C10 to select for resistant mutants. We discovered two mutations that confer resistance to the disruption of energy metabolism and allow for the growth of
Mtb
in high C10 concentrations, indicating that growth inhibition by C10 is associated with inhibition of respiration. Using these mutants as well as direct inhibitors of the
Mtb
electron transport chain, we provide evidence that inhibition of energy metabolism by C10 is neither sufficient nor necessary to potentiate killing by INH. Instead, we find that C10 acts downstream of INH-NAD synthesis, causing
Mtb
to become particularly sensitive to inhibition of the INH-NAD target, InhA, without changing the concentration of INH-NAD or the activity of InhA, the two predominant mechanisms of potentiating INH. Our studies revealed that there exists a vulnerability in
Mtb
that can be exploited to render
Mtb
sensitive to otherwise subinhibitory concentrations of InhA inhibitor.

IMPORTANCE

Isoniazid (INH) is a critical frontline antibiotic to treat
Mycobacterium tuberculosis
(
Mtb
) infections. INH efficacy is limited by its suboptimal penetration of the
Mtb
-containing lesion and by the prevalence of clinical INH resistance. We previously discovered a compound, C10, that enhances the bactericidal activity of INH, prevents the emergence of INH-resistant mutants, and re-sensitizes a set of INH-resistant mutants to INH. Resistance is typically mediated by
katG
mutations that decrease the activation of INH, which is required for INH to inhibit the essential enzyme InhA. Our current work demonstrates that C10 re-sensitizes INH-resistant
katG
-hypomorphs without enhancing the activation of INH. We furthermore show that C10 causes
Mtb
to become particularly vulnerable to InhA inhibition without compromising InhA activity on its own. Therefore, C10 represents a novel strategy to curtail the development of INH resistance and to sensitize
Mtb
to sub-lethal doses of INH, such as those achieved at the infection site.
Draft genomes of two phylotype I and II
Ralstonia solanacearum
species complex (RSSC) isolates causing bacterial wilt in tomato plants from Costa Rica
Authors: Galiano-Murillo Fiorella , Salas-Lara Vidal , Echandi Carlos , Brenes-Guillén Laura , Uribe-Lorío Lorena 
Published: January 2024

ABSTRACT

Bacteria from RSSC hold agricultural significance as they are the causal agents of bacterial wilt. Here, we report the draft genomes of two bacteria extracted from vascular tissues of infected tomato plants. Isolate RALF-MA was classified as
Ralstonia pseudosolanacearum
(phylotype I) and RALSA-MA as
Ralstonia solanacearum
(phylotype II).
Improving gene set enrichment analysis (GSEA) by using regulation directionality
Authors: Wang Biwen , van der Kloet Frans , Kes Mariah B. M. J. , Luirink Joen , Hamoen Leendert W. 
Published: January 2024

ABSTRACT

To infer the biological meaning from transcriptome data, it is useful to focus on genes that are regulated by the same regulator, i.e., regulons. Unfortunately, current gene set enrichment analysis (GSEA) tools do not consider whether a gene is activated or repressed by a regulator. This distinction is crucial when analyzing regulons since a regulator can work as an activator of certain genes and as a repressor of other genes, yet both sets of genes belong to the same regulon. Therefore, simply averaging expression differences of the genes of such a regulon will not properly reflect the activity of the regulator. What makes it more complicated is the fact that many genes are regulated by different transcription factors, and current transcriptome analysis tools are unable to indicate which regulator is most likely responsible for the observed expression difference of a gene. To address these challenges, we developed the gene set enrichment analysis program GINtool. Additional features of GINtool are novel graphical representations to facilitate the visualization of gene set analyses of transcriptome data, the possibility to include functional categories as gene sets for analysis, and the option to analyze expression differences within operons, which is useful when analyzing prokaryotic transcriptome and also proteome data.

IMPORTANCE
Measuring the activity of all genes in cells is a common way to elucidate the function and regulation of genes. These transcriptome analyses produce large amounts of data since genomes contain thousands of genes. The analysis of these large data sets is challenging. Therefore, we developed a new software tool called GINtool that can facilitate the analysis of transcriptome data by using prior knowledge of gene sets controlled by the same regulator, the so-called regulons. An important novelty of GINtool is that it can take into account the directionality of gene regulation in these analyses, i.e., whether a gene is activated or repressed, which is crucial to assess whether a regulon or functional category is affected. GINtool also includes new graphical methods to facilitate the visual inspection of regulation events in transcriptome data sets. These and additional analysis methods included in GINtool make it a powerful software tool to analyze transcriptome data.
Primary small intestine angiosarcoma mimicking Crohn’s disease
Authors: Thaveenthiran Prasanthan , Bae Lily , Wewelwala Chandika , Zhou Kevin 
Published: January 2024

A man in his 40s presented to an emergency department after experiencing worsening abdominal pain for 2 days. Contrast-enhanced CT of the abdomen and pelvis revealed circumferential mural thickening and luminal narrowing of the distal ileum and upstream dilatation of the small intestine, indicating small intestine obstruction. This prompted emergency laparotomy, where two lesions in the distal ileum were identified as the source of his bowel obstruction and resected. Immunohistochemistry of the resected segment revealed a primary small intestine angiosarcoma acting positively for vascular markers ERG and CD31. A subsequent positron emission tomography (PET) scan revealed positive mediastinal metastatic lymphadenopathy without organ metastases.Following his surgery, the patient recovered well and was promptly referred to an oncology unit at a specialised health centre for further treatment. Primary small intestine angiosarcoma is a rare entity in which patients present with non-specific symptoms requiring prompt tissue diagnosis to facilitate multidisciplinary management.