bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unveiling Genetic Basis Associated With Manganese Content in Turkish Common Bean (Phaseolus vulgaris L.) Germplasm Through a Genome‐Wide Association Study
Authors: Altaf Muhammad Tanveer , Nadeem Muhammad Azhar , Ayten Sefa , Aksoy Emre , Sönmez Ferit , Çiftçi Vahdettin , Baloch Faheem Shehzad 
Published: November 2024

ABSTRACTMicronutrient deficiencies, such as manganese (Mn), pose significant global health risks, affecting millions of people worldwide and leading to serious health conditions. Biofortifying crops, notably common beans, offer a sustainable solution to combat these deficiencies. This study aimed to uncover the genetic basis associated with Mn content in Turkish common bean (Phaseolus vulgaris) germplasm through a genome‐wide association study (GWAS), which is crucial for developing nutrient‐rich bean varieties. Here, we examined variation among 183 common bean accessions, collected from 19 provinces of Turkey and identified the genetic basis linked to seed Mn content. Genotype by environment interaction significantly influenced Mn content (p < 0.05). The mean Mn content was observed 31.69 mg kg−1 across the germplasm. Bingol‐16 had the lowest, while Malatya‐59 had the highest Mn contents. Stability analysis was performed using the ‘STABILITYSOFT’ method and found 10 stable accessions. The cluster constellation plot was generated using JMP statistical software. A total of 7900 DArTseq markers were used for association analysis, identifying 16 markers across four chromosomes (Pv2, Pv5, Pv7 and Pv11). Notably, markers DArT‐3374915 and DArT‐3375187 exhibited consistent associations across different environments, making them promising candidates for Mn‐focused breeding programmes. Gene annotation and interactome analysis, including BLAST searches and protein–protein interaction analysis, revealed associations of candidate genes with Mn concentration regulation, shedding light on potential mechanisms underlying Mn accumulation in common beans. Our findings lay a foundation for marker‐assisted breeding efforts in common bean improvement.
Transcriptional and functional characterization in the terpenoid precursor pathway of the early land plant Physcomitrium patens
Authors: Horn A. , Lu Y. , Astorga Ríos F. J. , Toft Simonsen H. , Becker J. D. 
Published: November 2024

Abstract
Isoprenoids comprise the largest group of plant specialized metabolites. 1‐deoxy‐D‐xylulose‐5‐phosphate synthase (DXS) is one of the major rate‐limiting enzymes in their biosynthesis. The DXS family expanded structurally and functionally during evolution and is believed to have significantly contributed to metabolic complexity and diversity in plants. This family has not yet been studied in Physcomitrium patens or other bryophytes.
Here, we assessed the degree of evolutionary expansion in the DXS family in bryophytes and, more specifically, in P. patens using phylogenetic analysis. Transcriptome profiling was applied to investigate tissue‐specific, developmental, and environmental responses, such as salt stress, in the DXS family. Moreover, the effect of salt stress on terpenoid biosynthesis was monitored through metabolomics.
The phylogenetic analysis of DXS revealed that a structural expansion occurred in bryophytes, but not in P. patens. Functional complementation assay revealed functional activity in all four copies. Comparative transcriptomics showed tissue‐ and condition‐specific divergence in the expression profiles of DXS copies and demonstrated specific stress responses for PpDXS1D, particularly to salt stress. These findings coincide with increased flux in the pathway towards downstream metabolites under salt stress. Additionally, co‐expression network analysis revealed significant differences between the co‐expressed genes of the DXS copies and illustrated enrichment of stress‐responsive genes in the PpDXS1D network.
These results suggest that the DXS family in P. patens is conserved but undergoes differential transcriptional regulation, which might allow P. patens to fine‐tune DXS levels under different conditions, such as abiotic stress.
Combined use of NBPT and micronutrients in granulated or coated urea: A new approach to reduce ammonia volatilization losses from soil
Authors: Cassim Bruno Maia Abdo Rahmen , Lisboa Izaias Pinheiro , Degryse Fien , da Silva Rodrigo C. , Prestes Clelber Vieira , Lavres José , Otto Rafael 
Published: November 2024

AbstractN‐(n‐Butyl) thiophosphoric triamide (NBPT) is the most widely adopted urease inhibitor, used to reduce ammonia (NH3) volatilization from urea. Micronutrients such as boron (B), zinc (Zn), nickel (Ni) and molybdenum (Mo) are also reported to inhibit urease, serving simultaneously as plant nutrients. However, there is little information on the potential synergistic or antagonistic effects of NBPT and micronutrients on urea protection. The aim of this study was to evaluate NH3 volatilization losses, soil pH and soil mineral nitrogen content (‐N and ‐N) after application of urea coated or granulated with the micronutrients B, Zn, Ni or Mo, individually. Thereafter, the fertilizers were applied combined and not associated with NBPT. Ammonia volatilization was measured in a closed static chamber under controlled conditions. Urea granulated with B and Zn reduced NH3‐N volatilization circa 30% compared with untreated urea, while Mo and Ni had no effect. NBPT stabilizer had the greatest effect on NH3‐N volatilization (44%–59% reduction), but was less effective (only 20%–34% reduction) when urea was coated with B, Zn or Mo. On the other hand, when B and Zn were incorporated via granulation, the efficiency of NBPT was not reduced, likely because of the physical separation. These findings demonstrate that granulating urea with B or Zn combined with an NBPT‐coating can be a valuable strategy to reduce NH3 volatilization losses while also supplying micronutrients and hence potentially increase yields in agricultural production systems.
Okay in intercultural lingua franca interactions between Chinese and British postgraduate students
Authors: Sabbah‐Taylor Angela , Jenks Christopher J. 
Published: November 2024

AbstractThe forms and functions of okay have been investigated extensively in contexts where interlocutors speak the same language (e.g., German, Hungarian, and Swedish). Conversely, comparatively few studies have been conducted on how okay is used among people who do not share the same first language, such as lingua franca encounters. This article narrows this gap by investigating the use of okay in face‐to‐face tandem language learning between Chinese Expanding Circle users of English and British Inner Circle users of English. Using applied conversation analysis on a large corpus of 36 h of video recordings, the findings demonstrate that okay is used by both groups of speakers to manage comprehension in two ways: (1) okay is used to display sufficient understanding and (2) okay is used to display insufficient understanding. Although both groups of speakers use okay to claim sufficient and insufficient understanding, there are small, nuanced ways that the British Inner Circle users of English and Chinese Expanding Circle users of English differ in the use of discourse markers. These findings suggest that much more work is needed to fully understand how discourse markers are used in lingua franca interactions and world Englishes contexts.
Global solutions to semilinear parabolic equations driven by mixed local–nonlocal operators
Authors: Biagi Stefano , Punzo Fabio , Vecchi Eugenio 
Published: November 2024

AbstractWe are concerned with the Cauchy problem for the semilinear parabolic equation driven by the mixed local–nonlocal operator , with a power‐like source term. We show that the so‐called Fujita phenomenon holds, and the critical value is exactly the same as for the fractional Laplacian.
Roughness Investigations on In-Service High-Pressure Compressor Blades—Part I: An Automated Process for High-Fidelity Roughness Measurements
Authors: Vasilopoulos Ilias , Rostamian Mirco , Voigt Matthias , Meyer Marcus , Mailach Ronald 
Published: November 2024

Abstract
The two-part publication deals with roughness investigations on in-service high-pressure compressor (HPC) blades, both in terms of measurements and simulations. In this article (Part I), an automated process for performing detailed surface roughness measurements of the blades has been developed. Specifically, a highly accurate Alicona sensor (20x lens; capable of capturing roughness values down to 0.1μm) was combined with a pick-and-place robotic arm, and the system was trained to conduct roughness measurements on all the different rotor blades of a 10-stage HPC. First, the Alicona measuring device is validated against a NanoFocus device of similar accuracy. Then, a detailed measurement of the roughness on the suction and pressure side of Rotor 2 is demonstrated, using a 100-point grid. This process is further accelerated by using a reduced number of measuring points. The location of those points has been determined by numerical optimization that aims at minimizing the error between a radial basis function (RBF)-based approximation model and the detailed measured roughness distribution. Finally, a summary of the roughness measurements through the entire HPC is given (rotors only; before and after cleaning of the blades at an ultrasonic bath) and the article ends with a discussion of the results.
Genome drafts of
Lotmaria passim
strains C2 and C3 isolated from honey bees in Spain
Authors: Ruiz José Luis , Marin Arturo , Carreira de Paula Jessica , Gómez-Moracho Tamara , García Olmedo Pedro , Andrés-León Eduardo , Solano Parada Jennifer , Orantes Bermejo Francisco , Osuna Antonio , de Pablos Luis Miguel 
Published: November 2024

ABSTRACT

Lotmaria passim
is a highly prevalent parasite of honey bees. Herein is reported the draft genome sequences of
L. passim
C2 and C3 strains of 27.15 Mbp and 26.94 Mbp, respectively. The genomes were sequenced using Illumina MiSeq platform and will allow for further comparative and functional genomics studies.
Complete mitochondrial genome sequence of giant freshwater prawn,
Macrobrachium rosenbergii
of Bangladesh
Authors: Pal Dipta Chandra , Hasan Md. Mahmud , Khan Shakila Nargis , Karim Muhammad Manjurul 
Published: November 2024

ABSTRACT

We report the complete mitochondrial genome sequence of the giant freshwater prawn (
Macrobrachium rosenbergii
) from Bangladesh. The circular genome is 15,766 base pairs long, with a GC content of 38.1%, and contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region.
Draft genome sequences for
Neonectria magnoliae
and
Neonectria punicea,
canker pathogens of
Liriodendron tulipifera
and
Acer saccharum
in West Virginia
Authors: Petronek Hannah M. , Kasson Matt T. , Metheny Amy M. , Stauder Cameron M. , Lovett Brian , Lynch Shannon C. , Garnas Jeff R. , Kasson Lindsay R. , Stajich Jason E. 
Published: November 2024

ABSTRACT

The fungal genus
Neonectria
contains many phytopathogenic species currently impacting forests and fruit trees worldwide. Despite their importance, a majority of
Neonectria
spp. lack sufficient genomic resources to resolve suspected cryptic species. Here, we report draft genomes and assemblies for
Neonectria magnoliae
NRRL 64651 and
Neonectria punicea
NRRL 64653.
Complete genome sequence of
Franconibacter pulveris
SL.qac10, a putative QAC-resistant isolate from an indoor built environment
Authors: Liu S. , Leung K. M. , Lai G. K. K. , Griffin S. D. J. 
Published: November 2024

ABSTRACT

Franconibacter pulveris
SL.qac10 was isolated at a school in Hong Kong from swabs of flooring frequently cleaned with a quaternary ammonium compound (QAC)-based disinfectant. Its complete genome, a single chromosome and circular plasmid totalling 4.88 Mbp (56.50% G + C), was established by hybrid assembly.
Identification of a putative novel polycyclic aromatic hydrocarbon-biodegrading gene cluster in a marine
Roseobacteraceae
bacterium
Sagittula
sp. MA-2
Authors: Abe Mayuko , Sakai Miharu , Kanaly Robert A. , Mori Jiro F. 
Published: November 2024

ABSTRACT

The ability to biodegrade polycyclic aromatic hydrocarbons (PAHs) and the catabolic enzymes responsible for PAH biotransformation in marine bacteria belonging to the family
Roseobacteraceae
remain largely unexplored despite their wide distribution and highly diverse physiological traits. A bacterial isolate within
Roseobacteraceae
originating from coastal seawater,
Sagittula
sp. strain MA-2, that biotransformed phenanthrene and utilized it as a growth substrate was found to possess a putative PAH-degrading gene cluster on one of the eight circular plasmids in its genome. Subsequent comprehensive investigations utilizing bacterial genomes in public databases revealed that gene clusters potentially homologous to this newly found cluster are widely but heterogeneously distributed within
Roseobacteraceae
and a few non-
Roseobacteraceae
(
Paracoccaceae
and
Rhizobiaceae
) strains from saline environments. Catabolic functions of the enzymes encoded in strain MA-2 were predicted through the profiling of phenanthrene biotransformation products by liquid chromatography-electrospray ionization high-resolution mass spectrometry and substrate docking simulations using predicted three-dimensional structures of selected proteins, and phenanthrene biodegradation pathways were proposed. Strain MA-2 appeared to biodegrade phenanthrene via two separated, concurrent pathways, namely the salicylate and phthalate pathways. This study serves as the first investigation into the functional genes potentially responsible for PAH biodegradation conserved in
Roseobacteraceae
bacteria, expanding scientific understanding of the physiological repertoire evolved in this ubiquitous marine bacterial group.

IMPORTANCE

The ocean is often characterized as the terminal destination for persistent polycyclic aromatic hydrocarbon (PAH) environmental pollutants; however, the ability to biodegrade PAHs and the corresponding enzymes conserved among marine bacteria are less understood compared to their terrestrial counterparts. A marine bacterial isolate,
Sagittula
sp. strain MA-2, belonging to the family
Roseobacteraceae
—a widely distributed and physiologically diverse marine bacterial group—was found to possess a functional gene cluster encoding enzymes potentially responsible for PAH biodegradation in its genome and exhibit the ability to biodegrade the three-ring PAH, phenanthrene. Intriguingly, gene clusters potentially homologous to this cluster were also distributed broadly across genomes from different
Roseobacteraceae
genera in public databases, which has not been previously investigated. The knowledge provided here expands our understanding of the physiology of
Roseobacteraceae
and may be applied to explore biotechnologically useful bacteria that contribute to the remediation of polluted marine environments or high-salinity wastewater.
Virulence-associated variants in
Cryptococcus neoformans
sequence type 93 are less likely to be associated with population structure compared to independent rare mutations
Authors: Jackson Katrina M. , Kabbale Kisakye Diana , Macchietto Marissa , Meya David , Tiffin Peter , Nielsen Kirsten 
Published: November 2024

ABSTRACT

Cryptococcus neoformans
is a pathogenic yeast that is the causative agent of cryptococcal meningitis. While it is well known that the genotype of
C. neoformans
impacts patient outcomes, the reason for this association has not been well elucidated. In this study, we examined the relationship between two subpopulations in the sequence type 93 clade of
C. neoformans
: ST93A and ST93B. We found extensive linkage disequilibrium (LD) among the single nucleotide polymorphisms (SNPs) that differentiate ST93A from ST93B. We also found differences in the extent of linkage among SNPs within each subpopulation; LD was more extensive within ST93B than ST93A. SNPs associated with virulence were in long-range linkage disequilibrium with less frequency than recurrent SNPs not associated with virulence. We investigated the karyotype of ST93A and ST93B using contour-clamped gel electrophoresis and long-read sequencing and found that the extensive long-range linkage was not due to chromosomal rearrangements. Overall, we found that the two subpopulations in ST93 are driven by SNPs in LD. We additionally found that recurrent SNPs associated with virulence were less frequently evolutionarily linked and were two times more likely to be independent, congruent mutations rather than tied to phylogeny.

IMPORTANCE

Cryptococcus neoformans
is an important pathogen that is widely distributed and ubiquitous in the environment. The majority of the human population has a latent, controlled infection suggesting that
C. neoformans
is uniquely adapted to cause infection. In spite of this, the reason
C. neoformans
is a pathogen remains unknown; interestingly, most environmental isolates are avirulent but are genetically very similar to disease-causing virulent isolates. Recent evidence from genome-wide association studies shows that small mutations in key virulence-associated genes are associated with the virulence of specific isolates. The data presented here provide an evolutionary framework for those small mutations. The mutations that impact disease are not being collected over long-term evolution. The mutations may instead occur independently during infection. Identifying these genes that are more likely to be mutated during infection will be fundamental for understanding
C. neoformans
virulence.
Spleen tyrosine kinase inhibitors disrupt human neutrophil swarming and antifungal functions
Authors: Hopke Alex , Viens Adam L. , Alexander Natalie J. , Mun Seok Joon , Mansour Michael K. , Irimia Daniel 
Published: November 2024

ABSTRACT

Neutrophils communicate with one another and amplify their destructive power through swarming, a collective process that synchronizes the activities of multiple neutrophils against one target. The sequence of activities contributing to swarming against clusters of fungi has been recently uncovered. However, the molecular signals controlling the neutrophils’ activities during the swarming process are just emerging. Here, we report that spleen tyrosine kinase (SYK) inhibitors severely impair neutrophil swarming responses, resulting in the complete loss of fungal restriction. These findings are enabled by a microscale platform to probe the biology of human neutrophils swarming against uniformly sized clusters of growing
Candida albicans
, a representative opportunistic fungal pathogen. We take advantage of the ability to monitor large arrays of swarms and quantify the effect of multiple chemical inhibitors on different phases of human neutrophil swarming. We show that inhibitors that interfere with PI3Ky signaling disrupt the regulation of the initiation of swarming, while the activation of JNK signaling is essential for the activation of biochemical antifungal functions. Furthermore, we reveal that granulocyte colony-stimulating factors (GCSF and GM-CSF) can partially rescue the antifungal functions of neutrophils exposed to SYK inhibitors. These findings advance our understanding of neutrophil swarming biology in humans and lay the foundation for novel therapeutics that may restore neutrophil function during immunosuppression.

IMPORTANCE

Neutrophils can amplify their destructive power through swarming, a crucial process against large targets that individual neutrophils cannot destroy. However, the molecular mechanisms controlling this process are just emerging. Here, we leveraged microscale tools to probe the biology of swarming against fungi. We used multiple chemical inhibitors and mapped SYK, PI3Ky, and JNK signaling roles during human neutrophil swarming against fungal clusters of
Candida albicans
. We also found that treating human neutrophils with GCSF and GM-CSF rescues some neutrophil antifungal function during SYK inhibition. These findings advance our understanding of swarming biology in humans while laying the foundation for developing therapeutics that enhance neutrophil function during immunosuppression.
Internal cooling system effects to heat transfer and tool wear in turning operations of titanium alloys Ti6Al4V
Authors: Soori Mohsen , Karimi Ghaleh Jough Fooad 
Published: November 2024

Internal cooling systems are essential for turning operations to improve the efficiency and quality of the machining process. In this paper, application of the virtual machining system is developed to analyze the effects of internal cooling systems on heat transfer and tool wear in turning operations of titanium alloys Ti6Al4V. The cutting forces as well as cutting temperature along machining paths are simulated in the virtual machining system to predict and analyze the effects of internal cooling system to the heat transfer and tool wear during turning operations. The coolant flow inside the internal cooling channels of a rotating cutting tool is simulated using computational fluid dynamics. Next, utilizing the modified Johnson–Cook model, the cutting temperature during turning operations is determined. The finite element method is employed to predict tool wear by applying the Takeyama–Murata analytical method. To validate the study, experimental works are implemented using turning machine tool. The cutting settings during experimental works are feed rate of 0.3 mm/rev, depth of cut of 2 mm, and cutting speed of 75 m/min. Thus, using the proposed virtual machining system, the performance of internal cooling system can be enhanced to increase cutting tool life and surface quality of machined parts in turning operations.
Knowledge Mapping of Aspergillus‐Related Research in Respiratory Medicine: A Bibliometric Analysis Based on English‐Language Articles Spanning 1975 to 2022
Authors: Jiang Fan , Li Xuemei , Qiao Qing , Zhang Ge , Zhang Yanmei , Su Lin 
Published: November 2024

Background: Aspergillus has become the second most common causative agent of invasive fungal infections and is the leading cause of death from fungal infections.Methods: English‐language publications ranging from 1975 to 2022 collected from the Web of Science Core Collection database were analyzed visually using VOSviewer, R package Bibliometrix, Scimago graphic, Gephi, Pajek, and Microsoft Excel 365. Literature search using the advanced search function in WoSCC with the search formula “TS=(Aspergillus).” The inclusion criteria were as follows: (1) article type = article; (2) time span = 1975–2022; (3) topic = “Medical Mycology”; (4) research field = “Respiratory System, Internal Medicine”; (5) language type = English.Results: As of February 21, 2023, studies of Aspergillus in respiratory medicine included 1065 articles with 41,308 cumulative citations. The United States ranked first in terms of the highest number of publications (n = 320). Udice French Research University was the institution with the highest number of publications (n = 40). The author with the highest number of publications was Denning (n = 32). Based on the CiteSpace analysis result, the keywords with the nature of a Burst Citation were “epidemiology,” “chronic pulmonary aspergillosis,” “galactomannan,” “guideline,” “sensitization,” and “randomized trail.” Besides the keywords, it was found that as of 2022, only the topics “allergic bronchopulmonary aspergillosis” and “invasive pulmonary aspergillosis” are still active with a large number of papers published, according to the results of the CiteSpace analysis of the cited literature.Conclusions: The bibliometric results indicated the current hot research hotspots of Aspergillus were as follows: (1) research directly related to Aspergillus (epidemiology, risk factors, early diagnosis methods, and methods of novel antifungal treatment, e.g., galactomannan); (2) studying coinfections of Aspergillus with other pathogens: For example, COVID‐19 could focus on studying the immune status of patients with COVID‐19‐associated pulmonary aspergillosis (CAPA) to guide individualized immunotherapy and individualized management of patients with CAPA.