bluuebunny/crossref_metadata_2025_split huggingface dataset:
Physiological and transcriptomic analysis provides novel insight into growth in Kam sweet rice under different nitrogen supplies
Authors: Amin Bakht , Luo Jun , Shi Jian , Huang Weiting , Fang Zhongming 
Published: January 2024

AbstractKam Sweet Rice (KSR) is a rice cultivar cultivated for thousands of years in China. Proper and balanced use of nitrogen sources is essential for achieving optimal growth and yield in KSR. This study was carried out to find the most effective hydroponic nutrient solution for cultivating and promoting the growth of KSR. Different nitrogen treatments were applied to KSR cultivars GouDan (GD), GouHa (GH), HongHe (HH), LeiLongGang (LG), and ZaiBianXiaoXiangHe (ZH), resulting in noticeable changes in both growth and physiological traits. Our findings revealed that D3 treatment [1.2 mM NH4Cl + 2.4 mM NaNO3+ neutral amino acids (0.1 mM Ser + 0.2 mM Thr + 0.2 mM Gly + 0.2 mM Pro +0.3 mM Ala)] had a notable positive impact on the growth of GH and ZH which showed the best performance in terms of plant height, root length and fresh weight when compared to the control (CK). Through transcriptome analysis, we discovered that these treatments altered the expression levels of genes associated with carbon metabolism, photosynthesis, and nitrogen pathways within 40 days. Interestingly, by altering the growth and tillering in rice transgenic plants, we validated the role of amino acid transporter OsAAP13 identified in transcriptome profiling, underscoring its significance. Our results are helpful for large‐scale production of KSR with the key methods for controlling the growth of KSR. It is a valuable asset for future investigations aimed at unravelling the intricate mechanisms governing plant growth in the context of different nitrogen supplies.
The president and the vice president: Different types of partnerships for a unique power couple
Authors: Prémont Karine 
Published: January 2024

AbstractAs the vice presidency evolves over time, the way we assess vice presidents' activities and influence also needs to change. We must consider the type of partnership that the president and the vice president develop together, which determines not only the latter's involvement in the decision‐making process but also the scope of his or her influence. Since partnerships can change from one term to another and according to the issues, they can help explain the fluctuations of vice presidents' influence within and between administrations, but they also enhance our comprehension of the evolution of executive power by emphasizing the dynamics of the connection between its principal components—the presidency and the vice presidency. This article introduces a new typology accounting for four different partnerships: communication, coordination, cooperation, and collaboration. This typology distinguishes between weak and strong partnerships, depending on the level of influence they allow the vice presidents to exert. Partnerships are defined by a series of criteria related to the selection of the running mate, the tasks of the vice president within the administration, and the quality of his or her relationship with the president.
How to make calibration less painful—A proposition for an automatic, reliable and time‐efficient procedure
Authors: Świder Karolina , Moratti Stephan , Bruña Ricardo 
Published: January 2024

AbstractIn behavioral and neurophysiological pain studies, multiple types of calibration methods are used to quantify the individual pain sensation stimuli. Often, studies lack a detailed calibration procedure description, data linearity, and quality quantification and omit required control for sex pain differences. This hampers study repetition and interexperimental comparisons. Moreover, typical calibration procedures require a high number of stimulations, which may cause discomfort and stimuli habituation among participants. To overcome those shortcomings, we present an automatic calibration procedure with a novel stimuli estimation method for intraepidermal stimulation. We provide an in‐depth data analysis of the collected self‐reports from 70 healthy volunteers (37 males) and propose a method based on a dynamic truncated linear regression model (tLRM). We compare its estimates for the sensation (t) and pain (T) thresholds and mid‐pain stimulation (MP), with those calculated using traditional estimation methods and standard linear regression models. Compared to the other methods, tLRM exhibits higher R2 and requires 36% fewer stimuli applications and has significantly higher t intensity and lower T and MP intensities. Regarding sex differences, t and T were found to be lower for females compared to males, regardless of the estimation method. The proposed tLRM method quantifies the calibration procedure quality, minimizes its duration and invasiveness, and provides validation of linearity between stimuli intensity and subjective scores, making it an enabling technique for further studies. Moreover, our results highlight the importance of control for sex in pain studies.
Agency in waiting: innovation and repetition in a novel Turkish Cypriot nationalist commemoration
Authors: Bahceci Sergen 
Published: January 2024

AbstractThis paper focuses on the Dawn Watch commemoration in northern Cyprus that has been organised since 2010 to mark the anniversary of Turkey's military operation/invasion on 20 July 1974. I argue that the Dawn Watch utilises the innovative ritual practice of ‘keeping watch' to subjectivise participating Turkish Cypriots as the ‘guards/watchmen' who have made Turkey's military presence in Cyprus possible. This novel commemoration seeks to address growing disinterest in Turkish nationalist narratives and commemorations in northern Cyprus, which conventionally reduce Turkish Cypriots to historically unimportant figures who were merely ‘liberated' by Turkey. By adopting the innovative ritual practice of ‘keeping watch', the Dawn Watch provides participants with a new way of participating in an old nationalist narrative.
Home safety hazards associated with unintentional poisoning among children aged 0–5 years in Mongolia: A case–control study
Authors: Sambuu Tsetsegee , Bayanbat Bat‐Amgalan , Naidan Oyunbileg , Badarch Tumen Ulzii , Mukhtar Yerkyebulan , Ichikawa Masao 
Published: January 2024

AbstractObjectiveTo examine the association between home safety hazards and unintentional poisoning in children in Mongolia.MethodsWe conducted a case–control study using structured questionnaires to investigate safety behaviours, safety equipment use, and home hazards in households with or without children aged 0–5 years who had suffered from poisoning at home (i.e., cases and controls). We recruited 190 cases (105 medicinal and 84 non‐medicinal poisonings, and one each) at the National Center for Maternal and Child Health and 379 controls in the communities between 1 March and 30 October 2021.ResultsThere were large differences between cases' and controls' households in safety behaviours and home hazards: the failure to store all medicines out of reach of children (68% of cases vs. 25% of controls), the failure to store all medicines safely (out of reach, locked or non‐existent) (61% vs. 22%), the failure to put all medicines away immediately after use (77% vs. 43%), the presence of things that a child could climb on to reach high surfaces (82% vs. 67%), the presence of medicines transferred into different containers (28% vs. 9%) and the presence of household products transferred into different containers (28% vs. 16%). These home safety hazards were strongly associated with poisoning after controlling for confounders.ConclusionChildren's risk of unintentional poisoning was strongly associated with the unsafe storage of potentially poisonous agents by caregivers and home hazards. Since unsafe storage is widespread, a fail‐safe approach such as child‐resistant closure of medicines and household products should be considered.
The CsAP2‐09‐CsWRKY25‐CsRBOH2 cascade confers resistance against citrus bacterial canker by regulating ROS homeostasis
Authors: Li Qiang , Xian Baohang , Yu Qiyuan , Jia Ruirui , Zhang Chenxi , Zhong Xin , Zhang Miao , Fu Yongyao , Liu Yiqi , He Houzheng , Li Man , Chen Shanchun , He Yongrui 
Published: January 2024

SUMMARYCitrus bacterial canker (CBC) is a serious bacterial disease caused by Xanthomonas citri subsp. citri (Xcc) that adversely impacts the global citrus industry. In a previous study, we demonstrated that overexpression of an Xcc‐inducible apetala 2/ethylene response factor encoded by Citrus sinensis, CsAP2‐09, enhances CBC resistance. The mechanism responsible for this effect, however, is not known. In the present study, we showed that CsAP2‐09 targeted the promoter of the Xcc‐inducible WRKY transcription factor coding gene CsWRKY25 directly, activating its transcription. CsWRKY25 was found to localize to the nucleus and to activate transcriptional activity. Plants overexpressing CsWRKY25 were more resistant to CBC and showed higher expression of the respiratory burst oxidase homolog (RBOH) CsRBOH2, in addition to exhibiting increased RBOH activity. Transient overexpression assays in citrus confirmed that CsWRKY25 and CsRBOH2 participated in the generation of reactive oxygen species (ROS) bursts, which were able to restore the ROS degradation caused by CsAP2‐09 knockdown. Moreover, CsWRKY25 was found to bind directly to W‐box elements within the CsRBOH2 promoter. Notably, CsRBOH2 knockdown had been reported previously to reduce the CBC resistance, while demonstrated in this study, CsRBOH2 transient overexpression can enhance the CBC resistance. Overall, our results outline a pathway through which CsAP2‐09‐CsWRKY25 transcriptionally reprograms CsRBOH2‐mediated ROS homeostasis in a manner conducive to CBC resistance. These data offer new insight into the mechanisms and regulatory pathways through which CsAP2‐09 regulates CBC resistance, highlighting its potential utility as a target for the breeding of CBC‐resistant citrus varieties.
Endoglin mutants retained in the endoplasmic reticulum exacerbate loss of function in hereditary hemorrhagic telangiectasia type 1 (HHT1) by exerting dominant negative effects on the wild type allele
Authors: Gariballa Nesrin , Badawi Sally , Ali Bassam R. 
Published: January 2024

AbstractHereditary hemorrhagic telangiectasia (HHT) is an autosomal dominant disorder affecting 1 in 5000–8000 individuals. Hereditary hemorrhagic telangiectasia type 1 (HHT1) is the most common HHT and manifests as diverse vascular malformations ranging from mild symptoms such as epistaxis and mucosal and cutaneous telangiectases to severe arteriovenous malformations (AVMs) in the lungs, brain or liver. HHT1 is caused by heterozygous mutations in the ENG gene, which encodes endoglin, the TGFβ homodimeric co‐receptor. It was previously shown that some endoglin HHT1‐causing variants failed to traffic to the plasma membrane due to their retention in the endoplasmic reticulum (ER) and consequent degradation by ER‐associated degradation (ERAD). Endoglin is a homodimer formed in the ER, and we therefore hypothesized that mixed heterodimers might form between ER‐retained variants and WT protein, thus hampering its maturation and trafficking to the plasma membrane causing dominant negative effects. Indeed, HA‐tagged ER‐retained mutants formed heterodimers with Myc‐tagged WT endoglin. Moreover, variants L32R, V105D, P165L, I271N and C363Y adversely affected the trafficking of WT endoglin by reducing its maturation and plasma membrane localization. These results strongly suggest dominant negative effects exerted by these ER‐retained variants aggravating endoglin loss of function in patients expressing them in the heterozygous state with the WT allele. Moreover, this study may help explain some of the variability observed among HHT1 patients due to the additional loss of function exerted by the dominant negative effects in addition to that due to haploinsufficiency. These findings might also have implications for some of the many conditions impacted by ERAD.
Collapsing Pressures of Bessemer Steel Lap-Welded Tubes, Three to Ten Inches in Diameter
Authors: Stewart Reid T. 
Published: January 2024

Abstract
This research was undertaken for the purpose of supplying an urgent demand for reliable information on the behavior of modern wrought tubes when subjected to fluid collapsing pressure. Every means known to engineering science that could aid in the accomplishment of this undertaking has been used, and every possible effort made to get at the truth and have the research yield trustworthy data. It was planned and executed under the immediate direction of the author, at the McKeesport works of the National Tube Company, and has occupied for its completion, during a period of four years, the time of from one to six men.
Metabolic model predictions enable targeted microbiome manipulation through precision prebiotics
Authors: Marinos Georgios , Hamerich Inga K. , Debray Reena , Obeng Nancy , Petersen Carola , Taubenheim Jan , Zimmermann Johannes , Blackburn Dana , Samuel Buck S. , Dierking Katja , Franke Andre , Laudes Matthias , Waschina Silvio , Schulenburg Hinrich , Kaleta Christoph 
Published: January 2024

ABSTRACT

While numerous health-beneficial interactions between host and microbiota have been identified, there is still a lack of targeted approaches for modulating these interactions. Thus, we here identify precision prebiotics that specifically modulate the abundance of a microbiome member species of interest. In the first step, we show that defining precision prebiotics by compounds that are only taken up by the target species but no other species in a community is usually not possible due to overlapping metabolic niches. Subsequently, we use metabolic modeling to identify precision prebiotics for a two-member
Caenorhabditis elegans
microbiome community comprising the immune-protective target species
Pseudomonas lurida
MYb11 and the persistent colonizer
Ochrobactrum vermis
MYb71. We experimentally confirm four of the predicted precision prebiotics, L-serine, L-threonine, D-mannitol, and γ-aminobutyric acid, to specifically increase the abundance of MYb11. L-serine was further assessed
in vivo
, leading to an increase in MYb11 abundance also in the worm host. Overall, our findings demonstrate that metabolic modeling is an effective tool for the design of precision prebiotics as an important cornerstone for future microbiome-targeted therapies.

IMPORTANCE

While various mechanisms through which the microbiome influences disease processes in the host have been identified, there are still only few approaches that allow for targeted manipulation of microbiome composition as a first step toward microbiome-based therapies. Here, we propose the concept of precision prebiotics that allow to boost the abundance of already resident health-beneficial microbial species in a microbiome. We present a constraint-based modeling pipeline to predict precision prebiotics for a minimal microbial community in the worm
Caenorhabditis elegans
comprising the host-beneficial
Pseudomonas lurida
MYb11 and the persistent colonizer
Ochrobactrum vermis
MYb71 with the aim to boost the growth of MYb11. Experimentally testing four of the predicted precision prebiotics, we confirm that they are specifically able to increase the abundance of MYb11
in vitro
and
in vivo
. These results demonstrate that constraint-based modeling could be an important tool for the development of targeted microbiome-based therapies against human diseases.
The first report of the mobile colistin resistance gene,
mcr-10.1
, in Kenya and a novel mutation in the
phoQ
gene (S244T) in a colistin-resistant
Enterobacter cloacae
clinical isolate
Authors: Kigen Collins , Muraya Angela , Wachira James , Musila Lillian 
Published: January 2024

ABSTRACT

This study describes the identification of the
mcr-10.1
gene in a clinical isolate of an ST1
Enterobacter cloacae
isolate cultured in 2015 in Kenya. The isolate was multidrug resistant, phenotypically non-susceptible to various antibiotics, including colistin. Whole genome sequence analyses indicated carriage of chromosomally encoded antimicrobial resistance genes and the colistin-resistant gene
mcr-10.1
located on a 72-kb plasmid designated pECC011b with an IncFIA(HI1) replicon directly adjacent to tyrosine recombinase gene,
xerC
, and downstream of an IS
KPn26
insertion sequence. Studies have shown that expression of
mcr-10.1
may not be sufficient to confer colistin resistance, but a novel non-synonymous mutation (S244T) was identified in the
phoQ
gene known to influence colistin resistance within lipid modification pathways, which could have complemented the
mcr-10.1
resistance mechanism.
In silico
analysis of the mutant
phoQ
protein shows the location of the mutation to be at the Histidine kinases, Adenyl cyclases, Methyl-accepting proteins and Phosphatases (HAMP) region, which plays a crucial role in the protein’s activity. This study and our previous report of
mcr-8
in
Klebsiella pneumoniae
indicate the presence of mobile
mcr
genes in the
Enterobacterales
order of bacteria in Kenya. The study points to the importance of regulation of colistin in the animal industry and enhancing surveillance in both human and animal health to curb the spread of
mcr
genes and accurately assess the risks posed by these mobile genetic elements in both sectors.

IMPORTANCE

This paper reports the detection of new colistin resistance mechanisms in Kenya in a clinical isolate of
Enterobacter cloacae
in a patient with a healthcare-associated infection. The plasmid-mediated resistance gene,
mcr-10.1
, and a novel amino acid mutation S244T in the
phoQ
gene, located in a region of the protein involved in membrane cationic stability contributing to colistin resistance, were detected. Colistin is a critical last-line drug for multidrug-resistant (MDR) gram-negative human infections and is used for treatment and growth promotion in the animal industry. The emergence of the resistance mechanisms points to the potential overuse of colistin in the animal sector in Kenya, which enhances resistance, threatens the utility of colistin, and limits treatment options for MDR infections. This study highlights the need to enhance surveillance of colistin resistance across sectors and strengthen One Health policies that ensure antimicrobial stewardship and implementation of strategies to mitigate the spread of antibiotic resistance.
Diversification of gene content in the
Mycobacterium tuberculosis
complex is determined by phylogenetic and ecological signatures
Authors: Silva-Pereira Taiana Tainá , Soler-Camargo Naila Cristina , Guimarães Ana Marcia Sá 
Published: January 2024

ABSTRACT

We analyzed the pan-genome and gene content modulation of the most diverse genome data set of the
Mycobacterium tuberculosis
complex (MTBC) gathered to date. The closed pan-genome of the MTBC was characterized by reduced accessory and strain-specific genomes, compatible with its clonal nature. However, significantly fewer gene families were shared between MTBC genomes as their phylogenetic distance increased. This effect was only observed in inter-species comparisons, not within-species, which suggests that species-specific ecological characteristics are associated with changes in gene content. Gene loss, resulting from genomic deletions and pseudogenization, was found to drive the variation in gene content. This gene erosion differed among MTBC species and lineages, even within
M. tuberculosis
, where L2 showed more gene loss than L4. We also show that phylogenetic proximity is not always a good proxy for gene content relatedness in the MTBC, as the gene repertoire of
Mycobacterium africanum
L6 deviated from its expected phylogenetic niche conservatism. Gene disruptions of virulence factors, represented by pseudogene annotations, are mostly not conserved, being poor predictors of MTBC ecotypes. Each MTBC ecotype carries its own accessory genome, likely influenced by distinct selective pressures such as host and geography. It is important to investigate how gene loss confer new adaptive traits to MTBC strains; the detected heterogeneous gene loss poses a significant challenge in elucidating genetic factors responsible for the diverse phenotypes observed in the MTBC. By detailing specific gene losses, our study serves as a resource for researchers studying the MTBC phenotypes and their immune evasion strategies.

IMPORTANCE

In this study, we analyzed the gene content of different ecotypes of the
Mycobacterium tuberculosis
complex (MTBC), the pathogens of tuberculosis. We found that changes in their gene content are associated with their ecological features, such as host preference. Gene loss was identified as the primary driver of these changes, which can vary even among different strains of the same ecotype. Our study also revealed that the gene content relatedness of these bacteria does not always mirror their evolutionary relationships. In addition, some genes of virulence can be variably lost among strains of the same MTBC ecotype, likely helping them to evade the immune system. Overall, our study highlights the importance of understanding how gene loss can lead to new adaptations in these bacteria and how different selective pressures may influence their genetic makeup.
Transcriptomic and metabolomic analysis unveils a negative effect of glutathione metabolism on laccase activity in
Cerrena unicolor
87613
Authors: Zhang Long-Bin , Qiu Ting-Ting , Qiu Xiu-Gen , Yang Wu-Wei-Jie , Ye Xiu-Yun , Meng Chun 
Published: January 2024

ABSTRACT

The white rot fungus
Cerrena unicolor
87613 has been previously shown to be a promising resource in laccase production, an enzyme with significant biotechnological applications. Conventional methods face technical challenges in improving laccase activity. Attempts are still being made to develop novel approaches for further enhancing laccase activity. This study aimed to understand the regulation of laccase activity in
C. unicolor
87613 for a better exploration of the novel approach. Transcriptomic and metabolomic analyses were performed to identify key genes and metabolites involved in extracellular laccase activity. The findings indicated a strong correlation between the glutathione metabolism pathway and laccase activity. Subsequently, experimental verifications were conducted by manipulating the pathway using chemical approaches. The additive reduced glutathione (GSH) dose-dependently repressed laccase activity, while the GSH inhibitors (APR-246) and reactive oxygen species (ROS) inducer (H
2
O
2
) enhanced laccase activity. Changes in GSH levels could determine the intracellular redox homeostasis in interaction with ROS and partially affect the expression level of laccase genes in
C. unicolor
87613 in turn. In addition, GSH synthetase was found to mediate GSH abundance in a feedback loop. This study suggests that laccase activity is negatively influenced by GSH metabolism and provides a theoretical basis for a novel strategy to enhance laccase activity by reprogramming glutathione metabolism at a specific cultivation stage.

IMPORTANCE

The production of laccase activity is limited by various conventional approaches, such as heterologous expression, strain screening, and optimization of incubation conditions. There is an urgent need for a new strategy to meet industrial requirements more effectively. In this study, we conducted a comprehensive analysis of the transcriptome and metabolome of
Cerrena unicolor
87613. For the first time, we discovered a negative role played by reduced glutathione (GSH) and its metabolic pathway in influencing extracellular laccase activity. Furthermore, we identified a feedback loop involving GSH, GSH synthetase gene, and GSH synthetase within this metabolic pathway. These deductions were confirmed through experimental investigations. These findings not only advanced our understanding of laccase activity regulation in its natural producer but also provide a theoretical foundation for a strategy to enhance laccase activity by reprogramming glutathione metabolism at a specific cultivation stage.