bluuebunny/crossref_metadata_2025 huggingface dataset:
A cotton mitochondrial alternative electron transporter, GhD2HGDH, induces early flowering by modulating GA and photoperiodic pathways
Authors: Billah Masum , Renju Liu , Wei Hu , Qanmber Ghulam , Da Yan , Lan Yang , Qing‐di Yan , Fuguang Li , Zhaoen Yang
Published: June 2024

D‐2‐hydroxyglutarate dehydrogenase (D2HGDH) is a mitochondrial enzyme containing flavin adenine dinucleotide FAD, existing as a dimer, and it facilitates the specific oxidation of D‐2HG to 2‐oxoglutarate (2‐OG), which is a key intermediate in the tricarboxylic acid (TCA) cycle. A Genome‐wide expression analysis (GWEA) has indicated an association between GhD2HGDH and flowering time. To further explore the role of GhD2HGDH, we performed a comprehensive investigation encompassing phenotyping, physiology, metabolomics, and transcriptomics in Arabidopsis thaliana plants overexpressing GhD2HGDH. Transcriptomic and qRT‐PCR data exhibited heightened expression of GhD2HGDH in upland cotton flowers. Additionally, early‐maturing cotton exhibited higher expression of GhD2HGDH across all tissues than delayed‐maturing cotton. Subcellular localization confirmed its presence in the mitochondria. Overexpression of GhD2HGDH in Arabidopsis resulted in early flowering. Using virus‐induced gene silencing (VIGS), we investigated the impact of GhD2HGDH on flowering in both early‐ and delayed‐maturing cotton plants. Manipulation of GhD2HGDH expression levels led to changes in photosynthetic pigment and gas exchange attributes. GhD2HGDH responded to gibberellin (GA3) hormone treatment, influencing the expression of GA biosynthesis genes and repressing DELLA genes. Protein interaction studies, including yeast two‐hybrid, luciferase complementation (LUC), and GST pull‐down assays, confirmed the interaction between GhD2HGDH and GhSOX (Sulfite oxidase). The metabolomics analysis demonstrated GhD2HGDH's modulation of the TCA cycle through alterations in various metabolite levels. Transcriptome data revealed that GhD2HGDH overexpression triggers early flowering by modulating the GA3 and photoperiodic pathways of the flowering core factor genes. Taken together, GhD2HGDH positively regulates the network of genes associated with early flowering pathways.
Morpho‐histology of co‐occurrence of somatic embryos, shoots, and inflorescences within a callus of Limonium ‘Misty Blue’
Authors: Raha Priyanka , Khatua Ishita , Saha Gourab , Adhikari Sinchan , Gantait Saikat , Bandyopadhyay Tapas Kumar
Published: June 2024

This is the first attempt to report the co‐occurrence of somatic embryos, shoots, and inflorescences and their sequential development from stem cell niches of an individual callus mass through morpho‐histological study of any angiosperm. In the presence of a proper auxin/cytokinin combination, precambial stem cells from the middle layer of a compact callus, which was derived from the thin cell layer of the inflorescence rachis of Limonium, expressed the highest level of totipotency and pluripotency and simultaneously developed somatic embryos, shoots, and inflorescences. This study also proposed the concept of programmed cell death during bipolar somatic embryo and unipolar shoot bud pattern formation. The unique feature of this research was the stepwise histological description of in vitro racemose inflorescence development. Remarkably, during the initiation of inflorescence development, either a unipolar structure with open vascular elements or an independent bipolar structure with closed vascular elements were observed. The protocol predicted the production of 6.6 ± 0.24 and 7.4 ± 0.24 somatic embryos and shoots, respectively, from 400 mg of callus, which again multiplied, rooted, and acclimatised. The plants' ploidy level and genetic fidelity were assessed randomly before acclimatisation by flow cytometry and inter simple sequence repeats (ISSR) marker analysis. Finally, the survivability and flower quality of the regenerated plants were evaluated in the field.
Natural variation in root traits identifies significant SNPs and candidate genes for phosphate deficiency tolerance in Zea mays L.
Authors: Rajput Prakriti , Urfan Mohammad , Sharma Shubham , Hakla Haroon Rashid , Nandan Brij , Das Ranjan , Roychowdhury Rajib , Chowdhary Sikander Pal
Published: June 2024

Phosphorus (P) is a crucial macronutrient required for normal plant growth. Its effective uptake from the soil is a trait of agronomic importance. Natural variation in maize (339 accessions) root traits, namely root length and number of primary, seminal, and crown roots, root and shoot phosphate (Pi) contents, and root‐to‐shoot Pi translocation (root: shoot Pi) under normal (control, 40 ppm) and low phosphate (LP, 1 ppm) conditions, were used for genome‐wide association studies (GWAS). The Bayesian‐information and Linkage‐disequilibrium Iteratively Nested Keyway (BLINK) model of GWAS provided 23 single nucleotide polymorphisms (SNPs) and 12 relevant candidate genes putatively linked with root Pi, root: shoot Pi, and crown root number (CRN) under LP. The DNA‐protein interaction analysis of Zm00001d002842, Zm00001d002837, Zm00001d002843 for root Pi, and Zm00001d044312, Zm00001d045550, Zm00001d025915, Zm00001d044313, Zm00001d051842 for root: shoot Pi, and Zm00001d031561, Zm00001d001803, and Zm00001d001804 for CRN showed the presence of potential binding sites of key transcription factors like MYB62, bZIP11, ARF4, ARF7, ARF10 and ARF16 known for induction/suppression of phosphate starvation response (PHR). The in‐silico RNA‐seq analysis revealed up or down‐regulation of candidate genes along with key transcription factors of PHR, while Uniprot analysis provided genetic relatedness. Candidate genes that may play a role in P uptake and root‐to‐shoot Pi translocation under LP are proposed using common PHR signaling components like MYB62, ARF4, ARF7, ARF10, ARF16, and bZIP11 to induce changes in root growth in maize. Candidate genes may be used to improve low P tolerance in maize using the CRISPR strategy.
Robert Park and Norbert Elias's contributions to ethnic and racial studies: A relational approach
Authors: Webb Andrew
Published: June 2024

Since Weber's work on ethnic affinities, two centuries have passed in which scholars have drawn on sociological traditions in attempts to capture the characteristics and complexities of ethnic and racial phenomena. While some authors' works have been critically acclaimed and widely cited, others remain somewhat more peripheral, including two of sociology's more famous names from the classical cannon: Robert Park and Norbert Elias. In this paper I present these seminal thinkers' central ideas, discussing some of the crucial points of convergence, as well as limitations and divergences between them, and conclude with some of the contributions that might be applicable for studying ethnic and racial phenomena as intrinsically relational and processual. I suggest that this approach is valuable for avoiding dichotomising tendencies frequently found in ongoing debates between primordialist, constructivist, situationalist, and instrumental accounts of intergroup identities. I note that neither Elias nor Park's individual approaches are sufficient as self‐contained theoretical frameworks for the task of advancing an understanding relational ethnicity, but it is precisely in their conceptual convergencies where there is potential for moving forwards.
The novel HLA‐C*07:1089 allele, identified by Sanger dideoxy nucleotide sequencing in a Chinese individual
Authors: Wu Xue‐qiong , Yang Xiao‐zhu , An Lin , Li Ye‐mo , Yang Ting
Published: June 2024

HLA‐C*07:1089 differs from HLA‐C*07:02:01:01 by one nucleotide in exon 3.
Detection of the novel HLA‐DRB5*01:01:01:07 allele by Pacific Biosciences HiFi sequencing in a Chinese individual
Authors: Li Zihang , Han Yue , Yang Xiaodan , Zhang Weifeng , Gao Peng
Published: June 2024

HLA‐DRB5*01:01:01:07 differs from HLA‐DRB5*01:01:01:01 by two nucleotide changes in intron 1 and intron 2.
Identification of the novel HLA‐C*01:02:01:74Q and ‐C*15:02:01:63 alleles in individuals from Madhya Pradesh
Authors: Rajak Jyoti , Firfire Alfiya , Tambe Manisha , D'Silva Selma Z. , Singh Meenakshi
Published: June 2024

Allele variants HLA‐C*01:02:01:74Q and ‐C*15:02:01:63 differ from ‐C*01:02:01:01 and ‐15:02:01:01 by a single nucleotide, respectively.
Characterisation of the novel HLA‐DQA1*04:14N allele by next‐generation sequencing
Authors: Gatouillat Grégory , Walencik Alexandre , Tabary Thierry , Tonye‐Libyh Marcelle , Giusti Delphine
Published: June 2024

HLA‐DQA1*04:14N differs from HLA‐DQA1*04:01:01:03 by a single nucleotide deletion in codon 113 in exon 3.
The novel HLA‐DRB1*14:265 allele was likely generated by recombination
Authors: Ocejo‐Vinyals J. Gonzalo , Toriello María , Walias David , Mota‐Pérez Nerea , Balas Antonio
Published: June 2024

Description of the novel HLA‐DRB1*14:265 allele.
The trade effect of regional trade agreements in the presence of duty drawbacks
Authors: Hayakawa Kazunobu , Laksanapanyakul Nuttawut , Mukunoki Hiroshi
Published: June 2024

Before regional trade agreements (RTAs) come into force, some firms enjoy duty‐free imports using other tariff regimes such as a duty drawback (DD) regime. For such firms, the use of RTA tariff regimes will not provide additional benefits in terms of duty exemption. In this study, we examine the trade effects of RTAs in the presence of a DD regime. We theoretically demonstrate that firms that switch from a DD to an RTA regime will either increase or decrease their imports. Subsequently, we empirically analyse the effect of this switching on imports using firm‐level trade data from Thailand. The empirical results show that switching firms either increase or do not change their imports. Our data also suggest that this increase in imported inputs is used to produce goods for the domestic market, not the export market. We also reveal that relatively small‐sized firms tend to switch to the RTA regime, while relatively large‐sized firms continue importing under the DD regime even after the entry of RTAs into force. With these results, we discuss the implication for the magnitude of trade creation effects of RTAs under the presence of DD regimes.
Modelling rice competition with Leptochloa fusca, Bidens frondosa and Ammannia coccinea in transplanted rice cultivation
Authors: Umurzokov Mirjalol , Bo Aung Bo , Cho Kwang Min , Lim Soo‐Hyun , Kim Do‐Soon , Kim Jin‐Won , Lee Jeongran , Park Sang‐Un , Park Kee Woong
Published: June 2024

A 2‐year field experiment was conducted in Daejeon, South Korea, to investigate changes in the growth parameters of rice plants during the growth and model the rice yield loss as affected by the competition with Leptochloa fusca, Bidens frondosa and Ammannia coccinea under transplanted rice cultivation. Compared with B. frondosa and A. coccinea, L. fusca significantly reduced the number of tillers at the early growth stage, resulting in more reduction in the number of panicles and other yield components such as the number of spikelets, ripened grain ratio and the ultimate rice yield at the later growth stage. Among the components, the panicle number was the most negatively and positively correlated with weed density and rice yield, respectively. Cousens' rectangular hyperbola model predicted that weed competitiveness value represented by parameter β was 0.0337 and 0.0572 for L. fusca, 0.0124 and 0.0165 for B. frondosa and 0.0059 to 0.0061 for A. coccinea in 20.8 and 15.2 hill m−2 rice densities, respectively, indicating the competition effect of L. fusca on rice yield was greater than that of B. frondosa and A. coccinea. Weed densities corresponding to a 50% reduction in the rice yield were 27 and 18 for L. fusca, 81 and 61 for B. frondosa and 169–164 for A. coccinea in 20.8 and 15.2 hill m−2 rice densities, respectively. Weeds are more competitive in low‐density rice plots, leading to greater yield loss. In addition, the economic thresholds (ET) are positively correlated with rice densities and negatively correlated with weed competitiveness. Although low‐density rice transplanting may offer economic benefits during cultivation, optimal rice density and weed control strategies are important for securing a high yield. Therefore, the model and findings could be applied to decision‐making systems in rice farming where weed interference is present.
Estridor, punta del iceberg en granulomatosis con poliangeítis: presentación de un caso
Authors: Espitia Caro Greis Patricia , Martín M. Myriam Lorena , Aluja Jaramillo Felipe , Villegas María Camila
Published: June 2024

Introducción: La granulomatosis con poliangeítis es una vasculitis autoinmune, necrosante y granulomatosa asociada con la presencia de anticuerpos anticitoplasma de neutrófilo. Afecta vasos de pequeño calibre y afecta especialmente la vía área superior e inferior, y en menor frecuencia otros órganos como el riñón. Objetivo: Reseñar el caso de una paciente pediátrica de 10 años de edad con granulomatosis con poliangeítis y su sustancial respuestas clínica y paraclínica luego del tratamiento. Presentación del caso: paciente con un cuadro de 6 meses de estridor, tos seca y disnea de grandes esfuerzos, manejada con corticoide sistémico y nebulizado. A partir de los estudios realizados se investigó el diagnóstico de granulomatosis con poliangeítis, cuyo resultado de anticuerpos anticitoplasma de neutrófilo fue positivo por inmunofluorescencia: p-ANCA 1:320, ELISA: antimieloperoxidasa positivo. Ello confirmo la sospecha diagnóstica. Conclusión: la granulomatosis con poliangeítis es una rara enfermedad en pediatría, y se requiere una alta sospecha diagnóstica y un tratamiento temprano para mejorar el pronóstico de los pacientes.
Semi-Analytical Solution for a Single-Phase Thermal Conduction Problem of a Hollow-Cylinder With a Growing or Receding Inner Radius
Authors: Kumar Pavan , Segall Albert , Drapaca Corina
Published: June 2024

A semi-analytical solution for the thermal conduction of a single phase, homogeneous, circular, hollow-cylinder with a growing or receding inner radius at a constant rate under unit-loading was derived using conformal mapping, Laplace transformation, and a Zakian series representation of the inverse Laplace transform. All solutions allow for convection on the fixed outer radius. Predictions were compared to finite element simulations with excellent agreement observed. Given the changing thickness, thermal transients could not reach true steady-state equilibrium, especially for faster growth or recession rates. Indeed, the temperature states become somewhat linear with respect to time, reflecting the constant velocity of growth or recession. In practice, the resulting solutions can be used to determine temperatures during machining, wear, erosion, corrosion, and/or additive manufacturing, especially for lower temperature solid-state methods such as cold-spray.
Global Sensitivity Analysis of Ultrasonic Testing Simulations of Slot-Like Defects With Multifidelity Modeling
Authors: Liu Yen-Chen , Miorelli Roberto , Leifsson Leifur , Reboud Christophe , Calmon Pierre
Published: June 2024

In this paper, an efficient global sensitivity analysis (GSA) method for simulation-based ultrasonic testing (UT) of slot-like defects using multifidelity modeling with novel termination criterion is proposed. GSA quantifies the effect of quantities of interest with variability (e.g., position, height, and angle) on the output (e.g., amplitude). GSA with Sobol’ indices requires the use of Monte Carlo simulations (MCS) when dealing with nonlinear problems having many parameters. It is impractical to perform GSA directly on high-fidelity physics-based models due to their long evaluation times and the large number of required samples. Multifidelity methods construct surrogate models based on data from an accurate high-fidelity model (HFM) and fast low-fidelity models (LFMs). The multifidelity surrogates evaluate quickly and can be used in lieu of the HFM to accelerate the GSA. Conventional multifidelity methods construct the surrogate to meet a prespecified error metric before using it within an analysis. This requires a separate set of testing data and an often arbitrary error metric threshold. To avoid these, a novel multifidelity modeling termination criterion for GSA is proposed that is based on the absolute relative change of the Sobol’ indices. The proposed approach is demonstrated on a simulated UT case inspecting a slot-like defect with three uncertainty variables. The results show a potential for significant reduction in computational cost compared with conventional approaches.
Combined Effect of Surface Irregularities and Applied Voltage on the Behavior of Hole-Entry Spherical Hybrid Journal Bearings Lubricated With an Electro-Rheological Fluid
Authors: Tomar Adesh Kumar , Sahu Krishnkant , Sharma Satish C. , Marian Max
Published: June 2024

Surface irregularities substantially affect the performance of tribological systems. The influence of three-dimensional surface irregularities on the behavior of hole-entry spherical hybrid journal bearings has been investigated. Recently, smart fluids have been employed in several applications to improve their performance. The interactive effect of electro-rheological (ER) fluid and surface irregularities has also been studied. The modified Reynolds equation and restrictor flow equation have been solved using the finite element technique with appropriate boundary conditions. The results show that consideration of surface irregularities on the bearing surface enhances bearing stability. Spherical hybrid journal bearings lubricated by ER fluid increase minimum fluid film thickness and minimize the possibility of metal-to-metal contact. It is found that the combined effect of surface irregularities and ER fluid significantly improved the bearing performance parameters than individual behavior. The bearing designer is anticipated to benefit from the current model.
An Enhanced Modeling Framework for Bearing Fault Simulation and Machine Learning-Based Identification With Bayesian-Optimized Hyperparameter Tuning
Authors: Ortiz Ricardo , Miranda-Chiquito Piedad , Encalada-Davila Angel , Marquez Luis E. , Tutiven Christian , Chatzi Eleni , Silva Christian E.
Published: June 2024

Monitoring the condition of rotating machinery offers a salient tool for predictive maintenance of rolling elements subjected to continuous working loads, wear, fatigue, and degradation. In this study, an enhanced computational tool for bearing fault simulation and feature extraction is proposed. A subsequent identification scheme is realized, through Bayesian optimization of hyperparameters, including support vector classifier (SVC), gradient boosting (GBoost), random forest (RF), extreme gradient boosting (XBoost), light gradient boosting machine (LightGBM), and categorical boosting (CatBoost). The proposed hyperparameter optimization technique stands out from traditional methods by offering a more informed and efficient pathway to optimal performance in predictive maintenance. By using Bayesian optimization for hyperparameter tuning of machine learning models, which has not been extensively explored in this field, our approach shows significant advancements. Typical instances of bearing faults like inner race, outer race, and ball faults are considered. The analysis relies on the extraction of statistical and engineering characteristics from the collected response signals, including kurtosis, root mean square, peak, and ridge factor. Highly influential variables are highlighted on the basis of feature selection and importance algorithms, allowing bearing fault classification. We demonstrate that SVC and LightGBM produce over 97% of accuracy at low computational cost. This approach constitutes a robust and scalable framework for similar applications in engineering diagnostics.
Analysis of Exergy Efficiency and Influencing Factors of Tube Heating Furnace in Oilfield Enterprises
Authors: Cheng Qinglin , Zhou Ruiwen , Wang Lu , Lv Lili
Published: June 2024

In the energy consumption of surface engineering systems in oilfield enterprises, heating furnaces account for a significant proportion. Therefore, it is necessary to analyze and study their operational performance. This article conducts an exergy analysis of tubular heating furnaces from the perspective of energy quality. First, an exergy balance model and exergy analysis evaluation criteria are established for the energy system of the heating furnace. Then, the internal and external exergy losses in the heating furnace's energy system are comprehensively considered to identify weak points in the energy system and reflect the utilization of energy quality. The exergy analysis results show that the highest proportion of exergy losses in the heating furnace system is attributed to the heat transfer process. The excess air coefficient, exhaust temperature, and outer surface temperature of the furnace are inversely proportional to exergy efficiency. Based on the static exergy analysis results, measures to improve the exergy efficiency of the heating furnace are proposed: controlling the excess air coefficient within a reasonable range, reducing the exhaust temperature, and lowering outer surface temperature of the furnace. These measures can effectively enhance the energy utilization level of the tubular heating furnace and provide reference and assistance in meeting emission reduction requirements.
Numerical analysis of high vacuum packaging efficiency for narrow structured devices
Authors: Mei Zhengwei , Wang Siwei , Lin Wenyu , Wang Xudi , Wang Yuqing
Published: June 2024

High vacuum packaging is the key manufacturing technology of passive vacuum devices. The inherent characteristics of narrow and long space and large surface-to-volume ratio make it challenging to effectively remove the desorption gas inside the device. To this end, the pressure distribution of two standard packaging methods during the pump-down process is investigated using the two-dimensional diffusion equation. Experiments and simulations show that a pressure gradient persists within the slit even when pumping reaches the quasi-equilibrium state. In addition, a Monte Carlo method based on the cosine law reveals that the high-frequency collisions of gas molecules with the walls impede the pumping process. Furthermore, the results indicate that for tube pumping, the number of collisions of gas molecules with the wall during transport within the gap is inversely proportional to the gap height. For edge pumping, the number of collisions is inversely proportional to the square of the gap height. This provides a theoretical basis for efficient high vacuum packaging and long-term pressure maintenance for passive vacuum devices.
PERSPECTIVE: Analysis of thixotropic timescale
Authors: Joshi Yogesh M.
Published: June 2024

Thixotropy is characterized by a time-dependent rise in viscosity under no or weak flow conditions and a decrease in viscosity over time when subjected to strong flow conditions. The characteristic timescale associated with the thixotropic phenomenon, particularly how the viscosity increases with time, has been termed the thixotropic timescale. Several approaches have been suggested in the literature for estimating the thixotropic timescale. The most prominent approach, however, infers it from a specific form of a kinetic expression for structure parameter evolution. In this paper, we study the various kinds of structural kinetic models. By carefully analyzing the same, we propose a parameter for the thixotropic timescale associated with the most generic form of kinetic expression for structure parameter evolution. We observe that increasing the thixotropic timescale weakens the thixotropic character of a system when the viscosity of the structural kinetic model continuously increases over time and eventually diverges under quiescent conditions. We also propose a new phenomenological measure of the thixotropic timescale: τthix=(dlnη/dt)−1, where η is viscosity and t is time. The proposed definition allows a straightforward and unique way to determine the thixotropic timescale through experiments and agrees well with the conventional notion of thixotropy.
The Lreu_1276 protein from
Limosilactobacillus reuteri
represents a third family of dihydroneopterin triphosphate pyrophosphohydrolases in bacteria
Authors: Kachi Kaede , Sato Takaaki , Nagasawa Maina , Cann Isaac , Atomi Haruyuki
Published: June 2024

Tetrahydrofolate is a cofactor involved in C
1
metabolism including biosynthesis pathways for adenine and serine. In the classical tetrahydrofolate biosynthesis pathway, the steps removing three phosphate groups from the precursor 7,8-dihydroneopterin triphosphate (DHNTP) remain unclear in many bacteria. DHNTP pyrophosphohydrolase hydrolyzes pyrophosphate from DHNTP and produces 7,8-dihydroneopterin monophosphate. Although two structurally distinct DHNTP pyrophosphohydrolases have been identified in the intestinal bacteria
Lactococcus lactis
and
Escherichia coli
, the distribution of their homologs is limited. Here, we aimed to identify a third DHNTP pyrophosphohydrolase gene in the intestinal lactic acid bacterium
Limosilactobacillus reuteri
. In a gene operon including genes involved in dihydrofolate biosynthesis, we focused on the
lreu_1276
gene, annotated as Ham1 family protein or XTP/dITP diphosphohydrolase, as a candidate encoding DHNTP pyrophosphohydrolase. The Lreu_1276 recombinant protein was prepared using
E. coli
and purified. Biochemical analyses of the reaction product revealed that the Lreu_1276 protein displays significant pyrophosphohydrolase activity toward DHNTP. The optimal reaction temperature and pH were 35°C and around 7, respectively. Substrate specificity was relatively strict among 17 tested compounds. Although previously characterized DHNTP pyrophosphohydrolases prefer Mg
2+
, the Lreu_1276 protein exhibited maximum activity in the presence of Mn
2+
, with a specific activity of 28.2 ± 2.0 µmol min
−1
mg
−1
in the presence of 1 mM Mn
2+
. The three DHNTP pyrophosphohydrolases do not share structural similarity to one another, and the distribution of their homologs does not overlap, implying that the Lreu_1276 protein represents a third structurally novel DHNTP pyrophosphohydrolase in bacteria.

IMPORTANCE

The identification of a structurally novel DHNTP pyrophosphohydrolase in
L. reuteri
provides valuable information in understanding tetrahydrofolate biosynthesis in bacteria that possess
lreu_1276
homologs. Interestingly, however, even with the identification of a third family of DHNTP pyrophosphohydrolases, there are still a number of bacteria that do not harbor homologs for any of the three genes while possessing other genes involved in the biosynthesis of the pterin ring structure. This suggests the presence of an unrecognized DHNTP pyrophosphohydrolase gene in bacteria. As humans do not harbor DHNTP pyrophosphohydrolase, the high structural diversity of enzymes responsible for a reaction in tetrahydrofolate biosynthesis may provide an advantage in designing inhibitors targeting a specific group of bacteria in the intestinal microbiota.
The SAMHD1-MX2 axis restricts HIV-1 infection at postviral DNA synthesis
Authors: Guo Haoran , Yang Wanying , Li Huili , Yang Jiaxin , Huang Yuehan , Tang Yubin , Wang Shijin , Ni Fushun , Yang Weiming , Yu Xiao-Fang , Wei Wei
Published: June 2024

HIV-1 replication is tightly regulated in host cells, and various restriction factors have important roles in inhibiting viral replication. SAMHD1, a well-known restriction factor, suppresses HIV-1 replication by hydrolyzing intracellular dNTPs, thereby limiting the synthesis of viral cDNA in quiescent cells. In this study, we revealed an additional and distinct mechanism of SAMHD1 inhibition during the postviral cDNA synthesis stage. Using immunoprecipitation and mass spectrometry analysis, we demonstrated the interaction between SAMHD1 and MX2/MxB, an interferon-induced antiviral factor that inhibits HIV-1 cDNA nuclear import. The disruption of endogenous MX2 expression significantly weakened the ability of SAMHD1 to inhibit HIV-1. The crucial region within SAMHD1 that binds to MX2 has been identified. Notably, we found that SAMHD1 can act as a sensor that recognizes and binds to the incoming HIV-1 core, subsequently delivering it to the molecular trap formed by MX2, thereby blocking the nuclear entry of the HIV-1 core structure. SAMHD1 mutants unable to recognize the HIV-1 core showed a substantial decrease in antiviral activity. Certain mutations in HIV-1 capsids confer resistance to MX2 inhibition while maintaining susceptibility to suppression by the SAMHD1-MX2 axis. Overall, our study identifies an intriguing antiviral pattern wherein two distinct restriction factors, SAMHD1 and MX2, collaborate to establish an alternative mechanism deviating from their actions. These findings provide valuable insight into the complex immune defense networks against exogenous viral infections and have implications for the development of targeted anti-HIV therapeutics.

IMPORTANCE

In contrast to most restriction factors that directly bind to viral components to exert their antiviral effects, SAMHD1, the only known deoxynucleotide triphosphate (dNTP) hydrolase in eukaryotes, indirectly inhibits viral replication in quiescent cells by reducing the pool of dNTP substrates available for viral cDNA synthesis. Our study provides a novel perspective on the antiviral functions of SAMHD1. In addition to its role in dNTP hydrolysis, SAMHD1 cooperates with MX2 to inhibit HIV-1 nuclear import. In this process, SAMHD1 acts as a sensor for incoming HIV-1 cores, detecting and binding to them, before subsequently delivering the complex to the molecular trap formed by MX2, thereby immobilizing the virus. This study not only reveals a new antiviral pathway for SAMHD1 but also identifies a unique collaboration and interaction between two distinct restriction factors, establishing a novel line of defense against HIV-1 infection, which challenges the traditional view of restriction factors acting independently. Overall, our findings further indicate the intricate complexity of the host immune defense network and provide potential targets for promoting host antiviral immune defense.
Draft genome sequence of
Bacillus atrophaeus
TL401, a biocontrol bacterium with plant growth-promoting properties
Authors: Peng Wanrong , Guo Xueying , Shi Hongli , Yang Xingyong
Published: June 2024

Bacillus atrophaeus
strain TL401 exhibits biocontrol activity against
Botrytis cinerea
on tomato and plant growth promotion. Here, we present the draft genome sequence of strain ITL401, which includes a circular chromosome with 4,213,034 bp and a guanine-cytosine content of 43.39%.
A single-source nosocomial outbreak of
Aspergillus flavus
uncovered by genotyping
Authors: Gewecke A. , Hare R. Krøger , Salgård C. , Kyndi L. , Høg M. , Petersen G. , Nahimana D. , Abou-Chakra N. , Knudsen J. D. , Rosendahl S. , Vissing N. H. , Arendrup M. C.
Published: June 2024

During construction work (2017–2019), an increase in
Aspergillus flavus
infections was noted among pediatric patients, the majority of whom were receiving amphotericin B prophylaxis. Microsatellite genotyping was used to characterize the outbreak. A total of 153
A
.
flavus
isolates of clinical and environmental origin were included. Clinical isolates included 140 from 119 patients. Eight patients were outbreak-related patients, whereas 111 were outbreak-unrelated patients from Danish hospitals (1994–2023). We further included four control strains. Nine
A. flavus
isolates were from subsequent air sampling in the outbreak ward (2022–2023). Typing followed Rudramurthy et al.(S. M. Rudramurthy, H. A. de Valk, A. Chakrabarti, J. Meis, and C. H. W. Klaassen, PLoS One 6:e16086, 2011,
https://doi.org/10.1371/journal.pone.0016086
). Minimum spanning tree (MST) and discriminant analysis of principal components (DAPC) were used for cluster analysis. DAPC analysis placed all 153 isolates in five clusters. Microsatellite marker pattern was clearly distinct for one cluster compared to the others. The same cluster was observed in an MST. This cluster included all outbreak isolates, air-sample isolates, and additional patient isolates from the outbreak hospital, previously undisclosed as outbreak related. The highest air prevalence of
A. flavus
was found in two technical risers of the outbreak ward, which were then sealed. Follow-up air samples were negative for
A. flavus
. Microsatellite typing defined the outbreak as nosocomial and facilitated the identification of an in-hospital source. Six months of follow-up air sampling was without
A. flavus
. Outbreak-related/non-related isolates were easily distinguished with DAPC and MST, as the outbreak clone’s distinct marker pattern was delineated in both statistical analyses. Thus, it could be a variant of
A. flavus
, with a niche ability to thrive in the outbreak-hospital environment.

IMPORTANCE

Aspergillus flavus
can cause severe infections and hospital outbreaks in immunocompromised individuals. Although lack of isogeneity does not preclude an outbreak, our study underlines the value of microsatellite genotyping in the setting of potential
A. flavus
outbreaks. Microsatellite genotyping documented an isogenic hospital outbreak with an internal source. This provided the “smoking gun” that prompted the rapid allocation of resources for thorough environmental sampling, the results of which guided immediate and relevant cleaning and source control measures. Consequently, we advise that vulnerable patients should be protected from exposure and that genotyping be included early in potential
A. flavus
outbreak investigations. Inspection and sampling are recommended at any site where airborne spores might disperse from. This includes rarely accessed areas where air communication to the hospital ward cannot be disregarded.
Protocol for the development of a reporting guideline for umbrella reviews on epidemiological associations using cross-sectional, case-control and cohort studies: the Preferred Reporting Items for Umbrella Reviews of Cross-sectional, Case-control and Cohort studies (PRIUR-CCC)
Authors: Solmi Marco , Cobey Kelly , Moher David , Ebrahimzadeh Sanam , Dragioti Elena , Shin Jae Il , Radua Joaquim , Cortese Samuele , Shea Beverley , Veronese Nicola , Hartling Lisa , Pollock Michelle , Egger Matthias , Papatheodorou Stefania , Ioannidis John P , Carvalho Andre F
Published: June 2024

Introduction

Observational studies are fraught with several biases including reverse causation and residual confounding. Overview of reviews of observational studies (ie, umbrella reviews) synthesise systematic reviews with or without meta-analyses of cross-sectional, case-control and cohort studies, and may also aid in the grading of the credibility of reported associations. The number of published umbrella reviews has been increasing. Recently, a reporting guideline for overviews of reviews of healthcare interventions (Preferred Reporting Items for Overviews of Reviews (PRIOR)) was published, but the field lacks reporting guidelines for umbrella reviews of observational studies. Our aim is to develop a reporting guideline for umbrella reviews on cross-sectional, case-control and cohort studies assessing epidemiological associations.

Methods and analysis

We will adhere to established guidance and prepare a PRIOR extension for systematic reviews of cross-sectional, case-control and cohort studies testing epidemiological associations between an exposure and an outcome, namely Preferred Reporting Items for Umbrella Reviews of Cross-sectional, Case-control and Cohort studies (PRIUR-CCC). Step 1 will be the project launch to identify stakeholders. Step 2 will be a literature review of available guidance to conduct umbrella reviews. Step 3 will be an online Delphi study sampling 100 participants among authors and editors of umbrella reviews. Step 4 will encompass the finalisation of PRIUR-CCC statement, including a checklist, a flow diagram, explanation and elaboration document. Deliverables will be (i) identifying stakeholders to involve according to relevant expertise and end-user groups, with an equity, diversity and inclusion lens; (ii) completing a narrative review of methodological guidance on how to conduct umbrella reviews, a narrative review of methodology and reporting in published umbrella reviews and preparing an initial PRIUR-CCC checklist for Delphi study round 1; (iii) preparing a PRIUR-CCC checklist with guidance after Delphi study; (iv) publishing and disseminating PRIUR-CCC statement.

Ethics and dissemination

PRIUR-CCC has been approved by The Ottawa Health Science Network Research Ethics Board and has obtained consent (20220639-01H). Participants to step 3 will give informed consent. PRIUR-CCC steps will be published in a peer-reviewed journal and will guide reporting of umbrella reviews on epidemiological associations.
Applying ordered network analysis to video-recorded physician–nurse interactions to examine communication patterns associated with shared understanding in inpatient oncology care settings
Authors: Popov Vitaliy , Tan Yuanru , Manojlovich Milisa
Published: June 2024

Objectives

The main aim of this study was to demonstrate how ordered network analysis of video-recorded interactions combined with verbal response mode (VRM) coding (eg, edification, disclosure, reflection and interpretation) can uncover specific communication patterns that contribute to the development of shared understanding between physicians and nurses. The major hypothesis was that dyads that reached shared understanding would exhibit different sequential relationships between VRM codes compared with dyads that did not reach shared understanding.

Design

Observational study design with the secondary analysis of video-recorded interactions.

Setting

The study was conducted on two oncology units at a large Midwestern academic health care system in the USA.

Participants

A total of 33 unique physician–nurse dyadic interactions were included in the analysis. Participants were the physicians and nurses involved in these interactions during patient care rounds.

Primary and secondary outcome measures

The primary outcome measure was the development of shared understanding between physicians and nurses, as determined by prior qualitative analysis. Secondary measures included the frequencies, orders and co-occurrences of VRM codes in the interactions.

Results

A Mann-Whitney U test showed that dyads that reached shared understanding (N=6) were statistically significantly different (U=148, p=0.00, r=0.93) from dyads that did not reach shared understanding (N=25) in terms of the sequential relationships between edification and disclosure, edification and advisement, as well as edification and questioning. Dyads that reached shared understanding engaged in more edification followed by disclosure, suggesting the importance of this communication pattern for reaching shared understanding.

Conclusions

This novel methodology demonstrates a robust approach to inform interventions that enhance physician–nurse communication. Further research could explore applying this approach in other healthcare settings and contexts.
Quality improvement initiative ‘S-A-F-H’ to reduce healthcare-associated neonatal sepsis in a tertiary neonatal care unit
Authors: Kallimath Aditya , Patnaik Suprabha K , Malshe Nandini , Suryawanshi Pradeep , Singh Pari , Gareghat Reema , Nimbre Vinaya , Ranbishe Kalyani , Kamble Archana Gautam , Ambekar Vishwas
Published: June 2024

Background

Neonatal sepsis is a leading cause of morbidity and mortality among admitted neonates. Healthcare-associated infection (HAI) is a significant contributor in this cohort.

Local problem

In our unit, 16.1% of the admissions developed sepsis during their stay in the unit.

Method

We formed a team of all stakeholders to address the issue. The problem was analysed using various tools, and the main contributing factor was low compliance with hand hygiene and handling of intravenous lines.

Interventions

The scrub the hub/aseptic non-touch technique/five moments of hand hygiene/hand hygiene (S-A-F-H) protocol was formulated as a quality improvement initiative, and various interventions were done to ensure compliance with hand hygiene, five moments of hand hygiene, aseptic non-touch technique. The data were collected and analysed regularly with the team members, and actions were planned accordingly.

Results

Over a few months, the team could reduce the incidence of HAI by 50%, which has been sustained for over a year. The improvement in compliance with the various aspects of S-A-F-H increased.

Conclusions

Compliance with hand hygiene steps, five moments of hand hygiene and an aseptic non-touch technique using quality improvement methodology led to a reduction in neonatal sepsis incidence in the unit. Regular reinforcement is required to maintain awareness of asepsis practices and implementation in day-to-day care and to bring about behavioural changes.
Secondary uses of electronic prescribing and pharmacy data in UK hospital care: a national survey
Authors: Chaudhry Navila Talib , Benn Jonathan , Franklin Bryony Dean
Published: June 2024

Electronic hospital pharmacy (EHP) systems are ubiquitous in today’s hospitals, with many also implementing electronic prescribing (EP) systems; both contain a potential wealth of medication-related data to support quality improvement. The reasons for reuse and users of this data are generally unknown. Our objectives were to survey secondary use of data (SUD) from EHP and EP systems in UK hospitals, to identify users of and factors influencing SUD.

A national postal survey was sent out to all hospital chief pharmacists with pre-notifications and follow-up reminders. Descriptive statistical analysis was performed.

Of 187 hospital organisations, 65 (35%) responded. All had EHP systems (for ≥20 years) and all reused data; 50 (77%) had EP systems (established 1–10 years) but only 40 (80%) reused data. Reported facilitators for SUD included medication safety, providing feedback, benchmarking, saving time and patient experience. The purposes of SUD included audits, quality improvement, risk management and general medication-related reporting. Earlier introduction of SUD could provide an opportunity to heighten local improvement initiatives.

Data from EHP systems is reused for multiple purposes. Evaluating SUD and sharing experiences could provide richer insight into potential SUD and barriers/factors to consider when implementing or upgrading EP/EHP systems.
Role of coproduction in the sustainability of innovations in applied health and social care research: a scoping review
Authors: Overton Charlotte , Tarrant Carolyn , Creese Jennifer , Armstrong Natalie
Published: June 2024

Background

Innovations such as toolkits and frameworks are developed through applied health and social care research, to address identified gaps in quality or safety of care. The intention is to subsequently implement these innovations into practice to bring about improvements. Challenges can arise from poor choice of implementation strategies or lack of alignment to local contexts. Research has identified the importance of involving and engaging patients, health professionals and other stakeholders in the design and delivery of the underpinning research, and in informing subsequent implementation. However, how and why such coproduction influences the sustainability of innovations in health and social care is unclear.

Objective

The objective of this scoping review is to identify and present the available evidence regarding the role of coproduction in the sustainability of innovations in applied health and social care research.

Inclusion criteria

This scoping review includes papers related to the role of coproduction in the sustainability of innovations in applied health and social care research published in peer-reviewed journals. The review is limited to articles reporting applied health and social care research conducted in the United Kingdom.

Methods

Scopus, Web of Science, CINAHL and MEDLINE were searched for studies. Titles and abstracts were screened by two independent reviewers for assessment against the inclusion criteria, followed by a full-text review and data extraction. Data were extracted using a data extraction form developed by the reviewers. The completed forms were imported into NVivo and analysed using basic qualitative content analysis.

Results

Our review provides insight into the role of coproduction in the sustainability of innovations in applied health and social care research. Our findings highlight that sustainability is a dynamic process, supported by coproduction activities such as ongoing collaborative partnerships; these can be planned for in both the research design and implementation phases of a project.
Addressing challenges in vector control: a review of current strategies and the imperative for novel tools in India’s combat against vector-borne diseases
Authors: Kumar Gaurav , Baharia Rajendra , Singh Kuldeep , Gupta Sanjeev Kumar , Joy Sam , Sharma Amit , Rahi Manju
Published: June 2024

Vector-borne diseases (VBDs) exert a substantial burden across the world, especially in tropical countries. Malaria, chikungunya, dengue, visceral leishmaniasis, lymphatic filariasis and Japanese encephalitis are among the public health concerns for India. One of the major pillars for the containment of VBDs is vector control and different tools have been employed for several decades. These range from chemical insecticides used in indoor residual sprays, space sprays, fogging, treated bednets and larvicides to biological control methods such as larvivorus fishes and environmental control and modification measures such as source reduction. However, these methods are increasingly becoming less effective due to several reasons such as insecticide resistance, outdoor biting, behavioural changes in vectors for biting and resting, climate change, movement of population, vector incursion to newer areas and others. It is essential to develop and test new tools for vector control to surmount these challenges. Though focusing on India’s public health concerns, the new tools enumerated here can be tested by any country with similar epidemiological and environmental conditions. The promising new vector control tools are insecticide-treated nets with synergist and/or pyrrole chlorfenapyr, alternatives/additions to synthetic pyrethroids like neonicotinoids, clothianidin for indoor residual spray, newer formulations such asBacillus sphaericusfor use in larvicides, attractive toxic sugar baits, especially to curtail outdoor transmission, endectocides like ivermectin for use in animals/humans, insecticidal paints, spatial repellents, insecticide-treated wearables and others. Genetic modification technologies (Sterile Insect Technique/Incompatible Insect Technique/Wolbachia transfection) are also upcoming strategies. Among the six VBDs, India is committed to the elimination of three (malaria, visceral leishmaniasis and lymphatic filariasis) and it will require additional and/or novel tools to overcome the roadblocks in our current journey to the goal of control/elimination of these VBDs.