bluuebunny/crossref_metadata_2025_split huggingface dataset:
Leaf Rust Infection Phakopsora pachyrhizi on Seven Soybean Varieties in Pine Agroforestry System
Authors: Septariani D N , Supyani  , Jannah M 
Published: June 2024

Abstract
The agroforestry farming system is an alternative to increasing soybean production in Indonesia. However, in its cultivation, there are obstacles in the form of attacks by leaf rust pathogens. Leaf rust caused by the P. pachyrhizi fungus can reduce soybean production, depending on the variety and environmental conditions. This research was conducted from June to September 2023 on the KHDTK (Kawasan Hutan dengan Tujuan Khusus) Forestry Alas Bromo, Karanganyar, Central Java, Indonesia, to explore the leaf rust incidence in soybean varieties. This research used a completely randomized block design (CRBD) consisting of seven soybean variety treatments: Anjasmoro, Argomulyo, Dena-1, Dena-2, Denasa-1, Denasa-2, and Devon-1, and repeated three times. The variable observed was disease incidence. The results showed that all soybean varieties tested could be infected with the leaf rust pathogen. The lowest leaf rust infection was found in the Devon-1 variety (6.0%), and the highest infection occurred in the Dena-1 variety (20.0%). This is thought to be related to genetic traits and environmental conditions strongly influencing the growth and development of the P. pachyrhizi pathogen.
Rods, tubes, wires, and sheets
Authors: Dierking Ingo , Martins Figueiredo Neto Antônio 
Published: June 2024

AbstractMore lyotropic phase forming rod-like and plate-like materials are introduced, not so much natural mineral materials but rather laboratory made modern materials and biomaterials. Rod-like systems that are discussed are the classic example of the tobacco mosaic viruses, cellulose nanocrystals which have more recently attracted much attention, gold nanorods with their plasmonic properties, titanium dioxide, and cadmium selenide. These are followed by carbon nanotubes, ZnO, silver, and boron nitride nanowires, before several different nanosheet materials are discussed, such as graphene and graphene oxide, as well as other plate-like nanostructures such as MoS2 and MXenes. Their applications as fibres and in fabrics is pointed out.
Prior infections and effectiveness of SARS-CoV-2 vaccine in test-negative studies: a systematic review and meta-analysis
Authors: Tsang Tim K , Sullivan Sheena G , Huang Xiaotong , Wang Can , Wang Yifan , Nealon Joshua , Yang Bingyi , Ainslie Kylie E C , Cowling Benjamin J 
Published: June 2024

Abstract
Prior infection with SARS-CoV-2 can provide protection against infection and severe COVID-19. We aimed to determine the impact of preexisting immunity on vaccine effectiveness (VE) estimates. We systematically reviewed and meta-analyzed 66 test-negative design studies that examined VE against infection or severe disease (hospitalization, intensive care unit admission, or death) for primary vaccination series. Pooled VE among studies that included people with prior COVID-19 infection was lower against infection (77%; 95% CI, 72-81) and severe disease (86%; 95% CI, 83-89) compared with studies that excluded people with prior COVID-19 infection (pooled VE against infection: 87% [95% CI, 85-89]; pooled VE against severe disease: 93% [95% CI, 91-95]). There was a negative correlation between VE estimates against infection and severe disease, and the cumulative incidence of cases before the start of the study or incidence rates during the study period. We found clear empirical evidence that higher levels of preexisting immunity were associated with lower VE estimates. Prior infections should be treated as both a confounder and effect modificatory when the policies target the whole population or are stratified by infection history, respectively.
Characterizing an amidase and its operon from actinomycete bacteria responsible for paraben catabolism
Authors: Takenoya Mihoko , Hiratsuka Yoshiaki , Shimamura Kaho , Ito Shinsaku , Sasaki Yasuyuki , Yajima Shunsuke 
Published: June 2024

Abstract
Hydrazidase from Microbacterium hydrocarbonoxydans was revealed to catalyze synthetic hydrazide compounds, enabling the bacteria to grow with them as a sole carbon source, but natural substrates have remained unknown. In this study, kinetic analyses of hydrazidase with parabens showed that the compounds can be substrates. Then, methylparaben induced gene expressions of the operon containing hydrazidase and ABC transporter, and the compound as a sole carbon source was able to grow the bacteria. Furthermore, homology search was carried out revealing that several actinomycetes possess hydrazidase homologs in the operon. Among those bacteria, an amidase from Pseudonocardia acaciae was subjected to a kinetic analysis and a structure determination revealing similar but not identical to those of hydrazidase. Since parabens are reported to exist in plants and soil, and several actinomycetes code the homologous operon, the enzymes with those operons may play a physiologically important role for bacterial survival with use of parabens.
Assay for okadaic acid O-acyl transferase using HPLC-FLD
Authors: Terauchi Masato , Komazaki Yuki , Yoshino Atsushi , Cho Yuko , Kudo Yuta , Yotsu-Yamashita Mari , Konoki Keiichi 
Published: June 2024

ABSTRACT
Dinophysistoxin 1 (DTX1, 1) and okadaic acid (OA, 2), produced by the dinoflagellates Dinophysis spp. and Prorocentrum spp., are primary diarrhetic shellfish toxins (DSTs), which may cause gastric illness in people consuming such as bivalves. Both compounds convert to dinophysistoxin 3 (DTX3, 3; generic name for 1 and 2 with fatty acids conjugated at 7-OH) in bivalves. The enzyme okadaic acid O-acyl transferase (OOAT) is a membrane protein found in the microsomes of the digestive glands of bivalves. In this study, we established an in vitro enzymatic conversion reaction using 4-nitro-2,1,3-benzoxadiazole (NBD)-OA (4), an OA derivative conjugated with (R)-(-)-4-nitro-7-(3-aminopyrrolidin-1-yl)-2,1,3-benzoxadiazole (NBD-APy) on 1-CO2H, as a substrate. We detected the enzymatically produced 3, NBD-7-O-palmitoyl-OA (NBD-Pal-OA), using high-performance liquid chromatography-fluorescence detection. We believe that an OOAT assay using 4 will facilitate the fractionation and isolation of OOAT in the future.
OLB-AC: toward optimizing ligand bioactivities through deep graph learning and activity cliffs
Authors: Yin Yueming , Hu Haifeng , Yang Jitao , Ye Chun , Goh Wilson Wen Bin , Kong Adams Wai-Kin , Wu Jiansheng 
Published: June 2024

Abstract

Motivation
Deep graph learning (DGL) has been widely employed in the realm of ligand-based virtual screening. Within this field, a key hurdle is the existence of activity cliffs (ACs), where minor chemical alterations can lead to significant changes in bioactivity. In response, several DGL models have been developed to enhance ligand bioactivity prediction in the presence of ACs. Yet, there remains a largely unexplored opportunity within ACs for optimizing ligand bioactivity, making it an area ripe for further investigation.

Results
We present a novel approach to simultaneously predict and optimize ligand bioactivities through DGL and ACs (OLB-AC). OLB-AC possesses the capability to optimize ligand molecules located near ACs, providing a direct reference for optimizing ligand bioactivities with the matching of original ligands. To accomplish this, a novel attentive graph reconstruction neural network and ligand optimization scheme are proposed. Attentive graph reconstruction neural network reconstructs original ligands and optimizes them through adversarial representations derived from their bioactivity prediction process. Experimental results on nine drug targets reveal that out of the 667 molecules generated through OLB-AC optimization on datasets comprising 974 low-activity, noninhibitor, or highly toxic ligands, 49 are recognized as known highly active, inhibitor, or nontoxic ligands beyond the datasets’ scope. The 27 out of 49 matched molecular pairs generated by OLB-AC reveal novel transformations not present in their training sets. The adversarial representations employed for ligand optimization originate from the gradients of bioactivity predictions. Therefore, we also assess OLB-AC’s prediction accuracy across 33 different bioactivity datasets. Results show that OLB-AC achieves the best Pearson correlation coefficient (r2) on 27/33 datasets, with an average improvement of 7.2%–22.9% against the state-of-the-art bioactivity prediction methods.

Availability and implementation
The code and dataset developed in this work are available at github.com/Yueming-Yin/OLB-AC.
Genopyc: a Python library for investigating the functional effects of genomic variants associated to complex diseases
Authors: Gualdi Francesco , Oliva Baldomero , Piñero Janet 
Published: June 2024

Abstract

Motivation
Understanding the genetic basis of complex diseases is one of the main challenges in modern genomics. However, current tools often lack the versatility to efficiently analyze the intricate relationships between genetic variations and disease outcomes. To address this, we introduce Genopyc, a novel Python library designed for comprehensive investigation of how the variants associated to complex diseases affects downstream pathways. Genopyc offers an extensive suite of functions for heterogeneous data mining and visualization, enabling researchers to delve into and integrate biological information from large-scale genomic datasets.

Results
In this work, we present the Genopyc library through application to real-world genome wide association studies variants. Using Genopyc to investigate the functional consequences of variants associated to intervertebral disc degeneration enabled a deeper understanding of the potential dysregulated pathways involved in the disease, which can be explored and visualized by exploiting the functionalities featured in the package. Genopyc emerges as a powerful asset for researchers, facilitating the investigation of complex diseases paving the way for more targeted therapeutic interventions.

Availability and implementation
Genopyc is available on pip https://pypi.org/project/genopyc/.The source code of Genopyc is available at https://github.com/freh-g/genopyc. A tutorial notebook is available at https://github.com/freh-g/genopyc/blob/main/tutorials/Genopyc_tutorial_notebook.ipynb. Finally, a detailed documentation is available at: https://genopyc.readthedocs.io/en/latest/.
Multimodal pretraining for unsupervised protein representation learning
Authors: Nguyen Viet Thanh Duy , Hy Truong Son 
Published: June 2024

Abstract
Proteins are complex biomolecules essential for numerous biological processes, making them crucial targets for advancements in molecular biology, medical research, and drug design. Understanding their intricate, hierarchical structures, and functions is vital for progress in these fields. To capture this complexity, we introduce Multimodal Protein Representation Learning (MPRL), a novel framework for symmetry-preserving multimodal pretraining that learns unified, unsupervised protein representations by integrating primary and tertiary structures. MPRL employs Evolutionary Scale Modeling (ESM-2) for sequence analysis, Variational Graph Auto-Encoders (VGAE) for residue-level graphs, and PointNet Autoencoder (PAE) for 3D point clouds of atoms, each designed to capture the spatial and evolutionary intricacies of proteins while preserving critical symmetries. By leveraging Auto-Fusion to synthesize joint representations from these pretrained models, MPRL ensures robust and comprehensive protein representations. Our extensive evaluation demonstrates that MPRL significantly enhances performance in various tasks such as protein–ligand binding affinity prediction, protein fold classification, enzyme activity identification, and mutation stability prediction. This framework advances the understanding of protein dynamics and facilitates future research in the field. Our source code is publicly available at https://github.com/HySonLab/Protein_Pretrain.
Rates of Resistance to Ceftazidime-Avibactam and Ceftolozane-Tazobactam Among Patients Treated for Multidrug-Resistant Pseudomonas aeruginosa Bacteremia or Pneumonia
Authors: Shah Sunish , Kline Ellen G , Haidar Ghady , Squires Kevin M , Pogue Jason M , McCreary Erin K , Ludwig Justin , Clarke Lloyd G , Stellfox Madison , Van Tyne Daria , Shields Ryan K 
Published: June 2024

Abstract
Among consecutive patients with multidrug-resistant Pseudomonas aeruginosa bacteremia or pneumonia we found those treated with ceftazidime-avibactam were more likely to develop resistance (defined as ≥4-fold increased MIC) than those treated with ceftolozane-tazobactam (40% vs 10%; P = .002). Ceftazidime-avibactam resistance was associated with new mutations in ampC and efflux regulatory pathways.
Limited efficacy of a commercial microbial inoculant for improving growth and physiological performance of native plant species
Authors: Wong Wei San , Ruscalleda-Alvarez Jaume , Yong Jean W H , Stevens Jason C , Valliere Justin M , Veneklaas Erik J 
Published: June 2024

Abstract
Soil microbial inoculants are increasingly being explored as means to improve soil conditions to facilitate ecological restoration. In southwestern Western Australia, highly biodiverse Banksia woodland plant communities are increasingly threatened by various factors including climate change, land development and mining. Banksia woodland restoration is necessary to conserve this plant community. The use of microbial inoculation in Banksia woodland restoration has not yet been investigated. Here, we evaluated the efficacy of a commercial microbial inoculant (GOGO Juice, Neutrog Australia Pty Ltd) for improving the performance of 10 ecologically diverse Banksia woodland plant species in a pot experiment. Plants were subjected to one of two watering regimes (well-watered and drought) in combination with microbial inoculation treatments (non-inoculated and inoculated). Plants were maintained under these two watering treatments for 10 weeks, at which point plants in all treatments were subjected to a final drought period lasting 8 weeks. Plant performance was evaluated by plant biomass and allocation, gas exchange parameters, foliar carbon and nitrogen and stable isotope (δ15N and δ13C) compositions. Plant xylem sap phytohormones were analysed to investigate the effect of microbial inoculation on plant phytohormone profiles and potential relationships with other observed physiological parameters. Across all investigated plant species, inoculation treatments had small effects on plant growth. Further analysis within each species revealed that inoculation treatments did not result in significant biomass gain under well-watered or drought-stressed conditions, and effects on nitrogen nutrition and photosynthesis were variable and minimal. This suggests that the selected commercial microbial inoculant had limited benefits for the tested plant species. Further investigations on the compatibility between the microorganisms (present in the inoculant) and plants, timing of inoculation, viability of the microorganisms and concentration(s) required to achieve effectiveness, under controlled conditions, and field trials are required to test the feasibility and efficacy in actual restoration environments.
Who will take the bait? Using an embedded, experimental study to chart organization-specific phishing risk profiles and the effect of a voluntary microlearning among employees of a Dutch municipality
Authors: Spithoven Remco , Drenth Anthonie 
Published: June 2024

Abstract
Phishing can lead to data leaks or infiltration of computer networks. Protection against the risks of phishing is particularly important for public organizations such as municipalities, that process a large amount of sensitive personal information and whose operational processes can have major societal impact. This makes phishing a direct threat to operational continuity and the reputation of the organization and raises the question of how public organizations can combat this effectively and which resources they can deploy to mitigate the risks of phishing. In this experiment, two test phishing emails were sent to the total population of one of the 15 largest Dutch municipalities. We performed an embedded experiment, with employees experiencing the risks of phishing first hand with extensive attention for the ethics of this approach. Senior and middle-aged employees clearly run the biggest risk of becoming victims of phishing at this specific organization, but they are not automatically prepared to do an online, educational microlearning on phishing. This is also the case for young staff. Less voluntary education should be aimed at these groups of employees in this organization to make them and the organization, more resilient to the risks of phishing. Also, the microlearning did not have an effect on the results of our participants. We advocate a tailor-made approach of offline training to raise awareness and resilience against phishing among employees of public organizations, municipalities, and organizations in general. Our experimental design can be reused in this direction. We conclude to also look at how never-clickers think and act, with further theoretical substantiation and research into the application of the human-as-solution approach..
Genome report: First reference genome of Vaccinium floribundum Kunth, an emblematic Andean species
Authors: Albuja-Quintana Martina , Pozo Gabriela , Gordillo-Romero Milton , Armijos Carolina E , Torres Maria de Lourdes 
Published: June 2024

Abstract
Vaccinium floribundum Kunth, known as “mortiño,” is an endemic shrub species of the Andean region adapted to harsh conditions in high-altitude ecosystems. It plays an important ecological role as a pioneer species in the aftermath of deforestation and human-induced fires within paramo ecosystems, emphasizing its conservation value. While previous studies have offered insights into the genetic diversity of mortiño, comprehensive genomic studies are still missing to fully understand the unique adaptations of this species and its population status, highlighting the importance of generating a reference genome for this plant. ONT and Illumina sequencing were used to establish a reference genome for this species. Three different de novo genome assemblies were generated and compared for quality, continuity and completeness. The Flye assembly was selected as the best and refined by filtering out short ONT reads, screening for contaminants and genome scaffolding. The final assembly has a genome size of 529 Mb, containing 1,317 contigs and 97% complete BUSCOs, indicating a high level of integrity of the genome. Additionally, the LTR Assembly Index of 12.93 further categorizes this assembly as a reference genome. The genome of V. floribundum reported in this study is the first reference genome generated for this species, providing a valuable tool for further studies. This high-quality genome, based on the quality and completeness parameters obtained, will not only help uncover the genetic mechanisms responsible for its unique traits and adaptations to high-altitude ecosystems but will also contribute to conservation strategies for a species endemic to the Andes.
Acute kidney injury after radical gastrectomy: incidence, risk factors, and impact on prognosis
Authors: Zhang Benlong , Li Li , Gao Yunhe , Wang Zijian , Lu Yixun , Chen Lin , Zhang Kecheng 
Published: June 2024

Abstract

Background
Acute kidney injury (AKI) is a serious adverse event often overlooked following major abdominal surgery. While radical gastrectomy stands as the primary curative method for treating gastric cancer patients, little information exists regarding AKI post-surgery. Hence, this study aimed to ascertain the incidence rate, risk factors, and consequences of AKI among patients undergoing radical gastrectomy.

Methods
This was a population-based, retrospective cohort study. The incidence of AKI was calculated. Multivariate logistic regression was used to identify independent predictors of AKI. Survival curves were plotted by using the Kaplan–Meier method and differences in survival rates between groups were analyzed by using the log-rank test.

Results
Of the 2,875 patients enrolled in this study, 61 (2.1%) developed postoperative AKI, with AKI Network 1, 2, and 3 in 50 (82.0%), 6 (9.8%), and 5 (8.2%), respectively. Of these, 49 patients had fully recovered by discharge. Risk factors for AKI after radical gastrectomy were preoperative hypertension (odds ratio [OR], 1.877; 95% CI, 1.064–3.311; P = 0.030), intraoperative blood loss (OR, 1.001; 95% CI, 1.000–1.002; P = 0.023), operation time (OR, 1.303; 95% CI, 1.030–1.649; P = 0.027), and postoperative intensive care unit (ICU) admission (OR, 4.303; 95% CI, 2.301–8.045; P &lt; 0.001). The probability of postoperative complications, mortality during hospitalization, and length of stay in patients with AKI after surgery were significantly higher than those in patients without AKI. There was no statistical difference in overall survival (OS) rates between patients with AKI and without AKI (1-year, 3-year, 5-year overall survival rates of patients with AKI and without AKI were 93.3% vs 92.0%, 70.9% vs 73.6%, and 57.1% vs 67.1%, respectively, P = 0.137).

Conclusions
AKI following radical gastrectomy is relatively rare and typically self-limited. AKI is linked with preoperative hypertension, intraoperative blood loss, operation time, and postoperative ICU admission. While AKI raises the likelihood of postoperative complications, it does not affect OS.
Robotic-assisted thoracic surgery training in France: a nation-wide survey from young surgeons
Authors: Clermidy Hugo , Fadel Guillaume , Bottet Benjamin , Belaroussi Yaniss , Eid Maroua , Armand Elsa , Baste Jean-Marc , Pages Pierre-Benoit , Fourdrain Alex , Al Zreibi Charles , Madelaine Leslie , Saiydoun Gabriel ,   AJCTCV, Bernard Chloé , Jungling Marie , Aiouaz Hayat , Vasse Solenne , Buschiazzo Antoine , Borchiellini Paul , Cattan Johann , Saade Saadé 
Published: June 2024

Abstract

OBJECTIVES
Evaluate theoretical and practical training of thoracic surgeons-in-training in robotic-assisted thoracic surgery (RATS) in France.

METHODS
A survey was distributed to thoracic surgeons-in-training in France from November 2022 to February 2023.

RESULTS
We recruited 101 thoracic surgeons-in-training (77% response rate). Over half had access to a surgical robotics system at their current institution. Most (74%) considered robotic surgery training essential, 90% had attended a robotic procedure. Only 18% had performed a complete thoracic robotic procedure as the main operator. A complete RATS procedure was performed by 42% of fellows and 6% of residents. Of the remaining surgeons, 23% had performed part of a robotic procedure. Theoretical courses and simulation are well developed; 72% of residents and 91% of fellows had undergone simulation training in the operating room, at training facilities, or during congress amounting to &lt;10 h (for 73% of the fellows and residents), 10–20 h (17%), 20–30 h (8%) or &gt;30 h (3%). Access to RATS was ≥1 day/week in 71% of thoracic departments with robotic access. Fellows spent a median of 2 (IQR 1–3) semesters in departments performing robotic surgery. Compared with low-volume centres, trainees at high-volume centres performed significantly more complete robotic procedures (47% vs 13%; P = 0.001), as did fellows compared with residents.

CONCLUSIONS
Few young surgeons perform complete thoracic robotic procedures during practical training, and access remains centre dependent. Opportunities increase with seniority and exposure; however, increasing availability of robotic devices, theoretical formation, and simulation courses will increase opportunities.