bluuebunny/crossref_metadata_2025 huggingface dataset:
The gapless genome assembly and multi-omics analyses unveil a pivotal regulatory mechanism of oil biosynthesis in the olive tree
Authors: Lv Jiaojiao , Jiang Chengying , Wu Wenjun , Mao Kaili , Wei Qianqian , Zheng Yuming , Gao Chengyu , Niu Zhiming , Jin Gaoming , Zhang Rong , Mao Juan , Chen Baihong , Ren Guangpeng , Yang Yongzhi , Wan Dongshi
Published: June 2024

Olive is a valuable oil-bearing tree with fruits containing high levels of fatty acids. Oil production is a multifaceted process involving intricate interactions between fatty acid biosynthesis and other metabolic pathways that are affected by genetics and the developmental stages of the fruit. However, a comprehensive understanding of the underlying regulatory mechanisms is still lacking. Here, we generated a gap-free telomere-to-telomere assembly for Olea europaea cv. ‘Leccino’, representing an olive genome with the highest contiguity and completeness to date. The combination of time-course metabolomics and transcriptomics datasets revealed a negative correlation between fatty acid and flavonoid biosynthesis in the initial phase of olive fruit development, which was subject to an opposing regulatory mechanism mediated by the hub transcription factor MYC2. Multifaceted molecular assays demonstrated that MYC2 is a repressor of fatty acid biosynthesis by downregulating the expression of BCCP2 (biotin carboxylase carrier protein 2), while it acts as an activator of FLS (flavonol synthase), leading to an increase in flavonoid synthesis. Furthermore, the expression of MYC2 is regulated by fluctuations of methyl jasmonate content during olive fruit development. Our study completes a high-quality gapless genome of an olive cultivar, and provides new insight into the regulatory mechanisms underlying the biosynthesis of fatty acids and flavonoids in its fruit.
Drivers of bitter crab disease occurrence in eastern Bering Sea snow crab (Chionoecetes opilio)
Authors: Balstad Laurinne J , Fedewa Erin J , Szuwalski Cody S
Published: June 2024

A recent population collapse of eastern Bering Sea (EBS) snow crab (Chionoecetes opilio) led to the first-ever closure of the snow crab fishery in 2022. The population collapse, caused, in part, by unprecedented warming, was preceded by peaks in juvenile snow crab density (2018) and bitter crab disease (BCD, Hematodinium sp.; 2016), a fatal crustacean disease. Annual bottom trawl surveys in the EBS show high year-to-year spatiotemporal variation in BCD-infected crab, yet it remains unclear what ecological drivers might explain the variation. We used statistical models of BCD presence/absence to examine the relative importance of intrinsic and extrinsic factors as drivers of BCD. We found a dome-shaped relationship between temperature and BCD presence, and results suggest that 2–4°C bottom temperatures are more likely to support BCD. Matching with past work across the globe, we find that stations with high population density of small, new shell crab are most likely to be BCD-positive. While our work highlights the challenges of disease monitoring in the EBS, our results indicate that indirect management measures related to snow crab rebuilding and recruitment may be more appropriate than directed fisheries management in mitigating BCD impacts.
hp-version C1-continuous Petrov–Galerkin method for nonlinear second-order initial value problems with application to wave equations
Authors: Wang Lina , Zhang Mingzhu , Tian Hongjiong , Yi Lijun
Published: June 2024

We introduce and analyze an $hp$-version $C^{1}$-continuous Petrov–Galerkin (CPG) method for nonlinear initial value problems of second-order ordinary differential equations. We derive a-priori error estimates in the $L^{2}$-, $L^{\infty }$-, $H^{1}$- and $H^{2}$-norms that are completely explicit in the local time steps and local approximation degrees. Moreover, we show that the $hp$-version $C^{1}$-CPG method superconverges at the nodal points of the time partition with regard to the time steps and approximation degrees. As an application, we apply the $hp$-version $C^{1}$-CPG method to time discretization of nonlinear wave equations. Several numerical examples are presented to verify the theoretical results.
Connecting detailed photosynthetic kinetics to crop growth and yield: a coupled modelling framework
Authors: He Yufeng , Wang Yu , Friedel Douglas , Lang Meagan , Matthews Megan L
Published: June 2024

Photosynthesis and crop growth are inseparable processes that govern plant carbon assimilation and allocation. An accurate model description of these processes can bridge dynamics at the leaf and canopy levels, assisting in identifying potential photosynthetic improvements that can be converted into increased yield. Integrating multiscale biophysical processes and achieving computational effectiveness for seasonal simulations, however, are challenging. Here, we present a fully coupled modelling framework that integrates a metabolic model of C3 photosynthesis (ePhotosynthesis) and a semi-mechanistic crop growth model (BioCro). We replaced the leaf-level Farquhar photosynthesis model in BioCro with the ePhotosynthesis model that mechanistically describes the photosystem electron transport processes and the C3 carbon metabolism including the Calvin–Benson–Bassham cycle and the photorespiratory pathway. The coupled BioCro-ePhotosynthesis model was calibrated to represent a soybean cultivar and developed to be operationally fast for seasonal simulations. As an example of model application, we conducted a global sensitivity analysis of 26 enzymes under an average daytime intercepted radiation of 400 µmol m−2 s−1, identifying 2 enzymes, phosphoglycerate kinase (PGK) and phosphoribulokinase (PRK), which had the largest impact on the leaf-level assimilation. Increasing PGK and PRK by 2-fold was predicted to increase the leaf-level assimilation by 8.3 % and the final seed yield by 6.75 % ± 0.5 % over 4 years of observed field climate data. The coupled BioCro-ePhotosynthesis model provides a seamless and efficient integration between the leaf-level metabolism and the field-level yield over a full growing season. The coupled model could be further applied to investigate non-steady-state photosynthetic processes such as non-photochemical quenching.
LEAP: LLM instruction-example adaptive prompting framework for biomedical relation extraction
Authors: Zhou Huixue , Li Mingchen , Xiao Yongkang , Yang Han , Zhang Rui
Published: June 2024

Objective

To investigate the demonstration in large language models (LLMs) for biomedical relation extraction. This study introduces a framework comprising three types of adaptive tuning methods to assess their impacts and effectiveness.

Materials and Methods

Our study was conducted in two phases. Initially, we analyzed a range of demonstration components vital for LLMs’ biomedical data capabilities, including task descriptions and examples, experimenting with various combinations. Subsequently, we introduced the LLM instruction-example adaptive prompting (LEAP) framework, including instruction adaptive tuning, example adaptive tuning, and instruction-example adaptive tuning methods. This framework aims to systematically investigate both adaptive task descriptions and adaptive examples within the demonstration. We assessed the performance of the LEAP framework on the DDI, ChemProt, and BioRED datasets, employing LLMs such as Llama2-7b, Llama2-13b, and MedLLaMA_13B.

Results

Our findings indicated that Instruction + Options + Example and its expanded form substantially improved F1 scores over the standard Instruction + Options mode for zero-shot LLMs. The LEAP framework, particularly through its example adaptive prompting, demonstrated superior performance over conventional instruction tuning across all models. Notably, the MedLLAMA_13B model achieved an exceptional F1 score of 95.13 on the ChemProt dataset using this method. Significant improvements were also observed in the DDI 2013 and BioRED datasets, confirming the method’s robustness in sophisticated data extraction scenarios.

Conclusion

The LEAP framework offers a compelling strategy for enhancing LLM training strategies, steering away from extensive fine-tuning towards more dynamic and contextually enriched prompting methodologies, showcasing in biomedical relation extraction.
Using machine learning to improve anaphylaxis case identification in medical claims data
Authors: Kural Kamil Can , Mazo Ilya , Walderhaug Mark , Santana-Quintero Luis , Karagiannis Konstantinos , Thompson Elaine E , Kelman Jeffrey A , Goud Ravi
Published: June 2024

Objectives

Anaphylaxis is a severe life-threatening allergic reaction, and its accurate identification in healthcare databases can harness the potential of “Big Data” for healthcare or public health purposes.

Materials and methods

This study used claims data obtained between October 1, 2015 and February 28, 2019 from the CMS database to examine the utility of machine learning in identifying incident anaphylaxis cases. We created a feature selection pipeline to identify critical features between different datasets. Then a variety of unsupervised and supervised methods were used (eg, Sammon mapping and eXtreme Gradient Boosting) to train models on datasets of differing data quality, which reflects the varying availability and potential rarity of ground truth data in medical databases.

Results

Resulting machine learning model accuracies ranged from 47.7% to 94.4% when tested on ground truth data. Finally, we found new features to help experts enhance existing case-finding algorithms.

Discussion

Developing precise algorithms to detect medical outcomes in claims can be a laborious and expensive process, particularly for conditions presented and coded diversely. We found it beneficial to filter out highly potent codes used for data curation to identify underlying patterns and features. To improve rule-based algorithms where necessary, researchers could use model explainers to determine noteworthy features, which could then be shared with experts and included in the algorithm.

Conclusion

Our work suggests machine learning models can perform at similar levels as a previously published expert case-finding algorithm, while also having the potential to improve performance or streamline algorithm construction processes by identifying new relevant features for algorithm construction.
Electromembrane extraction of drugs of abuse and prescription drugs from micropulverized hair
Authors: Schüller Maria , Bergh Marianne Skov-Skov , Pedersen-Bjergaard Stig , Øiestad Elisabeth Leere
Published: June 2024

Hair analysis can provide chronological insights into past drug use for months to years after drug administration. In comparison to analyses from other biological matrices, such as blood and urine, sample pretreatment is often tedious and not environmental friendly. In this study, we present a more environmental friendly approach to hair analysis using micropulverized hair and electromembrane extraction for the efficient extraction of 15 drugs of abuse, prescription drugs, and metabolites from hair. The optimized extraction method, involving micropulverization, demonstrated comparable yields to the standard approach of cutting and overnight incubation. A 15-min extraction method using a commercial electromembrane extraction prototype was developed and validated according to forensic guidelines, using only 10 µL of organic solvent per sample. The final method, employing HPLC–MS–MS with a biphenyl column, exhibited good linearity, precision, and sensitivity. An AgreePrep assessment comparing the environmental impact of our method with the standard routine method, involving overnight incubation and conventional liquid–liquid extraction, was conducted. This is the first time micropulverized hair has been subjected to electromembrane extraction.
First successful downhole testing of the permeability logging prototype
Authors: Li Ning , Wang Kewen , Lu Junqiang , Liu Peng , Xiao Chengwen , Wu Hongliang , Guo Qingbin , Fan Huajun , Men Baiyong , Feng Zhou , Li Yusheng
Published: June 2024

This article reports on the successful downhole testing of the prototype permeability logging instrument, developed by the Li Ning Innovation Team of PetroChina. The test was carried out on 3 March 2024 in the Ren 91 standard well in Huabei (North China). In this article, we analysed the instrument characteristics of porosity logging measurement, saturation logging measurement, and permeability logging measurement in three stages of development, as well as the current research status of continuous depth-permeability measurement in the wellbore formations. We highlighted the basic principle of permeability logging measurement with Stoneley waves and pointed out the main challenges in the development of permeability logging measurement devices and on-site application research.
Anatomical and Surface Electron Microscopic Investigation of the Tongue and Laryngeal Prominence in the Red-Eyed Turtle Dove (Streptopelia semitorquata, Rüppel 1837)
Authors: Igbokwe Casmir Onwuaso , Mbajiorgu Felix Ejikeme , Bello Umar Muhammed
Published: June 2024

This study investigated the morphology of tongue and laryngeal structures in red-eyed dove and related it to feeding habits. Samples were examined using gross anatomy, scanning electron microscopy (SEM), and histological techniques. The tongue conformed to the shape of the lower beak, and the apex with a pointed tip, body, and root were distinguished. A median grove was apparent, and a papillary crest with pointed triangular papillae separated the body from the root. The length of the tongue, its width (body), and the percentage of the length of the lower jaw occupied by the tongue were, on average, 12.5 mm, 2.3 mm, and 57.3%, respectively. SEM showed highly desquamated dorsal epithelium with pointed papillae-like projections. The papillary crest presented pointed papillae of about 20–22. Salivary openings were apparent in the root, surrounded by mucosal folds and blunt papillae. Laryngeal prominence was irregularly triangular shaped and elevated. The rim of the glottis showed glandular pinpointed marks. Typical cornified multilayered mucosal epithelium was present in the apex and decreased caudally. Hyaline entoglossal cartilage and adjoining connective tissue were present in the body and apex. Numerous tubuloalveolar glands were seen in the body and root. The rim of the glottis showed mucous intraepithelial glands. The rostral and caudal lingual glands indicated positive reaction to neutral and acidic mucins. This study demonstrated a morphofunctional relationship of the tongue of a red-eyed dove to its diet.
Evidence for non-zero turbulence in the protoplanetary disc around IM Lup
Authors: Flaherty Kevin , Hughes A Meredith , Simon Jacob B , Reina Alicia Smith , Qi Chunhua , Bai Xue-Ning , Andrews Sean M , Wilner David J , Kóspál Ágnes
Published: June 2024

The amount of turbulence in protoplanetary discs around young stars is critical for determining the efficiency, timeline, and outcomes of planet formation. It is also difficult to measure. Observations are still limited, but direct measurements of the non-thermal, turbulent gas motion are possible with the Atacama Large Millimeter/submillimeter Array (ALMA). Using CO(2–1)/$^{13}$CO(2–1)/C$^{18}$O(2–1) ALMA observations of the disc around IM Lup at $\sim 0.4$ arcsec ($\sim$60 au) resolution we find evidence of significant turbulence, at the level of $\delta v_{\rm turb}=(0.18-0.30)$c$_\mathrm{ s}$. This result is robust against systematic uncertainties (e.g. amplitude flux calibration, mid-plane gas temperature, disc self-gravity). We find that gravito-turbulence as the source of the gas motion is unlikely based on the lack of an imprint on the rotation curve from a massive disc, while magneto-rotational instabilities and hydrodynamic instabilities are still possible, depending on the unknown magnetic field strength and the cooling time-scale in the outer disc.
Automated detection and analysis of coronal active region structures across solar cycle 24
Authors: Gass Daniel G , Walsh Robert W
Published: June 2024

Observations from NASA’s Solar Dynamic Observatory Atmospheric Imaging Assembly were employed to investigate targeted physical properties of coronal active region structures across the majority of solar cycle 24 (From 2010 May to end of 2020 December). This is the largest consistent study to date which analyses emergent trends in structural width, location, and occurrence rate by performing an automatic and long-term examination of observable coronal and chromospheric limb features within equatorial active region belts across four extreme ultraviolet wavelengths (171, 193, 211, and 304 Å). This has resulted in over 30 000 observed coronal structures and hence allows for the production of spatial and temporal distributions focused upon the rise, peak, and decay activity phases of solar cycle 24. Employing a self-organized-criticality approach as a descriptor of coronal structure formation, power-law slopes of structural widths versus frequency are determined, ranging from -1.6 to -3.3 with variations of up to 0.7 found between differing periods of the solar cycle, compared to a predicted Fractal Diffusive Self-Organized Criticality (FD-SOC) value of -1.5. The North–South hemispheric asymmetry of these structures was also examined with the Northern hemisphere exhibiting activity that is peaking earlier and decaying slower than the Southern hemisphere, with a characteristic ‘butterfly’ pattern of coronal structures detected. This represents the first survey of coronal structures performed across an entire solar cycle, demonstrating new techniques available to examine the composition of the corona by latitude in varying wavelengths.
Exploring galaxy evolution time-scales in clusters: insights from the projected phase space
Authors: Sampaio V M , de Carvalho R R , Aragón-Salamanca A , Merrifield M R , Ferreras I , Cornwell D J
Published: June 2024

Galaxies infalling into clusters undergo both star formation quenching and morphological transformation due to environmental effects. We investigate these processes and their time-scales using a local sample of 20 191 cluster and 11 674 field galaxies from Sloan Digital Sky Survey. By analysing morphology as a function of distance from the star formation main sequence, we show that environmental influence is especially pronounced for low-mass galaxies, which emerge from the green valley (GV) with early-type morphologies before their star formation is fully suppressed. Using the galaxies’ positions in the clusters’ projected phase space, we examine the evolution of blue cloud, GV, and red-sequence fractions as a function of time since infall. Interestingly, the GV fraction remains constant with time since infall, suggesting a balanced flow of galaxies in and out of this class. We estimate that galaxies less massive than $10^{10}\,\rm {\rm M}_{\odot }$ spend approximately 0.4 Gyr in the GV. By comparing quenched and early-type populations, we provide further evidence for the ‘slow-then-rapid’ quenching model and suggest that it can also be applied to morphological transitions. Our results indicate that morphological transformation occurs at larger radii than complete star formation quenching. About 75 per cent of galaxies undergoing morphological transition in clusters are spirals evolving into S0s, suggesting that infalling galaxies retain their discs, while massive ellipticals are relics of early merger events. Finally, we show it takes approximately 2.5 and 1.2 Gyr after the delay time ($\sim 3.8 {\,\rm Gyr}$) for the population of low-mass galaxies in clusters to reach a 50 per cent threshold in quenched and early-type fraction, respectively. These findings suggest morphological transition precedes full star formation quenching, with both processes possibly being causally linked.
Chrononutrition in Critical Illness
Authors: Sagun Eylul , Akyol Asli , Kaymak Cetin
Published: June 2024

Circadian rhythms in humans are biological rhythms that regulate various physiological processes within a 24-hour time frame. Critical illness can disrupt the circadian rhythm, as can environmental and clinical factors, including altered light exposure, organ replacement therapies, disrupted sleep–wake cycles, noise, continuous enteral feeding, immobility, and therapeutic interventions. Nonpharmacological interventions, controlling the ICU environment, and pharmacological treatments are among the treatment strategies for circadian disruption. Nutrition establishes biological rhythms in metabolically active peripheral tissues and organs through appropriate synchronization with endocrine signals. Therefore, adhering to a feeding schedule based on the biological clock, a concept known as “chrononutrition,” appears to be vitally important for regulating peripheral clocks. Chrononutritional approaches, such as intermittent enteral feeding that includes overnight fasting and consideration of macronutrient composition in enteral solutions, could potentially restore circadian health by resetting peripheral clocks. However, due to the lack of evidence, further studies on the effect of chrononutrition on clinical outcomes in critical illness are needed. The purpose of this review was to discuss the role of chrononutrition in regulating biological rhythms in critical illness, and its impact on clinical outcomes.
Get2PrEP2—A Provider Messaging Strategy to Improve PrEP Uptake: A Randomized Controlled Quality Improvement Project
Authors: Zucker Jason , Castor Delivette , Theodore Deborah , Carnevale Caroline , Osilama Eshiemomoh , Archer Norman , Bonadonna Lily , Wadden Elena , Morley Nicholas , Huang Simian , Meyers Kathrine , Cohall Alwyn , Gordon Peter , Sobieszczyk Magdalena E
Published: June 2024

Introduction

HIV preexposure prophylaxis (PrEP), a key strategy for preventing HIV transmission, requires awareness and access to PrEP services. Although all patients should be made aware of HIV PrEP; the diagnosis of bacterial sexually transmitted infections (STIs) is an important indicator of potential HIV PrEP need. In a previous evaluation of Get2PrEP (G2P), we found that an electronic medical record laboratory comments did not increase the frequency of PrEP discussions between patients and providers. In Get2PrEP2 (G2P2), we hypothesized that active, personalized messaging to providers about HIV PrEP would increase the documentation of PrEP discussions, referrals, and/or provision of HIV PrEP to individuals diagnosed with an STI.

Methods

G2P2 was a parallel 3-arm, unblinded, randomized controlled design. Participants were allocated 2:1 to intervention or control. Participants in the intervention arm were further allocated to receive provider messaging through the electronic medical record chat message or e-mail.

Results

The 191 randomized encounters resulted in a modest 7.8% (odds ratio, 1.078; confidence interval, 1.02–1.13) increase in documented PrEP discussions in intervention encounters versus none in the standard care group. There was no statistical difference by intervention modality. All documented discussions occurred in the outpatient or emergency department and were more frequent in women and those aged <25 years.

Discussion

An e-mail or electronic medical record chat message sent to providers of patients testing positive for an STI had a small but significant effect on documented patient-provider PrEP discussions. Further investigation is required to determine whether provider messaging can increase PrEP uptake among eligible patients and longer-term outcomes.
Bulk Rock and Olivine Chemistry and Isotopes of 106–58 Ma Basalts from Liaodong Peninsula and its Adjacent Areas: Implications for Secular Evolution of the Big Mantle Wedge in Eastern China
Authors: Zhang Chao , Ma Qiang , Hong Lubing , Dai Hong-Kun , Ma Liang , Xu Yigang , Zheng Jianping , Cao Hui-Ying
Published: June 2024

The subducting Pacific slab stagnates in the mantle transition zone and creates a big mantle wedge (BMW) system in East Asia. A similar BMW structure may have already existed since the Early Cretaceous (>120 Ma), but how such a structure evolved from Early Cretaceous to the present day remains unclear. We address this issue by comparing compositions and source heterogeneity of the 106–58 Ma basalts from Liaodong Peninsula and its adjacent areas (LPAA) in eastern China, with those formed in the modern BMW setting. The LPAA basalts display oceanic island basalts–like trace element patterns. Elemental and isotopic compositions of these basalts and their olivine phenocrysts point to peridotite and two recycled components in their source. One recycled component is altered lower oceanic crust given the low δ18Oolivine (2.8–5.2‰) of the ~99 Ma Liaoyuan alkali basalts. The second component consists of altered upper oceanic crust and pelagic sediments indicated by high δ18Oolivine (>6.0‰), represented by the ~58 Ma Luanshishanzi alkali basalts. The depleted mantle-like isotopes of these two components suggest derivation from a young HIMU source with characteristics of the Izanagi plate (e.g. Indian Ocean-type Sr-Nd-Pb-Hf isotopes), which may have resided in the mantle transition zone at that time. Our results reveal strong similarities between chemical and source characteristics of the mantle sampled by the 106–58 Ma LPAA basalts and those derived from the modern BMW. This implies that the BMW structure has been present since the Early Cretaceous, probably having lasted more than 120 Myr, and modulating the chemical properties of the upper mantle and influencing a variety of geological processes.
Automated quantification of wrist bone marrow oedema, pre- and post-treatment, in early rheumatoid arthritis
Authors: Yiu Chungwun , Griffith James Francis , Xiao Fan , Shi Lin , Zhou Bingjing , Wu Su , Tam Lai-Shan
Published: June 2024

Objective

Bone inflammation (osteitis) in early RA (ERA) manifests as bone marrow oedema (BME) and precedes the development of bone erosion. In this prospective, single-centre study, we developed an automated post-processing pipeline for quantifying the severity of wrist BME on T2-weighted fat-suppressed MRI.

Methods

A total of 80 ERA patients [mean age 54 years (s.d. 12), 62 females] were enrolled at baseline and 49 (40 females) after 1 year of treatment. For automated bone segmentation, a framework based on a convolutional neural network (nnU-Net) was trained and validated (5-fold cross-validation) for 15 wrist bone areas at baseline in 60 ERA patients. For BME quantification, BME was identified by Gaussian mixture model clustering and thresholding. BME proportion (%) and relative BME intensity within each bone area were compared with visual semi-quantitative assessment of the RA MRI score (RAMRIS).

Results

For automated wrist bone area segmentation, overall bone Sørensen–Dice similarity coefficient was 0.91 (s.d. 0.02) compared with ground truth manual segmentation. High correlation (Pearson correlation coefficient r = 0.928, P < 0.001) between visual RAMRIS BME and automated BME proportion assessment was found. The automated BME proportion decreased after treatment, correlating highly (r = 0.852, P < 0.001) with reduction in the RAMRIS BME score.

Conclusion

The automated model developed had an excellent segmentation performance and reliable quantification of both the proportion and relative intensity of wrist BME in ERA patients, providing a more objective and efficient alternative to RAMRIS BME scoring.
Data hazards in synthetic biology
Authors: Zelenka Natalie R , Di Cara Nina , Sharma Kieren , Sarvaharman Seeralan , Ghataora Jasdeep S , Parmeggiani Fabio , Nivala Jeff , Abdallah Zahraa S , Marucci Lucia , Gorochowski Thomas E
Published: June 2024

Data science is playing an increasingly important role in the design and analysis of engineered biology. This has been fueled by the development of high-throughput methods like massively parallel reporter assays, data-rich microscopy techniques, computational protein structure prediction and design, and the development of whole-cell models able to generate huge volumes of data. Although the ability to apply data-centric analyses in these contexts is appealing and increasingly simple to do, it comes with potential risks. For example, how might biases in the underlying data affect the validity of a result and what might the environmental impact of large-scale data analyses be? Here, we present a community-developed framework for assessing data hazards to help address these concerns and demonstrate its application to two synthetic biology case studies. We show the diversity of considerations that arise in common types of bioengineering projects and provide some guidelines and mitigating steps. Understanding potential issues and dangers when working with data and proactively addressing them will be essential for ensuring the appropriate use of emerging data-intensive AI methods and help increase the trustworthiness of their applications in synthetic biology.
Privacy versus transparency: It's time to look at the data
Authors: Noseda Filippo
Published: June 2024

In previous articles published in this Review, (‘FATCA, CRS and Public BO registers: a report on the direction of travel—the next 12 months’, 28 Trusts & Trustees (2022), 482–487. https://academic.oup.com/tandt/article/28/6/482/6586702; ‘FATCA and CRS: Recent EU judgment on public BO registers shines a light on the direction of travel’, 29 Trusts & Trustees (2023), 469–474. https://academic.oup.com/tandt/article/29/6/469/7163198) the author argued for a balanced approach to the whole issue of transparency in the area of taxation. The underlying legal analysis touched on data protection and Human Rights legislation, and was supported by eloquent opinions from data protection experts in the European Union. Now it’s time to look at the hard data supporting both sides of the argument.
IXThe Seventeenth Century, Part I
Authors: Martin Catherine Gimelli , Timmis Patrick , Stelzer Emily , Dyck Paul , James Anne , Urban David V
Published: June 2024

This chapter has seven sections: 1. General; 2. Bacon; 3. Browne; 4. Burton; 5. Herbert; 6. Donne; 7. Milton. Sections 1 and 2 are by Catherine Gimelli Martin; section 3 is by Patrick Timmis; section 4 is by Emily Stelzer; section 5 is by Paul Dyck; section 6 is by Anne James; section 7 is by David V. Urban.
Reshaping the Primary Cell Wall: Dual Effects on Plant Resistance to Ralstonia solanacearum and Heat Stress Response
Authors: Desaint Henri , Gigli Alessandro , Belny Adrien , Cassan-Wang Hua , Martinez Yves , Vailleau Fabienne , Mounet Fabien , Vernhettes Samantha , Berthomé Richard , Marchetti Marta
Published: June 2024

Temperature elevation drastically affects plant defense responses to Ralstonia solanacearum and inhibits the major source of resistance in Arabidopsis thaliana, which is mediated by the receptor pair RRS1-R/RPS4. In this study, we refined a previous genome-wide association (GWA) mapping analysis by using a local score approach and detected the primary cell wall CESA3 gene as a major gene involved in plant response to  R. solanacearum at both 27°C and an elevated temperature, 30°C. We functionally validated  CESA3 as a susceptibility gene involved in resistance to  R. solanacearum at both 27 and 30°C through a reverse genetic approach. We provide evidence that the  cesa3mre1 mutant enhances resistance to bacterial disease and that resistance is associated with an alteration of root cell morphology conserved at elevated temperatures. However, even by forcing the entry of the bacterium to bypass the primary cell wall barrier, the  cesa3mre1 mutant still showed enhanced resistance to  R. solanacearum with delayed onset of bacterial wilt symptoms. We demonstrated that the  cesa3mre1 mutant had constitutive expression of the defense-related gene  VSP1, which is upregulated at elevated temperatures, and that during infection, its expression level is maintained higher than in the wild-type Col-0. In conclusion, this study reveals that alteration of the primary cell wall by mutating the cellulose synthase subunit CESA3 contributes to enhanced resistance to R. solanacearum, remaining effective under heat stress. We expect that these results will help to identify robust genetic sources of resistance to  R. solanacearum in the context of global warming.

[Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Identification, Characteristics, and Fungicide Efficacy of Seed-Associated Fungi of Saposhnikovia divaricata in Northeast China
Authors: Zhang Xue , Liu Jinxin , Li Yonggang , Xue Baiyan , Bai Yunlong
Published: June 2024

Saposhnikovia divaricata (Trucz.) Schischk. is one of the traditional medicinal herbs in Northeast China, and its roots are used for medicinal purposes. In 2020, a fungus isolated from S. divaricata seeds was observed to cause root rot of seedlings and leaf and stem spot of adult plants in Shuangyashan, Heilongjiang, China. Based on morphological and molecular data, isolates of all fungi were identified as Alternaria alternata. To our knowledge, this is the first report of A. alternata isolated from S. divaricata seeds in China. The carrying rate of S. divaricata seeds from 20 different collection sites reached 100% in 70% of the sites in Hulunbeier area, Inner Mongolia, China. The A. alternata isolate could infect the roots of cucumber, sorghum, mung bean, and maize seedlings and cause root rot. Considering the control of seed-associated fungal diseases, prochloraz 45% EW had the best control effect of 92.6%, followed by flusilazole 400 g liter−1 EC (88.9%) and azoxystrobin + propiconazole 18.7% SE (70.7%) of 15 fungicides. Further field control efficacy showed that 45% prochloraz EW had an 80% control efficacy on the disease at a dose of 0.225 g liter−1. It is recommended that soaking seeds and spraying are the best treatments for controlling seed-associated fungi and leaf spot on S. divaricata caused by A. alternata. Therefore, the aforementioned methods can effectively prevent the occurrence of fungal diseases of S. divaricata and provide a way to reduce reinfestation in the field.
Survey of Heterodera glycines Population Abundance and Virulence Phenotypes During 2021 to 2022 in Heilongjiang Province
Authors: You Jia , Wang Jiajun , Tian Runze , Wang Siru , Yu Ying , Xu Lijian , Zhou Changjun , Pan Fengjuan , Chen Jingsheng , Sui Yueyu , Hu Yanfeng
Published: June 2024

Soybean cyst nematode (SCN), Heterodera glycines, poses a significant threat to global soybean production. Heilongjiang, the largest soybean-producing province in China, contributes more than 40% to the country’s total yield. This province has much longer history of SCN infestation. To assess the current situation in Heilongjiang, we conducted a survey to determine the SCN population density and virulence phenotypes during 2021 to 2022 and compared the data with a previous study in 2015. A total of 377 soil samples from 48 counties representing 11 major soybean-planting regions were collected. The prevalence of SCN increased from 55.4% in 2015 to 59% in the current survey. The population densities ranged from 80 to 26,700 eggs and juveniles per 100 cm3 of soil. Virulence phenotypes were evaluated for 60 representative SCN populations using the H. glycines (HG) type test, revealing nine different HG types. The most common virulence phenotypes were HG types 7 and 0, accounting for 56.7 and 20% of all SCN populations, respectively. The prevalence of populations with a female index (FI) greater than 10% on PI 548316 increased from 64.5% in 2015 to 71.7%. However, the FI on the commonly used resistance sources PI 548402 (Peking) and PI 437654 remained low at 3.3%. These findings highlight the increasing prevalence and changing virulence phenotypes of SCN in Heilongjiang. They also emphasize the importance of rotating soybean varieties with different resistance sources and urgently identifying new sources of resistance to combat SCN.
Procyanidin C1 inhibits bleomycin‐induced pulmonary fibrosis in mice by selective clearance of senescent myofibroblasts
Authors: Shao Min , Qiu Yujia , Shen Mengxia , Liu Wei , Feng Dandan , Luo Ziqiang , Zhou Yan
Published: June 2024

Pulmonary fibrosis is a formidable challenge in chronic and age‐related lung diseases. Myofibroblasts secrete large amounts of extracellular matrix and induce pro‐repair responses during normal wound healing. Successful tissue repair results in termination of myofibroblast activity via apoptosis; however, some myofibroblasts exhibit a senescent phenotype and escape apoptosis, causing over‐repair that is characterized by pathological fibrotic scarring. Therefore, the removal of senescent myofibroblasts using senolytics is an important method for the treatment of pulmonary fibrosis. Procyanidin C1 (PCC1) has recently been discovered as a senolytic compound with very low toxicity and few side effects. This study aimed to determine whether PCC1 could improve lung fibrosis by promoting apoptosis in senescent myofibroblasts and to investigate the mechanisms involved. The results showed that PCC1 attenuates bleomycin (BLM)‐induced pulmonary fibrosis in mice. In addition, we found that PCC1 inhibited extracellular matrix deposition and promoted the apoptosis of senescent myofibroblasts by increasing PUMA expression and activating the BAX signaling pathway. Our findings represent a new method of pulmonary fibrosis management and emphasize the potential of PCC1 as a senotherapeutic agent for the treatment of pulmonary fibrosis, providing hope for patients with pulmonary fibrosis worldwide. Our results advance our understanding of age‐related diseases and highlight the importance of addressing cellular senescence in treatment.
Time to Pregnancy and Life Expectancy: A Cohort Study of 18 796 Pregnant Couples
Authors: Lindahl-Jacobsen R. , Petersson M. Tavlo , Priskorn L. , Skakkebæk N. E. , Juul A. , Kristensen D. M. , Eisenberg M. L. , Jensen T. K.
Published: June 2024

(Abstracted from Hum Reprod 2024;39(3):595–603)

It is hypothesized that the well-evidenced global decline in reproductive health may, together with behavioral factors, be contributing to the world’s declining fertility and to a soon-expected decreasing global population. Time to pregnancy (TTP), defined as the time to success to conceive under unprotected intercourse, is a commonly used population measure of fecundity, defined as an individual’s capacity to reproduce irrespective of pregnancy intentions.
Maternal and Fetal Safety Outcomes After In Utero Stem Cell Injection: A Systematic Review
Authors: Sagar Rachel L. , Walther-Jallow Lilian , Götherström Cecilia , Westgren Magnus , David Anna L.
Published: June 2024

(Abstracted from Prenatal Diagnosis 2023;43:1622–1637)

Congenital diseases often have a significant impact on individuals both prenatally and postbirth, and treatment options are quite limited until after delivery. In utero stem cell transplantation (IUSCT) is one method that can be used to treat congenital diseases prenatally, and primarily use hematopoietic or mesenchymal stem cells.
Neonatal Survival After Serial Amnioinfusions for Bilateral Renal Agenesis: The Renal Anhydramnios Fetal Therapy Trial
Authors: Miller Jena L. , Baschat Ahmet A. , Rosner Mara , Blumenfeld Yair J. , Moldenhauer Julie S. , Johnson Anthony , Schenone Mauro H. , Zaretsky Michael V. , Chmait Ramen H. , Gonzalez Juan M. , Miller Russell S. , Moon-Grady Anita J. , Bendel-Stenzel Ellen , Keiser Amaris M. , Avandhani Radhika , Jelin Angie C. , Davis Jonathan M. , Warren Daniel S. , Hanley Daniel F. , Watkins Joslynn A. , Samuels Joshua , Sugarman Jeremy , Atkinson Meredith A.
Published: June 2024

(Abstracted from JAMA 2023;330:2096–2105)

Bilateral renal agenesis is a congenital anomaly of the fetal urinary tract that results in the absence of amniotic fluid by the second trimester. This occurs in roughly 1 in 3000 births and often results in depressurization of fetal airways, impaired pulmonary development, and lethal pulmonary hypoplasia at birth.vvvvvv
Metformin Plus Insulin for Preexisting Diabetes or Gestational Diabetes in Early Pregnancy: The MOMPOD Randomized Clinical Trial
Authors: Boggess Kim A. , Valint Arielle , Refuerzo Jerrie S. , Zork Noelia , Battarbee Ashley N. , Eichelberger Kacey , Ramos Gladys A. , Olson Gayle , Durnwald Celeste , Landon Mark B. , Aagaard Kjersti M. , Wallace Kedra , Scifres Christina , Rosen Todd , Mulla Wadia , Valent Amy , Longo Sherri , Young Laura , Marquis M. Alison , Thomas Sonia , Britt Ashley , Berry Diane
Published: June 2024

(Abstracted from JAMA 2023;330(22):2182–2190)

Preexisting type 2 diabetes in pregnant people increases the risk for adverse pregnancy outcomes, intrapartum complications, and neonatal hypoglycemia at birth. To achieve normal maternal glucose levels and optimize pregnancy outcomes, management includes maternal blood glucose monitoring, dietary management, and insulin therapy.
Vaginal Progesterone for Preventing Preterm Birth and Adverse Perinatal Outcomes in Twin Gestations: A Systematic Review and Meta-analysis
Authors: Conde-Agudelo Agustin , Romero Roberto , Rehal Anoop , Brizot Maria L. , Serra Vicente , Da Fonseca Eduardo , Cetingoz Elcin , Syngelaki Argyro , Perales Alfredo , Hassan Sonia S. , Nicolaides Kypros H.
Published: June 2024

(Abstracted from Am J Obstet Gynecol 2023;229:599–616.e3)

Preterm birth represents a significant burden to both healthcare systems and individuals. Complications resulting from preterm birth are a leading cause of death in newborns in the first weeks of life and account for 36% of all neonatal deaths, increasing the risk of both short- and long-term complications.
Qualitative Assessment of Vulvovaginal Health Information on Social Media
Authors: Bhuiyan Julia , Addison Jessica , Hassan Areej
Published: June 2024

(Abstracted from J Pediatr Adolesc Gynecol 2024;37:33–38)

Recent years have given way to an exponential rise in social media platforms as major hubs for dissemination and access of health information. This increase has occurred most dramatically in the social media usage of adolescents and young adults (AYAs), with more than 84% of adults aged 18–29 years and 95% of adolescents aged 13–17 years using at least one social media platform in 2021 and 2022, respectively.
Dexamethasone for Cardiac Surgery
Authors: Myles Paul S. , Dieleman Jan M. , Munting Karin E. , Forbes Andrew , Martin Catherine A. , Smith Julian A. , McGiffin David , Verheijen Lieke P. J. , Wallace Sophie , Ueoka M. , Dutton M. , Robertshaw S. , Clarris M. , Neylan A. , Hulley A. , Warwarek S. , Painter T. , Heyman K. , Falland R.-L. , Pieterse J. , Fiddes R. , Marriott A. , Dieleman J. , Cope J. , Clark-Mackay E. , van Dijk D. , Wietsma N.E. , Monteiro de Olivieira N. P. , Oey L. W. L.
Published: June 2024

Background:

High-dose corticosteroids have been used to attenuate the inflammatory response to cardiac surgery and cardiopulmonary bypass, but patient outcome benefits remain unclear. The primary aim was to determine whether using dexamethasone was superior to not using dexamethasone to increase the number of home days in the first 30 days after cardiac surgery. Our secondary aim was to evaluate efficiency, value, and impact of the novel trial design.

Methods:

This pragmatic, international trial incorporating a prerandomized consent design favoring local practice enrolled patients undergoing cardiac surgery across seven hospitals in Australia and The Netherlands. Patients were randomly assigned to dexamethasone 1 mg/kg or not (control). The primary outcome was the number of days alive and at home up to 30 days after surgery (“home days”). Secondary outcomes included prolonged mechanical ventilation (more than 48 h), sepsis, renal failure, myocardial infarction, stroke, and death.

Results:

Of 2,093 patients assessed for eligibility, 1,951 were randomized (median age, 63 yr; 80% male). The median number of home days was 23.0 (interquartile range, 20.1 to 24.1) in the dexamethasone group and 23.1 (interquartile range, 20.1 to 24.6) in the no dexamethasone group (median difference, 0.1; 95% CI, –0.3 to 0.5; P = 0.66). The rates of prolonged mechanical ventilation (risk ratio, 0.72; 95% CI, 0.48 to 1.08), sepsis (risk ratio, 1.02; 95% CI, 0.57 to 1.82), renal failure (risk ratio, 0.94; 95% CI, 0.80 to 1.12), myocardial infarction (risk ratio, 1.20; 95% CI, 0.30 to 4.82), stroke (risk ratio, 1.06; 95% CI, 0.54 to 2.08), and death (risk ratio, 0.72; 95% CI, 0.22 to 2.35) were comparable between groups (all P > 0.10). Dexamethasone reduced intensive care unit stay (median, 29 h; interquartile range, 22 to 50 h vs. median, 43 h; interquartile range, 24 to 72 h; P = 0.004). Our novel trial design was highly efficient (89.3% enrollment).

Conclusions:

Among patients undergoing cardiac surgery, high-dose dexamethasone decreased intensive care unit stay but did not increase the number of home days after surgery.
Methylene Blue in Septic Shock: A Systematic Review and Meta-Analysis
Authors: Fernando Shannon M. , Tran Alexandre , Soliman Karim , Flynn Barbara , Oommen Thomas , Wenzhe Li , Adhikari Neill K.J. , Kanji Salmaan , Seely Andrew J.E. , Fox-Robichaud Alison E. , Wax Randy S. , Cook Deborah J. , Lamontagne François , Rochwerg Bram
Published: June 2024

OBJECTIVES:

Although clinicians may use methylene blue (MB) in refractory septic shock, the effect of MB on patient-important outcomes remains uncertain. We conducted a systematic review and meta-analysis to investigate the benefits and harms of MB administration in patients with septic shock.

DATA SOURCES:

We searched six databases (including PubMed, Embase, and Medline) from inception to January 10, 2024.

STUDY SELECTION:

We included randomized clinical trials (RCTs) of critically ill adults comparing MB with placebo or usual care without MB administration.

DATA EXTRACTION:

Two reviewers performed screening, full-text review, and data extraction. We pooled data using a random-effects model, assessed the risk of bias using the modified Cochrane tool, and used Grading of Recommendations Assessment, Development, and Evaluation to rate certainty of effect estimates.

DATA SYNTHESIS:

We included six RCTs (302 patients). Compared with placebo or no MB administration, MB may reduce short-term mortality (RR [risk ratio] 0.66 [95% CI, 0.47–0.94], low certainty) and hospital length of stay (mean difference [MD] –2.1 d [95% CI, –1.4 to –2.8], low certainty). MB may also reduce duration of vasopressors (MD –31.1 hr [95% CI, –16.5 to –45.6], low certainty), and increase mean arterial pressure at 6 hours (MD 10.2 mm Hg [95% CI, 6.1–14.2], low certainty) compared with no MB administration. The effect of MB on serum methemoglobin concentration was uncertain (MD 0.9% [95% CI, –0.2% to 2.0%], very low certainty). We did not find any differences in adverse events.

CONCLUSIONS:

Among critically ill adults with septic shock, based on low-certainty evidence, MB may reduce short-term mortality, duration of vasopressors, and hospital length of stay, with no evidence of increased adverse events. Rigorous randomized trials evaluating the efficacy of MB in septic shock are needed.

REGISTRATION:

Center for Open Science (https://osf.io/hpy4j).