bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluating metagenomics and targeted approaches for diagnosis and surveillance of viruses
Authors: Buddle Sarah , Forrest Leysa , Akinsuyi Naomi , Martin Bernal Luz Marina , Brooks Tony , Venturini Cristina , Miller Charles , Brown Julianne R. , Storey Nathaniel , Atkinson Laura , Best Timothy , Roy Sunando , Goldsworthy Sian , Castellano Sergi , Simmonds Peter , Harvala Heli , Golubchik Tanya , Williams Rachel , Breuer Judith , Morfopoulou Sofia , Torres Montaguth Oscar Enrique 
Published: September 2024

Abstract

Background

Metagenomics is a powerful approach for the detection of unknown and novel pathogens. Workflows based on Illumina short-read sequencing are becoming established in diagnostic laboratories. However, high sequencing depth requirements, long turnaround times, and limited sensitivity hinder broader adoption. We investigated whether we could overcome these limitations using protocols based on untargeted sequencing with Oxford Nanopore Technologies (ONT), which offers real-time data acquisition and analysis, or a targeted panel approach, which allows the selective sequencing of known pathogens and could improve sensitivity.

Methods
We evaluated detection of viruses with readily available untargeted metagenomic workflows using Illumina and ONT, and an Illumina-based enrichment approach using the Twist Bioscience Comprehensive Viral Research Panel (CVRP), which targets 3153 viruses. We tested samples consisting of a dilution series of a six-virus mock community in a human DNA/RNA background, designed to resemble clinical specimens with low microbial abundance and high host content. Protocols were designed to retain the host transcriptome, since this could help confirm the absence of infectious agents. We further compared the performance of commonly used taxonomic classifiers.

Results
Capture with the Twist CVRP increased sensitivity by at least 10–100-fold over untargeted sequencing, making it suitable for the detection of low viral loads (60 genome copies per ml (gc/ml)), but additional methods may be needed in a diagnostic setting to detect untargeted organisms. While untargeted ONT had good sensitivity at high viral loads (60,000 gc/ml), at lower viral loads (600–6000 gc/ml), longer and more costly sequencing runs would be required to achieve sensitivities comparable to the untargeted Illumina protocol. Untargeted ONT provided better specificity than untargeted Illumina sequencing. However, the application of robust thresholds standardized results between taxonomic classifiers. Host gene expression analysis is optimal with untargeted Illumina sequencing but possible with both the CVRP and ONT.

Conclusions
Metagenomics has the potential to become standard-of-care in diagnostics and is a powerful tool for the discovery of emerging pathogens. Untargeted Illumina and ONT metagenomics and capture with the Twist CVRP have different advantages with respect to sensitivity, specificity, turnaround time and cost, and the optimal method will depend on the clinical context.
Host genetics and gut microbiota synergistically regulate feed utilization in egg-type chickens
Authors: Zhang Wenxin , Lan Fangren , Zhou Qianqian , Gu Shuang , Li Xiaochang , Wen Chaoliang , Yang Ning , Sun Congjiao 
Published: September 2024

Abstract
Background
Feed efficiency is a crucial economic trait in poultry industry. Both host genetics and gut microbiota influence feed efficiency. However, the associations between gut microbiota and host genetics, as well as their combined contributions to feed efficiency in laying hens during the late laying period, remain largely unclear.

Methods
In total, 686 laying hens were used for whole-genome resequencing and liver transcriptome sequencing. 16S rRNA gene sequencing was conducted on gut chyme (duodenum, jejunum, ileum, and cecum) and fecal samples from 705 individuals. Bioinformatic analysis was performed by integrating the genome, transcriptome, and microbiome to screen for key genetic variations, genes, and gut microbiota associated with feed efficiency.

Results
The heritability of feed conversion ratio (FCR) and residual feed intake (RFI) was determined to be 0.28 and 0.48, respectively. The ileal and fecal microbiota accounted for 15% and 10% of the FCR variance, while the jejunal, cecal, and fecal microbiota accounted for 20%, 11%, and 10% of the RFI variance. Through SMR analysis based on summary data from liver eQTL mapping and GWAS, we further identified four protein-coding genes, SUCLA2, TNFSF13B, SERTM1, and MARVELD3, that influence feed efficiency in laying hens. The SUCLA2 and TNFSF13B genes were significantly associated with SNP 1:25664581 and SNP rs312433097, respectively. SERTM1 showed significant associations with rs730958360 and 1:33542680 and is a potential causal gene associated with the abundance of Corynebacteriaceae in feces. MARVELD3 was significantly associated with the 1:135348198 and was significantly correlated with the abundance of Enterococcus in ileum. Specifically, a lower abundance of Enterococcus in ileum and a higher abundance of Corynebacteriaceae in feces were associated with better feed efficiency.

Conclusions
This study confirms that both host genetics and gut microbiota can drive variations in feed efficiency. A small portion of the gut microbiota often interacts with host genes, collectively enhancing feed efficiency. Therefore, targeting both the gut microbiota and host genetic variation by supporting more efficient taxa and selective breeding could improve feed efficiency in laying hens during the late laying period.
Engineering of fast-growing Vibrio natriegens for biosynthesis of poly(3-hydroxybutyrate-co-lactate)
Authors: Sun Xinye , Shang Yanzhe , Zhang Binghao , Guo Pengye , Luo Yuanchan , Wu Hui 
Published: September 2024

AbstractPoly(3-hydroxybutyrate-co-lactate) [P(3HB-co-LA)] is a highly promising valuable biodegradable material with good biocompatibility and degradability. Vibrio natriegens, owing to its fast-growth, wide substrate spectrum characteristics, was selected to produce P(3HB-co-LA). Herein, the crucial role of acetyltransferase PN96-18060 for PHB synthesis in V. natriegens was identified. Heterologous pathway of P(3HB-co-LA) was introduced into V. natriegens successfully, in addition, overexpression of the dldh gene led to 1.84 fold enhancement of the lactate content in P(3HB-co-LA). Finally, the production of P(3HB-co-LA) was characterized under different carbon sources. The lactate fraction in P(3HB-co-LA) was increased to 28.3 mol% by the modification, about 1.84 times of that of the control. This is the first successful case of producing the P(3HB-co-LA) in V. natriegens. Collectively, this study showed that V. natriegens is an attractive host organism for producing P(3HB-co-LA) and has great potential to produce other co-polymers.
Mouse testicular macrophages can independently produce testosterone and are regulated by Cebpb
Authors: Duan Nengliang , Ran Yuanshuai , Wang Huapei , Luo Ya , Gao Zhixiang , Lu Xingyu , Cui Fengmei , Chen Qiu , Xue Boxin , Liu Xiaolong 
Published: September 2024

Abstract
Background
Testicular macrophages (TM) have long been recognized for their role in immune response within the testicular environment. However, their involvement in steroid hormone synthesis, particularly testosterone, has not been fully elucidated. This study aims to explore the capability of TM to synthesize and secrete testosterone de novo and to investigate the regulatory mechanisms involved.

Results
Transcriptomic analysis revealed significant expression of Cyp11a1, Cyp17a1, Hsd3b1, and Hsd17b3 in TM, which are key enzymes in the testosterone synthesis pathway. qPCR analysis and immunofluorescence validation confirmed the autonomous capability of TM to synthesize testosterone. Ablation of TM in mice resulted in decreased physiological testosterone levels, underscoring the significance of TM in maintaining testicular testosterone levels. Additionally, the study also demonstrated that Cebpb regulates the expression of these crucial genes, thereby modulating testosterone synthesis.

Conclusions
This research establishes that TM possess the autonomous capacity to synthesize and secrete testosterone, contributing significantly to testicular testosterone levels. The transcription factor Cebpb plays a crucial role in this process by regulating the expression of key genes involved in testosterone synthesis.
Adsorption of dibenzothiophene sulfone using Fe3+ and Fe6+-impregnated clay adsorbents
Authors: Alcaraz Maegan Gwyneth T. , Choi Angelo Earvin Sy , Dugos Nathaniel P. , Wan Meng-Wei 
Published: September 2024

AbstractIn this study, the adsorption of dibenzothiophene sulfone (DBTO) was investigated using clay minerals as adsorbents. Raw bentonite (BR) and raw activated clay (ACR) were impregnated with Fe3+ and Fe6+, creating bentonite-Fe3+ (BF3), bentonite-Fe6+ (BF6), activated clay-Fe3+ (ACF3), and activated clay-Fe6+ (ACF6). The surface functional groups, surface morphology, and surface area of the raw and modified adsorbents were studied through Fourier transform infrared spectroscopy, a scanning electron microscope, and Brunauer, Emmett, and Teller analysis, respectively. Batch experiments on simulated oil were done to test the effect of adsorption time (0.5–24 h), adsorption dosage (0.3–1.5 g), and adsorption temperature (30–50 °C). The results of the experiments showed the suitability of the pseudo-second order kinetic model on the clay adsorbent and sulfone system. This suggests that chemisorption is the rate-limiting step of the reaction. Equilibrium isotherms indicated the adherence of DBTO onto BR and BF3 to the Freundlich model, implying the heterogeneous adsorption of the sulfones onto the adsorbents. The systems of DBTO with BF6, ACR, ACF3, and ACF6 showed a better fit with the Dubinin-Radushkevich model. This denotes that adsorption happens through the filling of sulfones of the micropores on the adsorbent. Lastly, thermodynamic studies revealed the endothermic and non-spontaneous nature of the clay adsorbents and sulfone systems. The experiments showed that the impregnation of Fe3+ and Fe6+ lowered the desulfurization ability of the adsorbents. This could be due to the iron ions being hard acids and the sulfones being soft bases, thus showing lower compatibility than the raw counterparts of the adsorbents. Comparison with related studies showed that the prepared adsorbents, namely BF3 (5.1 mg g−1) and BF6 (6.4 mg g−1), had a higher adsorption capacity than Ni2+-loaded activated carbon (4.9 mg g−1) and activated clay (4.1 mg g−1). The study shows that BR (7.2 mg g−1) is the best-performing adsorbent, which can be set as the direction for future research. This study is a step toward the commercialization of oxidative desulfurization methods.
Explore the most recent developments and upcoming outlooks in the field of dental nanomaterials
Authors: Alsuraifi Ali , Sulaiman Zainab M. , Mohammed Noor Alhuda R. , Mohammed Jassim , Ali Sarah Kareem , Abdualihamaid Yousef Husam , Husam Fatimah , Ayad Abdullah 
Published: September 2024

Abstract
Background
The rapid evolution of nanotechnology has fundamentally transformed both medical and dental fields. By harnessing nanomaterials, researchers have unlocked the ability to replicate natural tissue structures and properties, significantly enhancing integration processes. Notably, nanostructures have emerged as pivotal elements in oral medicine, particularly in combating dental caries and enhancing outcomes in dental implants and maxillofacial surgeries.

Main body of the abstract
Nanostructures play multifaceted roles in oral health, promoting osseointegration and expediting healing processes in dental procedures. The impact of these materials extends to improving the adhesive strength and overall properties of dental composites. This review critically evaluates the influence of nanointerfaces on the longevity of dental restorations, exploring innovative nanotechnological interventions aimed at augmenting restoration durability. Furthermore, recent strides in nanodentistry are discussed, highlighting breakthroughs in oral health diagnostics, preventative strategies, and treatment modalities essential for achieving and sustaining optimal oral health.

Short conclusion
Incorporating nanotechnology into dental practice presents exciting prospects for advancing oral healthcare. From enhancing restoration durability to revolutionizing diagnostics and treatments, nanotechnology offers transformative solutions that hold significant promise for the future of oral health management.
Deep eutectic solvent strategy for green extraction of chlorogenic acid from sea buckthorn: optimization and sustainability
Authors: Saddique Iqra , Akram Sumia , Rubab Saima , Sadiqa Ayesha , Raza Ali , Mushtaq Muhammad , Ghauri Mohsin Ahmad 
Published: September 2024

Abstract
Background
Sea buckthorn (Hippophae rhamnoides), a deciduous species plant, is widely distributed around the globe, and native to the cold-temperate regions of Europe and Asia. This medicinal herb contains several bioactive constituents including chlorogenic acid. The conventional methods used for the extraction of phenolic antioxidants from natural herbs often result in low yields, high toxicity, and pose environmental hazards limiting their effectiveness and scalability. Therefore, green extraction techniques using deep eutectic solvents, composed of natural, non-toxic, and biodegradable components were applied for extraction of chlorogenic acid from sea buckthorn weed. Fourteen deep eutectic solvent mixtures were prepared and evaluated for extraction yield of chlorogenic acid. Parameters such as hydrogen bond donor-to-hydrogen bond acceptor ratio, liquid-to-solid ratio, shaking speed, and shaking time were optimized for the best mixture.

Results
The combination of lactic acid and maltose (1:1) was found to give best extraction yield using response surface methodology. The deep eutectic solvent system under optimum conditions produced 12.2 g/100 g of crude extract sea buckthorn containing 174.7 mg gallic acid equivalents (mg GA)/g) of extract. Moreover, the optimized extract exhibited appreciable radical scavenging capacity (91%), trolox equivalent antioxidant capacity (11.2% of extract), and inhibition of peroxide in linoleic acid (80.6%). High-performance liquid chromatography-based characterization revealed the extracts contained chlorogenic acid (20.1 mg/g of extract) as the major constituent.

Conclusions
In summary, the adoption of DES for the extraction of bioactive phenolic constituents from sea buckthorn offers multiple benefits, including economic efficiency, enhanced extraction performance, and environmental sustainability. The findings of this study not only advance the understanding of DES in phytochemical extraction but also pave the way for broader application of green solvents in the natural products industry. Future research should focus on further optimizing DES formulations and scaling up the extraction process to fully realize the potential of this innovative extraction method in commercial applications.
Aquamimicry (Copefloc technology): an innovative approach for sustainable organic farming with special reference to shrimp aquaculture
Authors: Deepti Mutum , Meinam Martina , Devi Ng Chinglembi , Singh Soibam Khogen , Devi Wangkheimayum Malemnganbi 
Published: September 2024

AbstractWith the rising demand for fish worldwide, aquaculture's contribution to the global food supply is crucial. To conserve natural resources by relying less on water supplies and minimizing land use, different cutting-edge technologies have been developed. These innovative, cutting-edge technologies should emphasize on environmental conservation and eco-safety by imparting environmental benefits, biosecurity safeguards, environmentally sound activities, mitigating substantial environmental concerns, and transmission of diseases. Shrimp farming has historically produced the highest profits in the aquaculture industry. The sector holds promise for foreign earnings and has boomed worldwide. Aquamimicry technology is one of the many novel technologies that have shown promising results in achieving long-term sustainability in the thriving shrimp farming sector. This novel method simulates a natural environment in controlled conditions by harnessing heterotrophic microorganisms thereby offering benefits for low-oxygen-intensive farming practices. Maintaining a specific C:N ratio in this system with the help of probiotics allows heterotrophic bacteria to make use of the nitrogenous metabolites released by food and waste matter, hence facilitating in preserving water quality, and providing protein-rich live feed i.e., copepods. As we all are well aware that feed cost makes up more than half of the entire cost of production in most culture system. Therefore, this innovation not only aids in maintaining water quality and health of the organism but also significantly reduces the reliance on supplementary feed, rendering it a profitable long-term strategy for aquaculture. Although the concept has been around for a while, aquaculture farmers are yet to adopt this method as information is sparse. The current review focuses on elucidating the underlying process, existing knowledge, and future prospects of aquamimicry technology, also known as Copefloc technology, to accelerate the advancements in shrimp farming industry.
Ultrafast X-ray laser-induced explosion: How the depth influences the direction of the ion trajectory
Authors: De Santis Emiliano , Dawod Ibrahim , André Tomas , Cardoch Sebastian , Timneanu Nicusor , Caleman Carl 
Published: September 2024

Abstract
Single particle imaging using X-ray lasers is a technique aiming to capture atomic resolution structures of biomolecules in their native state. Knowing the particle's orientation during exposure is crucial for method enhancement. It has been shown that the trajectories of sulfur atoms in a Coulomb exploding lysozyme are reproducible, providing orientation information. This study explores if sulfur atom depth influences explosion trajectory. Employing a hybrid collisional-radiative/molecular dynamics model, we analyze the X-ray laser-induced dynamics of a single sulfur ion at varying depths in water. Our findings indicate that the ion spread-depth relationship depends on pulse parameters. At a photon energy of 2 keV, high-charge states are obtained, resulting in an increase of the spread with depth. However, at 8 keV photon energy, where lower charge states are obtained, the spread is essentially independent with depth. Finally, lower ion mass results in less reproducible trajectories, opening a promising route for determining protein orientation through the introduction of heavy atoms.
Multiple Primary Paragangliomas in a Pediatric Patient With von Hippel Lindau: A Diagnostic Dilemma
Authors: Magnan Katelin , Wang Qian , Meade Julia 
Published: September 2024

Abstract
Pheochromocytoma and paragangliomas (PPGLs) are rare chromaffin cell tumors arising from neural crest tissue. The majority of these tumors are nonmetastatic, with complete cure achieved through surgical resection. PPGLs have been associated with several hereditary cancer syndromes, including von Hippel-Lindau (VHL). We present the case of a 10-year-old patient with VHL and a history of 2 asynchronous pheochromocytomas requiring bilateral adrenalectomies who presented with a new 1.2 cm × 1.3 cm × 1.5 cm nodular structure between the superior pole of the right kidney and the intrahepatic inferior vena cava. The patient was noted to have hypertension but was otherwise asymptomatic. Positron emission tomography-DOTA-(Tyr)3-octreotate revealed a metabolically active retrocrural lymph node. Based on these imaging findings and laboratory studies showing elevated plasma normetanephrine, clinical suspicion was highest for metastatic pheochromocytoma. The patient underwent surgical resection of multiple abdominal tumors. Pathology ultimately favored a diagnosis of multiple primary paragangliomas rather than metastatic disease. With this shift in diagnosis, the patient was managed with surgery alone. One year later, he has no signs of disease recurrence. Long-term surveillance imaging and screening with fractionated plasma metanephrines is indicated to monitor for new tumors in the setting of VHL and 3 prior endocrine tumors.
Single-Institution Experience of Larotrectinib Therapy for Patients With NTRK Fusion-Positive Thyroid Carcinoma
Authors: Elghawy Omar , Barsouk Adam , Heidlauf Alec , Chen Simon , Cohen Roger B , Sun Lova 
Published: September 2024

Abstract

Context
The real world efficacy and tolerabiltiy of NTRK inhibitor larotrectinib has not yet been reported in the literature although trial data has shown promising results.

Objective
We report a retrospective analysis of patients with thyroid cancer harboring NTRK fusions who underwent treatment with larotrectinib.

Methods
A single-institution, retrospective case series of patients with NTRK fusion-positive thyroid cancers treated with neurotrophic tyrosine receptor kinase (NTRK) inhibitors from January 1, 2007, to January 1, 2023, was performed. This study was conducted at a single academic tertiary referral center. Patients with confirmed NTRK-fusion thyroid cancer who received larotrectinib were included. Larotrectinib was administered in accordance with clinical judgment from oncology providers. The primary end point was progression-free survival (PFS).

Results
Eight patients with NTRK fusion-positive thyroid cancer treated with larotrectinib were identified: 4 with papillary thyroid cancer (PTC) (50%), 3 with poorly differentiated thyroid cancer (PDTC) (38%), and 1 with anaplastic thyroid cancer (ATC) (12%). The median PFS (mPFS) for all patients was 24.7 months (95% CI, 11.3-38.1). mPFS in PTC was higher than PDTC (34.6 months [24.7-48.7 months] vs 17.5 [7.1-21.1 months]; P = .017). The median overall survival (OS) was 43.8 months (29.8-56.8 months) overall. The single patient with ATC had a PFS and OS of 23 months. Two patients remained on treatment/alive at data cutoff, with a duration of response of 33.5 months and a median follow-up of 52 months. Patients achieved 1 complete response (12%), 6 partial responses (75%), and 1 stable disease (12%).

Conclusion
In this single-institution cohort of patients with NTRK fusion-positive thyroid cancer, NTRK inhibition led to an mPFS of 25 months, with survival surpassing historic benchmarks for ATC and PDTC.