bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome assembly of Hibiscus sabdariffa L. provides insights into metabolisms of medicinal natural products
Authors: Kim Taein , Lee Jeong Hun , Seo Hyo Hyun , Moh Sang Hyun , Choi Sung Soo , Kim Jun , Kim Sang-Gyu 
Published: July 2024

Abstract
Hibiscus sabdariffa L. is a widely cultivated herbaceous plant with diverse applications in food, tea, fiber, and medicine. In this study, we present a high-quality genome assembly of H. sabdariffa using more than 33 Gb of high-fidelity (HiFi) long-read sequencing data, corresponding to ∼20× depth of the genome. We obtained 3 genome assemblies of H. sabdariffa: 1 primary and 2 partially haplotype-resolved genome assemblies. These genome assemblies exhibit N50 contig lengths of 26.25, 11.96, and 14.50 Mb, with genome coverage of 141.3, 86.0, and 88.6%, respectively. We also utilized 26 Gb of total RNA sequencing data to predict 154k, 79k, and 87k genes in the respective assemblies. The completeness of the primary genome assembly and its predicted genes was confirmed by the benchmarking universal single-copy ortholog analysis with a completeness rate of 99.3%. Based on our high-quality genomic resources, we constructed genetic networks for phenylpropanoid and flavonoid metabolism and identified candidate biosynthetic genes, which are responsible for producing key intermediates of roselle-specific medicinal natural products. Our comprehensive genomic and functional analysis opens avenues for further exploration and application of valuable natural products in H. sabdariffa.
ONeSAMP 3.0: estimation of effective population size via single nucleotide polymorphism data from one population
Authors: Hong Aaron , Cheek Rebecca G , De Silva Suhashi Nihara , Mukherjee Kingshuk , Yooseph Isha , Oliva Marco , Heim Mark , W. Funk Chris , Tallmon David , Boucher Christina 
Published: July 2024

Abstract
The genetic effective size (Ne) is arguably one of the most important characteristics of a population as it impacts the rate of loss of genetic diversity. Methods that estimate Ne are important in population and conservation genetic studies as they quantify the risk of a population being inbred or lacking genetic diversity. Yet there are very few methods that can estimate the Ne from data from a single population and without extensive information about the genetics of the population, such as a linkage map, or a reference genome of the species of interest. We present ONeSAMP 3.0, an algorithm for estimating Ne from single nucleotide polymorphism data collected from a single population sample using approximate Bayesian computation and local linear regression. We demonstrate the utility of this approach using simulated Wright–Fisher populations, and empirical data from five endangered Channel Island fox (Urocyon littoralis) populations to evaluate the performance of ONeSAMP 3.0 compared to a commonly used Ne estimator. Our results show that ONeSAMP 3.0 is broadly applicable to natural populations and is flexible enough that future versions could easily include summary statistics appropriate for a suite of biological and sampling conditions. ONeSAMP 3.0 is publicly available under the GNU General Public License at https://github.com/AaronHong1024/ONeSAMP_3.
gNOMO2: a comprehensive and modular pipeline for integrated multi-omics analyses of microbiomes
Authors: Arikan Muzaffer , Muth Thilo 
Published: July 2024

Abstract

Background
In recent years, omics technologies have offered an exceptional chance to gain a deeper insight into the structural and functional characteristics of microbial communities. As a result, there is a growing demand for user-friendly, reproducible, and versatile bioinformatic tools that can effectively harness multi-omics data to provide a holistic understanding of microbiomes. Previously, we introduced gNOMO, a bioinformatic pipeline tailored to analyze microbiome multi-omics data in an integrative manner. In response to the evolving demands within the microbiome field and the growing necessity for integrated multi-omics data analysis, we have implemented substantial enhancements to the gNOMO pipeline.

Results
Here, we present gNOMO2, a comprehensive and modular pipeline that can seamlessly manage various omics combinations, ranging from 2 to 4 distinct omics data types, including 16S ribosomal RNA (rRNA) gene amplicon sequencing, metagenomics, metatranscriptomics, and metaproteomics. Furthermore, gNOMO2 features a specialized module for processing 16S rRNA gene amplicon sequencing data to create a protein database suitable for metaproteomics investigations. Moreover, it incorporates new differential abundance, integration, and visualization approaches, enhancing the toolkit for a more insightful analysis of microbiomes. The functionality of these new features is showcased through the use of 4 microbiome multi-omics datasets encompassing various ecosystems and omics combinations. gNOMO2 not only replicated most of the primary findings from these studies but also offered further valuable perspectives.

Conclusions
gNOMO2 enables the thorough integration of taxonomic and functional analyses in microbiome multi-omics data, offering novel insights in both host-associated and free-living microbiome research. gNOMO2 is available freely at https://github.com/muzafferarikan/gNOMO2.
Haplotype-resolved genome and mapping of freezing tolerance in the wild potato Solanum commersonii
Authors: Dong Jianke , Li Jingwen , Zuo Yingtao , Wang Jin , Chen Ye , Tu Wei , Wang Haibo , Li Chenxi , Shan Yacheng , Wang Ying , Song Botao , Cai Xingkui 
Published: July 2024

Abstract
Solanum commersonii (2n = 2x = 24, 1EBN, Endosperm Balance Number), native to the southern regions of Brazil, Uruguay, and northeastern Argentina, is the first wild potato germplasm collected by botanists and exhibits a remarkable array of traits related to disease resistance and stress tolerance. In this study, we present a high-quality haplotype-resolved genome of S. commersonii. The two identified haplotypes demonstrate chromosome sizes of 706.48 and 711.55 Mb, respectively, with corresponding chromosome anchoring rates of 94.2 and 96.9%. Additionally, the contig N50 lengths are documented at 50.87 and 45.16 Mb. The gene annotation outcomes indicate that the haplotypes encompasses a gene count of 39 799 and 40 078, respectively. The genome contiguity, completeness, and accuracy assessments collectively indicate that the current assembly has produced a high-quality genome of S. commersonii. Evolutionary analysis revealed significant positive selection acting on certain disease resistance genes, stress response genes, and environmentally adaptive genes during the evolutionary process of S. commersonii. These genes may be related to the formation of diverse and superior germplasm resources in the wild potato species S. commersonii. Furthermore, we utilized a hybrid population of S. commersonii and S. verrucosum to conduct the mapping of potato freezing tolerance genes. By combining BSA-seq analysis with traditional QTL mapping, we successfully mapped the potato freezing tolerance genes to a specific region on Chr07, spanning 1.25 Mb, with a phenotypic contribution rate of 18.81%. In short, current research provides a haplotype-resolved reference genome of the diploid wild potato species S. commersonii and establishes a foundation for further cloning and unraveling the mechanisms underlying cold tolerance in potatoes.
Phospholipid production and signaling by a plant defense inducer against Podosphaera xanthii is genotype-dependent
Authors: Margaritopoulou Theoni , Baira Eirini , Anagnostopoulos Christos , Vichou Katerina-Eleni , Markellou Emilia 
Published: July 2024

Abstract
Biotrophic phytopathogenic fungi such as Podosphaera xanthii have evolved sophisticated mechanisms to adapt to various environments causing powdery mildews leading to substantial yield losses. Today, due to known adverse effects of pesticides, development of alternative control means is crucial and can be achieved by combining plant protection products with resistant genotypes. Using plant defense inducers, natural molecules that stimulate plant immune system mimicking pathogen attack is sustainable, but information about their mode of action in different hosts or host genotypes is extremely limited. Reynoutria sachalinensis extract, a known plant defense inducer, especially through the Salicylic acid pathway in Cucurbitaceae crops against P. xanthii, was employed to analyze the signaling cascade of defense activation. Here, we demonstrate that R. sachalinensis extract enhances phospholipid production and signaling in a Susceptible to P. xanthii courgette genotype, while limited response is observed in an Intermediate Resistance genotype due to genetic resistance. Functional enrichment and cluster analysis of the upregulated expressed genes revealed that inducer application promoted mainly lipid- and membrane-related pathways in the Susceptible genotype. On the contrary, the Intermediate Resistance genotype exhibited elevated broad spectrum defense pathways at control conditions, while inducer application did not promote any significant changes. This outcome was obvious and at the metabolite level. Main factor distinguishing the Intermediate Resistance form the Susceptible genotype was the epigenetic regulated increased expression of a G3P acyltransferase catalyzing phospholipid production. Our study provides evidence on phospholipid-based signaling after plant defense inducer treatment, and the selective role of plant’s genetic background.
Clinical Impact of Plasma Metagenomic Next-Generation Sequencing on Infection Diagnosis and Antimicrobial Therapy in Immunocompromised Patients
Authors: Yin Guankun , Yin Yuyao , Guo Yifan , Sun Lingxiao , Ma Shuai , Chen Hongbin , Wang Qi , Wang Hui 
Published: July 2024

Abstract

Background
The clinical impact of plasma metagenomic next-generation sequencing (mNGS) on infection diagnosis and antimicrobial therapy in immunocompromised patients with suspected infection remains unclear.

Methods
Between March and December 2022, 424 cases with fever, infection history, mechanical ventilation, or imaging abnormalities underwent plasma mNGS testing at a single center. Eleven patients had received solid organ transplantation, and the remaining patients were categorized into febrile neutropenia (FN), non-neutropenia (NN), and non-transplant and non-hematologic disease (NTHD) groups based on immunosuppression severity. The diagnostic rate of infection and the utilization of antimicrobial agents based on mNGS were assessed.

Results
The use of mNGS significantly improved the diagnostic rates for fungi in the FN (65.1%, P = .001) and NN (58.8%, P = .008) groups versus the NTHD group (33.3%). Positive impacts associated with therapy were significantly greater than negative impacts across all 3 groups (all P &lt; .001), and the utilization of escalation therapy was significantly more frequent in the FN group than in the NN group (P = .006). More than 70% of cases with negative mNGS results across the 3 groups underwent de-escalation therapy, with more than one-third being discontinued, preventing antimicrobial overuse.

Conclusions
Plasma mNGS has a clinically confirmed positive impact in immunocompromised patients with neutropenia, improving the diagnosis of fungal infections and antimicrobial therapy.
Quantification of Total Sulfites in Shrimp by BIOFISH 300/3000 SUL Method, Collaborative Study: Final Action 2021.09
Authors: Garate Jone , Ortiz de Zarate Itziar , Gonzalez Roberto , Añorga Larraitz , Salleres Sandra 
Published: July 2024

Abstract

Background
In December 2021, the BIOFISH 300 SUL method for the determination of total sulfites in shrimp was adopted as a First Action Official Method of AnalysisSM by the AOAC INTERNATIONAL.

Objective
A collaborative study was conducted in February 2023 in order to test the reproducibility of the method.

Methods
The method is based on the use of a benchtop biosensor device that relates the concentration of sulfite to a quantifiable electric current signal. The sensing element, the Biotest, harbors an enzyme that specifically oxidizes sulfite, and the reaction products are electrochemically detected by the device in less than 3 min. The sulfite is extracted from the solid using an aqueous-based buffer solution, which ensures that all sulfite is present as a free anion.

Results
Eleven collaborators participated in the study of nine different shrimp samples. Values of repeatability and reproducibility relative standard deviation (RSDr and RSDR) obtained from the statistical analysis of valid data ranged from 2.1–8.1% and 7.5–14.3%, respectively, for shrimp samples above the quantification limit of the method, set at 7 mg/kg.

Conclusion
These results showed good repeatability and reproducibility of the method, even at concentrations below the legal threshold for sulfite in food, where the reference optimised Monier-Williams (OMW) method shows relatively high imprecision.

Highlights
On the basis of these results, the enzymatic amperometric biosensor method developed by BIOLAN Microbiosensores was adopted as Final Action Official Method in September 2023.
Dietary Spirulina effects in Eimeria-challenged broiler chickens: growth performance, nutrient digestibility, intestinal morphology, serum biomarkers, and gene expression
Authors: Alagbe Emmanuel Oluwabukunmi , Schulze Hagen , Adeola Olayiwola 
Published: July 2024

Abstract
This study investigated the growth performance, nutrient utilization, and intestinal health responses of Eimeria-challenged broiler chickens to dietary Spirulina (Arthrospira platensis). On day 1, birds were assigned to 2 diets supplemented with Spirulina (0 or 5 g/kg) in a randomized complete block design. The birds within each diet were divided into 2 Eimeria-challenge groups (challenge or no-challenge) and that resulted in a 2 × 2 factorial arrangement with 2 levels each of Spirulina and challenge on day 14. On day 15, the birds in the challenge or no-challenge groups were orally gavaged with a solution containing Eimeria oocysts or 1% PBS, respectively. Samples were collected on days 21 and 26 (6- and 11-d post-infection; dpi). Data collected from days 1 to 26 were analyzed using the MIXED procedure of SAS. Birds that were fed Spirulina-supplemented diets had increased (P &lt; 0.05) BW gain, gain-to-feed ratio, and total tract retention nitrogen from days 14 to 21. The ileal villus perimeter and area, serum catalase, HMOX1 and SOD1 jejunal abundance were all increased (P &lt; 0.05) in birds fed Spirulina-supplemented diets on day 21 (6 dpi). However, there was no effect on bone ash or oocyst count. From days 21 to 26, there was a tendency (P = 0.059) for a Spirulina × Challenge interaction on the BW gain of birds. Moreover, dietary Spirulina addition increased (P &lt; 0.05) serum catalase, total antioxidant capacity, ileal villus perimeter, tibia bone ash, and the relative mRNA expression of HMOX1, SOD1, claudin 1, and TNFα in the jejunal mucosa of birds on day 26 (11 dpi). On both 6 and 11 dpi, the Eimeria challenge negatively (P &lt; 0.05) impacted growth performance, gut morphology, and the relative mRNA expression of genes. Overall, assessing the impact of Spirulina in broilers revealed its positive antioxidant, immune-modulating, and health benefits. However, its dietary addition did not completely reverse the Eimeria-induced effects in these birds. Ultimately, this study outlines the positive properties of dietary Spirulina beyond its use in the diet of healthy broiler chickens.
VP1 of human and murine noroviruses recognizes glycolipid sulfatide via the P domain
Authors: Tsukamoto Bunta , Kurebayashi Yuuki , Takahashi Tadanobu , Abe Yusuke , Ota Ryohei , Wakabayashi Yoshiki , Nishiie Anju , Minami Akira , Suzuki Takashi , Takeuchi Hideyuki 
Published: July 2024

Abstract
Noroviruses are a prevalent cause of human viral gastroenteritis, yet the precise mechanisms underlying their infection cycle, particularly their interactions with and entry into cells, remain poorly understood. Human norovirus (HuNoV) primarily targets human small intestinal epithelial cells, within which 3-O-sulfogalactosylceramide (sulfatide) ranks among the most abundant glycosphingolipids (GSLs). While sulfatide involvement in the binding and infection mechanism of several viruses has been documented, its interaction with noroviruses remains underexplored. This study investigated whether noroviruses interact with sulfatide. We found that the recombinant viral capsid protein VP1 of HuNoV (genogroups I and II) and murine norovirus (genogroup V) exhibited robust binding to sulfatide compared with other tested GSLs using enzyme-linked immunosorbent assay, thin-layer chromatography binding assay and real-time quantitative reverse transcription polymerase chain reaction binding assay. VP1 also bound 3-O-sulfated lactosylceramide, which shares the 3-O-sulfated galactose moiety with sulfatide. However, both VP1 and its P domain, identified as the sulfatide-binding domain, exhibited limited binding to structural analogues of sulfatide and other sulfated compounds. These findings suggest a specific recognition of the 3-O-sulfated galactose moiety. Notably, we found that sulfatide is a novel binding target for norovirus particles. Overall, our findings reveal a previously unknown norovirus–sulfatide interaction, proposing sulfatide as a potential candidate for norovirus infection receptors.
Dedicated Breast CT: Getting Ready for Prime Time
Authors: Aminololama-Shakeri Shadi , Boone John M 
Published: July 2024

Abstract
Dedicated breast CT is an imaging modality that provides true 3D imaging of the breast with many advantages over current conventional breast imaging modalities. The addition of intravascular contrast increases the sensitivity of breast CT substantially. As such, there are immediate potential applications in the clinical workflow. These include using breast CT to replace much of the traditional diagnostic workup when faced with indeterminate breast lesions. Contrast-enhanced breast CT may be appropriate as a supplemental screening tool for women at high risk of breast cancer, similar to breast MRI. In addition, emerging studies are demonstrating the utility of breast CT in neoadjuvant chemotherapy tumor response monitoring as well as planning for surgical treatment options. While short exam times and fully 3D imaging in a noncompressed position are advantages of this modality, limited coverage of chest wall/axilla due to prone positioning and use of ionizing radiation are drawbacks. To date, several studies have reported on the performance characteristics of this promising modality.
Ocular findings in Jansen metaphyseal chondrodysplasia
Authors: Obiezu Fiona , Magone De Quadros Costa M Teresa , Huryn Laryssa A , Pan Kristen , Almpani Konstantinia , Ninan Anisha , Roszko Kelly L , Weinstein Lee S , Gafni Rachel I , Ferreira Carlos R , Lee Janice , Collins Michael T , Jha Smita 
Published: July 2024

Abstract
Jansen metaphyseal chondrodysplasia (JMC) is an ultra-rare disorder caused by germline heterozygous PTHR1 variants resulting in constitutive activation of parathyroid hormone type 1 receptor. A description of ocular manifestations of the disease is lacking. Six patients with JMC underwent a detailed ophthalmic evaluation, spectral-domain optical coherence tomography (OCT), visual field testing, and craniofacial CT scans. Five of 6 patients had good visual acuity. All patients had widely spaced eyes; 5/6 had downslanted palpebral fissures. One patient had proptosis, and another had bilateral ptosis. Two patients had incomplete closure of the eyelids (lagophthalmos), one had a history of progressive right facial nerve palsy with profuse epiphora, while the second had advanced optic nerve atrophy with corresponding retinal nerve fiber layer (RNFL) thinning on OCT and significant bilateral optic canal narrowing on CT scan. Additionally, this patient also had central visual field defects and abnormal color vision. A third patient had normal visual acuity, subtle temporal pallor of the optic nerve head, normal average RNFL, but decreased temporal RNFL and retinal ganglion cell layer analysis (GCA) on OCT. GCA was decreased in 4/6 patients indicating a subclinical optic nerve atrophic process. None of the patients had glaucoma or high myopia. These data represent the first comprehensive report of ophthalmic findings in JMC. Patients with JMC have significant eye findings associated with optic canal narrowing due to extensive skull base dysplastic bone overgrowth that appear to be more prevalent and pronounced with age. Progressive optic neuropathy from optic canal narrowing may be a feature of JMC, and OCT GCA can serve as a useful biomarker for progression in the setting of optic canal narrowing. We suggest that patients with JMC should undergo regular ophthalmic examination including color vision, OCT, visual field testing, orbital, and craniofacial imaging.
Evidence for peri-lacunar remodeling and altered osteocyte lacuno-canalicular network in mouse models of myeloma-induced bone disease
Authors: Evans Holly , Andrews Rebecca , Abedi Fatma Ali , Sprules Alexandria , Trend Jacob , Lovric Goran , Green Alanna , Chantry Andrew , Clarkin Claire , Brown Janet , Lawson Michelle 
Published: July 2024

Abstract
Myeloma bone disease (MBD) affects ~90% of multiple myeloma patients, but current treatment options are suboptimal. Therefore, to successfully develop new therapies or optimize current ones, we must improve our fundamental knowledge of how myeloma affects bone microstructure and function. Here, we have investigated the osteocyte lacuno-canalicular network (LCN) in MBD, as bone porosity affects bone quality and resilience. We used the syngeneic 5TGM1-C57BL-Kalwrij and the xenograft U266-NSG models at end stage and compared them to healthy controls (naïve). Micro-computed tomography (μCT) and histomorphometry indicated the 5TGM1 and U266 models developed mild and extensive MBD, respectively, with the U266 model producing large osteolytic lesions. High-resolution synchrotron micro-CT (SR-μCT) revealed significant osteocyte lacunae changes in U266 bones but not 5TGM1, with a reduction in lacunae number and sphericity, and an increase in lacunae volume compared with naïve. Canalicular length, visualized using histological Ploton silver staining, appeared significantly shorter in 5TGM1 and U266 bones compared with naïve. Canalicular area as a proportion of the bone was also decreased by 24.2% in the U266 model. We observed significant upregulation of genes implicated in peri-lacunar remodeling (PLR), but immunohistochemistry confirmed that the osteocyte-specific protein sclerostin, a known driver of PLR, was unchanged between MBD and naïve bones. In summary, we have demonstrated evidence of PLR and altered organization of the osteocyte LCN in MBD mouse models. The next step would be to further understand the drivers and implications of PLR in MBD, and whether treatments to manipulate PLR and the LCN may improve patient outcomes.