Homologous recombination deficiency should be tested for in patients with advanced stage high-grade serous ovarian cancer aged 70 years and over.

OBJECTIVE: Due to limited data on homologous recombination deficiency (HRD) in older patients (≥ 70 years) with advanced stage high grade serous ovarian cancer (HGSC), we aimed to determine the rates of HRD at diagnosis in this age group. METHODS: From the Phase 3 trial VELIA the frequency of HRD and BRCA1/2 pathogenic variants (PVs) was compared between younger (< 70 years) and older participants. HRD and somatic(s) BRCA1/2 pathogenic variants (PVs) were determined at diagnosis using Myriad myChoice® CDx and germline(g) BRCA1/2 PVs using Myriad BRACAnalysis CDx®. HRD was defined if a BRCA PV was present, or the genomic instability score (GIS) met threshold (GIS ≥ 33 & ≥ 42 analyzed). RESULTS: Of 1140 participants, 21% were ≥ 70 years. In total, 26% (n = 298) had a BRCA1/2 PV and HRD, 29% (n = 329) were HRD/BRCA wild-type, 33% (n = 372) non-HRD, and 12% HR-status unknown (n = 141). HRD rates were higher in younger participants, 59% (n = 476/802), compared to 40% (n = 78/197) of older participants (GIS ≥ 42) [p < 0.001]; similar rates demonstrated with GIS ≥ 33, 66% vs 48% [p < 0.001]. gBRCA PVs observed in 24% younger vs 8% of older participants (p < 0.001); sBRCA in 8% vs 10% (p = 0.2559), and HRD (GIS ≥ 42) not due to gBRCA was 35% vs 31% (p = 0.36). CONCLUSIONS: HRD frequency was similar in participants aged < 70 and ≥ 70 years (35% vs 31%) when the contribution of gBRCA was excluded; rates of sBRCA PVs were also similar (8% v 10%), thus underscoring the importance of HRD and BRCA testing at diagnosis in older patients with advanced HGSC given the therapeutic implications.

Isolation, Plant Growth-Promoting Properties, and Whole-Genome Sequence of a Novel Paenibacillus Species.

This work aimed to isolate and characterize a novel chitin-degrading bacterium from Yok Don National Park, Vietnam, for crop production studies. Among the chitinolytic isolates, strain YSY-4.3 was selected, which grew rapidly and produced a large halo around the colony. 16S rDNA analysis indicated that the strain is a novel species in the genus paenibacillus, and an in vitro evaluation showed that the strain produced phytohormones (IAA, GA3, and zeatin), biofilms, and siderophores; possessed cellulase; and exerted antifungal activity. The whole genome of the strain was 5,628,400 bp with 49.3% GC content, 5056 coding sequences, 48 tRNA, and 1 rRNA. It shared the highest values of digital DNA-DNA hybridization (67.4%) and average nucleotide identity (89.54%) with those of Paenibacillus woosongensis B2_4 (CP126084.1), suggesting a novel species. Of the coding sequences, 4287 proteins were identified by COG, and 2561 were assigned by KEGG. The genome contained at least 51 genes involved in plant growth and resistance to heavy-metal toxicity and 359 carbohydrate-active enzymes. The chitinolytic system of the strain was composed of 15 enzymes, among them, PsChiC, which contained a GH18 catalytic domain and a GH5 catalytic domain, had not been previously reported. In addition, the genome possessed 15 gene clusters encoding antimicrobial metabolites, 10 of which are possible novel clusters. This study expands knowledge regarding novel chitinolytic bacteria from Yok Don National Park and provides a valuable gene resource for future studies.

Endophytic bacterial dataset of the Cavendish banana grown in Dak Lak Province of Vietnam using 16S rRNA gene metabarcoding.

The Cavendish banana (Musa cavendishii L.) is one of the main perennial crops grown in Dak Lak Province of Vietnam. However, data on the endophytic bacterial community of this plant are unknown. In this work, a representative sample, mixing from 5 root samples collected from five banana gardens (the Dwarf Cavendish cultivar) in Dak Lak, was used for analyzing the endophytic microbiome using 16S rRNA gene metabarcoding. Results showed that 5 phyla, 7 classes, 20 orders, 31 families, and 47 genera of endophytic bacteria were identified from the sample. Bacteria belonging to phylum Proteobacteria were the most predominant, with 72.64%, and functions involved in biosynthesis were the most abundant, with 75.35%, of the endophytic bacterial community. Data help to understand the endophytic bacterial community of the Cavendish banana cultivated in Dak Lak, Vietnam. These data can be useful for further experiments concerning relationships between the growth of the Cavendish banana and endophytic bacteria. This is the first report on the endophytic bacteria of the Cavendish banana cultivated in Dak Lak, Vietnam.

16S rRNA metagenomic dataset on endophytic bacterial community of the cashew plant (Anacardium occidentale L.) grown in Dak Lak Province of Vietnam.

Vietnam is currently one of the largest producers and exporters of cashew nuts in the world. Cashew (Anacardium occidentale L.) is one of the main industrial crops cultivated in Dak Lak Province of Vietnam. Comprehending the endophytic bacteria of this plant, a new biofertilizer for sustainable cashew nut production can be progressed. In this report, the cashew root sample was collected from cashew fields in 2021 in Dak Lak. The DNeasy Powersoil kit was used to extract the genomic DNA of endophytic bacteria from the root sample. The 16S rRNA genes (V1-V9 regions) were amplified by PCR, and libraries of amplicons were prepared using the Swift amplicon 16S plus ITS panel kit. The Illumina MiSeq platform was applied to sequence amplicon libraries using 16S rRNA metagenomics. Taxonomic analyses showed that Gammaproteobacteria (38.77 %) and Alphaproteobacteria (37.76 %) were the predominant classes among the endophytic bacteria. Functional analyses revealed that biosynthesis (72.78 %) was the primary function of the endophytic bacterial community. Raw sequences (Fastq files) have been deposited in Mendeley Data [1]. The obtained data provide insight into the endophytic bacterial community of cashews cultivated in Dak Lak Province of Vietnam. The data are valuable for further developing a new biofertilizer for cashew nut production using endophytic bacteria. Ours is the first report about endophytic bacterial communities of cashews cultivated in this province as well as the Central Highlands of Vietnam.

Whole genome sequence data of Paenibacillus tyrfis YSS-72.2.G2, a chitinolytic bacterium newly isolated from a National Park of Vietnam.

Paenibacillus tyrfis YSS-72.2.G2 is a soil chitinolytic bacterium newly isolated from Yok Don National Park of Vietnam. Our previous results demonstrated that this bacterium was a strong chitinase producer, possessed plant growth promotion, and had high activity against phytopathogenic fungi. However, the genome sequence of this strain is unknown. This work aimed to establish data on the genome sequence of P. tyrfis YSS-72.2.G2 and its chitinase system for further assessments regarding biocontrol mechanisms and plant growth promotion. The P. tyrfis YSS-72.2.G2 genome is 7,756,121 bp in size and 53.4 % G+C. It harbors 6,948 protein-coding genes, 5 rRNA genes, 82 tRNA genes, 4 ncRNA genes, 99 pseudo genes, and 5 CRISPR arrays. Genes involved in heavy metal resistance (5 genes), iron acquisition (5 genes), and IAA biosynthesis (5 genes) were predicted in the genome. There were 234 carbohydrate-active enzymes found in this genome; among them, 13 enzymes possibly possess activity against phytopathogens. Chitin-degrading system of YSS-72.2.G2 contains 15 chitinolytic enzymes. In addition, 28 gene clusters coding for antimicrobial metabolites were identified, of these, 14 show no sequence similarities to the known clusters. The raw sequences were submitted to the Sequence Read Archive on the National Center for Biotechnology Information with accession number PRJNA946889. The genome sequence of P. tyrfis YSS-72.2.G2 has been deposited in the DDBJ/GenBank/EMBL database under accession number NZ_BSDJ00000000. Data provide insight into the genomic information of strain YSS-72.2.G2. This is the first work reporting data on the genome sequence of P. tyrfis isolated from Vietnam.

Data on annotation and analysis of genome sequence of Paenibacillus elgii YSY-1.2, a promising chitinase-producing, plant-growth-promoting, and biocontrol agent.

The bacterium Paenibacillus elgii YSY-1.2 was recently isolated from soil collected from Yok Don National Park in Vietnam. Previous experiments showed this bacterium possesses high chitin-degrading activity, plant-growth promotion, and biocontrol capacity. Here, we report the draft genome sequence of strain YSY-1.2 for further characterizations related to crop production. The genome sequencing was performed using the DNBSeq-G99 with the Illumina platform. The draft genome of P. elgii YSY-1.2 has 8,240,519 bp in length and comprises 135 contigs. It has an N50 of 315,408 bp and a GC% of 52.8%. The genome contains 7498 protein-coding genes, 87 tRNA genes, and 1 rRNA gene. Among the protein-coding sequences, 6610 were assigned by COG, while 3230 were assigned by KEGG. The genome possesses at least 61 genes involved in environmental adaptation and plant growth promotion. Additionally; there are 258 carbohydrate-active enzymes deduced from the genome; among them, at least 14 may contribute to the biocontrol capacity. The chitin-degrading system of strain YSY-1.2 contains 16 chitinolytic enzymes, comprising 10 chitinases, 4 ß-N-acetylhexosaminidases, and 2 auxiliary activities. Furthermore, 32 gene clusters encoding antimicrobial metabolites were identified from the genome, with 17 showing no sequence similarities to reported clusters. Data provide an insight into the genomic information of strain YSY-1.2 and could lead to valuable further explorations and applications in crop production. This is the first report describing the genome sequence of P. elgii isolated from Vietnam.

Data on gene cloning, expression, purification, and characterization of the glycoside hydrolase family 11 from Bacillus velezensis.

Bacillus velezensis RB.IBE29 is a chitinolytic bacterium originally isolated from the rhizospheric soil of black pepper grown in Vietnam. This bacterium is a strong biocontrol agent against plant pathogens and possesses a novel chitinase system. Genome sequences available in CAZy database revealed B. velezensis possesses one gene encoding xylanase belonging to glycoside hydrolase family 11; however, this enzyme has yet to be un-experimentally characterized. In this work, xyA gene was isolated from the genomic DNA of strain RB.IBE29 and cloned in Escherichia coli DH5α cells using the pUC19 vector. Sequencing analysis showed that the ORF of xyA contains 642 bp and encodes the deduced xylanase with 213 aa and 23.27 kDa. The domain structure of the enzyme has a signal peptide and a family 11 catalytic domain. xyA (without peptide sequence) was successfully expressed in E. coli BL21-CodonPlus (DE3)-RIPL cells using the pColdII vector and purified using the HisTrap FF column. Purified recombinant xylanase degraded xylan substrates, had the highest hydrolytic activity at 55°C in 20 mM sodium phosphate buffer (pH 6.0), and MgCl2, CoCl2, and MnCl2 enhanced the enzymatic activity. Nucleotide sequence of xyA was submitted to the DDBJ/GenBank/EMBL under accession number LC779040. This is the first data on the gene cloning, expression, purification, and characterization of the glycoside hydrolase family 11 from B. velezensis.

Machine learning-enhanced gesture recognition through impedance signal analysis.

Gesture recognition is a crucial aspect in the advancement of virtual reality, healthcare, and human-computer interaction, and requires innovative methodologies to meet the increasing demands for precision. This paper presents a novel approach that combines Impedance Signal Spectrum Analysis (ISSA) with machine learning to improve gesture recognition precision. A diverse dataset that included participants from various demographic backgrounds (five individuals) who were each executing a range of predefined gestures. The predefined gestures were designed to encompass a broad spectrum of hand movements, including intricate and subtle variations, to challenge the robustness of the proposed methodology. The machine learning model using the K-Nearest Neighbors (KNN), Gradient Boosting Machine (GBM), Naive Bayes (NB), Logistic Regression (LR), Random Forest (RF), and Support Vector Machine (SVM) algorithms demonstrated notable precision in performance evaluations. The individual accuracy values for each algorithm are as follows: KNN, 86%; GBM, 86%; NB, 84%; LR, 89%; RF, 87%; and SVM, 87%. These results emphasize the importance of impedance features in the refinement of gesture recognition. The adaptability of the model was confirmed under different conditions, highlighting its broad applicability.

Epcoritamab monotherapy in patients with relapsed or refractory follicular lymphoma (EPCORE NHL-1): a phase 2 cohort of a single-arm, multicentre study.

BACKGROUND: A standard of care and optimal duration of therapy have not been established for patients with multiply relapsed or refractory follicular lymphoma. The aim of this study was to evaluate epcoritamab, a novel CD3 × CD20 bispecific antibody, in the third-line and later setting of follicular lymphoma. METHODS: EPCORE NHL-1 is a multicohort, single-arm, phase 1-2 trial conducted at 88 sites across 15 countries. Here, we report the primary analysis of patients with relapsed or refractory follicular lymphoma in the phase 2 part of the trial, which included the pivotal (dose expansion) cohort and the cycle 1 optimisation cohort. Eligible patients were aged 18 years or older, had relapsed or refractory CD20+ follicular lymphoma (grade 1-3A), an Eastern Cooperative Oncology Group performance status of up to 2, and had received at least two previous lines of therapy (including an anti-CD20 monoclonal antibody and an alkylating agent or lenalidomide). Patients were treated with subcutaneous epcoritamab 48 mg in 28-day cycles: weekly in cycles 1-3, biweekly in cycles 4-9, and every 4 weeks until disease progression or unacceptable toxicity. To mitigate the risk and severity of cytokine release syndrome, in the pivotal cohort, cycle 1 consisted of a step-up dosing regimen of a 0·16-mg priming dose on day 1 and a 0·80-mg intermediate dose on day 8, followed by subsequent 48-mg full doses and prophylactic prednisolone 100 mg; in the cycle 1 optimisation cohort, a second intermediate dose of 3 mg on day 15, adequate hydration, and prophylactic dexamethasone 15 mg were evaluated during cycle 1 to further reduce risk and severity of cytokine release syndrome. Primary endpoints were independently reviewed overall response rate for the pivotal cohort and the proportion of patients with grade 2 or worse and any-grade cytokine release syndrome for the cycle 1 optimisation cohort. Analyses were done in all enrolled patients who had received at least one dose of epcoritamab. This study is registered with ClinicalTrials.gov, NCT03625037, and is ongoing. FINDINGS: Between June 19, 2020, and April 21, 2023, 128 patients (median age 65 years [IQR 55-72]; 49 [38%] female and 79 [62%] male) were enrolled and treated in the pivotal cohort (median follow-up 17·4 months [IQR 9·1-20·9]). The overall response rate was 82·0% (105 of 128 patients; 95% CI 74·3-88·3), with a complete response rate of 62·5% (80 of 128; 95% CI 53·5-70·9). The most common grade 3-4 treatment-emergent adverse event was neutropenia in 32 (25%) of 128 patients. Grade 1-2 cytokine release syndrome was reported in 83 (65%) of 128 patients; grade 3 cytokine release syndrome was reported in two (2%). Immune effector cell-associated neurotoxicity syndrome was reported in eight (6%) of 128 patients (five [4%] grade 1; three [2%] grade 2). Between Oct 25, 2022, and Jan 8, 2024, 86 patients (median age 64 years [55-71]; 37 [43%] female and 49 [57%] male) were enrolled and treated in the cycle 1 optimisation cohort. The incidence of cytokine release syndrome was 49% (42 of 86 patients; eight [9%] grade 2; none of grade 3 or worse), with no reported immune effector cell-associated neurotoxicity syndrome. INTERPRETATION: Epcoritamab monotherapy showed clinically meaningful activity in patients with multiply relapsed or refractory follicular lymphoma, and had a manageable safety profile. FUNDING: Genmab and AbbVie.

Assessment of the Effectiveness of Ultrasound-Guided Needle Aspiration of Lactating Breast Abscesses.

Objective: To evaluate the effectiveness of ultrasound-guided needle aspiration in treating lactating breast abscesses. Methods: This study was conducted in Bach Mai Hospital, from 6/2020 to 7/2021. Lactating patients with breast abscesses underwent ultrasound-guided aspiration followed by antibiotics therapy. Results: There were 59 lactating patients with 82 breast abscesses. Most of the abscesses had heterogeneous echogenicity, no capsule, and a size smaller than 5cm. Bacterial culture results showed that 85.4% of cases were Methicillin-resistant Staphylococcus aureus. The number of aspirations was from 1 to 5. The cure rate was 91.5%, and 5.3% of these cases had a complication associated with galactocele after treatment. Conclusion: Ultrasound-guided needle aspiration is a minimally invasive treatment option for lactating breast abscesses with a high complete cure rate and good cosmetic results.

Efficient Isolation and Long-term Red Fluorescent Nanodia-mond Labeling of Umbilical Cord Mesenchymal Stem Cells for the Effective Differentiation into Hepatocyte-like Cells

Abstract Fluorescent nanodiamond (FND) has been used for long-term cell labeling and in vivo cell tracking because they have good at photostability and biocompatibility. In this study, we evaluate the effect of fluorescent nanodiamond labeling on in vitro culture and differentiation of human umbilical cord mesenchymal stem cells (hUCMSCs) into hepatocyte-like cells (HLCs). For hepatic differentiation of hUCMSCs, cells were induced with human hepatocyte growth factor, nicotinamide and Dexamethasone. FND was supplied in two experimental groups with 20 μg/mL and 100 μg/mL in 2 hours. The cell was assessed for FND uptake by laser scan microscopy and flow cytometry methods. The effect of FND on hUCMSCs was evaluated by the cell viability and growth assays as well as the differentiation throughout of morphology alterations or gene expression of anfa-fetoprotein, albumin, and hepatocyte nuclear factor 4α. The results showed that the labeling of hUCMSCs is efficient and easy and there was significant cellular uptake of FND. We did not observe any negative impacts of FND to the cell viability and growth. FND can be utilized for the long-term labeling and tracking of hUCSCs and HLCs in vivo studies.