title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=173 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Assessment of genotype by environment and yield performance of tropical maize hybrids using stability statistics and graphical biplots link: https://peerj.com/articles/18624 last-modified: 2024-11-29 description: BackgroundEnhancing maize grain yield in tropical regions faces significant challenges due to variability in agroclimate, soil conditions, and agroecosystems. Understanding genotype (G) by environment (E) interaction (GEI) in plant breeding is crucial for selecting and developing high-yielding genotypes adapted to diverse environments.MethodsTen maize hybrids, including eight candidates and two commercial varieties, were evaluated across ten environments in Indonesia using a randomized complete block design with three replications. The GEI effect and yield stability were assessed using stability statistics, additive main effects and multiplicative interaction model (AMMI), and genotype + genotype × environment (GGE) biplot methods.Results and DiscussionAnalysis of variance revealed a significant GEI effect, indicating differences in hybrid responses for grain yield (GY), allowing for stability analysis. G01 showed the highest GY based on the best linear unbiased prediction (BLUP) across environments. Correlation analysis indicated strong associations between stability statistics (YSi and S(6)) and GY, aiding in the selection of high-yielding hybrids. The integration of AMMI with the BLUP method, and weighted average of absolute scores (WAASB), enabled precise measurement of genotype stability. Overall, G01 (R0211), G04 (R0105), G05 (R0118), and G07 (R0641) emerged as high-yielding, stable hybrids based on stability statistics, AMMI, GGE biplot, and WAASB rankings. These hybrids offer promising candidates for maize genetic improvement programs in tropical regions. creator: Dedy Supriadi creator: Yusuf Mufti Bimantara creator: Yuniel Melvanolo Zendrato creator: Eko Widaryanto creator: Kuswanto Kuswanto creator: Budi Waluyo uri: https://doi.org/10.7717/peerj.18624 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Supriadi et al. title: Vascular synovial phenotype indicates poor response to JAK inhibitors in rheumatoid arthritis patients: a pilot study link: https://peerj.com/articles/18631 last-modified: 2024-11-29 description: ObjectiveRheumatoid arthritis (RA) is a chronic autoimmune inflammatory disease, characterized by significant individual variations in treatment response. Predicting treatment response remains a formidable challenge. This study aims to identify predictors within the synovium associated with the response to JAK inhibitor therapy in RA patients, employing a retrospective approach.MethodsA retrospective analysis was conducted on 27 RA patients who underwent synovial biopsy and received JAK inhibitor therapy for at least three months at our center, from January to November 2023. These patients had comprehensive clinical records. Based on their response to JAK inhibitor therapy, as measured by the ACR20 criteria, they were categorized into non-responder and responder groups. We compared clinical data (including sex, age, disease duration), laboratory findings (RF, ACPA, ESR, CRP, etc.), DAS28-CRP scores, and synovial pathology features—such as synovial lining hyperplasia, neovascularization, stromal activation, inflammatory infiltration, and the expression of CD3, CD20, CD68, and CD138 markers in the synovium—between the two groups.ResultsThe rate of non-responder to JAKi was found to be 33.3% (nine cases out of a total of 27 patients). Non-responders, when compared to responders, exhibited longer disease duration, more pronounced synovial neovascularization alongside reduced infiltration of labeled CD20+ and CD138+ cells in the synovium. Multivariate regression analysis identified synovial neovascularization and disease duration as independent predictors of a poor response to JAK inhibitor treatment.ConclusionsThe presence of vascular phenotype with low inflammation within the synovium of RA patients is an indicator of poor response to JAK inhibitor therapy, highlighting its potential as a predictive marker for treatment outcomes. creator: Mengxia Liu creator: Pengcheng Liu creator: JianBin Li creator: Yiping Huang creator: Rui Wu uri: https://doi.org/10.7717/peerj.18631 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Liu et al. title: Expression of CK7, CK19 and p16 in HPV-mediated oropharyngeal squamous cell carcinoma link: https://peerj.com/articles/18286 last-modified: 2024-11-28 description: BackgroundThe incidence of oropharyngeal squamous cell carcinoma (OPSCC) mediated by human papilloma virus (HPV) has been steadily increasing worldwide. The specific pathogenesis of HPV-mediated head and neck squamous cell carcinoma (HNSCC) usually induces carcinogenesis in the oropharynx and the roles of CK7, CK19 and p16 in the carcinogenesis mechanism of HPV-mediated OPSCC still remain uncertain.MethodsWe collected case data and paraffin samples of 69 cases of OPSCC and 40 cases of OSCC from July 2009 to December 2021. Immunohistochemistry was performed on serial paraffin sections from all cases to analyze the expression patterns of CK7, CK19, and p16. HPV-mediated (p16+) and non-HPV-mediated OPSCC were differentiated based on p16 expression. Three to six fields were selected from each case for observation of the expression intensity, localization, and interrelationship of the three proteins.ResultsIn both cancerous nests and pericancerous normal epithelium of OPSCC, various expression combinations of CK7, CK19 and p16 were observed, including CK7+CK19+p16+, CK7−CK19+p16+, and CK7+CK19+p16−, while no expression of CK7+CK19−p16+ was found. The expression of CK7 with CK19, CK7 with p16, and CK19 with p16 all showed consistency in OPSCC (P < 0.05) while only the expression of CK7 and CK19 demonstrated consistency in OSCC (P < 0.05). The positive rates and H-scores for CK7/CK19 in HPV-mediated (p16+) OPSCC were significantly higher than those in non-HPV-mediated OPSCC and OSCC (P < 0.05).ConclusionsThese results suggest that CK7, CK19 and p16 may relate to HPV-mediated OPSCC. The interaction of CK7, CK19 and p16 may affect the development of HPV-mediated OPSCC. creator: Qizhang Yan creator: Pengning Chen creator: Xinyu Chen creator: Guanxi Chen creator: Lin Luo creator: Ping Ruan creator: Dahai Yu creator: Xiaojuan Zeng creator: Mengyu Zhou uri: https://doi.org/10.7717/peerj.18286 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Yan et al. title: Effects of temperature and size class on the gut digesta microbiota of the sea urchin Tripneustes ventricosus link: https://peerj.com/articles/18298 last-modified: 2024-11-28 description: BackgroundUnderstanding the dynamics of the gut microbiota in sea urchins is crucial for comprehending the ecological balance in marine ecosystems. The gut microbiota plays a vital role in nutrient metabolism, immune system modulation, and pathogen protection. The microbial composition and dynamics of naturally occurring sea urchin Tripneustes ventricosus have yet to be thoroughly investigated. We hypothesized the gut microbiota of T. ventricosus in the Caribbean, varies across life stages and seasons.MethodsThirty-six naturally occurring large individuals and six small individuals (42 animals) were collected from shallow waters on the northeastern coast of Puerto Rico in February and August of 2019. The fecal pellet’s microbiota was characterized by sequencing V4 region of the 16S rRNA gene.ResultsWe found significant differences in the composition of fecal pellet microbiota between seasons and life stages. Phylum Bacteroidota had greater relative abundance in August, while Firmicutes was more dominant in February. Propionigenium and Roseimarinus had greater relative abundance in August, while Candidatus Hepatoplasma, and Kistimonas had greater relative abundance in February. Differences in the gut digest microbiota were not found between small and large urchins, but small urchins displayed a slightly higher diversity and dominance of Bacteroidota and Proteobacteria, while large urchins exhibited a greater relative abundance of Fusobacteria and Desulfobacterota. However, the genera Ferrominas and Propionigenium counts were significantly lower in small individuals.DiscussionThis is the first report for this species in the Caribbean region and adds to our comprehension of the microbiota of the white sea urchin across collection periods and size classes, highlighting the dynamic nature of the gut microbiota. creator: Ruber Rodríguez-Barreras creator: Eduardo L. Tosado-Rodríguez creator: Anelisse Dominicci-Maura creator: Filipa Godoy-Vitorino uri: https://doi.org/10.7717/peerj.18298 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Rodríguez-Barreras et al. title: Exploration of severe early childhood caries microbiota through a novel developed nutrient enriched microbiological medium, high through-put 16S rRNA sequencing and culturomics link: https://peerj.com/articles/18312 last-modified: 2024-11-28 description: IntroductionSevere early childhood caries (S-ECC) is a widespread disease that harms children physically and mentally. Microorganisms are regarded as the dominant etiology of caries, however, S-ECC microbiome remains largely unknown, nearly 1/4 of them remained uncultivated. To explore S-ECC microbiota, a new bacterial medium, nutrient-enriched microbiological medium (NEMM) was designed in this study.MethodsEleven fresh S-ECC dental plaque samples were collected and cultivated in both NEMM and SHI medium (reference medium) for 0, 1, 3, 6, 9, 15, 21 and 28 days under aerobic and anaerobic conditions. Thereafter, the cultures were harvested, together with their corresponding clinical S-ECC dental plaque samples, for high through-put 16S rRNA sequencing and culturomics. The single colonies were cultured for further confirmation by sequencing the full length of the 16S rRNA gene after bacterial genomic DNA extraction and PCR amplification.ResultsEither NEMM or SHI medium showed a significant decrease in bacterial alpha diversity compared to clinical dental plaque samples by high throughput 16S rRNA sequencing analysis, indicating a larger room for the improvement of both media. NEMM displayed more living bacteria, abundant bacteria species, uncultured bacteria and capacities in carbohydrate transport and metabolism than SHI medium. The dynamic changes in bacterial community composition over time indicated that some bacteria tended to be enriched at specific time points. Culturomics and identification of bacterial species results were further confirmed by the high throughput 16S rRNA sequencing results.ConclusionWe developed a new medium NEMM that could support S-ECC microbiota growth with a higher yield of living bacteria, higher abundance and capacity, and be suitable for cultivating oral uncultured bacteria via culturomics technology. creator: Yixin Zhang creator: Yang Chen creator: Chang Diao creator: Haojie Lin creator: Jingqi Zhu creator: Ruiqing Sun creator: Meng Wang creator: Yuke Chen creator: Hanzhang Zhou creator: Zixi Dong creator: Bin Xia creator: Yixiang Wang uri: https://doi.org/10.7717/peerj.18312 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhang et al. title: Pereskia bleo augments NK cell cytotoxicity against triple-negative breast cancer cells (MDA-MB-231) link: https://peerj.com/articles/18420 last-modified: 2024-11-28 description: BackgroundNatural killer cells (NK cells) are essential in cancer immunosurveillance in the body as they can recognize cancer cells that lacking MHC class 1 on their surface. Regulatory cytokines, including interleukin (IL)-18, IL-12, IL-10, IL-8, interferon-γ (IFN-γ), and secretory granules like perforin and granzyme are involved in NK cell-mediated cytotoxicity. Stimulating NK cells cytotoxicity towards cancer cells is an ideal strategy to combat cancer naturally. Medicinal plants have been reported to enhance immunity, with Pereskia bleo (P. bleo) particularly noteworthy due to its abundant bioactive compounds and ability to activate immune cells. This study aimed to evaluate the potential of methanol extract of P. bleo leaves (MEPB) for enhancing NK cell cytotoxicity against triple-negative human breast cancer cells (MDA-MB-231).MethodsThe optimal concentration of MEPB to activate NK cells was determined using healthy blood samples, assessing the expression of IL-12, IL-18, IL-10, IL-8, IFN-γ, perforin, and granzyme B via an enzyme-linked immunosorbent assay (ELISA). NK cell purity from healthy donors and breast cancer patients was determined using specific antibodies, and the number of NK cells was assessed using flow cytometry and a hemocytometer. A co-culture experiment, ELISA, and apoptosis assay were used to evaluate NK-mediated cytotoxicity pathways.ResultsELISA data indicated that MEPB at 7.5 µg/ml significantly increased the expression of IFN-γ, IL-12, IL-18, perforin, and granzyme B while decreasing IL-8 and IL-10 expression after 20 hrs of incubation. The average NK cell purity was 87.09 ± 0.043%. Breast cancer patients exhibited lower NK cell counts than healthy donors. Co-culture experiments demonstrated that NK cells induced apoptosis in MDA-MB-231 breast cancer cells in the presence of MEPB by increasing perforin, granzyme B, and IFN-γ expression in both healthy donors and breast cancer patients-experimental groups. P. bleo enhances NK cell activation, promoting the apoptosis of triple-negative human breast cancer cells (MDA-MB-231), suggesting the potential use of MEPB leaves as an anti-cancer immunostimulant. creator: Taif Kareem Khalaf creator: Norzila Ismail creator: Nor Amalia Nazri creator: Naveed Ahmed creator: Aidy Irman Yajid creator: Rohimah Mohamud creator: Ramlah Kadir uri: https://doi.org/10.7717/peerj.18420 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Khalaf et al. title: Analysing the spatial variation of soil respiration during the early growing season of different grasslands in China link: https://peerj.com/articles/18480 last-modified: 2024-11-28 description: BackgroundAs one of the most essential vegetation types, grasslands play a vital role in the global carbon cycle. However, current researches on the spatial variation (SV) of soil respiration (Rs) in grasslands faces great uncertainties.MethodsThe SV of Rs was analysed by obtaining Rs during the early growing season of three types of grasslands (i.e., alpine meadow, desert steppe, and typical steppe) and related impact factors at 19 sites.ResultsThe results demonstrated that during the early growing season, the Rs of the alpine meadow was the highest, followed by the typical steppe and desert steppe. Moreover, soil temperature was the primary factor affecting the SV of Rs in desert steppe. In contrast, soil water content influenced the SV of Rs in typical steppe. This study increases our understanding of the SV of Rs during the early growing season of different grasslands. It provides an important reference for accurately estimating the SV of Rs in grasslands at various time scales. creator: Jie Liu creator: Ni Huang creator: Li Wang creator: Xiaoyu Lin creator: Luying Zhu creator: Zheng Niu creator: Yuelin Zhang creator: Wensheng Duan uri: https://doi.org/10.7717/peerj.18480 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Liu et al. title: A comprehensive review of oncogenic Notch signaling in multiple myeloma link: https://peerj.com/articles/18485 last-modified: 2024-11-28 description: Multiple myeloma remains an incurable plasma cell cancer with radical case-by-case heterogeneity. Because of this, personalized and disease-specific biology of multiple myeloma must be understood for the discovery of effective molecular targets. The highly evolutionarily conserved Notch signaling pathway has been extensively described as a multifaceted driver of the multiple myeloma disease process—contributing to both intrinsic effects of malignant cells and to widespread remodeling of the tumor microenvironment that further facilitates disease progression. Namely, Notch signaling amongst malignant cells promotes increased proliferation, tumor-initiating capacity, drug resistance, and invasiveness. Moreover, Notch signaling between malignant cells and cells of the tumor microenvironment leads to increased osteodegenerative disease and angiogenesis. This comprehensive review will discuss both the intrinsic implications of pathological Notch signaling in multiple myeloma and the extrinsic implications of Notch signaling in the multiple myeloma tumor microenvironment. Additionally, the genetic origins of Notch signaling dysregulation in multiple myeloma and current attempts at targeting Notch therapeutically will be reviewed. While the subject has been reviewed previously, recent developments in the intervening years demand a revised synthesis of the literature. The aim of this work is to introduce and thoroughly synthesize the current state of knowledge in this vein of research and to highlight future directions for both new and in-the-field scientists. creator: Justin Roosma uri: https://doi.org/10.7717/peerj.18485 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Roosma title: The impact of doctor–patient communication on medication adherence and blood pressure control in patients with hypertension: a systematic review link: https://peerj.com/articles/18527 last-modified: 2024-11-28 description: BackgroundThis systematic review aims to present existing evidence concerning the effects of doctor–patient communication on medication adherence and blood pressure control in hypertensive patients.MethodsTwo researchers independently conducted comprehensive searches of five databases and screened relevant studies published from the inception of these databases up to July 21, 2024. The titles, abstracts, and full texts of all the retrieved articles subsequently underwent rigorous duplicate screening, according to predefined inclusion and exclusion criteria. We then synthesized the findings in a narrative format of the included studies. Finally, two researchers independently assessed study quality.ResultsEighteen observational studies encompassing 21,542 patients and seven randomized controlled trials with 2,804 patients were included in the systematic review. Diverse approaches were employed for evaluating doctor–patient communication and medication adherence in these studies, with identified themes including communication content and communication skills. Various facets of doctor–patient communication, including patient satisfaction with doctor–patient communication, the specific content discussed, the style of communication, the comprehensive communication skills of doctors, and the duration of these conversations, were scrutinized. In general, the results suggest a promising link between effective doctor–patient communication and increased medication adherence and blood pressure control. Nonetheless, the presence of nuanced variations and subtle distinctions within the literature underscores the imperative for deeper exploration and consideration in clinical practice. Additionally, effective communication interventions must attain a certain threshold of intensity and endure for an adequate duration.ConclusionThis review underscores the pivotal role of robust doctor–patient communication in improving both medication adherence and blood pressure control. Nevertheless, additional research may be warranted to address the disparities and subtleties in the literature and to establish precise implications for clinical practice. Moreover, in clinical practice, strategies to enhance doctor–patient communication should be incorporated, given the potential to improve medication adherence and blood pressure control among hypertensive patients.Trial registrationSystematic review registration: PROSPERO with registration number CRD42024503112. creator: Jianwei Zeng creator: Yuqiang Gao creator: Chen Hou creator: Tao Liu uri: https://doi.org/10.7717/peerj.18527 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zeng et al. title: Understanding the progress of COVID-19 transmission in a rural district: a social network approach link: https://peerj.com/articles/18571 last-modified: 2024-11-28 description: BackgroundSocial interactions within and between communities influenced the spread of COVID-19. By using social network analysis (SNA), we aimed to understand the effect of social interaction on the spread of disease in a rural district.MethodA retrospective record review study using positive COVID-19 cases and contact-tracing data from an area in Malaysia was performed and analysed using the SNA method through R software and visualised by Gephi software. The justification for utilizing SNA is its capability to pinpoint the individuals with the highest impact and accountability for the transmission of COVID-19 within the area, as determined through SNA.ResultAnalysis revealed 76 (4.5%) people tested positive for COVID-19 from 1,683 people, with 51 (67.1%) of the positive ones being male. Outdegrees for 38 positive people were between 1 and 12, while 41 people had 1–13 indegree. Older males have a higher outdegree, while younger females have a higher outdegree than other age groups among same-sex groups. Betweenness was between 0.09 and 34.5 for 15 people. We identified 15 people as super-spreaders from the 42 communities detected.ConclusionWomen play a major role in bridging COVID-19 transmission, while older men may transmit COVID-19 through direct connections. Thus, health education on face mask usage and hand hygiene is important for both groups. Working women should be given priority for the work-from-home policy compared to others. A large gathering should not be allowed to operate, or if needed, with strict adherence to specific standard operating procedures, as it contributes to the spread of COVID-19 in the district. The SNA allows the identification of key personnel within the network. Therefore, SNA can help healthcare authorities recognise evolving clusters and identify potential super-spreaders; hence, precise and timely action can be taken to prevent further spread of the disease. creator: Juliana Mansor creator: Nazarudin Safian creator: Fatimah Abdul Razak creator: Halim Ismail creator: Muhammad Haikal Ghazali creator: Noriah Ismail uri: https://doi.org/10.7717/peerj.18571 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Mansor et al.